One of the most common viral elements that persist in human genomes is a chunk of DNA called an Alu repeat. Alus constitute at least 13% of the human genome; there were over 300 copies in Totary-Jain’s mega-cluster. She suspected that those Alu repeats were turning on the immune system in the placenta. But her colleagues cautioned her against going down that road.

“The advice I was given was: ‘Don’t touch Alus, don’t work with Alus, forget about Alus,’” Totary-Jain said. The multitude of Alus in the genome makes it tough to unpack what a specific set may be doing.

But the data implicating Alus was too compelling to ignore. After years of careful experiments, Totary-Jain’s team showed that in the placenta, transcripts of Alu repeats formed snippets of double-stranded RNA — a molecular silhouette our cells recognize as viral in origin. Sensing the fake virus, the cell responded by producing interferon lambda.

“The cell is effectively dressing up as an infectious agent,” Kagan said. “The result is that it convinces itself that it’s infected, and then operates as such.”

Simmering Immunity

Immune responses can be destructive, and antiviral responses especially so. Because viruses are at their most dangerous when they’re already inside a cell, most immune strategies that target viral infections work in part by damaging and killing infected cells.

For that reason, cells cry “Virus!” at their own risk. In most tissues, Alu sequences are highly suppressed so that they never get a chance to mimic a viral attack. And yet that is the exact scenario the placenta seems to create on purpose. How does it balance the health of the growing embryo with a potentially risky immune response?

In experiments with mice, Totary-Jain’s team found that the placenta’s double-stranded RNAs and ensuing immune response didn’t seem to hurt the developing embryos. Instead they protected the embryos from Zika virus infection. The placental cells were able to toe the line — conferring protection on the embryos without cuing a self-destructive immune response — because they called in the gentler defenses of interferon lambda.

Typically the first responders to double-stranded Alu RNA escapees are type I and type II interferons, which quickly recruit destructive immune cells to the site of an infection, leading to tissue damage and even autoimmune disease. Interferon lambda, on the other hand, is a type III interferon. It acts locally by communicating only with cells within the tissue, generating a milder immune response — one that can be sustained long term in the placenta.

How placental cells manage to activate only interferon lambda, keeping the immune response simmering but never boiling over, is still a mystery. But Totary-Jain has an idea about why placental cells evolved this trick that other cells seemingly avoid: Since the placenta is discarded at birth, perhaps it can afford to take immune risks that other tissues can’t.

The findings reveal a new strategy the placenta has for protecting the fetus, apart from mom’s immune system. Since the mother’s immune response is dampened during pregnancy to prevent attacks on the genetically distinct embryonic cells, the placenta has had to develop extra defenses for the growing baby it supports.

However, this trick — a low-level immune response generated by a fake virus — may not be limited to the placenta. Researchers from Columbia University recently described a similar phenomenon in neurons. They observed RNAs from different genomic elements bound together in double strands to produce an immune response. In this instance, the immune system called in a more destructive type I interferon, but it was produced at low levels. The authors surmised that chronic low-level inflammation in the brain may keep infections under control, preventing major inflammation and neuronal death.

It’s possible, then, that this kind of immune trickery is more common than anyone thought. By studying how the immune system seems to break its own rules, scientists can better define what the rules are in the first place.

Quanta is conducting a series of surveys to better serve our audience. Take our biology reader survey and you will be entered to win free Quanta merchandise.