December 1, 2005 (Vol. 25, No. 21)
Insights on the Adoption and Utilization of this Often Maligned Technology
As protein arrays have become increasingly consistent and reliable, more scientists have begun to incorporate them into their proteomics experiments.
Researchers are attracted by the technology’s ability to detect protein expression quicker and easier than traditional approaches, such as 2-D gel electrophoresis and mass spectrometry. By allowing scientists to look at multiple protein interactions simultaneously, the seemingly insurmountable challenge of characterizing an organism’s proteome is within reach.
While there is tremendous excitement about the potential of protein arrays to further our understanding of protein expression, function, and structure on a microscopically global level, there is also hesitancy, on behalf of many scientists, to adopt a technology that is often still perceived as unstable and irreproducible.
“Protein Microarrays: Technology Adoption and Utilization,” a report released in September by market research firm BioInformatics (Arlington, VA), provides insights from over 800 life scientists about the technology’s current limitations and their future expectations.
Although no longer considered a new technology, 47% of study participants have been using protein microarrays in their research for six months or less, suggesting a relatively slow rate of adoption since its emergence in the late 1990s. However, this statistic and the fact that 69% of future users plan on using protein arrays within 12 months or less suggests that scientists might now be more receptive to the technology than they were a year ago.
According to the Bioinformatics study, the top three suppliers of treated protein microarray surfaces for self-printing are PerkinElmer Life and Analytical Sciences (www.perkinelmer.com), Eppendorf (www.eppendorf.com), and GE Healthcare (www. gehealthcare.com).
Clontech (www.clontech.com) and Invitrogen (www.invitrogen.com) are top suppliers of commercially available protein microarrays.
Bio-Rad (www.biorad.com), Agilent (www.agilent.com), and PerkinElmer are top suppliers of protein microarray readers.
Notwithstanding the optimism that the “time is right” to sell protein microarray products and services, there is a worrying trend with regard to the technology’s perceived usefulness. 53% of proteomics researchers who do not plan to use protein arrays in their research state that the technology is not necessary for achieving their experimental objectives.
A possible explanation for this belief is that technologies similar in function, such as 2-D gel electrophoresis and mass spectrometry, are utilized less frequently than some of the more popular immuno-based techniques.
This preference is particularly evident for respondents uninterested in using protein microarrays. These nonusers employ 2-D gel electrophoresis less frequently than current and even future protein microarray users.
Addressing these objections by repositioning their technology and educating scientists about the technology’s utility are two ways suppliers can try to overcome a nonuser’s resistance and acquire new protein microarray customers.
For example, free sample arrays and a no obligation trial-period might entice some nonusers, however, published reports in the literature demonstrating the technology’s validity and proof of functionality would be equally effective in changing a respondent’s mind. Also, the recommendation of a colleague and/or collaborator is quite important.
Because of technical difficulties in creating enough high-quality capture agents to populate a broad or high-density platform, many suppliers are developing arrays with more focused content. Popular types of arrays currently utilized are antibodies, signaling proteins, and cytokines.
Cytokines, in particular, lend themselves to this type of thematic targeting due to their pleiotropism, multifunctionality, and redundancy. These characteristics limit the number of proteins that need to be included on a single array.
Study participants planning on adopting protein microarray technology are shifting their emphasis toward more complex protein classes. Specifically, academic scientists would also like to study membrane receptors and transcriptional regulators, while industrial scientists are particularly interested in membrane receptor proteins.
Due to the fact that arrays of membrane proteins also require immobilizing-associated lipid molecules, suppliers hoping to meet this emerging need will be faced with additional manufacturing challenges.
In contrast to cytokines, transcriptional regulators are more functionally diverse and target-specific. Microarrays of these proteins will require more density to achieve complete coverage. This raises an important issue for suppliers of how to do so cost-effectively.
In addition to tackling increasing array complexity, suppliers must also address the question of array density. Because of cross-reactivity and printing challenges, the initial expectation that protein microarrays would mimic the high density of DNA microarrays was never realized.
Data from this study supports this industry trend. Currently, 68% of study respondents using protein microarrays focus on subsets of proteins, usually fewer than 100 of them per array.
This emphasis on lower density arrays will diminish, however, as future users adopt the technology. Only 54% of these researchers plan on using arrays with less than 100 proteins printed on them.
The upcoming shift to higher density arrays is even more evident when comparing the specific preferences of the study participants. 27% of current users utilize arrays with less than 25 proteins printed on them and 28% of future users plan to utilize arrays with 1011,000 proteins printed on them.
While impractical just a couple of years ago, higher density arrays are now more technically feasible and economical. Furthermore, a portion of this increased density will need to come only from “spot replicates” as future users will expect their arrays to contain two to three replicates per spot instead of primarily just two replicates per spot that current users prefer.
This distinction translates into less unique moieties that need to be printed per array to achieve higher densities.
Researchers who participated in this study are also looking for guidance on how best to apply it. Demonstrating proof-of-concept for new applications would be the most desired improvement. Given the potential to use protein microarrays to facilitate expression profiling, studies of protein-protein and protein-drug interactions, and activity measurements, it is understandable that some scientists are overwhelmed at their options and wonder, “what is the technology particularly appropriate for, especially as it relates to my own research objectives?”
Whole Proteome Arrays
Scientists also would be interested in whole-proteome arrays, particularly of human and mouse origin. Additionally, they would like the ability to array functional membrane proteins, which has been a major technical hurdle from the technology’s inception.
Innovations, whether they are more futuristic, like merging protein micoarrays with microfluidics, or practical, such as improving protein binding and detection, are not nearly as important to respondents.
To overcome the technical challenges that presently limit increasing protein microarray complexity and density, suppliers are looking to improve protein array substrate materials and surface chemistries, arraying reagents, detection techniques, and the use of miniaturization and automation.
This trend in increased density will culminate in a receptive market for the whole proteome array of human and mouse. A major challenge suppliers face will be to ensure that the majority of meaningful biological problems that can be answered with a whole proteome array can be done so quantitatively and with real-time measurements.