Regulation of cell fate decisions

Mr. Atchuta Srinivas Duddu’s interview with Bio Patrika hosting “Vigyan Patrika”, a series of author interviews. Mr. Duddu is currently a PhD student in the Cancer Systems Biology Laboratory of Dr. Mohit Kumar Jolly at the Centre for BioSystems Science and Engineering, Indian Institute of Science Bangalore. Mr. Duddu completed his M. S. (ECE) from University of California San Diego and B. Tech. (Instrumentation) from IIT Kharagpur. He published a paper titled “Multi-stability in cellular differentiation enabled by a network of three mutually repressing master regulators” as the first author in Journal of the Royal Society Interface (2020).

How would you explain your paper’s key results to the non-scientific community?

Phenotype refers to any of the observable characteristics or traits of an organism. This includes traits we generally see like eye color, face structure and more, traits that may not be visible to the naked eye but measurable like biochemical and physiological properties and various behavioral traits as well. All these phenotypes are coded by genes present in our DNA. The phenotypes are not set in stone and are sometimes subject to external factors resulting in switching phenotypes. One such example is the Epithelial/Mesenchymal transitions where epithelial cells change into mesenchymal cells due to changes in its local environment or by being triggered in a signaling pathway. Regulation among genes coding the phenotypes is required for the switching to happen. Genes regulate signaling via transcription factors (TFs) and proteins.

Apart from phenotypic switching, gene regulation is indispensable for embryonic development, as a single cell zygote divides and multiplies into a huge number of cells varying in function, structure and behavior (with different phenotypes). During the developmental process, a frequently occurring gene regulatory network for the cell fate decisions is the Toggle Switch (Figure 1A).

Figure 1. A) Toggle Switch network, two mutually repressing transcription factors B) Toggle Triad network, three mutually repressing transcription factors.

The network of mutual repression between transcription factors corresponding to the two cell fates (here A and B) results in a bistable system. The progenitor cell (the cell before committing to a fate) can result in an expression level of either {A-high, B-low} or {A-low, B-high} thus deciding its fate. We have studied a similar network, a Toggle Triad, but with the progenitor cell differentiating possibly into three primary types of cells (here A, B and C, Figure 1B). The outcome qualitatively is not as apparent as for Toggle Switch and motivated the study. Our simulations show that Toggle Triad enables tristability with the most common states being TF of one of the cell fates being expressed more relative to the other two or ‘single positive’ states i.e. {A-high, B-low, C-low} or {A-low, B-high, C-low} or {A-low, B-low, C-high}. Furthermore, three more hybrid states or ‘double-positive’ states were observed with intermediary expression levels of two of the TFs with the other expressed low especially with self-activation for the three cell fates (Figure 2).

Figure 2. Waddington landscape for a toggle triad. Modified Waddington’s landscape to demonstrate the differentiation of three distinct ‘single positive’ states (states A, B and C), and three putative ‘double positive’ states (hybrid states A/B, A/C and C/B) from a common progenitor. These six states can be obtained from a toggle triad with/without self-activation.

We have extended the network results to the case of CD4+ helper T-cells differentiating into Th1, Th2 or Th17. Experimental investigations have already shown self-activation for Th1 and Th2 along with toggle switch behavior between them as well as the existence of hybrid Th1/Th2 and Th1/Th17 states suggesting toggle switch with self-activation behavior. Our model offers similar toggle switch connecting all three transcription factors, thus forming a toggle triad which explains the tristability of the network and persistence of hybrid states too.

What are the possible consequences of these findings for your research area?

The model presented supports the hypothesis, mixed cellular phenotypes (hybrid states possessing characteristics of two or more cell types) are stable cellular identities with specific functional traits, and not just a transient co-expression of these lineage determining transcription factors, as seen often in common progenitor cells. Our model offers insights into the dynamics of cell differentiating as well as outlining principles for designing tristable systems synthetically. Our work paves the way for further investigation into the dynamics and principles of more gene regulatory networks and possibilities of application in the area like cellular reprogramming, the process of reverting cells into their pluripotent forms and synthetic biology, the creation or redesigning of biological devices or systems.

What was the exciting moment (eureka moment) during your research?

The first exciting moment for me was when I read the first set of papers suggested by my PI. I am from an engineering background and did not have too much of interaction with biology. These papers opened my insight to the mechanisms of genetic coding, cellular reprogramming and understanding diseases as intelligent outcomes and many related concepts. The next such moment came when I started to realize how so many mathematical concepts I have yet to learn and then apply to investigate. I did have a few more moments, and I believe that I will keep on having these moments in plenty whenever I read a new paper, learn a new mathematical method or make my code efficient.

What do you hope to do next?

The phenotypic switching has a regulation on its reversibility or irreversibility else we would see different cells continuously switching their fates, function and structure leading to pandemonium. We are planning to extend the work we have done on the Toggle Triad to include this regulation on reversibility and irreversibility. The mathematical framework is to be developed, which would improve our model and yield a better understanding of the biological scenario. We also plan on extending the model to more extensive networks to find their design principles and topological effects on the system.

Where do you seek scientific inspiration?

Reading different papers and articles, having discussions, debates and solving problems with my lab mates and friends and learning in the process are what drive me and inspire me to continue my research. I like the everyday life that I have right now, and it allows me to keep a good perspective on my career.

How do you intend to help Indian science improve?

I do not know how I can directly do that right now. I think focusing on my research work and completing my PhD would be a step towards contributing to science. I believe active participation in increasing science discussion and awareness in my personal and professional community is how I will be contributing to Indian science. I am an artist and am currently exploring scientific illustration. I think art as a tool would help me towards this goal.

Reference

Duddu AS, Sahoo S, Hati S, Jhunjhunwala S, Jolly MK. Multi-stability in cellular differentiation enabled by a network of three mutually repressing master regulators. J. R. Soc. Interface 2020, 17: 20200631.

Email: atchutaduddu@iisc.ac.in

Originally published at http://biopatrika.com on October 12, 2020.

Bio- Biology; Patrika: Magazine. An integrated platform for “Vigyan patrika”, “Margdarshak”, “BioKonnect” and “Jobs”. Indian Science highlights.

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