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

BMC Cancer. 2023 Jan 13;23(1):45. doi: 10.1186/s12885-023-10532-y.

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.

Keywords: Head and neck squamous cell carcinoma; Immune cell infiltration; Immunotherapy sensitivity; Prognostic model; Tumor microenvironment.

Publication types

  • Meta-Analysis

MeSH terms

  • Algorithms*
  • Cytoskeletal Proteins
  • Head and Neck Neoplasms* / genetics
  • Head and Neck Neoplasms* / therapy
  • Humans
  • Immunotherapy
  • Intracellular Signaling Peptides and Proteins
  • Prognosis
  • Squamous Cell Carcinoma of Head and Neck / genetics
  • Squamous Cell Carcinoma of Head and Neck / therapy
  • Transcription Factors
  • Tumor Microenvironment / genetics

Substances

  • WIPF1 protein, human
  • Cytoskeletal Proteins
  • Intracellular Signaling Peptides and Proteins
  • MORF4L2 protein, human
  • Transcription Factors