In Germany, approximately 30-50% of Oropharyngeal squamous-cell carcinoma (OPSCC) are related to human papillomaviruses (HPV), of which 90% are caused by HPV-16. The analysis of cancer-associated antigens is needed to develop antigen-specific immunotherapy and to determine the level of personalization required for therapeutic cancer vaccines.
Human leucocyte antigen (HLA) ligands from fresh frozen OPSCC biopsies were analyzed. HLA molecules were extracted from tumor tissue using immunoaffinity chromatography. HLA-bound peptides were subjected to high performance liquid chromatography (HPLC) and tandem mass spectrometry (MS/MS). Tumor-exclusive antigens in OPSCC were identified by comparative profiling against an in-house benign and malignant database. Additionally, whole exome sequencing of RNA and DNA isolated from the respective cancer biopsies was performed to complement the database.
To date, HLA ligandomes from 28 OPSCC (15 HPV+; 13 HPV-) patients were analyzed. Compared to the benign samples database, 148 source proteins were tumor-exclusive for HLA class I and 200 source proteins for HLA class II. The mean number of tumor-exclusive proteins per sample was 6.0 (0-14) for HLA class I and 7.7 for HLA class II (0-41) respectively. Among the tumor exclusive proteins for HLA class I, 23 had not been detected in other malignant tumor ligandomes (n = 703 samples) and 75 for HLA class II (n = 433 samples). A principal component analysis of the HLA-ligandomes from HPV+ and HPV- revealed significant differences between the two groups. For HLA-class I, 85 tumor-exclusive proteins were only found in HPV+ and 55 in HPV-, whereas 8 proteins were found in both groups. Among the 200 HLA class II tumor-exclusive proteins, 96 were only found in HPV+ and 95 in HPV- respectively, whereas 9 were shared by HPV+ and HPV-.
The analysis of HLA-ligandomes from OPSCC revealed tumor-exclusive and newly discovered antigens. We found clear differences between the HLA ligandomes of HPV+ and HPV- patients. These differences need to be taken into account for therapeutic vaccination strategies. The level of personalization needed for such vaccines remains to be determined.
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University of Ulm, Clinician Scientist Programme.
S. Laban: Honoraria (institution), Advisory / Consultancy, Travel / Accommodation / Expenses: Merck Sharp & Dohme (MSD); Honoraria (institution), Advisory / Consultancy, Travel / Accommodation / Expenses: Bristol-Myers Squibb; Honoraria (institution), Advisory / Consultancy, Travel / Accommodation / Expenses: AstraZeneca; Honoraria (institution): Merck Serono. P.J. Schuler: Advisory / Consultancy: Bristol-Myers Squibb. T.K. Hoffmann: Honoraria (institution), Advisory / Consultancy: Merck Sharp & Dohme (MSD); Honoraria (institution): Bristol-Myers Squibb; Honoraria (institution): Merck Serono. H. Rammensee: Advisory / Consultancy, Leadership role, Shareholder / Stockholder / Stock options, Officer / Board of Directors: Immatics; Advisory / Consultancy, Leadership role, Shareholder / Stockholder / Stock options, Officer / Board of Directors: CureVac; Advisory / Consultancy, Leadership role, Shareholder / Stockholder / Stock options, Officer / Board of Directors: Synimmune. All other authors have declared no conflicts of interest.