1Protagen AG

Protagen AG

Otto-Hahn-Str. 15

44227 Dortmund

+49-231-9742 6300

Successful Strategy for Systematic Identification of Novel Biomarkers

Technologieforum Diagnostik – Frankfurt, 27./28. Nov. 2006

Dr. Jens Beator

Director Protein Biochips

Jens.beator@protagen.de

JB/26.11.2006 Slide: 2

Fact Sheet

Corporation on stocks „Aktiengesellschaft“Legal form:

34Employees:

- Bruker Daltonik GmbH, Bremen - Vivascience AG, Hannover- Serva Electrophoresis GmbH, Heidelberg

Industrial partners:

Otto-Hahn-Str. 15

44227 Dortmund

Germany

Location:

Established: 1997

Protagen AG

2Protagen AG

JB/26.11.2006 Slide: 3

Products & Services - Overview

JB/26.11.2006 Slide: 4

Business Strategy

Valu

e / R

even

ues

2000 2004 2008

FeeFee--forfor--serviceservice

and Bioand Bio--ITIT

Protein Biochip Protein Biochip

ProductionProduction

Time

Horizon 1

Horizon 2

Horizon 3

Diagnostics Diagnostics

andand

TherapeuticsTherapeutics

2010

3Protagen AG

> 80 autoimmune disease are currently known

„Autoimmune diseases, with the exception of rheumatoid arthritis

and autoimmune thyroiditis, are individually rare, but together they

affect approximately 5 percent of the population in Western

Countries.“

Davidson & Diamond, 2001, N Engl J Med, Vol. 345, No. 5, 340-350

Biomarkers in Autoimmune Diseases

Commonly accepted autoimmune diseases (AID),

in-vitro diagnosis by autoantibodies (profiles) as “biomarkers”:

Type 1 diabetes, autoimmune thyroiditis, systemic lupus erythematodes,

rheumatoid arthritis, mixed connective tissue disease, Sjögren’s syndrome,

pemphigoid diseases, ….

Autoimmune Diseases – Open Questions

Inciting antigens unknown in many AID:

Juv. idiopathic arthritis, inflammatory bowel disease (Morbus Crohn, Colitis

ulcerosa, …), psoriatic arthritis, …

Autoimmune reactions in important other diseases:

Multiple Sclerosis, Alzheimer, breast cancer, prostate cancer, ….

What are the (auto)antigens?

Which autoantibody profiles are suitable biomarkers?

4Protagen AG

JB/26.11.2006 Slide: 7

hEx1 Protein Expression Library

• Derived from human fetal braintissue with largest diversity of expressed genes193.500 human protein expression clones with His-tagsbacterial clones grown on PVDF filtersinducible protein expression

• 37.200 protein expressing clonesreact with anti-His antibody

• 16 000 different gene products available for binding assays

2533 different clusters (multiple clones of same gene)

13550 singletons

Büssow et al. 1998,

Lüking, Gutjahr, Cahill, Lehrach, Protagen & MPI f. Molecular Genetics, unpublished

The Unique Resource for Biomarker Discovery

JB/26.11.2006 Slide: 8

MACROarrays:

the only product and the largest human protein diversity for

reproducible, unbiased screening

• hEx1 Protein Expression Library (other libraries available)

• Manufactured using robotic systemsFull traceability & identification of clonesReproducible screening product with 16,000 different expression clones

• Low sample consumption (0.5 ml/sample)

• Large amount of antigen available for antibody binding

Unique Strength of the Technology

5Protagen AG

JB/26.11.2006 Slide: 9

Patient and control samples

Screening of 37,000 human expression clones

Generation of a putative

disease specific protein subset

Bioinformatical Analysis

0

2

4

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Protein 1 Protein 2 Protein 3 Protein 4 Protein 5 Protein 5 Protein 6 Protein 7 Protein 8 Protein 9

Putative auto-antigens

Facto

r

Factor19

Factor20

Factor21

Factor22

Factor23

Factor24

Factor1

Factor2

Factor3

Factor4

Factor5

Factor6

Factor7

Factor8

Factor9

Factor10

Factor11

Bioinformatical analysisIndication-specificmultiplex biochip

Identification of Biomarkers - Strategy

Patient

Sample

Control

Sample

JB/26.11.2006 Slide: 10

MACROarray Serum Screening: Alopecia areata

Identification of 23 protein expressing clones,

detected by antibodies in two or more of the five patient pools,

not recognized by serum from 11 controls.

