Author: MIT News

Ever since freezers were invented, the life sciences industry has been reliant on them. That’s because many patient samples, drug candidates, and other biologics must be stored and transported in powerful freezers or surrounded by dry ice to remain stable.

The problem was on full display during the Covid-19 pandemic, when truckloads of vaccines had to be discarded because they had thawed during transport. Today, the stakes are even higher. Precision medicine, from CAR-T cell therapies to tumor DNA sequencing that guides cancer treatment, depends on pristine biological samples. Yet a single power outage, shipping delay, or equipment failure can destroy irreplaceable patient samples, setting back treatment by weeks or halting it entirely. In remote areas and developing nations, the lack of reliable cold storage effectively locks out entire populations from these life-saving advances.

Cache DNA wants to set the industry free from freezers. At MIT, the company’s founders created a new way to store and preserve DNA molecules at room temperature. Now the company is building biomolecule preservation technologies that can be used in applications across health care, from routine blood tests and cancer screening to rare disease research and pandemic preparedness.

“We want to challenge the paradigm,” says Cache DNA co-founder and former MIT postdoc James Banal. “Biotech has been reliant on the cold chain for more than 50 years. Why hasn’t that changed? Meanwhile, the cost of DNA sequencing has plummeted from $3 billion for the first human genome to under $200 today. With DNA sequencing and synthesis becoming so cheap and fast, storage and transport have emerged as the critical bottlenecks. It’s like having a supercomputer that still requires punch cards for data input.”

As the company works to preserve biomolecules beyond DNA and scale the production of its kits, co-founders Banal and MIT Professor Mark Bathe believe their technology has the potential to unlock new health insights by making sample storage accessible to scientists around the world.

“Imagine if every human on Earth could contribute to a global biobank, not just those living near million-dollar freezer facilities,” Banal says. “That’s 8 billion biological stories instead of just a privileged few. The cures we’re missing might be hiding in the biomolecules of someone we’ve never been able to reach.”

From quantum computing to “Jurassic Park”

Banal came to MIT from Australia to work as a postdoc under Bathe, a professor in MIT’s Department of Biological Engineering. Banal primarily studied in the MIT-Harvard Center for Excitonics, through which he collaborated with researchers from across MIT.

“I worked on some really wacky stuff, like DNA nanotechnology and its intersection with quantum computing and artificial photosynthesis,” Banal recalls.

Another project focused on using DNA to store data. While computers store data as 0s and 1s, DNA can store the same information using the nucleotides A, T, G, and C, allowing for extremely dense storage of data: By one estimate, 1 gram of DNA can hold up to 215 petabytes of data.

After three years of work, in 2021, Banal and Bathe created a system that stored DNA-based data in tiny glass particles. They founded Cache DNA the same year, securing the intellectual property by working with MIT’s Technology Licensing Office, applying the technology to storing clinical nucleic acid samples as well as DNA data. Still, the technology was too nascent to be used for most commercial applications at the time.

Professor of chemistry Jeremiah Johnson had a different approach. His research had shown that certain plastics and rubbers could be made recyclable by adding cleavable molecular bonds. Johnson thought Cache DNA’s technology could be faster and more reliable using his amber-like polymers, similar to how researchers in the “Jurassic Park” movie recover ancient dinosaur DNA from a tree’s fossilized amber resin.

“It started basically as a fun conversation along the halls of Building 16,” Banal recalls. “He’d seen my work, and I was aware of the innovations in his lab.”

Banal immediately saw the potential. He was familiar with the burden of the cold chain. For his MIT experiments, he’d store samples in big freezers kept at -80 degrees Celsius. Samples would sometimes get lost in the freezer or be buried in the inevitable ice build-up. Even when they were perfectly preserved, samples could degrade as they thawed.

As part of a collaboration between Cache DNA and MIT, Banal, Johnson, and two researchers in Johnson’s lab developed a polymer that stores DNA at room temperature. In a nod to their inspiration, they demonstrated the approach by encoding DNA sequences with the “Jurassic Park” theme song.

The researchers’ polymers could encompass a material as a liquid and then form a solid, glass-like block when heated. To release the DNA, the researchers could add a molecule called cysteamine and a special detergent. The researchers showed the process could work to store and access all 50,000 base pairs of a human genome without causing damage.

“Real amber is not great at preservation. It’s porous and lets in moisture and air,” Banal says. “What we built is completely different: a dense polymer network that forms an impenetrable barrier around DNA. Think of it like vacuum-sealing, but at the molecular level. The polymer is so hydrophobic that water and enzymes that would normally destroy DNA simply can’t get through.”

As that research was taking shape, Cache DNA was learning that sample storage was a huge problem from hospitals and research labs. In places like Florida and Singapore, researchers said contending with the effects of humidity on samples was another constant headache. Other researchers across the globe wanted to know if the technology would help them collect samples outside of the lab.

“Hospitals told us they were running out of space,” Banal says. “They had to throw samples out, limit sample collection, and as a last-case scenario, they would use a decades-old storage technology that leads to degradation after a short period of time. It became a north star for us to solve those problems.”

A new tool for precision health

Last year, Cache DNA sent out more than 100 of its first alpha DNA preservation kits to researchers around the world.

“We didn’t tell researchers what to use it for, and our minds were blown by the use cases,” Banal says. “Some used it for collecting samples in the field where cold shipping wasn’t feasible. Others evaluated for long term archival storage. The applications were different, but the problem was universal: They all needed reliable storage without the constraint of refrigeration.”

Cache DNA has developed an entire suite of preservation technologies that can be optimized for different storage scenarios. The company also recently received a grant from the National Science Foundation to expand its technology to preserve a broader swath of biomolecules, including RNA and proteins, which could yield new insights into health and disease.

