Reengineering cancer tumors to self-destruct and kill drug-resistant cells

Treating cancer can sometimes feel like a game of whack-a-mole. The disease can become resistant to treatment, and clinicians never know when, where, or how much resistance might emerge, leaving them behind. But a team led by researchers at Penn State University has found a way to reprogram the disease’s course and engineer tumors that are easier to treat.

They created a modular genetic circuit that turns cancer cells into a “Trojan horse,” causing them to self-destruct and kill nearby drug-resistant cancer cells. Tested on human cell lines and mice as a proof of concept, the circuit thwarted a wide range of resistance.

The results were published today, July 4, in the journal Biotechnology of natureThe researchers have also filed a provisional patent application for the technology described in the paper.

“This idea came out of frustration. We’re not doing a bad job of developing new therapies to treat cancer, but how can we think about potential cures for more advanced cancers?” said Justin Pritchard, the Dorothy Foehr Huck and J. Lloyd Huck Early Career Associate Professor of Biomedical Engineering and senior author of the paper.

“Selection genes represent a powerful new paradigm for evolution-driven cancer therapy. I like the idea that we can use the inevitability of a tumor’s evolution against it.”

New personalized cancer treatments often fail, not because the treatments aren’t effective, but because of the inherent diversity and heterogeneity of cancer, Pritchard said. Even if a first-line treatment is effective, resistance eventually develops and the drug stops working, allowing the cancer to come back.

Clinicians then find themselves back at square one and repeat the process with a new drug until resistance emerges again. The cycle intensifies with each new treatment until there are no other options available.

“It’s like playing whack-a-mole. You don’t know what mole is going to show up next, so you don’t know what the best drug is going to be to treat the tumor. We’re always on the defensive, unprepared,” said Scott Leighow, a postdoctoral researcher in biomedical engineering and lead author of the study.

The researchers wondered if they could go further. Could they eliminate resistance mechanisms before cancer cells had a chance to evolve and appear in unexpected ways? Could they force a specific “mole” onto the chart, one that they preferred and were willing to fight?

What started as a thought experiment is proving effective. The team created a modular circuit, or dual-switch gene drive, to introduce a mutation in the EGFR gene into non-small lung cancer cells. This mutation is a biomarker that existing drugs on the market can target.

The circuit has two genes, or switches. The first acts as a selection gene, allowing researchers to turn drug resistance on and off, like a light switch. When the first switch is turned on, the genetically modified cells become temporarily resistant to a specific drug—in this case, a drug for non-small cell lung cancer.

When the tumor is treated with the drug, the drug-sensitive native cancer cells are killed, leaving behind the cells engineered to resist and a small population of drug-resistant native cancer cells. The engineered cells eventually grow and outcompete the resistant native cells, preventing them from amplifying and developing new resistance.

The resulting tumor contains mostly genetically modified cells. When the first switch is turned off, the cells become sensitive to drugs again. The second switch is the therapeutic payload. It contains a suicide gene that allows the modified cells to make a diffusible toxin that can kill both the modified cells and neighboring unmodified cells.

“Not only does it kill the modified cells, it also kills the surrounding cells, which are the resistant native population,” Pritchard said. “That’s critical. That’s the population you want to get rid of so the tumor doesn’t grow back.”

The team first simulated tumor cell populations and used mathematical models to test the concept. Then they cloned each switch, packaged them separately into viral vectors, and tested their functionality individually in human cancer cell lines. They then coupled the two switches together into a single circuit and tested it again. When the circuit proved effective in vitro, the team repeated the experiments in mice.

But the team didn’t just want to know if the circuit worked, they wanted to know if it could work in every possible way. They subjected the system to resistance testing using complex genetic libraries of resistance variants to see if the genetic drive system could work robustly enough to counter all the genetic ways in which resistance could arise in cancer cell populations.

And it worked: A handful of engineered cells can take control of the cancer cell population and eradicate high levels of genetic heterogeneity. Pritchard said that’s one of the study’s greatest strengths, conceptually and experimentally.

“The beauty of this situation is that we are able to target cancer cells without knowing what they are, without waiting for them to grow or for resistance to develop, because by that point it’s too late,” Leighow said.

Researchers are now working on how to translate this genetic circuit so that it can be delivered safely and selectively to growing tumors and, ultimately, to metastatic disease.

Other authors on the study include Marco Archetti, associate professor of biology; Shun Yao, postdoctoral researcher in biology; Ivan Sokirniy, a graduate student at the Huck Institutes of the Life Sciences; and Joshua Reynolds and Zeyu Yang, members of the Department of Biomedical Engineering. Co-author Haider Inam was a doctoral student in biomedical engineering at the time of the research and is currently a research scientist at the Broad Institute of MIT and Harvard. Dominik Wodarz, a professor at the University of California, San Diego, also contributed to the study.