World's only technology that consistently produces full-length, correctly folded, functional proteins - Sengenics
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Misfolded proteins are washed away Only correctly folded proteins are immobilised World’s only technology that consistently produces full-length, correctly folded, functional proteins Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Agenda for today’s presentation 2 1. Company 2. Technology 3. Case Studies 4. Study Design Cambridge roots Protein folding Autoantibodies Samples Main collaborators Protein function Diagnostics Study design Team Performance Response prediction Business case Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Sengenics is a 12-year old British biotech company with a solid global footprint 3 2020 2021 2008 A c q ui r ed b y m u l t i - bi l l i on d o l l a r , l i f e - s c i enc e f o c used, S w e di s h f i r m C a m b r i dge s p i n - out B o s t on R & D f a c i l i t y 2016 P r o t e i n p r o d uct i on a n d h i g h- t hr oughput a s s ay f a c i l i t y i n A s i a Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Sengenics KREX immunoproteomics platform leveraged by 100+ institutions 4 9 o u t o f t o p 1 0 P h a r m a g lo b a lly 10 a c a d e m ic in s t it u t io n s 6 a c ad e m ic in s t it u t io n s > 5 0 p r o je c t s Member of Cancer, Inflammation & Immunity, and Neuroscience Steering Committees 2 7 a c a d e m ic in s t it u t io n s > 2 00 p r o je c t s I n d us t r i a l a d v i s or y b o a r d m e mber Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Wide repertoire of research studies and IP 5 Type 1 Type 2 Type 3 Core Tech Patents Sero-diagnostics Drug ADR-Response 14 Granted 3 Filed 1 Filed 1 Filed 20+ Unfiled 16 Unfiled 2 Unfiled Group 1 - Preparing protein arrays with Aging Sjogren’s Anti TNF marker tag to immobilise proteins Oral Cancer Zika Anti IL Group 2 - Protein Variant Arrays NSCLC Melanoma Anti CTLA-4 Group 3 - BCCP tag Type II Diabetes Malaria Anti PDL1 Group 4 - Cytosolic Accessory Proteins Parkinson’s Gastric Cancer Other drugs Group 5 - Drug discovery Alzheimer’s Crohn’s Prostate Cancer RA Lupus Breast Cancer Confidential © 2008–2021 Sengenics Corporation Pte Ltd
The core principle of our KREX protein folding technology 6 > BCCP: compact, inert, folding marker > Biotin is attached ONLY to correctly folded proteins > Misfolded proteins misfold BCCP > BCCP loses its biotinylation activity > Only correctly folded proteins are attached Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Unique surface chemistry 7 > No conventional purification: Simultaneous purification and immobilisation PROTEINS > KREX proteins retain folded structure and function in the behave as if aqueous environment they are in > Streptavidin tetramers covalently bound to hydrogel free solution layer COO- COO- > Single attachment point ensures COO- consistent orientation of COO- COO- proteins > Proteins are immobilised onto proprietary streptavidin-coated HYDROGEL > Proteins are projected 50 Angstroms from the glass surface Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Immobilise various biomolecules associated with complex diseases on KREX arrays 8 PTM & complex protein Bacterial protein Peptide DNA Viral protein
QC of KREX protein arrays demonstrates performance required for downstream assays 9 1. Biotinylated marker 15. Biotinylated marker 14. Control pPro10 8. No name 11. No name 4. SH3GL1 3. STAT5A 6. ERCC5 13. KRAS2 5. GPHN 7. GPC3 12. GAS7 9. HRAS 10. SAV1 2. SSX1 Spot diameter ~25nm 202+/-33 streptavidin units per mm2 Dual wavelength scan of an on-array c-Myc Distance between streptavidin units assay: Red = Cy5-biotin BSA controls (red); 52.9+/-3.1 nm Green = C-terminally c-myc-tagged antigens 40,000 binding units / 200mm2 spot Western blot analysis Anti-c-myc assay Streptavidin density Confidential © 2008–2021 Sengenics Corporation Pte Ltd
