Scientists combine CRISPR and DNA barcoding to track cancer growth

April 3, 2018 by Ker Than, Stanford University
Stanford researchers say the combination of CRISPR-Cas9 and DNA barcoding could allow scientists to replicate in the lab the kind of genetic diversity observed in cancer patients. Credit: Courtesy Monte Winslow

Stanford scientists have found a way to modify pairs of cancer-related genes in the lungs of mice and then precisely track individual cells of the resulting tumor – a combined technique that could dramatically speed up cancer research and drug development.

The work could finally allow scientists to mimic and then study the of cells found in tumors outside of the lab.

"Human cancers don't have only one tumor-suppression mutation – they have combinations. The question is, how do different mutated genes cooperate or not cooperate with one another?" said Monte Winslow, a geneticist at Stanford's School of Medicine and a senior author of the study, published in the April 2 issue of the journal Nature Genetics.

Just a few years ago, such a mapping study would have been a monumental, years-long effort. It would have required breeding several lineages of genetically modified mice, each with a different pair of inactivated tumor suppressor genes. To explore all of the possible combinations, hundreds or thousands of mice would have been needed.

In contrast, Winslow and his colleagues conducted their experiments in a few months involving fewer than two dozen mice. "We've analyzed more genotypes of lung tumors than the whole field has in 15 years," Winslow said.

A wild idea

The team achieved this result using CRISPR-Cas9 – a powerful gene-editing tool that can easily replace, modify, or delete genetic sequences inside organisms – to create multiple, genetically distinct tumors in the lungs of individual animals. "We can induce thousands of clonal tumors in a single mouse," Winslow said.

However, in order to draw useful conclusions about the combinatory effects of different gene mutations, the scientists needed a precise way to label and track the growth of different tumors. Here again, conventional techniques – which involved trying to excise and compare the sizes of individual tumors – were insufficient.

"Not only was it extremely slow, but how do you pluck out a tumor that's weirdly shaped, or one that's stuck to another tumor?" said study coauthor Ian Winters, a graduate student in Winslow's lab. "We needed a better way to quantify tumor sizes."

The solution came from an unexpected source. Dmitri Petrov, an evolutionary biologist at Stanford who is a senior author of the new study, had been working with Stanford physicist Daniel Fisher and geneticist Gavin Sherlock to develop DNA barcoding as a way of investigating rapid evolution in yeast. When Petrov learned about the experiments in Winslow's group, he thought that the technique might also work in mice.

"Dmitri's the sort of guy who has a lot of wild ideas, and at first, we didn't think that what he was suggesting was possible," Winslow said. "But after we thought about it for a couple of days, we realized that, well, actually, maybe we can do that."

Counting barcodes

Petrov's idea was to attach short, unique sequences of DNA to individual tumor cells inside mice lungs. Each sequence functions as a heritable genetic barcode, and as each cancer seed cell divides, growing into a tumor, the number of barcodes also multiplies.

Now, instead of having to painstakingly cut out individual tumors, the scientists could take an entire cancerous lung, grind it up, and then use high-throughput DNA sequencing and computational analysis to very precisely determine how big a tumor is by counting how often its barcodes pop up. By tallying different barcodes, scientists can compare tumor sizes much more quantitatively than was previously possible.

"This is 10 steps forward in our ability to model human cancer," said Petrov, who is the Michelle and Kevin Douglas Professor in the School of Humanities and Sciences. "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."

Genetic diversity

The combination of CRISPR-Cas9 and DNA barcoding could allow scientists to replicate in the lab the kind of genetic diversity observed in cancer patients. "It gets around this fear of the complexity of cancer," Winters said. "We've known for decades that human tumors are extremely complex and different from patient to patient, but how do you actually recreate that so you can study it? It's not by doing it one at a time. Now, we can model 30 different genetic variations of a cancer simultaneously."

One striking finding from the team's mapping study is that many are context dependent – that is, they only affect cancer growth in the presence or absence of another gene. "We are now in a good position to understand how key cancer drivers interact with each other, and why tumors with the same mutations sometimes grow to be very large and sometimes not," said study co-first author Christopher McFarland, a postdoctoral scholar in Petrov's lab.

