Dynamic nature of RNA modifications and their influence in neurological diseases

• Applicant: Professorin Dr. Stefanie Kaiser
• Subject Area: Biochemistry ; Analytical Chemistry ; Pharmacy
• Term: from 2017 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 373254728

• Final Report Year: 2024

Final Report Abstract

Ribonucleic acid (RNA) has been known at least since its global use as a vaccine against Covid-19. The rapid availability of the vaccine is based on RNA modifications, small changes in RNA introduced by enzymes, which fulfil a variety of biological functions. As part of my Emmy Noether project, I investigated natural RNA modifications (epitranscriptome) in humans that are associated with neurological diseases. At the project start I developed mass spectrometry-based methods to determine the physiological quantities of RNA modifications and to make their dynamics measurable. Together with my team, I investigated the enzymes that incorporate modifications into tRNA in healthy humans and are simultaneously absent in patients with neurological hereditary diseases. Together with international partners, we not only succeeded in demonstrating the lack of tRNA modification but also in better understanding the cellular consequences of their absence. Although it has not yet been conclusively clarified, in most cases we have established a connection between the loss of tRNA modification and changes in protein formation. This malformation of the proteins is probably decisive for the disease in patients. In the case of Alzheimer's disease, we were able to show in cell culture that artificially produced but correctly modified tRNA prevents the malformation of protein formation, which represents a first RNA-based therapeutic approach. A total of 19 publications related to the biological context of the Emmy Noether Project were produced, as well as 21 further publications that utilized the technologies and instrument of the project.

Link to the final report

https://doi.org/10.21248/gups.91562

Publications

• TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. Molecular and Cellular Biology, 37(21).
  Dewe, Joshua M.; Fuller, Benjamin L.; Lentini, Jenna M.; Kellner, Stefanie M. & Fu, Dragony
  
• Benefits of stable isotope labeling in RNA analysis. Biological Chemistry, 400(7), 847-865.
  Asadi-Atoi, Paria; Barraud, Pierre; Tisne, Carine & Kellner, Stefanie
  
• Cytosine-5 RNA methylation links protein synthesis to cell metabolism. PLOS Biology, 17(6), e3000297.
  Gkatza, Nikoletta A.; Castro, Cecilia; Harvey, Robert F.; Heiß, Matthias; Popis, Martyna C.; Blanco, Sandra; Bornelöv, Susanne; Sajini, Abdulrahim A.; Gleeson, Joseph G.; Griffin, Julian L.; West, James A.; Kellner, Stefanie; Willis, Anne E.; Dietmann, Sabine & Frye, Michaela
  
• Formation of tRNA Wobble Inosine in Humans Is Disrupted by a Millennia-Old Mutation Causing Intellectual Disability. Molecular and Cellular Biology, 39(19).
  Ramos, Jillian; Han, Lu; Li, Yan; Hagelskamp, Felix; Kellner, Stefanie M.; Alkuraya, Fowzan S.; Phizicky, Eric M. & Fu, Dragony
  
• Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis. Genes, 10(1), 26.
  Borland, Kayla; Diesend, Jan; Ito-Kureha, Taku; Heissmeyer, Vigo; Hammann, Christian; Buck, Amy H.; Michalakis, Stylianos & Kellner, Stefanie
  
• Surpassing limits of static RNA modification analysis with dynamic NAIL-MS. Methods, 156, 91-101.
  Reichle, Valentin F.; Kaiser, Steffen; Heiss, Matthias; Hagelskamp, Felix; Borland, Kayla & Kellner, Stefanie
  
• Time-resolved NMR monitoring of tRNA maturation. Nature Communications, 10(1).
  Barraud, Pierre; Gato, Alexandre; Heiss, Matthias; Catala, Marjorie; Kellner, Stefanie & Tisné, Carine
  
• Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro. Nucleic Acids Research, 48(7), e41-e41.
  Hagelskamp, Felix; Borland, Kayla; Ramos, Jillian; Hendrick, Alan G.; Fu, Dragony & Kellner, Stefanie
  
• Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder. RNA, 26(11), 1654-1666.
  Ramos, Jillian; Proven, Melissa; Halvardson, Jonatan; Hagelskamp, Felix; Kuchinskaya, Ekaterina; Phelan, Benjamin; Bell, Ryan; Kellner, Stefanie M.; Feuk, Lars; Thuresson, Ann-Charlotte & Fu, Dragony
  
• Production and purification of endogenously modified tRNA-derived small RNAs. RNA Biology, 17(8), 1104-1115.
  Drino, Aleksej; Oberbauer, Vera; Troger, Conor; Janisiw, Eva; Anrather, Dorothea; Hartl, Markus; Kaiser, Steffen; Kellner, Stefanie & Schaefer, Matthias R.
  
• Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6. Nucleic Acids Research, 49(2), 1006-1022.
  Selmi, Tommaso; Hussain, Shobbir; Dietmann, Sabine; Heiß, Matthias; Borland, Kayla; Flad, Sophia; Carter, Jean-Michel; Dennison, Rebecca; Huang, Ya-Lin; Kellner, Stefanie; Bornelöv, Susanne & Frye, Michaela
  
• Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo. Nature Communications, 12(1).
  Heiss, Matthias; Hagelskamp, Felix; Marchand, Virginie; Motorin, Yuri & Kellner, Stefanie
  
• Instrumental analysis of RNA modifications. Critical Reviews in Biochemistry and Molecular Biology, 56(2), 178-204.
  Yoluç, Yasemin; Ammann, Gregor; Barraud, Pierre; Jora, Manasses; Limbach, Patrick A.; Motorin, Yuri; Marchand, Virginie; Tisné, Carine; Borland, Kayla & Kellner, Stefanie
  
• Quantification of Modified Nucleosides in the Context of NAIL-MS. Methods in Molecular Biology, 279-306. Springer US.
  Heiss, Matthias; Borland, Kayla; Yoluç, Yasemin & Kellner, Stefanie
  
• The Stress-Dependent Dynamics of Saccharomyces cerevisiae tRNA and rRNA Modification Profiles. Genes, 12(9), 1344.
  Yoluç, Yasemin; van de Logt, Erik & Kellner-Kaiser, Stefanie
  
• Different modification pathways for m1A58 incorporation in yeast elongator and initiator tRNAs. Nucleic Acids Research, 51(19), 10653-10667.
  Yared, Marcel-Joseph; Yoluç, Yasemin; Catala, Marjorie; Tisné, Carine; Kaiser, Stefanie & Barraud, Pierre
  
• Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry. Accounts of Chemical Research, 56(22), 3121-3131.
  Ammann, Gregor; Berg, Maximilian; Dalwigk, Jan Felix & Kaiser, Stefanie M.
  
• Temporal resolution of NAIL-MS of tRNA, rRNA and Poly-A RNA is overcome by actinomycin D. RSC Chemical Biology, 4(5), 354-362.
  Hagelskamp, Felix; Borland, Kayla; Ammann, Gregor & Kaiser, Stefanie M.
  
• Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1870(1), 166857.
  Pereira, Marisa; Ribeiro, Diana R.; Berg, Maximilian; Tsai, Andy P.; Dong, Chuanpeng; Nho, Kwangsik; Kaiser, Stefanie; Moutinho, Miguel & Soares, Ana R.