Dr Ian Tobias is a post-doctoral researcher in the Mitchell laboratory in the Department of Cell & Systems Biology (CSB) working on neural stem cells. He is a member of the Chippewas of the Nawash Unceded First Nation. Upon starting his position in CSB, he earned a Provost Post-Doctoral Fellowship.

Dr Tobias spoke with Research Communications Officer Neil Macpherson on his research, his time at U of T and his future plans at the University of Guelph.

This interview has been edited and condensed for clarity.

New and Specialized Roles for Stem Cells

Neil Macpherson

Congratulations on completing your post-doctoral research on neural stem cells at the Mitchell lab in the Department of Cell and Systems Biology. You recently released a paper from this work on the pre-print server BioRxiv. Could you tell us a bit more about the work you do and how you started out?

Ian Tobias

Thanks! I started on this project shortly after the University of Toronto began reopening its research and learning spaces with preventative measures in place to control the spread of the COVID-19 virus, so about three years ago.

My project involves using stem cells as a tool to understand how different parts of the genome regulate the development of the myriads of cell types that exist in our bodies.

I’m fascinated by how these cells take on new and more specialized roles within the developing organism. I always find myself thinking about how embryonic and fetal cells interpret their environment and then adopt these fates at very specific places and times.

Heads or Tail in Developing Neural Cells

Neil Macpherson
What were the main findings from your study?

Ian Tobias

In our most recent study, the main finding is that there is a very specific regulatory region of the mouse genome that controls the level of the DNA binding protein called Sox2 in certain types of neural cells.

Within the last five years, there’s been a critical mass of research and technological development that shed light on how some neural cells can become located to the head of the organism to become types of neurons found in the brain, while others become located to the trunk of the body to create spinal neurons.

We knew that the levels of Sox2 had a role in allocating neural cells to the head or the tail end of the embryo and now we’ve found a Sox2 regulatory region that helps to determine this very specific regional fate amongst a broader range of fates normally available to neural progenitors.

Neil Macpherson
Is this region only found in mice?

Ian Tobias

The regions we’re looking at specifically seem to be strongly conserved in animals with a vertebral column, so something with a defined head and tail. When we look closely at how the region contributes to genetic activation, we see it is actually a collection of multiple elements which are important for increasing the overall level of Sox2.

It likely plays a role in ensuring that neural progenitor cells found in our brain activate the Sox2 gene properly within the head of the embryo to keep this specific identity, rather than becoming the neural cells found further down the trunk of the animal.

Genome Editing on Neural Progenitors

Neil Macpherson

That head or tail difference is really interesting. So what tools did you use to examine effects on this differentiation from mutations in the regulatory region?

Ian Tobias

We used neural progenitor cells to mimic the process of neural development and we found that this activator region for the Sox2 gene is important for the neural cells to look and behave like progenitor cells found in the developing brain.

With this region removed, the neural progenitor cells look and behave like progenitor cells found in the trunk and spinal cord rather than cranial progenitor cells.

Neil Macpherson
So your discovery was accomplished by removing a region of DNA from the cells. How is that done?

Ian Tobias
The genome is a very large series of molecules organized across separate DNA assemblies that we call chromosomes. We can target very small regions of these chromosomes with molecular scissors that cut and paste at or around the genes in our DNA. This is called genome editing.

So, if we suspect a region of playing a role in regulating how the genome is used by cells during development, we can engineer these molecular scissors to cut at the margins of what we think is important.

Often, this type of experiment actually removes the whole piece of DNA from the genome, and if the cells are able to tolerate the removal of that piece of the genome, then we can see how their abilities and appearance are affected.

Neil Macpherson
So the neural progenitor cells tolerate the removal of the Sox2 regulatory region and become trunk cells instead of brain cells. Does that mean that is there a trunk Sox2 enhancer? Or is Sox2 off in the trunk but on in the head?

Ian Tobias

Sox2 is expressed throughout the central nervous system, which includes the developing spinal cord. But the regulatory regions that direct Sox2 gene activation in those tissues have not yet been characterized in mammals.

Neil Macpherson

That’s a really interesting result. Is there an example of how this affects neural development in vertebrates?

Ian Tobias

Given the very strong underlying importance of this region to brain development, we think that mutations that substantially disrupt the function of this region wouldn’t be well-tolerated.

We know that genetics plays a significant role in these processes and we’re learning more about it every day. Unfortunately, many hereditary disorders result from errors in these developmental processes, and they are largely untreatable.

There are also statistical associations between certain genetic changes that might be found in this region within different groups of people and a predisposition to neuropsychiatric conditions like schizophrenia. However, the link behind this right now is speculative and it would require studies in living organisms to tease out processes like behaviour and psychiatry.

What Comes Next?

Neil Macpherson
When you first make a discovery, like finding out that this form of genetic control can change neural cell fate, how quickly do you start to build on that discovery?

Ian Tobias
We’re currently still in the stage where we’re manipulating a single cell type and doing very targeted transitions between cell fates. All of these cultures done in a laboratory setting have different tradeoffs.

For what comes next, I think some of the best examples of how mutations that affect stem cell function are those that have been associated with malformations of the brain. There are great studies using  emerging three-dimensional models of development to characterize how changes in our DNA relate to heritable diseases.

These techniques allow neural cells or embryonic cells self-assemble and tell us what they can and cannot form based on the minimal cues we provide will be a very interesting next step.

Evolutionary Forces on the Nervous System

Neil Macpherson
What implication do these results have, for example for understanding neural development?

Ian Tobias
I think the discovery of the biological function of this genomic region helps explain how the nervous system of mammals differentiates into regions with very specific forms and functions.

