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A Platform Approach to Functional Potency Assay Development for Gene Therapy Products

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A Platform Approach to Functional Potency Assay Development for Gene Therapy Products absorption.com A PLATFORM APPROACH TO FUNCTIONAL POTENCY ASSAY DEVELOPMENT FOR GENE THERAPY PRODUCTS November 20, 2019 Karen Doucette, Director of Operations Gene Therapy Analytical Development Summit Renaissance Boston Waterfront Hotel TABLE OF CONTENTS • Streamlining development of functional potency assays • Case studies for diverse product types with custom and complex MOA • Bridging the gap between R&D and cGMP for commercially viable potency assays 2 Copyright 1999-2019 Absorption Systems LLC TYPES OF GENE THERAPY PRODUCTS Multiple delivery systems: Plasmid DNA Viral vectors Bacterial vectors Human gene editing Patient-derived cellular gene therapy Selection based on: Tissue tropism Packaging capacity Immunogenicity Image: CBER, US FDA Mechanism of action depends on: https://www.fda.gov/vaccines-blood-biologics/cellular-gene-therapy-products/what-gene-therapy In vivo or ex vivo Vector or non-vector Viral vector or non-viral vector 3 Copyright 1999-2019 Absorption Systems LLC IN VITRO RELATIVE POTENCY Potency is defined as “the specific ability or capacity of the product…to effect a given result.” Validation Parameters: Accuracy Precision (Repeatability, Intermediate Precision) Specificity Linearity and Range System Suitability Robustness 4 Copyright 1999-2019 Absorption Systems LLC GENE THERAPY MECHANISM(S) OF ACTION Multi-Step Process Based on Central Dogma of Molecular Biology 1. Gene is delivered to cell 2. Gene is turned on Potency assay must reflect expression and activity 3. Gene encodes for protein 4. Protein is functional Infection Transcription Translation Activity Protein functions Vector/ • Antibody DNA mRNA Protein Function • Enzyme Plasmid • Messenger • Structure • Transport • Storage Gene Cell Nucleus Cytoplasm Body • Channels • Binding • Other 5 Copyright 1999-2019 Absorption Systems LLC STEP 1 - INFECTION Multi-Step Process Based on Central Dogma of Molecular Biology 1. Gene is delivered to cell DOE for Transduction Efficiency 2. Gene is turned on MOI Time Points Enhancers 3. Gene encodes for protein 1x104 24 hr Sodium butyrate 4. Protein is functional 1x105 48 hr Neuraminidase 72 hr Etoposide Infection None Virus: AAV2-CMV-GFP Cells: HEK293 cells (P48) Vector/ No AAV-GFP 4 MOI 1x105 DNA mRNA Protein Function MOI 1x10 Plasmid FSC Gene Cell Nucleus Cytoplasm Body MFI119 MFI605 GFP 6 Copyright 1999-2019 Absorption Systems LLC CASE STUDY 1 - TRANSDUCTION EFFICIENCY (CAPSID) Design: • AAV9-GFP under ubiquitous promoter • 6 cell lines selected for screening based on literature for potential be permissibility to AAV9 • 2 MOIs • With and without enhancer (neuraminidase) Transduction Efficiency Screening Conclusions: 120 • 2 cell lines were transducible without enhancer (#2 100 and #6) • Enhancer increased transduction in 5 of 6 cell lines 80 (green bars) 60 without enhancer • Cell line #6 had the highest transduction efficiency, 40 and comparable efficiency with and without enhancer, with enhancer 20 so this cell line was selected % of expressing cells GFP 0 1 2 3 4 5 6 Cell Line # 7 Copyright 1999-2019 Absorption Systems LLC STEP 2 - TRANSCRIPTION Multi-Step Process Based on Central Dogma of Molecular Biology 1. Gene is delivered to cell 2. Gene is turned on 3. Gene encodes for protein 4. Protein is functional Infection Transcription Vector/ Ubiquitous Tissue-Specific DNA mRNA Protein Function Plasmid Promoters Promoters (TSP) CMV Liver CßA Retina EF1a Brain Gene Cell Nucleus Cytoplasm Body SV40 Others 8 Copyright 1999-2019 Absorption Systems LLC CASE STUDY 2 - TRANSDUCTION EFFICIENCY (PROMOTER) Design: • AAV5-XXX-eGFP • Cell line from target tissue MOI 1E5 / CMV • Ubiquitous promoter (top panels) and tissue-specific promoter (TSP, bottom panel) • 2 MOIs • With and without enhancers (sodium butyrate and etoposide) MOI 1E6 / CMV Conclusions: • Capsid is permissible to the cell line MOI 1E6 / TSP • Enhancers increased transduction with ubiquitous promoter • Cell line does not contain sufficient endogenous transcription factors for TSP 9 Copyright 1999-2019 Absorption Systems LLC STEP 3 - TRANSLATION Multi-Step Process Based on Central Dogma of Molecular