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Stanford researchers track cancer growth with genome editing, DNA barcoding
CRISPR crabs. (Courtesy of Stanford News)

Stanford researchers track cancer growth with genome editing, DNA barcoding

A novel technique developed by Stanford scientists combines genome editing and DNA barcoding to more accurately and efficiently track the effects of cancer-related genetic interactions in the lungs of mice, according to a Stanford News press release. The study, conducted by Stanford geneticist Monte Winslow, was published in the April issue of the scientific journal “Nature Genetics.”

Winslow’s research will allow scientists to replicate and analyze the genetic diversity of cells found in tumors of cancer patients, dramatically improving the rate of cancer research and drug development.

Overall, the study aims to help researchers better understand how cancer-related genetic interactions trigger tumor growth in vivo.

“Human cancers don’t have only one tumor-suppression mutation — they have combinations,” said Winslow. “The question is, how do different mutated genes cooperate or not cooperate with one another?”

Conventional techniques that facilitate mapping research of this kind require an enormous expenditure of resources, including the breeding of several lineages of genetically modified mice under a long period of observation. To mimic and observe all the possible genetic combinations, a study would have involved hundreds or thousands of mice. Winslow’s lab saw results in just a few months, and their study required fewer than two dozen mice.

“We’ve analyzed more genotypes of lung cancer tumors than the whole field has in 15 years,” Winslow said.

Winslow’s lab developed a method that incorporates CRISPR-Cas9 — a gene-editing tool that allows researchers to easily modify DNA sequences — and DNA barcoding – a process where scientists attach a short genetic marker to individual tumor cells — to analyze pairwise combinations of tumor suppressor alterations. The lab used CRISPR-Cas9 to induce the growth of genetically-distinct tumors in the lungs of individual mice.

However, simply inducing tumor growth is not sufficient to draw useful conclusions about the effects of interactions of genetic mutations. To identify and track the growth of tumors, Winslow enlisted the help of Stanford evolutionary biologist Dmitri Petrov, also a senior author of the study. Petrov suggested the technique of DNA barcoding — as each cancer seed cell divides into a tumor, the number of heritable DNA barcodes also multiplies.

DNA barcoding allows Winslow’s lab to more quantitatively analyze the size of cancerous tumors in mice. Researchers can study a cancerous mouse lung using computational methods to tally how often the barcode attached to the tumor appears.

“We can now generate a very large number of tumors with specific genetic signatures in the same mouse and follow their growth individually at scale and with high precision. The previous methods were both orders of magnitude slower and much less quantitative,” said Petrov.

“This is 10 steps forward in our ability to model human cancer,” Petrov added.

 

Contact Alex Tsai at aotsai ‘at’ stanford.edu.

About Alex Tsai

Alex Tsai ’21 is a writer for The Daily’s campus life beat. She was born and raised in Hong Kong for 13 years and moved to La Jolla, CA for high school. Alex walked onto the varsity lacrosse team this year and is interested in computer science.