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Proteomics Pioneer: Joseph Loo on Saliva Research and Other Proteomic Work at UCLA

Joseph Loo
University of California Los Angeles/Keck Mass Spectrometry and Proteomics Technology Center

At A Glance

Name: Joseph Loo

Position: Director of University of California Los Angeles/Keck Mass Spectrometry and Proteomics Technology Center; UCLA professor of biological chemistry and biochemistry, since 2001.

Background: Scientist and mass spectrometry group leader at Pfizer, 1992-2001.

Postdoc and senior research scientist in laboratory of Richard Smith, Pacific Northwest National Laboratory, 1988-1992.

PhD in Fred McLafferty's laboratory, Cornell University, 1987.

Last week, ProteoMonitor reported on the half-year-old Human Salivary Proteome Project (see PM 4/1/2005). This week, ProteoMonitor spoke with Joseph Loo, the co-chair of the project and the director of the UCLA/Keck Mass Spectrometry and Proteomics Technology Center, to find out about his background and the proteomics work being done at UCLA on saliva as well as other biological samples.

What were you doing before you joined UCLA?

My PhD is from Cornell with Fred McLafferty in mass spectrometry. After that, I went to Dick Smith's lab at PNNL as a post doc, working on electrospray ionization and mass spectrometry. And then I stayed there for an extra two years as a staff member there, and after that I went to what was then called Parke Davis Pharmaceuticals, but now it's called Pfizer, in Ann Arbor, Michigan. I was a staff scientist there. I eventually got to the point where I was running a mass spectrometry group. I was trying to develop tools to help the drug-discovery part, and trying to integrate the mass spectrometry and drug discovery efforts, and then we eventually formed a proteomics group that was looking for biomarkers for disease or biomarkers for efficacy of drugs. The proteomics group started probably in the middle 1990's. Then in 2001, I left Pfizer to take this faculty position at UCLA.

What kind of projects were you working on in Dick Smith's lab?

When I was a postdoc with Dick, John Fenn had not yet published his paper on the electrospray ionization of proteins. So essentially, right after I started, Fenn's work just started to come out. The early part of my work was trying to essentially exploit what Fenn had developed and really push it towards large protein analysis, and then eventually towards protein sequencing. A lot of our work was based on just finding the right conditions for detection of proteins from mixtures, trying to see if we could sequence proteins using electrospray, and then integrating that with separation tools. Back then, Dick was very interested in capillary electrophoresis and electrospray, so that was also part of my project.

Did you apply all of that when you went to Pfizer?

We applied some of it. We never did apply the capillary electrophoresis to mass spectrometry. But at Pfizer, I was initially hired to run this very large mass spectrometer that they had just purchased, and to really advise and build the group up so that we had sufficient mass spectrometry tools to look at the proteins.

The company didn't really know where proteomics was going to go, so it was actually a little premature to form a group solely dedicated to proteomics. They didn't realize what the potential was for proteomics in any kind of area for drug discovery. So we had lots of discussions. We probably spent a couple of years discussing how proteomics would be integrated in discovery or even in drug development. Biomarkers hadn't even come up at that point as far as a topic for proteomics research.

So the proteomics group we had formed back then was really a merging of the analytical group that I was running and a biology group that had special expertise in 2D-gel electrophoresis and other protein characterization tools. It was almost like a hobby for us at the beginning. The hobby was the proteomics part.

What did you start working on once you got to UCLA?

So at UCLA, they were looking for a faculty member who could help establish a proteomic presence at UCLA. There hadn't been really anything organized until around the time that I came. UCLA had just secured a fairly substantial research grant from the Keck foundation to establish a proteomic core facility. The university was looking for somebody who knew how to spend money essentially to ramp up a proteomics facility. So that's what I've been doing. The first couple of years were just setting up the facility, and the next couple of years have been just advising people who want to look at proteomics for research purposes, and helping them to design experiments and use the facility.

Were you working on particular research problems when you started?

The original plan was that I would initially just start the proteomic facility, and after it got going, it would have a life of its own and I would just take over my own research activities. But in fact, it's actually a 50-50 proposition. There's still a lot of education going on, and the facility is still morphing into something that's a little different from what I anticipated.

My own research interests are primarily in tools development. Since I'm primarily a mass spectrometrist, we try to push the mass spectrometry method and the protein chemistry method for protein sequencing and protein identification. It's all fairly integrated into the facility. Anything that we develop we put down into the facility.

We're trying to increase the throughput for protein identification mixtures, trying to exploit things on the electrophoresis end. We're trying to integrate the electrophoresis with the mass spectrometry.

I have one collaboration with the school of engineering and the chemistry department. We're trying to build a protein chip involving microfluidics. We're trying to do nanoscale protein sequencing on a small chip using mass spectrometry on the detection end.

I have another set of students who are interested in looking at very large proteins and protein complexes and using mass spectrometry as the detection end. We're interested in what's the largest protein complex we can identify; what's the largest protein complex we can see by mass spectrometry. And identifying all the proteins that are present within the complex.

