What is the name of the methodology?
Polytope mouse
OI Name
Jacco van Rheenen
What is the methodology good for?
Tracing the fate of individual cells and their progeny remains a challenging task. Here, we introduce ‘Polytope’, an epitope barcoding system capable of generating up to 512 unique color codes that can be read out by both imaging and DNA/RNA sequencing.
What is/are the main advantages of this methodology over related technologies?
While imaging-based fate-mapping using e.g. fluorescent markers (e.g. confetti, luciferase) can provide spatial information, it generally lacks complexity due to limited label diversity, resulting in diminished capture of comprehensive lineages and fate maps. Our polytope system can generate up to 512 unique color codes, providing the often needed label diversity.
What are the most important limitations of the methodology?
The system requires antibody staining and can therefore not be done on living cells or tissues.
What type of samples are compatible with methodology?
Cancer cell lines | Primary cells in culture | Organoids | Primary tissue |
possibly | Yes | possibly | Yes |
What future develops to the methodology are you planning, in any?
The current polytope is localized in the nucleus and requires fixation and permeabilization of cells and tissues for labeling the different bar codes. We are currently working on the second generation of this mouse model where the barcode is localized at the membrane at the outside of the cells, so that barcoded cells in tissues can be labelled and isolated by flow cytometry. Moreover, we are working on the 3 generation that is based on the expression of fluorophores, so labelling is no longer needed.
If someone outside your lab wants to use the methodology, what is the best option?
A) What do you need to provide them to make it work?
- Need to perform the first experiments together in the van Rheenen lab
- This will enable the optimalization and training of a person from their lab
- After that, we can provide protocols to perform in their own lab.
B) Is there any minimal expertise/equipment others need to work with the methodology?
Multi-color microscopes, bioinformatic skills, mouse experience
Name one or more people in your lab that are experienced with the methodology
- Tom van Leeuwen
- Lali Noguera Delgado
Who originally developed the methodology?
The technologies was developed by the Daniel Postrach when he was a PhD student in the van Rheenen lab, and finished it when he was in the Hans-Reimer Rowald group. More info can be found in the following pre-print: https://www.biorxiv.org/content/10.1101/2024.11.20.624484v1