Franz M. Gerner, PhD - Principal Consultant
Franz Gerner brings 30+ years of hands-on expertise in AAV gene therapy CMC, with a proven track record of solving complex manufacturing challenges that others couldn't crack. From groundbreaking PhD research optimizing AAV production at Ludwig-Maximilians-University to leading Technical Operations at multiple gene therapy companies — including as Chief Technology Officer at Excision BioTherapeutics — Franz combines deep scientific knowledge with practical business acumen to help clients achieve their CMC goals on time and within budget.
Franz provides comprehensive AAV CMC expertise spanning process development, analytical methods, regulatory strategy, and manufacturing optimization. What truly sets him apart is combining this breadth with unique hands-on capabilities: facilities design from a CMC/process perspective (not just architectural engineering), plasmid optimization and redesign for improved AAV production, and vector optimization expertise delivering up to 100-fold potency improvements. This integrated approach covers the entire development lifecycle from vector design through commercial readiness, across all AAV serotypes and production platforms..
PROFESSIONAL SNAPSHOT
Current Role:
Principal Consultant, South Mountain Advanced Therapies Consultants (2023-Present)
Previous Leadership:
Chief Technology Officer, Excision BioTherapeutics (2021-2023)
Vice President, Technical Operations, Sio Gene Therapies (2019-2021)
Senior Director, Technical Innovation & Process Development, REGENXBIO (2014-2019)
Scope & Experience:
30+ years in AAV gene therapy CMC across multiple companies
International reach: Supporting programs across North America, Europe, and globally
Comprehensive AAV expertise: All serotypes (AAV1-9) and production platforms
Full lifecycle experience: Research through commercial readiness
Education:
PhD, Virology/Biochemistry, Ludwig-Maximilians-University, Munich, Germany (2007)
Diplom-Chemist (equivalent to M.S.), Ludwig-Maximilians-University (1995)
Innovation:
3 patents in AAV production and purification
Multiple peer-reviewed publications
Editorial Advisory Board, Cell and Gene Therapy Insights (2023-present)
DEMONSTRATED IMPACT
Manufacturing Excellence
Developed scalable AAV manufacturing platform achieving 7-fold yield improvement with >80% purity enhancement
Led cross-functional teams of 25+ scientists delivering multiple clinical trial supplies on schedule
Reduced COGS per patient by 30-50% through strategic manufacturing optimization
Directed teams in scaling processes from research scale to clinical-scale manufacturing (200L+)
Established internal manufacturing capabilities including equipment selection, facility design, team building, and cell line development for improved yield and consistency
Vector Optimization & Innovation
Optimized vector design delivering up to 100-fold potency improvements — transforming program economics and enabling previously unviable programs
Engineered viral vectors including ITR modifications for self-complementary AAV and refined expression cassettes for enhanced performance and reduced immunogenicity
Patents in AAV manufacturing: scalable clarification, anion exchange chromatography, and scalable production methods
Identified, evaluated, and implemented new technologies that became industry best practices for enhanced yields and quality
Regulatory & Quality Leadership
Authored CMC sections (Module 3) for multiple successful IND submissions and coordinated timely responses to FDA and EMA regulatory queries
Established GMP-compliant manufacturing and quality control operations
Developed comparability strategy for process changes ensuring regulatory acceptance
Conducted technical audits of vendors and CDMOs for manufacturing capability assessment
Phase-appropriate development planning balancing risk and resource allocation
Business & Strategic Leadership
As CTO, oversaw Technical Operations strategy for multiple viral and non-viral gene therapy programs
Built highly efficient teams meeting budget targets and timeline commitments
Managed departmental budgets, resource allocation, and cross-functional coordination across R&D, preclinical, clinical, and regulatory departments
Analyzed cost per patient and provided technical assessments to inform strategic business and investment/M&A decisions
Directed technology transfer to multiple CDMOs with zero delays to clinical timelines
PROFESSIONAL BACKGROUND
South Mountain Advanced Therapies Consultants (2023-Present)
Independent Consultant
Supporting clients across the full spectrum of AAV gene therapy CMC: manufacturing and analytics for early-stage clinical trials, viral vector design optimization, GMP facility planning, external manufacturing strategy, comparability planning, and due diligence from a CMC perspective
Excision BioTherapeutics, Inc. (2021-2023)
Chief Technology Officer
Led Technical Operations for multiple viral and non-viral gene therapy programs.
Key Achievements:
Established comprehensive Technical Operations strategy encompassing process development, analytical development, manufacturing, QC, supply chain, and QA
Managed departmental budget and conducted cost per patient analysis
Built and led efficient technical team meeting all budget and timeline goals
Sio Gene Therapies, Inc. (2019-2021)
Vice President, Technical Operations
Directed all Technical Operations activities supporting on-time clinical trial material supply.
