Clinical translation of a NexGen platform for quantifying protein networks in human biospecimens

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Project Summary/Abstract Due to technological limitations, there are no validated assays for quantifying the majority of human proteins in clinical biospecimens, and thus most of the human proteome is clinically inaccessible. Because most modern cancer therapies act on proteins, our inability to quantify proteins is an impediment to the translation of targeted therapies. Furthermore, proteins act as interconnected “networks,” and thus we must be able to quantify panels of proteins in cancers to assess the activity of pathways and networks that determine treatment responses. Our project aims to translate (for use in clinical trial settings) a multiplex protein assay for quantifying tumor suppressor proteins and cell signaling networks that response to DNA damage- a critical network targeted by current drug discovery efforts. The assay is based on a NextGen platform for quantifying protein panels uses targeted, multiple reaction monitoring mass spectrometry (MRM-MS), which complements existing protein assay technologies and overcomes many of the technological limitations, including enabling multiplexing of assays for many proteins in a single network. MRM has been extensively validated in the preclinical space but has not yet been adapted for clinical trials. Our multidisciplinary team brings together academic partners with diverse expertise (MRM-MS, analytical chemistry, clinical chemistry, pathology, statistics, bioengineering, protein biochemistry) with an industrial partner (AstraZeneca) that has extensive experience in drug development and clinical trials. Successful adaptation of this MRM-based assay panel to the clinical trial setting will provide a road map and standard operating protocols (SOPs) for translation of additional MRM-based assay panels (>1,500 assays are already publicly available at https://assays.cancer.gov/).