Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency Journal Article

   

Authors:	Solovyov, A.; Behr, J. M.; Hoyos, D.; Banks, E.; Drong, A. W.; Thornlow, B.; Zhong, J. Z.; Garcia-Rivera, E.; McKerrow, W.; Chu, C.; Arisdakessian, C.; Zaller, D. M.; Kamihara, J.; Diao, L.; Fromer, M.; Greenbaum, B. D.
Article Title:	Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency
Abstract:	Somatic mobilization of LINE-1 (L1) has been implicated in cancer etiology. We analyzed a recent TCGA data release comprised of nearly 5000 pan-cancer paired tumor-normal whole-genome sequencing (WGS) samples and ~9000 tumor RNA samples. We developed TotalReCall an improved algorithm and pipeline for detection of L1 retrotransposition (RT), finding high correlation between L1 expression and “RT burden” per sample. Furthermore, we mathematically model the dual regulatory roles of p53, where mutations in TP53 disrupt regulation of both L1 expression and retrotransposition. We found those with Li-Fraumeni Syndrome (LFS) heritable TP53 pathogenic and likely pathogenic variants bear similarly high L1 activity compared to matched cancers from patients without LFS, suggesting this population be considered in attempts to target L1 therapeutically. Due to improved sensitivity, we detect over 10 genes beyond TP53 whose mutations correlate with L1, including ATRX, suggesting other, potentially targetable, mechanisms underlying L1 regulation in cancer remain to be discovered. © The Author(s) 2025.
Keywords:	genetics; mutation; genetic analysis; neoplasm; neoplasms; metabolism; gene expression; algorithms; protein p53; rna; gene expression regulation; gene expression regulation, neoplastic; algorithm; tumor suppressor protein p53; li-fraumeni syndrome; tumor; tp53 protein, human; heterogeneity; long interspersed nucleotide elements; atrx protein, human; cancer; humans; human; whole genome sequencing; transcriptional regulator atrx; multiomics; long interspersed nuclear element; x-linked nuclear protein
Journal Title:	Nature Communications
Volume:	16
ISSN:	2041-1723
Publisher:	Nature Publishing Group
Date Published:	2025-02-28
Start Page:	2049
Language:	English
DOI:	10.1038/s41467-025-57271-1
PUBMED:	40021663
PROVIDER:	scopus
PMCID:	PMC11871128
DOI/URL:	https://www.scopus.com/inward/record.uri?eid=2-s2.0-85219644811&doi=10.1038%2fs41467-025-57271-1&partnerID=40&md5=dca422e795ae2e408eed0b12bdb20c5c
Notes:	Erratum issued, see DOI: 10.1038/s41467-025-58288-2 -- The MSK Cancer Center Support Grant (P30 CA008748) is acknowledge in the PDF -- Corresponding authors is MSK author: Alexander Solovyov and Benjamin D. Greenbaum -- Source: Scopus

https://synapse.mskcc.org/synapse/works/has_related_data_chk/223829