The overall premise of the Targeted Pathway Analysis Core (TPAC) is to steer investigators through introductory "discovery" lipidomics and proteomics experiments toward statistically powered, targeted experiments aimed at measuring biological pathways relevant to diabetes and metabolism.
This structure is designed to leverage our state-of-the-art approaches to these -omics technologies at both UCLA and UCSD, while addressing the NIH’s guidelines for improved rigor and transparency. The TPAC consolidates mass spectrometry –omics experiments within a single core, with lipidomics led by Oswald Quehenberger at UCSD and proteomics led by Julian Whitelegge at UCLA.
The heart of the core will be the user interface that will provide DRC investigators consultation with highly experienced core directors and custom experimental options that go far beyond the typical capabilities of institutional fee-for-service facilities.
We thus anticipate a three-phased process in which investigators first seek advice on entry level experiments, followed by design of quantitative discovery experiments in experimental systems to identify relevant pathways, finally leading to targeted measurements in translational settings, according to the following aims:
- Provide a user interface. Central to the TPAC will be the user interface led by Julian Whitelegge at UCLA and Oswald Quehenberger/Edward A. Dennis at UCSD. These scientists have been involved in high-throughput mass spectrometry-based –omics since the field arose. Efforts at both institutions have evolved with the field, gaining vast experience working on a diverse group of projects with a variety of collaborators. The Core will guide DRC investigators through discovery experiments toward statistically powered, targeted mass spectrometry suitable for translation to the clinic. The Core will promote interactions and synergy between investigators from San Diego (UCSD and the Salk Institute) and Los Angeles (UCLA, LA Biomed and Cedars-Sinai), as well as between other DRC Biomedical Cores, particularly the Genomics and Epigenetics Core at UCSD and the Metabolic and Molecular Physiology Core at UCLA.
- Provide sophisticated discovery services. The TPAC core will provide a variety of mass spectrometry –omics experiments covering quantitative discovery lipidomics and proteomics. The TPAC will accept samples from exploratory studies in patients, mice and cells, using serum and tissue samples and cells generated/obtained by DRC investigators. Experiments will be designed in consultation with the TPAC leadership, and resulting samples treated expeditiously, with rapid turnover at a discounted cost subsidized by the core. Guidance with data interpretation and bioinformatics will be achieved in consultation with the core and other resources at the UCSD and UCLA campuses. The goal is to illuminate the most important pathways in the experimental state under investigation.
- Provide DRC investigator-driven quantitative assays of molecular pathways relevant to diabetes and its complications in human and animal-model tissues and cells. Successful achievement of aims 1 and 2 will yield selected panels of lipids and proteins that report upon pathways, readying investigators to scale experiments to the next level. Targeted measurements of chosen molecules and pathways will be performed with internal standards to yield actual concentrations within experimental samples, rapidly performed such that larger cohorts can be analyzed to improve statistical power. The goal will be for these targeted pathway analyses to be suitable for translational assays for use in clinical investigation.