KREX arrays exhibit exceptional sensitivity, specificity and consistency 10 Very high specificity High signal:noise ratio and clearly interpretable hits Obviates conventional blood draw and cold chain As little as 1µl Collect samples during flare-ups of serum or plasma Leverages sensitivity of sample KREX platform Highly reproducible Exceptional sensitivity Duplicate samples exhibit exceptional performance Limit of detection is 10pg/ml range and consistency Single digit µl levels of sample can be used (Pearson correlation >0.97) Five orders of magnitude dynamic range Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Proteins on KREX arrays have been functionally validated 11 > Kinases auto-phosphorylate and Kinase inhibition assays correlate with published data > DNA binding proteins bind DNA – p53 mutant proteins exhibit differential binding of labelled oligo > Indirect functional assays Kinases autophosphorylate P53 mutants bind labelled Autoimmune disease hits in the presence of ATP DNA oligo with different Kd values correlate with published data Confidential © 2008–2021 Sengenics Corporation Pte Ltd
KREX proteins form multimers and are functional on the array 12 HETERODIMERS TRIMERS ON-ARRAY PTMs FUNCTIONAL ASSAYS The detection of the 58 kDa Western blot analyses of expressed Quantifying the effect of post-translational On-chip phosphorylation of p53 by hexahistidine-tagged β-subunit (lower HA variants protein. Two samples modifications on autoantibody casein kinase II (CKII) boxes in red) and a band at ~90 kDa (denatured and non-denatured recognition: neoantigens in colorectal (upper boxes in red) under semi-native proteins) of each HA variant were run cancer. Protein arrays were incubated in assay conditions of all TCR proteins provides side-by-side on SDS-PAGE gels. buffer containing ATP in the presence evidence for heterodimer complex Arginine deimidation to citrullene on chip and absence of CKII formation during protein expression in using peptide arginine deimidase 4. Results: Specific phosphorylation of insect cell. S392 was detected using residue specific antiphosphoserine primary Only the β-subunit was detected at ~58 antibody with detection by secondary kDa under denaturing/reducing antibody-peroxidase conjugate and conditions. chemiluminescence. Mutations with “X” denote truncations due to introduction of premature stop codons and therefore lack S392 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
KREX arrays exhibit exceptional consistency with CV% values of
Diverse microarray product & antigen range 14 High-throughput Quantification of Simultaneous screening of Multi-antigen, autoantibody profiling autoantibodies to 200+ 100+ wild-type and multi-domain COVID-19 against 1600+ proteins clinically relevant CT antigens mutant p53 antibody test Confidential © 2008–2021 Sengenics Corporation Pte Ltd
15 Identify all the autoantigens and antigens that make up the Using Orvar, the totality of all possible autoantigens and neoantigens representing a given disease and its sub-types can be identified The total number of antigens if you add all possible variants of human proteins, splice variants of those human proteins and neoantigens is in the millions Use KREX to clone, express and attach every single autoantigen or antigen on to a Sengenics protein array Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Autoantigens identified using Orvar are clinically relevant 16 Tissue from Colorectal Cancer (CRC) individuals (cancer and adjacent normal tissue) were characterised