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Priyabrata Pattnaik, PhD
Director & Head of Biologics Operations
Asia Pacific
Production and
purification of
Viral vectors for
gene and cell
therapy
applications
The cell & gene therapy market is poised for rapid growth
with projections reaching ~$10B in 5 years
Source: Seed Planning; METI; Kuick Research; Med Market Diligence;Transparency market research
Global market
size & CAGR
USD B
Products in
the pipeline
74
74
34
54
75
Stem cell
therapy
106
17
14
Cellular
therapy,
other
123
15
Gene
therapy
144
16
Phase I
Phase II
Phase III
10
9
1
12
8
3
2020
+36% p.a.
20182012
Kuick research (India)
See Planning/
METI (Japan)
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 20162
The cell & gene therapy market can be split into 3 broad segments...
Description and
examples Major players
Cell & gene
therapy
Non-geneti-
cally modified
cell therapies
• Purified populations of
allogeneic cells are
expanded and injected
topically
• E.g., mesenchymal stem
cells
Viral gene
therapies
• Drug product is virus
particle, injected into
patient topically (or
systemically)
• E.g., Spark’s night-
blindness therapy
• Autologous patient cells are
extracted, genetically
modified using viral
transduction, then reinfused
into the patient
• E.g., CAR T-cell therapy
Genetically
modified cell
therapies
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 20163
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
3 broad segments
Gene Therapy Stem-cell Therapy Cell Immunotherapy
Gene Therapy
Stem-cell Therapy
Cell Immunotherapy
 Nucleic acid
 Lenti/Adeno virus-based delivery
 Somatic or germline
 Stem cells banking
 Replace or regenerate organs and tissue
 Broad use of bone marrow in ALL
 Autogenetic CAR-T
1. Most common
2. Immune cells separation
3. Lentivirus-based delivery
4. Chimeric Antigen Receptors (CARs)
 Allogeneic modified T cells
1. Industrialized trend
2. Genetic modification of immune cells
3. Allogeneic T cell generation
4. Lentivirus-based delivery or genome edit (CRISPR)
CAR-TVirus
Stem cells
T-cells
Virus
CAR-T
4
Methods for producing genetically modified T-cells for
immunotherapy
Source: Bure et al. (2016) Automation of CAR-T Cell Adoptive Immunotherapy Bioprocessing. Bioprocess International, 14(4)s: 22-31.
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 20165
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Overall Process Map of CAR-T
T-cell separation
Virus generation
GMP-grade lentivirus
 Recovery rate= 70%
 2.5*109 virus per trial
 5*106 titer/ml
 500ml bulk
T-cell modification
 MOI=5
 1.7*109 virus per trial
Car-T Cell Amplification
Reintroduction
 5*106 CAR-T/kg
 E.g.: 70 kg weighting
 3.5*108 CAR-T per trial
6
7 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Viral Vectors For Gene Therapy
Introduction
Gene Therapy – Main Applications:
• Treat Heridatery Single-Gene Defects.
• Cancer
• Cardiovascular Diseases
• Ocular Diseases
• Infectious Diseases
• Other Diseases Where Gene Transfer Will Have an Impact
Main Features for Virus-Based Vectors:
• Lacks Viral Genes Involved in Replication.
• Expression Cassette is Cloned into the Vector.
• Helper Function is Provided in trans
• Co-Transfection of Vector Genome and Packaging Construct Produce Recombinant Vecotor
8
~60% of the vaccines undergoing clinical trials are viral based.
 ~ 640 viral vaccines
 ~ 200 viral vectors
 ~ 60 virus like particles
 Another ~240 gene therapy products in development that utilize
the same technology.
Example of vectors:
 Adenovirus (70-100 nm)
 Lentivirus (80-100 nm)
 HSV (300 nm)
Viral Vectors – Introduction
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
9 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Features AAV Lentivirus
Genome ssDNA ssRNA(+)
Virus Coat Non-Enveloped Enveloped
Diameter 18 – 26nm 80 – 130nm
Packaging size 4.5 kb 8 kb
Infection Range Dividing & Non-Dividing Cells Mostly Dividing
Post Infection Mostly Non-Integrating* Integrates into Host Genome
Gene Expression Long lasting (?) Prolonged
Main Advantage Non-pathogenic; Non-inflamatory Persistent Gene Transfer
Main Disadvantage Small packaging capacity Oncogenesis may occur
Characteristics of AAV & Lentivirus
^ AAV (mainly serotype 2) may integrate into Chromosome 19
10 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
AAV Serotype Tissue Tropism
AAV1 Muscle, Heart, Ocular, CNS
AAV2 CNS, Kidney, Muscle, Testes
Various in vitro applications
AAV4 Lung,
AAV5 Lung, CNS, Ocular, Pancreas
AAV6 Lung, Heart
AAV7 Muscle, Liver
AAV8 Liver, Muscle, Ocular, CNS, Heart
AAV9 Lung, Liver, Muscle, Heart, CNS, Kidney, Testes
AAVrh10 Pleura, CNS
Other Various
AAV Serotypes and Tissue Tropism
11 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
 Transient Transfection Mediated by PEI or Calcium Phosphate. Co-transfection of AAV
production cells with 3 plasmids:
• Plasmid with AAV ITR and the gene of interest
• Plasmid with AAV rep/cap
• Plasmid providing the helper genes isolated from adenovirus.
