Journal Article

DKFZ-2026-01789

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer.

Pribus, S. J. ; Osredek, I. ; Otonicar, J. (First author)DKFZ* ; Simovic-Lorenz, M. (First author)DKFZ* ; Giovenino, C.DKFZ* ; Rademacher, A.DKFZ* ; Wille, S. J.DKFZ* ; Berzain Battioni, C.DKFZ* ; Scherer, M.DKFZ* ; Manzano-Sanchez, S.DKFZ* ; Kienzle, A.DKFZ* ; Parekh, U.DKFZ* ; Villacorta, L. ; Benes, V. ; Sant, P.DKFZ* ; Mallm, J.-P.DKFZ* ; Brand, K. ; Rippe, K.DKFZ* ; Riemer, A.DKFZ* ; Sültmann, H.DKFZ* ; Plass, C.DKFZ* ; Stankovic, M. ; Korbel, J.DKFZ* ; Rausch, T. ; Ernst, A. (Last author)DKFZ*

2026
Springer Nature [London]

Abstract: 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.

Note: #EA:B420#LA:B420#

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Contributing Institute(s):

1. Genominstabilität in Tumoren (B420)
2. DKTK HD zentral (HD01)
3. Chromatin-Netzwerke (B066)
4. Epigenomik (B370)
5. Immuntherapie und -prävention (D410)
6. Single-cell Open Lab (W192)
7. Krebsgenomforschung (B063)
8. Mechanismen der genetischen Variation und Datenwissenschaft (B480)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2026

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Database coverage:
; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Agriculture, Biology and Environmental Sciences ; Current Contents - Life Sciences ; Current Contents - Physical, Chemical and Earth Sciences ; DOAJ Seal ; Essential Science Indicators ; Fees ; IF >= 15 ; JCR ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection ; Zoological Record

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