Introduction: HPV± HNSCC differ in their biology and response to treatment, particularly radiotherapy, with HPV+ being more sensitive. HNSCC cell lines recapitulate this difference in vitro. Materials and Methods: To identify protein expression differences between HPV± HNSCC cells in an open, unbiased approach, we performed a mass spectrometric comparison of 7 HPV+ and 6 HPV- HNSCC lines with reported differences in radiosensitivity. Results: We identified a total of 3603 proteins. As expected, the HPV surrogate marker p16 was found to be expressed at far higher levels in HPV+ samples. 273 proteins were found to be differentially expressed with a p-value of >0.05 (Students T-test, uncorrected) and a fold change of ≥1.5. Some results of differentially expressed factors obtained in previous HPV±OPSCC tissue comparisons by our own and other groups were recapitulated in cell lines, while other prominently differentially expressed factors did not differ in cell lines, for example the MCM proteins of the replicative helicase complex. Four proteins with reported DNA repair functions were downregulated in HPV+ HNSCC cells, and one reported radiosensitivity factor was upregulated. In addition, several interferon-induced genes were expressed at reduced levels. Functional characterisation of promising proteins is ongoing. Conclusions: We identified hypothesis-generating differences between HPV+ and HPV- HNSCC cell lines, some of which will be further investigated for their mechanistic role and clinical relevance. As HPV± cell lines differ in the expression of several proteins from tumour tissue, while other features are well recapitulated, the question in which aspects they do or do not reflect tumour behaviour will be further investigated.

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