Franz M. Gerner, PhD — Principal Consultant and Founder
Franz Gerner brings 30+ years of AAV gene therapy CMC experience and senior technical leadership, most recently as Chief Technology Officer at a gene therapy company. From PhD research to leading Technical Operations at multiple gene therapy companies, Franz combines deep scientific knowledge with practical business judgment — engaging at every level the program requires, from data review and CDMO oversight to setting strategy with CEOs and boards, and supporting life sciences investors with independent technical due diligence and COGS analysis.
Franz partners with biotech and pharma drug developers across all program stages — from fractional Head of CMC or interim CTO leadership for early-stage biotechs to CMC strategy support for clinical and commercial-stage programs. He works with manufacturers and CDMOs on process and analytical optimization, technology transfer, and facility evaluation and design input from an operational perspective. He also supports investors and strategic partners with technical due diligence and COGS analysis.
What sets Franz apart is the combination of breadth and hands-on capability: cell line and process optimization delivering up to 7-fold yield improvement, plasmid optimization, vector engineering with up to 100-fold potency improvements, facility evaluation and design input from an operational perspective, and technical due diligence supporting acquisition, in-licensing, and COGS-per-patient analyses. This integrated experience covers the full AAV lifecycle from preclinical strategy through commercial readiness, across multiple serotypes and production platforms.
Professional Snapshot
Current Role:
Principal Consultant and Founder, 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 and New Technologies, REGENXBIO (2018-2019)
Senior Director, Process Development, REGENXBIO (2014-2018)
Scope & Experience:
30+ years in AAV gene therapy CMC across multiple companies
International reach: supporting programs across North America, Europe, Asia-Pacific and beyond
Comprehensive AAV expertise: Multiple serotypes (AAV 1-9 and AAVrh10) and production platforms
Full lifecycle experience: Research through commercial readiness
Education:
PhD in Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany (2007). Doctoral research in the AAV gene therapy group of Prof. Michael Hallek at the LMU Gene Center; dissertation: “Optimierung des Adeno-assoziierten Virus Vektorsystems für die in vivo Anwendung” (Optimization of the Adeno-Associated Virus Vector System for In Vivo Application)
Diplom-Chemiker (equivalent to M.S. in Chemistry), Ludwig-Maximilians-Universität München, Germany (1995). Diploma thesis performed at the Max Planck Institute of Biochemistry, Department of Virology, under Prof. Dr. Hofschneider: “Stable synthesis of recombinant Sendai virus surface proteins F and HN in eukaryotic cells”, part of a gene therapy program developing producer cell lines for recombinant virus production
Innovation:
Inventor on three granted US patents as well as multiple pending patent applications in AAV gene therapy
Multiple peer-reviewed publications
Editorial Advisory Board, Cell and Gene Therapy Insights (2022-present)
CMC Steering Committee Member, American Society of Gene & Cell Therapy (ASGCT) (2025-present)
Demonstrated Impact
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 improved yields and quality across programs
Manufacturing Excellence
Developed scalable AAV manufacturing platform delivering up to 7-fold yield improvement while substantially improving product purity through systematic cell line and process optimization across serotypes
Built and led a 25-person PD team improving AAV processes and manufacturing material at 200 L scale for preclinical and analytical use, with the resulting process transferred to a CDMO for clinical manufacturing
Reduced COGS per patient by 30-50% through strategic manufacturing optimization
Established internal manufacturing capabilities including equipment selection, facility design input, team building, and cell line development for improved yield and consistency
Analytical Development & Method Innovation
Developed analytical strategy and characterization plans for AAV programs, overseeing teams executing methods spanning titer, capsid characterization, potency, and impurity testing
Designed sampling plan strategies determining material requirements for release testing, characterization, stability, and retain samples
Coordinated multi-site analytical testing across internal teams and external CROs, ensuring data quality, method comparability, and timeline reliability
Track record of advancing analytical methods ahead of regulatory requirements — from early qPCR-based titer methods (2000) to current strategic guidance preparing client programs for evolving FDA expectations
Regulatory & Quality Leadership
Authored CMC sections (Module 3) for multiple IND submissions and coordinated timely responses to FDA and EMA regulatory queries
Established GMP-compliant manufacturing and quality control operations
Developed comparability strategies for process changes to support 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 a clinical-stage AAV-CRISPR program
Built highly efficient teams meeting budget targets and timeline commitments
Managed company-wide CMC budgets, resource allocation, and cross-functional coordination across R&D, preclinical, clinical, and regulatory functions
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)
Principal Consultant and Founder
Supporting drug developers, manufacturers and CDMOs, as well as investors and strategic partners across the full spectrum of AAV gene therapy CMC through project-based and retainer consulting — including manufacturing and analytical strategy, viral vector design optimization, GMP facility planning, external manufacturing strategy, comparability planning, and technical due diligence. Fractional Head of CMC or interim CTO leadership available for early-stage drug developers requiring senior CMC oversight without a full-time commitment.
