A meta-validated immune infiltration-related gene model predicts prognosis and immunotherapy sensitivity in HNSCC

Abstract

Background Tumor microenvironment (TME) is of great importance to regulate the initiation and advance of cancer. The immune infiltration patterns of TME have been considered to impact the prognosis and immunotherapy sensitivity in Head and Neck squamous cell carcinoma (HNSCC). Whereas, specific molecular targets and cell components involved in the HNSCC tumor microenvironment remain a twilight zone. Methods Immune scores of TCGA-HNSCC patients were calculated via ESTIMATE algorithm, followed by weighted gene co-expression network analysis (WGCNA) to filter immune infiltration-related gene modules. Univariate, the least absolute shrinkage and selection operator (LASSO), and multivariate cox regression were applied to construct the prognostic model. The predictive capacity was validated by meta-analysis including external dataset GSE65858, GSE41613 and GSE686. Model candidate genes were verified at mRNA and protein levels using public database and independent specimens of immunohistochemistry. Immunotherapy-treated cohort GSE159067, TIDE and CIBERSORT were used to evaluate the features of immunotherapy responsiveness and immune infiltration in HNSCC. Results Immune microenvironment was significantly associated with the prognosis of HNSCC patients. Total 277 immune infiltration-related genes were filtered by WGCNA and involved in various immune processes. Cox regression identified nine prognostic immune infiltration-related genes (MORF4L2, CTSL1, TBC1D2, C5orf15, LIPA, WIPF1, CXCL13, TMEM173, ISG20) to build a risk score. Most candidate genes were highly expressed in HNSCC tissues at mRNA and protein levels. Survival meta-analysis illustrated high prognostic accuracy of the model in the discovery cohort and validation cohort. Higher proportion of progression-free outcomes, lower TIDE scores and higher expression levels of immune checkpoint genes indicated enhanced immunotherapy responsiveness in low-risk patients. Decreased memory B cells, CD8+ T cells, follicular helper T cells, regulatory T cells, and increased activated dendritic cells and activated mast cells were identified as crucial immune cells in the TME of high-risk patients. Conclusions The immune infiltration-related gene model was well-qualified and provided novel biomarkers for the prognosis of HNSCC.

Type I conventional dendritic cells and CD8+ T cells predict favorable clinical outcome of head and neck squamous cell carcinoma patients

“…However, there are limited investigations exploring the tumor immune landscape in detail. So far, most studies have focused on detecting the presence of T cells using immunohistochemistry or bulk gene expression profiles of tumor samples ( 26 – 29 ). Several groups reported a positive impact of high densities of CD8 + T cells on the survival and relapse of HNSCC patients ( 5 , 27 ).…”

Deciphering COPS5 influence on immune infiltration and prognosis in head and neck squamous cell carcinoma

“…Several studies have made significant progress in establishing prognostic models for HNSCC to predict patient survival. These models have been constructed using various biological factors and gene sets, including immune-related long non-coding RNAs [ 14 ], immune infiltration-related genes [ 15 ], ferroptosis-related genes [ 16 ], N6 methyladenosine (m6A) regulator-related genes [ 17 ], and ion channel related genes [ 18 ]. These models, constructed using Lasso regression, have proven effectiveness in predicting patient survival rates, as well as the response to of immunotherapy.…”

Macrophage Profiling in Head and Neck Cancer to Improve Patient Prognosis and Assessment of Cancer Cell–Macrophage Interactions Using Three-Dimensional Coculture Models

“…The vast majority of HNCs are squamous cell carcinomas, and they are divided into several subtypes according to the primary tumor localization (oral cavity, nasopharynx, oropharynx, hypopharynx, and larynx) [ 2 ]. Head and neck tumors are associated with high levels of morbidity and mortality [ 3 ]. The overall 5-year survival rate of HNC is less than 50%, and this has remained unchanged over the past several decades [ 4 ], although novel therapeutic strategies have been proposed.…”