Biomarker Discovery: Ubiquitin Pathway Protein Microarrays

DESCRIPTION (provided by applicant): Bioinformatics and biochemical analysis suggests that the human genome encodes ~ 100 proteins known as deubiquitinating enzymes (DUBs). DUBs constitute an important class of enzymes that deconjugate ubiquitin and ubiquitin-like proteins (UBL) from their target proteins. Protein uniquitination serves many functions in the cell, including proteasome-mediated degradation of poly-ubiquitin tagged proteins. DUBs are thus key regulators that play a very important role in the fate of cellular proteins. In Phase I it was proposed to study a limited number of DUBs to test the feasibility of a catalytically active array as well as a DUB array for serum biomarkers. This study has been completed successfully and, for Phase II, LifeSensors plans to develop an array covering most of the deUBLases and selected Ub-ligases (UBL-enzymes) for profiling serum samples; specifically, two types of array are proposed: (1) a complete UBL-enzyme antibody array to monitor signature(s) of UBL-enzymes associated with disease and normal states; and (2) an array in which all of the UBL enzymes are utilized to monitor human sera for auto-antibodies that may serve as biomarkers in health and disease. UBL-enzyme microarrays developed in this study will represent important advances for research, biomarker discovery, diagnostics/prognostics, and therapeutics. The ubiquitin pathway is the most conserved pathway of eukaryotic origin. Aberrations in such highly conserved pathways are likely to lead to pathologies. The expression of various DUBs has been associated with diseases such as cancer, diabetes, and neurodegenerative disease (PD, AD), to name a few. Over- or under-expression of proteins in disease states tend to elicit elevated or diminished auto-antibody production against those proteins. Thus, auto-antibody profiling can help to identify the type and stage of a disease. The ubiquitin pathway and DUBs in particular are emerging as sources of novel therapeutic targets, and the development of UBL-enzyme arrays that identify signatures in disease tissue will doubtless facilitate target validation as well as serve as biomarkers. Given the Phase I success, a comprehensive plan for the development of UBL-enzyme microarrays from the human genome has been proposed. A key aspect of this plan is a collaboration with the Fred Hutchinson Cancer Research Center wherein the new UBL-enzyme biomarker arrays will be characterized by screening from among the institute's many human serum repositories. PUBLIC HEALTH RELEVANCE: The ubiquitin- and ubiquitin-related pathways play a central role in cellular homeostasis and regulation. These pathways involve a Yin/Yang of conjugation and deconjugation of the small ubiquitin-like proteins to target proteins. Dysregulation of these pathways has been implicated in cancer, inflammatory and cardiovascular diseases, and neurodegeneration. LifeSensors proposes to develop an assay technology for the majority of the members of these pathways, over 100 distinct proteins. This assay has the potential to identify new biomarkers for the early diagnosis of these diseases.