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Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns.

ABSTRACT: BACKGROUND:Esophageal squamous cell carcinoma (ESCC) cells are heterogeneous, easily develop radioresistance, and recur. Single-cell RNA-seq (scRNA-seq) is a next-generation sequencing method that can delineate diverse gene expression profiles of individual cells and mining their heterogeneous behaviors in response to irradiation. Our aim was using scRNA-seq to describe the difference between parental cells and cells that acquired radioresistance, and to investigate the dynamic changes of the transcriptome of cells in response to FIR. RESULTS:We sequenced ESCC cell lines KYSE180 with and without fractionated irradiation (FIR). A total of 218 scRNA-seq libraries were obtained from 88 cells exposed to 12?Gy (KYSE-180-12?Gy), 89 exposed to 30?Gy (KYSE-180-30?Gy), and 41 parental KYSE-180 cells not exposed to FIR. Dynamic gene expression patterns were determined by comprehensive consideration of genes and pathways. Biological experiments showed that KYSE-180 cells became radioresistant after FIR. PCA analysis of scRNA-seq data showed KYSE-180, KYSE-180-12?Gy and KYSE-180-30?Gy cells were discrete away from each other. Two sub-populations found in KYSE-180-12?Gy and only one remained in KYSE-180-30?Gy. This sub-population genes exposure to FIR through 12?Gy to 30?Gy were relevant to the PI3K-AKT pathway, pathways evading apoptosis, tumor cell migration, metastasis, or invasion pathways, and cell differentiation and proliferation pathways. We validated DEGs, such as CFLAR, LAMA5, ITGA6, ITGB4, and SDC4 genes, in these five pathways as radioresistant genes in bulk cell RNA-seq data from ESCC tissue of a ESCC patient treated with radiotherapy and from KYSE-150 cell lines. CONCLUSIONS:Our results delineated the divergent gene expression patterns of individual ESCC cells exposure to FIR, and displayed genes and pathways related to development of radioresistance.

SUBMITTER: Yang L

PROVIDER: S-EPMC6659267 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns.

Yang Ling L Zhang Xiaoyan X Hou Qiang Q Huang Ming M Zhang Hongfang H Jiang Zhenzhen Z Yue Jing J Wu Shixiu S

BMC genomics 20190725 1

<h4>Background</h4>Esophageal squamous cell carcinoma (ESCC) cells are heterogeneous, easily develop radioresistance, and recur. Single-cell RNA-seq (scRNA-seq) is a next-generation sequencing method that can delineate diverse gene expression profiles of individual cells and mining their heterogeneous behaviors in response to irradiation. Our aim was using scRNA-seq to describe the difference between parental cells and cells that acquired radioresistance, and to investigate the dynamic changes o ...[more]

PMID: 31345182

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Project description:BackgroundEsophageal squamous cell carcinoma (ESCC) is causing a high mortality rate due to the lack of efficient early prognosis markers and suitable therapeutic regimens. The prognostic role of genes responsible for the acquisition of radioresistance in ESCC has not been fully elucidated.AimTo establish a prognostic model by studying gene expression patterns pertinent to radioresistance in ESCC patients.MethodsDatasets were obtained from the Gene Expression Omnibus and The Cancer Genome Atlas databases. The edgeR, a Bioconductor package, was used to analyze mRNA expression between different groups. We screened genes specifically responsible for radioresistance to estimate overall survival. Pearson correlation analysis was performed to confirm whether the expression of those genes correlated with each other. Genes contributing to radioresistance and overall survival were assessed by the multivariate Cox regression model through the calculation of βi and risk score using the following formula: .ResultsWe identified three prognostic mRNAs (cathepsin S [CTSS], cluster of differentiation 180 [CD180], and SLP adapter and CSK-interacting membrane protein [SCIMP]) indicative of radioresistance. The expression of the three identified mRNAs was related to each other (r > 0.70 and P < 0.05). As to 1-year and 3-year overall survival prediction, the area under the time-dependent receiver operating characteristic curve of the signature consisting of the three mRNAs was 0.716 and 0.841, respectively. When stratifying patients based on the risk score derived from the signature, the high-risk group exhibited a higher death risk and shorter survival time than the low-risk group (P < 0.0001). Overall survival of the low-risk patients was significantly better than that of the high-risk patients (P = 0.018).ConclusionWe have developed a novel three-gene prognostic signature consisting of CTSS, CD180, and SCIMO for ESCC, which may facilitate the prediction of early prognosis of this malignancy.

Dataset Information

Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns.

Publications

Single-cell RNA-seq of esophageal squamous cell carcinoma cell line with fractionated irradiation reveals radioresistant gene expression patterns.

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