Proteomics and Cancer
Transcript of Proteomics and Cancer
1
Proteomics and Cancer
Proteomics and Cancer
Vladimir Valera, M.D, PhDJSPS Postdoctoral fellow
First Department of SurgeryNiigata University
Japan Society for the Promotion of Science (JSPS)Science Dialogue Program at Niitsu Senior High School
Niitsu, Niigata September 4th 2006
Proteomics and CancerProteomics and Cancer
• What is Proteomics?
• Why to study the Proteome?
• Why Cancer?
• How do we study the proteome
• What do we see?
• How do we use the results?
• How translate the results to patients’ care?
• Proteomics and Cancer only?
Proteomics and CancerProteomics and Cancer
• What is Proteomics?
The Proteome: the collection of proteins that are expressed by (or present in) a cell or tissue at a given moment
Proteomics and CancerProteomics and Cancer
• Why to study the Proteome?
Genomics Genes (DNA)
The Information
Transcriptomics mRNA
The Message
Proteomics Proteins
The Actors
Why to study the Proteome?Why to study the Proteome?
• The function of a protein depends on its structure and interactions, neither of which can be predicted accurately based on sequence information alone
• Genomics and Transcriptomics are coarse tools for large-scale functional analysis.
• The abundance of a given transcript may not reflect the abundance of the corresponding protein.
• Protein diversity is generated post-transcriptionally.
• Protein activity often depends on post-translational modifications, which are not predictable from the level of the corresponding transcript.
• The function of a protein often depends on its localization.
Proteomics and CancerProteomics and Cancer
•Why Cancer?Cancer is one of the main causes of death in the world
Is a public health problem
Proteomics will help to the identification of Genes and Proteins responsible for or implicated in the disease
Potentially curable
Proteomics will allow early detection
It is cheaper to prevent than to treat the disease
How do we study the proteome?How do we study the proteome?
• Electrophoresis
Gel electrophoresis
2 Dimensional Electrophoresis (2DE)
Capillary electrophoresis (CE)
• Liquid Chromatography (LC)
• Mass Spectrometry (MS)
• Combination: 2DE-MS, CE-MS, LC-MS
• Microarray Technology
ElectrophoresisElectrophoresis
ElectrophoresisElectrophoresis
Proteomics and CancerProteomics and Cancer
• 2 Dimensional Gel Electrophoresis (2DE)
Polyacrylamide Gels
1st dimension: pI(Isoelectric focusing)
2nd dimension: MW (molecular weight)
ElectrophoresisElectrophoresis
First Dimension: Isoelectric Focusing
ElectrophoresisElectrophoresis
First Dimension: Isoelectric Focusing
First Dimension Second Dimension
2 Dimensional Gel Electrophoresis2 Dimensional Gel Electrophoresis
2 Dimensional Gel Electrophoresis2 Dimensional Gel Electrophoresis
First Dimension
Second
Dimension
Differential Expression Proteomics
Differential Expression Proteomics
Differential Expression Proteomics
Differential Expression Proteomics
Proteomics and CancerProteomics and Cancer
• Capillary electrophoresis (CE)
Proteomics and CancerProteomics and Cancer
• Liquid Chromatography• High Performance Liquid Chromatography (HPLC)
• Ion exchange chromatography (IE)
• Affinity chromatography (AC)
• 2-D Liquid Chromatography• HPLC-IE, HPLC-AC etc.
Liquid ChromatographyLiquid Chromatography
Liquid ChromatographyLiquid Chromatography
Liquid ChromatographyLiquid Chromatography
Size Charge
Affinity
Proteomics and CancerProteomics and Cancer
• Mass Spectrometry (MS)
Mass SpectrometryMass Spectrometry
MALDI-TOF Mass SpectrometryMALDI-TOF Mass Spectrometry
ESI Mass SpectrometryESI Mass Spectrometry
ESI Mass SpectrometryESI Mass Spectrometry
Mass Spectra Analysis by Bioinformatics Algorithms
Peptide SequencePeptide Sequence
Proteomics and CancerProteomics and Cancer
• Combination of techniques:
2DE-MS, CE-MS, LC-MS
Combination of TechniquesCombination of Techniques
Capillary IEF
Mass Spectrometry
1-D or 2-D Liquid Chromatograpy/Mass
Spectrometry 2D-LC-MS
Combination of TechniquesCombination of Techniques
Proteomics and CancerProteomics and Cancer
Microarray Technology
Protein MicroarraysProtein Microarrays
Proteomics and CancerProteomics and Cancer
• What do we see?
• What do we look for?
Bands
What do we see?What do we see?
Spots
What do we see?What do we see?
Mass Spectra
What do we see?What do we see?
Peptide lists
What do we see?What do we see?
What do we look for?What do we look for?
Expression patterns
Expression patterns
What do we look for?What do we look for?
What do we look for?What do we look for?
Expression patterns
What do we look for?What do we look for?
How do we use the results? How do we use the results?
Proteomics and CancerProteomics and Cancer
• How translate the results to patients’ care?
Proteomics and CancerProteomics and Cancer
• Proteomics and cancer biomarkers only?
•Plant genomics and proteomics
•Marine Biology
http://gene64.dna.affrc.go.jp/RPD/database_en.html
The Rice ProteomeThe Rice Proteome
Callous 1 week after flowering
Proteomics and Marine BiologyProteomics and Marine Biology
Zebrafish
Medaka
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Thank you for your attention!
Thank you for your attention!