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