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Steven Bodovitz on Protein Biochips in Current and Future Markets

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At A Glance

Name: Steven Bodovitz

Age: 35

Position: Principal and co-founder of BioPerspectives (formerly BioInsights), since 1999

Experience: Author and consultant for numerous biotechnology reports, including The proteomics bottleneck: strategies for preliminary validation of potential biomarkers and drug targets, 2004; Protein biomarker strategies, 2003; Multidimensional proteomics, 2003; The protein biochip content problem, 2003; and The proteomics market, 2003.

Wrote more than 15 business plans for biotechnology companies

Education: PhD in neuroscience from Northwestern University

 

Steven Bodovitz is one of sev eral biotechnology consultants who spent about three months this year putting together a report that evaluates protein biochips within the biotechnology and pharmaceutical markets.

The report, which came out last week, predicted that protein biochip systems would increase in market worth from $170 million last year to $430 million in 2007 and $545 million in 2008 (see brief, page 5).

ProteoMonitor caught up with Bodovitz last week to ask him about his experience and expert opinions within the proteomics field.

How did you get recruited into doing this study involving protein and genomic biochips?

Well, I have a PhD in neurobiology from Northwestern where I worked on the molecular mechanisms of Alzheimer’s disease. And after finishing grad school, I started looking into consulting and this was 1997, so one of the really hot areas was genomics — it was the beginning of the genomics boom. Originally I did some work looking at DNA microarrays and I did a report actually covering DNA chips and protein chips as well. And then I was a co-founder of a company called BioInsights, and at BioInsights we also did a report covering all the different types of chips — and this was in 1999. And then in 2000, it became clear that the protein chips were really rapidly coming onto the scene, rapidly progressing. So we did a report on protein chips — this was the first report that looked at just the protein chip… In the first report we did in 1999, we covered just four companies. And then we did our next report in 2000 — we had about 20 companies at that point, and now, for the most recent report, we’ve covered 60 companies. So, I got into proteomics basically from the business side, looking at what were the most interesting markets. It was sort of a big twist going from academic research into biotech business consulting.

How would you say the field has changed since you did your first report back in 1999?

There’s been a lot of changes. In 1999, DNA microarrays were definitely the most interesting area of microarrays. There were a lot of different microarray companies producing DNA microarrays and since then the field has definitely turned. Most of the original players aren’t really competing any more, so now it’s just the big players that are left. Whereas in the protein chip area, it’s still in expansion mode.

There’s tons of little companies, tons of emerging companies and there’s no real dominant player yet in protein chips. In the current market, the majority of the revenues in 2003 are from three companies: BioCore, Ciphergen, and Luminex, but the field is harder to dominate, just because of the diversity of technologies. In the protein biochip world, there are a lot of smaller companies also trying to gain traction in the market.

Describe the bottleneck in going from protein biochips to drug development.

One of the things that is compelling about protein biochips is that they have a large application within the drug discovery and development process. So they could impact the process in multiple different ways. I think the bottleneck is a good place to start in talking about drug development. If you look at all the discovery technologies both in genomics and proteomics, they’ve been very successful at identifying potential drug targets. If you go to any conference, you’ll hear people give a talk about these things — they take their healthy and their diseased [samples] and they run it through mass spec, and they always find different goods.

There’s just huge amounts of potential targets. The challenge though is validation. The real question is which of these changes is real. Which of these changes that connect to a diseased state are not just spurious, due to other variables and not the disease. The problem is that these methods like mass spec and 2D gels are great for initial discovery and not so good for the screening part, when you want to really just test it over and over again and show that it holds up in different conditions. Mass spec lacks some of the throughput to screen these potential ones. That’s where the chips have a great potential. They are ideal for screening because they’re an inexpensive way to test that these changes are holding up across different patients, different sample collection methods, different time of day, different treatment for the patients, whatever you can throw at it. You want to test all those things, and that requires throughput more than anything else.

For example, Caprion has reported up to ten percent of proteins in serum can change between diseased and normal — this is sort of on the high end I’ve heard for percentage of changes. So you see all these changes. You could keep running your mass spec over and over again, but it’s more cost-effective to take a protein chip against those changes. You just measure all the proteins at one time, using a protein chip. That’s the idea.

What are some of the newest developments within the biochip field?

One issue with the biomarkers is that traditionally they’ve mostly been with a single protein, and the question now is if we can combine more analyses together on the same chip to increase the power of the analysis. And they’ve actually shown that you can use patterns on the chip to distinguish and predict — whether it’s do you respond better to a certain drug, or better therapeutic outcome, or better diagnostics.

They’ve established that patterns can enable some things in diagnostics that wouldn’t be possible otherwise. The danger is that you could actually complicate things more than you want by using patterns. So you have to prove that the patterns are actually going to be worthwhile. With patterns, you definitely want to use something like a protein biochip for parallel analysis.

What would you say are some of the differences between the 60 companies you analyzed that makes one more competitive than another?

We actually divided the market into interaction biochips versus capture biochips. Capture ones use antibodies to capture and bind to a target protein, and then you can measure the level after the capture. On the interaction side, you’re looking more at an interaction beyond just capture. So you would immobilize proteins or peptides and see what they interact with.

For example, there’s a company called Proteometrics that was acquired by Invitrogen, and they used this technology for immobilizing proteins from almost the entire yeast proteome. There are many companies doing things similar to that — we call those interaction chips. Still, there’s definitely more companies doing capture biochips than interaction biochips.

What are some of the obstacles in the field?

There hasn’t really been that much content — that’s one of the things that’s kind of holding the industry back. Mostly people have been dividing and conquering — making best use of available content. For example, there’s lots of good antibodies for cytokines. The most common protein biochip is one that looks at cytokine levels. Other companies are looking at different kind of pathways, for example signal transduction pathways. We definitely need to have more content. I think everyone would agree about that.

The market has definitely been changing over the last couple of years — it’s pretty much been moving from grandiose ideas like immobilizing 10,000 different antibodies on a high-density platform to more realistic goals. I’d say the state-of the-art chip now holds about 100 to 120 antibodies. One of the biggest wildcards in the market is what it talked about with Invitrogen — they have that chip with all the different yeast proteins on that — that’s definitely a wild card for the market. People are skeptical as to if you can really do protein biochemistry on the surface of a chip. So it’ll be interesting to see how that plays out.

What draws you to and keeps you in the field of proteomics?

Basically, I have a love of science and research. I found that I worked on one part of one protein for four and a half years in graduate school. What I do now involves just amazing amounts of variety — it’s fascin ating. There a lot of bold ideas and a huge variety of topics. I’ve really enjoyed that. It’s kind of like being a kid in a candy store.

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