Dr. Rohini Datta is currently a Postdoctoral Research Fellow in the lab of Jin Billy Li at the Department of Genetics, Stanford School of Medicine, Stanford University, USA. The work presented here was done as part of her PhD thesis in the lab of Prof. Raghavan Varadarajan at the Molecular Biophysics Unit, Indian Institute of Science, Bangalore. Dr. Rohini published a paper entitled “A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing” as a first author in Proceedings of the National Academy of Sciences USA (2020).
Author interview
How would you explain your paper’s key results to the non-scientific community?
Despite decades of research, an effective HIV vaccine that stimulates the production of neutralizing antibodies remains elusive. These antibodies not only bind to the virus but also prevent further infection. Our recent paper introduces a new method to rapidly identify the target sites (epitopes) of these neutralizing antibodies on HIV viruses.
We focused on the HIV envelope glycoprotein (Env), the main surface protein of HIV. We introduced cysteine molecules on the surface of the Env protein, then added a chemical label that binds to these cysteines. When these labeled viruses were treated with neutralizing antibodies, the labels blocked antibody binding. The viruses that survived were sequenced to identify the antibody target sites.
Identifying epitopes in sera (blood samples with mixed antibodies) is usually difficult. Our method allowed us to identify multiple epitopes targeted by antibodies from an HIV-infected patient who could naturally withstand infection without therapy—such individuals are called “elite neutralizers” and are very rare. Knowledge of the epitopes targeted by elite neutralizers can help design better HIV vaccines. Our method can also be adapted for other viruses like SARS-CoV-2.
“[…] Enables identification of epitopes directly on infectious HIV viruses.”
What are the possible consequences of these findings for your research area?
Our method allows epitope identification directly on infectious HIV viruses, offering an advantage over older methods that rely on purified proteins or surface displays. It’s a major step forward in the field.
This technique allows high-throughput mapping of neutralizing antibody epitopes without requiring expensive equipment like X-ray crystallography or cryo-EM. It also distinguishes between neutralizing and non-neutralizing antibodies, the former being crucial for vaccine development.
What was the exciting moment (eureka moment) during your research?
The most exciting moment was discovering the specific epitopes targeted by antibodies in the ‘elite neutralizer’ patient. These antibodies target two distinct epitopes on the HIV Env protein, contributing to the patient’s natural resistance to HIV. These experiments were made possible with the help of Dr. Luke Elizabeth Hanna from NIRT, Chennai, who provided the patient sera.
What do you hope to do next?
I hope this technology will be widely used to identify neutralizing antibody epitopes in emerging viral infections like SARS-CoV-2. At Stanford, I’m studying RNA editing by ADAR deaminases. My long-term goal is to explore how RNA molecules regulate viral infection pathways.
Where do you seek scientific inspiration?
I draw inspiration from mentors, teachers, and peers. Prof. Varadarajan’s guidance during my PhD was invaluable. At Stanford, Prof. Li’s mentorship makes research exciting and intellectually stimulating.
I’m also inspired by female scientists like Marie Curie, Lise Meitner, Rachel Carson, Dorothy Hodgkin, and Rita Levi-Montalcini. Their perseverance in the face of adversity is deeply motivating.
How do you intend to help Indian science improve?
At IISc, I participated in outreach programs, including training high school teachers from underprivileged schools. I’ve mentored several interns, many of whom are now pursuing PhDs in India. I also contribute to science journalism through The Wire Science. I will continue to support Indian science through outreach, mentorship, and science communication.
Reference
Datta R, Roy Chowdhury R, Manjunath K, Hanna LE, Varadarajan R.
A facile method of mapping HIV-1 neutralizing epitopes using chemically masked cysteines and deep sequencing. Proc Natl Acad Sci USA. 117(47):29584-29594 (2020).
DOI: https://doi.org/10.1073/pnas.2010256117
Current Affiliation:
Postdoctoral Research Fellow, Department of Genetics, Stanford School of Medicine, Stanford University, USA
Postdoctoral Advisor: Prof. Jin Billy Li
Twitter: https://twitter.com/dattarohini
Learn more about Prof. Varadarajan’s lab: http://mbu.iisc.ac.in/~rvgrp/home.html
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