on Orvar: Plasma samples from CRC and healthy individuals were screened against existing KREX proteins KREX proteins Positive on both platforms: Wild-type antigens 13.7% Positive on Orvar only: Neoantigens 9.8% 54.9% New autoantigens 21.6% Homologue autoantigens to KREX proteins which may contain overlapping surface epitopes reactive to the bound autoantibodies GO enrichment analysis: Results indicate % of antigens with high significance (adjusted p-values < 0.01) Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Autoantibodies are superior biomarkers compared to DNA, RNA and proteins 17 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
90% of autoantibodies bind to dis-continuous, conformational epitopes 18 Continuous Dis-continuous Folding independent Folding dependent Non-conformational Conformational epitope 1. *Barlow, D. J., Edwards, M. S., & Thornton, J. M. (1986). Continuous and discontinuous protein antigenic determinants. Nature, 322(6081), 747–748; 2. *Van Regenmortel, M. H. V. (2006, May). Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines. Journal of Molecular Recognition, 19(3), 183–187. Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Sengenics apps: use protein array technology to diagnose and stratify patients 19 CANCER AUTOIMMUNE NEURO CANCER AUTOIMMUNE Early diagnosis of diseases using Predict response and ADRs autoantibodies for cancer and autoimmune drugs using autoantibodies Diagnosis and screening of infectious diseases MICROBES Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Autoantibody assay protocol 20 Microarray Scanner 1. Add sample – 1 to 10μl (Serum, Plasma, CSF, Lung lavage, Tissue homogenate) 2. Autoantibodies in sample bind quantitatively to proteins on array 3. Scan to Quantify Autoantibody signal by adding anti-IgG secondary antibody Confidential © 2008–2021 Sengenics Corporation Pte Ltd
ORVAR autoantigen discovery work flow 21 Autoantigens from tissue source aAb from patient serum 1. Use ORVAR to identify the auto-proteome of interest using patient tissue source and serum 2. Use KREX to clone, express and attach every single autoantigen on to a Sengenics protein array 3. High-throughput quantification of autoantibodies for intra-disease stratification Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Case Study Cancer diagnostics in Melanoma 22 > Stage I/II Melanoma patients (n=124) vs controls (n=121) profiled on Sengenics Immunome arrays “The test, billed as a world first, is designed to make it easier to spot the skin cancer before it becomes fatal, according to researchers.” - BBC, 18 July 2018 139 biomarkers based on cut-off of positive score >5. A panel 10 biomarkers was selected based on a Biomarkers appear primarily related to general VEGFb, p53, MITF, KIT and MLANA have previously been random forest and classification tree analysis, resulted a cancer pathways, including apoptosis, associated with cancer and Melanoma combined sensitivity 84% and specificity 79% and an AUC of pathways associated with the immune 0.828. Biomarkers Panel : ZBTB7B, PRKCH, TP53, PCTK1, response and cell cycle, p53 signaling and the PQBP1, UBE2V1, IRF4, MAPK8_tv2, MSN and TPM1 MAPK signalling pathway, the main pathway associated with melanomagenesis Zaenker, Pauline et al. 2018 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Case Study Stratification of Melanoma patients to Pembro using autoantibodies 23 250000 CTAG2 24A 200000 Average RFU NY-ESO-1 24B > Study Design: 150000 24C 100000 > Metastatic melanoma, BRAF mutant patients, treated 24D 50000 with either Pembrolizumab (anti-PD-1) 24E 0 COL6A1 DDX53 ITGB1 SPANXC NANOG PBK TYR BAGE4 DPPA4 GAGE1 GAGE5 MAGEA4v2 MAGEA5 MAGEB6 MAPK3 TPTE PRKCZ SILV CDC25A CDK7 CTAG2 p53 