Mathias Uhlen

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SALSS August 21, 2009
Mathias Uhlen AlbaNova University Center Royal
Institute of Technology (KTH) Stockholm, Sweden
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• 18th century - biology
• 19th century - chemistry
• 20th century - physics
• 21st century - medicine

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Organism
Proteins
DNA/RNA
Cells
Molecule Information Function
Building-block DNA Digital Memory
4 bases Protein Analogue Chemistry
20 amino acids
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• Bacteria (1995)
• Yeast (1996)
• Worm (1998)
• Fruit fly (1999)
• Plant (2000)
• Human (2001)

DNA sequence in public databases more than
doubles every year
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Ronaghi, Uhlen Nyren (1998) Science 281,
363-365.

• Pyrosequencing (1998) - sequencing by synthesis
  (SBS)
• 454 instrument (2005) - pyrosequencing-based SBS
  (100 Mb)
• Solexa instrument (2006) - fluorescent-based SBS
  (1 Gb)
• SOLID (2007) - hybridization/ligation-based (2-3
  Gb)
• PacBio (2010) - single molecule SBS (100 Gb per
  hour)

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Generated with 454 (pyrosequencing)
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Catalysis
Signaling
Structures
Regulation
Defence
Enzyme
Hormone /Receptor
Collagen
DNA-binding protein
Antibody
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Leucine zipper DNA
Insulin
HIV Reverse Transcriptase
Collagen
Fungal Lipase
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Protein profiles
Protein parts list
RNA profiles
Genomics
Interactomics
Systems biology
Pathways, Biomarkers, Drug Targets
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26 SEPTEMBER 2008VOL 321 PAGES 1758-1761
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The Swedish Human Proteome Resource program

• Funding from Knut and Alice Wallenberg
  Foundation started 2003
• Eight sites KTH, Uppsala, KI, Malmö, Seoul,
  Beijing, Shanghai and Mumbai
• 100 employees at KTH and Uppsala University
  (altogether 200 researchers)
• A publicly available Human Protein Atlas

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• 75 FTEs at KTH, Stockholm (main site)
• 30 FTEs at Uppsala University (clinical site)
• Lund/Malmö hospital (clinical validation)
• KI (brain atlas)

Seoul site
Beijing site
Mumbai site (15 FTEs)
Shanghai site
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Dr. Sanjay Navani

• 15 certified pathologists
• All images available through internet
• Web-based annotation system

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• One partner in Korea (Seuol)
• Two partners in China (Shanghai and Bejing)
• Use FedEx to ship samples
• Pay on delivery (to Sweden)
• Cost reduction (4-5x)

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• Tissue profiling using IHC
• - 48 normal tissues
• - 20 cancer tissues
• Cell profiling using IHC
• - 47 cell lines
• - 12 clinical cell samples
• Subcellular profiling using IF
• - 3 cell lines

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LIver
Pancreas
Kidney
Heart
Endometrium
Small intestine
Fallopian tube
Breast
Testis
Brain (cerebellum)
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Proteins expressed in normal cells
Fraction of expressed proteins ()
Fraction of cells ()
Proteins
Cell types
6.800 antibodies towards (gt25 of all protein
encoding genes) 65 normal cell types (from 45
different tissue types)
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Uhlén et al (2005) A human protein atlas for
normal and cancer tissues based on antibody
proteomics Mol Cell Proteomics. 4(12)1920-32.
www.proteinatlas.org
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http//www.proteinatlas.org/rodentbrain/
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Status - HPR

• Number of human protein encoded genes (UniProt)
  20,331

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• 8,832 antibodies
• 6,844 genes (33,7)

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• Funding from Knut and Alice Wallenberg Foundation
• 2,500 genes per year (including 500 from
  collaborators)
• First draft of the human proteome by 2014
• Long-term objective paired antibodies to all
  human proteins

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Atlas Antibodies AB - Background

• Company started February 1, 2006
• Spinout from The Human Protein Atlas (HPA)
  program
• Located in Stockholm, Sweden
• Manufacturing, QC
• Inventory, distribution
• Customer and technical support
• RD
• 12 employees
• More than 100 FTEs involved through the academic
  HPA program

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• 100 persons involved in the HPR program (R)
• AA has 12 FTEs (D and IPR)

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• Obtains 50 aliquots of each antibody generated
• Web-shop (Google-based sales)
• Worldwide distribution directly from Stockholm
• Over night delivery to US and Europe by FedEx
• Over 500 customers in 30 countries
• 15 months after product launch

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• Identification of cancer origin (metastasis)
• Outcome prognosis (stratification)
• Treatment prognosis (stratification)
• Malignancy marker (benign versus malign)

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Micro arrays for serum/plasma analysis
Antibody microarrays
serum microarrays
Suspension bead arrays
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76 antibodies
Collaboration with John Bell and Mark McCarthy,
Oxford University, UK
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• spiked recombinant proteins
• assay performed in the standardized manner

Collaboration with Hanno Langen, Roche,
Switzerland
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Kidney disease
Objective find biomarkers for kidney toxicity
Peter Nilsson Jochen Schwenk Rebecca
Rimini Ulrika Igel Linn Fagerberg Jesper
Hedberg, AstraZeneca
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Target selection
AZ-list 335 ENSG-ID
ok PrEST-array
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Abs included
( 92 unique ENSG-ID)
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Result overview
Assay 2
Assay 1
Signal significantly higher than noise
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Plasma profiles
GN - Glomerulonephritis
Paired controls
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Plasma profiles
HPA 49
HPA 67
HPA30
HPA67
HPA23
HPA45

• Seven potential biomarkers discovered

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Validation of the HPA23 protein target

• HPA23 toxicity marker for all four kidney diseases

• An independent (paired) antibody yields same
  results
• These need to be further validated in larger
  patient cohorts

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7,000 ab/year
5,000 ab/year

• Short-term objective
• gt1,000,000 assays per month
• 20-30 projects in parallel in the discovery phase

Schwenk et al, manuscript in prep
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• A Swedish effort to map the human proteins
• All data publicly available
• First draft of the human proteome by 2014
• Comprehensive tools box of reagents for systems
  biology

Tissue-specificity is achieved by precise
regulation of protein levels in space and time.
Different tissues in the body acquire their
unique characteristics by controlling not which
proteins are expressed but how much of each is
produced.
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The Swedish HPR-team
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Text
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• New center for high-throughput biology
• Focus on core facilities with expensive
  infrastructure
• Prioritize next generation sequencing (more than
  50 of the core funding)
• Provide space for groups with relevant expertise
  in high-throughput biology
• Broad clinical focus including cancer, human
  genetics and infectious diseases
• Strong focus on bioinformatics and systems
  biology

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