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Ciphergen s Biomarker Alliance With Bayer May Be Significant Boost to SELDI Platform

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Ciphergen's cancer biomarker alliance with Bayer Pharmaceuticals, announced this week, marks the first time Ciphergen has made a long-term, formal agreement with a large pharma company to use its SELDI platform to help identify study patients likely to respond to a drug candidate.

The deal could potentially give a big financial boost to Ciphergen, which has been struggling with slumping SELDI sales and shortfalls in revenues (see PM 4/8/2004). While financial terms of the deal were not disclosed, Ciphergen said it would receive upfront fees and milestone payments.

In addition, the deal may represent a boost to the SELDI platform, and to makers of protein biomarker platforms in general, whose technologies have taken a back seat to genomic biomarkers as emerging drug-development tools.

Separately, investors, collaborators, and customers are still waiting for details of the "pivotal diagnostics deal" Ciphergen promised to disclose before the end of June. It was not immediately clear whether the Bayer deal represents that collaboration, or a part of it, though a report from investment bank Pacific Growth Equities said it is not.

Speaking about the Bayer deal, Robert Bower, a visiting assistant professor of pathology at the University of Pittsburgh said, "I think it's exciting because I think proteomics offers a good opportunity to monitor and sub-classify patient populations for toxicity, and for finding out which subclass of patients will best benefit from a drug. It's good to see a large pharma company that is a player in that arena."

Bowser co-founded a company last year based on SELDI-based biomarkers for amyotrophic lateral sclerosis (see Proteomics Pioneer).


"I think it's exciting because I think proteomics offers a good opportunity to monitor and sub-classify patient populations for toxicity, and for finding out which subclass of patients will best benefit from a drug."

While Ciphergen has had big pharma clients in the past who have made short-term contracts to use its biomarker discovery centers, or to use the company's biomarker-discovery services, the Bayer deal is Ciphegen's first expanded, long-term agreement with a large pharma that involves joint discovery and validation of biomakers.

Under terms of the agreement, Ciphergen will use its SELDI-TOF-MS platform to help Bayer identify cancer-related biomarkers and develop an assay that may be used in Bayer clinical trials for an undisclosed cancer compound under development at the German pharma. Ciphergen will analyze patient samples from Phase II clinical trials at its Pharmaceutical Biomarker Discovery Center laboratory in Malvern, Pa.

Bayer representatives did not respond in time for this article. A Ciphergen spokeswoman said she did not have any more information on the cancer compound. Other Ciphergen officials did not return calls for comment.

According to Bayer's website, the company has a cancer drug in Phase II and Phase III trials called sorafenib, or BAY 43-9006. The drug has been used to treat patients with advanced primary liver cancer and advanced kidney cancer. It has also been used in combination with other chemotherapeutic agents to treat patients with advanced metastatic melanoma.

Asked what it will take for the SELDI platform to become widely adopted by big pharma and by the FDA, the way that genomic biomarkers have been adopted, William Bigbee, the director of the proteomics facility at the University of Pittsburgh Cancer Institute's Hillman Cancer Center, said that the technology will have to be proven to be reproducible across laboratories, and across individuals and populations.

"To what degree can a given lab, on a given machine, reproduce one of these complex profiles from day to day? Or another machine in another laboratory? The technology must be reproducible and portable," said Bigbee. "And the second question is, 'To what degree can you reproduce the observation in different sets of patients within different populations?' Can that same predictive algorithm prove to be biologically robust?"

Bigbee noted that the adoption of SELDI can be accelerated if the biomarkers are not based on a pattern profile, but rather on a panel of identified proteins.

Another issue facing the SELDI platform is the sensitivity and specificity of the SELDI-based biomarkers, Bowser added.

"I'm assuming that Ciphergen has convinced Bayer that whatever panel [of biomarkers] they have is reproducible and has a high level of specificity and sensitivity," he said.

To be sure, alliances between pharma companies and proteomic biomarker companies are not unique. Caprion, for example, has allied itself with MDS Pharma Services (see ProteoMonitor 6/24/2005), and recently expanded its protein biomarker collaboration with Wyeth to include disease-state biomarkers in the areas of asthma and renal cell carcinoma.

By allying itself with Bayer, Ciphergen is further pushing itself down the path from a tools company to a biomarker discovery system company, Bigbee said.

"My view of Ciphergen is they had an old way of going about this, which was to sell instruments and chips to researchers and big pharma," said Bigbee. "Now, Ciphergen is expanding their business model to try to package themselves as a broader biomarker discovery system with an in-house set of expertise and protocols that allows them to align themselves with companies like Bayer that are related to therapeutic drugs."

During its first quarter earnings conference call in May, Ciphergen promised that it would announce a pivotal diagnostics deal before the end of June (see PM 5/13/2004). It remains to be seen whether the deal with Bayer is the "pivotal diagnostics deal," or if another deal will be announced. A report from investment bank Pacific Growth Equities said that the Bayer deal is not the diagnostic alliance Ciphergen has promised to disclose before the end of June.

— Tien-Shun Lee ([email protected])

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