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HUPO Initiative Seeks Projects to Bridge Gap Between Proteomics, Stem Cell Research

SEOUL – The real work begins now.
In June the Human Proteome Organization and the International Society for Stem Cell Research officially kicked off a joint initiative to explore the use of proteomic methods for the evaluation of stem cells in drug development efforts.
At HUPO’s annual conference here this week, officials made it clear that the eight-man committee formed to carry out the task has a lot of work ahead of it.
In the months since the initiative, called the Proteome Biology of Stem Cells, was officially launched during ISSCR’s annual meeting in Australia, the committee has been working to solidify its goals and to decide what projects to proceed with in an effort by both organizations to bring together experts from both fields.
The group is still soliciting ideas for collaborative studies, but has identified three potential projects and hopes to begin at least two within a year’s time, committee members said.
Overall, the initiative’s goals include providing a platform for investigators in stem cell proteomics to discuss and disseminate their work; establishing the proteomic requirements for stem cell biology; and promoting collaborations between researchers in both fields, said Jeroen Krijgsveld, a committee member from Utrecht University in the Netherlands.
While the scientific literature is filled with studies focused on stem cells, the number of published studies applying proteomics methods to stem cell research has been limited. A search on PubMed comes up with only about 300 such reports.
Stem cells have been studied on the genomic level for years, Krijgsveld told ProteoMonitor at HUPO, but “The basic thought is that there are many questions in stem cell [research] that can only be answered by a proteomics type of approach,” he said.
As HUPO was putting the initiative together, the organization cited the knowledge gap that exists between stem cell scientists and proteomics researchers. Because both are such highly specialized areas, expertise in both fields has been rare and difficult to find.
“The only way to bridge this gap and derive optimal benefit from what each field has to offer, is to bring together the specialists from both fields to discuss needs, possibilities, requirements, and conditions that will have to be resolved before collaborative efforts can be successful,” HUPO said in a document describing the initiative [See PM 06/21/07]
This week, Albert Heck of the Netherlands Proteomics Center and the chair of he HUPO stem cell initiative reiterated that notion. “I think only in close collaborations between the stem cell biologists and the proteomics people, can [we] learn each other’s strengths and each other’s weaknesses and then target some specific areas where proteomics can really add things that you [can’t achieve otherwise],” he said.
After the ISSCR meeting in Australia, the Proteome Biology group identified three possible topics for collaborative studies. One would look at whether glycopeptide analysis could be of value in defining embryonic stem cells by their surface markers. Another would determine whether systemic understanding of stem cell differentiation can be enhanced by proteomic analyses.
And the one that Heck and Krijgsveld say may have best chance of being carried out: A collaborative study on the need for cell surface markers in human embryonic cells studies that can be met with proteomic technologies.
“Several people now are actively looking at surface markers and using protocols to isolate surface proteins from stem cells and characterizing them by mass spec, so I think that will be an area to explore a little bit,” Krijgsveld said.
The group is continuing to gather additional ideas for collaborative studies, as well.
A year from now, Heck said, he hopes the group will have started two projects. “The players should be known, the objective should be known, and hopefully even some work should be done already,” he said. “I don’t think that sounds too ambitious because part of it is just joining efforts that are done now already.”

“Several people now are actively looking at surface markers and using protocols to isolate surface proteins from stem cells and characterizing them by mass spec, so I think that will be an area to explore a little bit.”

He and Krijgsveld acknowledge that the initiative faces significant challenges including the stem cell research community’s unfamiliarity with proteomics and its potential to add to the stem cell knowledge base.
The two have written an opinion piece on the use of proteomic technologies in stem cell research that they hope to publish in a stem cell journal. The editor of the journal, however, did not know what proteomics is and asked for a sidebar explaining it.
Heck also said that there is skepticism among many stem cell scientists of how proteomics can help them.
“One of the things we need to do is educate these people, and I think I’m always very open about the limitations of our techniques,” Heck said. “And I think it’s important that we bring that message as well.”
He and Krijgsveld also said that the current political climate in countries such as the US and Germany, where embryonic stem cells are a source of controversy, could pose challenges to the initiative, though they added that because the HUPO initiative is looking at all areas of stem cells, not just embryonic ones, that could be minimized.
“I think one of the problems is that every country has different regulations and different rules. Of course if [the laws] were everywhere the same, it would be easier, but we’re not going to exclude countries because they have certain policies,” Heck said.
The makeup of the committee has also changed since June. Paul Simmons, the president of ISSCR, who had been pegged as co-chair of the committee, is no longer on the committee, though he will remain involved in its work, Heck said.
Three additional members have been added ­– Krijgsveld, Steve Oh at the Bioprocessing Technology Institute in Singapore, and Ihor Lemischka at Princeton University.
They join previously named committee members Heck, Christine Mummery at Hubrecht Institute, the Netherlands; Anthony Whetton at the University of Manchester, UK; Bonghee Lee from Gachon University Gil Medical Center, South Korea; and Martin Pera from the University of Southern California.
Other committee chairs, aside from Heck, will be named in the near future, Heck said.

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