Excision BioTherapeutics, Inc. (2021-2023)
Chief Technology Officer
Led Technical Operations for clinical-stage AAV-CRISPR program, engaging from process and analytical strategy through CDMO oversight, with accountability for on-time CMC responses to FDA and company-wide CMC strategy and budget oversight.
Key Achievements:
Established comprehensive Technical Operations strategy encompassing process development, analytical development, manufacturing, QC, supply chain, and QA
Managed company-wide CMC budget and conducted cost per patient analysis
Built and led efficient technical team meeting all budget and timeline goals
Sio Gene Therapies, Inc. (formerly Axovant Gene Therapies, Ltd.) (2019-2021)
Vice President, Technical Operations
Directed Technical Operations for AAV gene therapy programs at Sio, including manufacturing strategy and CDMO oversight across multiple programs 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 analytical strategy, including method qualification and validation planning to prepare programs for late-stage development
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 up to 7-fold AAV yield improvement while substantially improving product purity through systematic cell line and process optimization
Supported formulation and device compatibility for improved stability and administration
Authored IND development and manufacturing sections and supervised technology transfer to CDMOs
Conducted technical due diligence supporting acquisition evaluation and in-licensing assessments, as well as COGS-per-patient analyses informing strategic decisions
Omnia Biologics, Inc. (2013-2014)
Director of Process Development and Manufacturing
Supported process development and GMP manufacturing operations at a CDMO serving biotech clients.
Key Achievements:
Gained operational experience with GMP manufacturing readiness, quality systems, and CDMO client management from the manufacturer's perspective
Wellstat Ophthalmics Corp. (2006-2013) (formerly Advanced Vision Therapies, Inc.)
Senior Scientist
Designed and executed gene therapy approaches using recombinant AAV and lentiviral vectors for ophthalmic indications.
Key Achievements:
Developed and improved production and purification methods for AAV and lentiviral vectors with reliable, consistent results within tight timelines
Established analytical methods for characterization and quantification of viral vectors and process-related contaminants
Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany (1999-2005)
Graduate Student (PhD Research)
Foundational research in AAV vector optimization.
PhD Thesis: “Optimierung des Adeno-assoziierten Virus Vektorsystems für die in vivo Anwendung” (Optimization of the Adeno-Associated Virus 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
Established methods that informed subsequent AAV vector development work
Theragene Biomedical Laboratories GmbH, Martinsried, Germany (1997-1999)
(Formerly a subsidiary of Octapharma; now Octapharma Biopharmaceuticals)
Research Scientist
Built laboratory operations and designed research projects for a newly founded gene therapy startup.
Key Achievements:
Set up, equipped, and maintained new laboratories
Completed milestones well ahead of schedule while reducing costs by 10%
Reported directly to the CSO of parent company Octapharma
Max Planck Institute of Psychiatry, Munich, Germany (1995-1997)
Research Scientist
Early AAV vector research in neuroscience.
Key Achievements:
Established a novel AAV-based antisense approach to reduce expression of an endogenous receptor
Why Work with Franz?
Deep Technical Expertise
Beyond strategic advice, Franz works on actual technical problems. With a PhD in Chemistry and 30+ years specializing in AAV gene therapy CMC, he brings the technical depth required for complex client challenges.
Full Lifecycle Experience
From vector design through commercial readiness, Franz has worked across every stage of AAV development. He understands how early decisions shape late-stage outcomes.
Business Acumen
As a former Chief Technology Officer managing company-wide CMC strategy and budgets, Franz understands that technical excellence must align with timelines, budgets, and strategic objectives. This includes representing CMC programs to investors and boards, and translating technical decisions into business and economic terms that non-CMC stakeholders can act on.
Proven Innovation
Multiple patents and publications demonstrate a track record of developing novel solutions for AAV manufacturing and analytics. Franz brings systematic problem-solving and a willingness to innovate when standard approaches reach their limits.
Regulatory Knowledge
Direct experience preparing CMC content for pre-IND packages, authoring and reviewing Module 3 sections for IND submissions, and drafting CMC responses to FDA and EMA queries. Franz knows what regulators expect and how to present programs effectively.
Industry Network and Relationships
Three decades in gene therapy means deep industry relationships — from CDMOs and analytical CROs to fill-finish specialists, equipment vendors, cold chain and logistics providers, as well as facility design partners.