AP

6Protagen AG

JB/26.11.2006 Slide: 11

1 21 and 2 show the results of two separate screens of the same

patient, screened separately on two arrays; > 80% reproducibility

MACROarray Reproducibility

Dilated Cardiomyopathy study, Horn et al. 2006

JB/26.11.2006 Slide: 12

� Using purified proteins printed on protein biochips

� 20 patient sera / 10 control sera from normal individuals

� 7 Disease control sera from patients with psoriasis, hand and foot

eczema or skin allergy

patient

sample 9

1

2

3

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5

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9

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12

1

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control

sample 57

disease control

skin eczema

sample 5

1

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7

8

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12

4

5

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Diagnostic Protein Biochip: Alopecia areata

= Alopecia-associated proteins

Confirmation of MACROarray-identified antigens

7Protagen AG

JB/26.11.2006 Slide: 13

MACROarrays Used for Biomarker Discovery

• Systemic Lupus erythematodes (SLE mouse model)Gutjahr, C., ….. Cahill, DJ (2005) Mouse protein arrays from a TH1 cell cDNA library for antibody screening and serum profiling. Genomics 85, 285–296

• Alopecia areata (hair loss) Lüking A., …. Cahill, DJ (2005)

Profiling of alopecia areata autoantigens based on protein microarray technology. Mol. Cell Proteomics 4:1382–90

• Dilated Cardiomyopathy (DCM)Horn, S., …. Cahill, DJ (2006)Profiling humoral auto-immune repertoire of dilated cardiomyopathy (DCM) patients and development of a disease-associated protein chipProteomics 6: 605 - 613

JB/26.11.2006 Slide: 14

Protagen Patent Position

Patented UNIclone® platform technology

• Creation and use of protein expression libraries

• Use of recombinant products originating from expression

libraries in array formats

• Protagen has exclusive worldwide license

from Max-Planck-Society, Germany

Protagen’s patent position

• Unique and solid position for protein arrays

• Freedom-to-operate towards products &

cooperations in the Life Science industry

8Protagen AG

JB/26.11.2006 Slide: 15

A B C E F G HD

Capturing antibody

Detecting antibody

Secondary antibody

Label

Immobilized protein

Interacting protein Small compound

Protagen Protein Biochips

JB/26.11.2006 Slide: 16

Quantitative binding profiles of biotherapeutics

Antibody A Antibody B Receptor Fusion

Antigen Antigen Antigen

UNIchip® AV-400 UNIchip® AV-400 UNIchip® AV-400

Example: UNIchip® AV-400, Launch 2005

Patented design with antigen calibrator

9Protagen AG

JB/26.11.2006 Slide: 17

Antigen Discovery for Multiple Sclerosis

Systematic discovery of novel Multiple Sclerosis autoantigens

in a BMBF-supported project

• Identification of putative autoantigens using MACROarrays

• Screening patient cohorts using purified antigens on protein biochips

• Disease control: acute disseminated encephalomyelitis (ADEM), healthy controls

• Clinical partner:Dr. Sebastian SchimrigkNeurologische Klinik der Ruhr Universität Bochum, St. Josef HospitalArbeitsgruppe NeuroimmunologieTherapie und Studienzentrum für Multiple Sklerosis

JB/26.11.2006 Slide: 18

Discovery of Putative Multiple Sclerosis Antigens

MS patient serum on hEx1 MACROarray

10Protagen AG

JB/26.11.2006 Slide: 19

Development and production of protein biochips with

recombinant antigens for diagnostic multiplex assays, patented

• MACROarray processing

• Clone selection & identification

• High-throughput protein expression & purification

• Screening & bioinformatic analysis

• Manufacturing quantitative protein biochips

Unique Strength of Protagen

JB/26.11.2006 Slide: 20

Protagen AG

Otto-Hahn-Str. 1544227 DortmundGermany

T +49-231-9742 6300F +49-231-9742 6301www.protagen.deinfo@protagen.de