 Wild Type Adenovirus Infection Into Cell Lines with AAV rep/cap Genes and AAV Vector.
 Infection using two HSV viruses harboring the gene of interest and the rep/cap genes to
produce AAV.
 Infecting sf9 cells with two baculoviruses harboring the gene of interest and the rep/cap
genes to produce AAV.
Production Modes for Recombinant AAV
 Sufficient Production of
virus vector copies
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201612
Adenovirus vectors manufacturing
Key requirements and needs
 Antigens attributes
have to meet pre-set
Critical Quality
Attributes
 Reproducibility &
consistency
 Biosafety
 Sufficient recovery to
achieve acceptable
economics
 Ex: nucleic acid
content, product
identity & safety, etc.
Titer
Regulatory
Recovery
Purity &
Quality
Process Schematics of AAV vector production and Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201613
UF/DF Benzonase
Treatment
Primary
Purification
Chromatography
Media and Inoculums
Preparation
Cell growth in Bioreactor
HEK 293 Cells
Virus Inoculation
Transfection
Virus
Harvest
(Lysis)
Primary
Clarification
UF/DF
Sterile
Filtration
Secondary
Clarification
Secondary
Purification
ChromatographyFill & Finish
Thaw and
Expand
Cells and
Seeds
Optional Benzonase
Treatment
Process Schematics of AAV vector production and Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201614
UF/DF Benzonase
Treatment
Primary
Purification
Chromatography
Media and Inoculums
Preparation
Cell growth in Bioreactor
HEK 293 Cells
Virus Inoculation
Transfection
Virus
Harvest
Primary
Clarification
UF/DF
Sterile
Filtration
Secondary
Clarification
Secondary
Purification
ChromatographyFill & Finish
Thaw and
Expand
Cells and
Seeds
Optional Benzonase
Treatment
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201615
Amplification & culture of HEK-293
Bioreactors
T-Flasks*
*Source: Wang and Rivière (2015) Manufacture of tumor-
and virus-specific T lymphocytes for adoptive cell therapies,
Cancer Gene Therapy (2015) 22, 85–94.
Segura et al., Biotechnology & Bioengineering, 2005,
90 : 391-404
Virus Total Protein DNA
MCB
Innoculation
Shake/spin
Sf-9
HEK 293
EB66® Cells
BHK21
Sf-9
HEK 293
EB66® Cells
16
Minimize Your Process Development Efforts
Leverage Merck’s Experience with Various Cell Lines in Mobius® Bioreactors
CHO
Hybridoma
SP 2/0
Vero
h-MSC
T cells
HepaRG®
Adherent
Suspension
Public references at the bench (2 L) … and production scale (50 to 2000 L)
Vero
Power/Volume
Agitation speed
MDCK
S2
Drosophilia
mAb / Rec-
protein
Virus
Production
(Suspension)
Cell
Therapy
Virus
production
(Adherent)
h-MSC
HepaRG®
CHO
Hybridoma
*application data available
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
17 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
• Standard media: EX-CELLTM 293 Serum-Free
Medium for HEK 293 Cells in suspension
• Custom media on demand
• Supplements
Cell culture Media preparation
Durapore® or
Express® 0.22 or
0.1 µm
Sterilizing
Or Viresolve®
Barrier (available
soon)
Lynx sterile
connectors
18 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Bioreactor Biosafety: Preventing contamination
Control
Protect
 Maximum control of animal derived materials
 In-coming test of critical materials
 Move to animal free raw materials processes.
 Recombinant versions of Trypsin, insulin, albumin etc
(Cellprime® range).
• As a minimum: sterile filtration of cell culture
media (Express SHC for example)
• Implementation of a Mycoplasma or a Virus
barrier: filtration of cell culture media for
example using Viresolve® barrier
• Sterile Sampling with NovaSeptum
• Aervent filters for the aeration (0.22µ)
• Sterile connectors (Lynx)
Process Schematics of AAV vector production and Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201619
UF/DF Benzonase
Treatment
Primary
Purification
Chromatography
Media and Inoculums
Preparation
Cell growth in Bioreactor
HEK 293 Cells
Virus Inoculation
Transfection
Virus
Harvest
(Lysis
AAV)
Primary
Clarification
UF/DF
Sterile
Filtration
Secondary
Clarification
Secondary
Purification
ChromatographyFill & Finish
Thaw and
Expand
Cells and
Seeds
Optional Benzonase
Treatment
20 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
 Adherent cells may be lysed in situ or
detached from the growth substrates
 Lysis can happen by freeze-thaw lysis,
mechanical homogenization or
chemically via the use of surfactants.
 Large volume suspension cultures may
be treated with surfactants, e.g. Triton
X-100, or homogenized with a
mechanical device.
 Nuclease treatment is incorporated
following lysis to reduce viscosity and
facilitate subsequent filtration and
chromatography steps.
