Retrotransposon Activity in Chronic Lymphocytic Leukemia: Associations with RNA Splicing and TP53 Dysfunction

Abstract

Retroelements (RE), particularly autonomous Long Interspersed Element-1 (LINE-1), function as potent drivers of genomic instability in various malignancies. While normally silenced by epigenetic mechanisms, their reactivation in cancer cells can drive tumor evolution. TP53 is known to repress LINE-1 transcription; however, the consequences of TP53 dysfunction on retrotransposition and transcriptional activity in chronic lymphocytic leukemia (CLL) remain unknown. To investigate the relationship between TP53 status, LINE-1 retrotranspositional potential, and transcriptomic alterations, we utilized a multi-omics approach, combining a highly sensitive NGS protocol for detecting novel LINE-1 insertions with transcriptomic profiling of transposable elements and protein-coding genes. We applied these methods to a cohort of CLL patients stratified by the presence or absence of TP53 clonal evolution and to CLL-derived cell lines MEC1 and HG3, including CRISPR/Cas9-engineered TP53 mutants. Genomic analysis revealed no evidence of widespread somatic retrotransposition, suggesting that CLL exhibits resistance against de novo LINE-1 insertions. Conversely, transcriptomic profiling uncovered distinct transposon expression signatures aligned with patterns of TP53 mutation status evolution. Notably, differentially expressed genes were significantly enriched in the RNA splicing pathway, indicating that while LINE-1 elements remain largely constrained at the genomic level, their transcriptomic activity may influence cellular rewiring, affecting patterns of TP53 mutation clonal evolution. Based on these results, we argue that the pathogenic contribution of retroelements in CLL lies in transcriptomic dysregulation and splicing alterations, rather than in direct DNA damage caused by LINE-1 insertions.