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Devyser Eyes Early Detection of Transplant Rejection With DNA Sequencing Tests

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NEW YORK – Following receipt of a €750,000 ($909,000) Eurostars-2 grant earlier this month, Swedish firm Devyser Diagnostics has launched a project to develop a plasma-based next-generation sequencing (NGS) assay for the early detection of kidney transplant rejection.

The company also expects to soon receive a CE mark for its Chimerism NGS kit, which identifies hematopoietic stem cell transplant (HSCT) rejection using cellular material from bone marrow cells.

Devyser, launched in 2004 by Chief Operating Officer Ulf Klangby, Chief Technology Officer Anders Hedrum, and medical advisor Dan Hauzenberger, initially sought to create assays for monitoring chimerism for stem cell transplants.

However, Klangby said that the expensive costs of performing next-generating sequencing (NGS) initially limited his team from developing a routine assay to monitor transplant status, therefore pausing development. Devyser instead chose to create testing kits for hereditary conditions such as prenatal aneuploidy. In 2019, the firm resumed research into assays that guided targeted cancer therapies and for post-transplant monitoring.

Devyser's kidney NGS assay will analyze donor-derived circulating cell-free DNA (dd-cfDNA) in the bloodstream stemming from tissue damage, driven by the recipient's immune system attacking the transplanted organ. Klangby explained that a release of DNA from the organ, which differs from the recipient's own genome, produces chimerism in the bloodstream.

The process begins by collecting about 2 ml of plasma from a blood collection tube drawn from a patient at a routine checkup during their first year after transplantation. The team extracts DNA from the plasma, followed by PCR-based library prep and NGS.

Devyser then analyzes the sequencing results through an informatics step to measure the percentage of donor and recipient DNA fraction to provide information to support long-term graft and patient survival.

While the firm is developing the kidney assay to run on Illumina's sequencing instruments, Klangby noted that the assay itself will be platform-agnostic.

Klangby said that the kidney assay will be useful to establish quantitative measurements of an analyte, rather than for qualitative measurements. He pointed out that the technology is based on clonal sequencing of individual DNA fragments, which "in theory … makes it powerful for quantitative" analysis.

As part of the three-year "Sensitive Chimerism Quantification Graft Rejection" (ENVISAGE) project with the University Hospital of Zurich, Devyser will further optimize the kidney assay using the hospital's biobank on organ transplant data.

The ENVISAGE project will determine how early in a patient's transplant journey the assay will be able to identify organ rejection. Devyser will also use the project to identify specific DNA biomarkers that will reduce background sequencing noise and help distinguish between donor and recipient DNA.  

By improving the kidney test's sensitivity and specificity, Klangby believes it can eventually help detect and quantify chimerism in patients with other types of solid-organ transplants, such as heart, lung, and pancreas transplants.

"We know that … heart transplants release even more cell-free DNA into the bloodstream," Klangby said. "Even though the mass of the heart is not very big, the contact surface to the blood is very big, so there's significant amounts of DNA."

As Devyser moves along with the ENVISAGE project, the firm also anticipates receiving a CE mark later this year for the Chimerism NGS kit.

HSCTs transfer stem cells from peripheral blood or bone marrow in a matched donor to a recipient struggling with conditions like cancers or autoimmune diseases, including multiple sclerosis and acute myeloid leukemia. After the patient undergoes a round of treatment to eradicate diseased cells, new stem cells are reintroduced and grafted to the body's bone marrow and potentially rebuild the patient's immune system over time.

In certain cases, however, the recipient's body can reject the transplant cells and cause long-term complications, such as chronic graft-versus-host disease and various organ toxicities.

Like Devyser's planned kidney assay, its commercial HSCT assay performs chimerism analysis to establish the rate of rejection to donor material. However, the method analyzes genomic material from stem cells in the recipient's bone marrow instead of cell-free DNA in the patient's bloodstream.

"In [the] case of solid organ transplantation follow-up, an increase in donor DNA fraction is indicative of organ damage and rejection," Klangby explained. "In [the] case of stem cell transplantation follow-up, an increase of recipient DNA fraction is indicative of disease relapse or a graft failure."

Klangby argues that the HSCT assay, which includes 24 indel biomarkers, can replace both single tandem repeat-based and real-time PCR methods through increased performance and usability.

The complete workflow for both assays can be completed within one to two business days, from sample collection to data analysis, Klangby added.  

Future work

In addition to ENVISAGE, Devyser aims to work with other labs and physicians to improve the sensitivity of the kidney assay, including groups that the firm has previously collaborated with on the Chimerism NGS kit.

"We are also in discussions with a couple partners in the US to validate the bone marrow transplant test, including hospitals and biotech companies," Klangby said, though he declined to name them.

Devyser currently holds a patent family related to the use of its NGS platform for solid and HSCTs in the US, Chinese, and European markets.

While Klangby declined to comment on the cost of the eventual CE-IVD version of the Chimerism NGS kit and the envisioned kidney assay, he believes that tests will ensure an overall lower cost of monitoring transplant rejection for the healthcare system. He emphasized that current kidney transplant management is extremely expensive due to the cost of inhibitors and the risk of acute rejection that can lead to dialysis.

"If we can manage to prolong the length of the kidney by 10 percent, which is almost a year, the number of available organs will increase by 20 percent every year," Klangby said. "So, more people [will be able to] receive transplants and the cost of patient management will drop."

Klangby believes the kidney assay will offer clear advantages to current methods, which he said only monitor rejection, in earlier stages because it measures the cfDNA leakage and ongoing tissue damage from the transplant. By monitoring the level of dd-cfDNA in the recipient's bloodstream, a physician can determine how quickly the patient's immune system will reject the organ.

"Thanks to the careful selection of genetic markers used in the assay, the lab can fit more samples on one NGS flowcell and then significantly reduce the sequencing cost per sample," Klangby said. "The assay design requires the lab to spend less than 45 minutes [of] hands-on time for running the whole procedure, a significant reduction of labor-related cost."

Klangby said that both NGS assays will come as a "complete kitted solution," which he expects will simplify lab procedures and help reduce the costs of monitoring for transplant rejections. The workflow also includes a software tool for data analysis to reduce data handling and reporting complexity.

After completing the ENVISAGE project, Devyser anticipates offering the kidney assay either through an early-access program or for research use in Europe prior to applying for a CE mark.

Fredrik Alpsten, CEO of Devyser, said that the firm is also currently looking at different routes to raise funds to push into international markets. While Alpsten declined to comment on specific plans for expansion, he expects the firm to launch the assays in the US market on its own instead of with a commercial partner.