Cell lysis to release virus particles
Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201621
Clarification
Centrifugation
 Centrifugation allows effective removal of microcarriers, but not so much for
cell/debris separation; the viral yield recovery is typically low (≤30-50%)
 Post-centrifugation clarification using double layer PES filter offer low throughput
due to insufficient clarity of the post-centrifuge viral supernatant and cause
additional losses of viral yield
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201622
Clarification strategies
Cell density & size matters
Low
Concentration
High
Concentration
Small particles
Colloids
Charged
Depth Filters
TFF Filters
Surface Filters
Non-charged
Depth Filters
 Filter capacities
depend on cell
density and degree
of lysis and particle
size distribution
Large/hard
particles
Milligard, Polysep,
Polygard CN
Polygard CR, Clarisolve 60HX
Prostak, Pellicon 2
Millistak+
Clarisolve 20/40 MS
23 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Case study: Clarification of AAV8
• Adeno-associated virus harvest clarification. Previous process
using a competitive depth filter.
• Clarisolve 20 MS was selected for primary clarification
• No pre-treatment required
• Adeno-associated virus harvest clarification. Previous process
using a competitive depth filter.
• Clarisolve 60 HX was tested for primary clarification.
 Increase of 4 x throughput vs previous depth filtration
filter = reduction of footprint
• No pre-treatment required
Depth filtration based clarification – primary
AAV case studies
20MS: Polypropylene &
Millistak® media
60HX: Polypropylene
media construction with
no (+)-charged resin
binder and no DE offer
inert surface, hence no
virus binding issues
24 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
 Millistak+ D0HC can be also used for the clarification
of virus lysates despite of (+) charges (cellulose
fibers with Diatomaceous earths).
 Can be an option to test side by side with Clarisolve
(similar format, same holder for large scale) & NFF
filters
 Example: Capacity range from 30 – 300 L/m2 for
Adenovirus from Per.C6 cell harvest
Depth filtration based clarification
Millistak+ for primary clarification
25 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
NFF based clarification of AAV
Filtration train example
Cell/Virus
Harvest
Polysep II
1.2/0.5 µm
Durapore
0.45µm
Pellicon 2
Biomax 100-300kDPolygard CR
5µm
OR
Clarigard
3 µm
Clarification
Bioburden
reduction
Concentration
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201626
Clarification systems with Single Use flow paths
Semi-automated systems
For POD formats (Millistak+
& Clarisolve®
For NFF filter capsules
Process Schematics of AAV vector production and Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201627
UF/DF Benzonase
Treatment
Primary
Purification
Chromatography
Media and Inoculums
Preparation
Cell growth in Bioreactor
HEK 293 Cells
Virus Inoculation
Transfection
Virus
Harvest
Primary
Clarification
UF/DF
Sterile
Filtration
Secondary
Clarification
Secondary
Purification
ChromatographyFill & Finish
Thaw and
Expand
Cells and
Seeds
Optional Benzonase
Treatment
Solution: Genetically engineered endonuclease that cleaves all forms of
DNA and RNA.
 Presence of Mg2+ (1-2 mM) is required for enzyme activity.
 One unit of Benzonase® degrades approximately 37µg DNA in 30 min to as
low as 3-8 base pairs (<6 kDa).
 Benzonase® can be detected with dedicated ELISA kit. Sensitivity 0.2 ng/ml
Nucleic Acid Digestion
Benzonase® Endonuclease
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201628
Regulatory:
<10 ng nucleic
acid/dose
Characteristics
Origin Serratia marcescens
Expression E. Coli K-12 mutant
Molecular mass ~ 30 KD
Isoelectric point 6.85
Functional in pH range 6-10
Temperature 0-42°C
Bioprocess International, February 2014
Parameters Biomax 300kD
Feed flow (l/min/m²) 6
TMP (bar) <0.3
Initial flux (LMH) 30
Final flux (LMH) 30
Average flux (LMH) 30
Volumetric Concentration
Factor
10
Diafiltration volume 2
Purification: First Step
Target: 25-fold conc + DF, vector recovery of 90%
Success Criteria
 Good yield & Retention
 Higher purity and
Contaminant Removal
- hcDNA
- HCP
- Spent Benzonase
Solution
Permeate control
Pellicon 2 Biomax 300 kD, V Screen for Lentivirus
100 kD for AAV
Lentivirus & AAV: Typical TFF process parameters
29
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201629
TFF-MF (0.1-0.65 µm) and Open UF (300-1000 kDa)
optimization
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201630
Process Schematics of AAV vector production and Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201631
UF/DF Benzonase
Treatment
Primary
Purification
Chromatography
Media and Inoculums
Preparation
Cell growth in Bioreactor
HEK 293 Cells
Virus Inoculation
Transfection
Virus
Harvest
Primary
Clarification
UF/DF
Sterile
Filtration
Secondary
Clarification
Secondary
Purification
ChromatographyFill & Finish
Thaw and
Expand
Cells and
Seeds
Optional Benzonase
Treatment
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201632
Purification of AAV Using cation exchange Fractogel EMD SO3- as
primary step
“The recovery from the Fractogel SO3 − column was almost
100% based on the infective viral particle recovery. In our
laboratory the Fractogel SO3 − has consistently shown a
recovery between 80 and 100%, which is dependent upon
the extraction procedures and the variability in the infective
viral particle assay”
+ Benzonase®
Fractogel® EMD
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201633
Purification of AAV
Ion exchange schemes
(A) Two-step purification protocol involving a strong cation exchange chromatography
resin (Fractogel SO3-) followed by a strong anion exchange resin (Fractogel TMAE)
(B) Capture of the AAV vector by anion exchange chromatography using a strong anion
exchange resin (Fractogel TMAE) with subsequent polishing by gel filtration
chromatography.
