Bio Patrika interviews Dr. Trivedi on her thoughts about “CRISPR-Cas9 based genome engineering resource for studying lipid signalling”

Dr. Deepti Trivedi’s interview with Bio Patrika hosting “Vigyan Patrika”, a series of author interviews. Dr. Trivedi heads the Fly Facility at Bangalore Life Science Cluster, Bangalore. Deepti’s paper as a first author in eLife journal (2020) entitled “A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signalling” is a collaboration between Fly Facility and Prof Raghu Padinjat’s laboratory at National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore.

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

CRISPR-Cas9 based genome engineering, which gained momentum as a favorite genome engineering tool in recent years, has made it easier than ever before to ask fundamental biological questions using precise genetic tools. Our paper in eLife is a collaboration between Fly Facility and the lab of Prof Raghu Padinjat. Prof Padinjat’s lab is interested in role of phosphoinositide (PI) signaling in various physiologically relevant intracellular processes. PI signaling is very important since alteration in levels of specific PI components is found to be the underlying cause of many diseases, including cancer, diabetes and several neurological disorders.

In this project, we have generated CRISPR-Cas9 based resources to systematically manipulate every component of PI signaling in eukaryotic cells. In Drosophila, this makes a total of 103 genes. As a proof of principle, we have used these resources to mutate each of these genes, specifically in Drosophila eyes and wings. We showed that several of these genes are important for eyes and wing development. These resources are now available to everybody where they can be used to manipulate PI levels in the Drosophila tissue of their choice and can address questions of their specific interest.

Figure 1. Graphical abstract representing the work done in the paper. Illustration by Dr. Vishnu Janardan.

“[…] we have generated CRISPR-Cas9 based resources to systematically manipulate every component of PI signaling in eukaryotic cells.”

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

Many questions in the field of PI signaling have been difficult to address simply because of the lack of genetic resources to address them. Since there are many genes and isoforms in the PI signaling pathway of higher organisms, Drosophila makes a wonderful model system to address these questions. Although there are only a few type of PIs, their involvement in several mutually exclusive cellular functions suggests a tight spatiotemporal regulation. This tight regulation is brought about by metabolic enzymes and specific binding proteins, which by themselves are perhaps regulated. Our toolkit offers the researcher to now address these kinds of questions in a tissue-specific manner. This will help in a better understanding of specific genetic pathways and phenotypes in PI signaling. This also opens up a possibility of picking up other signaling pathways and generating specific resources.

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

Since this project involves large scale resource generation, there were many exciting moments throughout the course. The first construct generation, the first transgenic flies, the first mutant generation and then the first screen phenotype, all were exciting, demanded facility wide celebration and we didn’t shy away from these celebrations of little successes. Of course, during the process, we generated close to 300 CRISPR constructs, more than 100 fly stocks and a large number of mutants, and their combinations. At some point, generating them became a routine process, with a fair share of unique troubleshooting experiences. Overall, this project helped the facility build its capabilities, and made us ready to take up large scale projects with tremendous confidence.

What do you hope to do next?

This collaborative project with Prof Raghu Padinjat has been a great exercise in capacity and knowledge building for the Fly Facility. We hope to move forward with the experience gained with this specific project and offer ourselves for more such collaborations for other scientists and organizations. Meanwhile, we are also constantly improving our technical and scientific expertise and keeping us up-to-date.

Where do you seek scientific inspiration?

Strictly speaking, my scientific inspiration comes from scientists worldwide. I like to read about not just their scientific work, but also who they are as people, what inspires them and where they come from. I read biographies of scientists and their scientific journeys. Older generation scientists, such as my own MSc mentor late Prof Obaid Siddiqi, inspire me to no end. I think science has a huge potential not just for great discoveries and inventions but also to make the world a better place.

How do you intend to help Indian science improve?

The value of research facilities such as ours cannot be underestimated in recent years when on one hand resources seem to be dwindling, but on the other hand, nothing less than cutting edge is expected from the scientists. Fly facility offers services in a “institute and country agnostic” manner, making it the only facility, certainly in India, and perhaps worldwide, to offer a full service in generation CRISPR based mutants and doing genetic screens. We are also very open to any collaboration projects within the mandate of the fly facility and have already generated resources for a large number of Indian institutes. In this way, I hope we will be able to contribute our bit to the research community of India. We are also interested in outreach initiatives focused mostly on schools and colleges where we introduce Drosophila as a model organism.

Reference

Trivedi D, Cm V, Bisht K, Janardan V, Pandit A, Basak B, H S, Ramesh N, Raghu P. A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signalling. Elife. 2020;9:e55793.

Author introduction and research interests

I head the fly facility at Bangalore LifeScience Cluster. I have a PhD from University of Cambridge and postdoctoral experience from University of California, Los Angeles. I am interested in genome engineering and technology development in Drosophila.

Email: dtrivedi@ncbs.res.in

Read more about Dr. Raghu lab interest’s http://flyfat.ncbs.res.in/

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