TY  - JOUR
AU  - Milenkovic, Ivan
AU  - Cruciani, Sonia
AU  - Llovera, Laia
AU  - Lucas, Morghan C
AU  - Medina, Rebeca
AU  - Pauli, Cornelius
AU  - Heid, Daniel
AU  - Muley, Thomas
AU  - Schneider, Marc A
AU  - Klotz, Laura V
AU  - Allgäuer, Michael
AU  - Lattuca, Ruben
AU  - Lafontaine, Denis L J
AU  - Müller-Tidow, Carsten
AU  - Novoa, Eva Maria
TI  - Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures.
JO  - Molecular cell
VL  - 85
IS  - 1
SN  - 1097-2765
CY  - New York, NY
PB  - Elsevier
M1  - DKFZ-2024-02647
SP  - 177–190.e7
PY  - 2025
N1  - Molecular Cell, 85(1), pp. 177–190.e7, 2025
AB  - 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.
KW  - RNA modifications (Other)
KW  - cancer (Other)
KW  - classification (Other)
KW  - direct RNA sequencing (Other)
KW  - epitranscriptome (Other)
KW  - fingerprinting (Other)
KW  - nanopore (Other)
KW  - pseudouridine (Other)
KW  - rRNA (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:39662470
DO  - DOI:10.1016/j.molcel.2024.11.014
UR  - https://inrepo02.dkfz.de/record/295827
ER  -