34 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
 Best method of separation is ultra centrifugation, but has challenges of scalabaility.
 Ion exchange chromatography with dual shallow gradient (pH & conductivity) can be used.
 pI of empty particles could be higher than that of packaged virions.
AAV empty capsid separation
SOURCE: Okada et al., (Sep. 2009) Scalable Purification of Adeno-Associated Virus Serotype 1 (AAV1) and AAV8 Vectors, Using Dual Ion-Exchange Adsorptive Membranes. Human Gene Therapy, 20:1013–1021
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201635
TFF & chrom systems with Single Use flow paths
Fully automated, recipe driven
Chromatography TFF (UF/DF)
Controls Automated with recipe control CCP6
Operating
pressure
Up to 60 psi
Operable fluid
temp
4o
C-30o
C 4o
C-45o
C
Area
Column diameter: 60 – 350
mm
System 1: 0.5-2.5 m2
System 2: 2.5-5 m2
Sensors
Pre & post column
pH, conductivity, UV,
temperature, pressure
Added sensors for
conductivity, UV
Flow Rate
System 1: 0.1 – 2.2 L/min
System 2: 1.6 - 8L/min
System 1: up to 18 L/min
System 2: up to 28 L/min
Other
Linear & step gradient
mix: Mixing range 10-90%
Accuracy :+/-2 %
Mixing tank 50L to 100/200L
Optional jacketed
Process Schematics of AAV vector production and Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201636
UF/DF Benzonase
Treatment
Primary
Purification
Chromatography
Media and Inoculums
Preparation
Cell growth in Bioreactor
HEK 293 Cells
Virus Inoculation
Transfection
Virus
Harvest
Primary
Clarification
UF/DF
Sterile
Filtration
Secondary
Clarification
Secondary
Purification
ChromatographyFill & Finish
Thaw and
Expand
Cells and
Seeds
Optional Benzonase
Treatment
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201637
Screening for excipients that prevent AAV2 vector aggregation
SOURCE: Wright et al., 2005. Identification of Factors that Contribute to Recombinant AAV2 Particle Aggregation and Methods to Prevent Its Occurrence during Vector Purification and Formulation.
Mol. Ther., 12(1): 171-178.
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201638
Formulation
Storage & Transport
 Range of formulation buffers and excipients to ensure long-term stability
• Buffers (ex: Tris, HEPES, PBS)
• Salts (freeze-dry)
• Stabilizers (ex: Polysorbate)
• Polyols: Manitol, sorbitol, PEG
• Sucrose, Trehalose (coming soon)
 Emprove® dossier
 Single Use Mixing & transport technologies
39 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
 Bioburden monitoring is essential (<10 cfu/ml)
 Durapore 0.22µm filter can be used as final filter
and had to undergo retrospective validation
 Process need to operate at low pressure to avoid
product loss during filtration
 Lot release will depend on sterility testing of final
dosage form & filter IT test
Sterile filtration and storage
40 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Wide range of buffers in solid or liquid forms
• Biological buffers (organic, ex amino-acids)
• Purfication & formulation buffers (ex: NaOH, NaCl, PBS, etc..)
• Cleaning in place (ex: NaOH, HCl)
• Emprove® dossier c
Buffers
Liquid buffers: dual sourcing strategy
• Berlin, Germany (batch size: up to 2000 L)
• Irvine, Scotland (batch size: up to 10000 L)
41 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Final Filling
Component choice
Criteria
Gamma compatibility
>40kGy
Statement of animal origin
USP<88> Class VI
post-gamma >40kGy
USP<85> Endotoxin,
post-gamma >40kGy
USP<788> Particulates,
post-gamma >40kGy
USP<661> Physicochemical,
post-gamma >40kGy
Shelf life >2.5 years,
post-gamma>40kGy
Total Bioburden
pre gamma
Bacteriastatis/Fungistasis,
Post-gamma >40kGy
Configurable
Assembly
Component Library
All available
Components
Solutions from Merck for AAV vector production and Purification
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201642
Pellicon 2
Biomax 100 kD
Benzonase
ELISA Kit II
Mobius Mix
Fractogel TMAE
Express HPF > SHR Mobius Bioreactor
NovAseptum Sampling
Aervent (vent filter)
Mobius
Mix
Polygard CR 5µm
Clarisolve 60HX
Pellicon 2
Biomax 300 kD
Durapore
0.22µm
Polysep II
2.0/1.2
Fractogel DMAE
Mobius
Integrated
Fill Finish
Solutions
Thaw and
Expand
Cells and
Seeds
Optional Benzonase
Treatment
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201643
Benzonase® Treatment Clarification Intermediate TFF
Tangential Flow
Filtration
Last Step
Drug
Substance
First step
Cell thawing
Cell culture (perfusion) – 5 weeks Virus infection – 2 days
3-6weeks
USP
week 1 to 5
DSP
week 5
DSP
week 6
Final
Filtration
2 stage Ion Exchange Chromatography
Virus vector– Single Use Process manufacturing overview
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201644
Quality-control assays for clinical-grade AAV vectors
SOURCE: Arie van Oorschot (UniQure) Setting up a market scale manufacturing platform from scratch. Cell Culture World Conference. 23 February 2016
45 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Schematic of the manufacturing steps associated testing regimes for
a cell therapy production process
Source: Alison Armstrong (2016) Advances in Assay Technologies for CAR T-Cell Therapies. BioPahrm International, 28(2): 32-37.
