If you’re so smart, why haven’t you come up with a cure for the common cold? The question has long dogged microbiologists, immunologists, and molecular pharmacologists. Now, finally, these beleaguered scientists can point to a discovery that may win them grudging thanks, or at least convince their tormentors to formulate a new challenge.
The discovery is this: Temporarily disabling a host protein can effectively deny the common cold a foothold it needs to replicate inside host cells.
Several enteroviruses (EVs), including rhinoviruses (RVs) that cause the common cold, have been stopped in their tracks by denying them access to a protein called SET domain containing 3 (SETD3). This protein, an actin histidine methyltransferase, was identified in a genome-scale CRISPR screen devised by researchers at Stanford University.
These researchers, in collaboration with scientists at the University of California, San Francisco, used gene editing to randomly disable a single gene in individual human cells in a collection of the cells. The team effort culminated in a cell culture that contained, in the aggregate, cells lacking one or another of every gene in our genome.
The scientists infected the culture with RV-C15, an RV known to exacerbate asthma in children, and then with EV-C68, implicated in acute flaccid myelitis. In each case, some cells managed to survive infection and spawn colonies. The scientists were able to determine which gene in each surviving colony had been knocked out of commission.
While RV-C15 and EV-D68 are both EVs, they’re taxonomically distinct and require different host-cell proteins to execute their replication strategies. So, most of the human genes encoding the proteins each viral type needed to thrive were different, too. But there were only a handful of individual genes whose absence stifled both types’ ability to get inside cells, replicate, bust out of their temporary cellular abodes, and invade new cells.
One of these genes stood out—the gene encoding SETD3. “It was clearly essential to viral success, but not much was known about it,” said Jan Carette PhD, an associate professor of microbiology and immunology at Stanford and one of four leaders of the current research.
Carette and colleagues presented their findings September 16 in Nature Microbiology, in an article titled, “Enterovirus pathogenesis requires the host methyltransferase SETD3.” Not only does the article detail how SETD3 was identified, it also describes how mice bioengineered to completely lack SETD3 were protected against several EVs, including two distinct EVs that can cause paralytic and fatal encephalitis. In fact, the mice proved impervious to infection even when the viruses were injected directly into their brains soon after they were newly born.
“We identify SETD3 as critically important for viral infection by a broad panel of EVs, including rhinoviruses and non-polio EVs increasingly linked to severe neurological disease such as acute flaccid myelitis (EV-D68) and viral encephalitis (EV-A71),” the article’s authors wrote. “We show that cytosolic SETD3, independent of its methylation activity, is required for the RNA replication step in the viral life cycle.”
This work suggests that targeting SETD3 in our own cells could protect against EVs, which like all viruses travel light, by preventing them from foraging host cells for replication-essential factors. The approach, which exploits a vulnerability shared by EVs, could be effective against asthma, encephalitis, myocarditis, polio, and the common cold.
There are roughly 160 known types of RV, which helps to explain why getting a cold doesn’t stop you from getting another one a month later. Making matters worse, RVs are highly mutation-prone and, as a result, quick to develop drug resistance, as well as to evade the immune surveillance brought about by previous exposure or a vaccine.
The new approach could also be effective against EV-D68, an EV that since 2014 has been implicated in puzzling biennial bursts of a polio-like disease, acute flaccid myelitis, in the United States and Europe.
In their article, the researchers also explored how the protective effects could be explained at the molecular level: “Using quantitative affinity purification–mass spectrometry, we show that SETD3 specifically interacts with the viral 2A protease of multiple enteroviral species, and we map the residues in 2A that mediate this interaction. 2A mutants that retain protease activity but are unable to interact with SETD3 are severely compromised in RNA replication. These data suggest a role of the viral 2A protein in RNA replication beyond facilitating proteolytic cleavage.”
EVs, the scientists learned, have no use for the section of SETD3 that cells employ for routine enzymatic activity. Instead, enteroviruses cart around a protein whose interaction with a different part of the SETD3 molecule, in some as yet unknown way, is necessary for their replication.
“This gives us hope that we can develop a drug with broad antiviral activity against not only the common cold but maybe all enteroviruses, without even disturbing SETD3’s regular function in our cells,” Carette explained.
The researchers observed a 1000-fold reduction in a measure of viral replication inside human cells lacking SETD3, compared with controls. Knocking out SETD3 function in human bronchial epithelial cells infected with various rhinoviruses or with EV-D68 cut replication about 100-fold.