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Q&A: Jun Qin on China's PHOENIX Proteomics Center and the Chinese Human Proteome Project, Part II

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By Adam Bonislawski

Name: Jun Qin
Position: Chief Technical Officer, Mass Spectrometry, Pilot Hub of Encyclopedical proteomIX, Beijing, China; Associate Professor, Biochemistry & Molecular Biology and Molecular & Cellular Biology, Baylor College of Medicine
Background: PhD, Rockefeller University

At the Human Proteome Organization's 2010 annual meeting in Sydney, Chinese researchers announced plans to expand their work on HUPO's Human Liver Proteome Project into a Chinese Human Proteome Project that would seek to characterize the proteomes of human tissues broadly, covering proteins in blood, brain, lungs, and other organs.

A centerpiece of this project is a new national laboratory in Beijing called the Pilot Hub of Encyclopedical proteomIX, or PHOENIX, center, which the government plans to fund to the tune of ¥1.2 billion ($187 million). Over half of those funds were slated for the center's new mass spectrometry facility, to be headed by Baylor College of Medicine researcher Jun Qin.

Last week, at HUPO's 2011 meeting in Geneva, ProteoMonitor spoke to Qin about the PHOENIX center and how the Chinese Human Proteome Project is progressing one year after it was announced.

Below is an edited version of the interview, the second in a two-part installment. Part one can be found here.

So far the Chinese HUPO efforts have focused on liver. Now with the CHPP you're moving on to a variety of tissues and organs. How will that work be divided up? Are different centers taking on different organs and systems?

We're still in the planning stage. I think there will be leading centers, where, for example, a group will be in charge of a certain tissue, say, kidney, and then there will be a few other teams that are a part of it, playing a minor role. No one will have control over a particular thing. It will always be a team effort, but there will be leaders in the team effort. That's how the HLPP has been doing it.

Are you prioritizing any particular tissues or diseases to look at first?

That plan is being worked out. We are still working on the action plan.

Is there a timeline for when the action plan will be done and you'll start the actual work?

It's not finalized yet. I have a little bit different thinking about this, because I don't think you can plan that well. But the initial pilot phase I think is very important, because we want to demonstrate the feasibility first. I think [the project] will take around 20 years. That's how we think. Maybe if we try very hard and have adequate funding, we can finish this gigantic task in 20 years. So we are very realistic.

How will funding for the CHPP work?

It will be competitive. Every cycle – hopefully it will be like a five-year cycle – every five, six years we'll go out and compete [for funding] anew.

Do you have grant money lined up now?

It's not finalized, but I think the government is very supportive for this. There will be [requests for applications] coming out hopefully soon. The money isn't fixed. It's not like the government has said, "We've allocated this amount of money for you to do this project." The Ministry of Science and Technology and other funding agencies have said, "Oh, the HPP is an important direction for research in China, and we want to support this," but then they will send out RFAs [calling] for people to apply. So we're trying to organize different teams so we can have some very strong teams and then go in to apply for this [funding]. So anyone can form a team to apply for it.

How does CHPP fit into the HUPO HPP and the work being done by that project?

We strongly support the HUPO HPP, and the CHPP has a lot of similarities to the HUPO HPP. The strategy may be a little bit different, and the focus may be a little bit different. So we actually want to contribute more to the HUPO HPP. We're hoping that China can contribute maybe 30 percent of the [HUPO] HPP. For the Human Genome Project, China did one percent. For the Human Proteome Project, we hope to do more – maybe 30 percent or more. This isn't a competing project.

I think the HUPO HPP is still in the planning stage. People are still talking about strategy and how to do things. It's just a framework because there's no funding from HUPO. Everything depends on the funding agencies. So how exactly you do this no one knows because the funding agencies have different ideas of whether to fund you or how they fund you. The [National Cancer Institute] has [one] idea. The [National Institute of Diabetes and Digestive and Kidney Diseases] has another idea. The situation is China is, the government has said, "This is a good direction; we want to support it," but how we do it is up to us, up to the participants, because you basically come in with a proposal and say, "I want to do this in this way, and this is how much money I need." So I think we probably can start earlier. I can't see the way for HUPO HPP to do it in a coordinated way.

Because there's no coordinated funding?

Right, right. Because there's no money man. At the end there's always the money man telling you how to do it.

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Do you expect that the funding from the Chinese government for the CHPP will lead to a big increase in mass spec purchases by groups around the country?

I don't know, but probably not because the funding mechanism is such that this funding will be for projects. It will be limiting the purchasing of instruments. It's the same as a [National Institutes of Health] grant.

Will private industry be taking part in the CHPP as well?

That is in negotiations, but, yes, there will be collaborations between private companies and the government.

BGI recently mentioned that they planned to expand their proteomics capabilities (PM 06/17/2011). Are they a potential CHPP partner?

They will be a potential participant.

Regarding the PHOENIX Center, do you envision it as a place for the development of assays that can then be sent out for use in smaller labs around China? Will that sort of workflow have any place in the CHPP?

I know that's the American way. America has a lot of centers where people send assays to them and they do that screen. We don't have that plan yet. I think we're still maybe a little bit behind for that kind of thinking. I think the difference between the PHOENIX project and American projects is that [PHOENIX] is very focused on discovery because the first idea was actually you don't want to build a lot of centers redundantly. The idea was to concentrate the resources in one or two places where people can use it. That was the idea.

We have substantial validation [plans], but that validation still is higher throughput. Detailed validation and functional analysis is difficult to separate. I'm hoping that when people come here they will do their experiment and they will leave with one or two very solid leads, and then they will have a really reasonable hypothesis and they can then go back to their lab to do the real functional analysis and really nail it.

In addition to the discovery and verification, [the center will have] a functional analysis, translational medicine component. So the idea is we want to put all of these techniques and the expertise to use these techniques in the same building. So the way to do it is, if you're a biologist, say you have an interesting project. We will send out RFAs, and you will go in with your proposal and say, "I have this project; I want to map how transcription factors are activated during development. I think these techniques and instruments at the PHOENIX Center will help us." Then the committee will evaluate this grant and say, "OK, this is a good match for the PHOENIX Center," and then you will actually come to the center and stay there for three months or six months or whatever, and we'll do the discovery and validation together, and then you can go back and finish your functional analysis. That's the philosophy.


Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.

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