Lecture 9 - Metabolomics Flashcards
Define:
• Metabolomics
• Metabolome
Metabolomics:
• Quantitative analysis of all small molecules in a biological system
Metabolome:
• Full complement of small molecules in a sample
Describe the updated view of metabolism
- Genome
- Transcriptome
- Proteome
- Metabolome
Compare primary and secondary metabolites
Primary: core constituents in metabolic pathways
Secondary:
• small peptides etc.
What are the challenges in metabolomics?
- Integreation of non-linear networks
- 2,000 - 200,000 metabolites
- Extreme range of concentrations
- Do amplification technologies for metabolites
- Great rates of flux (i.e. changes very quickly)
What are the various platforms for metabolomics?
NMR:
• Nuclear magnetic resonance imaging
GC-MS:
• Gas chromatography mass spectrometry
LC:
• Liquid chromatography MS
Imaging MS
Describe the metabolic analysis pipeline
- Sample preparation
• Serum, saliva, etc - Sample extraction
- Sample analysis
• GC-MS
• LC-MS etc - Data analysis
Describe how metabolic analysis of single cells is performed
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How many metabolites have been identified in the human body?
2,900
i.e. almost 3000
List some applications of metabolomics
- Systems biology
- Diagnostics
- Therapeutics
- Toxicology
- Microbiology
etc.
Describe how metabolites can be used as biomarkers for health and disease
Metabolites have been identified as biomarkers of early stages of disease
These can be tested for to determine if an individual will get a disease before it becomes evident
The power of this will be to start therapy before irreversible damage has occurred
e.g. Alzheimer’s
• Recently a group in America have identified a metabolite (plasma phospholipids) that is a marker of early stage AD
• Levels were elevated in those normal controls that went on to develop AD over the course of the study
Describe the process of tissue imaging with MS
Describe the applications of this
- Frozen or chemically fixed tissue sections prepared
- Coating with chemical matrix
- MALDI-MS or DESI-MS performed:
• Laser directed at tissue
• Ions are excited and emitted from the tissue
• MS detector detects these ‘analyses’
• DESI-MS is the same, but does not need to be performed at high vacuums, rather at ambient pressure
Results:
• Spatial mapping of 1000’s of individual metabolites
Application: • Portable devices: • Rapid microbial diagnosis • Testing for pesticides on surface of food • Diagnosis during surgery
Describe the process of stable-isotope resolved metabolomics
What is the application of this?
- Sample preparation
• Cultured cells
• Microbes
• Animals - Labelling with stable isotopes
• e.g. Carbon-13 in glucose / amino acids - Sample extraction
- Sample analysis
• GC-MS
• LC-MS - Data analysis
- Flux-network; generation of model
Application:
• Allows us to see turnover of specific molecule in a system
• ‘Real time’ capturing of a system
What is Toxoplasma gondii?
- Single celled eukaryotic pathogen
- Infects 1/3rd of world population
- Causes toxoplasmosis
- Most infections are asymptomatic
- Causes diseases in new borns, mothers and the immunocompromised
Infection:
• Extracellular tachzoite taken up into vacuole
• Replication
• Egress from host cell
What has metabolomics told us about T. gondii?
Through the use of stable isotope resolved analysis, it has been determined that T. gondii:
- There is an enzyme that is crucial for the metabolism of T. gondii
- This previously unknown enzyme could be a novel drug target
How can metabolomics provide insights into causes of cancer?
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