HUPO President Sam Hanash spoke on his personal philosophy of proteomics in front of a packed room of scientists and journalists on day three of the HUPO Congress.
In his talk, Hanash stressed an approach that emphasizes a return to the basics and a breaking apart of complexity as two keys to “harnessing the complex human proteome.” He paid tribute to the enzymologists and “protein hunters” of the pre-genomic era, who out of necessity followed six biochemical principles that Hanash felt were lacking in current proteomics protocols: working with natural proteins, relying heavily on separation sciences, assessing functionality, determining cellular and sub-cellular distribution, studying protein-protein interactions and protein complexes, and producing hard quantitative data.
These days, he said, researchers work with recombinant proteins rather than natural proteins; cloning rather than separation science; assessment of roles rather than assessment of functionality; and artificial systems rather than natural environments for studying protein-protein interactions. Finding a cellular context and producing real quantitative data, he said, were nearly abandoned goals.
“I don’t think there will be a day when a new technology will fall through the ceiling and make us all happy,” Hanash said. Instead, he said, proteomics researchers should work with what they already have to come up with new protocols that will pursue the six lost principles. “We need to combine our current technologies to get high performance,” he said. He gave an example of an article published in the July 2002 issue of Nature Medicine, in which DNA microarrays were compared with 2D gels for predicting lung cancer outcome. Hanash said that identifying just 20 proteins with a simple 2D gel produced better predictions of survival than the more “advanced” microarray. “We do have the technologies in proteomics,” he said. “They are not the most perfect technologies, but with the technology we have today there’s a lot we can learn.”
Following the conclusion of the Congress, Sam Hanash shared his thoughts with ProteoMonitor in an e-mail interview on how the conference went, what HUPO still needs to do, and his post-presidential life:
How did this conference compare to last year’s?
Clearly, this conference was much bigger than last year’s in terms of attendance, exhibitors, and program. What went well is that the response that we received from participants was highly favorable. Still, we are only in our second year and much could be improved in terms of anticipating, for example, what people are going to be interested in and making sure that simultaneous sessions do not create too much conflict.
Why did HUPO choose Montreal as its headquarters, and why choose Beijing for the next Congress? Why was John Bergeron a good choice for HUPO president?
Montreal was chosen because [the city] made an enticing offer of providing support for headquarters in the form of space and partial funding for staff. Also, geography was also an important factor — Montreal being an easily accessible city with ease of employing foreign staff if needed. There is substantial interest and expertise in proteomics and biotechnology in Montreal. I cannot speak on behalf of the nominating committee and the entire HUPO Council as to why John Bergeron was chosen as the next president. I think important considerations were his eminent scientific reputation and his demonstrated commitment [to] and involvement in HUPO.
Beijing was chosen because we are starting a tradition of rotating continents for our Congress. The first was held in Europe, the second in North America and therefore for the third, Beijing was a good choice.
What were some of the most important themes that you felt came up at the conference?
The HUPO initiatives themselves were important themes that came up — they [seem] to be attracting a lot of interest.
What do you think are some technological improvements that could help HUPO’s objectives be achieved?
I think automation is very important. Most of the techniques we use in proteomics are tedious and automation would make life easier in addition to improving reproducibility. [But] this could be done with the basic techniques currently employed in proteomics. Miniaturization would also help a lot, given the sample size limitations particularly for clinical samples.
What are your post-HUPO president plans?
I would like to put greater emphasis on lab-based research, which I have not been able to devote as much time to as I would like.