Proteomic Fractionation Group at U Mass Medical School
At A Glance
Name: Sunny Tam
Position: Director, Proteomic Fractionation Group at University of Massachusetts Medical School Proteomic Consortium; Research associate professor, since Jan. 2005.
Background: Senior scientist and manager, protein sample preparation group, Charles River Proteomic Services, 2003-2004. Associate director, proteomic discovery & cell biology group, Texas Biotechnology, 2001-2003. Project leader, protein microarrays, Genometrix, 2000-2001. Program Leader, mast cell biology, Tanox, 1998-2000. Scientist, assay development and drug screening; target validation and functional analyses, Mitotix, 1993-1998. Postdoc, Harvard University School of Public Health, department of toxicology, 1991-1993. PhD in pathology and molecular biology, Boston University School of Medicine, 1990.
The University of Massachusetts Medical School announced last week that it has formed a Proteomics Consortium facility that brings together the school's proteomics and mass spectrometry resources with resources from Charles River Laboratories' old proteomics facility (see UMMS story). ProteoMonitor caught up with Sunny Tam, a former manager at Charles River Proteomic Services who joined UMMS after the unit shut down last December, to find out more about his background and his role in the new consortium.
How did you get into proteomics?
I received my PhD training from Boston University Medical School. I did mostly molecular cloning at that time. After that, I went to Harvard School of Public Health, and I did a lot of cell-cycle signaling in response to a number of chemical compounds, trying to look at cell-cycle checkpoints. At that time, I think genomic sequencing and this new area of proteomics were not around, though at that time we were already doing some Edmund degradation. It took easily a week just to transfer from a gel to a blot, and to try to do MS sequencing. Now it just takes a matter of minutes to do the same thing.
My experience has mostly been in the biotech industry for the past 12 years, ever since my days at Harvard. I got into proteomics slowly. The first seven years or so I was working in biotech companies — a couple of those. One was called Mitotix. At that time I started to become interested in some of these protein array technologies. I had always been interested in building things in a more high throughput manner, because working in drug screening, there was always that need to decipher through a lot of the information. So before the name 'proteomics' was even coined, I had that kind of interest to be able to analyze proteins in a high throughput manner.
I guess my entry point was after working at a couple biotech companies — the first one was called Mitotix. The second company was called Tanox. Mitotix was based in Cambridge, Mass., and now they're part of GPC Biotech. Tanox was in Houston, Texas. I was involved in a number of areas such as DNA chips, and also with protein arrays. That's when I started to move into the proteomic area. My starting point was really with protein arrays.
What did you do after you left Tanox?
After I left Tanox, I joined another company called Genometrix. That is really a microarray/high throughput genomic type of company. Unfortunately, with the stock market and the cash flow problem, the company closed down. I was one of the scientists developing a cytokine protein array. That was six to seven years ago. I was basically developing the platform technology, and trying to understand how to apply it in various situations. For instance, in certain types of inflammatory diseases, could they be used to do large-scale screening of disease tissues? So I was working with the tools to answer important questions later.
We had a number of collaborations also. One was with the Baylor College of Medicine. Unfortunately, the company closed just a year after I got there. We were barely getting the platform out into beta testing.
What did you do after that?
After Genometrix, I joined another company called Texas Biotech. In that company, I was heading both the protein arrays and proteomic efforts for drug development. Through that, we formed a collaboration with the University of Texas Medical Branch Galveston. Now they have one of the 10 proteomic centers funded by the National Heart Lung and Blood Institute. We were one of the corporate collaborators on that grant, and in less than two years we were able to bring a new program combining new technologies and starting to identify new drug targets. Those were really my most gratifying years. I thought I would be there for the next ten years, except in industry there's a lot of turnover. It was no fault of anyone — it was simply the financial market that dictated what can be done — and in the last couple of years, the economy went downhill, and the entire program had to be let go. So that's how I ended up at Charles River Proteomic Services.
At Charles River Labs we have served a lot of commercial clients, academic clients, in many areas, from quality control of recombinant proteins, to trying to do biomarker discovery, to working on a number of model organisms. I also have pushed the protein array into the reverse-fractionated lysate array. I was hoping to actually arrange all of the animal tissues from Charles River Labs, because it's a leader in terms of animal services and also animal models. But again, it was a financial decision. CRPS had only been around for a couple of years, and purely it was a business decision that I don't know all the details about, but basically CRPS no longer exists.
At CRPS, in terms of the protein array area, I tried to not only apply the arrays, but also use my background to see how we could expand the technology. In terms of 2D gel technology, I basically learned it from UTMB. At CRPS, we were also improving on existing technology. One of my associates, Doug Hinerfeld, along with my boss, John Pirro, worked with me at CRPS, and we made a lot of significant improvements in terms of doing high throughput 2D gel analysis. The three of us really incorporated some of the technologies from, let's say, Bio-Rad to improve on those technologies and make sure that we could run hundreds of gels reproducibly. 2D gels are an old fashioned technology, but they were highly reliable and highly reproducible in our hands.
