Lecture 9 - Metabolomics Flashcards
True or False
Metabolic defect nderlie nearly all disease, inlcuding many not traditionally associated with altered metabolism
true
Most drugs and diagnostic biomarkers are small moelcule..
metabolites (or derived from)
The key challenges of metabolism is how it is..
regulated in vivo
The new view of how cells operate is ehat kind of lineage?
genone - transcriptome - proteome - metabolome - phenotype
Lots of feedback within these levels
transciptome is what appears to be happening
proteome shows the functional capabilities
metabolome - shows the output of all of those interactions - close to phenotype
Changes in the metabolome are not only representative of the upstream regulation events, but also…
extracellular factors - highly sensitive read out of the physiological state of the cell
What is the definiion of metabolomics and metabolome?
the QUANTITATIVE analysis of all small molecules in a bio system
metabolome - the full complement of small moelcules in a sample
what is a ‘small molecule”
<1500 daltons in size
What are the challenges of sudying metabolites?
there are heaps
There are differences in concentration
Diverse chemistries - no amplication of the low molecualr weight in abundance with high sensitivity
There are very quick changes - ATP is used very quickly, hard to measure
Integration of the networks is very complicated
What are some analytical platforms?
NMR
Gas chromatography
mass spectrometry
liquid chromatograhy
Imaging Mass -spec (used to iage frozen sections of tissue)
What is the analysis pipeline for metabolomics?
prep the sample your interested - body fluids, hair, feces, cultured cells, microbes
Stop metabolism rapidly - super cooling
sample extraction
sample analysis 9NMR for instance)
Data analysis
methods to see the single cell need to be high in what due to all the metabolites being taken at once?
mass accuracy - the ability to differentiate molecules of very similar mass
What are the applications of metabollomics?
Fucntional genomics - enzyme function
Systems biology - new pthaways, regulation in vivo
Diagnostics - diseases
Bioengineering - improving plant/lifestock production
therapeutics/Toxicology - Drug metabolism
Microbiology - host / pathogen interactions
What is needed in terms of AD diagnosis?
new biomarkers for preclinical disease diagnosis in order to develop disease modifying agents or preventative therpaies
A study identified mulitvariate analysis, 10 metabolites that disgtinguished the pre-converted group from the controls, what did this lead to?
90% sensitivity of patients with these changes also showed AD signs in the following years
What is tissue imaging mass spectrometry
laser excited ions hat leave the tissue sampe and are detected by the mass spec.
new machines can do this at ambient temperature - can use it during surgery to identify a biomarker of cancer and work out how much to cut (depending on whether parts ave the biomarker or not)
steady state samples don’t tell you about the dynamics of what is making bio-products for instance
what is the next area trying to address this?
Stable-isotope labelling procedures
once labelled - you can extract the cells and analyse how much labelled isotope has integrated in to the cell and work out how much of it has turned over (i.e Carbon 12 replced with carbon 13)
folowing an increase in mass measures the turnover
Toxoplasma gondii infects 1/3 of world population - most are asymtomatic
what is special about its metabolism?
lacks a mitochondrial pyruvate dehydrogenase - hence was predicted to generate ATPP from glycolysis
BUT
found that TCA cycle intermedites were labelled with carbon13 - so there must be anther dhydrogenase that converts to acetly-cOA
Have now developed drug targets for this
True or false
Tissue imaging mass spectrometry can be used to measure metabolites in intact tissues (spatial information)
true
