Novel multiplex matrix network analysis method for the elucidation of protein-protein interaction signatures
While the genome is the molecular recipe, the proteome provides a glimpse into what is happening in real time. Like letters that join together to compose ‘words’, individual proteins can bind to form distinctive protein complexes, where the unique composition of each protein complex signals to the cell a specific message. The human genome was sequenced in 2003, but the different combinations that proteins can form remain largely uncharted due to technological limitations.
Although detecting the subtle changes in the proteome is no easy task, the lab of Adam Schrum was up for the challenge. Schrum and colleagues recently published an article in Science Signaling detailing the development of a new method, PiSCES (Proteins in Shared Complexes Detected by Exposed Surface Epitopes), capable of deciphering the molecular signatures unique to healthy and aberrant signaling networks associated with disease.
Photograph used with permission from Adam Schrum.
T cell antigen receptor (TCR) is capable of transmitting multiple messages, and in autoimmune diseases the message can be pathologic. Therefore, the protein complexes that form a signalosome around TCR were examined from 4 mm skin punch biopsies from the scalp of controls or patients with alopecia areata, an autoimmune disorder where T cells attack hair follicles. One of the strengths of this method is the ability to detect patterns even with limited biomaterial – a common limitation when working with patient samples.
His team was looking for unique combinations of protein associations that they could interpret via a matrix approach to generate a network analysis of specific protein signatures. Twenty proteins in a pairwise combination matrix resulted in the detection of 210 unique pairs of PiSCES. They found a preliminary signature that distinguishes control from disease, and the protein complexes involved point toward an unforeseen hypothesis about which signaling activities might drive disease. In the future, heterogeneity patterns identified across groups could be used to determine personalized treatments based on known patterns associated with treatment responsiveness.
When asked what inspired PiSCES, Shrum noted that “the prospect of obtaining network-level information about protein complexes driving biological signal transduction was quite enticing, but there really wasn’t a good technical approach that could provide rich information from clinical patient samples, mainly because they are so small. We needed something that could do this like an ELISA assay would, with that kind of sensitivity, and possibility for broad survey. The multiplex microsphere platform seemed very promising, like it could fit the bill, and it turned out to provide an informative protein interaction signature like we had hoped.”
Moving forward, Schrum hopes to translate his method from the lab to patients. Once concise, clinically relevant bio-signatures are identified, this subset could serve as the basis of a molecular diagnostic assay.
Want to hear directly from the authors? Download the Science Signaling podcast.
Want to read more? Visit Dr. Schrum’s faculty webpage for article access.
Interested in developing your own multiplex assay? Download the xMAP Cookbook to get started.
Luminex supports life science research with its Research Use Only (RUO) product portfolio. Not for use in diagnostic procedures.