Key Achievements:
Evaluated cost per patient for multiple programs in coordination with commercial team
Reviewed COGS from several CDMOs, informing manufacturing strategy
Led qualification and validation of analytical methods for late-stage programs
REGENXBIO, Inc. (2014-2019)
Senior Director, Technical Innovation and New Technologies (2018-2019)
Senior Director, Process Development (2014-2018)
Built internal process development capabilities and drove innovation agenda.
Key Achievements:
Established and led laboratory infrastructure and team of 25 personnel developing scalable manufacturing platform
Achieved 7-fold yield improvement with >80% purity enhancement through systematic optimization
Supported formulation and device compatibility for improved stability and administration
Authored IND development and manufacturing sections and supervised technology transfer to CDMOs
Omnia Biologics, Inc. (2013-2014)
Director of Process Development and Manufacturing
Led process development and GMP manufacturing for CDMO clients.
Gene Center, Ludwig-Maximilians-University, Munich (1999-2005)
Graduate Student (Ph.D. Research)
Pioneering research in AAV vector optimization.
PhD Thesis: "Optimization of the adeno-associated virus (AAV) vector system for in vivo application"
Key Contributions:
Significantly improved rAAV vector yield and purity through production and purification optimization
Developed detection methods for virus analysis
Fundamental work that continues to influence the field
WHY WORK WITH FRANZ?
Deep Technical Expertise
Not just strategic advice—Franz solves actual technical problems. With a PhD in Virology/Bio-chemistry and 30+ years specializing in AAV gene therapy CMC, he brings unmatched technical depth to client challenges.
Full Lifecycle Experience
From vector design concept through commercial readiness, Franz has lived every stage of AAV development. He understands how early decisions impact late-stage outcomes.
Regulatory Knowledge
Direct experience authoring regulatory submissions and interacting with FDA. Franz knows what regulators need to see and how to present it effectively.
Proven Innovation
Patents and multiple publications demonstrate a track record of developing novel solutions that advance the field. When standard approaches don't work, Franz innovates.
Business Acumen
As a former CTO, Franz understands that technical excellence must align with business realities—timelines, budgets, and strategic objectives matter.
Extensive Network
Thirty years in gene therapy means extensive industry relationships—from CDMOs and analytical service providers to equipment vendors and facilities design specialists. Franz helps clients find the right partners, evaluate technologies, and design optimal manufacturing facilities.
Client-Focused Approach
Flexible engagement models tailored to client needs—from hourly consulting to comprehensive program support. Responsive, practical, and focused on client success.
AREAS OF SPECIALIZATION
Vector Design & Optimization
Optimizing vectors for both therapeutic efficacy and manufacturing feasibility—these don't always align naturally, and Franz has deep expertise in balancing both.
Facility Design & Equipment Selection
Unlike consultants who only provide recommenda-tions, Franz works hands-on with equipment ven-dors, architects, and contractors. Expertise spans cleanroom design, equipment specification, utility planning, and workflow optimization—ensuring facilities are built right the first time.
Plasmid Manufacturing Strategy
Deep expertise in plasmid design and manufactur-ing for AAV production, including ITR stability optimi-zation, bacterial strain selection, and GMP-grade plasmid supply chain management.
Manufacturing / Process Development
Systematic optimization of upstream and down-stream processes to maximize yield, purity, and cost-effectiveness. Proven track record of dramatic improvements.
Empty Capsid Challenges
Extensive experience addressing one of the most pressing current challenges in AAV manufacturing — achieving regulatory specifications for full capsid content through optimized purification strategies.
Technology Transfer
Structured approach to transferring AAV processes between sites or to CDMOs. Ensures process con-sistency, comprehensive knowledge transfer, and successful implementation at receiving facilities through detailed protocols and hands-on support.
CDMO Selection & Management
Having worked with numerous CDMOs and trans-ferred multiple processes, Franz provides com-prehensive CDMO evaluation, selection guidance, and ongoing partnership management for success-ful outcomes.
Analytical Method Development
Development and validation of characterization methods, particularly for challenging measurements like empty/full capsid ratios and potency assays.
Due Diligence
Comprehensive technical assessment of AAV programs for investors, helping identify risks and opportunities before they become expensive problems.
Regulatory Strategy
Phase-appropriate CMC strategy that satisfies regulators while managing cost and timeline efficiently.
