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Lee Hartwell, President Bush, Andrew von Eschenbach, PerkinElmer, P&G Pharma, Digilab, Boehringer Ingelheim, ActivX, Pfizer, CTC, Agilent, Proteome Sciences, Medical Solutions, BioSystems


Lee Hartwell to Proteomics Scientists: The Biomarker Bottleneck Is in Discovery, Not Validation

Proteomics researchers have not discovered enough cancer-related biomarkers, and they should modify and accelerate their research efforts if protein biomarker identification and validation are to have an impact in battling the disease, according to Nobel laureate Lee Hartwell.

Contrary to one theory that the problem with protein biomarkers lies in validating candidate biomarkers, Hartwell argued that validation and even approval are not the reasons why so few reliable protein biomarkers are known. "I put the problem squarely in discovery," he said yesterday during his talk at the second annual US HUPO meeting, held in Boston this week. "We are not discovering markers effectively."

"Basic science has not had a big impact on cancer yet," said Hartwell, who is also president and director of the Fred Hutchinson Cancer Research Center. "There's an enormous opportunity ... for the whole proteomics industry and technologies to really have an impact on cancer."

He said in particular that improving molecular diagnostics will be the "most important thing" along that path.

Hartwell pointed out that while much scientific effort has gone into finding common SNPs that correlate to risk association for cancer, he believes protein biomarkers will be more effective in risk assessment, early detection, and cancer prevention. "Proteins are going to be even more informative" than the DNA-based diagnostics scientists use today, he said.

The discovery phase for biomarkers should be ramped up and multiplexed, he said. Whereas traditional drug discovery is limited to putting just one therapeutic in a patient or model organism at a time, a single serum or tissue sample from a patient can serve as a test for thousands of biomarkers at once, said Hartwell. Multiplexing in this way could make trials much more high-throughput and accelerate protein biomarker discovery, he said.

Hartwell also highlighted a need for efficient, low-cost assays to develop and validate candidate biomarkers. ELISA tests remain very expensive and time-consuming; scientists need highly sensitive assays that are far less costly and don't require them to develop two antibodies for each protein, he said. "I'm hopeful that within the next couple of years the bottleneck of assay development will not be limiting anymore."

One approach to dealing with this problem, and others related to proteomic technology, is working in very organized teams following the model laid out by the Human Genome Project, Hartwell said. Several such international biomarker-discovery teams already exist — he listed 11 in his talk — that have chosen to tackle a specific cancer. The teams, which are required to include expertise in mass spec, informatics, antibody development, clinical work, and mouse model research, are organized under HUPO. Anyone is welcome to form a team and take part. "I think the main value of participation is going to be learning from one another what works," Hartwell said.

Bush Taps von Eschenbach, Outspoken Supporter of Genomics, to Head FDA

President Bush this week nominated Andrew von Eschenbach to head the US Food and Drug Administration, a potentially significant move for the genomics community because von Eschenbach has been an outspoken supporter of genomic-related technologies in drug discovery.

The nomination was widely expected because von Eschenbach, who is director of the National Cancer Institute, has been acting-FDA commissioner since Lester Crawford resigned in September 2005.

Von Eschenbach's background in cancer, along with recent statements he made, suggest that his tenure as FDA head may encourage the use of genomics and other molecular technologies in medicine.

For example, as head of the NCI since 2002, von Eschenbach pushed a program of translational research, and in recent comments before a Senate subcommittee hearing he announced a goal to eliminate cancer by 2015 through an understanding of the interaction of genetics and other factors.

"Scientific advances and major discoveries from areas such as genomics, nanotechnology, proteomics, immunology, and bioinformatics allow us to envision a not too-distant future when a patient's genetic, lifestyle, and environmental risk for cancer can be combined with effective prevention and early intervention strategies especially for those at high risk," von Eschenbach was quoted as saying by the Biotechnology Industry Organization in April 2005.

Von Eschenbach was named acting commissioner of the FDA in September 2005 following the resignation of Lester Crawford, and he has held that title concomitantly with his NCI job.

Prior to being named NCI chief, von Eschenbach worked as a doctor and executive at the MD Anderson Cancer Center in Houston for 25 years, reaching the post of executive vice president and chief academic officer.

He earned a medical degree from Georgetown University School of Medicine in 1967, and worked as an instructor in urology at the University of Pennsylvania School of Medicine. From 1968 to 1971, von Eschenbach served as a Lieutenant Commander in the US Navy Medical Corps.

PerkinElmer Plans to Launch Suite of i-PROT Kits Within Six to 12 Months

PerkinElmer said last week that it intends to launch a commercial version of its newly-acquired i-PROT isobaric protein-labeling technology within six to 12 months.

