Single-cell CRISPR Screening for Nuclear Modulators of Mitochondrial Dysfunction

Summary

Mitochondria contain their own ~16.5kb small circular genome, the mitochondrial DNA (mtDNA). Unlike the diploid nuclear genome, cells contain hundreds to thousands of copies of mtDNA. When mutations arise, a cell may contain a mixture of different mtDNA molecules, called heteroplasmy. During development and aging, and in disease, mtDNA mutations can clonally expand to high heteroplasmy levels in single cells, leading to cell dysfunction and death. 

Project aims

The objective of this project is to understand how these mutations clonally expand, and why this process is accelerated in mitochondrial disease and other neurodegenerative disorders. High-throughput single cell functional genomic techniques combined with new animal models allow these questions to be tackled for the first time.

The student will apply novel single-cell sequencing technologies, to simultaneously sequence the mtDNA, transcriptome and chromatin accessibility, and then combine this with gene-disrupting technologies at the single-cell level (CROP-seq, Perturb-seq). We will take advantage of heteroplasmic mouse and patient-derived human cells established in the lab. Possibility exists to translate findings into an in vivo context, in Drosophila or mouse models of mitochondrial disease.

Basic knowledge of bioinformatic pipelines to analyse single-cell sequencing datasets is a plus, but the student will receive further bioinformatics training during the project.  

References  

  • Viscomi C, van den Ameele J, Meyer KC, Chinnery PF. Opportunities for mitochondrial disease gene therapy. Nat Rev Drug Discov. 2023 Jun;22(6):429-430. 
  • van den Ameele J*, Krautz R*, Cheetham SW*, Donovan APA, Llora-Batlle O, Yakob R, Brand AH. Reduced chromatin accessibility correlates with resistance to Notch activation. Nat Commun. 2022 Apr 25;13(1):2210. *Contributed equally.  
  • van den Ameele J, Hong YT, Manavaki R, Kouli A, Biggs H, McIntyre Z, Horvath R, Yu-Wai-Man P, Reid E, Williams-Gray CG, Bullmore ET, Aigbirhio FI, Fryer TD, Chinnery PF. [11C]PK11195-PET brain imaging of the mitochondrial translocator protein in mitochondrial disease. Neurology. 2021;96(22):e2761-e2773. 
  • van den Ameele J, Brand AH. Neural stem cell temporal patterning and brain tumour growth rely on oxidative phosphorylation. eLife. 2019;8:e47887.   

Contact details

Dr Jelle van den Ameele (jv361@cam.ac.uk) Neurology and Mitochondrial Biology Unit  

Co-supervised with Patrick Chinnery

Opportunities

This project is open to applicants who want to do a:

  • PhD
  • MPhil