ALL-tRNAseq enables robust tRNA profiling in tissue samples
| العنوان: | ALL-tRNAseq enables robust tRNA profiling in tissue samples |
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| المؤلفون: | Chantal Scheepbouwer, Ernesto Aparicio-Puerta, Cristina Gomez-Martin, Heleen Verschueren, Monique van Eijndhoven, Laurine E. Wedekind, Stavros Giannoukakos, Nathalie Hijmering, Lisa Gasparotto, Hilde T. van der Galien, Roos S. van Rijn, Eleonora Aronica, Robby Kibbelaar, Vivi M. Heine, Pieter Wesseling, David P. Noske, W. Peter Vandertop, Daphne de Jong, D. Michiel Pegtel, Michael Hackenberg, Tom Wurdinger, Alan Gerber, Danijela Koppers-Lalic |
| المساهمون: | Pathology, AII - Inflammatory diseases, ANS - Cellular & Molecular Mechanisms, Child and Adolescent Psychiatry & Psychosocial Care, Neurosurgery, ANS - Neurovascular Disorders, ANS - Systems & Network Neuroscience, CCA - Cancer Treatment and Quality of Life, Human genetics, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, AII - Cancer immunology, CCA - Cancer biology and immunology, CCA - Imaging and biomarkers, Amsterdam Neuroscience - Neurovascular Disorders, Amsterdam Neuroscience - Systems & Network Neuroscience, AII - Infectious diseases |
| المصدر: | Genes & development, 37(5-6), 243-257. Cold Spring Harbor Laboratory Press Scheepbouwer, C, Aparicio-Puerta, E, Gomez-Martin, C, Verschueren, H, van Eijndhoven, M, Wedekind, L E, Giannoukakos, S, Hijmering, N, Gasparotto, L, van der Galien, H T, van Rijn, R S, Aronica, E, Kibbelaar, R, Heine, V M, Wesseling, P, Noske, D P, Vandertop, W P, de Jong, D, Pegtel, D M, Hackenberg, M, Wurdinger, T, Gerber, A & Koppers-Lalic, D 2023, ' ALL-tRNAseq enables robust tRNA profiling in tissue samples ', Genes and Development, vol. 37, no. 5-6, pp. 243-257 . https://doi.org/10.1101/gad.350233.122 Genes and Development, 37(5-6), 243-257. Cold Spring Harbor Laboratory Press |
| سنة النشر: | 2023 |
| مصطلحات موضوعية: | tissue samples, Genetics, cancer, high-throughput sequencing, transfer RNA, Developmental Biology |
| الوصف: | 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. |
| اللغة: | English |
| تدمد: | 0890-9369 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d1b9244df37517aa537b551f1c722c3d http://www.scopus.com/inward/record.url?scp=85151574209&partnerID=8YFLogxK |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....d1b9244df37517aa537b551f1c722c3d |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 08909369 |
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