ArticleJournal of oncology2021
Identification and Validation of Three PDAC Subtypes and Individualized GSVA Immune Pathway-Related Prognostic Risk Score Formula in Pancreatic Ductal Adenocarcinoma Patients.
Article in Journal of oncology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 23 citations in OpenAlex.
- Article
- Article
- Establishment of a Lactylation-Related Gene Signature for Hepatocellular Carcinoma Applying Bulk and Single-Cell RNA Sequencing Analysis.International journal of genomics · 2025Article
- Distance-depending transcriptome changes of pancreatic stellate cells in paracrine pancreatic ductal adenocarcinoma co-culture models.Scientific reports · 2024Article
- Article
- Genomic and algorithm-based predictive risk assessment models for benzene exposure.Frontiers in public health · 2024Article
- A glycolysis-related gene signatures in diffuse large B-Cell lymphoma predicts prognosis and tumor immune microenvironment.Frontiers in cell and developmental biology · 2023Article
- Article
- Immune-related gene signature associates with immune landscape and predicts prognosis accurately in patients with skin cutaneous melanoma.Frontiers in genetics · 2022Article
- Identification of Specific Cervical Cancer Subtypes and Prognostic Gene Sets in Tumor and Nontumor Tissues Based on GSVA Analysis.Journal of oncology · 2022Article
- Construction of five cuproptosis-related lncRNA signature for predicting prognosis and immune activity in skin cutaneous melanoma.Frontiers in genetics · 2022Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith the progress of precision medicine treatment in pancreatic ductal adenocarcinoma (PDAC), individualized cancer-related medical examination and prediction are of great importance in this high malignant tumor and tumor-immune microenvironment with changed pathways highly enrolled in the carcinogenesis of PDAC.
methodsHigh-throughput data of pancreatic ductal adenocarcinoma were downloaded from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. After batch normalization, the enrichment pathway and relevant scores were identified by the enrichment of immune-related pathway signature using gene set variation analysis (GSVA). Then, cancerous subtype in TCGA and GEO samples was defined through the NMF methods by cancertypes packages in R software, respectively. Subsequently, the significance between the characteristics of each TCGA sample and cancer type and the significant prognosis-related pathway with risk score formula is calculated through t-test and univariate Cox analysis. Next, the prognostic value of gained risk score formula and each significant prognosis-related pathway were validated in TCGA and GEO samples by survival analysis. The pivotal hub genes in the enriched significant prognosis-related pathway are identified and validated, and the TIMER database was used to identify the potential role of hub genes in the PDAC immune environment. The potential role of hub genes is promoting the transdifferentiation of cancer-associated fibroblasts.
resultsThe enrichment pathway and relevant scores were identified by GSVA, and 3 subtypes of pancreatic ductal adenocarcinoma were defined in TCGA and GEO samples. The clinical stage, tumor node metastasis classification, and tumor grade are strongly relative to the subtype above in TCGA samples. A risk formula about GSVA significant pathway "GSE45365_WT_VS_IFNAR_KO_CD11B_DC_MCMV_INFECTION_DN ∗ 0.80 + HALLMARK_GLYCOLYSIS ∗ 16.8 + GSE19888_CTRL_VS_T_CELL_MEMBRANES_ACT_MAST_CELL_DN ∗ 14.4" was identified and validated in TCGA and GEO samples through survival analysis with significance. DCN, VCAN, B4GALT7, SDC1, SDC2, B3GALT6, B3GAT3, SDC3, GPC1, and XYLT2 were identified as hub genes in these GSVA significant pathways and validated in silico.
conclusionsThree pancreatic ductal adenocarcinoma subtypes are identified, and an individualized GSVA immune pathway score-related prognostic risk score formula with 10 hub genes is identified and validated. The predicted function of the 10 upregulated hub genes in tumor-immune microenvironment was promoting the infiltration of cancer-associated fibroblasts. These findings will contribute to the precision medicine of pancreatic ductal adenocarcinoma treatment and tumor immune-related basic research.
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Registered trials
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