We analysed the levels and repair of DSBs and SSBs/alkali-labile sites (ALSs) in HeLa and HNSCC cell lines using γH2AX and 53BP1 foci (as a surrogate marker of DSBs) and alkaline comet assays (for SSBs/ALSs) following PBT at increasing LET. Here, TP53BP1 is linked to head and neck squamous cell carcinoma.