Text · study · 2026
Comprehensive epigenomic profiling reveals diagnostic and prognostic biomarkers in oral squamous cell carcinoma
Listed in NCBI GEO
Objective: The number of patients with oral cancer is increasing, and despite advances in diagnostic techniques and the development of novel therapies, survival rates have not significantly improved.
Description
Therefore, innovative approaches that serve as potential therapeutic targets and diagnostic markers are required. The epigenome plays a critical role in maintaining cellular homeostasis and regulating the expression of genes associated with cancer.
Among epigenetic mechanisms, super-enhancers (SEs) are key regulatory regions that drive gene expression. However, the epigenomic landscape of oral squamous cell carcinoma (OSCC) remains relatively underexplored compared with that of other carcinomas.
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Methods
In this study, we performed ChIP-seq analysis of histone H3 lysine 27 acetylation (H3K27ac) in OSCC cell lines to identify SE regions. The Cancer Genome Atlas (TCGA) datasets of head and neck cancer (HNC) were analyzed to examine the clinical samples. Results: We detected several coding genes and non-coding RNAs that were potentially regulated by SEs.
Fur- thermore, we identified SE-controlled genomic regions that are specific to OSCC by integrating genome-wide expression analyses. Analysis of the TCGA dataset revealed that several of these genes were upregulated in tu- mors and were associated with the prognosis of patients. Conclusions: Collectively, our findings demonstrate that ChIP-seq analysis combined with public database valida- tion provides a novel strategy for identifying potential diagnostic markers in OSCC.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE344nnn/GSE344708 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE344708 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1516581 ncbi.nlm.nih.gov/bioproject/PRJNA1516581 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by array · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- Cancer 75%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE344708 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-array | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |