Atlas Antibodies AB and The Human Protein Atlas. Hong Kong, August 10, 2012

Transcription

1 Atlas Antibodies AB and The Human Protein Atlas Hong Kong, August 10, 2012

2 Company Overview Founded in February 2006 Spinout from The Human Protein Atlas (HPA) project Exclusive commercial rights to HPA Antibodies Exclusive rights to founders inventions Antibody reagents and diagnostics/discovery Headquarter located in Stockholm, Sweden Solid financial position Cash flow positive since 2008

3 Commercial Opportunities Make the HPA Antibodies available to researchers world wide Manufacturing, marketing and sales of the HPA Antibodies Protect interesting biomarkers Evaluate and patent protect Evaluate and patent protect interesting biomarkers

4 Antibody Reagents 12,300 antibodies targeting >10,000 human proteins Developed by researcher for research IHC analysis of 700 samples with each antibody In depth annotation by pathologist of each sample IF for subcellular localization studies 2,500 new antibodies added annually 99% of catalogue in stock Customers world wide

5 Diagnostics Tissue diagnostics Biomarkers for metastasis diagnosis, treatment prediction and prognosis Candidate screening in the world s largest human protein expression database of expression profiling in 700 normal and tumor derived tissue samples Antibody based validation in large patient cohorts Antibodies for >60% of the all human proteins Premium quality TMAs Blood diagnostics Blood markers for diagnosis and relapse prognosis Suspension bead arrays 150,000 immunoassays per day < 50 μl sample to screen all human protein targets

6 Towards a knowledge-based Human Protein Atlas

7 The Human Protein Atlas Antibody based proteomics initiative (started in 2003) > 125M$ Funding from the Wallenberg Foundation (non-profit) > 100 full time employees in R&D and Production Generation and use of antibodies to functionally explore the human proteome KTH, Stockholm (antibody generation) Uppsala University (clinical site) Lund/Malmö hospital (clinical site) SiLifLbSt SciLifeLab Stockholm (biobank b and cell profiling) 12,238 genes with protein expression profiles based on 15,598 antibodies ( org) (>14,000 genes at next release September 10, 2012)

8 The Human Protein Atlas Project Team KTH, Stockholm (antibody generation) Uppsala University (clinical site) Lund/Malmö hospital (clinical validation) SciLifeLab Stockholm (biobank and cell profiling) Seoul site Shanghai site Mumbai site

9 Antibody Development Process in the HPA-project 1. Antibody generation 2. Application specific validation 3. Protein expression profiling Protein Atlas Berglund et al (2008). A gene-centric human protein atlas for expression profiles based on antibodies. Mol Cell Proteomics

10 Bioinformatics Antigen Design (HPA) In house developed antigen design software Specificity by design amino acids (PrEST) Avoid transmembrane regions and signal peptides Avoid high regional and/or local sequence identity to other human proteins

11 Molecular Biology PrEST Cloning g( (HPA) PrEST selection RNA QC Primer design RNA panels RT PCR Plasmid maxiprep A,B,C,D Agarose check Digestion of vector Restriction CIP ing vector Ligation Testing quality of competent cells Preparation of competent cells Transformation Patching Phi amplification Cycle sequencing Purification ABI sequencing Sequence evaluation Single cell streaks Glycerol stock Plasmid miniprep Protein Factory Micro Array Team Long term storage Cloning from RNA pools (RT-PCR) or cdna clones Solid-phase cloning using biotinylated primers and magnetic beads. Validation by DNA sequencing 800 clones per month

12 Protein Factory Target Expression and Purification (HPA) P T7 His ABP PrEST Target expression and purification Recombinant expression in E.coli Rosetta 600 new antigens per month Validation by mass spectrometry (MALDI and ESI) Purity analysis by SDS-PAGE Quantification by BCA-assay

13 Immunotechnology Antibody Purification (HPA) Target specific antibodies Three step antigen based affinity purification 1. Depletion of unwanted specificity 2. Capture of antigen specific pool 3. Desalting and buffer exchange 470 array-approved approved antibodies per month Nilsson et al, Towards a human protein atlas: High-throughput generation of mono-specific antibodies for tissue profiling Proteomics 5 (2005)

14 Protein Arrays (HPA) Tag specific antibodies Antigen affinity purified antibodies Analysis of 120 new antibodies every week Antibody Purification QC Validation of antibody specificity (384 proteins/msab) Nilsson et al, Towards a human protein atlas: High-throughput generation of mono-specific antibodies for tissue profiling Proteomics 5 (2005)

15 Western blot (HPA) M R U P L T Supportive Uncertain Not supportive Standard set up: Two Human Cell lines (RT-4, U-251) Human Plasma (Depleted of HSA/IgG) Two Human Tissue lysates (Liver, Tonsil) Protocol: Primary antibody 1:250 Chemiluminescence detection (Data provided by: HPA, Cajsa Älgenäs)

