When a gene quality-control mechanism fails, abnormal RNA strands may contribute to cancer and neurodegeneration microbiologystudy

Failure of a gene-reading quality-control mechanism called Integrator leaves cells littered with abnormal RNA strands that increase cell stress and may contribute to diseases such as cancer and neurodegeneration, a new study has found.

The research, published in Cell, is the first to reveal the consequences of such failures. In doing so, it explains some of the symptoms seen in patients with Integrator mutations that have stumped doctors and suggests a path toward treatment.

“Normally, you can look at the altered gene activity in patients with a mutation and understand how you get from there to the patient’s symptoms. But with Integrator, the gene activity doesn’t explain the symptoms,” said senior author Karen Adelman, the Edward S. Harkness Professor of Biological Chemistry and Molecular Pharmacology in the Blavatnik Institute at Harvard Medical School.

“We discovered that it’s not certain genes causing the symptoms, it’s the abundance of poor-quality, incomplete RNAs that are made when Integrator is mutated,” she said.

The results call for more attention to incomplete RNAs, which have been generally overlooked in research and medicine.

“I’ve been studying gene transcription for a long time, and the focus has always been on measuring the amount of mature, full-length RNA made from each gene,” Adelman said. “We’re proposing that the immature RNA that most studies ignore is the very thing that causes cell stress and damage.”

The new work opens the door to better understanding diseases associated not just with Integrator mutations but with other, similar malfunctions in RNA production.

The importance of finishing the gene marathon

Integrator is one of many protein complexes in the cell nucleus that help control which genes can be “read” and ultimately translated into the proteins that perform the functions of life.

Adelman and colleagues—led by first author Apoorva Baluapuri, research fellow in biological chemistry and molecular pharmacology in the Adelman Lab—focused on Integrator because mutations in it have been linked to neurologic and blood disorders, cancers, ciliopathies, developmental abnormalities, and other diseases.

Integrator ensures that the machinery preparing to read a gene sequence can make it all the way to the end of the gene. That can be quite a challenge for very long genes.

“It’s like how race officials don’t let any random person show up to run the Boston Marathon; they hold time trials to make sure runners can finish,” Adelman said.

But sometimes, when there’s a mutation in the Integrator complex, machinery that’s not up to the task sneaks into the gene.

“It’s like letting me start a marathon. It would be okay for a short distance, but I’d never make it to the end,” Adelman said.

This results in incomplete RNAs that contain potentially harmful sequences called introns.

Many researchers had assumed that these RNAs get destroyed before they’re able to leave the nucleus and therefore don’t harm the cell.

“No one had studied what happens when you let this faulty machinery read genes,” Adelman said. “People had never asked, “Is there an intron making its way into the cytoplasm and hanging out?'”

Her team asked—and found a concerning answer.

Stressed-out cells

Studying cell cultures, the researchers found that the abnormal RNAs do leave the nucleus, and when they reach the cytoplasm, they can fold back on themselves and make double-stranded RNA—something typically seen only when a cell is infected by a virus.

Further experiments revealed that both the drop in proper Integrator function and the rise of double-stranded RNAs stimulate a cell-wide stress pathway known as the integrated stress response. Chronic activation of this response has been seen in aging, neurodegeneration, and cancer. Some researchers argue it also plays a major role in cognitive and metabolic disorders.

When the team looked in tissue samples from patients with Integrator mutations, they observed the same stress response.

“We didn’t realize the extent to which shoddy, immature RNAs would cause trouble,” Adelman said.

But there is good news.

The team found that a molecule called PKR (protein kinase R) contributes to the stress response when it recognizes the double-stranded RNA—and that treating cells with PKR inhibitors relieved the stress.

The results indicate that targeting PKR could be a promising avenue for treating illnesses arising from Integrator mutations. Researchers have a head start: Many PKR inhibitors are already in development, and studies suggest that some FDA-approved drugs, including the diabetes drug metformin, also suppress PKR.

Hidden in plain sight

Most scientific and diagnostic tests don’t detect unprocessed, doubled-over RNAs. Adelman’s team had to develop a method to study them.

Scientists and clinicians alike have been contacting her lab seeking to test patient samples or learn how to detect the RNAs themselves.

“We’re hearing from clinicians who haven’t been satisfied with the understanding of how mutations in Integrator or other transcription regulators cause their patients’ disease,” Adelman said. “They say, ‘Ah ha! This could be it.’ That may be the most gratifying aspect of this work.”

Adelman and colleagues emphasize that while the study is opening the field’s eyes to a new disease mechanism, double-stranded RNAs won’t explain every disorder linked to malfunctions in complexes like Integrator.

“It’s something to add to a diagnostic checklist if a patient has a mutation in a gene transcription regulator and their genotype and phenotype [symptoms] don’t seem connected,” she said.

The team’s insights do suggest why Integrator mutations seem to have an outsize effect on neurons: Neuronal genes are the longest in the human genome.

“Those are the marathons the unfit machinery is least likely to finish running.”