Scientists link mysterious snippets of DNA to cell growth and tumor suppression

DNA evolutionary tree
It’s been 80 million years since our our evolutionary branch diverged from mice — so why do we share some fragments of DNA that are essentially unchanged? (Fred Hutch News Service Illustration / Kim Carney)

Why do some strings of genetic code remain virtually unchanged despite tens of millions of years of evolutionary divergence? A newly published study that takes advantage of the gene-editing technique known as CRISPR has found that at least some of those DNA strings are essential to keep healthy cells growing and block the growth of tumor cells.

The research, published today in Nature Genetics, is the “first study finding large-scale importance of these highly conserved elements,” senior author Rob Bradley of Seattle’s Fred Hutchinson Cancer Research Center said in a news release.

Bradley and his colleagues say unraveling the mysteries of those ultra-conserved elements could lead to new avenues for cancer treatment.

The study started out with a molecular analysis focusing on specialized snippets of DNA known as poison exons. Such snippets regulate the activity of cells by shutting off the production of particular proteins. They’ve been called “kill switches” for cellular functions. When they go haywire, they can cause maladies such as epilepsy. But when they work the way they’re supposed to, they can “poison” the production of undesirable proteins and keep cells on the right track.

Scientists have previously noticed an overlap between poison exons and ultra-conserved elements, but they weren’t able to nail down exactly why the ultra-conserved poison exons were so essential. When they knocked out the target exons, one by one, they didn’t see much of an effect on cell survival.

The Fred Hutch team took a wider-angle approach: They made use of a CRISPR gene-editing enzyme that was modified with guide-RNA molecules to hunt down and snip out hundreds of poison exons from the genomes of mice, rats and humans.

Bradley and the study’s lead author, Fred Hutch researcher James Thomas, call their technique “paired guide RNAs for alternative exon removal,” or pgFARM (pronounced like “pig farm”). “What’s unique about what James did is not the approach per se, but that he’s doing it in high throughput,” Bradley said.

The researchers identified 465 poison exons that were highly conserved between species — as well as another 91 poison exons that weren’t so highly conserved. They found that many of the ultra-conserved exons performed similar functions, which explains why knocking out just one of them at a time didn’t have much of an effect. But when bunches of the highly conserved exons were snipped out at the same time, the cells died off in a lab dish.

As a follow-up, the team tested the role of poison exons in live mice that had lung tumors. Many of the exons were essential for normal cell growth, just as they were for the cells in the lab dish. Even more intriguingly, some of the exons had tumor-suppressing effects that were “clinically relevant,” the researchers reported.

Tumor-fighting poison exons tended to turn up within the genes that govern RNA splicing, a vital part of the cell’s protein-making machinery. Those exons may well rein in RNA-splicing factors that could otherwise promote tumor growth.

Scientists are already working on techniques to fix RNA-splicing problems that contribute to a wide variety of diseases — and Thomas is hopeful that ultra-conserved poison exons could point the way to new molecular targets specific to cancer treatment.

“Once you find a target, it’s easy to build upon the previous technology that exists for therapeutics,” he said.

In addition to Thomas and Bradley, the authors of the Nature Genetics study, “RNA Isoform Screens Uncover the Essentiality and Tumor-Suppressor Activity of Ultraconserved Poison Exons,” include Jacob Polaski, Qing Feng, Emma De Neef, Emma Hoppe, Maria McSharry, Joseph Pangallo, Austin Gabel, Andrea Belleville, Jacqueline Watson, Naomi Nkinsi and Alice Berger.

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