Quality, Science and Services You Can Trust
 Merck Life Science (SAFC and BioReliance) provide the greatest array of process
development, manufacturing and testing support services for our clients.
 Viral Based Gene Therapy products (Adenovirus, AAV, Retrovirus, Lentivirus, others)
 Cell Banking
 Viral Banking
 Bulk Drug Substance
 Bulk Drug Product
 Custom Assay Development
 BioSafety Testing
Viral Vector Production at SAFC Carlsbad Facility
Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201646
47 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
Merck offers wide range of technology, tools
and services for Production and purification of
Viral vectors for gene and cell therapy
Thank You
Priyabrata Pattnaik, PhD
priyabrata.pattnaik@merckgroup.com
@pattnaik_p
https://sg.linkedin.com/in/priyabratapattnaik
https://plus.google.com/109816383630328905377

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Production and purification of Viral vectors for gene and cell therapy applications

  • 1. Priyabrata Pattnaik, PhD Director & Head of Biologics Operations Asia Pacific Production and purification of Viral vectors for gene and cell therapy applications
  • 2. The cell & gene therapy market is poised for rapid growth with projections reaching ~$10B in 5 years Source: Seed Planning; METI; Kuick Research; Med Market Diligence;Transparency market research Global market size & CAGR USD B Products in the pipeline 74 74 34 54 75 Stem cell therapy 106 17 14 Cellular therapy, other 123 15 Gene therapy 144 16 Phase I Phase II Phase III 10 9 1 12 8 3 2020 +36% p.a. 20182012 Kuick research (India) See Planning/ METI (Japan) Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 20162
  • 3. The cell & gene therapy market can be split into 3 broad segments... Description and examples Major players Cell & gene therapy Non-geneti- cally modified cell therapies • Purified populations of allogeneic cells are expanded and injected topically • E.g., mesenchymal stem cells Viral gene therapies • Drug product is virus particle, injected into patient topically (or systemically) • E.g., Spark’s night- blindness therapy • Autologous patient cells are extracted, genetically modified using viral transduction, then reinfused into the patient • E.g., CAR T-cell therapy Genetically modified cell therapies Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 20163
  • 4. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 3 broad segments Gene Therapy Stem-cell Therapy Cell Immunotherapy Gene Therapy Stem-cell Therapy Cell Immunotherapy  Nucleic acid  Lenti/Adeno virus-based delivery  Somatic or germline  Stem cells banking  Replace or regenerate organs and tissue  Broad use of bone marrow in ALL  Autogenetic CAR-T 1. Most common 2. Immune cells separation 3. Lentivirus-based delivery 4. Chimeric Antigen Receptors (CARs)  Allogeneic modified T cells 1. Industrialized trend 2. Genetic modification of immune cells 3. Allogeneic T cell generation 4. Lentivirus-based delivery or genome edit (CRISPR) CAR-TVirus Stem cells T-cells Virus CAR-T 4
  • 5. Methods for producing genetically modified T-cells for immunotherapy Source: Bure et al. (2016) Automation of CAR-T Cell Adoptive Immunotherapy Bioprocessing. Bioprocess International, 14(4)s: 22-31. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 20165
  • 6. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Overall Process Map of CAR-T T-cell separation Virus generation GMP-grade lentivirus  Recovery rate= 70%  2.5*109 virus per trial  5*106 titer/ml  500ml bulk T-cell modification  MOI=5  1.7*109 virus per trial Car-T Cell Amplification Reintroduction  5*106 CAR-T/kg  E.g.: 70 kg weighting  3.5*108 CAR-T per trial 6
  • 7. 7 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Viral Vectors For Gene Therapy Introduction Gene Therapy – Main Applications: • Treat Heridatery Single-Gene Defects. • Cancer • Cardiovascular Diseases • Ocular Diseases • Infectious Diseases • Other Diseases Where Gene Transfer Will Have an Impact Main Features for Virus-Based Vectors: • Lacks Viral Genes Involved in Replication. • Expression Cassette is Cloned into the Vector. • Helper Function is Provided in trans • Co-Transfection of Vector Genome and Packaging Construct Produce Recombinant Vecotor
  • 8. 8 ~60% of the vaccines undergoing clinical trials are viral based.  ~ 640 viral vaccines  ~ 200 viral vectors  ~ 60 virus like particles  Another ~240 gene therapy products in development that utilize the same technology. Example of vectors:  Adenovirus (70-100 nm)  Lentivirus (80-100 nm)  HSV (300 nm) Viral Vectors – Introduction Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
  • 9. 9 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Features AAV Lentivirus Genome ssDNA ssRNA(+) Virus Coat Non-Enveloped Enveloped Diameter 18 – 26nm 80 – 130nm Packaging size 4.5 kb 8 kb Infection Range Dividing & Non-Dividing Cells Mostly Dividing Post Infection Mostly Non-Integrating* Integrates into Host Genome Gene Expression Long lasting (?) Prolonged Main Advantage Non-pathogenic; Non-inflamatory Persistent Gene Transfer Main Disadvantage Small packaging capacity Oncogenesis may occur Characteristics of AAV & Lentivirus ^ AAV (mainly serotype 2) may integrate into Chromosome 19
