Metabolomics and Exposome Core

Core Overview

The Metabolomics and Exposome Core located at the Nutrition Research Institute (NRI) encourages collaborations that promote the use of untargeted and targeted metabolomics in basic, clinical, and translational research focused on environmental health, and precision nutrition. The measurement of perturbations in metabolism that arise from disease, dysfunction, or exposure (e.g., chemicals, drugs, nutrients, foods, stress) is referred to as metabolomics. The measurement of all exposures and the impact on endogenous metabolism is referred to as the Exposome.

Metabolomics involves the analysis of the low molecular weight complement of cells, tissues, or biological fluids, and makes it feasible to profile (metabotyping) the biochemistry of an individual or system. The untargeted metabolomics profile includes signals for endogenous compounds (that map to biochemical pathways), as well as signals of exogenously derived components (e.g., chemicals, drugs, nutrients), enabling biomarker discovery and providing mechanistic insights for medical and nutritional applications, as well as environmental research.

The use of metabolomics in precision medicine often involves the development of biomarkers to detect, stage, and monitor disease, as well as the study of how individuals respond to drug treatment. Similarly, in the field of precision nutrition, individuals have different nutrient requirements, and individuals respond differently to nutrient intake. Individuals also have many types of exposures to drugs, chemicals, and foods that can cause metabolic perturbations. Genetics, polymorphisms, and metabolic individuality can all contribute to the adverse or positive responses of an individual - and the intersection between genomics, metabolomics, and the environment (e.g., foods, nutrients, chemicals, drugs, lifestyle) comprises the focus of the Metabolomics and Exposome Core at the NRI.

The NRI Metabolomics and Exposome Core uses a variety of quantitative targeted analytical methods, and untargeted metabolomics for the simultaneous detection of signals derived from endogenous compounds (i.e., those known to map to biochemical pathways) and exogenous compounds (e.g., drugs, chemicals, and nutrients).

This core is directed by Dr. Susan Sumner who has served as the PI/Director of the NIH Common Fund Eastern Regional Comprehensive Metabolomics Resource Core since 2012, and the Director of the untargeted analysis core for a NIEHS-funded Children's Health Exposure Analysis Resource Hub since 2016.

Untargeted Metabolomics and Exposome Sub-Core

We have developed a number of platforms to use for the study of endogenous and exogenous compounds that represent the metabolome and the exposome.

The Untargeted Metabolomics and Exposome Sub-Core provides:

Expert opinion related to study design, sample selection/collection and storage, proposal review and development, manuscript development and review.

Untargeted analysis using a variety of analytical methods:

Ultra High Performance Liquid Chromatography (UPLC) coupled with Mass Spectrometry
- The core uses a variety of orbitrap (Orbi), and time of flight (TOF) mass spectrometry systems for the detection of signals following separation by UPLC.
- These UPLC-MS untargeted methods enable the detection of tens of thousands of signals associated with the metabolome/exposome.
- Metabolites are assigned through matching retention-time (RT), Mass (MS), and MS/MS to in-house library established under conditions identical to the methods used for analysis of the study samples.
  - Our core has a retention-time, MS, MS/MS library with approximately 600 endogenous compounds, 130 environmentally relevant chemicals, and 30 medications and illicit drugs.
  - This library grows as we work with collaborators to obtain standards and identify signals associated with the metabolome/exposome.
- Signals that do not match to our in-house libraries are annotated through the use of literature and publicly available external libraries.
  - We are using innovative methods for peak picking and big data analytics to annotate signals.

Nuclear magnetic resonance (NMR) spectroscopy

NMR is a highly reproducible metabolomics platform with exceptional longitudinal stability. NMR can detect, with semi-quantitation, hundreds of signals. Signals are assigned to metabolites through library matching, and using the structural information provided by the NMR chemical shift and coupling patterns.

Targeted Metabolite Analysis

Quantitative targeted analysis of 188 endogenous metabolites (acylcarnitines, amino acids, biogenic amines, hexoses, phosphatidylcholines and sphingolipids) is conducted using the Biocrates Absolute IDQ p180 Kit and LC-MS/MS.
NMR is used to quantitate targeted analytes – such as those know to derive from microbial metabolism.
Additional targeted assays including choline, betaine, phosphatidylcholine, sphingomyelinin, phosphocholine, and glycerophosphocholine, dimethyl-glycine, TMAO, or creatinine are available through the Targeted Metabolic Profiling Sub-Core.

High-throughput, relative quantitation analysis using the RayBiotech array to acquire data for 42 or 80 cytokines in human samples, 62 cytokines in mouse samples and 34 cytokines in rat samples.

Specialized set-up for quantitative targeted analysis

Statistics and Multivariate Data Analysis is used to identify patterns and data trends that show the association of signals with phenotypic responses under investigation. These methods include supervised and unsupervised multivariate analyses, descriptive statistics, hypothesis testing and modeling (e.g., linear and logistic regression, structural equation modeling, random forest models).

Pathway Analysis is used to map identified signals to biochemical pathways via specialized software, and expert biochemist interpretation.

Targeted Metabolic Profiling Sub-Core

The Targeted Metabolic Profiling Sub-Core is focused on quantitative LC-MS assays related to 1-carbon metabolism:

Choline, phosphocholine, glycerophosphcholine, betaine, dimethylglycine, phosphatidylcholine, sphingomyelin, and TMA/TMAO in various combinations. These metabolites can be measured in plasma, urine, breast milk, and foods (LC-MS/MS).

S-adenosylhomocysteine (SAH) and s-adenosylmethionine (SAM) in tissue samples, and homocysteine in plasma (LC-MS/MS).

Total folate using a biological method.

Tissue BHMT enzyme activity in a radiological assay.

The Core also has cell sorting capabilities using a BD Aria III fluorescence activated cell sorter (FACS). Sorts can be optimized for purity, yield or single cell modes, into 2 or 4 tubes. The Aria III is equipped with blue (488 nm), green (561 nm), red (633 nm) and violet (405 nm) lasers with 11 detectors allowing for forward scatter (FSC), side scatter (SSC) and up to 10 colors.

A Zeiss Axio Imager A1 microscope and camera are available for hourly rental. This microscope has brightfield, darkfield, differential phase interference contrast (DIC), polarization contrast (PO) and fluorescence capabilities.

Leadership and Staff

Name	Role	Phone	Email	Location
Susan Sumner, PhD	Director, Metabolomics and Exposome Core	(704) 250-5066	susan_sumner@unc.edu	Kannapolis, NC
Steven Zeisel, MD, PhD	Director, Targeted Metabolic Profiling Sub-Core	(919) 843-4731	steven_zeisel@unc.edu	Kannapolis, NC
Susan McRitchie	Core Manager, Untargeted Metabolomics and Exposome Sub-Core	(704) 250-5067	susan_mcritchie@unc.edu	Kannapolis, NC
Sunil Hwang	Core Manager, Targeted Metabolic Profiling Sub-Core (Kannapolis)	(704) 250-5041	sunil_hwang@unc.edu	Kannapolis, NC
Qing Shi	Core Manager, Targeted Metabolic Profiling Sub-Core (Chapel Hill)	(919) 966-7162	qing_shi@med.unc.edu	Chapel Hill, NC

Location and hours of operation


NRI Metabolomics and Exposome Lab	500 Laureate Way, Kannapolis, NC 28081
8am-5pm M-F

Links and Resources

Contacts

Name	Role	Phone	Email	Location
John Easterbrook	NORC Managing Director	(919) 962-0948	john.easterbrook@unc.edu	Chapel Hill, NC