Vipul Shukla, Ph.D.

Cracking the folded code in our DNA

FUNDED BY: the generosity of The Tullie Family

What was the goal of your SPARK project?

My SPARK proposal was aimed at understanding the biological significance of unusual folded codes, known as G-folds in the genome. G-folds form in regions of DNA with a high abundance of “Gs”, which is one of the four letters that make up DNA (A, T, G and C). For the last several decades, researchers have focused on understanding the mechanisms by which the linear sequence of letters in our DNA is read and interpreted within cells but we know very little about how cells, decipher the information encoded in unusual DNA structures, such as G-folds.

To answer this question with my SPARK project, I focused on two important objectives. The first objective was to develop new technologies to detect G-folds in normal cells, as well as their altered formation in cancer cells. My second objective was to identify precisely how our cells read and interpret information encoded in G-folds.

Pivoting during a pandemic

During the pandemic, more than ever, our research relied on teamwork. While the past year presented unique challenges to normal work routines, and even prevented access to the lab for several weeks. Through the constant support from fellow colleagues and leadership at LJI, I was able to make the anticipated progress in accomplishing the objectives that I set out for my SPARK proposal.

SPARK project results:

We used a special chemical called NMM to detect G-folds in normal cells while also studying their perturbations during the development of cancer. We then used this newly developed NMM-based detection method to measure G-fold levels in normal cells and revealed a striking increase in the levels of G-fold structures in blood cancer cells that arise upon loss of certain DNA modifying proteins. Using unbiased genome-wide approaches, we also found that G-folds are a “fragility signature” in DNA and represent common sites in the genome where DNA frequently breaks. These DNA breaks are a hallmark of many different cancers.

Next, I set out to understand the mechanisms by which the information encoded in G-folds is relayed inside cells. I performed a mass-spectrometry screen to identify specific G-fold recognizing proteins. Since proteins are the key functional units in cells, this approach shed light on the biological functions of G-fold structures. We were able to identify several previously unknown G-fold interacting proteins. As we hypothesized, many of the G-fold recognizing proteins that we identified through our screen are known to be essential for controlling key functional genomic states, thereby further endorsing the notion that G-folds represent a critical and underappreciated code in the genome.

In summary, these findings have implications towards our fundamental understanding of genome biology and represent a crucial step towards elucidating the biological functions of these enigmatic DNA structures.

What’s next for this project?

In close alignment with the mission of the SPARK program, the research I performed under this project has opened up several new areas of investigation that I plan to pursue in my own independent laboratory. These studies highlighted G-folds as unique vulnerabilities that could be therapeutically targeted in cancer cells, and we intend to follow up on this in future studies. I’m also excited to share that this work has just been accepted for publication in a premier peer-reviewed journal, Nature Immunology, so it will be published very soon. My collaborators and I are also working to further modify the chemical NMM to generate more reagents that we could apply to precisely map the location of G-folds across the entire genome. We are actively working on this aspect of the project and hope to develop a robust G-fold mapping method in the near future to chart G-fold structures in normal and cancer genomes.

What’s next for Vipul?

I recently accepted a faculty position at Northwestern University in Chicago, IL, where I plan to expand on this work. During the term of my SPARK award, I also received independent research funding in the form of the prestigious “K99/R00 pathway to independence award” from the National Cancer Institute, which will allow me to continue this research in my laboratory. I also plan to build on data generated from my SPARK project and apply for more independent funding from the National Institutes of Health and other organizations to carry this work forward.