When HUPO held court at Versailles last month, about 880 participants from 34 countries heeded its call to the three-day Human Proteome Organization First World Congress.
While many of the talks were delivered by what some attendants regarded as the “usual suspects” — the keynote speakers included Nobel Prize winner Alfred Gilman, systems biology expert Lee Hood, and mass spectrometry maestro Matthias Mann — more than 250 posters from researchers in academia and industry gave a broad overview of what is going on in proteomics laboratories throughout the world. Topics ranged from the “Use of quadrupole-linear ion trap mass spectrometer in combination with nanoscale 2D-LC for the analysis of C. elegans proteins” to a “Proteomic analysis of the human alcoholic brain.” More than 50 posters and presentations came from scientists in the US, followed, in numbers, by those from Germany, the UK, France, and Korea. Most other European countries, as well as Russia, Canada, and China also had plenty to show, while Japan’s research seemed somewhat underrepresented.
The program comprised both scientific talks by academic and industry researchers and science policy discussions ranging from the current status of the HUPO initiatives to human proteome efforts around the world, and collaborations between industry and academia. The discussion spurred by this dense program of lectures, posters, and panels sometimes spilled out of the Palais des Congrès, and into the bistros and brasseries in town where debate continued until late at night over bottles of Beaujolais Nouveau.
Gilbert Omenn from the University of Michigan invited researchers to join HUPO’s Plasma Proteome Initiative, outlining its soon-to-start pilot project (see ProteoMonitor 11-18-02). His appeal seemed to bear fruit: on Sunday at 8 am, a roomful of potential participants gathered before the first morning session to find out about ways to contribute.
However, not everyone was convinced that the pilot project, which aims to compare different methods for studying plasma proteins by analyzing small plasma samples, is the way to go. According to Dennis Hochstrasser from the University of Geneva, pooling samples, a strategy pursued by GeneProt, a company he co-founded, is the only way to detect low-abundance proteins. “Shipping samples to labs…will not unravel the complexity of the human plasma,” Hochstrasser said. Furthermore, he and others pointed out the need for good sample quality control. Finally, Hochstrasser also urged HUPO to address questions of intellectual property, without which companies like GeneProt might not be able to participate in the Plasma Proteome Initiative. This view was echoed by Lorne Taichman, corporate associate at Johnson&Johnson. “The conflict of interest regarding intellectual ownership is a vexing issue,” he said, with no simple solution. Nevertheless, J&J is planning to provide support for the initiative. Taichman told ProteoMonitor that the more than 160 companies under J&J’s umbrella are currently working out the level of support, which will be below $1 million.
But very likely, the public will have to do most of the work, said Lee Hood, who urged HUPO to publish its data immediately, without IP-related restrictions. “Don’t make the information confidential and proprietary,” he said.
Carl Merril from the NIH cautioned, however, that non-specific discovery projects, like the human plasma protein initiative, are a tough sell to granting agencies. A NIH protein disease database, for example, no longer receives any funding, he said. Merril also pointed out that decades of data on plasma proteins already exist in the scientific literature.
On the other side of the world, Korea and China appear to be racheting up their proteomics efforts. Young-Ki Paik, director of the Yonsei Proteome Research Center at Yonsei University, reported that the Korean branch of HUPO, KHUPO, has more than 600 members so far. The Korean government, he said, has supported a 10-year cancer and immune disease program by the Ministry of Science and Technology that started this year and is funded with $5 million per year; a human plasma proteome project, to be launched in January 2003 by the Ministry of Health and Welfare and funded with $3 million per year over about eight years; and a proteome informatics and protein production program, funded by less than $2 million per year over five years, from the Ministry of Commerce and Industry.
Fuchu He of the Beijing Institute of Radiation Medicine talked about China’s HUPO, or CHUPO. The National Natural Science Foundation of China, which is part of the Chinese government, has been funding a so-called “Proteomics Initiative of China” with $5 million over five years since 1998. The aim of this initiative has been to set up proteomics platforms at universities and research institutes across the country. Also, $35 million over five years from the Ministry of Science and Technology has gone towards proteomics projects related to human disease since 2001. The same ministry started funding liver proteomics research this year with $40 million over four years. Finally, the ministry will launch a program to study liver and its diseases “from bench to bedside” by the end of this year. This five-year program, which will include proteomics research, is expected to be funded with more than $200 million. With regard to the HUPO initiatives, He reported that the Chinese government pledged to make “more contributions to the Human Proteome Project than to the Human Genome Project and the rice genome project.”
Europe, on the other hand, appears to be doing proteomics piecemeal. According to Julio Celis of the Danish Cancer Society, there are “no mechanisms for large-scale projects envisioned by HUPO” in Europe. Only five percent of the total European Union research budget is distributed by the EU, he said — the rest remains in the member countries. However, there are ongoing discussions to establish one or more European Research Councils, he added. Under the 6th European Framework Program, a multi-year funding program of the EU that starts next year, consortia of European universities, research centers, and small- to medium-sized companies can apply for funding for so-called “networks of excellence.” Although each of these may obtain up to $10 million per year, Celis said, the money has to be split up among the numerous participants. The EU is expected to make its first calls for proposals by the end of the year. These will include the areas of structural proteomics, protein-protein interactions, bioinformatics, cancer proteomics and oncogenomics, and arrays.
The German Federal Ministry of Education and Research has also supported proteomics projects with a total of about $153 million so far, including new technologies for proteome analysis, systems biology, human proteome analysis, and a “Protein Structure Factory,” according to Angelika Görg from the Technical University Munich. A German Society for Proteome Research was founded last year.
In France, the government has set up centers for proteomics at 12 locations, according to Jean Rossier of the Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris. Finally, proteomics efforts are also getting underway in Japan and Russia. The next HUPO bioinformatics workshop will take place in Moscow in March 2003.