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 genetic diversity of cells found in tumors outside of the lab.

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

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, 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.

Dmitri Petrov, an evolutionary biologist at Stanford who is a senior author of the new study, had been working 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.

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 cut out individual tumors painstakingly, 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. 

"We can now generate a huge 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."

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 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.

"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."