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Outreach and Education Core


Overview

Despite rapid advances in metabolomics technologies and the need for understanding the human metabolome, metabolomics applications in biomedical research remain limited. This is partly due to the combination of lack of awareness in the value of large-scale metabolic understanding, inadequate access to high end instrumentation, and a lack of experience in experimental design, sample handling/processing, and complex data analysis and biochemical interpretation. The purpose of this Core is to provide the proper outreach, training, education, and support to overcome most barriers to integrating metabolomics approaches into mainstream basic and translational research.

The facility offer an annual hands on Workshop that covers practical experience in sample preparation, data acquisitions and reduction, accompanied by overawes of analytical and theoretical principles by the Center Staff and invited experts. The Workshop is accompanied by a one-day Symposium in which cutting edge research is presented by leading practitioners, to demonstrate how metabolic studies can be integrated into basic and translational programs. The Center runs a Pilot Program as a means to acquire preliminary data to foster the use of metabolic studies as part of a research program. The Center develops methods and validates them as SOPs that are deposited at DRCC. Videos of many of the procedures used are also available for download. The Center welcomes visits by interested researchers at all levels.

What is Metabolomics?

Living cells are maintained under non-equilibrium conditions, which requires constant input of energy. The cells must also maintain their infrastructure, and perform tissue-specific tasks, all of which need energy and raw material. Metabolism is the set of processes that convert exogenous compounds to metabolic energy, which drives biochemical reactions within the cell, maintains homeostasis, provides the means to do work (e.g. contraction, movement, action potentials, secretion and so forth), for cellular repair, and to divide. Metabolism responds to exogenous signals as represented by diet and pollutants for example, and local environments (microenvironment) as represented by the conditions prevailing outside cells in tissues. As such, metabolism is a sensitive indicator of pathology.

Therefore, the ability to measure global metabolism in quantitative detail is of fundamental importance in all aspects of biology. Metabolomics provides the technical means to carry out global analyses of metabolism, by identifying and quantifying a large fraction of all of the metabolites present in a cell, and how they change in response to perturbations within relevant metabolic networks. Metabolomics therefore requires high-end analytical instrumentation, of which mass spectrometry and NMR together are the most appropriate technologies. Informatics is the third critical component of metabolomics to interpret the observations in a biological context. Careful sample preparation and processing is the often overlooked first critical component in metabolomics, which is necessary to prevent excessive perturbation and degradation of the observed metabolites. And appropriate experimental design and adherence to this design is the zeroth critical component of metabolomics.

Other Definitions and Descriptions

What is Stable Isotope-Resolved Metabolomics (SIRM)?

Global metabolomics, the quantification of a large number of metabolites in tissue or biofluids can identify disease states or response to therapeutics by reference to the normal condition. However, determining specific mechanisms, such as detecting which pathways are impacted in particular cell types within a tissue by measuring metabolic fluxes, requires additional information as many metabolites are present in different amounts in different cell types or within compartments of cells, as well as participating in several pathways simultaneously. To identify the precursor-product relationships, it is necessary to distinguish different sources of carbon, nitrogen etc. which necessitates some means of “labeling” individual atoms so that their fate can be traced through metabolic pathways. Traditionally this was achieved using radioisotopes. However, stable isotopes have several advantages, including being wholly biocompatible, and also individual atoms within a metabolite are easily distinguishable by NMR and mass spectrometry.

The general approach we have developed, which we call Stable Isotope Resolved Metabolomics or SIRM, combines the power of global (untargeted) metabolic profiling with atom-resolved tracking of metabolites during metabolic transformations within cells, tissue or whole organisms. The cell culture, tissue, or organism is provided with a source metabolite that is enriched at any or all of the atoms with a stable isotope (like 13C or 15N with natural abundances 1.1 % and 0.37%, respectively), and the products are analyzed by NMR and MS at different times after treatment. The specific isotopomer and isotopologue distributions in the various product metabolites are determined, along with the total amounts of the metabolites, which together provide detailed information about the relative importance of intersecting and parallel pathways. For example, lactate can be produced directly from glucose by lactic fermentation, as well as by glutaminolysis; the relative contributions from these independent pathways is readily determined from the isotope distributions in the lactate using either 13C-enriched glucose or glutamine as labeled sources. At the same time such labeling schemes provide simultaneous information about the flow of carbon through the pentose phosphate pathway, glycolysis, hexosamine pathway, the Krebs cycle and lipid biosynthesis among others.

Pilot and Feasibility Grants

The purpose of the Pilot and Feasibility Grants is to promote the use of stable isotope-resolved metabolomics in the broader research community via the use of this Center. They are specifically designed to support projects that will provide preliminary data for new extramural grant proposals that incorporates metabolomics into new areas of biomedical research. The expected outcome is to broaden the use of metabolomics in the broader research community and to foster collaborations and partnerships with the Center.