  • 10. 10 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 AAV Serotype Tissue Tropism AAV1 Muscle, Heart, Ocular, CNS AAV2 CNS, Kidney, Muscle, Testes Various in vitro applications AAV4 Lung, AAV5 Lung, CNS, Ocular, Pancreas AAV6 Lung, Heart AAV7 Muscle, Liver AAV8 Liver, Muscle, Ocular, CNS, Heart AAV9 Lung, Liver, Muscle, Heart, CNS, Kidney, Testes AAVrh10 Pleura, CNS Other Various AAV Serotypes and Tissue Tropism
  • 11. 11 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016  Transient Transfection Mediated by PEI or Calcium Phosphate. Co-transfection of AAV production cells with 3 plasmids: • Plasmid with AAV ITR and the gene of interest • Plasmid with AAV rep/cap • Plasmid providing the helper genes isolated from adenovirus.  Wild Type Adenovirus Infection Into Cell Lines with AAV rep/cap Genes and AAV Vector.  Infection using two HSV viruses harboring the gene of interest and the rep/cap genes to produce AAV.  Infecting sf9 cells with two baculoviruses harboring the gene of interest and the rep/cap genes to produce AAV. Production Modes for Recombinant AAV
  • 12.  Sufficient Production of virus vector copies Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201612 Adenovirus vectors manufacturing Key requirements and needs  Antigens attributes have to meet pre-set Critical Quality Attributes  Reproducibility & consistency  Biosafety  Sufficient recovery to achieve acceptable economics  Ex: nucleic acid content, product identity & safety, etc. Titer Regulatory Recovery Purity & Quality
  • 13. Process Schematics of AAV vector production and Purification Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201613 UF/DF Benzonase Treatment Primary Purification Chromatography Media and Inoculums Preparation Cell growth in Bioreactor HEK 293 Cells Virus Inoculation Transfection Virus Harvest (Lysis) Primary Clarification UF/DF Sterile Filtration Secondary Clarification Secondary Purification ChromatographyFill & Finish Thaw and Expand Cells and Seeds Optional Benzonase Treatment
  • 14. Process Schematics of AAV vector production and Purification Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201614 UF/DF Benzonase Treatment Primary Purification Chromatography Media and Inoculums Preparation Cell growth in Bioreactor HEK 293 Cells Virus Inoculation Transfection Virus Harvest Primary Clarification UF/DF Sterile Filtration Secondary Clarification Secondary Purification ChromatographyFill & Finish Thaw and Expand Cells and Seeds Optional Benzonase Treatment
  • 15. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201615 Amplification & culture of HEK-293 Bioreactors T-Flasks* *Source: Wang and Rivière (2015) Manufacture of tumor- and virus-specific T lymphocytes for adoptive cell therapies, Cancer Gene Therapy (2015) 22, 85–94. Segura et al., Biotechnology & Bioengineering, 2005, 90 : 391-404 Virus Total Protein DNA MCB Innoculation Shake/spin
  • 16. Sf-9 HEK 293 EB66® Cells BHK21 Sf-9 HEK 293 EB66® Cells 16 Minimize Your Process Development Efforts Leverage Merck’s Experience with Various Cell Lines in Mobius® Bioreactors CHO Hybridoma SP 2/0 Vero h-MSC T cells HepaRG® Adherent Suspension Public references at the bench (2 L) … and production scale (50 to 2000 L) Vero Power/Volume Agitation speed MDCK S2 Drosophilia mAb / Rec- protein Virus Production (Suspension) Cell Therapy Virus production (Adherent) h-MSC HepaRG® CHO Hybridoma *application data available * * * * * * * * * * * * * * * * * * * * * Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016
  • 17. 17 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 • Standard media: EX-CELLTM 293 Serum-Free Medium for HEK 293 Cells in suspension • Custom media on demand • Supplements Cell culture Media preparation Durapore® or Express® 0.22 or 0.1 µm Sterilizing Or Viresolve® Barrier (available soon) Lynx sterile connectors
  • 18. 18 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Bioreactor Biosafety: Preventing contamination Control Protect  Maximum control of animal derived materials  In-coming test of critical materials  Move to animal free raw materials processes.  Recombinant versions of Trypsin, insulin, albumin etc (Cellprime® range). • As a minimum: sterile filtration of cell culture media (Express SHC for example) • Implementation of a Mycoplasma or a Virus barrier: filtration of cell culture media for example using Viresolve® barrier • Sterile Sampling with NovaSeptum • Aervent filters for the aeration (0.22µ) • Sterile connectors (Lynx)
  • 19. Process Schematics of AAV vector production and Purification Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201619 UF/DF Benzonase Treatment Primary Purification Chromatography Media and Inoculums Preparation Cell growth in Bioreactor HEK 293 Cells Virus Inoculation Transfection Virus Harvest (Lysis AAV) Primary Clarification UF/DF Sterile Filtration Secondary Clarification Secondary Purification ChromatographyFill & Finish Thaw and Expand Cells and Seeds Optional Benzonase Treatment
