Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures
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- dc.contributor.author Milenkovic, Ivan
- dc.contributor.author Cruciani, Sonia
- dc.contributor.author Llovera Nadal, Laia
- dc.contributor.author Lucas, Morghan C.
- dc.contributor.author Medina, Rebeca
- dc.contributor.author Pauli, Cornelius
- dc.contributor.author Heid, Daniel
- dc.contributor.author Muley, Thomas
- dc.contributor.author Schneider, Marc A.
- dc.contributor.author Klotz, Laura V.
- dc.contributor.author Allgäuer, Michael
- dc.contributor.author Lattuca, Ruben
- dc.contributor.author Lafontaine, Denis L. J.
- dc.contributor.author Müller-Tidow, Carsten
- dc.contributor.author Novoa, Eva Maria
- dc.date.accessioned 2025-02-28T13:03:47Z
- dc.date.embargoEnd info:eu-repo/date/embargoEnd/2025-12-10
- dc.date.issued 2025
- dc.description.abstract Mammalian ribosomal RNA (rRNA) molecules are highly abundant RNAs, decorated with over 220 rRNA modifications. Previous works have shown that some rRNA modification types can be dynamically regulated; however, how and when the mammalian rRNA modification landscape is remodeled remains largely unexplored. Here, we employ direct RNA sequencing to chart the human and mouse rRNA epitranscriptome across tissues, developmental stages, cell types, and disease. Our analyses reveal multiple rRNA sites that are differentially modified in a tissue- and/or developmental stage-specific manner, including previously unannotated modified sites. We demonstrate that rRNA modification patterns can be used for tissue and cell-type identification, which we hereby term "epitranscriptomic fingerprinting." We then explore rRNA modification patterns in normal-tumor matched samples from lung cancer patients, finding that epitranscriptomic fingerprinting accurately classifies clinical samples into normal and tumor groups from only 250 reads per sample, demonstrating the potential of rRNA modifications as diagnostic biomarkers.
- dc.embargo.liftdate 2025-12-10
- dc.format.mimetype application/pdf
- dc.identifier.citation Milenkovic I, Cruciani S, Llovera L, Lucas MC, Medina R, Pauli C, et al. Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures. Mol Cell. 2025 Jan 2;85(1):177-190.e7. DOI: 10.1016/j.molcel.2024.11.014
- dc.identifier.doi http://dx.doi.org/10.1016/j.molcel.2024.11.014
- dc.identifier.issn 1097-2765
- dc.identifier.uri http://hdl.handle.net/10230/69753
- dc.language.iso eng
- dc.publisher Elsevier
- dc.relation.ispartof Mol Cell. 2025 Jan 2;85(1):177-190.e7
- dc.rights © Elsevier http://dx.doi.org/10.1016/j.molcel.2024.11.014
- dc.rights.accessRights info:eu-repo/semantics/embargoedAccess
- dc.subject.keyword RNA modifications
- dc.subject.keyword Cancer
- dc.subject.keyword Classification
- dc.subject.keyword Direct RNA sequencing
- dc.subject.keyword Epitranscriptome
- dc.subject.keyword Fingerprinting
- dc.subject.keyword Nanopore
- dc.subject.keyword Pseudouridine
- dc.subject.keyword rRNA
- dc.title Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/acceptedVersion