TECHNICAL EXPERTISE
Production Methods
Transient transfection (PEI, calcium phosphate, lipid-based)
Baculovirus/Sf9 systems
Stable producer and packaging cell lines
Platform selection and optimization
Plasmid Design & Manufacturing
ITR stability optimization for AAV production (deletion strategies, sequence modifications)
Plasmid design optimization (genomic load, CpG content, regulatory elements
Bacterial strain selection (Stbl2, SURE, DH10B) for ITR-containing plasmids
Manufacturing process development and scale-up optimization
GMP-grade plasmid manufacturing and supply chain management
Plasmid characterization and quality control (isoform percentage, residuals, safety testing)
Purification Technologies
Affinity chromatography (POROS CaptureSelect, AVIPURE AAV resin)
Ion exchange chromatography (Capto Q, other AEX resins and monolith)
Tangential flow filtration / ultrafiltration
CsCl and iodixanol ultracentrifugation
Depth filtration and clarification
Analytical Methods
Titer: qPCR, ddPCR, ELISA, A260/A280
Capsid Content: AUC, AEX-HPLC, TEM, CDMS
Characterization: LC-MS/MS (VP ratios), Capillary Western blot, CE-SDS
Potency: Cell-based transduction assays, functional assays
Impurities: HCP, HCD, residual plasmid, process-related impurities
Safety: Sterility, endotoxin, mycoplasma, rcAAV
Formulation & Fill-Finish
Formulation buffer development and optimization
Fill-finish process development
Semi-automated vs. fully automated systems
Compatibility and stability studies
Vector Platforms
AAV: All natural serotypes (AAV1-9), engineered variants, single-strand and self-complementary
Plasmid DNA: Regulatory-grade manufacturing and banking
Manufacturing Infrastructure
Facility design from CMC and process perspective
Equipment selection, specification, and vendor evaluation
Cleanroom layout optimization and material flow design
Utility requirements assessment (power, gas, cooling water)
AAV-specific material compatibility evaluation
Pocess & Technology Transfer
CDMO technology transfer coordination and oversight
Comparability protocol development and assessment
Tech transfer documentation and knowledge management
Regulatory & Quality
CMC section authoring of regulatory submissions
FDA and EMA interaction
GMP manufacturing strategy
Vendor audit support
Quality systems implementation strategy
Deviation and CAPA management
Comparability protocols
Business & Strategy
Cost of goods analysis
Manufacturing cost optimization
CDMO evaluation and selection
Due diligence and technical assessment
Departmental budget management
Strategic planning and resource allocation
Technology assessment and selection (platform evaluation, vendor comparison)
Program timeline management and critical path analysis
Risk assessment and mitigation strategies
PUBLICATIONS & PATENTS
Patents
Scalable clarification process for recombinant AAV production (WO/2019/212921)
Anion exchange chromatography for recombinant AAV production (WO/2019/241535)
Scalable method for recombinant AAV production (WO/2020/033842)
Editorial & Review Activities
Editorial Advisory Board: Cell and Gene Therapy Insights (2023-present)
Peer Reviewer: Molecular Therapy Methods & Clinical Development
Speaking Engagements & Industry Participation
Roundtable participant: "The Cell & Gene Therapy Journey: Discovery to Commercialization" - Charles River Cell & Gene Therapy Summit, San Francisco, CA (2025)
Roundtable participant: "Viral Vector Gene Therapy Journey (from Discovery to Commercialization)" - Charles River Cell and Gene Therapy Summit, London, UK (2024)
Roundtable participant: "Viral Vector Production Process Intensification: Analytics, Automation, In-line Testing"
- Cell and Gene Therapy Insights (2021) View PublicationInvited speaker: "Challenges of comparing the quantity and quality of different AAV manufacturing methods" - Cell and Gene Therapy Innovation Summit, Berlin, Germany (2019)
Invited speaker: "Monolith Columns for purification of AAV" - Bioprocess International Europe, Monolith Symposium, Portoroz, Slovenia (2018)
Invited speaker: "Process Development Strategies for Viral Vectors used in Gene Therapy" - Bioprocess International Europe, Amsterdam, The Netherlands (2018)
PROFESSIONAL AFFILIATIONS
Memberships
American Society of Gene Therapy (ASGCT)
Member since 2000CMC Committee Member
(2025-present) - Newly appointed
European Society of Gene & Cell Therapy (ESGCT)
Member since 2016International Society for Pharmaceutical Engineering (ISPE)
Member since 2018Parenteral Drug Association (PDA)
Member since 2020International Society for BioProcess Technology (ISBiotech)
Member 2010-2023
PERSONAL PHILOSOPHY
"The best gene therapy is the one that reaches patients. Technical excellence is essential, but it must be balanced with practical considerations—timelines, budgets, and regulatory requirements. My goal is to help clients navigate complex CMC challenges with solutions that are scientifically sound, regulatorily acceptable, and commercially viable. Every program is different, and cookie-cutter approaches rarely work in gene therapy. I pride myself on understanding each client's unique situation and providing tailored solutions that work in their specific context."
READY TO DISCUSS YOUR PROGRAM?
Whether you're facing specific technical challenges, planning your manufacturing strategy, or evaluating potential partners, Franz brings the expertise and experience to help you succeed.
Schedule a confidential, no-obligation consultation to discuss how SMAT Consultants can support your AAV program.