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In Conversation: Research Fellow Sanjeev Shukla, Ph.D.

Photo of Sanjeev Shukla, Ph.D.

Sanjeev Shukla, Ph.D. (Photo: J. Summers, SPGM, FNL)

Among the multiple alterations present in cancer cells are an abundance of aberrant mRNA transcripts. Whether this abnormal gene transcription is a by-product of cellular transformation or whether it represents aberrant splicing that contributes altered proteins to cancer cells is not yet clear.

CCR: Sanjeev, your research path is a bit unusual. What prompted you to switch your earlier research focus on prognostic biomarkers for oral cancers to the world of alternative splicing and its regulation?

Sanjeev: Actually, from my perspective, I have not changed my focus. My ultimate goal is to contribute to cancer research by unraveling the basic mechanisms that enable cancer cells to churn out aberrant splice products, and biomarkers are among these products. I realized that in order to understand cancer’s aberrant proteins, I need to thoroughly understand the mechanism of alternative splicing, and I need to know its regulators.

CCR: Did you come to CCR as a Visiting Fellow to help you achieve those goals?

Sanjeev: Yes, it offered me the opportunity of a mutually beneficial collaboration. I knew what my long-range goal was, and I discovered that Shalini Oberdoerffer’s lab could provide me with the training and technical tools to ask the right preliminary questions about the mechanism of alternative splicing. Shalini’s interests are more focused upon alternative pre-mRNA splicing in maturing immune cells, but we share an interest in deconstructing all the regulators and steps involved in alternative splicing, and she has the perfect CD45 pre-mRNA model system to study the regulators.

CCR: Have you mastered the basic mechanism of alternative splicing or gathered any preliminary data toward your ultimate goal of deconstructing alternative splicing’s link to cancer?

Sanjeev: Yes. I am pleased with our progress so far. Shalini and I knew that alternative splicing decisions are determined by the ability of weak splice sites to compete with strong splice sites for detection by the spliceosome, but we did not know how epigenetic factors could alter this process. We have discovered a key regulatory role for DNA methylation. And it regulates splicing in a most unusual manner.

CCR: What exactly does methylation do to alter the basic splicing mechanism?

Sanjeev: We discovered a novel mechanism for regulation of alternative splicing via DNA methylation. In lymphocytes, the mechanism of CD45 exon 5 splicing was not clear. We found that a protein called CTCF usually binds to exon 5 DNA. Now CTCF’s usual role is to form DNA loops and give chromatin a spatial conformation. So this might mean that epigenetic modifications may be maintained on DNA to aid the spliceosome in the process of exon selection. DNA methylation regulates CTCF binding, and that, in turn, regulates alternative splicing. So by slowing down pol II, CTCF might be providing time for the splicing machinery to both recognize the exon 5 splice site and incorporate exon 5 into the CD45 mRNA transcript. Isn’t that fascinating?

CCR: Have you given any thought to how you will mentor your own Postdoctoral Fellow in the future when you run your own lab?

Sanjeev: I plan to repeat the same approach that worked for me at CCR. I think the key is for the Postdoctoral Fellow to think clearly about his overarching career goal. Then I would suggest that he or she shop for the lab that can offer the technology and training that can best help him or her to approach the questions that need to be answered to reach that goal.

As the head of the lab, I plan to expect that type of focus from my prospective Postdoctoral Fellows, and I expect the candidates to articulate their “big picture” goals to me. Then I will explain what expertise and technology training my lab can bring to bear upon their goals.