Lecture 9 - Metabolomics

Question 1

True or False

Metabolic defect nderlie nearly all disease, inlcuding many not traditionally associated with altered metabolism

Answer 1

true

Question 2

Most drugs and diagnostic biomarkers are small moelcule..

Answer 2

metabolites (or derived from)

Question 3

The key challenges of metabolism is how it is..

Answer 3

regulated in vivo

Question 4

The new view of how cells operate is ehat kind of lineage?

Answer 4

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

Question 5

Changes in the metabolome are not only representative of the upstream regulation events, but also…

Answer 5

extracellular factors - highly sensitive read out of the physiological state of the cell

Question 6

What is the definiion of metabolomics and metabolome?

Answer 6

the QUANTITATIVE analysis of all small molecules in a bio system

metabolome - the full complement of small moelcules in a sample

Question 7

what is a ‘small molecule”

Answer 7

<1500 daltons in size

Question 8

What are the challenges of sudying metabolites?

Answer 8

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

Question 9

What are some analytical platforms?

Answer 9

NMR

Gas chromatography
mass spectrometry
liquid chromatograhy
Imaging Mass -spec (used to iage frozen sections of tissue)

Question 10

What is the analysis pipeline for metabolomics?

Answer 10

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

Question 11

methods to see the single cell need to be high in what due to all the metabolites being taken at once?

Answer 11

mass accuracy - the ability to differentiate molecules of very similar mass

Question 12

What are the applications of metabollomics?

Answer 12

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

Question 13

What is needed in terms of AD diagnosis?

Answer 13

new biomarkers for preclinical disease diagnosis in order to develop disease modifying agents or preventative therpaies

Question 14

A study identified mulitvariate analysis, 10 metabolites that disgtinguished the pre-converted group from the controls, what did this lead to?

Answer 14

90% sensitivity of patients with these changes also showed AD signs in the following years

Question 15

What is tissue imaging mass spectrometry

Answer 15

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)

Question 16

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?

Answer 16

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

Question 17

Toxoplasma gondii infects 1/3 of world population - most are asymtomatic

what is special about its metabolism?

Answer 17

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

Question 18

True or false

Tissue imaging mass spectrometry can be used to measure metabolites in intact tissues (spatial information)

Answer 18

true