Our story
New technologies can challenge how we see the world — opening doors to the study of previously impenetrable scientific problems and inspiring breakthroughs. At the same time, the latest instrumentation cannot displace thoughtful experiment designs that test scientific hypotheses. Our group brings both aspects together, creating a space where leading-edge technology draws in people dedicated to undertaking the most challenging and rewarding science: a space for discovery.Established in 2012 with a gift of $10 million from the Marron family, the Donald B. and Catherine C. Marron Cancer Metabolism Center at Memorial Sloan Kettering is one of those spaces. This initiative focused on understanding the many ways cancer cells tap into the body’s supply of nutrients to fuel their growth, and it has provided the infrastructure necessary to uncover fundamental insights into cancer’s behavior and vulnerabilities. The group has since grown into a self-sustaining scientific enterprise within MSK and enhances the work of research programs across the institution.
Lab Overview
As part of the Donald B. and Catherine C. Marron Cancer Metabolism Center, the Cell Metabolism core is dedicated to advancing the study of metabolism in cancer and other diseases. Our mission is to support investigators in their efforts to better understand complex biological systems by providing expertise in the direct measurement of small molecules— metabolites, which are key readouts of cellular and systemic processes. We collaborate with researchers on a diverse array of translational projects, ranging from dissecting the intricacies of cancer cell metabolism and host-gut microbiome interactions to mapping metabolic pathways in other various biological contexts.To achieve these goals, we leverage a suite of analytical technologies, including gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) platforms to navigate through various targeted and untargeted metabolomics questions that are customized to answer each research question. These complementary techniques enable precise measurement of a broad range of metabolites, offering key insights into metabolic pathways. This data can be utilized to uncover differential expression, identify potential biomarkers, and characterize metabolite structures.In addition to mass spectrometry-based approaches, we provide access and utilize non-MS technologies for measuring critical metabolic parameters, such as nutrient consumption, oxygen uptake, and other indicators of cellular bioenergetics. These tools enable a holistic view of metabolic activity in diverse experimental models.Beyond supporting research, the Cell Metabolism core is deeply committed to education and training. Over the years, we have contributed to educational programs designed to empower scientists to explore and creatively apply state-of-the-art metabolomics technologies. These have included workshops, hands-on training sessions, and collaborative learning opportunities aimed at building technical expertise and encouraging innovative approaches to scientific inquiry. By fostering creativity and providing a strong foundation in metabolomics, we aim to inspire a new generation of researchers and accelerate innovation in the field.For inquiries, or to learn more about our services, please contact Dr. Justin Cross, Core Director ([email protected])
Technologies
The Cell Metabolism Core is equipped with advanced analytical instruments for small molecule analysis, including multiple liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) systems. These platforms enable comprehensive metabolomics and lipidomics analyses, leveraging extensive libraries and databases of annotated compounds to ensure broad coverage and high-quality data for every sample.Our metabolomics and lipidomics workflows are designed to provide detailed profiling of metabolites and lipids across diverse biological systems. These analyses can be conducted in both targeted and untargeted modes, offering the flexibility to address hypothesis-driven research as well as exploratory studies. For specialized research questions, we also have the capability to customize or create panels tailored to specific biological pathways or processes, ensuring the analytical approach aligns with the goals of each study.
In addition to routine profiling, the Core supports stable isotope tracing, enabling detailed investigations of metabolic flux and pathway dynamics. Our untargeted approaches facilitate the identification of potential biomarkers and the discovery of novel metabolites and lipids, driving new insights into metabolic processes and biological mechanisms.True to our mission of fostering innovation, we routinely develop custom analytical methods to meet project-specific needs. Whether quantifying unique metabolites or designing entirely new workflows, we collaborate closely with internal and external researchers to provide tailored solutions that address their scientific challenges.
Nutrient Consumption
Our YSI 7000 enzymatic analyzer measures glucose, glutamine, and lactate levels in cell culture media and is used to determine cellular nutrient consumption rates.
Oxygen Consumption
Seahorse XFe96 and XFp Extracellular Flux Analyzers are available for the measurement of oxygen consumption and extracellular acidification.
Cell Growth and Viability
The ACEA xCELLigence MP provides the real-time measurements of cell proliferation and viability. A hypoxia chamber is also available for maintaining cells in low oxygen.
Sample Preparation
A variety of instruments and protocols are available for the homogenization of extraction of metabolites and lipids from cells, cell culture media, tissue, serum/plasma, urine and fecal material. A Gerstel MPS instrument is used to automate chemical derivatizations.
Gas Chromatography–Mass Spectrometry – Targeted
2 Agilent GC-MS systems with 5975 mass selective detectors are used to measure derivatized organic acids, amino acids, fatty acid methyl esters and short chain fatty acids, by relative and absolute quantitation, and using EI and CI ionization.
Liquid Chromatography–Mass Spectrometry – Targeted
The laboratory uses an Agilent 6230 time-of-flight (TOF) and 6545 Q-TOF LC-MS instruments for the relative quantitation of polar metabolites from cells, plasma and tissue extracts. Dedicated chromatographic methods are used for distinct chemical classes of metabolites including reverse phase, HILIC and ion pair methods. Our Thermo Vantage triple quadrupole LC-MS is used for the targeted quantitation of metabolites, including Acyl CoA profiling, cyclic nucleotides and modified DNA bases.
Untargeted metabolite profiling
Our Agilent 6550 LC Q-TOF and Agilent 7200 GC Q-TOF instruments are used for microbiome-related and lipidomic metabolite profiling. We use recursive feature finding workflows and multivariate statistical strategies in the analysis of large metabolomics datasets. We also integrate data from other ‘omic scale technologies, such as gene expression data and 16S ribosomal profiling of microbial communities, in order to generate hypotheses and inform future targeted experiments.
Isotope Tracing and Flux Measurements
Stable isotope tracing experiments using 13C, 2H and 15N stable isotope tracing, local flux calculations and IROA analysis are undertaken on a collaborative basis.
Analytical Pharmacology
Our AB SCIEX API 4000 with Shimadzu HPLC, fluorescence and UV detection is used for targeted quantitation small molecule pharmaceuticals. We generate supporting data for stage phase I/II clinical trials including DMPK studies, drug metabolite identification and bioavailability studies.