Courses

* New online courses are being developed for the Graduate Program in Toxicology at the University of Kentucky.
  • Training videos are available here.

Older Courses

  • CHEM 648 - Systems Biochemistry: Principles and Practices, Dept. of Chemistry, University of Louisville
  • CHEM 652 - Practical Approaches to Metabolomics, Dept. of Chemistry, University of Louisville
  • CHEM 528 - Contemporary Methods of Synthesis and Analysis I, Dept. of Chemistry, University of Louisville

Symposia, Workshops, and Seminars

2007_metabolomics_symposium_group_photo.jpg
Group photo for the 2007 Metabolomics Symposium

Upcoming Events

Prior Events


Outreach

Visiting Researchers

Developing research scientists of all levels are welcome to work side-by-side with the Center's core faculty and staff learning Metabolomics techniques and applying them to their particular research interests. Students and junior faculty from laboratories across campus, around the state, throughout the nation and from around the world contribute to the interdisciplinary cross-pollination of ideas that is a very important objective for the Center. Please contact us for opportunities to visit.

Recent contributions have been made by the following:
  • Marilia Dias- Sao Paulo. shRNA of enzymes for SIRM studies in cancer cells.
  • Dan Crooks-NCI Bethesda. Metabolomics of SDH mutant kidney cancers
  • Nicola Consolini-U. Bologna
  • Katarina Fritz-Graz, Austria. SIRM studies of ATGL
  • Sandra Gomes - Sao Paulo. Sample preparation for SIRM studies of glutaminase C in cancer cells.
  • Scott Jones – Medicine at University of Louisville. Natural products involved in pre-Parkinson’s disease symptoms.
  • Anne Le - Johns Hopkins University. SIRM analysis of MYC expression in cancer cells.
  • Santiago Moralli – University of Barcelona. High-throughput metabolite analysis, specifically the study of the lipidome and its changes during cell cycle progression and tumor transformation.
  • Jason Podrabsky - Oregon State. GC-MS analysis of killifish embryos.
  • Miriam Porquet – University of Barcelona. Study of metabolic and lipid profiles of mouse embryogenic fibroblast cell lines using LTQ FT MS and GCMS techniques and software to describe the metabolic importance of the lack of two key enzymes (CDK4 and CDK6) in the cell cycle.
  • Chris Ricketts and Youfeng Yang - NCI SIRM studies of metabolic reprogramming in fumarate hydrate null cells
  • Pankaj Seth - Beth Israel Deaconess, Boston. SIRM analysis of LDH-A knockdowns in cancer cells.
  • Mariia Yuneva – University of California, San Francisco. Molecular regulatory mechanisms of the MYConcogene in mammalian cells.

Undergraduate

Kathleen_Marshall_in_Fan_Lab.JPG
Kathleen Marshall in Fan Lab
Undergraduate students participate in all aspects of research including conducting their own projects, developing analytical methods, and preparing platform and poster presentations.



Students mentored by Center faculty:
Student Project Dates Home Town Mentor
Alex Belshoff Arsenic Detoxification: Inhibition of Glutathione Production Results in Increased Arsenic Accumulation June 2007-May 2008 Louisville KY Teresa Fan
Sabine Dhakal   June-Oct. 2007 Nepal Teresa Fan
Kathleen Marshall   June 2007-May 2008 Leitchfield KY Teresa Fan
Mark Capece   2008 Davis CA Teresa Fan
Ben King   2008   Teresa Fan
Patrick Mullaney   2008-20012 Louisville KY Hunter Moseley
Abigail Hoskins   2008-2012 Floyds Knobs IN Hunter Moseley
Timothy Cook   2008-2011 Paducah KY Hunter Moseley
M. Habib Energy metabolism in rat skeletal muscle Summer 2008   Andrew Lane
Martin McKinney Stable Isotope Resolved Metabolomics Analysis of Ribonucleotide and RNA Metabolism Summer 2008   Andrew Lane
Sabrina Shatzman   2009-2012   Teresa Fan
G. Bousamra P-31 NMR based energy metabolism in rat tissue Summer 2010 Louisville KY Andrew Lane
Joshua Mitchell Developing Computational Tools for Molecular Comparison and Metabolic Placement of Detectable Uncharacterized Metabolites 2010-2012 Frankfort KY Hunter Moseley
Rima Patel   2010-2011 Louisville KY Hunter Moseley
Craig Clemons   2010-2013 Fairdale, KY Hunter Moseley
Zelalem Mekonnen   Summer 2011   Teresa Fan
Austin McCuiston Lipidomics of Microvesicles in Human Lung Cancer Cells for Cancer Detection Summer 2011   Andrew Lane
Joshua Mabrey   Fall 2011 Bardstown KY Hunter Moseley
Elizabeth Lorch   2011-2012 Park Hills, KY Hunter Moseley
Andrew McCollam   2011-2013 Floyds Knobs IN Hunter Moseley
Eugene Hinderer   2011-2013 Greenville IN Hunter Moseley
John Taylor Hans   2011-2013 Louisville, KY Hunter Moseley
Annabelle Carrell   2011-2013 Crescent Springs, KY Hunter Moseley
Arren Carter   2011-2013 Columbus, OH Hunter Moseley
L. Cornwell Exosomal lipid analyses in cancer 2011-2013 Louisville, KY Andrew Lane
Indraneel Reddy   2013 Louisville, KY Hunter Moseley
C. Kinslow SIRM analysis of primary human NSCLC cells 2013 New York, NY Andrew Lane
Tamas Nagy   2014-2015 Lexington, KY Hunter Moseley
Michael Yurek   2014-2015 Lexington, KY Hunter Moseley
Yvonne Johnson   2014-2015 Louisville, KY Hunter Moseley
Ashir Amin   2014-2015   Hunter Moseley

