Identification and risk modelling of bacterial lipopolysaccharide-related subtypes in head and neck squamous cell carcinoma to predict prognostic and immunological properties

Background

Head and neck squamous cell carcinoma (HNSC) is the most common form of head and neck cancer, and lipopolysaccharide (LPS), a component of Gram-negative bacteria, plays a vital role in modulating immune function. The study aimed to uncover bacterial LPS-associated subtype signatures that could predict the prognosis and effectiveness of immunotherapy for HNSC patients.

Methods

First, transcriptome data from patients with HNSC were downloaded from the Cancer Genome Atlas (TCGA) database, and the samples consisted of 522 primary tumour tissues and 44 adjacent normal tissues. Non-Negative Matrix Factorization (NMF) clustering was used to perform cluster analysis on the samples. Univariate, multivariate, and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses were performed to identify prognostic characteristic genes and develop a risk model. This model was validated in independent Gene Expression Omnibus (GEO) data sets: GSE41613. The receiver operating characteristic (ROC) curves were constructed and the Area Under the Curve (AUC) values were calculated for 1-, 3- and 5-year ROC curves to assess model performanc. In addition, we utilized ssGSEA to explore differences in immune infiltration between risk groups. Finally, drug sensitivity analyses was performed using the pRRophitic algorithm.

Results

We identified 2 subtypes and 9 LPS-related biomarkers in HNSC. ROC curves demonstrated that these signature genes were effective in predicting patient prognosis. Compared to the high-risk group, the low-risk group had higher immunologic infiltration levels and greater response to immunotherapy. Finally, we identified potential drugs including 5-Fluorouracil, Bleomycin, Cetuximab, and Vinblastine that might be more suitable for the treatment of low-risk patients.

Conclusion

In summary, we identified novel LPS-related molecular subtypes and developed a prognostic model, describing their immunological characteristics that may provide valuable insights for the prognosis of HNSC patients.