Q136x p53 S46A ROPN1 SPO11 CALM1 CXorf48.1 FES LIP1 NY-CO-45 p53 K382R AKT1 MAGEA11 5T4/TPBG CSAG2 GDF3 OIP5 SPAG9 SSX2A XAGE3av1 SYCP1 > Patient sera collected at different points of treatment (baseline, post-treatment 1, 2 etc.) > Sera screened on the KREX arrays for the quantification of autoantibodies towards CT antigens 25000 p53 S15A p53 S46A 20000 > Figures show autoantibody profiles across 3 Average RFU p53 K382R 15000 p53 p53 L344P C141Y patients treated with Pembro whom were reported P53 T18A 10000 to have; 47A 5000 47B > complete response (top) 0 > disease progression (middle) COL6A1 DDX53 ITGB1 MAGEA4v2 MAGEA5 MAGEB6 TYR PBK BAGE4 DPPA4 GAGE1 GAGE5 MAPK3 SPANXC NANOG TPTE CDK7 CTAG2 PRKCZ FES ROPN1 SILV CALM1 CDC25A SPO11 AKT1 5T4/TPBG CSAG2 CXorf48.1 GDF3 LIP1 MAGEA11 NY-CO-45 OIP5 p53 K382R p53 Q136x p53 S46A SPAG9 SSX2A SYCP1 XAGE3av1 > initially stable and then disease progression (bottom) 300000 DDX53 > Differences in autoantibody signatures observed 250000 suggest the platform’s potential in providing a 200000 MAGEB6 MAGEB1 Average RFU CTAG2 NY-ESO-1 practical route to patient stratification prior to 150000 51A 100000 treatment 51C 50000 0 51D COL6A1 DDX53 ITGB1 BAGE4 DPPA4 MAGEA4v2 MAGEA5 MAGEB6 GAGE1 GAGE5 PBK SPANXC MAPK3 NANOG TPTE TYR CDK7 CTAG2 FES ROPN1 CALM1 PRKCZ SILV CDC25A SPO11 AKT1 CSAG2 CXorf48.1 GDF3 LIP1 MAGEA11 NY-CO-45 p53 K382R p53 Q136x p53 S46A 5T4/TPBG OIP5 SPAG9 SSX2A SYCP1 XAGE3av1 Source: Unpublished data in collaboration with ONCJRI Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Case Study Diagnostic biomarkers in SLE 24 > Two independent studies both identified well-known SLE autoantigens TROVE2 (Ro60) and SSB (La) showing the most significant difference between SLE and healthy cohorts. (Study 1: 86 SLE patients vs 90 matched healthy individuals Study 2: 10 SLE patients vs 10 healthy individuals) > These studies also identified previously reported SLE autoantigens such as PRM1 (U.S. Patent Application No. 14/418,700). The array also validated other previously reported SLE autoantigens PSME3 (also known as Ki) (M. Matsushita, 2004) Volcano plot summarising the results from a comparison analysis of 86 SLE Comparison analysis of 10 SLE patients VS 10 matched healthy samples run on the patients VS 90 matched healthy samples run on the Sengenics Immunome Sengenics Immunome array in Study 2 array in Study 1 Lewis, M. J., et. al. 2018 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Case Study Autoimmune patient stratification in Lupus 25 > Autoantibody profiles stratify SLE patients significantly based on disease trajectories – potential therapeutic targets based on severity > Identified autoantigens cluster into functional groups, hinting at differing underlying pathogenic mechanisms and possibly at differing treatments for the SLE subgroups > 13 of the novel antigens directly implicated in SLE pathogenesis B Unsupervised clustering of the autoantibody repertoire revealed Two key themes emerged: cluster 2 autoantigens centred around four distinct SLE clusters (1a, 1b, 2, 3) in discovery and validation SMAD2 and SMAD5 were linked to TGF-b/Wnt/BMP signalling; cohort. These clusters represent distinct molecular subtype of SLE cluster 3 autoantigens were implicated in TLR/NF-kB signalling, and different response to treatment apoptosis regulation, and B and T lymphocyte development. Lewis, M. J., et. al. 2018 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Case Study Autoimmune patient stratification in Lupus 26 > Autoantibody profiles stratify SLE patients significantly based on disease trajectories – potential therapeutic targets based on severity > Identified autoantigens cluster into functional groups, hinting at differing underlying pathogenic mechanisms and possibly at differing treatments for the SLE subgroups > 13 of the novel antigens directly implicated in SLE pathogenesis Red = subgroup 1a Purple = subgroup B-cell-directed therapies? 