Are you collaborating with any companies in developing the protein chip?

Not really. I am an advisor to a small biotech company called HK Pharmaceuticals. But they're very small. The environment right now for investing in biotech companies is not very good - certainly not like four years ago. We're trying to help [HK Pharmecuticals] lift off the ground. They're very much interested in developing a mass spectrometry platform to help companies identify which proteins might be binding to a drug target that they didn't anticipate, as far as toxicity is concerned. And a lot of the tools that we're developing could probably be applied towards that goal.

This protein chip that we're working on, one of the first samples that we'll be likely using is saliva. Saliva is so easy to collect. For an early detection method for a disease like cancer, saliva really presents itself as a fairly simple type of analysis. And if we can integrate this on a chip platform and make it readily available to a lot of people, I think the methods are simple enough that anyone can apply this. So saliva will be one of the first fluids that we'll be testing on this protein chip.

Right now with the protein chip, we can integrate a lot of the steps that we do for protein identification, like trypsin digestion and sample cleanup on the chip, and then put that on a MALDI mass spectrometer. But we haven't actually tested on a real sample yet, and I think saliva will be the first one.

What kind of content does the chip has on it?

The chip is really just a platform for moving fluids at will to any position you want on the chip. So what the chip will have are reservoirs for the protein chemistry that you need to have. It will have a method for peptide separation, sample cleanup. It will be designed such that you just sort of load the reagents on the chip, and you put it into your instrument, and there are pre-programmed steps for the fluid to move around to do the chemistry, and then the detection is still the mass spectrometry part.

The chip is kind of like a Gilson 215 liquid handler, only in a foot print that's no bigger than a credit card.

We've published a couple of papers on the early data. The development of the chip is actually from two groups: The engineering group is run by CJ Kim, and the chemistry part, as far as the surface chemistry is concerned, is run by Robin Garell. My part in this whole thing is really the biology part and the integration with the mass spectrometry.

How did you get involved with the Human Salivary Proteome Project? Did you get involved because you planned to use the protein chip to analyze saliva?

No. I'm can't even remember how I got involved. How I became interested in saliva was that the LA Times published an article in their health section on using saliva as a diagnostic fluid for markers of disease, and even markers for cavities. The article was really written about a group of researchers at the University of Southern California, not at UCLA. I read the article, I had just come to UCLA. I thought, that's kind of interesting - saliva is pretty easy to collect, and here's a bunch of people that are interested in proteins. So I cut the article out and I filed it away. I didn't even realize at that point that UCLA had a dental school. I had no idea.

Then around a year later, David Wong, [the head of the HSPP], approached me. He was looking for somebody who was an expert in proteomics, and he asked me if I would be interested in collaborating with him in starting this small effort in proteomics of saliva. And I was interested in it. I was already interested in saliva before, just based on that article.

And it turns out that he was collaborating with that group from USC. So we all kind of got involved, and then this big RFA came out from the dental part of NIH, and that's when we really got going and formed this group of people who are interested in looking at salivary diagnostics.

Do you see your protein chip as being used with saliva in some kind of home diagnostic test?

Probably not the chip that we've been talking about, because you need a power supply. But I've seen the diabetes test where you do the pin prick - you still have to put it in some sort of hand-held instrument to do the reading. So I don't know - maybe. I think that's so far in the future that we haven't even begun thinking about it. I don't expect patients to have this device in a home, but I could see it perhaps in a doctor's office.

What other projects are you working on?

For the last couple of years, I've been working with a professor at the medical school who is in the asthma center. His project is to understand the role of air pollution in asthma. So our project is funded by NIH to look at proteome profiles of samples collected initially on cell lines, and now we've moved to lung fluid from mice which have been exposed to diesel particles collected from the atmosphere. I believe the diesel particles were actually collected in Los Angeles. And we have been finding that proteins are differentially expressed when they are exposed to different levels of these diesel particles. Many of these proteins are modified post translationally, and there's an oxidative stress mechanism that's involved. So a lot of these markers are either phosphorylated, or they're tyrosines that they converted to nitro-tyrosine. Many of these are markers for inflammation. Some might be markers specifically for asthma.

So we're trying to identify a protein marker that we can validate that might be an indication that for say a kid who grows up in Los Angeles near a freeway - if we can measure this protein and it's elevated at a certain point in time during their life - then, there's a fairly good chance that this person's going to develop asthma.

And then once we know what these markers are, if we can identify if they're causative or not, that might also lead to a potential therapy.

What are you looking to do in the future?

Other than just expand the proteomics facility, I'm still just very interested in applying the basics of mass spectrometry to biology problems. There's still much to learn and much to develop in the field of mass spectrometry, and that's really where my heart is. But certainly working with the biologists and the medical researchers on campus has been quite pleasant, and it really complements that side of me. You can't develop an analytical tool without understanding what the application might be, and that's what the medical researchers really bring to my attention.

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