Biology 1. Gene is delivered to cell 2. Gene is turned on 3. Gene encodes for protein 4. Protein is functional Infection Transcription Translation Specificity from endogenous protein: Vector/ DNA mRNA Protein Function Plasmid Subtract background from NTC Knock out endogenous with CRISPR Knock down endogenous with LV-shRNA Gene Cell Nucleus Cytoplasm Body 10 Copyright 1999-2019 Absorption Systems LLC CASE STUDY 3 – CELL LINE DEVELOPMENT ABCG2/BCRP Knockdown VC Cell line with endogenous expression Lentiviral shRNA constructs with 5 different sequences Western blot and RT-qPCR to confirm reduced expression Stable knockdown cell line used for FDA-recommended functional activity assays 11 Copyright 1999-2019 Absorption Systems LLC STEP 4 - ACTIVITY Multi-Step Process Based on Central Dogma of Molecular Biology 1. Gene is delivered to cell 2. Gene is turned on 3. Gene encodes for protein 4. Protein is functional Infection Transcription Translation Activity Protein Functions Vector/ DNA mRNA Protein Function • Antibody Plasmid • Enzyme • Messenger • Structure • Transport Gene Cell Nucleus Cytoplasm Body • Storage • Channels • Binding • Other 12 Copyright 1999-2019 Absorption Systems LLC FUNCTIONAL POTENCY ASSAY EXAMPLES Enzyme Transporter Transcription Ligand Interaction Factor X X X X E X Y Promoter Y Y Y Y LC-MS/MS for LC-MS/MS for ELISA or cell-based PLA assay for X binding formation of accumulation of ddPCR for mRNA bioassay for binding of X to Y with no known product Y substrate X expression of Y causing downstream Y downstream mechanism e.g. RPE65 ABCA4 훃-catenin VEGF ?? Therapeutic Gene 13 Copyright 1999-2019 Absorption Systems LLC TIMELINES FOR CUSTOM POTENCY ASSAYS Start functional potency assay development as early as possible Phase 1/2 Phase 3 Start bridging the gap from R&D to cGMP once assay feasibility is established Potency Feasibility/ Development/ Qualification Spec Setting Validation Assay POC Optimization 4-6 months 4-6 months 3-6 months 3-6 months 3-6 months Maintain a development narrative to justify assay conditions based on product knowledge 14 Copyright 1999-2019 Absorption Systems LLC BRIDGING THE GAP R&D BRIDGE GMP R&D scientists with different skill sets Establish assay-specific time and Multiple GMP analysts must be trained in Analysts for POC (cell culture, molecular material requirements for training new multiple lab techniques for a single assay biology, bioassay, analytical) analysts on custom assays Explore commercial sources and GMP R&D grade, may come from academic grade material during assay GMP grade supplied by approved vendors Reagents or non-GMP sources with no incoming optimization, gather data to set specs and part of reagent management system reagent specifications for critical reagents QA begin vendor qualifications, and Vendors May not be approved by QA explore alternatives if vendor does not Approved by QA meet quality requirements Begin IOPQ process, and plan for May not be validated or have Validated (IOPQ) with inter- and intra-lab Equipment feasibility and cost of establishing redundancy redundancy redundancy of customized equipment Pursue validation package if available, Validated (i.e., meet Part 11/ Annex 11 data Software May not be validated establish compliant work-around integrity requirements for unique logins, audit procedures if not trail, etc.) Protocol driven and recorded in lab Transferred to SOP and forms, with system Processes Process map, involve QC lab early notebooks and sample suitability criteria established 15 Copyright 1999-2019 Absorption Systems LLC BRIDGING THE GAP Using traditionally R&D assays for GMP release Involve the QC lab early Business Process Modeling and Notation (BPMN) Prepare QA to qualify R&D vendors and Example: What the task of splitting a cell culture flask looks like in BPMN validate R&D equipment & software Each Task of the assay/SOP can be mapped in a similar fashion Process Map to streamline transfer to GMP Robust Reproducible Compliant R&D protocol step of “Split flask” = a 4-6 step process in a method SOP 16 Copyright 1999-2019 Absorption Systems LLC TO LEARN MORE Meet our experts here at the conference or Visit any of our locations Boston – Philadelphia - San Diego https://www.absorption.com/kc/potency-assay-guide-2019/ 17 Copyright 1999-2019 Absorption Systems LLC absorption.com THANK YOU .
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