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Down syndrome is the most common genetic disorder, impacting about 1 in 700 newborns around the world. At some point during their first hours and days of embryonic development, their dividing cells fail to properly wriggle a chromosome pair away from each other, leaving an extra copy where it shouldn’t be. Although scientists have known for more than six decades that this extra copy of chromosome 21 causes the cognitive impairment people with Down syndrome experience, exactly how it happens remains a matter of debate.

The dominant hypothesis is that people with this syndrome make too much of the proteins encoded in the genes that reside on chromosome 21, and that this overexpression alters the timing, pattern, or extent of neurodevelopment. This theory has a name: the “gene dosage effect.”

But in recent years, scientists using new RNA sequencing techniques to study cells from pairs of twins — one with Down syndrome and one without — have repeatedly turned up a curious pattern. It wasn’t just the genes on chromosome 21 that had been cranked way up in individuals with Down syndrome. Across every chromosome, gene expression had gone haywire. Something else was going on.

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On Thursday, a team from the Massachusetts Institute of Technology reported in Cell Stem Cell that it may have found a surprising culprit: senescent cells, the same types implicated in many diseases of aging. The study was small and preliminary, and some experts want to see it replicated in samples from more individuals before buying into its interpretations. But they are nevertheless intriguing.

Intriguing because those are the same types of cells that pile up and pollute tissues as people get older, and because so many companies are now rushing to develop drugs that clear senescent cells from the body.

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“That senescence might be playing a role in the neuropathology of Down syndrome is very interesting,” said Tamir Chandra, a molecular geneticist at the University of Edinburgh who was not involved in the new study. “That opens a new door for exploring potential interventions.”

Senescence is a natural stress response in which cells lose their ability to divide. It prevents old, often glitchy cells from proliferating out of control and causing cancer. Senescent cells secrete cytokines, a chemical signal that tags them for destruction by the immune system. But as people age, their immune system has a harder time keeping up. Senescent cells accumulate, bathing tissues in a cytokine stew that leads to systemic inflammation. Chandra and others have found that the cells also undergo internal changes; the chromosomes collapse and compact, altering the types of genes the cells express.

Hiruy Meharena had never heard of that phenomenon, when in 2016, he asked his postdoctoral adviser, Li-Huei Tsai, director of the the Alana Down Syndrome Center and the Picower Institute for Learning and Memory at MIT, if he could use a new method for measuring the three-dimensional architecture of DNA to look inside the brain cells of people with Down syndrome. He wanted to know what it could tell them about what was causing the gene expression scrambling other groups had been finding.

He and his colleagues spent years using different methods to measure the differences between two copies and three copies of chromosome 21 in neural progenitor cells, and they began to see very drastic genomic rearrangements. Meharena’s team concluded that these cells — which give rise to neurons and other tissues of the central nervous system — simply don’t have enough room to accommodate the extra copy of chromosome 21. The result of this overcrowding is a reorganization of the 3D shape of the entire genome of the developing brain.

“The nucleus of a cell is like an elevator when it’s full of people,” said Meharena. “It’s already at capacity, and then this one additional chromosome wants to come in, so every other chromosome squishes together to make space.”

The nucleus is not an infinitely expanding organelle. At its core is DNA that’s more loosely coiled so that it’s more easily expressed — the genes are more accessible to the cell’s protein-making machinery. Out toward the periphery the DNA condenses, meaning those areas are expressed little or not at all. But add an extra chromosome into the mix, and things start to get weird. DNA on the periphery gets dislodged and the other chromosomes start folding in on themselves; out becomes in, in becomes out, off becomes on, and to some extent, on becomes off.

At first the researchers didn’t know what to make of the results. “The data kept leading us into uncharted territories, so we just kept chasing it and chasing it,” Meharena told STAT. “It wasn’t until late in the game that we realized what we were seeing closely resembled senescence.”

