Twins aren’t as rare as you might think. In fact, every human harbors many of them — in our genes.
About two-thirds of human genes have their own doppelgänger, a duplicated copy that often shares overlapping functions within the cell. Cancer cells can take advantage of gene twins, relying on one to stay alive if its pair is lost. But now, scientists have developed a method to turn gene twins to their advantage when studying cancer and seeking new drug targets.
In work published today in the journal Cell Reports, Fred Hutchinson Cancer Research Center scientists describe an approach that allows them to knock out genes in tandem, which could help identify which gene pairs may play a role in cancer, and which could make for attractive therapeutic targets.
“This project grew out of the recognition that due to extensive gene duplication, we may not be detecting the function of those duplicated genes in typical CRISPR screens — or really any genetic assay where you only knock out one gene at a time,” said Hutch cancer geneticist Dr. Alice Berger, who led the work and holds the Innovators Network Endowed Chair.
Cancer cells exploit gene twins’ overlapping activities, relying on one gene twin to keep key cellular processes going after the first is lost. Researchers studying genes one at a time may miss a gene’s effects on cancer, not suspecting that its twin is pulling the strings in the background. It might lead them to dismiss a key cancer gene (and its therapeutic potential) — a misstep that Berger and her team hope their approach can help scientists avoid.
“We saw the potential for using [this phenomenon] to identify drug targets and other important cancer genes that had been missed,” she said.
There isn’t a single answer to why our DNA contains so many genetic doubles. In some cases, they may be playing a role so essential to survival that cells always need a backup. In others, gene duplicates start traveling along diverging evolutionary trajectories, retaining some overlapping activities, but also picking up critical new functions unique to each twin.
Berger and graduate student Phoebe Parrish recognized that finding the twins that have maintained critical functional overlap (called “paralogs” in scientific jargon) could have two different therapeutic uses.
“The first one is that we can just identify paralogs that are important for cancer that had been missed [before],” Berger said. “We might be able to target both paralogs with the same small molecule [drug] because they’re so much like each other.”
Some cancer drugs already work by blocking two paralogs with one therapeutic. Ibrance (palbociclib) and Kisquali (ribociclib), which have been approved for treatment of certain kinds of breast cancer, each inhibit both CDK4 and CDK6, enzymes that regulate cell proliferation. Perhaps the team could identify other pairs with the same co-druggable potential.
The other situation in which scientists could take advantage of gene twins is in the case of cancers that are forced to rely heavily on one gene twin after having lost the other. In theory, these cells would become extremely vulnerable to drugs that target the surviving twin.
“If you could have a specific inhibitor of one of those paralogs, then you could specifically target tumors that have lost the other paralog,” Berger explained. “Then you would have a therapeutic window in the tumor compared to the surrounding normal cells.”
Berger and Parrish worked with Hutch computational biologist and holder of the McIlwain Family Endowed Chair in Data Science Dr. Robert Bradley, and Bradley Lab postdoctoral fellow Dr. James Thomas, to tackle the problem by extending a genetic engineering approach they’d developed previously, called pgFARM, for paired guide RNAs for alternative exon removal. Though Bradley and Thomas used pgFARM to figure out why certain DNA sequences have remained unchanged for millions of years, the team quickly realized that they could adapt it to answer other genetic questions.
In this case, the researchers decided to tweak their approach so they could remove two genes at once. They dubbed this approach pgPEN, for paired guide RNAs for paralog gENetic interaction mapping.
Using pgPEN, Berger and Parrish conducted what they believe to be the largest survey of gene paralogs to date. Studying genes pair by pair, rather than one by one, gave them new insights into cancer and its potential vulnerabilities.
The researchers found that about 12% of gene pairs exhibit what scientists call “synthetic lethality.” This means that removing both twins at the same time tanks cells’ survival, but cells can get by if either one or the other remains. These synthetic lethal gene pairs included CDK4 and CKD6, which have been linked to many tumor types, including breast cancer and melanoma, as well as new pairs whose potential as drug targets has not yet been explored.
The team also found that gene pairs could shape cancer biology. They identified 10 sets of gene twins that promote cell proliferation when lost together, suggesting that different gene pairs could be involved in both promoting and restraining cancer development.
Now, Berger and her team plan to take the next step toward nominating future drug targets. They’ll validate their top twin hits to confirm that cells that have lost one twin are more sensitive to inhibitors of the other twin as compared to cells that have both twins to rely on.
"It's incredibly exciting to see how CRISPR has enabled us to better understand the genome, but the ultimate goal is to be able to use this information to help people," Berger said. "The hard work now begins to move these discoveries toward the clinic."
The work was funded by the Lung Cancer Research Foundation, the National Science Foundation, the National Institutes of Health, the Washington Research Foundation, the Prevent Cancer Foundation, a Stephen H. Petersdorf Lung Cancer Research Award, the Edward P. Evans Foundation, the Leukemia & Lymphoma Society, the Mark Foundation for Cancer Research, the Paul G. Allen Frontiers Group and the Department of Defense Breast Cancer Research Program.
Sabrina Richards, a senior editor and writer at Fred Hutch Cancer Center, has written about scientific research and the environment for The Scientist and OnEarth Magazine. She has a PhD in immunology from the University of Washington, an MA in journalism and an advanced certificate from the Science, Health and Environmental Reporting Program at New York University. Reach her at srichar2@fredhutch.org.
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