ArticleFrontiers in oncology2021
Systematic Chromatin Accessibility Analysis Based on Different Immunological Subtypes of Clear Cell Renal Cell Carcinoma.
Article in Frontiers in oncology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Establishment of a Seven-Gene Signature Associated with CD8International journal of molecular sciences · 2023Trial
- Machine learning driven multiomics analysis identifies disulfidptosis associated molecular subtypes in ovarian cancer.Scientific reports · 2025Article
- Single-cell multi-omics and spatial transcriptomics reveal the transcriptional regulatory landscape of clear cell renal cell carcinoma.Translational andrology and urology · 2025Article
- Construction of ferroptosis and pyroptosis model to assess the prognosis of gastric cancer patients based on bioinformatics.Translational cancer research · 2024Article
- Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort.Nature communications · 2023Article
- Relationship between ATOH1 and tumor microenvironment in colon adenocarcinoma patients with different microsatellite instability status.Cancer cell international · 2022Article
- Comprehensive Analysis of the Immune Cell Infiltration Landscape and Immune-Related Methylation in Retinoblastoma.Frontiers in genetics · 2022Article
- Identification and Validation of the Pyroptosis-Related Molecular Subtypes of Lung Adenocarcinoma by Bioinformatics and Machine Learning.Frontiers in cell and developmental biology · 2021Article
- Research Progress of Tumor Microenvironment Targeted Therapy for Clear Cell Renal Cell Carcinoma.Cancer control : journal of the Moffitt Cancer CenterReview
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14 authors.
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Abstract
backgroundRecent research of clear cell renal cell carcinoma (ccRCC) is focused on the tumor immune microenvironment (TIME). Chromatin accessibility is critical for regulation of gene expression. However, its role in different immunological subtypes of ccRCC based on immune cell infiltration has not been systematically studied.
methodsFive hundred thirty patient data from The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) were adopted to estimate immune cell infiltration. Twenty-four types of immune cells were evaluated with single-sample Gene Set Enrichment Analysis (ssGSEA). Patients were divided into two clusters based on immune cell infiltration. Systematic chromatin accessibility analysis was conducted based on the two clusters.
resultsWe compared the relative expression of the immune gene signatures among 530 patients of TCGA-KIRC using ssGSEA. Overall survival (OS) analysis revealed 10 types of immune cells were significantly associated with prognosis. Patients were divided into two clusters based on 24 types of immune cell infiltration. Immune cell signals as well as PD-1/PD-L1 signal were higher in cluster 1. Among the two clusters, 2,400 differential peaks were found in TCGA-KIRC Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) data. The distribution of differential peaks and prognosis-related immune cells in 23 chromosomes are essentially the same. There is no peak distribution downstream. The proportion of peaks upstream of the 5' transcription start site decreases, and both sides of binding regions of the TSS 0.1-1 kb becomes smaller. Enrichment analysis of GO and KEGG of these differential peaks showed that they are remarkably related to the immune regulation in tumor microenvironment. Known motifs and
conclusionThe abnormality of chromatin accessibility may play an important regulatory role in ccRCC immunity.
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