IGSB Core Faculty Richard Jones Illuminates protein networks in 1 step
Illuminating protein networks in 1 step
A new assay capable of examining hundreds of proteins at once and enabling new experiments that could dramatically change our understanding of cancer and other diseases has been invented by a team of University of Chicago scientists.
Described today in the journal Nature Methods, the new micro-western arrays combine the specificity of the popular “Western blot” protein assay with the large scale of DNA microarrays. The technique will allow scientists to observe much of a cell’s intricate protein network in one experiment rather than peeking at one small piece at a time.
“The proteins are the actual machines that are doing everything in the cell, but nobody’s been able to examine them in depth because it’s been too complicated. Now, we can begin to do that with this new method,” said Richard B. Jones, senior author and assistant professor at and the University of Chicago’s Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology.
Since the 1970’s, laboratories have used Western blots to measure proteins. Cellular material is loaded into a gel and proteins of different sizes are separated by an electric field. A protein is then targeted by an antibody, allowing scientists to measure the amount present in the cells.
The method has led to numerous findings across the field of cell biology, but is limited by a need for large amounts of cell material and expensive antibodies, and the inability to measure more than a handful of proteins at a time. With hundreds or even thousands of proteins involved in cellular networks, scientists were restricted to observing only a small fraction of protein activity with each experiment.
“When you walk into a dark room and don’t have much information, it’s difficult to predict where everything is going to be,” Jones said. “If someone can simply turn on the light, you don’t have to progress one step at a time by bumping into things. With this new technology, you can potentially see everything at the same time.”
Micro-western arrays adapt the technology of the micro-array, typically used to assess the expression of thousands of genes in a single experiment, to proteins. With pre-printed micro-western array gels, essentially comprising 96 miniature Western blots, scientists can compare the levels of hundreds of proteins simultaneously, or compare dozens of proteins under dozens of treatment conditions in one shot. Mere nanoliters of cell material and antibodies are needed for the experiments, reducing cost and maximizing the information obtained from a single sample.
To demonstrate the potential of the micro-western array, Jones and colleagues from the University of Chicago and the Massachusetts Institute of Technology looked at the behavior of proteins in a cancer cell line with elevated amounts of epidermal growth factor receptor (EGFR).
“We started asking questions about what we could do that no one else could previously do,” Jones said. “We could actually reproducibly see 120 things at a time rather than looking at 1 or 2 or 5.”
The experiments found that activating EGFR simultaneously activated several other receptors in the cell – a new discovery that may explain why some tumors become resistant to cancer therapies.
With more information, the method may potentially be used clinically for more precise diagnoses of cancer and other diseases that can direct individualized treatment.
“In the clinic, you’re limited by the fact that typically most cancers are diagnosed by one or two markers; you’re looking for one or two markers that are high or low then trying to diagnose and treat an illness,” Jones said. “Here, we can potentially measure a collection of proteins at the same time and not just focus on one guess. We’ve never been able do that before.”
Other scientists in the field of systems biology said that micro-western arrays would make possible experiments that were previously beyond the scope of laboratory methods.
“I think this is really a breakthrough technology that allows us to monitor in close to real time the activity profiles of modified signaling proteins, which is essentially impossible right now,” said Andrea Califano, professor of biomedical informatics at Columbia University. “This opens up a completely new window in terms of the molecular profiling of the cell.”
“One of the biggest hurdles for systems biology is the struggle for high density, dynamic and quantitative data, and the micro-western array method will go a long way to address this problem,” said Walter Kolch, director of Systems Biology Ireland and Professor at University College Dublin. “It is a fine example of generating exciting new technology from applying a new idea to an old method.”
The paper, “Systems analysis of EGF receptor signaling dynamics with micro-western arrays,” will be published online in Nature Methods on Sunday, January 24th. Also credited as authors on the paper are Mark F. Ciaccio and Chih-Pin Chuu from the University of Chicago and Joel P. Wagner and Douglas A. Lauffenburger from the Massachusetts Institute of Technology.
The work was funded by The University of Chicago Comprehensive Cancer Center, the American Cancer Society, the Cancer Research Foundation, the Illinois Department of Public Health, the National Institutes of General Medical Sciences, the National Cancer Institute, and the National Science Foundation.
The 10-week Chicago Center for Systems Biology summer REU program kicked off this past Tuesday. Students will work in the labs of Kevin White, Michael Rust, Richard Carthew, Rick Morimoto and Ilya Ruvinsky, on projects ranging from circadian rhythms in cyanobacteria to Drosophila development.
Two major gifts will build momentum behind the University of Chicago’s leadership in biomedical computation by assembling experts in the field and furnishing them with the tools to use “big data” to understand and treat disease. Kevin White and Robert Grossman will lead the Pancreatic Cancer Genomic Medicine Initiative, which aims to improve care for patients with this disease using genomic and physiological data.
Barbara Stranger and colleagues take a systems approach, integrating GWAS, eQTL and protein interaction data, to demonstrate that loci associated with inflammatory disease susceptibility are enriched for genomic signatures of recent evolutionary selection. Their analyses suggest that natural selection for pathogen-defense mechanisms through human evolution may underlie modern susceptibility to inflammatory diseases.
The annual list, published by Federal Computer Week, recognizes government, industry and academic leaders who have played pivotal roles in the federal government IT community.
In response to the community-wide interest in High Throughput Screening, the Chicago Biomedical Consortium is offering a 1:1 HTS Matching Grant Program to help fund innovative small molecule discovery. The intent of this program is to support pilot projects involving bio medically-relevant targets using a HTS facility located at one of the CBC universities, including the IGSB’s Cellular Screening Center.
By mapping the bindings sites of nuclear receptors, chromatin state markers and transcription factors associated with breast cancer, IGSB Director Kevin White and colleagues construct a network representing different types of regulatory relationships. Their analyses identifies transcriptions factors with previously unsuspected roles in breast cancer and enables predictions of responses to therapy.