Cytocentric Visionaries: Tim Downing, PhD

This post contains excerpts from an interview that Dr. Alicia Henn, Chief Scientific Officer of BioSpherix, conducted with Dr. Timothy Downing. Our conversation was edited for brevity and clarity.

In the last post, Dr. Downing introduced us to his work on the Epigenomics of Cell Reprogramming and talked about some technical limitations. Today we talk in more depth about controlling the microenvironment for in vitro cell research.

Here at the Cytocentric Blog, we are always trying to take the cell’s point of view, advocating for the most physiologically relevant environment for the cell in vitro. How much do we know about epigenetics in vivo?

TD: That’s a hard question. There’s been a lot of data generated by isolating primary tissues and seeing the DNA methylation and histone modification profiles across the genome. You can sort cells and see what the epigenetic profile is. That way we’re able to see how epigenetics are changing throughout development in an in vivo context. With this approach, however, there’s only so much you can do, especially when you’re talking about human cells and working with fresh human tissues.

So we try to expand primary cells in culture or create stable cells lines to stay within certain ethical guidelines. But in this case we lose a bit more information when we culture cells in a dish without considering how this non-native environment influences cell identity at the epigenetic level, especially from a material standpoint. Obviously chemical factors, growth factors, and cell-cell signaling are not the same as you would have in an in vivo context. There are a slew of other components that we can’t normalize for.

So we’re limited in what we can understand from in vitro work by how much the microenvironment differs from in vivo?

TD: I would say in vivo we’re limited and also we’re limited in vitro because we haven’t found the ideal physiological, or pathophysiological, environment to mimic.

My work looks at how the biophysical microenvironment influences cells. There’s a lot of interest in the adhesome, and how it changes when outside the body, but it’s a tough system to control for because there are so many variables and gene expression might not be relevant to protein levels or even functional protein units.

That’s why I was very excited to see what BioSpherix has going on because the only way to really know what variable, or how one variable, is influencing your cell culture is by controlling them. If you can’t control them all, you can only make estimations. With this type of control, my hope is to understand how the extracellular microenvironment influences cell behavior so we can make better predictions.

So if you could take any kind of equipment to measure your cell’s responses, and put it inside a closed environment, where you could control not only liquid chemical factors but also bioactive gases, what equipment would that be?

TD: Equipment to measure anything that happens in a physiological context like rigidity of a substrate, dynamic or static stress, mechanical strain, and shear stress from fluid flow. These are all mechanical cues that exist inside of the body that are difficult to control for. When you combine those with oxygen gradients, and what we call hypoxia, it becomes very difficult to control for all of these things.

I would like to be able to put my own tools, and those of other labs, inside a space where you can control oxygen, to answer questions about how they all integrate to influence cell behavior.

The moment you take a single cell out of its environment, there are going to be changes.

It’s like my favorite line in the movie Pocahontas, ‘You can never step in the same river twice.’ Once you go to a certain place with a cell, I’m not going to say it’s impossible to get back there because obviously we have things like reprogramming, but how do you get it back to that original state? It’s very difficult.

Our interview with Dr. Downing is continued in our next blog post in which he tells us about his path to this point and what impact he would like to have on the field.

If you would like to be considered for a Cytocentric Visionary feature, please contact us here and tell us how your work fits the Cytocentric Principles.

 Tim Downing interview: Part 1, Part 2, Part 3