CPRIT Core Facility Support Award (CFSA) RP210227: Cancer Metabolomic and Proteomic Core Facility.
Introduction
The cancer research community increasingly recognizes that genomic and transcriptomic analysis alone are often insufficient for understanding the complexity and heterogeneity of cancer. Insights provided by additional proteomic and metabolomic characterization are required for identification of actionable therapeutic targets and response biomarkers applicable to precision oncology. Recent research has also demonstrated that stringent quality control, continuous management, and strong bioinformatics support are required for success of multiomics studies. To this end, we built the infrastructure and advanced technologies for comprehensive integration of all major omics on clinically relevant samples. We focus our efforts on processing and analysis of human tumors in PDXs and clinical investigational studies with the goal of supporting discoveries that more directly impact patient care.
Methods
The core performs splitting of frozen or OCT-embedded tissues, conducts sample quality control, and distributes samples to all technology platforms for profiling. Mass spectrometry-based proteomics includes TMT-based multiplexed methods for profiling of ~10,000 proteins and up to 25,000 phosphosites, and identification of protein interactions. A targeted proteomic RPPA (reverse phase protein array) platform provides sensitive quantification of ~250 proteins and phosphosites representing major oncogenic signaling pathways, and an epigenetic panel of 40 chromatin modifiers and 20 histone modifications. Metabolomics offers targeted assays for up to 700 known metabolites, isotopomer-based flux assays in cells and in vivo, unbiased lipidomics, and BioCrates platform. Bioinformatics tools includes workflow pipelines for management and analysis of large omics data sets and for integration of data sets across different omics platforms.
Results
Over the past five years we have supported more than 400 cancer projects and 100 publications for ~150 laboratories. Several technology development studies were also published independently by the core. We support numerous grant applications, resulting in 12-15 new awards per year with total annual funding of ~$19.5M. The types of basic discoveries by our omics platforms include identification of pathways involved in tumor progression, pathways and mechanisms associated with therapy resistance, identification of signatures for cancer subtypes, metastasis, EMT, and immune microenvironment, and identification of novel therapeutic targets and vulnerabilities. Our facility has optimized multiomics workflow, streamlined inter-facility communications, and standardized data organization and bioinformatics pipelines to provide proper sample-matched analysis. We demonstrate this workflow on a flagship project characterizing eight new PDX models of bladder cancer and their matching patient tumor sources. We performed total RNA sequencing, whole exome sequencing, MS proteome and phosphoprofiling, BioCrates steady-state targeted panel of metabolites, and oncopathways by RPPA consistently across this cohort. The multiomic analysis highlighted conservation of profiles from patient samples to the established PDXs. We are now exploring these data to propose testing specific targetable vulnerabilities such as an overactivity in kinase cascades supported by multiple omics.
Conclusion
To support high quality basic cancer research projects for a broad range of investigators, our core has standardized microscaled methods and workflows for collection and processing of preclinical PDX models and human cancer specimens under conditions appropriate for application of multiomic analysis from the same sample. Our integrated technology network of four primary and several collaborative BCM Advanced Technology Cores creates a unique opportunity for single-source approach in comprehensive characterization of the genomic, transcriptomic, proteomic, and metabolic environment of human tumors.