Linear DNA Crosses the Line between Tags and Therapeutics

Applied DNA Sciences exploits the long and short of amplicon production

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James A. Hayward
James A. Hayward, PhD, ScD

Short fragments of linear DNA are used for molecular tagging in a variety of industries, from textiles to pharmaceuticals, to provide product authentication and ingredient traceability. Applied DNA Sciences is now translating its expertise in the molecular tagging industry to the biopharma industry. Its subsidiary, LineaRx, is manufacturing large, gene-sized fragments of linear DNA for companies researching or developing gene-based therapies or diagnostics, as well as for its own gene therapy program. This parallel path to growth addresses both the development and distribution sides of the biopharma industry, which bodes well for overall organizational success.

The parent company’s short fragments and the subsidiary’s long fragments both involve the large-scale production of specific DNA sequences using the polymerase chain reaction (PCR). Alongside this commonality, there is this significant difference: The short fragments are nonfunctional, whereas the long fragments are functional (and suitable for therapeutic applications).

The use of linear DNA for gene-based therapies challenges the historic use of bacterially fermented plasmids, which produce circular DNA and risk introducing bacterial contaminants such as foreign DNA and endotoxins.

“For gene therapy, we can introduce functional, therapeutic DNA to patients without using viral or retroviral vectors (many of which originally were pathogens),” says James A. Hayward, PhD, ScD, chairman, president, and CEO of Applied DNA Sciences. “The insertion is episomal in the nucleus. DNA isn’t inserted in the chromosome. The linear DNA can withstand a fair number of cell divisions, surviving one to two weeks in mice.”

The company’s patents suggest that the survival times of linear DNA in the nucleus can be tuned as required. Such tuning is advantageous, Hayward points out, in the case of vaccines, enabling antigens to be made in the body only long enough to raise an immune response. Transient expression lowers the risk and seriousness of unintended consequences.

Applied DNA Sciences formed LineaRx in September 2018 as a wholly owned subsidiary to apply its expertise in the large-scale PCR development of linear DNA to vaccines and to gene and cellular therapies. The company functions as a CRO and CMO, but it is also working with partners to develop therapies, notably a cancer vaccine and a CAR T-cell immunotherapy.

Creating the new subsidiary provides a distinct focus for each company’s sales team. Beyond that, the decision to develop a therapeutic program with partners enhances market visibility for the technology and scientific evidence of the value of linear DNA in drug development. The decision to also develop and manufacture therapeutic DNA as a CRO and CMO positions LineaRx to supply custom DNA now to the growing gene-therapy market, Hayward explains. The decision looks straightforward on paper, but drug development is, inevitably, a long, challenging, and very risky process for even experienced drug companies.

From cotton to CAR T cells

The applications for molecular tagging are measured in hundreds of thousands of metric tons. Consequently, to reach that market, Applied DNA Sciences had to find a way to manufacture short fragments of linear DNA to scale. Its solution centered on increasing the efficiency of its manufacturing processes and increasing the size of the amplicons it manufactured.

Originally, the technology was used to track products to their origin. For example, Hayward says, “DNA tags would be added to cotton at the cotton gin, which are proximal to the cotton farm. But the utility of molecular tags goes far beyond that.” It enables third-party verification of particular claims. For example, although you can’t verify that  raw ingredients are grown under sustainable conditions just by tagging them, you can use molecular tags to verify that a particular raw ingredient is the same one that was verified as sustainable by a third party. Therefore, molecular tagging provides a layer of assurance that a product ingredient hasn’t been diverted or replaced in transit between the supplier and the manufacturing customer.

“Success in scaling up our molecular tagging manufacturing led us to entertain thoughts of the relevance of amplicons for therapeutics,” Hayward notes. Like any product company, Applied DNA Sciences researched the opportunity.

The promise of linear DNA

“We dipped our toes in the pharmaceutical waters by presenting a poster and exhibiting at a global vaccine conference. We were overwhelmed by the strength of the audience response,” he recalls. The industry was grounded in plasmid production, so the realization that linear DNA could be produced at scale was an epiphany, he declares. By the time LineaRx was founded, its parent company had about a year’s experience in the pharmaceutical industry and already had shipped several thousand milligrams of linear DNA for both diagnostic and therapeutic applications.

Linear DNA that is short and nonfunctional scales well for industrial applications, but when linear DNA technology is translated to the life sciences industry, maintaining scalability is just one challenge. Amplicons need to be large enough to approximate the length of actual genes and to contain the control mechanisms allowing the DNA to be expressed in cells.

Those goals appear to have been achieved. As Hayward says, “We believe our linear DNA approach will yield more transcripts and protein per molecule of DNA, and that they’ll also survive longer in vivo.”

Early-stage therapeutic programs

LineaRx has two therapeutic programs in early-stage development. The lead program, an anti-DC19b CAR T-cell therapy, “has been in the clinic in Asia, where it was delivered successfully by both plasmid and retroviral vectors,” Hayward assents. “We acquired the rights to develop a linearized form for use in the United States. We’re working quickly to demonstrate the effectiveness of this approach.” It is based upon assembling effective constructs to generate high expression and high signal transduction in T cells. “There’s every expectation this will prove relevant to both solid and hematologic tumors,” he insists.

The other preclinical program, a nucleic acid–based cancer vaccine targeting the overexpression of telomerase, has shown immunogenicity in mice. It is being developed in partnership with Takis Biotech and EvviVax for applications in cats and dogs. This approach helps the vaccine accumulate data before it is translated to human trials.

LineaRx also is developing a concept for adoptive cell therapies. The basic premise is to place artificial intelligence–enabled, DNA-producing PCR devices in hospitals throughout the United States. Adhering to cGMP standards, local clinicians could use these devices to replicate the genes needed for their patients’ gene therapies. “That opens the opportunity for fast, highly personalized cell therapies,” he says. Still in its early stages, this therapy will need a large pharma partner for development and commercialization.

While advancing these programs, LineaRx continues working as a CRO/CMO. In November, for example, it announced a shipment of linear DNA to Technogenetics for use in kits to detect autoimmunity and infectious disease.

Parallel opportunities

“It’s very exciting to us to bring value to patients and to the supply chain in large, complex ecosystems like textiles, cannabis, and pharmaceuticals,” Hayward says. Applied DNA Sciences and LineaRx provide a two-pronged approach to a global problem.

First, Applied DNA Sciences provides the tracking technology to verify that the product that’s delivered actually is the product the customer paid for. The World Health Organization estimated in 2017 that 10% of medical products in low- and middle-income countries are “substandard or falsified.” “Their impact on morbidity and mortality can justifiably be characterized as a disease state!” Hayward adds. Molecular tagging goes a long way toward preventing much of that harm.

Then, LineaRx takes therapeutics another step further by developing a form of DNA that has the potential to make cancer, immune, and gene therapy, more accessible. “There’s a range of opportunities,” Hayward observes.

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