  • 20. 20 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016  Adherent cells may be lysed in situ or detached from the growth substrates  Lysis can happen by freeze-thaw lysis, mechanical homogenization or chemically via the use of surfactants.  Large volume suspension cultures may be treated with surfactants, e.g. Triton X-100, or homogenized with a mechanical device.  Nuclease treatment is incorporated following lysis to reduce viscosity and facilitate subsequent filtration and chromatography steps. Cell lysis to release virus particles Purification
  • 21. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201621 Clarification Centrifugation  Centrifugation allows effective removal of microcarriers, but not so much for cell/debris separation; the viral yield recovery is typically low (≤30-50%)  Post-centrifugation clarification using double layer PES filter offer low throughput due to insufficient clarity of the post-centrifuge viral supernatant and cause additional losses of viral yield
  • 22. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201622 Clarification strategies Cell density & size matters Low Concentration High Concentration Small particles Colloids Charged Depth Filters TFF Filters Surface Filters Non-charged Depth Filters  Filter capacities depend on cell density and degree of lysis and particle size distribution Large/hard particles Milligard, Polysep, Polygard CN Polygard CR, Clarisolve 60HX Prostak, Pellicon 2 Millistak+ Clarisolve 20/40 MS
  • 23. 23 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Case study: Clarification of AAV8 • Adeno-associated virus harvest clarification. Previous process using a competitive depth filter. • Clarisolve 20 MS was selected for primary clarification • No pre-treatment required • Adeno-associated virus harvest clarification. Previous process using a competitive depth filter. • Clarisolve 60 HX was tested for primary clarification.  Increase of 4 x throughput vs previous depth filtration filter = reduction of footprint • No pre-treatment required Depth filtration based clarification – primary AAV case studies 20MS: Polypropylene & Millistak® media 60HX: Polypropylene media construction with no (+)-charged resin binder and no DE offer inert surface, hence no virus binding issues
  • 24. 24 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016  Millistak+ D0HC can be also used for the clarification of virus lysates despite of (+) charges (cellulose fibers with Diatomaceous earths).  Can be an option to test side by side with Clarisolve (similar format, same holder for large scale) & NFF filters  Example: Capacity range from 30 – 300 L/m2 for Adenovirus from Per.C6 cell harvest Depth filtration based clarification Millistak+ for primary clarification
  • 25. 25 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 NFF based clarification of AAV Filtration train example Cell/Virus Harvest Polysep II 1.2/0.5 µm Durapore 0.45µm Pellicon 2 Biomax 100-300kDPolygard CR 5µm OR Clarigard 3 µm Clarification Bioburden reduction Concentration
  • 26. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201626 Clarification systems with Single Use flow paths Semi-automated systems For POD formats (Millistak+ & Clarisolve® For NFF filter capsules
  • 27. Process Schematics of AAV vector production and Purification Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201627 UF/DF Benzonase Treatment Primary Purification Chromatography Media and Inoculums Preparation Cell growth in Bioreactor HEK 293 Cells Virus Inoculation Transfection Virus Harvest Primary Clarification UF/DF Sterile Filtration Secondary Clarification Secondary Purification ChromatographyFill & Finish Thaw and Expand Cells and Seeds Optional Benzonase Treatment
  • 28. Solution: Genetically engineered endonuclease that cleaves all forms of DNA and RNA.  Presence of Mg2+ (1-2 mM) is required for enzyme activity.  One unit of Benzonase® degrades approximately 37µg DNA in 30 min to as low as 3-8 base pairs (<6 kDa).  Benzonase® can be detected with dedicated ELISA kit. Sensitivity 0.2 ng/ml Nucleic Acid Digestion Benzonase® Endonuclease Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201628 Regulatory: <10 ng nucleic acid/dose Characteristics Origin Serratia marcescens Expression E. Coli K-12 mutant Molecular mass ~ 30 KD Isoelectric point 6.85 Functional in pH range 6-10 Temperature 0-42°C Bioprocess International, February 2014
  • 29. Parameters Biomax 300kD Feed flow (l/min/m²) 6 TMP (bar) <0.3 Initial flux (LMH) 30 Final flux (LMH) 30 Average flux (LMH) 30 Volumetric Concentration Factor 10 Diafiltration volume 2 Purification: First Step Target: 25-fold conc + DF, vector recovery of 90% Success Criteria  Good yield & Retention  Higher purity and Contaminant Removal - hcDNA - HCP - Spent Benzonase Solution Permeate control Pellicon 2 Biomax 300 kD, V Screen for Lentivirus 100 kD for AAV Lentivirus & AAV: Typical TFF process parameters 29 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201629