We basically have also transferred this technology to the University of Massachusetts now too.
When did you join U Mass Medical School?
Just in January. Because when CRPS closed down, since we were already doing a number of work projects for the U Mass Medical School faculty members, the school felt that it was an important technology that could benefit people on campus, so they basically invited us to form the 2D gel group on campus. Already on campus, they have a couple of really good mass spectrometry groups, and they have more sensitive [mass spec] equipment than what we had at Charles River Labs. For instance, the LTQ they have on campus is 100 times more sensitive than the LCQ we had at Charles River Labs. But the mass spectrometry equipment changes almost monthly, so it's also very difficult to keep up with the technology. I think CRPS at that time was lacking. What we purchased two years ago would soon become outdated, and another place such as UMMS would buy much better equipment two years later.
When you were hired by UMMS, was it to develop the new Proteomics Consortium?
Well, the main goal was to continue to serve the U Mass Medical School faculty members. We were already doing a lot of work for them in laboratories such as Craig Mello, the inventor of RNAi, and also a few other groups on campus such as Nathan Lawson — he works in the zebrafish area. There were quite a few faculty members that would continue to need our help in this technology.
What kind of proteomic work were you doing for them?
Mostly, it was, for instance, looking at some of the signal transduction and new protein complexes. We were trying to use 2D gels to identify new protein partners. A lot of times, when they have done a knockout or transgenic model, the next thing they want to know is what causes this change? And you can hone into specific pathways if you have antibodies. Under different stimulations and different time courses, you are going to see different protein complex formations. What we are able to bring onto the campus are the 2D gels that enable you to spread out the proteins from these immunocomplexes, and then do mass spec identifications looking at what are some of the proteins that bind to this protein of interest, what are the post-translational modifications?
I think our strength is also in upfront sample preparation. We take the principle of divide and conquer. In proteins, you could be dealing with hundreds or thousands of classes of proteins. They could be big, small, hydrophobic, hydrophilic. Some could have different folding. The heterogeneity is a major bottleneck in proteomics. What we do is develop different fractionation schemes. We've developed very highly reproducible and cost effective fractionation technologies.
We're able to fractionate into a less complex pool of proteins, spread them out onto a 2D gel, and interrogate the gels with different dyes to look at post translational modifications, and also quantitate differences with software such as Nonlinear Dynamics' software. The software itself costs close to $150,000 per copy, and we have that now also on campus. The software helps us to compare and match hundreds of gels from different treatment groups, and then use statistics to identify which proteins are differentially expressed. So we have all that information for scientists.
We have two groups on campus that are part of the consortium now. One is headed by Jim Evans, the other by John Leszyk. They would help people to identify proteins by mass spec. Proteomics really requires teams of experts and also a variety of equipment to deal with the complexity of proteins in disease versus control, or in quality control of different batches of protein.
How much of the CRPS equipment was bought by UMMS?
We bought a number of critical equipment at a negotiated price. Some of this is confidential information. I think CRPS really has helped us out in setting up this new facility. It's not that Charles River Labs does not treasure proteomics — they saw proteomics as a critical role — but it was just a pure business, dollars and cents, issue that they could not support the group in the company. But we are very grateful for the help from CRPS. Because without the help from CRPS, the consortium would not be possible. If we had to start from scratch and buy all this equipment, it would cost the school a significant amount of money. We were able to negotiate with CRPS to obtain this equipment at a very reasonable price. We need laser scanners, cutters, the 2D gel image software. We had to go through also a negotiation with Nonlinear Dynamics to allow the transfer of the 2D gel imaging software.
What is your lab in particular doing now?
Right now we do a lot of fractionations and depletions of very abundant proteins. Our strategy for fractionation depends on the particular protein. Besides depletion, we also fractionate proteins by isoelectric point and by hydrophobicity.
Traditionally, people doing mass spec would go through an ion-exchange column, and then a reverse phase. We also do that, and sometimes, depending on the abundance of the proteins of interest, we take some of these fractions and directly inject into the mass spec, or we could take the isolated material and use it to do protein labeling, like ICAT.
What do you think will be the future of your research, and of the Proteomics Consortium?
We want to take the proteomic technology to the next level. The technology can be improved significantly. Almost every month, there's a new type of mass spec equipment. Technology itself still has a long way to go. I hope that within the consortium I can continue to work on technologies such as protein labeling, because that would help us to understand more quantitative proteomics. Also, I'd like to work on more signal transduction, and also the protein microarray area which has been with me for many years. We're also trying to find ways we could do more high throughput type of mass spectrometry, because we have a Nanomate from Advion that we bought through Charles River Labs. That has a 96 well mass spec loader, so we're trying to work on new ways to fractionate proteins and then take advantage of the Nanomate to do more high throughput MS analysis.
These are my personal interests, but each member of the consortium has their own personal goals and interests.