Proteomes | Interview with One of the Authors—Dr. Shantanu Gupta

Name: Dr. Shantanu Gupta
Affiliation: Bioinformatics Multidisciplinary Environment (BioME) – Digital Metropole Institute (IMD), Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil

“DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance”
by Shantanu Gupta, Daner A. Silveira, José Carlos M. Mombach and Ronaldo F. Hashimoto
Proteomes 2025, 13(1), 6; https://doi.org/10.3390/proteomes13010006
Available online: https://www.mdpi.com/2227-7382/13/1/6

We recently had the opportunity to interview Dr. Shantanu Gupta, one of the authors of a recent paper published in Proteomes (ISSN: 2227-7382). He generously shared his perspective on his research, the challenges he’s encountered, and his personal journey in the field. The following is a brief interview with Dr. Gupta:

1. Could you tell us a little bit about yourself and your paper?
My research journey is centered at the intersection of bioinformatics, systems biology, and the role of non-coding RNAs in cancer, with a focus on decoding how cells make life-or-death decisions. I began developing the computational framework for this paper during my time at the University of São Paulo, and I’m now expanding this research line as a Visiting Associate Professor at the Bioinformatics Multidisciplinary Environment (BioME)-IMD at the Federal University of Rio Grande do Norte (UFRN).
My perspective is continually sharpened by my active role as a peer reviewer for over 150 international journals, which provides a broad, real-time view of the field. This was crucial for our paper, where we addressed a central challenge in cancer treatment: why do some tumors become resistant to therapy?
We developed a Boolean network model that reveals how the p53 protein and key non-coding RNAs interact as a coordinated system. Rather than working in isolation, these molecules form a decision-making network that determines whether a cell will undergo ferroptosis—a potent form of cell death—or survive and contribute to drug resistance.
What makes our approach unique is its systems-level logic. The model explains how cancer cells bypass death mechanisms, suggesting new strategies to overcome treatment resistance. This work was a collaborative effort with my colleagues Daner A. Silveira, José Carlos M. Mombach, and Ronaldo F. Hashimoto, whose expertise was invaluable. We were fortunate to have support from FAPESP and CNPq, without which this research would not have been possible.

2. What do you think made the academic community respond to your work so positively?
I believe that several factors contributed to the positive response. First, we addressed a genuine clinical problem—therapy resistance—that virtually every cancer researcher encounters. Second, by connecting established pathways like p53 with emerging fields like ferroptosis, we provided a bridge between different scientific communities.
The timing was also right. There's growing recognition that we need systems-level approaches to understand complex diseases like cancer. Our Boolean model offered an accessible yet powerful way to visualize these complex interactions. Perhaps most importantly, we didn’t just present data but offered a conceptual framework and testable hypotheses, encouraging collaboration across disciplines and inspiring new lines of investigation.

3. What do you think is the biggest challenge currently and the future directions in your area of research?
The biggest challenge remains cancer heterogeneity—each tumor, and even different regions of the same tumor, behaves uniquely. Capturing this complexity in models is extremely difficult.
Looking forward, I see the future in multi-scale, personalized systems modeling—integrating multi-omics data, signaling dynamics, and patient-derived information to
build digital representations of tumors. At BioME–IMD, UFRN, we are actively working toward this vision, developing computational frameworks that adapt as tumors evolve.
Such models could one day serve as predictive tools for precision oncology, helping clinicians simulate therapeutic responses before actual treatment. This integrative approach, combining systems biology with patient-centered data, is key to transforming computational discoveries into clinical impact.

4. What advice would you give to young scholars seeking to get into academia or publish their work?
I’d emphasize three principles that have guided my career.
First, cultivate intellectual fearlessness—don’t hesitate to work at the interface of disciplines. My own background in physics has deeply influenced how I think about biological systems. Physics teaches us to search for underlying principles and patterns, and that mindset is incredibly powerful when applied to the complexity of life sciences. Some of the most transformative discoveries happen when physics, biology, computation, and medicine converge.
Second, embrace the iterative nature of science. Each paper adds a piece to a larger puzzle. Your first work doesn’t need to answer everything—it just needs to ask the right, meaningful questions that move the field forward.
Third, engage deeply with the scientific community. This goes beyond just publishing. For me, this has meant taking on roles as an editorial board member for several journals. This experience isn't just about a title; it's a front-row seat to the publishing process, teaching you what makes a paper compelling, robust, and impactful—lessons you can directly apply to your own work. Collaboration and mentorship are the lifeblood of research. Be open, generous, and persistent—the rest will follow.

5. What is your impression of the publishing experience with the Proteomes journal?
My publishing experience with Proteomes was exceptionally positive. The peer review process was rigorous yet deeply constructive—the reviewers posed challenging questions that significantly improved the manuscript’s clarity and depth.
What stood out most was the journal’s commitment to intellectual quality over speed or profit. The editorial team fostered a genuine scientific dialog rather than a transactional process, and our revision rounds felt collaborative and purposeful.
I also appreciate the journal’s author-centered initiatives, like this interview series, which allow researchers to share the story behind their science and connect with a broader audience. It reflects a true dedication to advancing thoughtful, high-impact research within the scientific community.

6. How do you manage your time between research and daily life? Do you have any tips to share?
For me, effective time management is about balancing focused work with meaningful personal time. I dedicate mornings to deep research and writing, when concentration is highest. Afternoons are usually reserved for meetings, collaboration, mentoring, and my scholarly service work including peer review and editorial board responsibilities. Evenings often include teaching undergraduate and postgraduate students. Engaging with students and colleagues keeps me energized and frequently inspires new research ideas.
Equally important is making time for family. Sharing moments with them helps me recharge and maintain perspective, which is essential for sustaining creativity and productivity. Living in Natal, with its beautiful green-blue ocean and serene surroundings, makes it easier to enjoy these moments fully.
Ultimately, sustaining a research career is about rhythm—knowing when to dive deeply into the lab, classroom, or meetings, and when to pause to share time with family and reflect. Much like the rhythm of the ocean here in Natal, balance between intensity and stillness sustains both creativity and well-being, allowing science to remain not just a pursuit, but a passion.