Individual
DC projects
Research project
Understanding the impact of IEI on RNA processing and lifecycle with new methods
Rationale and Objectives
For IEIs that do not impede transcription, it is unclear of the produced RNA suffers from aberrations throughout its lifecycle such as mislocalization, delayed splicing, translation, or lowered lifetime. DC13 will study how IEIs affect the downstream processing and lifecycle of mutant RNAs by comparatively studying the impact on the RNA lifecycle dynamics of mutant versus wildtype RNAs.
(1) To develop a highly sensitive in situ proximity detection method that will allow annotating RNAs based on their functional state and hence study their lifecycle stage at single molecule resolution in multiplexed fashion, under conditions of disease and treatment.
(2) To combine this method with in situ detection of mutations and mutation corrections in cells and tissues to resolve the impact in spatial organization, cell-cell interactions and visual phenotypes.
(3) Apply the approaches in aims 1 and 2 together to identify the RNAs with IEI mutations at single molecule level in heterozygous samples isolated from patients and see how the RNA processing and utilization is affected. The exact target transcripts will be defined based on early transcriptomics results from the IMMERGE Network. The in situ mutation detection capabilities that DC13 will develop will further enable evaluation of the gene editing approaches by detection of gene corrections within the context of the spatial organization at the cell and tissue level.
Expected results
(1) Generalizable methods and protocols for RNA lifecycle stage annotation.
(2) Integratable approaches for in situ mutation detection.
(3) Identification of the impact of the chosen IEI mutations on RNA lifecycle dynamics.
Planned secondments
UKLFR to receive training on patient sample processing and learn about signaling pathways, m10-m12 (2 months); Alia Therapeutics to learn novel gene editing protocols, m18 (1 month); University of Basel to receive multi-omics analysis, m23-24 (2 months).
PhD programme
PhD in Bioinformatics, EMBL, Heidelberg, Germany