Undergraduate Seminars

Center faculty give metabolomics presentations tailored specifically for undergraduate students to promote a broader dissemination of the field and what it has to offer for future scientific careers.
  • October 2007- North Eastern Illinois University: Andrew Lane " Biological Chemistry: Structure, Thermodynamics and Function "
  • Fall 2010 - Berea College: Dr. Teresa Fan presenting "Metabolism: Old or Gold?".
  • Fall 2010 - Huntingdon College: Dr. Hunter Moseley presenting "Metabolic Modeling of Converging Metabolic Pathways. Analysis of Non-Steady State Stable Isotope-Resolved Metabolomics of UDP-GlcNAc and UDP-GalNAc."
  • August 2011 - Summer Student Program, JG Brown Cancer Center: “Clinical Applications of Stable Isotope-Resolved Metabolomics (SIRM) in Non Small Cell Lung Cancer”. Andrew Lane
  • July 2012 - Summer Student Program, JG Brown Cancer Center: “Understanding Cancer Through Metabolism”. Andrew Lane
  • June 2013 - NCI R25 Cancer Education Program, JG Brown Cancer Center: Dr. Hunter Moseley presented "The Omics Era".

High School

High School students participate in many aspects of our metabolomics research efforts to promote early interest in science. Many use this opportunity for senior science projects and present their efforts at regional science fairs.

Students mentored by Center faculty:
Student Grade Title of Poster/Award Date Ethnicity Mentor
Doug Lattimore High School Electrophoretic separation of proteins March 12 2005 African American Teresa Fan
Patrick Oechsli Junior High Cancer Cell Response to Selenium March 12 2005 Caucasian Teresa Fan
Li Zhang High School The Effect of Zinc on Rate of Fermentation March 11 2006 Asian Teresa Fan
Nambi Arumugam High School Effect of Selenium on Breast Cancer Cells (HTB29) March 11 2006 Asian Teresa Fan
Nambi Arumugam High School The Effect of Cadmium on Lung Cancer Cells (A549) February 1 2007 Asian Teresa Fan
Monali Haldankar High School “The Effect of the Metabolic Inhibitors 2-deoxyglucose and Dehydroepiandrosterone on Glucose Uptake and Lactate Secretion in A549 Human Lung Adenocarcinoma Cells”
Regional and State Science Fair winner
Fall 2008 Asian Andrew Lane
A. Duan High School “The Effect of the Metabolic Inhibitors 2-deoxyglucose and Dehydroepiandrosterone on Glucose Uptake and Lactate Secretion in A549 Human Lung Adenocarcinoma Cells “
Regional and State Science Fair winner
Fall 2008 Asian Andrew Lane
Rodney Folz Jr. High School “Developing Computational Tools for Molecular Comparison and Metabolic Placement of Detectable Uncharacterized Metabolites”
James Graham Brown Cancer Center 10th Annual Retreat
2010-2011 Caucasian Hunter Moseley
A. Duan High School “Urine microvesicles from cancer patients as biomarkers” Fall 2010 Asian Andrew Lane
Alison Davis Junior High "The Lengths of the Proteins in the Collagen Family compared to the Number of Single Nucleotide Polymorphisms." 2011-2012 Caucasian Hunter Moseley
Camille Rougier Junior High   2012-2013 Caucasian Hunter Moseley
Genghis Goodman High School   2014-2015 Asian Hunter Moseley

Broader Community

Center faculty and staff have also participated in many local conferences with audiences ranging from secondary school teachers to environmentalists. These presentations serve to educate the community about the discipline of Metabolomics and offer the instructional services of the Center to the community it serves. The following is a partial list:
Topic revision: r16 - 18 Mar 2015, HunterMoseley
 

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