Collaborative Research Holds Promise For Nanomedicine Through RNA-Based Materials

When UNC Charlotte researchers Kirill Afonin and Ian Marriott describe their labs’ RNA nanotechnology research, they use words that might at first seem non-scientific, including alphabet, library and language.

This is because their work – on multiple levels – deals with communication. They are working collaboratively to engineer better treatments for cancers and other diseases. Their research focuses on developing novel functional RNA-based nanomaterials that can communicate with each other or with cellular machinery, or respond to various stimuli.

To maximize the benefit of these nanostructures, it is critical for the researchers to understand – and influence – how the structures prompt immune responses within the body. Some immune responses can be harmful, while others can be beneficial.

To grasp their work, a good place to start is with a basic definition of RNA. Ribonucleic acid – or RNA – is present in living cells. Its main job is to serve as a messenger carrying instructions from DNA – deoxyribonucleic acid – to control the synthesis of proteins. RNA functions as an enzyme, a powerful regulator of gene expression, and a natural molecular scaffold due to its natural versatility and structural properties.

“Some primitive organisms, like plants for instance, don’t have immune systems the way we think about it, but they use RNA, in particular RNA interference processes, to fight pathogens,” he says.

The UNC Charlotte partnership draws on the expertise of Marriott, a Department of Biological Sciences faculty member with expertise in immunology and cell biology, and Afonin, a faculty member in the Department of Chemistry and the Nanoscale Science Ph.D. Program, who has expertise in computational and experimental RNA biology. Both faculty members have previously received the prestigious National Institutes of Health R01 research grants and many other funding awards.

They draw upon each other’s expertise and that of colleagues at UNC Charlotte and other universities and labs. They also hold high expectations for the postdoctoral fellows and graduate and undergraduate students in their labs, calling upon them to contribute meaningfully to the work.

“This is key because students have to learn the integrative nature of science,” Marriott says. “The days when you were studying one thing in an enclosed manner, or blinkered manner, is long gone. Now, science is integrated. Nobody can be an expert in everything. That is why everybody has to be working together as a team. These things are just too complex.”

These lead researchers, their lab teams, and colleagues elsewhere have published a number of academic papers documenting the research, including a paper in the journal Small, with lead author Brittany Johnson, who was a postdoctoral fellow in both labs at the time. Johnson has since moved to a research faculty position at UNC Charlotte and in November 2020, she, Afonin, Marriott, Nanoscale Science doctoral student Justin R. Halman and collaborators at Ball State University published a paper in Nucleic Acids Research.

The earlier paper in Small presented a set of 16 nanoparticle platforms that are highly configurable and that can be tuned to elicit the desired immune response or lack of response. Rationally designed programmable RNA nanostructures offer unique advantages in addressing contemporary therapeutic challenges such as distinguishing target cell types and responding to disease, the researchers found.

“Kirill has generated these therapeutic nucleic acids, and they are very novel because they overcome a lot of problems you have with these traditional nano-therapeutics,” Johnson says. “The ones he’s generated can be specifically engineered, and that’s one of the strongest things about them. You can engineer their melting temperature and their resistance to degradation in the body.” 

The researchers are measuring the physical and chemical properties of these particles, such as melting temperatures, stability in blood serum, dissociation constant, sizes, and composition. 

“All that is fed into the program,” Afonin says. “This program can be trained to recognize patterns. The program was able to find the strong connections between the physical properties and the immunological responses.”

The team is characterizing each of the nanoparticles in terms of their immunological responses.

“Kirill is putting together this library of nanoparticles, and our job with my lab is to throw those letters and words into a system to test what they do to the immune system,” Marriott says. “We know that a lot of our own cells can recognize certain shapes and forms of nucleic acids like RNA. We have these sensors inside our cells that recognize these foreign RNA molecules. Basically that’s a cue for the cell to let it know it is compromised.”

Their paper in Small documented the distinct immune responses to the RNA, which can self-assemble into different shapes or structures, as well as carry embedded functionalities, such as serving as a way to deliver therapeutics.

“We’ve got some tantalizing preliminary data that the distinct shapes themselves could be an influencing factor; rings and cubes and fibers will dictate a response,” Marriott says. “It’s not only the composition, but also the form that can actually dictate a response.”

Work is continuing on designing nanoparticles and testing them.

“I want to create an actual molecule language which can be used by these structures to communicate with the immune system,” Afonin says. “I want to make it so simple that you don’t have to be an immunologist, and you don’t have to be an RNA nanotechnologist. You will have already an alphabet. It’s like letters.”

A hurdle for all drug delivery systems, including this one, is that cells can see these RNA nanostructures as a threat.

“That’s the kind of thing that will provoke an immune response and maybe an inflammation and all that nasty, bad stuff such as a septic-type shock,” Marriott says.

“What we want to do is find the particular motifs that provoke particular responses that either are ignored by the cell, which could be good, or that are provoking not this bad inflammatory response, but maybe just certain responses that would be beneficial to fight a cancer.”

An example of a beneficial immune response would be how the body’s immune system responds to a vaccine.

Unlike chemotherapy, which is a brute-force type of treatment and targets all rapidly dividing cells, including “good” cells, the type of approach these researchers are developing is more specific and focused.

“In these therapeutics we are trying to design, we want them to be more targeted therapy,” says Justin Halman, a Ph.D. student in the nanoscale science program who is part of Afonin’s lab. “In this case, we’re looking for an immune response, and if we can generate a specific immune response, which we’re seeing as tailored by the composition, by the shape, by the structure of our nucleic acid nanoparticles, we could better combat these type of diseases.” 

The potential is enormous, Marriott says. “It will be totally transformative. It would be an unimaginably powerful tool. The idea that you could deliver whatever you wanted wherever you wanted, and engineer the host response to whatever it is you’re trying to combat, would be extraordinary.”

Words and Images: Lynn Roberson | Top Image: Kirill Afonin (left) works with doctoral student Justin Halman in his lab. | This article originally appeared in the spring 2018 issue of the CLAS print research magazine, Exchange. It was updated in early 2021 with new research information.