NIH grant supports KU study of DNA-protein cross-links

LAWRENCE — Identifying toxic DNA-protein cross-links (DPCs) and the cellular pathways to repair them are the goals of research underway by University of Kansas assistant professor of medicinal chemistry Luke Erber and his lab team. The research is being funded by a $1.8 million grant recently announced by the National Institute of General Medical Sciences, a unit of the National Institutes of Health.

DPCs are bulky protein lesions that chemically and irreversibly bond to DNA, disrupting essential functions like DNA replication and transcription. These disruptions can lead to genomic instability and are directly linked to accelerated aging, cancer, neurodegeneration and rare genetic diseases. Erber’s research within the KU School of Pharmacy could lead to improved efficacy of existing chemotherapies, advancement of early detection to limit toxic exposures and personalized cancer risk assessment to minimize toxicity.

“One major part of our research is understanding which metabolites in the cell contribute to DNA-protein cross-linking,” Erber said. “The other major part is understanding how these cross-links are repaired. What are the mechanisms or pathways that the cell uses to try to repair the DNA when this kind of damage occurs?”

DPCs can be caused by environmental agents such as ultraviolet light and even some types of chemotherapies. Endogenous agents, occurring naturally in the body, can also cause these cross-links. Metabolic conditions such as obesity, Type 2 diabetes mellitus and liver diseases are more susceptible to this kind of cellular dysfunction.

To help with the outsized task of identifying proteins and pathways of DNA repair, Erber is employing mass spectrometry, a unique approach in this field of research. 

“We want to make direct measurements of the DNA damage from the cell, not just correlations or associations,” Erber said. “The tremendously sensitive mass spectrometer allows us to do this. We can identify molecules by mass, and by applying a separation technique, we gain quantitative information that helps us with discovery of molecules at work or absent in the repair process.”

To identify and characterize DPC formation and repair, Erber’s team extracts DNA from cells with elevated levels of reactive endogenous agents. The DNA is separated down to the four DNA nucleosides, commonly known as A, T, G and C. Using mass spectrometry, the Erber team searches for changes to the masses of the four DNA nucleosides. These unique changes in mass permit identification of naturally occurring metabolites contributing to DNA damage. The research will include working with human cancer cells to investigate how repair functions are at work or stymied by the cancer cells.

An important part of the grant is being able to establish standards in the research to increase confidence in their methods and data, Erber said. The research is a complex and challenging area of study that demands standardization procedures that do not currently exist. Challenges of studying DPCs include extreme chemical heterogeneity, very low natural abundance, instability, cellular lethality and repair pathway redundancies. Since DPCs are technically hostile to almost all standard molecular biology techniques, Erber’s team will be focused on developing small molecule standards to accurately detect and measure DPCs.

Understanding how enzymes impact the cell repair function in the cross-linking environment could potentially lead to therapeutic solutions. That is beyond Erber’s current research through this NIH grant, but he said he is hopeful the research will help inform future research in this area.

Erber said he is grateful for the NIH grant not only from the research aspect but also because of the learning that will come from it. 

“The education and training of our graduate and undergraduate students is an important outcome of this funding as well,” he said. “There will also be substantial collaborations across the U.S. with individuals working in the same area. In fact, these collaborations have already been impactful in our research.”