Integration RNA bulk and single cell RNA sequencing to explore the change of glycolysis-related immune microenvironment and construct prognostic signature in head and neck squamous cell carcinoma

Highlights

• •

  High glycolysis level indicates poor prognosis of patients with head and neck squamous cell carcinoma.

• •

  RNA bulk and single cell RNA sequencing database of head and neck squamous cell carcinoma analysis showed that patients with high glycolysis levels had less infiltration of macrophages, T cells and monocytes.

• •

  The risk signature was verified by the external verification dataset, and the results show that the prediction effect is good.

• •

  In vitro functional and Western blot assays confirmed that the above five risk genes(MUCL1,TRIML2,RAB3B,SPINK6,IGSF11) affect tumor function and related to the process of glycolysis.

Abstract

Background

Glycolysis is an indispensable process for tumor cell,but the effect of glycolysis on the prognosis and immune cell infiltration of head and neck squamous cell carcinoma is not clear.

Methods

Based on RNA bulk and single cell RNA sequencing data of head and neck squamous cell carcinoma from The Cancer Genome Atlas(TCGA) and GSE195832, the effect of glycolysis level on immune cell infiltration was analyzed. Then, we obtained the prognostic genes related to glycolysis through survival analysis to construct prognostic risk signature. Our sample and GSE65858 datasets are used as external verification datasets to verify the validity of the signature. Finally, we used Western blot and cell function assays to determine the relationship between risk genes and glycolysis and the function of prognostic genes.

Result

The level of glycolysis was related to the prognosis of head and neck tumors ( P = 0.0044). The results of immune infiltration analysis of TCGA database showed that high level glycolysis subgroup had less infiltration of macrophages, T cells and monocytes. Results of single cell sequencing analysis validates the above results. Additionally, Five risk genes(MUCL1,TRIML2,RAB3B,SPINK6,IGSF11) were selected to construct signature.Risk score was an independent prognostic factor( P < 0.01). The external validation set also shows the same result. In vitro functional and Western blot assays confirmed that the above five genes affect tumor function and related to the process of glycolysis.

Conclusion

Glycolysis-related risk signatures can be used to predict the prognosis and immune infiltration of head and neck squamous cell carcinoma.