Developed by Agilix, the i-PROT technology enables quantitative comparison between proteins expressed in a number of different conditions, for example six or seven different time points (see ProteoMonitor 12/17/2004).

Prior to PerkinElmer's acquisition last week of the technology from Agilix, the i-PROT technology had been used by Toronto-based Protana as part of its proteomic services, but the technology had not been commercially sold, said Neil Cook, chief scientific officer of PerkinElmer's Life and Analytical Sciences division.

"Most academic researchers have not had access yet to this technology," said Cook. "It's our intention to get this technology in a workable format into the hands of researchers as fast as possible. We want to make sure the technology is as widely used as possible."

PerkinElmer will be launching a "whole range" of i-PROT kits based on different chemistries optimized for different applications, said Cook. He added that it is too early to discuss prices for the kits.

Cook said PerkinElmer intends to take advantage of its collaborator network to help "prioritize and drive applications" for the new technology.

"We will use the technology for our biomarker discovery programs, and we will work with key opinion leaders to develop novel applications of the technology," said Cook.

While ICAT labeling technology allows researchers to quantitatively compare protein expression between two different conditions, and iTRAQ labeling technology allows the comparison of four different conditions, i-PROT technology allows for comparison of more than four different conditions, Cook noted.

"The exciting thing is that up until now proteomics has largely been a black versus white type of procedure, where you look at healthy versus diseased, or before versus after," said Cook. "What this technology allows us to do is to get to all the shades of grey — to look at several different chemistries within a sample simultaneously."

P&G Pharma, Scuttling Internal Discovery, Will End Some Existing Vendor Contracts

Procter & Gamble Pharmaceuticals will retain some of its genomic-related alliances and end others after the company late last month decided to shutter its internal drug-discovery program.

"We are currently evaluating all of our discovery contracts," P&G spokesperson Tom Milliken said in an email message to ProteoMonitor sister publication GenomeWeb News today. "Some of them will remain open as originally planned, and others will not, depending upon the value that each adds to our new strategy." P&GP spokeswoman Paula Koenigs said the company's new strategy involves moving out of drug discovery and into external licensing agreements and drug acquisitions.

P&GP has many R&D collaboration with various genomic-related tool vendors. However, the company could not specify which would be affected by the closure.

The shuttered program means lost opportunities for existing collaborators, potential future allies, or past partners, such as Inpharmatica, which delivered model GPCRs last year to P&GP. The company last week said P&GP's decision closed the door for lead-optimization deals. "We could have expanded," said Vinod Mehta, senior vice president of business development at Inpharmatica. "Those opportunities in lead-optimization were affected."

Digilab Inks Biomarker-Discovery Deal with Boehringer Ingelheim

Digilab BioVision this week said it will work with Boehringer Ingelheim to identify new biomarkers.

Terms of the deal call for Digilab to use its Peptidomics technology to analyze quantitative peptide content of biological samples for Boehringer.

Additional details were not provided.

Digilab acquired Hanover, Germany-based BioVision last month to enhance its peptidome analysis technologies.

ActivX and Pfizer Expand Proteomics, Drug Discovery Deal

ActivX, a subsidiary of Tokyo-based Koran Pharmaceutical, said this week that it has renewed its agreement with Pfizer to encompass discovery to developmental stage projects across multiple research sites of Pfizer's Global Research and Development organization.

Under the terms of the agreement, ActivX will apply its chemical technologies and high-throughput protein analysis to a number of Pfizer programs spanning drug discovery, polemic profiling, compound selectivity and biological activity, and mechanisms of toxicity.

Financial terms of this transaction include an upfront technology access fee along with research support payments by Pfizer.

ActivX and Pfizer began their collaboration in February 2005.

CTC and Agilent to Bundle Autosampler/Chromatography Products

CTC Analytics will make its autosamplers available as original equipment on Agilent's LC, LC/MS, GC, and GC/MS products, Agilent said this week.

The OEM agreement encompasses PAL CTC systems for liquid injection, headspace injection, and SPME, including accessories, consumables, and service, said the company in a statement.

Financial details were not provided.

Proteome Sciences, Medical Solutions Ink Co-Marketing Deal

Proteome Sciences will market its ProteoShop platform with Medical Solutions' biomarker validation technologies as an integrated package for drug discovery and development.

Financial details were not discussed.

BioSystems International Licenses Northeastern's Biomarker Discovery Platform

BioSystems International will license from Northeastern University its monoclonal antibody-based biomarker-discovery and -development platform.

The platform was developed by scientists at Pfizer Fresnes Laboratories and Northeastern University. Pfizer retains rights to use the technology for its programs.

Terms of the agreement were not disclosed.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.