16 Western blot (HPA) Endogenous Protein 32% of all HPA antibodies are approved for western blot applications using default protocol (data from ). > 50% of all HPA Antibodies are validated for Western blot (Data provided by: HPA, Cajsa Älgenäs)

17 New Initiative (HPA) Recombinant Over-expressed Protein In total 1025 tested antibodies HPA standard setup % supportive Over-expression expression Lysates 84% supportive (Data provided by: HPA, Cajsa Älgenäs)

18 Protein Expression Profiling Proteins are organized into functional elements at different levelsels ORGANS TISSUES CELLS ORGANELLES IHC IF

19 Tissue Micro Arrays (HPA) Access to pathology archives at Uppsala University Hospital Extensive tissue material available Very ygood clinical follow up data Tissue quality Representative ti tissue samples Technical excellence in TMA manufacturing process

20 Standard IHC Package (HPA) Normal tissues: Surgical specimens with normal morphology 46 normal tissue types present All tissue types present in triplicates (from three patients) In total 144 samples Cancer tissues: 20 of the most common cancer types represented Duplicate samples from 12 different patients. In total 432 samples from 216 patients Cell lines: 46 cell lines (hematopoietic tumors, solid tumors) 12 clinical cell samples

21 Annotation and Curation of IHC Images (HPA) In total 634 tissue/cell cores

22 Immunohistochemical staining of human cerebellum using an antibody CAB towards neurofilament, light polypeptide.

23 Immunohistochemical staining of human heart using antibody HPA collagen, type VI, alpha 1

24 Previously Uncharacterized Proteins

25 Immunofluorescence (HPA) 3 human cell lines (A-431, U-2 OS, U251-MG) Confocal microscopy for subcellular annotation 4-color images >20% of antibodies validated for IF (increasing) U251 MG Brain Glial 1. Sample preparation (automated) - Fixation/Permeabilization - Immunofluorescent staining - Markers: nucleus, ER,cytoskeleton A 431 Skin Epithelial 2. Image acquisition (manual) - High-resolution - Multi channel images U 2 OS Bone Mesenchymal 3. Image annotation (manual) - Protein location - Intensity Barbe et al (2008). Toward a confocal subcellular atlas of the human proteome. Mol Cell Proteomics. 7:

26 Subcellular Annotation (HPA) Subcellular location (17 different locations) Staining intensity (negative, weak, moderate or strong) Staining characteristic (granular, speckled, smooth etc) Comments Stadler et al (2010) A single fixation protocol for proteome-wide immuno-fluorescence localization studies, J. Proteomics Apr 18;73(6):

27 Immunofluorescent staining of U-2 OS osteosarcoma cells shows positivity (green) in nucleus but not nucleoli

28 Immunofluorescent staining of U-251 MG malignant glioma cells shows positivity (green) in Golgi apparatus

29 The Human Protein Atlas ( Gene and protein data Subcellular localization Normal tissues and organs Cancer tissues Cell lines Antibody summary

30 The Human Protein Atlas Cancer tissues

31

32 The Human Protein Atlas Number of genes covered per release September (2005) (2006) (2007) (2008) (2009) (2010) (2010) (2011) (2011) (2012)

33 The next five years of the Human Protein Atlas Approximately 8 new genes completed per day First draft of the human proteome by 2015 (~ genes) Long-term objective: paired antibodies to all human proteins

34 The Swedish Protein Atlas Team Prof. Mathias Uhlén

35 Diagnostics and Biomarker Discovery

36 Cancer Diagnostics Large Unmet Need for Biomarkers Cancer is one of the most common causes of disease and death i the western world Biomarkers have an increasingly important role in development and utilization of cancer drugs There is a large unmet need for new and better cancer markers Early and correct diagnose for early and correct treatment Patient stratification for treatment selection Prediction of therapy response Prediction of tumor relapse Follow progression evaluate results from clinical studies

37 Cancers in the Human Protein Atlas 20 different types of cancer 216 patients 12 different patients of each type Tumors stratified according to histopathology

38 Companion Diagnostics (CDx) From ONE SIZE FITS ALL to TAILORED THERAPY From NICE TO HAVE to MUST HAVE components of a drug development strategy Using a companion test whether it looks for genetic, proteomic, or gene expression markers to predict if a drug will work in a patient or what kind of dose that person should take - will be the norm in the future

39 Tissue Biomarkers for Treatment Prediction Aim Identification of protein signatures to improve prediction of response to established therapies Purpose Identify patient groups responding to a therapy Strategy Select candidate markers in Human Protein Atlas Differential protein expression in cancer patients Analyze the response to treatment based on marker expression Patient t cohorts with treatment t t data and survival data

