After finding long, repetitive sequences in the genomes of seven kinds of cancer, researchers at Stanford Medicine and their colleagues developed a molecule that curbed their production.
December 14, 2022 - By Jackie Rocheleau
Research led by scientists at Stanford Medicine has shown that long, repetitive DNA sequences may have a role in gene regulation in seven types of cancer — and there may be a way to home in on those sequences to suppress the propagation of cancer cells.
Using a new algorithm to analyze more than 2,000 human cancer genomes, the researchers first identified the repetitive sequences, then created a molecule that targeted them in kidney cancer cells, finding that it slowed the production of, and sometimes killed, those cells.
Although the scientists aren’t sure what role the repetitive sequences play in cancer, they were encouraged that they appeared to have found a way to inhibit the creation of more cancer cells. “The most dramatic result was that you could actually target them and stop cell proliferation,” said Michael Snyder, PhD, professor and chair of the department of genetics.
From neurodegenerative disease to cancer
The project began not with cancer, but with a rare, neurodegenerative disease without a cure, Friedreich ataxia. Five years ago, Erwin, then a graduate student at the University of Wisconsin-Madison, was exploring the genetic underpinnings of Friedreich ataxia in hopes of filling the therapeutic void.
Erwin knew that DNA mutations called repeat expansions cause Friedreich ataxia, along with dozens of other serious conditions, many neurological. Repeat expansions are stretches of DNA that erroneously repeat themselves dozens to thousands of times in the genome.
Erwin developed a molecule called Syn-TEF1 that zeroed in on the repeat expansions causing Friedreich ataxia. These expansions disrupt the FXN gene and prevent RNA polymerase, the molecule that transcribes DNA to RNA (the molecular recipe for proteins), from properly transcribing the gene so cells can produce the corresponding protein, frataxin. At healthy levels, frataxin helps the powerhouse of the cell, mitochondria, generate energy and protects cells from reactive molecules called free radicals, which can be harmful. Without the RNA instructions, cells can’t produce the frataxin they need, which is particularly detrimental to the energy-demanding nervous system and heart.
Testing the molecule in cells from a Friedreich ataxia patient, Erwin saw that Syn-TEF1 successfully targeted the repeat expansion, helping RNA polymerase move through it to transcribe the FXN gene, bringing frataxin to normal levels. Due to its success in cells, researchers are now testing the safety and dosage of a version of Syn-TEF1 in Friedreich ataxia patients.
When Erwin came to Stanford, he wondered what role repeat expansions played in other diseases. Scientists haven’t found much of a role for repeat expansions in non-neurological conditions, but Erwin didn’t think that was because these mutations weren’t there. “I think it’s just that we haven’t looked,” he said.
A new therapeutic avenue
Long stretches of repetitive DNA aren’t easy to find in cancer genomes. The most commonly used cancer genome sequencing technology sequences only fragments of DNA. It then uses the fragments to piece together the whole genome. But the repeat expansions are often longer than the fragments, which may leave lengthy repeats hiding in plain sight.
The research team found a way around this obstacle. “We were able to use a tool that allows us to find expansions in sequences from whole genomes,” Erwin said.
Armed with this new tool, Erwin and his colleagues 2,622 cancer genomes from 2,509 patients, data obtained from the International Cancer Genome Consortium and the Cancer Genome Atlas.
With scant research on repeat expansions in cancer, it wasn’t clear what, if anything, they would find. But of the 29 different cancers they examined, the research team found 160 repeat expansions in seven cancers. They further saw that of those, 155 repeat expansions were specific to certain cancer subtypes — “meaning,” Erwin said, “if we detect [certain repeat expansions] in prostate cancer, we tend not to detect them in other cancers.”
To ensure they had found repeat expansions that were both specific to cancer and longer than the norm, the researchers compared each individual’s cancer cell genomes with genomes of their non-cancerous cells. Repetitive DNA sequences are found in healthy genomes, but it’s the expansion of these sequences that can lead to disease.
The repeat expansions were most common in prostate and liver cancers, with researchers detecting the repeats in 93% of prostate cancer genomes and 95% of liver cancer genomes. The repeats also occurred in ovarian cancer, kidney cancer, a brain cancer called pilocytic astrocytoma and a type of lung cancer called squamous cell carcinoma.
It’s possible, however, that there are more repeat expansions in the cancer genomes the researchers couldn’t detect. As sequencing technologies improve at analyzing longer stretches of DNA, Snyder predicts they’ll find more repeats in different cancers. “I think we’re just at the tip of the iceberg,” he said.
A molecule on the hunt
To see whether their results could lead to new directions for cancer treatment, the researchers piggybacked off Erwin’s earlier work and created a molecule, Syn-TEF3, to target a specific repeat expansion in kidney cancer cells, comparing it with a molecule without that targeting ability.
Syn-TEF3 slowed the production of or killed cells with the Syn-TEF3-specific repeat expansion. In cells without that expansion, the molecule had little effect. Similarly, the molecule that didn’t target the repeat expansion didn’t impart the benefits of Syn-TEF3, the researchers reported.
“To go right from discovery to potential therapeutic avenue was pretty unusual,” Snyder said. The researchers have a long way to go before testing their method in humans, but Snyder and the team are excited to explore it.
Researchers from Columbia University, New York Genome Center, Illumina, Northwestern University, the Hospital for Sick Children, the University of Toronto, the Veterans Affairs Palo Alto Health Care System and Yale University also contributed to the study.
The study was funded by the National Institutes of Health (grants U2CCA233311 and K99HG011467) and the Stanford Cancer Institute Postdoctoral Fellowship from the Ellie Guardino Research Fund.
About Stanford Medicine
Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit med.stanford.edu.