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An Introduction to Genomics
and Proteomics
Bo LönnerdalProgram of International & Community Nutrition
University of California, Davis
What is Genomics?
Techniques:
Northern blots
In situ hybridization
Microarray
Microchip
The study of genes and non-coding sequences of DNA in organisms
(transcriptomics)
Genomics marked the beginning of a new age in biology and
medicine
1900
1953
1977
1980
1983
1990
1994-98
1998
2000
2005
Watson and Crick identify DNA(the double helix) as the Chemical basis of heredity
DNA markers used to map human disease genes to chromosomal regions
Human Genome Projects (HPG) begins-an international effort to map and sequence all the genes in the human genome
DNA markers used to map human disease genes to chromosomal regions
Release of Human Genome Project
Sanger and Gilbert derive methods of sequencing DNA
Huntington disease gene mapped to chromosome 4
Genetic and physical mapping
Working Draft of the human genome sequencing complete
Rediscovery of Mendel's laws helps establish the science of genetics
Source: Health Policy Research Bulletin, volume 1 issue2, September 2001
Understanding traits, in particular diseases,
some inherited diseases results from the
change of 1 base in a DNA sequence
A screening process covering thousands of
potentially affected indicators of nutritional
status simultaneously
Biomarker discovery
Why study Genomics?
Samples? RNA needed !
Tissues (biopsies, placenta, PBMCs)Quick separation to minimize RNAse activityStorage at -80 C (+ RNAse inhibitors)
This has restricted the use of genomics in nutrition intervention studies
Mathematical tools
1. Normalization
2. Hierarchical clustering
3. Heat maps
4. Pathway analysis
Heat Map showing Hierarchical Clustering results
Genes are up- or down-regulated
FormulaVs
Breast-fed
Major Functions of Differentially Expressed Genes
• Cell cycle regulation
• Cytoskeleton remodeling• Cell migration
• Cell adhesion• Barrier function
• Immune response
• Signal transduction• AKT• PKC
Apoptosis
Cell cycle progression
Immune response
TranscriptionCell motility, structure and integrity
Cell adhesion
Trafficking
Matrix assembly
Metacore Gene PathwayFormula
VsBreast-fed
Red is up, Blue is down
Wnt Signalling
Signaling TranscriptionFactor
What is proteomics?The global analysis of the complete complement of proteins that make up a cell, tissue or body fluid
Why study proteomics?The genome/transcriptome is not sufficient to model and predict biological systems
Post-transcriptional modifications such as phosphorylation, proteolytic cleavage, etc. often regulate protein activities
The quantity of protein in a cell, tissue or organism is not always regulated by mRNA. Instead, translation and degradation play critical roles in determining the abundance of protein
Major applications of Proteomics
1. Proteome profiling (large scale identification of proteins
2. Comparative proteomics (quantitative proteomics)
- target identification and biomarker discovery
3. Functional proteomics
- antibody arrays to monitor proteins involved in various functions, e.g. the immune system
Process for proteomics
Protein separation
-- gel based, liquid chromatography (LC) based
Mass spectrometry
-- MALDI/TOF, MS/MS
Bioinformatics --- protein sequence database
-- SwissProt, NCBI
Sample preparation required
Remove major proteins (e.g. serum albumin, immunoglobulins, transferrin)
Concentrate minor components
Two-dimensional gel electrophoresis
MS analysis
Antibody arrays
Good for low-abundance proteins known to be involved in functions, e.g. cytokines/immune function
Predictions
In nutrition studies, transcript level changes are more subtle, yet significant, but the number of affected genes is often surprisingly high, turning interpretation into a real challenge. Therefore, data will need independent confirmation by assessing protein levels (proteomics).
Will be used considerably more in biomarker discoveryWill be used more for evaluations of outcomes, possibly coupled with phenotyping