Differential Gene Expression Analysis of TCGA mRNA Sequencing Data from Male Patients with and without Lymph Node Metastasis in Tongue Cancer
https://doi.org/10.21315/aos2024.1902.OA03
- Author:
Nam C-N Huynh
1
Author Information
1. Faculty of Odonto-Stomatology, University of Medicine and Pharmacy at Ho Chi Minh City, 652 Nguyen Trai, Ward 11, District 5, 749000, Ho Chi Minh City, Vietnam
- Publication Type:Journal Article
- Keywords:
Metastasis;
mRNA sequencing;
oral squamous cell carcinoma;
TCGA;
tongue cancer
- From:
Archives of Orofacial Sciences
2024;19(2):127-139
- CountryMalaysia
- Language:English
-
Abstract:
Differential Gene Expression Analysis of TCGA mRNA Sequencing Data from Male Patients with and without Lymph Node Metastasis in Tongue Cancer:Gene expression plays a crucial role in progression, invasion, and metastasis in many groups of oral
squamous cell carcinoma. Based on extensive patient data, no research has been done so far on the
differences in gene expression between groups of male patients with tongue squamous cell carcinoma
who drink alcohol and those who do not, about lymph node metastasis. Our study analysed differential
gene expression in male patients with and without lymph node metastasis in tongue cancer, utilising
messenger ribonucleic acid (mRNA) sequencing data from The Cancer Genome Atlas (TCGA)
program. Analysis was performed using R and bioinformatics tools to process mRNA sequencing data,
compare differential gene expression, and examine functional signaling pathways and survival analysis.
After screening the database, 38 out of 74 cases with metastasis were selected for the analysis. The
computational analysis identified a significant increase in cancer invasion transcription factors, such as
GATA2, SP1 and MYC in the metastatic group, whereas CREB1 was more associated with the nonmetastatic group. Functional analysis suggested new prognostic biomarkers for unfavourable outcomes
(TRIML2 and EXOSC4) and favourable outcomes (HS3ST4 and SFTPA1). New suggested markers for
oral and tongue cancer such as TRIML2, EXOSC4 are known for their role in non-oral cancer including
lung and liver cancer. Especially head and neck squamous cell carcinoma (HNSCC) survival analysis and
protein atlas investigation confirmed the indirect biological roles of found markers. The study indicates
that TRIML2 and EXOSC4 could serve as biological markers for predicting lymph node metastasis in
tongue squamous cell carcinoma among male patients who consume alcohol. These findings suggest
that gene expression profiles may play a role in the progression and metastasis of tongue cancer. Further
research is needed to validate these results and to develop targeted therapies for patients with tongue
cancer.
- Full text:2026060323124259887Differential Gene Expression.pdf
