WEEK 8 - Multiomics in Personalised Medicine and Biomarker Discovery Flashcards
(18 cards)
What is the difference between Personalised and Precision Medicine
Personalised Medicine - tailor therapy for the right person at the right time using molecular profiling
- look at pt histopathology, cell surface markers, genome)
Precision Medicine - takes into account individual variability in genes, environment and lifestyle for each person disease treatment + prevention
What are biomarkers
What are the 5 characteristics of an ideal biomarker
WHAT?
A characteristic that can be objectively measured and evaluated as an indicator for:
- normal biological process
- pathological process
- therapeutic response
IDEAL BIOMARKER:
- Can be objectively measured
- Safe and easy to measure
- Cost efficient to follow up
- Consistent across gender + ethnicity
Example:
- Cholesterol (CVD)
- Blood sugar (Diabetes)
- Genes, proteins, metabolites
How have multiomics technologies contributed in biomaker discover, drug development and personalised medicine
Multiomics - Looking at ALL / >1 molecule (mulecular profiling)
- Multiomics is an approach that combines experimental data generated by different omics techniques computational approaches
4 Omics Technologies:
1. Genomics
2. Transcriptomics
- study of all RNA
3. Proteomics
4. Metabolomics
Technology Platforms Used:
- Mass spectrometery
- Sequencing platforms
- Computational approaches
What are genomics
Sequencing and analysing of organism’s genome (all genes / DNA)
Genome:
- Organisims entire DNA (ALL genes)
How are genomics applied in drug and biomarker discovery, development and validation
- Differences in drug response was linked to variations in genes metabolising drug
- Cancer = 1st area to develop from genomic revolution
Drug Development:
1. Identify condition
2. Link to gene
3. Understand function of gene
4. Identify protien produced by gene
- can be drug target / gene therapy
- OR diagnostic marker
What are protemoics
Large scale anlaysis / study of proteins in an organism
2 Types:
1. Clinical Proteomics - research focuesd on primary samples (direct from pt)
2. Translational Proteomics - Understanding how change / biomarker can be used clincally
How are protemoics applied in drug and biomarker discovery, development and validation
- Can be used to identify biomarkers, for diagnostics
Analysing:
- Use mass spectrometry
- can identify post-translational modif.
- Large proteins use gel chromatography
WHY Study Proteins
- They are involved in almost all cellular proccesses
- e.g. metabolism, transport, storage, toxins, protection, support, enymes
- Genomics doesn’t pick up post-translational modifications
- how protein modified after synthesis
What are metabolomics
Identifying / analysis of all metabolites produced by organism
- e.g. lipids, sugars, amino acids
Metabolites:
- Can be polar or non-polar
- Small MW (< 1500 Da)
- Can be organic or inorganic
NOTE:
- Genes (DNA) and transcriptis (mRNA) produce proteins, enzymes (proteins) produce metabolites
How are metaolomics applied in drug and biomarker discovery, development and validation
Provide overview of the metabolic status
- easier to analyse due to small size
- cheaper to conduct
- Its the final downstream of gene transcription = closest to phenotype being studied
- Metabolites not only affected by genetics but also environment
- e.g. diet, drugs taken, sleep, excercise, smoking, alcohol
ANALYSIS:
- Use mass spectrometry (MS)
- Liquid Chromatography MS
- Gas Chromatography MS
ISSUE:
- Metabalome is complex, dynamic process that changes with time (age, diet)
Untargeted Metabolomics vs Targeted Metabolomics
Untargeted Metabolomics a.k.a. Global Metabolic Profiling
Untargeted Metabolomics / Analysis
- Analysis of many metabolites
- Provides a snapshot of global metabolism
Targeted Metabolomics
- Analysis of specific metabolites
- Metabolite could be: molecule of interest, drug, nutrient markers
- Provides understanding of how drug works
Advanced bio-analytic methodologies: Mass Spectrometry and its applications
Inc. Process / MoA
Mass Spectrometry:
- A versatile, selective and sensitve analysis methof
- Used for protiens, lipids, suagrs etc
- Can be used with chromatograpy (for analysis)
- Can be automated + work without constant supervision
- Generates large data sets via computational approach
- Can identify post-translational proteins
MoA:
1. Sample introduced
2. Ionisation
- sample passes through ions
- e.g. ESI, MALDI (most common)
- ESI = electron spray ionisation
- others: EI, CI, APCI
3. Analyser
- seperates ions based on mass
- inc. ToF, quadrupole, ion trap
4. Array of Ion Detectors
- take electronic signal produced + give us info
5. Data system = Data output
- links output to protein structure
How does ESI work
Mass Spectrometry - Ionisation Process
ESI - Electron Spray Ionisation
- Sample is sprayed with droplets containing ions
- Ions evaporate from surafce of droplets
- Ionisation of the metabolite / sample
NOTE:
- Used for metbaolites
- e.g. amino acids, lipids
- Soft ionisation method (ions are NOT destroyed)
- can be used with column chromatography
How does MALDI work
Mass Spectrometry - Ionisation Process
MALDI - Matrix Assisted Laser Desorption Ionisation
- Mix metabolite in organic matrix
- Matrix surrounds metabolite
= more suceptible for mass spectrometry - Irradation of matrix-metabolite complex
- Released complex is ionised
- Enters mass spectrometer
NOTE:
- Used for insoluble metabolite that can’t go through liquid chromatography
Time of Flight (ToF) MoA
An analyser method
Time of Flight - gives info about molecule size, properties
- Ions are sent through magnets + accelerated to have the same kinetic energy
- Ions travel through a vaccum + lan on detector
- Time taken produces a peak
- peak depends on mass of molecule
- heavier = land first
- lighter = travel further
Liquid Chromatography (LCMS)
Type of Mass Spectrometry (MS)
Separates molecules depending on affinity to polar liquid solvent
- Start with low organic (polar solvent)
- Increase solvent content
- As ↑ solvent some molecules dissociate from stationary phase + flow through column
- By point of high organic content = most molecules will be in mobile phase
Gas Chromatography MS (GCMS)
Type of Mass Spectrometry (MS)
Use temp. to separate molecules
- At low temp. most moelcules would in stationary phase
- Intermediate temp. = some molecules stationary and other moving with carrier gas
- Higher temp. = most molecules moving through column with carrier gas
What locations can biomarkers be identfied from
- Blood / Plasma / Serum
- Accessible, can be routinely collectec
- Levels affected by diet, huge range
- Plasma: albumin = majority of protein presence + hard to isolate protein biomarkers - Urine
- Accessible, routinely collected
- Conc. affected by time of day + fluid intake - Tissue
- Site of disease
- Inaccessible, harder to monitor - Cerebrospinal Fluid (CSF)
- Inaccessible, invasive, hard to monitor
What are the challenges in developing and validating biomarkers
In Personalised Medicine
- Limited understanding of genetic, molecular and cellular mechanisms for diseases
- Other omics (exc. genomics) need more development
- Genomics need larger scaled studies to validate biomarkers
- Bio-banking is expensive
- collection of UK residents health data
- Require training for researchers, HCP, regulators
- No clear identification of what a healthy individual is (for analysis)
