
NEW YORK – Cache DNA, a Massachusetts Institute of Technology spinout developing technology for long-term storage of DNA, is focusing on biobanking as a near-term application, touting a cheaper and less energy-intensive method for storing clinical research samples.
The firm's glass-based nucleic acid encapsulation technology, which also has potential applications in DNA-based data storage and computing, is enabling labs to preserve samples at ambient temperatures, rather than in power-consuming freezers, for a long time.
"When we look at this industry, we've seen a dizzying number of samples that have been generated, not only from the pandemic but on an ongoing basis, with everything from in vitro diagnostic tests to companion diagnostics," Cache CEO Mike Becich said. "There's so much precious information that's left on the table, and oftentimes labs are forced to make concessions, either throwing away the samples or only running a narrower panel, rather than thinking about more comprehensive whole-genome testing, or transcriptome, or epigenomic testing. … We're giving them an opportunity to archive those samples just in case, without having the budget balloon."
Cache has partnered with Euan Ashley’s group at Stanford University and with a group at Canada's Princess Margaret Cancer Centre, among other customers, which Becich declined to disclose. Oncology and rare disease research have fueled interest in Cache's technology, he added.
The firm, now based in San Carlos, California, raised a seed funding round in May. Becich said it was in the "mid- to high-single-digit" millions of dollars but declined to provide an exact figure. Climate Capital Bio, Exor Ventures, Hawktail, LifeX Ventures, Pillar VC, Trousdale Ventures, and Illumina participated in the round. Cache also participated in the old Illumina Accelerator program in 2022.
With biobanking, the firm is showing that its technology has uses other than DNA-based data storage applications, which remain out of reach. "The cost of DNA synthesis hasn't dropped as quickly as the industry hoped, but we still see positive signs in that direction," Becich said. "It's just a clear signal that we made the right choice focusing on the life sciences industry, where there is this immediate willingness to pay and need for high-quality bio storage."
Cache's technology is based on research from cofounder and MIT researcher Mark Bathe. In 2021, his lab showed it could pull out oligo-barcoded glass capsules containing information encoded in DNA using magnetic beads. The barcodes contain metadata about the contents and the "file system" enabled searches with Boolean logic.
In June, researchers from Cache and MIT published a paper in the Journal of the American Chemical Society on a new material for storing nucleic acids. They showed how their method, Thermoset-REinforced Xeropreservation (T-REX), was able to store DNA in glassy polymer networks. "This process successfully encapsulates DNA that spans different length scales, from tens of bases to gigabases, in a matter of hours compared to days with traditional silica-based encapsulation," the authors wrote. Cache has exclusively licensed the technology from MIT, Becich said.
Cache has seven full-time employees at the moment, in addition to a "large number" of contractors and consultants, Becich said. The firm is looking to grow once it secures its next funding round, which could happen next year.
Growing its staff could help Cache address the nucleic acid biobanking market, which is also on the rise. He estimated the addressable market at approximately $7 billion, about 10 percent of the broader $70 billion biobanking market.
"After touring a large number of [academic research centers], it is clear that the space that [freezers] occupy in labs is a major headache, especially for diagnostic labs who are operating on razor thin margins," Becich said. Maintenance contracts are expensive, and power failures could lead to emergencies.
Companies that have automated cold storage including Azenta Life Sciences and Hamilton are the biggest competition, but dried matrix and "macro encapsulation" — think metal capsules — are also options now.
Earlier this year, Cache and Princess Margaret researchers presented a poster at the 2024 American College of Medical Genetics and Genomics meeting with data on storage of formalin-fixed paraffin-embedded tumor-derived nucleic acid for use in whole-genome sequencing. Samples of 1 μg were split between freezer-based storage and Cache's approach, stored for four weeks, and then sequenced at 30X coverage. "Following variant analyses, we found genotype concordance exceeding 0.95 for SNPs and indels between encapsulated and unmodified samples," the authors wrote. "This high level of genotype concordance was also consistently observed across technical replicates of both sample types."
Cache has begun offering demo kits on its website, "just a box we're able to ship worldwide," Becich said.
Besides working on its next funding round, the firm is hoping to renew its Small Business Innovation Research grant from the National Science Foundation; a Phase II grant could be worth up to $1 million.