1b (e.g. Rituximab) Green = subgroup 2 Blue = subgroup 3 Non-B-cell-directed therapies? (e.g. cyclophosphamide) Lewis, M. J., et. al. 2018 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Publication Anti-TROVE2 Antibody Determined as a Predictive Marker for Adalimumab 27 Immunogenicity and Effectiveness in RA Good responders Anti-drug antibody (ADAb) positive vs negative patients at baseline and at week 24 of adalimumab therapy > Results: > Panel of top 8 biomarkers identified: autoantibodies Heat map showing clear against TROVE2, SSB, NDE1, ZHX2, SH3GL1, CARD9, distinction between poor PTON20, and KLHL12 and good (purple box) > Combined discriminatory power with: responders to adalimumab therapy > Sensitivity = 77% > Specificity = 81% Panel: 8 biomarkers Mean sensitivity: 0.774 Mean specificity: 0.806 Mean distribution plot from Mean accuracy: 0.790 random forest analysis showing a panel consisting of 8 biomarkers resulting in the most stable performance Anti-TROVE2 had the highest individual discriminating ability, and may serve as a novel predictor of adalimumab immunogenicity. Plasma autoantibody levels against TROVE2 correlated positively with ADAb titres and negatively with drug levels Chen, P. K. et. al., 2021 Patent no. 10202011473Y Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Proposed study design and phases to validation and commercialisation 28 Pilot study Validation Custom Clinical Matched samples Training and Signature ID FDA process Time points Validation set +Orvar proteins Regulatory 6 weeks 8 weeks 12 weeks 2500 2000 1500 1000 500 0 Samples Proteins Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Study design is dependent on disease type and heterogeneity 29 Percentage of Sample Size Estimation and Power Calculation for Various Diseases Category Type of Disease Power (%) Biomarkers 2% 1% 800 90.00% 153 250 Rheumatoid Arthritis 95.00% 189 309 Number of sample size estimation 700 99.00% 267 437 600 Autoimmune 90.00% 128 221 Sjogren’s syndrome 95.00% 149 256 500 99.00% 191 329 400 90.00% 91 116 Gastric Cancer 95.00% 113 143 300 99.00% 159 203 Cancer 200 90.00% 57 90 Non-small-cell lung 95.00% 66 104 100 carcinoma (NSCLC) Statistical 99.00% 85 134 Power 0 90.00% 160 182 Metabolic 0.9 0.95 0.99 0.9 0.95 0.99 0.9 0.95 0.99 0.9 0.95 0.99 0.9 0.95 0.99 0.9 0.95 0.99 Type 2 Diabetes (T2D) 95.00% 186 211 Disorder NSCLC Gastric Cancer T2D Sjogren Rheumatoid Parkinson 99.00% 239 271 Syndrome Athritis 90.00% 357 427 Neurological Parkinson 95.00% 442 528 Percentage of Biomarkers 2% 1% 99.00% 624 746 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Sengenics publications 30 Autoantibodies Targeting TLR and SMAD Pathways Define New Subgroups in Systemic Lupus Erythematosus Lewis, Myles J. et al. 2018 Identification of Novel Native Autoantigens in Rheumatoid Arthritis Poulsen, Thomas B. G. et al. 2020 A U T O I M M U N E Detection of Putative Autoantibodies in Systemic Lupus Erythematous using a Novel Native-conformation Protein Microarray Platform Mak, Anselm. et al. 2020 Anti-TROVE2 Antibody Determined by Immune-Related Array May Serve as a Predictive Marker for Adalimumab Immunogenicity and Effectiveness in RA Chen, Der-Yuan et al. 2021 Functional Protein Microarrays for Parallel Characterisation of P53 Mutants Boutell, Jonathan M. et al. 2004 Seromic Analysis of Antibody Responses in Non-Small Cell Lung Cancer Patients and Healthy Donors Using Conformational Protein Arrays Gnjatic, Sacha et al. 2009 Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation Duarte, Jessica et al. 2013 Serologic Autoantibodies as Diagnostic Cancer Biomarkers — A Review Zaenker, Pauline et al. 2013 C A N C E R Development Of A Novel, Quantitative Protein Microarray Platform for the Multiplexed Serological Analysis of Autoantibodies to Cancer-Testis Antigens Beeton-Kempen, Natasha et al. 2014 Novel Potential Serological Prostate Cancer Biomarkers Using CT100+ Cancer Antigen Microarray Platform in a Multi-Cultural South African Cohort Adeola, Henry A et al. 2016 Autoantibodies May Predict Immune-Related Toxicity: Results from a Phase I Study of Intralesional Bacillus Calmette–Guérin followed by Ipilimumab in Patients with Advanced Metastatic Melanoma Da Gama Duarte, Jessica et al. 2018 A Diagnostic Autoantibody Signature for Primary Cutaneous Melanoma Zaenker, Pauline et al. 2018 B cells and Antibody Production in Melanoma Da Gama Duarte, Jessica et al. 2018 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Sengenics publications 31 Augmentation of Autoantibodies by Helicobacter pylori in Parkinson’s Disease Patients May Be Linked to Greater Severity N E U R O Suwarnalata, Gunasekaran et al. 2016 Autoantibody Profile of Patients Infected with Knowlesi Malaria Liew, Jonathan et al. 2015 Identifying Protein Biomarkers in Predicting Disease Severity of Dengue Virus Infection Using Immune-Related Protein Microarray Soe, Hui Jen et al. 2018 M I C R O B I A L COVID-19 Antibody Testing: From Hype to Immunological Reality Blackburn, Jonathan M et al. 2020 Quantitative, Epitope-specific, Serological Screening of COVID-19 Patients Using a Novel Multiplexed Array-based Immunoassay Platform Blackburn, Jonathan M et al. 2020 A Novel Method to Identify Autoantibodies against Putative Target Proteins in Serum from beta-Thalassemia Major: A Pilot Study Sumera, Afshan et. al. 2020 O T H E R Potential Novel Proteomic Biomarkers for Diagnosis of Vertebral Osteomyelitis Identified using an Immunomics Protein Array Technique Chen, Chang-Hua et al. 2020 Protein Function Microarrays for Customised Systems-Oriented Proteome Analysis Blackburn, Jonathan M, and Shoko, Aubrey 2011 Advances in the Development of Human Protein Microarrays Duarte, Jessica G, and Blackburn, Jonathan M 2017 T E C H N O L O G Y Autoantibody-Based Diagnostic Biomarkers: Technological Approaches to Discovery and Validation Aziz, Farhanah et al. 2018 Applications of Functional Protein Arrays for Detection and Development of Autoantibody-based Diagnostics and Therapeutics Aziz, Farhanah et al. 2018 Confidential © 2008–2021 Sengenics Corporation Pte Ltd
Impact and benefits of using KREX and Orvar technologies 32 Use KREX protein arrays to discover high-accuracy autoantibody signatures Diagnose cancers/autoimmune diseases earlier Predict irAEs at baseline for IO and autoimmune drugs High PPV/NPV drug response prediction Intra-disease stratification Confidential © 2008–2021 Sengenics Corporation Pte Ltd
SEROMAX blood collection kit 33 How to use SEROMAX 1. Wipe alcohol swab across your fingertip 3. Prick finger by pushing lancet firmly down 5. Gently drip blood onto all 4 circles of the 2. Twist off the cap from the lancet with your other hand blood card 4. Press finger lightly towards the puncture 6. Insert blood card into the biohazard bag site to obtain blood before posting the box back to your service provider Sample collection kit which only requires a pin-prick amount of blood for quantifying antibodies or autoantibodies Obviates conventional blood draw and cold chain Leverages sensitivity of KREX platform Enables sample collection during flare-up events Confidential © 2008–2021 Sengenics Corporation Pte Ltd
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