With $24 million from the Chinese government and a mandate as co-president of next year’s International HUPO Congress in Beijing, Chinese HUPO president Fuchu He has pushed the acceleration button on the Human Liver Proteome Project.
“First we’ll get the working structure and working teams, then the standard operating procedure, third set up a specimen bank, and fourth [decide on] the platform and techniques,” He told ProteoMonitor this week, describing the project’s three-year pilot phase. As with the other major HUPO initiatives (see PM 10-10-03, 10-17-03, 10-24-03), HLPP leaders have made the establishment of standardized protocols a major priority for the pilot phase of this project. The HLPP will gather data from experimenters using different strategies for front-end and analysis techniques, He said, and then make some sort of assessment as to which techniques work best in which situations — a tactic similar to that taken by the organizers of the Human Plasma Proteome Project. Like the HPPP, He said that finding a good method for removing high-abundance proteins and enriching low-abundance proteins would be an important part of this process. “We hope to find a lot of studies for the enrichment of low-abundant proteins and also depletion of high- and middle-abundance proteins using antibodies. So we come [at it] from two sides,” He said. He added that he has so far tried various combinations of different mass spec analyses coupled with “microsequencing and microdigestion” for getting at the low-abundance proteins, and that “subcellular organelle isolation and biochemical fractionation with different characteristics of proteins or protein groups” were also on the plate for low-abundance enrichment possibilities.
He also intends to set up a bank of antibodies to all liver proteins as part of the Chinese portion of the umbrella HUPO antibody initiative (see PM 10-10-03); the antibodies could then be used as supplements to other low-abundance protein enrichment techniques. “That’s the reason we want to set it up in the pilot phase — because a lot of the scientific categories such as expression profiles, modification, localization, and protein-protein interactions could be identified with the antibodies,” he said. “For DNA and RNA we have recombinant technology and PCR, but for proteins we do not have these kinds of techniques for amplification.”
He is backing up his talk with results. In a lecture at the HUPO Congress, he presented his own data from a project his lab carried out analyzing the proteome of the human fetal liver. He said that he had identified a total of 2,395 proteins using a variety of techniques, including 1D gels, 2D gels, LC-MSMS, nano-MALDI MS, and the ZOOM IEF fractionator.
He did preliminary analyses of: sub-cellular distribution, the phosphoproteome, quantification, and correlation of the proteome of the human fetal liver with its transcriptome. He also used a combination of bioinformatics modeling and yeast-2-hybrid experiments to build a preliminary protein linkage map of 150 different interactions involving 664 proteins, or 50 percent of the known genes in the fetal liver. For the phosphoproteome profile, He used a simple 2D gel imaging technique.
The pilot phase of the HLPP, which will be carried out across participating countries in Europe and North America as well as in Asia, will have considerable funds at its disposal, including $12.5 million from the Canadian government and $10 to 15 million from the French government, in addition to the $24 million from the Chinese government and an as-yet undecided figure from US government organizations — all together a considerably higher sum than what has already been secured for the HPPP and the antibody initiatives, for example — and all this without notable corporate sponsorship, according to He.
He noted that the Chinese government’s particularly generous contribution was part of a larger initiative in liver disease, which, according to He, sets aside 1 percent of China’s GDP for liver disease diagnosis, prevention, and therapeutics (see PM 8-15-03). “It is a lot of money,” He said.
Following the pilot phase, which is set to wrap up in 2005, the “action phase” of the HLPP will begin in 2006 and will run through 2010. There will be nine parts to this phase, although He has labeled four categories as most important: expression profiling, compilation of the liver ORF-ome, completion of the antibody bank, and development of bioinformatics infrastructure. “These four categories are the basis for [fulfilling] our scientific objectives,” He explained. Of these, He said he believes that the modification profile will be the most difficult to complete, because “a lot of kinds of modification cannot be identified in a large scale so far.”
A date for the next HLPP meeting has not yet been set, according to He, but a teleconference will be held before the end of 2003 and an in-person meeting will be held before April 2004. The HUPO Congress in Beijing will be held in late October 2004.