A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis
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 da...
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.1022420/full |
| _version_ | 1828327411504119808 |
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| author | Liang Chen Xueming Zhang Qixiang Zhang Tao Zhang Jiaheng Xie Wei Wei Ying Wang Hongzhu Yu Hongkun Zhou |
| author_facet | Liang Chen Xueming Zhang Qixiang Zhang Tao Zhang Jiaheng Xie Wei Wei Ying Wang Hongzhu Yu Hongkun Zhou |
| author_sort | Liang Chen |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T19:54:59Z |
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| id | doaj.art-cf1b6c3a76594dd8b1f152fe7f6c854a |
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| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-13T19:54:59Z |
| publishDate | 2022-10-01 |
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| spelling | doaj.art-cf1b6c3a76594dd8b1f152fe7f6c854a2022-12-22T02:32:23ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-10-011310.3389/fimmu.2022.10224201022420A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysisLiang Chen0Xueming Zhang1Qixiang Zhang2Tao Zhang3Jiaheng Xie4Wei Wei5Ying Wang6Hongzhu Yu7Hongkun Zhou8Department of Hepatobiliary and Pancreatic Surgery, Conversion Therapy Center for Hepatobiliary and Pancreatic Tumors, First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, ChinaDepartment of Hepatobiliary and Pancreatic Surgery, Conversion Therapy Center for Hepatobiliary and Pancreatic Tumors, First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, ChinaDepartment of Neurosurgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, ChinaDepartment of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of Anesthesiology, Jiaxing First Hospital, Jiaxing, ChinaDepartment of Neurosurgery, Children's Hospital of Nanjing Medical University, Nanjing, ChinaDepartment of General Surgery, Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, ChinaDepartment of Hepatobiliary and Pancreatic Surgery, Conversion Therapy Center for Hepatobiliary and Pancreatic Tumors, First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, ChinaBackgroundAs 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.https://www.frontiersin.org/articles/10.3389/fimmu.2022.1022420/fullpancreatic cancernecroptosisprogrammed cell deathprognostic modelsingle-cell sequencing analysisbioinformatics |
| spellingShingle | Liang Chen Xueming Zhang Qixiang Zhang Tao Zhang Jiaheng Xie Wei Wei Ying Wang Hongzhu Yu Hongkun Zhou A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis Frontiers in Immunology pancreatic cancer necroptosis programmed cell death prognostic model single-cell sequencing analysis bioinformatics |
| title | A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis |
| title_full | A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis |
| title_fullStr | A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis |
| title_full_unstemmed | A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis |
| title_short | A necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis |
| title_sort | necroptosis related prognostic model of pancreatic cancer based on single cell sequencing analysis and transcriptome analysis |
| topic | pancreatic cancer necroptosis programmed cell death prognostic model single-cell sequencing analysis bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.1022420/full |
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