“This important innovation helps eliminate the cold chain and has the potential to unlock millions of genetic samples globally for Cache DNA to empower personalized medicine,” Bathe says. “Eliminating the cold chain is half the equation. The other half is scaling from thousands to millions or even billions of nucleic acid samples. Together, this could enable the equivalent of a ‘Google Books’ for nucleic acids stored at room temperature, either for clinical samples in hospital settings and remote regions of the world, or alternatively to facilitate DNA data storage and retrieval at scale.”

“Freezers have dictated where science could happen,” Banal says. “Remove that constraint, and you start to crack open possibilities: island nations studying their unique genetics without samples dying in transit; every rare disease patient worldwide contributing to research, not just those near major hospitals; the 2 billion people without reliable electricity finally joining global health studies. Room-temperature storage isn’t the whole answer, but every cure starts with a sample that survived the journey.”

Using tiny particles shaped like bottlebrushes, MIT chemists have found a way to deliver a large range of chemotherapy drugs directly to tumor cells.

To guide them to the right location, each particle contains an antibody that targets a specific tumor protein. This antibody is tethered to bottlebrush-shaped polymer chains carrying dozens or hundreds of drug molecules — a much larger payload than can be delivered by any existing antibody-drug conjugates.

In mouse models of breast and ovarian cancer, the researchers found that treatment with these conjugated particles could eliminate most tumors. In the future, the particles could be modified to target other types of cancer, by swapping in different antibodies.

“We are excited about the potential to open up a new landscape of payloads and payload combinations with this technology, that could ultimately provide more effective therapies for cancer patients,” says Jeremiah Johnson, the A. Thomas Geurtin Professor of Chemistry at MIT, a member of the Koch Institute for Integrative Cancer Research, and the senior author of the new study.

MIT postdoc Bin Liu is the lead author of the paper, which appears today in Nature Biotechnology.

A bigger drug payload

Antibody-drug conjugates (ADCs) are a promising type of cancer treatment that consist of a cancer-targeting antibody attached to a chemotherapy drug. At least 15 ADCs have been approved by the FDA to treat several different types of cancer.

This approach allows specific targeting of a cancer drug to a tumor, which helps to prevent some of the side effects that occur when chemotherapy drugs are given intravenously. However, one drawback to currently approved ADCs is that only a handful of drug molecules can be attached to each antibody. That means they can only be used with very potent drugs — usually DNA-damaging agents or drugs that interfere with cell division.

To try to use a broader range of drugs, which are often less potent, Johnson and his colleagues decided to adapt bottlebrush particles that they had previously invented. These particles consist of a polymer backbone that are attached to tens to hundreds of “prodrug” molecules — inactive drug molecules that are activated upon release within the body. This structure allows the particles to deliver a wide range of drug molecules, and the particles can be designed to carry multiple drugs in specific ratios.

Using a technique called click chemistry, the researchers showed that they could attach one, two, or three of their bottlebrush polymers to a single tumor-targeting antibody, creating an antibody-bottlebrush conjugate (ABC). This means that just one antibody can carry hundreds of prodrug molecules. The currently approved ADCs can carry a maximum of about eight drug molecules.

The huge number of payloads in the ABC particles allows the researchers to incorporate less potent cancer drugs such as doxorubicin or paclitaxel, which enhances the customizability of the particles and the variety of drug combinations that can be used.

“We can use antibody-bottlebrush conjugates to increase the drug loading, and in that case, we can use less potent drugs,” Liu says. “In the future, we can very easily copolymerize with multiple drugs together to achieve combination therapy.”

The prodrug molecules are attached to the polymer backbone by cleavable linkers. After the particles reach a tumor site, some of these linkers are broken right away, allowing the drugs to kill nearby cancer cells even if they don’t express the target antibody. Other particles are absorbed into cells with the target antibody before releasing their toxic payload.

Effective treatment

For this study, the researchers created ABC particles carrying a few different types of drugs: microtubule inhibitors called MMAE and paclitaxel, and two DNA-damaging agents, doxorubicin and SN-38. They also designed ABC particles carrying an experimental type of drug known as PROTAC (proteolysis-targeting chimera), which can selectively degrade disease-causing proteins inside cells.

Each bottlebrush was tethered to an antibody targeting either HER2, a protein often overexpressed in breast cancer, or MUC1, which is commonly found in ovarian, lung, and other types of cancer.

The researchers tested each of the ABCs in mouse models of breast or ovarian cancer and found that in most cases, the ABC particles were able to eradicate the tumors. This treatment was significantly more effective than giving the same bottlebrush prodrugs by injection, without being conjugated to a targeting antibody.

“We used a very low dose, almost 100 times lower compared to the traditional small-molecule drug, and the ABC still can achieve much better efficacy compared to the small-molecule drug given on its own,” Liu says.

These ABCs also performed better than two FDA-approved ADCs, T-DXd and TDM-1, which both use HER2 to target cells. T-DXd carries deruxtecan, which interferes with DNA replication, and TDM-1 carries emtansine, a microtubule inhibitor.

In future work, the MIT team plans to try delivering combinations of drugs that work by different mechanisms, which could enhance their overall effectiveness. Among these could be immunotherapy drugs such as STING activators.

The researchers are also working on swapping in different antibodies, such as antibodies targeting EGFR, which is widely expressed in many tumors. More than 100 antibodies have been approved to treat cancer and other diseases, and in theory any of those could be conjugated to cancer drugs to create a targeted therapy.

The research was funded in part by the National Institutes of Health, the Ludwig Center at MIT, and the Koch Institute Frontier Research Program.