The team's hybrid technique could also prove valuable for cancer drug testing. Pharmaceutical companies could test a drug on thousands of variations simultaneously to see which ones respond to treatment and – equally important – which ones don't.

"We can help understand why targeted therapies and immunotherapies sometimes work amazingly well in patients and sometimes fail," Petrov said. "We hypothesize that the genetic identity of tumors might be partially responsible, and we finally have a good way to test this."

Explore further: Can mice really mirror humans when it comes to cancer?

More information: Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice, Nature Genetics (2018). nature.com/articles/doi:10.1038/s41588-018-0083-2

Related Stories

Can mice really mirror humans when it comes to cancer?

January 18, 2018
A new Michigan State University study is helping to answer a pressing question among scientists of just how close mice are to people when it comes to researching cancer.

Cancer's gene-determined 'immune landscape' dictates progression of prostate tumors

January 12, 2018
The field of immunotherapy - the harnessing of patients' own immune systems to fend off cancer - is revolutionizing cancer treatment today. However, clinical trials often show marked improvements in only small subsets of ...

Study provides insight into link between two rare tumor syndromes

August 22, 2017
UCLA researchers have discovered that timing is everything when it comes to preventing a specific gene mutation in mice from developing rare and fast-growing cancerous tumors, which also affects young children. This mutation ...

Editing genes one by one throughout colorectal cancer cell genome uncovers new drug target

September 27, 2017
Cancers driven by mutations in the KRAS gene are among the most deadly. For decades, researchers have tried unsuccessfully to directly target mutant KRAS proteins as a means to treat tumors. Instead of targeting mutant KRAS ...

Biologists pinpoint a genetic change that helps tumors move to other parts of the body

April 6, 2011
MIT cancer biologists have identified a genetic change that makes lung tumors more likely to spread to other parts of the body. The findings, to be published in the April 6 online issue of Nature, offers new insight into ...

Two-drug combination may boost immunotherapy responses in lung cancer patients

November 30, 2017
Johns Hopkins Kimmel Cancer Center researchers and colleagues have identified a novel drug combination therapy that could prime nonsmall cell lung cancers to respond better to immunotherapy. These so-called epigenetic therapy ...

Recommended for you

Variants in non-coding DNA contribute to inherited autism risk

April 19, 2018
In recent years, researchers have firmly established that gene mutations appearing for the first time, called de novo mutations, contribute to approximately one-third of cases of autism spectrum disorder (ASD). In a new study, ...

Researchers discover link between gene variation and language

April 18, 2018
What shapes the basic features of a language?

Natural selection still at work in humans

April 18, 2018
Evolution has shaped the human race, with University of Queensland researchers finding signatures of natural selection in the genome that influence traits associated with fertility and heart function.

Gene therapy for beta-thalassemia safe, effective in people

April 18, 2018
In a powerful example of bench-to-bedside science showing how observations made in the lab can spark life-altering therapies in clinic, an international team of clinician-investigators has announced that gene therapy for ...

Potential lines of attack against prostate cancer

April 17, 2018
Researchers from The University of East Anglia (UEA) have contributed to the world's largest study into genes that drive prostate cancer – identifying 80 molecular weaknesses that could be targeted by drugs to treat the ...

Epstein-Barr virus linked to seven serious diseases

April 16, 2018
A far-reaching study conducted by scientists at Cincinnati Children's reports that the Epstein-Barr virus (EBV)—best known for causing mononucleosis—also increases the risks for some people of developing seven other major ...

2 comments

Adjust slider to filter visible comments by rank

Display comments: newest first

Spaced out Engineer
not rated yet Apr 03, 2018
Is there a map to Haah code to get ahead of the many body(biological) problem once they are flagged?
To hold the genetic identity in a spin liquid!
The human codex, and its apt ends that flirt with the efficient, though it may try to filter the ambient pinches.
Spaced out Engineer
not rated yet Apr 03, 2018
I hope not, seeing as how you people continue to bombard my ass with electromagnetism with the intent of increasing psychosis (https://www.bigge...en.com/) with total disregard for safety, health, hazard, cancer, or seizures.
But seeing as how this is just a reference in holography, the show must go on!
It is inescapable in its resolve.
Where is karma for the assholes with masers and ultrasound?

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.