40 RBM3 Prediction of Response to Platinum-Based Treatment RBM3 expression is associated with cisplatin sensitivity in epithelial ovarian cancer (EOC) Down regulation of RBM3 significantly reduces cisplatin sensitivity in ovarian cancer cells Expression of RBM3 in the cisplatin-sensitive A2780 ovarian cell line compared to the cisplatin resistant cell line A2780-Cp70 IHC staining and immunoblotting of RBM3 showing substantially lower RBM3 levels in A2780-Cp70 sirbm3 transfected A2780 cells treated with various concentration of cisplatin Ehlén et al., 2010, J Transl Med. Aug 20;8:78, Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer.

41 RBM3 Response to Oxaliplatin Treatment in Colorectal Cancer Survival of oxaliplatin (XELOX) treated stage III and IV colorectal cancer patients Patient material from population based prospective study (Malmö diet and cancer study) Patients stratified according to RBM3 expression All patient with high RBM3 levels l survived until end of study period Overall survival of patients with stage III and IV colorectal cancer treated with oxaliplatin. Patients are stratified into two groups based on RBM3 protein expression as determined by immunohistochemistry. All patients with high levels of RBM3 protein survived to the end of the study period as opposed to patients with low levels of RBM3 protein, of which none survived. UNPUBLISHED DATA (K JIRSTRÖM ET AL)

42 Metastasis Biomarker Panels Aim Identification of protein signatures to distinguish tumors of different types and origins from each other Purpose Accurately diagnose cancers of unknown primary Strategy 15 TMAs covering cancers from 18 different tissue types Validated with known metastasis biomarkers > 700 tumor samples (primary and metastasis) Candidate selection from Human Protein Atlas Cell- and tissue specific protein expression

43 SATB2 A diagnostic Marker for CRC in Metastatic Carcinoma SATB2 expression is restricted to glandular cells lining the lower GI tract and is primarily preserved in cancer cells of colorectal origin SATB2 offers a higher specificity than Cytokeratin 20 in clinical differential diagnostics SATB2 combined with CK20 identifies >95% of all colorectal carcinomas Prospective clinical study at Uppsala University Hospital SATB2 staining intensity in different cohorts corresponding to more than 1800 patients Magnusson et al., Am J Surg Pathol Jul;35(7): SATB2 in combination with Cytokeratin 20 identifies over 95% of all colorectal carcinomas

44 Blood Diagnostics Aim Identification of protein signatures to improve early diagnosis and treatment prediction Purpose Development of novel blood diagnostic products Strategy Suspension bead arrays Focus on oncology (early diagnosis and predictive markers) and cardiovascular markers (early diagnosis and predictive markers)

45 Fibulin 1 - A Blood Marker for Renal Impairment Three part collaboration (Astra Zeneca, KTH, Atlas Antibodies) Screening for markers of renal impairment Fibulin 1 - Candidate marker in renal impairment Analyzed in two independent cohorts Four different antibodies Neiman et al., J. Proteome Res. 2011, 10. Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment

46 Biomarker Discovery 20 active patent application families 4 approved patents t Type of biomarkers A diagnostic marker that show if a metastasis is of colorectal cancer origin Biomarker for treatment stratification in several major cancer forms

47 Research Reagents

48 Antibody Reagents 12,300 antibodies targeting >10,000 human proteins Developed by researcher for research IHC analysis of 700 samples with each antibody In depth annotation by pathologist of each sample IF for subcellular localization studies 2,500 new antibodies added annually 99% of catalogue in stock Customers world wide by

49 Competitive Advantages Unique Characterization >700 images available for each antibody In depth annotation by pathologist of each sample Antibodies against proteins not available through other suppliers Broad product catalogue All results publicly available through the Human Protein Atlas web portal ( tl

50 Global Distribution >12,300 antibodies targeting >10,300 different human proteins Over 6,000 users in more than 60 countries

51 Product Catalogue Development Number of HPA Antibodies available by the end of each year 2006 to 2011 Estimated number of HPA Antibodies available by the end of each year 2012 to No of Antibodies in Catalogue

52 Financial Development MUSD 50 5,0 4,0 3,0 20 2,0 1,0 0,0 1, Revenue (MUSD) Result (MUSD)

53 Summary Atlas Antibodies provides highly characterized antibodies developed by the academic HPA project 99 % of product catalogue in stock 700 IHC, IF and Western blot images per antibody 12,300 antibodies targeting more than 10, human proteins 2,500 new antibodies added annually All human proteins covered by 2015 More than 125 MUSD of secured funding to the HPA academic project (full production until 2015) Financially solid company with stable cash flow

54 Thank you!