A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis

Abstract

BackgroundAs a tumor type with high mortality and poor therapeutic effect, the pathogenesis of pancreatic cancer is still unclear. It is necessary to explore the significance of necroptosis in pancreatic cancer.MethodsPancreatic cancer transcriptome data were obtained from the TCGA database, ICGC database, and GSE85916 in the GEO database. The TCGA cohort was set as a training cohort, while the ICGC and GSE85916 cohort were set as the validation cohorts. Single-cell sequencing data of pancreatic cancer were obtained from GSE154778 in the GEO database. The genes most associated with necroptosis were identified by weighted co-expression network analysis and single-cell sequencing analysis. COX regression and Lasso regression were performed for these genes, and the prognostic model was established. By calculating risk scores, pancreatic cancer patients could be divided into NCPTS_high and NCPTS_low groups, and survival analysis, immune infiltration analysis, and mutation analysis between groups were performed. Cell experiments including gene knockdown, CCK-8 assay, clone formation assay, transwell assay and wound healing assay were conducted to explore the role of the key gene EPS8 in pancreatic cancer. PCR assays on clinical samples were further used to verify EPS8 expression.ResultsWe constructed the necroptosis-related signature in pancreatic cancer using single-cell sequencing analysis and transcriptome analysis. The calculation formula of risk score was as follows: NCPTS = POLR3GL * (-0.404) + COL17A1 * (0.092) + DDIT4 * (0.007) + PDE4C * (0.057) + CLDN1 * 0.075 + HMGA2 * 0.056 + CENPF * 0.198 +EPS8 * 0.219. Through this signature, pancreatic cancer patients with different cohorts can be divided into NCPTS_high and NCPTS_low group, and the NCPTS_high group has a significantly poorer prognosis. Moreover, there were significant differences in immune infiltration level and mutation level between the two groups. Cell assays showed that in CAPAN-1 and PANC-1 cell lines, EPS8 knockdown significantly reduced the viability, clonogenesis, migration and invasion of pancreatic cancer cells. Clinical PCR assay of EPS8 expression showed that EPS8 expression was significantly up-regulated in pancreatic cancer (*P<0.05).ConclusionOur study can provide a reference for the diagnosis, treatment and prognosis assessment of pancreatic cancer.

Single-Cell RNA Sequencing Analysis Reveals Metabolic Changes in Epithelial Glycosphingolipids and Establishes a Prognostic Risk Model for Pancreatic Cancer

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Combining single-cell and bulk RNA sequencing, NK cell marker genes reveal a prognostic and immune status in pancreatic ductal adenocarcinoma

“…The results indicated that NKCMGS had an impact the prognosis of PDAC patients in each clinical subgroups, which indicates a good prognostic value of NKCMGS. NKCMGS has higher stability and ability to identify high-risk patients compared to the model constructed by Zhang et al based on neuroendocrine, metabolism-related genes and the iron death-related signature constructed by Chen et al 42 , 43 .…”

Leveraging Diverse Regulated Cell Death for Prognostic Prediction of Pancreatic Cancer Using Machine Learning and Multi-omics Analysis

“…In previous investigations, several regulated cell death-related predictive signature have been reported in kinds of carcinoma, including pancreatic carcinoma. In combination with single-cell sequencing analysis and transcriptome analysis, a necroptosis-related signature consisting of POLR3GL, COL17A1, DDIT4, PDE4C, CLDN1, HMGA2, CENPF, and EPS8 had been constructed to predict pancreatic carcinoma prognosis (10). In addition, 14 ferroptosis-related genes were identi ed to establish a prognostic signature (11).…”