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EASTBIO Single cell multi-omics profiling of the brain for the study of neurological disease

  • Full or part time
    Dr C Sibley
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Second Supervisor: Emily Osterweil, CMVM University of Edinburgh
Recent research emphasises that neurological diseases involve a complex interplay of cell autonomous and non-cell autonomous events mediated by the different cell types in the brain (e.g.1). Accordingly, technologies to dissect this cellular heterogeneity are urgently required. A variety of scalable single cell profiling methods have accordingly been developed for monitoring individual cell chromatin dynamics, transcriptomes and proteomes2. However, no approach has yet been developed to allow monitoring of RNA and protein from the intracellular environment of the same cells in a truly scalable manner. Achieving this would dramatically enhance the power of single cell profiling studies and enable sophisticated systems biology methods to be applied across modalities.

In this project the student will develop and apply methods to i) simultaneously monitor the transcriptome and intracellular proteome from individual cells, and ii) simultaneously monitor the transcriptome and activity of specific regulatory RNA-binding proteins (RBPs) from individual cells with an adapted version of the powerful iCLIP method of which the Sibley lab is expert3. Notably, both workflows are closely related whilst pilot data has been generated in the Sibley lab demonstrating the feasibility of both. Initially the student will optimise both workflows in monocultures of immortalised human cells in which specific RBPs and other proteins are knocked out with RNAi. The techniques will be used to validate these perturbations alongside more traditional molecular biology methods (e.g. western blotting, qPCR, iCLIP). Next, the student will adapt the protocol for study of both the mouse and human brain where single nuclei rather than whole cells are profiled. Candidate RBPs to be profiled will be those involved in motor neuron disease (Sibley lab) and Fragile X syndrome (Osterweil lab) due to extensive supporting datasets which results can be related to. Last, the student will apply the methods to provide a high-resolution multi-modal view of already available disease-relevant tissue from patients and/or rodent models of the two diseases. Whilst the focus will be study of the brain, the technologies developed will be broadly applicable to other heterogenous cellular systems across evolution.

During the PhD the student will acquire a unique combination of both experimental and computational techniques. This will include standard molecular biology, cell culture, tissue processing, iCLIP and high throughput sequencing methods in the wet lab, and programming skills in the R, python, unix languages in the dry lab. The PhD will be supervised by Dr Sibley (90%) and Dr Osterweil (10%) who have extensive expertise covering the project methodology, diseases covered and model systems. The student will integrate into the University of Edinburgh’s globally recognised communities of leading RNA biologists and Neuroscientists, and benefit from excellent graduate training opportunities that are on offer at the School of Biology.


Funding Notes

The “Visit Website” button will take you to our Online Application checklist. Complete each step and download the checklist which will provide a list of funding options and guide you through the application process. Follow the instructions on the EASTBIO website (you will be directed here from our application checklist), ensuring you upload an EASTBIO application form and transcripts to your application, and ticking the box to request references. Your referees should upload their references using the EASTBIO reference form, in time for the 5th January deadline so please give them plenty of time to do this by applying early.

References


1 Serio A, Patani R. Concise Review: The Cellular Conspiracy of Amyotrophic Lateral Sclerosis. Stem Cells. 2018 Mar;36(3):293-303.

2 Stuart T, Satija R. Integrative single-cell analysis. Nat Rev Genet. 2019 May;20(5):257-272.

3 Sibley CR. Individual Nucleotide Resolution UV Cross-Linking and Immunoprecipitation (iCLIP) to Determine Protein-RNA Interactions. Methods Mol Biol. 2018;1649:427-454.

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

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