Once they did, they decided to test their hypothesis. They treated their cells with a combination of two senolytic drugs, dasatinib and quercetin. If the cells were truly senescent, then the medications should both reduce the number of senescent cells and reverse many of the structural DNA changes and gene expression disruptions. Which is exactly what happened.

But Meharena emphasized that the idea was just a proof of concept. “It wasn’t to show senolytics as a therapeutic intervention,” he said. “It’s still far too early for that.” Rather, he hopes that by identifying trisomy-induced senescence as a potential driver of the neurodevelopmental abnormalities seen in Down syndrome, his work might inspire new areas of research into future treatments.

Chandra also cautioned that testing existing experimental senolytic drugs to intervene in brain development amid Down syndrome would be premature. The drugs used in this study come with significant and dangerous side effects. And much more work needs to be done to ascertain what sort of role senescent cells play in driving the disease.

“Everyone thinks that senescent cells are always detrimental,” said Chandra. But in the last few years, studies have shown that these cells sometimes pick up new and useful functions. “Before we start injecting people with senolytic drugs, we really need to understand much better what these cells are doing in the brain,” he said.

The more immediate impact of the new study may be helping other researchers decide what not to do, said Chris Link, who studies neurodegenerative diseases at the University of Colorado, and worked on one of the papers that found widespread gene expression disruption in the cells of people with Down syndrome.

It may be the most common genetic disorder, but Down syndrome is also one of the most difficult to study. Unlike diseases caused by a single DNA letter typo or a more substantial mutation to a single gene, there aren’t easy ways to introduce an entire chromosome to cells in Petri dishes or animal models. The most widely used models are mice that have been engineered to have an extra long chromosome carrying mouse versions of two-thirds of the genes found on human chromosome 21. But they don’t fully recapitulate the physical crowding that Meharena’s data suggest might be a bigger part of the problem.

“So this might turn out to be an important observation for people to consider when making these mouse models — that maybe they can’t be as gene-centric as they have been,” said Link. There are also efforts to treat Down syndrome by silencing the extra chromosome. But if its size is as important as its activity, those efforts might not succeed.

“It’s somewhat of a scientific revelation that all these changes people have seen may be driven by these large-scale chromosomal associations,” said Link — provided the model holds up. When Link’s group compared the gene-expression profiles it found with what other groups found in people with Down syndrome, the patterns were really different. “So this is good work, but it needs to be replicated in more people to see if it’s truly a general phenomenon,” he said.

While skeptical, Link sees why this explanation is so tantalizing; it pulls together so many threads from across biology. Senescence, and the chronic inflammation it causes, is a hallmark of aging. Inflammation has also been offered as an explanation for the neuron die-offs observed in Alzheimer’s brains. People with Down syndrome age faster than other people, and they tend to get Alzheimer’s at much higher rates. They also have impaired immune systems, which may make it harder for their bodies to clear senescent cells. Studies have consistently found that people with Down syndrome have more senescent cells than other people. “So it all kind of fits,” Link said.

But in many ways, the new research raises as many questions as it answers. When Meharena and his collaborators repeated all their analyses with the stem cells they used to create the neural progenitor cells, all the cramming and genetic mayhem they’d observed disappeared. “Whatever disruption is happening is kicking in at the neural progenitor state,” he said.

So why are neural progenitor cells so sensitive to this extra chromosome when stem cells aren’t? What makes them so special? And what about other tissues, like those in the heart? Are they vulnerable to this nuclear reorganization too? Those are questions Meharena is now exploring with a lab of his own at the University of California, San Diego.

“If we can learn why stem cells seem to be able to incorporate the additional chromosome without any major issues, maybe we can apply that to therapeutic interventions,” he said. “At the very least, we hope it opens up new avenues for how we look at Down syndrome — that there seems to be this whole other element that plays on a different timeline that we really need to explore more.”

 

This story has been updated to correct the institution where Hiruy Meharena is currently employed. It is the University of California, San Diego, not the University of San Diego, as previously stated.

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