Rouhanifard Receives $3.4M NIH Grant to Discover RNA Modification Sites Using Pseudouridine Modified mRNA
BioE Assistant Professor Sara Rouhanifard was awarded a $3.4 million NIH R01 grant for “Synthetic mRNA Control Set for Nanopore-Based Pseudouridine Modification Profiling in Human Transcriptomes.” The research has the potential to vastly increase insight into the epitranscriptome—changes in chemical modifications of RNA that can affect gene expression within cells—which could help identify new therapeutic targets and lead to new classes of drugs.
Sara Rouhanifard, assistant professor of bioengineering, is leading a $3.4 million NIH R01 grant for “Synthetic mRNA Control Set for Nanopore-Based Pseudouridine Modification Profiling in Human Transcriptomes.” Co-investigators include Meni Wanunu, professor, College of Science and bioengineering affiliated faculty; and Ya-Ming Hou, professor of biochemistry and molecular biology at Thomas Jefferson University. The research has the potential to vastly increase insight into the epitranscriptome—changes in chemical modifications of RNA that can affect gene expression within cells. Cells use RNA to translate the instructions coded in their DNA into proteins—the workhorses of our basic life processes.
Engineered modifications to RNA molecules have been used to produce medical treatments like the mRNA vaccines recently administered to millions around the globe to combat COVID-19. Modifications to RNA also occur naturally, however, in mechanisms that are much less clear.
“The problem is that natural modifications are invisible to the technologies that exist today,” Rouhanifard explains. “We have no way of knowing where they are or measuring how much is there or figuring out what exactly they’re doing. We just have a couple of hints about what’s happening.”
Those hints often come from a device called a nanopore sequencer, which can be used to read out the sequence of individual segments of RNA with or without modifications. Even this remarkable capability, however, provides only a limited amount of information about naturally occurring modifications.
“It’s not quantitative,” Rouhanifard continues. “It’s a little bit murky. You can kind of see where modifications are, but you don’t know how many are there, and you’re not exactly sure what you’re looking at.”
She and her co-investigators have devised a new method of using a nanopore sequencer to locate and quantify previously unknown RNA modifications. They start by creating customized “control” RNA molecules, segments bearing known and site-specific modifications. Using the sequencer, they compare these controls to unmodified segments, establishing the differences between them. This information becomes a training set that is used by a machine-learning algorithm they have created to analyze the characteristics of each RNA modification in each defined sequence in much greater detail than previously possible.
This data could prove important in understanding how changes in the position and level of the RNA modification affect the function of a cell, or the health of an entire organism.
“Both the mapping position and the quantification level can change,” says Hou, “in stress, in a disease condition, or wherever there is perturbation of homeostasis of a cell. It’s important to understand how each change is associated with each disease state.”
Wanunu sees a parallel between advances in RNA modification detection and the epigenetics revolution a few decades ago, in which changes in a chromosome’s shape could affect gene expression as much as the sequences in DNA. That breakthrough led to new innovations in medical diagnosis and treatment, particularly of cancer.
“These methods are going to be the foundations for new discoveries,” he says of the team’s epitranscriptome research.
Rouhanifard agrees. “Suddenly you have this whole world opened up to you for new therapeutic targets and things you could manipulate to create new classes of drugs,” she says. “We’re just figuring out where RNA modifications are right now. Once you figure out where RNA modifications are and what their functions are, then you can engineer the system so that you can use it to improve human health.”
Award Source: NIH