Scientists have long understood that each of the roughly 20,000 genes in the human body carries the instructions for a single kind of protein. Researchers at Harvard Medical School have now found that instructions from separate genes—even genes on different chromosomes—can combine into chimeric mRNAs that produce previously unknown, functional proteins. The findings, published in Nature, point to potentially thousands of new chimeric proteins and show that at least some carry out important jobs in the body.
“Nobody knows these exist. Medicine doesn’t know they exist, the pharmaceutical industry doesn’t know they exist,” said senior author Ruaidhrí Jackson. “We’ve discovered an entirely new gene regulation system that could expand the known genome and proteome dramatically.” Jackson’s team doesn’t yet know how widespread the phenomenon is, but says chimeric proteins may contribute to poorly understood disease processes and could point to new drug targets.
Chimeric mRNA in humans had previously been documented mainly in cancer, where broken DNA scatters and genes fuse abnormally; sequencing results occasionally hinted it might also occur in healthy tissue, but standard techniques struggled to detect it reliably.
Using a newer method called direct RNA sequencing, the team compiled a list of over 30,000 chimeric mRNAs observed at least once in mammalian cells—the “dark genome” library, as Jackson calls it—and has so far profiled how almost 400 of these are regulated by inflammatory signals. The researchers found that healthy chromosomes can loop together in mouse cells during an immune response, bringing normally distant genes into proximity so the newly adjacent genes transcribe a single chimeric mRNA built from pieces of each one, producing a hybrid protein. “We thought we had a blueprint of every mRNA that is made in the body, and now we’re saying that was just page one,” Jackson said. “There are all these other combinations that can occur.” Detecting a chimeric mRNA, though, doesn't necessarily mean it creates a functional protein.
To test that, the team focused on one mouse chimera combining the genes for GSDMD and TMEM106A. GSDMD alone produces a protein that opens cell membranes during pyroptosis, in which immune cells burst open to trigger a large inflammatory response. They confirmed GSDMD-TMEM106A occurred naturally in two lab mouse strains and a wild-derived strain, then built a genetic tool to stop production of the chimeric protein alone, without disrupting normal GSDMD and TMEM106A.
Mice without the chimeric protein mounted a slower immune response and, when infected with Salmonella, were less able to fight off the bacteria. “They can’t control the bacterial infection,” Jackson said. “Nearly 50 percent of the immune process has been reduced without our chimeric protein, even though the normal GSDMD is still present. GSDMD needs our GSDMD-TMEM106A to function fully.” Given an endotoxin that causes sepsis, an extreme and potentially deadly immune response, 70 percent of mice without the chimeric protein survived a dose that would normally be lethal, because their immune response was milder than normal.
Working with Moderna, the researchers engineered an mRNA to boost GSDMD-TMEM106A production. Mice with elevated chimera levels did not survive even a mild endotoxin dose, but mice that both lacked the GSDMD gene and had elevated chimera levels had no response to the endotoxin at all—showing the chimera speeds up pyroptosis but cannot open cell membranes without GSDMD itself. Together, the results confirmed the chimeric protein is vital to the mouse inflammatory response.
“GSDMD-TMEM106A was initially discovered based on a single read in one of our samples. We were bracing ourselves for this to turn out to be nothing,” said co-first author Harry Kane. “It was very exciting when we found that GSDMD-TMEM106A was not only a real protein but also functional—it could modulate release of inflammatory molecules from cells.”
Jackson, Kane and their colleagues are now studying the molecular cues behind chimeric mRNA formation and evaluating other chimeric mRNAs for potential uses in medicine. “We want to find out which ones are operative in currently incurable diseases,” Jackson said. “We think we can find new players that have been completely overlooked by medicine, by pharma, by biomedical science in general.”
“Nobody knows these exist. Medicine doesn’t know they exist, the pharmaceutical industry doesn’t know they exist,” said senior author Ruaidhrí Jackson. “We’ve discovered an entirely new gene regulation system that could expand the known genome and proteome dramatically.” Jackson’s team doesn’t yet know how widespread the phenomenon is, but says chimeric proteins may contribute to poorly understood disease processes and could point to new drug targets.
Chimeric mRNA in humans had previously been documented mainly in cancer, where broken DNA scatters and genes fuse abnormally; sequencing results occasionally hinted it might also occur in healthy tissue, but standard techniques struggled to detect it reliably.
Using a newer method called direct RNA sequencing, the team compiled a list of over 30,000 chimeric mRNAs observed at least once in mammalian cells—the “dark genome” library, as Jackson calls it—and has so far profiled how almost 400 of these are regulated by inflammatory signals. The researchers found that healthy chromosomes can loop together in mouse cells during an immune response, bringing normally distant genes into proximity so the newly adjacent genes transcribe a single chimeric mRNA built from pieces of each one, producing a hybrid protein. “We thought we had a blueprint of every mRNA that is made in the body, and now we’re saying that was just page one,” Jackson said. “There are all these other combinations that can occur.” Detecting a chimeric mRNA, though, doesn't necessarily mean it creates a functional protein.
To test that, the team focused on one mouse chimera combining the genes for GSDMD and TMEM106A. GSDMD alone produces a protein that opens cell membranes during pyroptosis, in which immune cells burst open to trigger a large inflammatory response. They confirmed GSDMD-TMEM106A occurred naturally in two lab mouse strains and a wild-derived strain, then built a genetic tool to stop production of the chimeric protein alone, without disrupting normal GSDMD and TMEM106A.
Mice without the chimeric protein mounted a slower immune response and, when infected with Salmonella, were less able to fight off the bacteria. “They can’t control the bacterial infection,” Jackson said. “Nearly 50 percent of the immune process has been reduced without our chimeric protein, even though the normal GSDMD is still present. GSDMD needs our GSDMD-TMEM106A to function fully.” Given an endotoxin that causes sepsis, an extreme and potentially deadly immune response, 70 percent of mice without the chimeric protein survived a dose that would normally be lethal, because their immune response was milder than normal.
Working with Moderna, the researchers engineered an mRNA to boost GSDMD-TMEM106A production. Mice with elevated chimera levels did not survive even a mild endotoxin dose, but mice that both lacked the GSDMD gene and had elevated chimera levels had no response to the endotoxin at all—showing the chimera speeds up pyroptosis but cannot open cell membranes without GSDMD itself. Together, the results confirmed the chimeric protein is vital to the mouse inflammatory response.
“GSDMD-TMEM106A was initially discovered based on a single read in one of our samples. We were bracing ourselves for this to turn out to be nothing,” said co-first author Harry Kane. “It was very exciting when we found that GSDMD-TMEM106A was not only a real protein but also functional—it could modulate release of inflammatory molecules from cells.”
Jackson, Kane and their colleagues are now studying the molecular cues behind chimeric mRNA formation and evaluating other chimeric mRNAs for potential uses in medicine. “We want to find out which ones are operative in currently incurable diseases,” Jackson said. “We think we can find new players that have been completely overlooked by medicine, by pharma, by biomedical science in general.”