ALL-tRNAseq enables robust tRNA profiling in tissue samples.

Autor:	Scheepbouwer C; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands; c.scheepbouwer@amsterdamumc.nl d.koppers@math.leidenuniv.nl.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Aparicio-Puerta E; Genetics Department, Faculty of Science, University of Granada, 18071 Granada, Spain., Gomez-Martin C; Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Verschueren H; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., van Eijndhoven M; Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Wedekind LE; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Giannoukakos S; Genetics Department, Faculty of Science, University of Granada, 18071 Granada, Spain., Hijmering N; Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Gasparotto L; Department of Child and Adolescent Psychiatry, Emma Children's Hospital, Amsterdam UMC, Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., van der Galien HT; Department of Hematology, Medical Center Leeuwarden, 8934 AD Leeuwarden, the Netherlands.; HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands., van Rijn RS; Department of Hematology, Medical Center Leeuwarden, 8934 AD Leeuwarden, the Netherlands.; HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands., Aronica E; Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC location University of Amsterdam, 1105 AZ Amsterdam, the Netherlands., Kibbelaar R; HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands.; Department of Pathology, Pathology Friesland, 8917 EN Leeuwarden, the Netherlands., Heine VM; Department of Child and Adolescent Psychiatry, Emma Children's Hospital, Amsterdam UMC, Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Wesseling P; Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, University Medical Center Utrecht, 3584 CS Utrecht, the Netherlands., Noske DP; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Vandertop WP; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., de Jong D; Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Pegtel DM; Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Hackenberg M; Genetics Department, Faculty of Science, University of Granada, 18071 Granada, Spain., Wurdinger T; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Gerber A; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands., Koppers-Lalic D; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands; c.scheepbouwer@amsterdamumc.nl d.koppers@math.leidenuniv.nl.; Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.
Jazyk:	angličtina
Zdroj:	Genes & development [Genes Dev] 2023 Mar 01; Vol. 37 (5-6), pp. 243-257. Date of Electronic Publication: 2023 Feb 21.
DOI:	10.1101/gad.350233.122
Abstrakt:	Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. However, it remains unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research. (© 2023 Scheepbouwer et al.; Published by Cold Spring Harbor Laboratory Press.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu