Ancient microbial arms race sharpened our immune system—but also left us vulnerable

The influenza A virus, shown in a stylized scanning electron microscopic image, is one of many pathogens that take advantage of a 2-million-year-old evolutionary change in the surface of the human cell in order to slip inside it.

MedicalRF/Science Source

At a recent symposium on the evolution of infectious diseases, University of California, San Diego (UCSD), pathologist Nissi Varki noted that humans suffer from a long list of deadly diseases—including typhoid fever, cholera, mumps, whooping cough, measles, smallpox, polio, and gonorrhea—that don’t afflict apes and most other mammals. All of those pathogens follow the same well-trodden pathway to break into our cells: They manipulate sugar molecules called sialic acids. Hundreds of millions of these sugars stud the outer surface of every cell in the human body—and the sialic acids in humans are different from those in apes.

Varki and an international team of researchers have now traced how evolution may have scrambled to construct new defenses after that molecular vulnerability emerged in our distant ancestors. By analyzing modern human genomes and ancient DNA from our extinct cousins, the Neanderthals and Denisovans, the researchers detected a burst of evolution in our immune cells that occurred in an ancestor of all three types of human by at least 600,000 years ago.

As the researchers report in the current issue of Genome Biology and Evolution, these genetic changes may have sharpened the body’s defenses against the pathogens that evolved to exploit sialic acids—but created new vulnerabilities. In an added irony, they note, humans’ distinctive sialic acids were themselves once a defense against disease. The evolutionary saga is a vivid illustration of the competition between humans and microbes, says microbiologist Christine Szymanski of the University of Georgia, Athens, who is not a co-author. “This gives us a human perspective on how we have to keep changing to keep pace.”

The arena for this evolutionary arms race is the glycocalyx, a sugar coating that protects the outer membrane of all cells. It consists of a forest of molecules that sprout from the cell membrane. The sialic acids are at the tip of the tallest branches, sugar chains called glycans, which are rooted to fats and proteins deeper in the membrane.

Given their prominence and sheer number, sialic acids are usually the first molecules that invading pathogens encounter. Human cells are coated with one type of sialic acid, N-acetylneuraminic acid (Neu5Ac). But apes and most other mammals also carry a different one, N-glycolylneuraminic acid (Neu5Gc).

More than 2 million years ago, according to multiple molecular clock methods, a mutation in the CMAH gene on chromosome six made it impossible for human ancestors to produce Neu5Gc anymore; instead, they made more of another sialic acid, Neu5Ac. “We now know we had an ancient complete makeover of the surface of the human cells,” says evolutionary biologist Pascal Gagneux of UCSD, a co-author of the new paper. Birds, some bats, ferrets, and New World monkeys all separately made the same evolutionary change.

The change likely evolved as a defense against malaria, says UCSD physician-scientist Ajit Varki, senior author of the paper and Nissi Varki’s spouse. Malarial parasites that infect chimpanzees were no longer able to bind with the altered sialic acids on our red blood cells.  

But in the next million years or so, that mutation became a liability, as Neu5Ac became a favorite portal for a flurry of other pathogens. At the infectious disease symposium organized by UCSD’s Center for Academic Research and Training in Anthropogeny, researchers described how multiple diseases evolved to use Neu5Ac to enter cells or to evade immune cells.

Zone of infection

Sialic acids play key roles in both infection and immune response. Some pathogens use sialic acids, which sit on the outer edge of the cell membrane, to invade a cell. Those pathogens must also dodge sialic acid-binding immunoglobulin-type lectins (Siglecs), sentry molecules that can spot foreign sialic acids and signal whether to activate or inhibit an immune response.

Immune cellBody cellSialic acidsCell membraneInhibitionActivationGlycocalyxParasiteVirusesSiglecsBacteria

N. Desai/Science

Coronaviruses appear to be no exception. “Most coronaviruses infect cells in two steps—first by recognizing abundant sialic acids as binding sites to gain a foothold, and then seeking out the higher affinity protein receptors like ACE2,” Ajit Varki says. “Think of it like an initial handshake or introduction that is required before one can ask for a date.” Two preprints suggest the novel coronavirus, SARS-CoV-2, also docks with sialic acids before binding with the ACE2 receptor to pierce human cells.

In past studies, Ajit Varki and Gagneux suggested the makeover of the cell and the loss of Neu5Gc may have even contributed to the origin of a new species in our genus Homo. If a woman with only Neu5Ac sialic acids mated with a man who still expressed Neu5Gc, her immune system may have rejected that man’s sperm or the fetus that developed from it. This fertility barrier might have helped divide Homo populations into different species more than 2 million years ago, the researchers speculated.

But the sialic acid change also sparked a new arms race between pathogens and our ancestors. In the new study, the researchers scanned DNA for immune genes in six Neanderthals, two Denisovans, and 1000 humans, and looked at dozens of chimps, bonobos, gorillas, and orangutans as well. They found evolutionary changes that “markedly altered” one class of proteins—sialic acid-binding immunoglobulin-type lectins, or Siglecs—that usually sit on the surface of human immune cells and recognize sialic acids.

Siglecs are molecular sentries: They probe sialic acids to see whether they are familiar parts of our own bodies or foreign invaders. If Siglecs spot sialic acids that are damaged or missing, they signal immune cells to activate, rousing an inflammatory army to attack potential invaders or clean up damaged cells. If sialic acids instead appear to be normal parts of our own cells, other, inhibitory Siglecs throttle back immune defenses so as not to attack our own tissues (see graphic, above).

The researchers identified functional changes in the genomic DNA of eight out of 13 Siglecs encoded in a cluster in the CD33 gene on chromosome 19 in humans, Neanderthals, and Denisovans. This hot spot of evolution took place only in Siglec gene variants, not in nearby genes on the chromosome, suggesting natural selection favored these changes, presumably because they helped fight pathogens that target Neu5Ac.

Apes did not show these changes, says first author Naazneen Khan, an evolutionary biologist now at the University of Kentucky. Given the mutations’ presence in archaic hominins, this burst of evolution must have happened before our lineages diverged 600,000 years ago, but after the mutation in the CMAH gene arose more than 2 million years ago, perhaps in Homo erectus, thought to be an  ancestor of modern humans and Neanderthals.

Most Siglecs are found on immune cells, but in the new paper, the team reports that several of the human Siglecs that underwent evolutionary changes are expressed in other types of human cells, including some in the placenta, cervix, pancreas, gut, and brain. The appearance of Siglecs may have been a side effect of intense battles with pathogens that infected these tissues, Nissi Varki suggests.

Although the recently mutated Siglecs protect us from pathogens, they may also contribute to other diseases. Some of the genetically changed Siglecs are associated with inflammation and autoimmune disorders such as asthma and with meningitis. The researchers suggest the altered Siglecs may be constantly on high alert and do not dampen immune responses against our own tissues; they may even make some individuals more prone to the runaway inflammation seen in severe COVID-19.

Other researchers say the work underscores broad evolutionary principles. “This nicely shows that … natural selection is not always going for the optimal solution, because the optimal solution is changing all the time,” says Rita Gerardy-Schahn, a glycobiologist at Hannover Medical School in Germany, who was not part of the new work. “What is best for natural selection in the short run may be the wrong selection tomorrow.”

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