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<p>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 <i>APOBEC3B</i> and immune response pathways. In summary, our results support a model whereby L1 retrotransposition triggers downstream genomic instability and viral mimicry response.</p>

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Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月16日

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  • Sophia J. Pribus,
  • Ivana Osredek,
  • Jan Otoničar,
  • Milena Simovic-Lorenz,
  • Chiara Giovenino,
  • Anne Rademacher,
  • Sina Jasmin Wille,
  • Cecilia Berzain Battioni,
  • Michael Scherer,
  • Sergio Manzano-Sanchez,
  • Andreas Kienzle,
  • Urja Parekh,
  • Laura Villacorta,
  • Vladimir Benes,
  • Pooja Sant,
  • Jan-Philipp Mallm,
  • Karsten Brand,
  • Karsten Rippe,
  • Angelika B. Riemer,
  • Holger Sültmann,
  • Christoph Plass,
  • Mladen Stankovic,
  • Jan O. Korbel,
  • Tobias Rausch,
  • Aurélie Ernst

摘要

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.