ArticleJournal of gastrointestinal oncology2021
Identification of gene biomarkers and immune cell infiltration characteristics in rectal cancer.
Article in Journal of gastrointestinal oncology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 37 citations in OpenAlex.
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- Identification of novel diagnostic biomarkers associated with liver metastasis in colon adenocarcinoma by machine learning.Discover oncology · 2024Article
- The synergism of SMC1A cohesin gene silencing and bevacizumab against colorectal cancer.Journal of experimental & clinical cancer research : CR · 2024Article
- A New Risk Score Based on Eight Hepatocellular Carcinoma- Immune Gene Expression Can Predict the Prognosis of the Patients.Frontiers in oncology · 2021Article
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCompared with colon cancer, the increase of morbidity is more significant for rectal cancer. The current study set out to identify novel and critical biomarkers or features that may be used as promising targets for early diagnosis and treatment monitoring of rectal cancer.
methodsMicroarray datasets of rectal cancer with a minimum sample size of 30 and RNA-sequencing datasets of rectal adenocarcinoma (READ) were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. The method of robust rank aggregation was utilized to integrate differentially expressed genes (DEGs). The protein-protein interaction (PPI) network of the DEGs was structured using the STRING platform, and hub genes were identified using the Cytoscape plugin cytoHubba and an UpSet diagram. R software was employed to perform functional enrichment analysis. Receiver operating characteristic (ROC) curves based on the GEO data and Kaplan-Meier curves based on the TCGA data were drawn to assess the diagnostic and prognostic values of the hub genes. Immune cell infiltration analysis was conducted with CIBERSORT, and the diagnostic value and correlations between prognostic genes and infiltrated immune cells were analyzed by principal component analysis (PCA), ROC curves, and correlation scatter plots.
resultsA total of 137 robust DEGs were obtained by integrating datasets in GEO. Twenty-four hub genes, including CHGA, TTR, SAA1, SPP1, MMP1, TGFBI, COL1A1, and PCK1, were identified as a diagnostic gene biomarker group for rectal cancer, and SAA1, SPP1, and SI were identified as potential novel prognostic biomarkers. Functionally, the hub genes were mainly involved in the rectal cancer related interleukin (IL)-17 and proximal tubule bicarbonate reclamation pathways. Twelve sensitive infiltrated immune cells were identified, and were correlated with prognostic genes.
conclusionsThe integrated gene biomarker group combined with immune cell infiltration can effectively indicate rectal cancer.
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