Multiplexed gene-expression assays permit simultaneous rather than sequential measurement, increasing productivity and providing high-content data. The necessity to select a single target is eliminated, reducing hypothesis failure risk and eliminating the months/years of experiments needed to select a single target.
Pursuing drug discovery programs at the level of gene expression rather than at the level of proteins has at least three advantages. It eliminates the time needed to identify the protein targets and develop the required assays; it permits the program to remain multiplexed from start to finish; and combined with the quantitative precision of qNPA, it permits same assay comparison of efficacy, specificity, metabolism, and safety based on quantitative EC50 values.
Enabling gene-based drug discovery requires the capability for high-throughput screening and QSAR optimization, which is achieved by qNPA. Similarly, quantitative multiplexed diagnostic gene-expression assays are expected to provide more accurate understanding of disease state, stage, and subtype, and to monitor drug efficacy to guide effective therapy.
Making the disruptive change to measure a molecular signature (fingerprint) rather than a single target overcomes problems predicated on several generalities. High-throughput screening at the level of whole cells, much less whole organisms, is not typically pursued because of high false positive rates and difficulty differentiating direct/indirect compound effects that may change within an analog series. In vivo data is far less reproducible than in vitro data and less useful for optimization QSAR. Drugs and disease act in the whole organism, not in purified systems, and invariably side effects are discovered as programs move from cell-free to cellular, animal, and then human trials.
For example, agonists and antagonists in purified systems may exhibit mixed activity in cells or in vivo. The objective of therapy is to alter a disease phenotype that results from a molecular phenotype that is typically not measured at each stage of the drug discovery process or diagnostically. A molecular signature can provide both a qualitative measure as well as a quantitative measure of the molecular phenotype. Essentially, use of a molecular signature not only can be used to define the molecular phenotype, but it can also be used to increase the practical sensitivity of the assay.