Until recently, researchers could not see gene expression in an individual cell. Thanks to single cell sequencing techniques, they now can. But the timing of changes is still hard to visualize, as measuring the cell destroys it.

To address this, we developed an approach based on models in basic physics, explained Welch, treating the cells like they are masses moving through space and we are trying to estimate their velocity.

The model, dubbed MultiVelo, predicts the direction and speed of the molecular changes the cells are undergoing.

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Our model can tell us which things are changing firstepigenome or gene expression--and how long it takes for the first to ramp up the second, said Welch.

They were able to verify the method using four types of stem cells from the brain, blood and skin, and identified two ways in which the epigenome and transcriptome can be out of sync. The technique provides an additional, and critical, layer of insight to so called cellular atlases, which are being developed using single cell sequencing to visualize the various cell types and gene expression in different body systems.

By understanding the timing, Welch noted, researchers are closer to steering the development of stem cells for use as therapeutics.

One of the big problems in the field is the artificially differentiated cells created in the lab never quite make it to full replicas of their real-life counterparts, said Welch. I think the biggest potential for this model is better understanding what are the epigenetic barriers to fully converting the cells into whatever target you want them to be.

Additional authors on this paper include Chen Li, Maria C. Virgilio, and Kathleen L. Collins.

Paper cited: Single-cell multi-omic velocity infers dynamic and decoupled gene regulation, Nature Biotechnology. DOI: 10.1038/s41587-022-01476-y

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Mathematical model could bring us closer to effective stem cell therapies - Michigan Medicine