Client-Focused Approach
Flexible engagement models tailored to client needs — from project-based and retainer engagements to fractional Head of CMC or interim CTO leadership for early-stage drug developers requiring senior CMC oversight without a full-time commitment. Clients work directly with Franz throughout each engagement, combining senior-level perspective with hands-on technical involvement. Responsive, practical, and focused on client outcomes.
Areas of Specialization
Vector Design & Optimization
Optimizing AAV vectors for therapeutic efficacy and manufacturability — most design choices are compatible, but certain technical decisions around payload, capsid, and packaging can create downstream manufacturing challenges if not anticipated.
Plasmid Manufacturing Strategy
Plasmid design and manufacturing for AAV production — an under-recognized determinant of program success, where ITR stability, bacterial strain selection, and supply chain decisions can quietly drive yields and timelines.
Manufacturing / Process Development
Systematic optimization of upstream and downstream processes — combining hands-on technical knowledge with the cost discipline that translates yield improvements into program economics.
Empty Capsid Challenges
One of the most pressing current challenges in AAV manufacturing — meeting evolving regulatory specifications for full capsid content through purification strategy choices that often have to be made before clinical trial supplies are produced.
Analytical Method Development
Strategic oversight of analytical method development and validation — particularly for challenging measurements like empty/full capsid ratios, potency assays, and the analytical methods that anticipate evolving regulatory requirements.
Comparability
Demonstrating that material made before and after a process, scale, or site change is the same product — where the work is far cheaper to plan before the change than to reconstruct afterward from data that was never designed to support it.
Technology Transfer
Structured transfer of AAV processes between sites or to CDMOs — where success depends as much on knowledge transfer and protocol design as on the science itself.
CDMO Selection & Management
CDMO evaluation, selection, and ongoing partnership management — drawing on direct experience working with numerous CDMOs and transferring processes, providing perspective from both client and CDMO sides of the relationship.
Facility Evaluation & Equipment Selection
Facility evaluation and design input from a CMC and operational perspective — collaborating with equipment vendors, architects, and contractors so the facility is designed to support the manufacturing process from the start, not assessed only on paper.
Clinical Supply Chain & Logistics
International supply of frozen AAV material to clinical sites — where programs can lose material and time, and the highest-risk steps are often the handoffs between manufacturer, courier, depot, and site.
Regulatory Strategy
Phase-appropriate CMC strategy that satisfies regulators while managing cost and timeline efficiently — applying risk-based prioritization to know what FDA and EMA expect at each stage, what can responsibly wait, and where to focus investment.
Due Diligence
Technical assessment of AAV programs for investors and strategic partners — identifying risks and opportunities before they become expensive problems, with COGS modeling and platform feasibility evaluation grounded in real manufacturing experience.
In addition to consulting engagements, Franz is selectively open to board and Scientific Advisory Board (SAB) positions for early-stage gene therapy companies.
Patents & Industry Engagement
Granted Patents: AAV Manufacturing
Scalable clarification process for recombinant AAV production (US 12,365,865 B2)
Anion exchange chromatography for recombinant AAV production (US 12,070,702 B2)
Scalable method for recombinant AAV production (US 12,612,644 B2)
Patent Applications: Vector Design and Therapeutic Constructs
Gene therapy for neuronal ceroid lipofuscinoses (US 2021/0393802 A1)
Fully-human post-translationally modified antibody therapeutics (US 2022/0195462 A1)
Treatment of ocular diseases and metastatic colon cancer with human post-translationally modified VEGF-trap (CA 3079565 A1)
Publication & Citation Record
Editorial & Review Activities
Editorial Advisory Board: Cell and Gene Therapy Insights (2022-present)
Peer Reviewer: Molecular Therapy Methods & Clinical Development (ongoing)
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 & Cell Therapy (ASGCT)
Member since 2000CMC Steering Committee Member
(2025-present)
European Society of Gene & Cell Therapy (ESGCT)
Member since 2016International Society for Pharmaceutical Engineering (ISPE)
Member since 2018Parenteral Drug Association (PDA)
Member since 2020BLPN (Building Legendary Professional Networks, formerly Bullpen)
Founding Member since 2025
Invite-only, Member-Led Life Science Dealmaker ClubInternational 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, acceptable to regulators, and commercially viable. Every program is different, and cookie-cutter approaches rarely work in gene therapy. I take time to understand each client's unique situation and provide tailored solutions that work in their specific context."
Ready to Discuss Your AAV Program?
Whether you are advancing CMC strategy and execution, building manufacturing capability, optimizing existing processes, or conducting technical due diligence, you can leverage 30+ years of AAV gene therapy CMC experience spanning vector design, process and analytical development, regulatory strategy, and senior CMC leadership.
Direct collaboration with Franz throughout — strategic perspective grounded in hands-on technical depth across the full CMC lifecycle.