SNAP-X: Development of a Mutagenesis Strategy and High Density Protein Array to Comprehensively Display Protein Variants

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Project Summary SNAP-X: Development of a Mutagenesis Strategy and High Density Protein Array to Comprehensively Display Protein Variants PIs: Christopher L. Warren and Mary S. Ozers Personalized genomics will be realized when the results of full exome next-generation sequencing (NGS) can be understood in terms of protein functional effects. Distinguishing causal mutations from passenger mutations that have no effect remains the crucial problem to be solved before individual patient exome sequencing can be applied in the clinic. High-density protein arrays are an emerging solution to assessing functional variants. Preparation of individual mutational clones and spotting of protein variants onto arrays for functional assay using current methods is costly and time-consuming, not meriting the use of limited research and clinical resources. A high-throughput methodology for systematic mutational analysis of protein function is needed to spur advancements in clinical application of personalized genomics. We have previously developed a novel high density and high throughput peptide microarray platform technology, the SNAP-Tide array (Specificity and Affinity for PepTides), which can display up to one million unique peptides from the human proteome on a single glass slide, 100 times the peptide density of current commercial products. This increase in peptide density is possible because of our innovative synthesis process, in which peptide coding sequences on a standard DNA microarray are converted into RNA-barcoded peptides in vitro and addressed back to the array. In this proposal, we will innovate upon the SNAP-Tide platform to create the first available high-density array that displays proteins containing every amino acid substitution. Specifically, we will: 1) Design and synthesize the SNAP-X system to generate all possible amino acid variants of three cancer-related proteins; 2) Assess the quantity and functionality of the variant proteins synthesized on the SNAP-X array; 3) Using FoxA1 variants that have been identified through The Cancer Genome Atlas (TCGA) in breast cancer samples, validate the SNAP-X data by performing secondary experimental assays that segregate these FoxA1 variants by pathogenicity. The array format allows for rapid, simultaneous determination of protein activities such as ligand binding, protein-protein interactions, and protein-DNA interactions, thus providing information about individual amino acid side chain contributions to these activities. While there are other arrays that display full proteins, they do not display mutated versions of the proteins, nor do they reach the density of the SNAP-X platform. Additionally, our novel cell-free mutagenesis method reduces costs, material, and time to produce in vitro up to a million proteins with single amino acid substitutions. This technology will bridge NGS exome characterization, cancer phenotypes, and clinical outcomes.