Abstract
Background: LIM class homeobox (LHX) genes, an important subfamily of the homeobox genes, encode transcription factors that have a fundamental role during embryonic development. However, knowledge regarding the function and mechanism of LHXs in head and neck squamous cell carcinoma (HNSCC) is still lacking. Methods: We conduct a bioinformatic analysis to systematically explore the mRNA expression, clinical correlation, prognostic values, and underlying mechanisms of distinct LHXs in HNSCC. The differentially expressed mRNAs in the LIM homeobox gene family and their correlation with clinical variables were determined and verified with packages in software R. The prognosis values of LHXs expression levels were evaluated by Kaplan-Meier (KM) method and Cox proportional hazard model. Gene set enrichment analysis (GSEA) was conducted to understand the potential biological function of LHXs. The immune cell infiltration patterns were estimated through CIBERSORT and TIMER, and the methylation levels of LHXs in HNSCC were explored in UALCAN and MEXPRESS.Results: We found that among 12 LHXs, 8 genes (ISL1, LHX1-3, 5, 9, LMX1A, and LMX1B) showed altered expression in HNSCC tissues and detected significant correlations between their expression and clinical variables. Survival analysis revealed that LHX1, LHX5, LMX1A, LMX1B can serve as unfavorable prognosis predictors, and ISL1, LHX2, LHX9 can serve as favorable predictors in all HNSCC patients. Gene sets enrichment analysis and immune infiltration analyses showed that the aberrant expression of LHXs was closely related to cancer-associated processes and immune cell infiltration patterns. Finally, we observed hyper-methylation in the promoters of ISL1, LHX2, 5, 9, LMX1A, LMX1B and hypo-methylation in LHX3 promoter, suggesting the regulatory mechanism of LHXs abnormal expression may be related to aberrant DNA methylation. Conclusions: Our study found the oncogenic roles of LHX1,5 and LMX1B and the tumor-suppressor roles of ISL1 and LHX2 in patients with HNSCC, suggesting these LHXs as novel diagnostic and prognostic biomarkers for HNSCC.