Heterogeneity analysis and prognostic model construction of HPV negative oral squamous cell carcinoma T cells using ScRNA-seq and bulk-RNA analysis

Chunyan Li ¹, Zengbo Lv ¹, Chongxin Li ¹

⁰Department of Oncology, the First People's Hospital of Qujing City/the Qujing Affiliated Hospital of Kunming Medical University, 1 Yuanlin Road, Qujing, Yunnan, China.

Functional & Integrative Genomics +

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January 23, 2025

View abstract on PubMed

Summary

This study identifies T-cell marker genes to predict survival and immune infiltration in human papilloma virus (HPV)-negative oral squamous cell carcinoma (OSCC). A novel risk model aids in understanding T-cell roles in HPV-negative OSCC prognosis.

Area Of Science

Oncology
Immunology
Genomics

Background

T cells play a crucial role in tumor development and the tumor microenvironment (TME).
Human papilloma virus (HPV)-negative oral squamous cell carcinoma (OSCC) is a significant health concern.
Understanding T-cell dynamics is vital for predicting OSCC progression and treatment response.

Purpose Of The Study

To analyze T-cell marker gene expression profiles in HPV-negative OSCC.
To develop a predictive risk model for HPV-negative OSCC using T-cell genes.
To investigate the link between the risk score and immunotherapy response.

Main Methods

Single-cell RNA sequencing (scRNA-seq) of HPV-negative OSCC samples.
Cell-cell communication, trajectory, and pathway enrichment analyses.
Construction and validation of a T-cell-associated gene prognostic model using TCGA and GEO data.
Assessment of immune infiltration and qRT-PCR validation of key genes.

Main Results

Identified 774 differentially expressed T-cell-associated genes across five subtypes.
Developed a prognostic model predicting survival and TME immune infiltration.
High-risk group showed significantly upregulated expression of PMEPA1, SH2D2A, SMS, and PRDX4 compared to the low-risk group.

Conclusions

The study offers a valuable resource for understanding T-cell heterogeneity in HPV-negative OSCC.
Prognostic risk models based on T-cell genes provide insights into survival and immune infiltration.
Findings may guide personalized treatment strategies for HPV-negative OSCC patients.

Keywords:

Bulk-RNA HPV-negative oral squamous cell carcinoma Prognostic model ScRNA-seq T cells