Just to reiterate, one part of the nervous system develops towards the head. The other develops along with trunk of the body, eventually becoming our spinal cord and peripheral nervous system.

In my field of study, it’s exciting to consider that evolutionary forces may have encoded a genetic blueprint for the generation of spinal neurons or brain neurons to have their appropriate place in the body.

And they do it by using these enhancer regions that are responsible for interpreting positional information found within sections of our developing nervous system.

Neil Macpherson
How far away can you go from the idea of an organism with a head and a tail, to organisms that don’t have a strictly defined head and tail that still have this evolutionarily conserved region?

Ian Tobias
When we use data science to pool results across the web of life, we’re looking very closely at these evolutionary relationships. With respect to the groups of protein factors involved in neural cell allocation along the body axis, there are parallels to much simpler organisms – even those without a spinal cord. However, the DNA regions controlling the level of these proteins diverge much more across these evolutionary timescales.

Benefits of the Provost Postdoctoral Fellowship

Neil Macpherson
You mentioned that you started this work just as the university was opening again to the limited use of laboratory facilities.

One of the things that facilitated you starting that work was the Provost Postdoctoral Fellowship, which provides funding to support postdoctoral fellows from underrepresented groups, specifically Indigenous and Black researchers.

Can you share a little bit about how the Provost Postdoctoral Fellowship contributed to this project and to your success in moving forward with this project?

Ian Tobias
Yeah, I think I think that it gave me the breathing room I needed to stay on this path of discovery and scientific exploration.

I felt somewhat reassured that research institutions are continuing to put in the effort to welcome groups of scientists that face barriers to degree completion and representation in academia

I hope this is a genuine indication that research institutions want and value a diverse set of lived experiences, knowledge acquisition and sharing methods and it’s really motivated me to help create learning and research environments based on inclusion and connection between all people.

Lifting Undergraduate Learners

Neil Macpherson
That’s interesting that you talk about lifting other learners. You have also been teaching at the University of Toronto. Can you talk a little bit about how it felt to be able to develop those skills and to share your enthusiasm with undergraduates?

Ian Tobias
I’ve had a couple of contracts now as a sessional instructor in the Department of Cell and Systems Biology in the course called Stem Cell Biology, Developmental Models and Cell Therapeutics.

It’s a really interesting course that blends fundamental biology of stem cell populations and primitive organisms building up that complexity to mammalian species like rodent models, but also the stem cells that are relevant to potentially human health and disease progression or treatment.

It was a great opportunity to be able to engage more regularly with a highly motivated group of learners that find the topic refreshing and on a new frontier in biology and medicine.

I was able to elaborate more on emerging industries like regenerative medicine, tissue engineering, and drug discovery.

It’s always quite rewarding to see students engage with material that they can relate to and be excited about it in this way.

Starting a New Position at the University of Guelph

Neil Macpherson
Having done both research and teaching, you’ve now been hired for possession in at the University of Guelph as a professor. How will you be investigating neural development in your new position?

Ian Tobias
I’m really excited about my new position as Assistant Professor of Comparative Biomedical Science in the Department of Biomedical Sciences at Ontario Veterinary College, University of Guelph.

There, I plan to blend my expertise in developmental biology and functional genomics in a way that leverages the evolutionary relationships we can draw between the human genome and the genome of other mammals that make up the patient population of the Ontario Veterinary College.

I’ll be investigating the development of the parts of the nervous system that coordinate smooth movement and balance. To do this in multiple groups of species that have emerged over mammalian evolution, I will apply cutting-edge cellular programming technologies and genome engineering techniques.

Among my first steps, I’ll be tasked with identifying and understanding regulatory regions that are involved with the development of specific brain structures and engineering specific populations of neural cells that mimic these parts of the developing nervous system.

If the regulatory regions are shared across multiple species, we would like to know why they’re important to specific developmental processes.

And when I come across examples of where species are different in terms of gene regulation, I would like to understand how these regions contribute to the diversification of mammalian features or the emergence of specific genetic disorders.

Working with Animal Patients

Neil Macpherson
There are many canine breeds that are defined as breeds because they maintain their characteristics through selective breeding. But that also can lead to genetic disorders, for example, there is a higher degree of deafness in Dalmatian dogs. So, do you think just looking at different genes from dog patients and doing genomic analysis there that that might help?

Ian Tobias
Certainly. It’s an area of active investigation at major universities across the world. These artificially selected populations of domestic dogs are viewed as excellent models of comparative genomics and heritable disease.

I think just the scope of the genetic diversity across domestic dogs is dizzying. We’ve created 300 dog breeds in half as many years; you don’t get that level of diversification of traits and behaviors without substantial changes to the genome.

But we know that the human genome has hundreds and thousands of regions that remain to be characterized as far as their function is concerned.

So, we can figure out where in the genome these changes have been made and then try to work backwards from the function of that specific part of the genome to how it may have shaped all the unique forms and functions we see in humans and animals.

Reflecting on Research at U of T

Neil Macpherson
That’s really neat.

Alright, it’s great to hear about the work that you’ll be doing moving forward it, but I just wanted to sort of step back a bit and ask you as somebody at U of T: looking back at your time here, how do you feel about the environment for the research that you’ve done?

Ian Tobias
The research environment U of T is world class and I’m probably not the first to say that.

I’ve received excellent mentorship, specifically from within the Department of Cell & Systems Biology. The scientists that learn and work here empowered me to set out and build a research program around my strengths and expertise.

I feel grateful to have spent time conducting research here with some scientists and teaching an extremely motivated student population.

Neil Macpherson
Thank you for speaking with me and congratulations on your new position!