AccScience Publishing / EJMO / Online First / DOI: 10.36922/EJMO025260272
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ORIGINAL RESEARCH ARTICLE

Landscape of long interspersed element-1 and Alu chimeric transcripts in breast tumors

Jian Li1,2† ,  Yin Zhang2† ,  Yiting Zhou2 ,  Jianyou Liao2 ,  Yabin Guo2*
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1 Department of Clinic Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
2 Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
†These authors contributed equally to this work.
EJMO, 025260272 https://doi.org/10.36922/EJMO025260272
Received: 24 June 2025 | Revised: 18 July 2025 | Accepted: 1 August 2025 | Published online: 3 September 2025
© 2025 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution -Noncommercial 4.0 International License (CC-by the license) ( https://creativecommons.org/licenses/by-nc/4.0/ )
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Abstract

Introduction: Long interspersed element-1 (L1) and Alu elements are reported to regulate tumor development and progression by forming chimeric transcripts with diverse sequences. While these elements have been implicated in various cancers, the landscape of chimeric transcript formation in breast cancer remains poorly characterized.

Objective: Therefore, in this study, we comprehensively investigated the profiles of L1 and Alu chimeric transcripts in breast tumors by analyzing RNA sequences from The Cancer Genome Atlas (TCGA) database.

Methods: More than 50 billion paired-end RNA sequencing reads from 606 primary breast tumor tissues and 59 matched adjacent normal tissues from the TCGA database were aligned to L1 and Alu consensus sequences with Bowtie2 software and further analyzed.

Results: Our analysis revealed significantly elevated expression levels of L1 and Alu retrotransposons in breast tumor tissues compared to adjacent non-tumor tissues. Importantly, higher expression of L1 and Alu in breast tumors was associated with poorer 10-year overall survival, suggesting their potential as prognostic biomarkers. Further exploration demonstrated that L1 and Alu were extensively expressed in chimeric form with adjacent transcripts. A significant difference in the frequency of 651 L1-mRNA and 1,525 Alu-mRNA chimeric transcripts was observed between non-tumor and tumor tissues. Similarly, 1,009 L1-long non-coding RNA (lncRNA) and 2,575 Alu-lncRNA chimeric transcripts exhibited significantly different frequencies between non-tumor and tumor tissues. Functional enrichment analysis revealed that these differentially expressed chimeric genes played crucial roles in multiple facets of tumorigenesis, including metabolism, signal transduction, immunity, cell cycle regulation, and apoptosis.

Conclusion: Our findings demonstrate that Chimeric transcript formation with L1 and Alu retrotransposons represents a widespread phenomenon in breast cancer that impacts multiple oncogenic pathways. These results significantly expand our understanding of retrotransposon involvement in breast cancer and highlight potential novel targets for diagnostic and therapeutic development.

Keywords
Alu
Breast tumor
Long non-coding RNA
Long interspersed element-1
Retrotransposon
Funding
This work was supported by the National Natural Science Foundation of China (32170641 and 81872295 to YG).
Conflict of interest
The authors declare that they have no conflicts of interest.
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Eurasian Journal of Medicine and Oncology, Electronic ISSN: 2587-196X Print ISSN: 2587-2400, Published by AccScience Publishing
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