Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer
Bladder cancer is frequent and highly recurrent. Despite recent advances, knowledge gaps remain in molecular mechanisms underlying disease progression. In this study, we apply integrated multi-omic analyses to a cohort of 48 bladder cancer patients to comprehensively profile genetic, epigenetic, transcriptomic, and spatial features. Combining cell-free DNA sequencing, long-read tumor DNA-sequencing, RNA-sequencing, and spatial transcriptomics, we explore molecular alterations driving bladder cancer. We find frequent somatic LINE-1 (L1) insertions, and show that these L1 insertions are active and occur early in bladder cancer development. We link somatic L1 insertion with downstream genomic rearrangements and chromosomal instability, including increased structural variant and extrachromosomal DNA (ecDNA) counts in patients with high L1 counts. We identify variable ecDNA enrichment across tissue architecture, with highest enrichment overlapping differential expression of APOBEC3B and immune response pathways. In summary, our results support a model whereby L1 retrotransposition triggers downstream genomic instability and viral mimicry response.
Authors
- Aurélie Ernst (ORCID: https://orcid.org/0000-0002-8082-3677)
- Karsten Brand
- Milena Simović (ORCID: https://orcid.org/0000-0001-8835-6885)
- Urja Parekh (ORCID: https://orcid.org/0000-0003-3834-7010)
- Christoph Plass (ORCID: https://orcid.org/0000-0003-2554-3952)
- Holger Sültmann (ORCID: https://orcid.org/0000-0002-5257-8600)
- Laura Villacorta (ORCID: https://orcid.org/0000-0002-9509-8594)
- Tobias Rausch (ORCID: https://orcid.org/0000-0001-5773-5620)
- Chiara Giovenino (ORCID: https://orcid.org/0000-0003-2041-4019)
- Mladen Stanković (ORCID: https://orcid.org/0000-0001-7334-7150)
- Anne Rademacher (ORCID: https://orcid.org/0000-0003-3054-3121)
- Vladimı́r Beneš (ORCID: https://orcid.org/0000-0002-0352-2547)
- Jan Otoničar
- Andreas Kienzle (ORCID: https://orcid.org/0009-0008-4142-3196)
- Pooja Sant (ORCID: https://orcid.org/0000-0001-9301-3211)
- Jan‐Philipp Mallm (ORCID: https://orcid.org/0000-0002-7059-4030)
- Karsten Rippe (ORCID: https://orcid.org/0000-0001-9951-9395)
- Jan O. Korbel (ORCID: https://orcid.org/0000-0002-2798-3794)
- Sophia Pribus (ORCID: https://orcid.org/0009-0008-7041-0765)
- Michael Scherer (ORCID: https://orcid.org/0000-0001-7990-6179)
- Angelika Beate Riemer (ORCID: https://orcid.org/0000-0002-5865-0714)
- Sina Jasmin Wille (ORCID: https://orcid.org/0009-0000-1254-7431)
- Ivana Osredek (ORCID: https://orcid.org/0009-0007-1275-7122)
- Sergio Manzano-Sanchez
- Cecilia Berzain Battioni
Institutions
- German Cancer Research Center (DE)
- Heidelberg University (DE)
- University Hospital Heidelberg (DE)
- German Center for Infection Research (DE)
- Heidelberg Engineering (Germany) (DE)
- European Molecular Biology Laboratory (DE)
- DKFZ-ZMBH Alliance (DE)
- Medical University of Vienna (AT)
- Epigenomics (Germany) (DE)
- Stanford University (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-07-16
- DOI
- https://doi.org/10.1038/s41467-026-75399-6
- Primary Topic
- Bladder and Urothelial Cancer Treatments
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Deutsches Krebsforschungszentrum
- Deutsche Forschungsgemeinschaft
- Deutsche Krebshilfe