Multi-omics analysis of overexpressed tumor-associated proteins: gene expression, immunopeptide presentation, and antibody response in oropharyngeal squamous cell carcinoma, with a focus on cancer-testis antigens

Front Immunol. 2024 Jul 29:15:1408173. doi: 10.3389/fimmu.2024.1408173. eCollection 2024.

Abstract

Introduction: The human leukocyte antigen complex (HLA) is essential for inducing specific immune responses to cancer by presenting tumor-associated peptides (TAP) to T cells. Overexpressed tumor associated antigens, mainly cancer-testis antigens (CTA), are outlined as essential targets for immunotherapy in oropharyngeal squamous cell carcinoma (OPSCC). This study assessed the degree to which presentation, gene expression, and antibody response (AR) of TAP, mainly CTA, are correlated in OPSCC patients to evaluate their potential as immunotherapy targets.

Materials and methods: Snap-frozen tumor (NLigand/RNA=40), healthy mucosa (NRNA=6), and healthy tonsils (NLigand=5) samples were obtained. RNA-Seq was performed using Illumina HiSeq 2500/NovaSeq 6000 and whole exome sequencing (WES) utilizing NextSeq500. HLA ligands were isolated from tumor tissue using immunoaffinity purification, UHPLC, and analyzed by tandem MS. Antibodies were measured in serum (NAb=27) utilizing the KREX™ CT262 protein array. Data analysis focused on 312 proteins (KREX™ CT262 panel + overexpressed self-proteins).

Results: 183 and 94 of HLA class I and II TAP were identified by comparative profiling with healthy tonsils. Genes from 26 TAP were overexpressed in tumors compared to healthy mucosa (LFC>1; FDR<0.05). Low concordance (r=0.25; p<0.0001) was found between upregulated mRNA and class I TAP. The specific mode of correlation of TAP was found to be dependent on clinical parameters. A lack of correlation was observed both between mRNA and class II TAP, as well as between class II tumor-unique TAP (TAP-U) presentation and antibody response (AR) levels.

Discussion: This study demonstrates that focusing exclusively on gene transcript levels fails to capture the full extent of TAP presentation in OPSCC. Furthermore, our findings reveal that although CTA are presented at relatively low levels, a few CTA TAP-U show potential as targets for immunotherapy.

Keywords: HLA; antibody response (AR); cancer testis antigens (CTA); oropharyngeal squamous cell carcinoma (OPSCC); tumor-associated peptide (TAP).

MeSH terms

  • Adult
  • Aged
  • Antibody Formation / genetics
  • Antibody Formation / immunology
  • Antigen Presentation / immunology
  • Antigens, Neoplasm* / genetics
  • Antigens, Neoplasm* / immunology
  • Exome Sequencing
  • Female
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Male
  • Middle Aged
  • Multiomics
  • Oropharyngeal Neoplasms* / genetics
  • Oropharyngeal Neoplasms* / immunology
  • Squamous Cell Carcinoma of Head and Neck / genetics
  • Squamous Cell Carcinoma of Head and Neck / immunology

Substances

  • Antigens, Neoplasm

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. SL, HK, TH, TA, and JE were part of the research training group GRK-2254 (HEIST, 288342734) funded by DFG. SL was funded by University of Ulm within the Clinician Scientist Program.