Vipul Shukla, Ph.D.

Cracking the folded code in our DNA

FUNDED: JANUARY 2020
FUNDED BY: the generosity of The Tullie Family

Our DNA is often thought of as a “linear code,” that is encrypted through the combination of the four letters (A,T,G and C), which instructs the cells of our immune system to kill pathogens; the cells of our pancreas to produce insulin; or the cells of our heart to pump blood. However, recent studies have identified the existence of a more complex new code in our DNA. This new code compels DNA, which otherwise appears like a straight string, to fold itself into specialized structures called G-quadruplexes (or G-folds). The name “G-folds” comes from the high abundance of G, which is one of the four letters that makes our DNA.

Several decades of research have focused on understanding the mechanisms by which a linear sequence of letters in our DNA is read but we know very little about how the information encoded by G-folds is deciphered. Predictive models show that G-folds are commonly found at specific places in our genome, suggesting that they may be storing important information to carry out normal functions in many different cell types of our body.

Importantly, the formation of G-folds is significantly altered in many human diseases, including neurodegenerative disorders and several different cancers. The key to understanding why G-fold formation is increased in diseased states is to first understand their roles in normal cells. To do so, we first need to develop technologies that can aid in G-fold detection and discover mechanisms through which G-folds mediate their normal functions in a cell.

I have two primary objectives for my research proposal. The first objective is to develop new technologies that allow the detection of G-folds in normal cells as well as their altered formation in cancer cells. The second objective is to use an unbiased approach to identify the precise means by which the information encoded in the G-folds is read and interpreted in our cells. Together these studies will be valuable towards understanding the biology of these enigmatic structures and could potentially carve a path for the development of novel therapeutic approaches to target G-folds in human diseases.

Six-Month Project Update

My SPARK project goal is to decipher the biological functions of unusual DNA structures known as G-folds. Addressing our intent to devise novel methods for efficient G-fold detection, we’ve developed G-fold specific agents that we’re now testing in DNA sequencing applications to precisely map them across the entire genome. Using unbiased genome-wide approaches, I’m investigating the link between G-folds and accumulation of genomic instability, which is a common hallmark associated with development of many cancers. I’ve performed experiments geared towards exploring this relationship and we’re now analyzing these datasets to identify correlations and draw specific conclusions. In parallel, to understand how information encoded in G-folds is relayed in cellular systems, I’ve performed a mass-spectrometry screen to identify specific G-fold recognizing proteins. Since proteins are the key functional units in cells, using this experimental approach, I’ve identified several novel G-fold interacting proteins as a step towards elucidating the biological functions of these enigmatic DNA structures. I’m now functionally validating and assessing the biological significance of the interactions between G-folds and the candidate proteins. Notably, many of these candidate proteins are known to be essential for regulating the functional landscape in the genome. Together, these studies endorse the notion that G-folds represent a critical code in the DNA that is often deregulated in cancers.