Research Support Core for the Superfund Research Program

The Research Support Core will provide a wide range of high quality quantitative analytical services and stringently validated data, spanning diverse platforms such as metabolomics, epigenomics, and transcriptomics. The RSC leader is Dr. Dean Edwards, executive director of the BCM Advanced Technology Cores. This is a centralized facility that included matching institutional support of Cancer Center Shared Resources as matrix cores to fulfill the needs of both the Dan L Duncan Comprehensive Cancer Center and the Institution and minimize duplication of cores.

Dr. Edwards is also primary investigator of a CPRIT (Cancer Prevention and Research Institute) supported Cancer Proteomics and Metabolomics Core Facility, which provided funds for major expansion of the Cancer Center Proteomics Shared Resource and for start-up of the new Metabolomics Shared Resource. The co-leader is Dr. Nagireddy Putluri, who serves as technical director of the BCM Metabolomics core, and is a leader in the development of metabolic profiling and metabolic flux analysis.

To train investigators in designing, executing, and interpreting results of the state-of-art analytical techniques. RSC will commit to training and improving the capabilities of the Superfund investigators and trainees, and of the scientific community at large at Baylor College of Medicine and Rice University.

This core will establish a research support core that will be a central resource for metabolomics, transcriptomics, and proteomic studies, and RSC investigators will also collaborate with environmental science projects The goal is to support the Superfund projects with cutting edge quantitative profiling technologies, which includes: RNA-seq, metabolomics, reverse phase protein arrays (RPPA), and mass spectrum based proteomics.

Genomic and RNA Profiling Core (GARP): The Genomic and RNA Profiling Core provides researchers access to state-of-the-art genomics profiling technology and services including Next-Generation Sequencing on Illumina platforms (iSeq 100, NextSeq 500 and NovaSeq 6000) and the Nanostring nCounter technology for targeted gene interrogation. Our library prep automation system (SMARTer Apollo) enables us to process low- and high-throughput projects with minimal batch effects. Also available are automated DNA size selection on the Pippin HT and nucleic acid shearing on the Covaris LE220. GARP serves as a source for sample quality control, experimental design and NGS expertise.

Metabolomics Core: The Metabolomics Shared Resource provides various metabolomic procedures for discovery and validation of small molecular weight compound biomarkers of various diseases with state-of-the-art high mass spectrometry as the main technology platform. Services include quantitative targeted steady-state analysis of metabolites (up to 500 metabolites) for a wide range of analyte classes derived from biofluids, cell lines or tissues. Services also include measurement of flux in cell lines and in mice through various metabolic pathways by 13C-isotopomer methods, structural identification of unknown molecules and unbiased lipidomics profiling.

Mass Spectrometry Proteomics Core: The Mass Spectrometry Proteomics Core features state-of-the-art Thermo Scientific Orbitrap instruments (Lumos ETD Tribrid, Q-Exactive Plus, Fusion Tribrid, Explorer 480) and offers comprehensive service packages for proteome-wide label free quantitative profiling of cells and tissues, isolation and identification of protein complexes via immunoprecipitation and other affinity methods followed by mass spectrometry, post-translational modification analysis, and routine protein identification from purified samples. Full support is provided that includes project evaluation and design, biochemical purifications, mass spectrometry sequencing, and data analysis. 

Antibody-Based Proteomics Core: The Antibody-Based Proteomics Core provides highly customized services for targeted proteomics platforms that are valuable tools for both validation and protein biomarker discovery, particularly for low abundance regulatory proteins and activation states of proteins with phosphorylated antibodies. Services provided include reverse phase protein arrays (RPPA) with over 240 antibodies for total and phosphoproteins of major cell signaling pathways, and Luminex bead technology for multiplex quantitative analyses of intracellular and extracellular signaling proteins.