Integrative analysis of LINE-1 retrotransposition and mutational signatures in colorectal cancer

Abstract

Colorectal cancer (CRC) is one of the most common malignancies worldwide, and early-onset colorectal cancer (eoCRC), defined as diagnosis before the age of 50, is increasing globally through mechanisms that remain poorly understood. Long Interspersed Nuclear Element-1 (LINE-1) retrotransposons can become reactivated in cancer due to epigenetic dysregulation, contributing to genomic instability and structural variation. This study aimed to characterize somatic LINE-1 retrotransposition in colorectal tumors and to investigate its associations with clinical variables, driver gene alterations, and mutational signatures, with a particular focus on eoCRC.

Whole-genome sequencing (WGS) data from 61 microsatellite-stable (MSS) colorectal cancer patients from 5 countries in Europe and Asia were analyzed. Somatic LINE-1 insertion events were identified using a consensus pipeline integrating two complementary bioinformatic tools, TotalReCall and xTea. Downstream analyses assessed associations between insertion burden, clinicopathological features, somatic mutations in canonical driver genes, and mutational signature activity.

We identify a key limitation of conventional cancer genomics workflows, which may systematically overlook retrotransposon-mediated mutations and other complex insertional events. In particular, a somatic LINE-1 insertion affecting the tumor suppressor gene FBXW7 was not annotated as a driver alteration in standard analyses, despite being detected by dedicated retrotransposon-calling methods. Interestingly, FBXW7-mutant samples also exhibited a significantly higher overall LINE-1 insertion burden. LINE-1 retrotransposition activity was not associated with age at diagnosis, sex, alcohol consumption, or geographic origin. However, age-stratified analyses revealed that correlations between LINE-1 activity and specific mutational signatures including ID1, ID2, (polymerase slippage) SBS18 (oxidative DNA damage), and SBS2 (APOBEC deamination) were restricted to eoCRC tumors.

Together, these findings demonstrate that somatic LINE-1 retrotransposition contributes to shaping the genomic landscape of MSS colorectal cancer. The observed age-dependent correlation patterns highlight a context-specific role for retrotransposon activity in modulating genomic instability pathways, particularly in early-onset disease, with potential implications in tumor initiation and progression.