Unraveling LINE-1 retrotransposition in head and neck squamous cell carcinoma

The relevant role of LINE-1 (L1) retrotransposition in cancer has been recurrently demonstrated in recent years. However, the repetitive nature of retrotransposons makes their identification and detection inaccessible for clinical practice. Also, its clinical relevance for cancer patients is still limited. Here, we developed RetroTest, a new efficient method to quantify L1 activation based on targeted sequencing and a sophisticated bioinformatic pipeline, allowing its application in tumor biopsies. Firstly, we performed RetroTest benchmarking to confirm its high specificity and reliability. Then, we unraveled L1 activation in head-and-neck squamous cell carcinoma (HNSCC) according to an extensive patient cohort including all tumor stages. L1 retrotransposition estimation revealed a surprisingly early activation in HNSCC progression, contrary to its classical association with advanced stages. In addition, L1 activation together with genomic mutational profiling in normal adjacent tissues supported a field cancerization process, a phenomenon where a tissue develops multiple patches of cells with genetic and/or epigenetic alterations, increasing the risk of cancer development in that area. Overall, our results underline an early L1 activation in HNSCC and field characterization, raising L1 as a promising early diagnostic biomarker and supporting the importance of estimating L1 retrotransposition in clinical practice toward a more efficient diagnosis in HNSCC.