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Qiagen Makes Move toward Proteomics with Protagen CDx Development Deal

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NEW YORK(GenomeWeb) – Protein diagnostics firm Protagen this week announced a long-term collaboration agreement with Qiagen to provide its pharmaceutical partners access to technology that would advance the development of protein-based companion diagnostics for autoimmune disorders.

The deal is one of the most significant Protagen has announced since selling its subsidiary Protagen Protein Services to venture capital fund Zukunftsfond Heilbronn last year in order to focus on diagnostics development.

For Qiagen the agreement marks a move into proteomics for a firm that has traditionally focused on genomics.

Under the agreement, Qiagen will have access to Protagen's SeroTag platform, which allows researchers to simultaneously measure autoantibody levels for thousands of antigens to detect expression patterns linked to disease.

Qiagen declined to comment on the agreement, but said in a statement that the SeroTag technology can support Phase I to Phase IV drug development programs for autoimmune illnesses, as well as enable the development of companion tests for better disease diagnosis, patient stratification in clinical trials, and improved treatment strategies.

Protagen will have rights to intellectual property related to companion diagnostics developed under the agreement, particularly with regard to in vitro diagnostic kits and assays, CEO Stefan Müllner told GenomeWeb.

The collaboration, Müllner said, stemmed from Qiagen's desire to expand beyond its traditional focus on oncology CDx and into autoimmune disease, which, he said, is currently the second largest area of drug development.

"There is a huge demand for suitable CDx" in the autoimmune space, Müllner said, noting that this is Protagen's area of specialty. The company has research ongoing in rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis, systemic sclerosis, multiple sclerosis, and neuromyelitis optica, as well as an in-house CDx development program focused on predicting response of rheumatoid arthritis patients to treatment with methotrexate and anti-TNF-alpha drugs. 

One of the most prominent protein Dx firms in this space is Myriad Genetics' Crescendo Bioscience, which uses a panel of 12 proteins to assess rheumatoid arthritis patients. Acquired by Myriad this year for $270 million, Crescendo has been exploring the usefulness of its test, named Vectra DA, for predicting patient response to therapy.

As GenomeWeb reported this week, the company has begun collecting data aimed at showing that the test can predict which patients will respond to various therapies after failing to respond to methotrexate, which is the first-line treatment for the disease.

In its most recent earnings release, Myriad reported that Crescendo generated $10.8 million in revenues during Q4 2014.

Protagen's collaboration with Qiagen will not focus on any specific autoimmune diseases, Müllner said, adding that the SeroTag platform is suitable for investigation of a wide variety of autoimmune indications. 

The SeroTag platform uses bead-based arrays of full-length proteins to screen patient blood samples for autoantibodies characteristic of a given disease. Certain proteins produced by the body can elicit an immune response that can then be detected by measuring antibodies to that protein, and these immune responses can vary between diseased and healthy individuals.

Protagen's CDx development strategy is to identify such signatures and use them to track a patient's response to particular therapies. 

To this end, the company has what it asserts is the largest human antigen expression library in the world, a collection of more than 7,000 human proteins that includes more than 95 percent of published, disease-associated autoantigens. According to the company, all of these proteins have been sequence-verified by mass spectrometry.

While the majority of protein diagnostic work focuses on identifying differentially expressed proteins, there are certain potential advantages to an autoantibody-based approach, Müllner said. For instance, the body's immune response acts as a natural signal amplifier, meaning that autoantibodies to a protein can be present at significantly higher concentrations than the protein itself, providing a boost to assay sensitivity. Additionally, autoantibodies are in some cases more stable than traditional protein markers.

In its autoantibody-based approach, Protagen's SeroTag platform is similar to that of several other firms, most notably Arizona State University HealthTell, which uses arrays of random-sequence peptides to profile patient immune responses, and Opko Health, which is pursuing a similar approach for indications including Alzheimer's disease. 

A primary difference setting apart the SeroTag platform, Müllner said, is its use of full-length proteins as opposed to peptides. This provides a potential advantage in that the full-length proteins retain structural information that peptides don't, he said.

"Both technologies have their role. However, as the immune response is polyclonal and the majority of auto-antibodies produced by the immune system are directed against structural protein epitopes, Protagen employs proteins for autoantibody signature determination instead of peptides," he said. "Screening for unknown autoantibody signatures requires the highest number of possible structural epitopes, which are only present in full-length proteins." 

In this, Protagen's technology is perhaps most similar to an approach taken by another group of Arizona State Universityresearchers led by Karen Anderson and Joshua LaBaer. That team, which is currently working on autoantibody-based biomarkers for ovarian cancer, uses arrays of full-length proteins generated via LaBaer's nucleic acid programmable protein array (NAPPA) technology to detect autoantibodies linked to various diseases.

In an interview with GenomeWeb this week discussing the work, Anderson said that, while full-length proteins could offer certain advantages, she thought no one yet knew what would prove the best way of identifying autoantibody signatures in human serum, and that most likely there would not ultimately be a single best way.

"The antibody response is extremely diverse, and it can recognize both linear and conformational epitopes," she said.

The Protagen-Qiagen agreement has no specific timeline, Müllner noted, saying that "considering the often lengthy timelines associated with clinical development programs, the agreement is currently unrestricted."

In addition to the Qiagen deal, Protagen counts among its customers pharma firms including Pfizer, Biogen Idec, SuppreMol, and Bayer.

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