  • 30. TFF-MF (0.1-0.65 µm) and Open UF (300-1000 kDa) optimization Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201630
  • 31. Process Schematics of AAV vector production and Purification Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201631 UF/DF Benzonase Treatment Primary Purification Chromatography Media and Inoculums Preparation Cell growth in Bioreactor HEK 293 Cells Virus Inoculation Transfection Virus Harvest Primary Clarification UF/DF Sterile Filtration Secondary Clarification Secondary Purification ChromatographyFill & Finish Thaw and Expand Cells and Seeds Optional Benzonase Treatment
  • 32. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201632 Purification of AAV Using cation exchange Fractogel EMD SO3- as primary step “The recovery from the Fractogel SO3 − column was almost 100% based on the infective viral particle recovery. In our laboratory the Fractogel SO3 − has consistently shown a recovery between 80 and 100%, which is dependent upon the extraction procedures and the variability in the infective viral particle assay” + Benzonase® Fractogel® EMD
  • 33. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201633 Purification of AAV Ion exchange schemes (A) Two-step purification protocol involving a strong cation exchange chromatography resin (Fractogel SO3-) followed by a strong anion exchange resin (Fractogel TMAE) (B) Capture of the AAV vector by anion exchange chromatography using a strong anion exchange resin (Fractogel TMAE) with subsequent polishing by gel filtration chromatography.
  • 34. 34 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016  Best method of separation is ultra centrifugation, but has challenges of scalabaility.  Ion exchange chromatography with dual shallow gradient (pH & conductivity) can be used.  pI of empty particles could be higher than that of packaged virions. AAV empty capsid separation SOURCE: Okada et al., (Sep. 2009) Scalable Purification of Adeno-Associated Virus Serotype 1 (AAV1) and AAV8 Vectors, Using Dual Ion-Exchange Adsorptive Membranes. Human Gene Therapy, 20:1013–1021
  • 35. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201635 TFF & chrom systems with Single Use flow paths Fully automated, recipe driven Chromatography TFF (UF/DF) Controls Automated with recipe control CCP6 Operating pressure Up to 60 psi Operable fluid temp 4o C-30o C 4o C-45o C Area Column diameter: 60 – 350 mm System 1: 0.5-2.5 m2 System 2: 2.5-5 m2 Sensors Pre & post column pH, conductivity, UV, temperature, pressure Added sensors for conductivity, UV Flow Rate System 1: 0.1 – 2.2 L/min System 2: 1.6 - 8L/min System 1: up to 18 L/min System 2: up to 28 L/min Other Linear & step gradient mix: Mixing range 10-90% Accuracy :+/-2 % Mixing tank 50L to 100/200L Optional jacketed
  • 36. Process Schematics of AAV vector production and Purification Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201636 UF/DF Benzonase Treatment Primary Purification Chromatography Media and Inoculums Preparation Cell growth in Bioreactor HEK 293 Cells Virus Inoculation Transfection Virus Harvest Primary Clarification UF/DF Sterile Filtration Secondary Clarification Secondary Purification ChromatographyFill & Finish Thaw and Expand Cells and Seeds Optional Benzonase Treatment
  • 37. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201637 Screening for excipients that prevent AAV2 vector aggregation SOURCE: Wright et al., 2005. Identification of Factors that Contribute to Recombinant AAV2 Particle Aggregation and Methods to Prevent Its Occurrence during Vector Purification and Formulation. Mol. Ther., 12(1): 171-178.
  • 38. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201638 Formulation Storage & Transport  Range of formulation buffers and excipients to ensure long-term stability • Buffers (ex: Tris, HEPES, PBS) • Salts (freeze-dry) • Stabilizers (ex: Polysorbate) • Polyols: Manitol, sorbitol, PEG • Sucrose, Trehalose (coming soon)  Emprove® dossier  Single Use Mixing & transport technologies
  • 39. 39 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016  Bioburden monitoring is essential (<10 cfu/ml)  Durapore 0.22µm filter can be used as final filter and had to undergo retrospective validation  Process need to operate at low pressure to avoid product loss during filtration  Lot release will depend on sterility testing of final dosage form & filter IT test Sterile filtration and storage
  • 40. 40 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Wide range of buffers in solid or liquid forms • Biological buffers (organic, ex amino-acids) • Purfication & formulation buffers (ex: NaOH, NaCl, PBS, etc..) • Cleaning in place (ex: NaOH, HCl) • Emprove® dossier c Buffers Liquid buffers: dual sourcing strategy • Berlin, Germany (batch size: up to 2000 L) • Irvine, Scotland (batch size: up to 10000 L)
  • 41. 41 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Final Filling Component choice Criteria Gamma compatibility >40kGy Statement of animal origin USP<88> Class VI post-gamma >40kGy USP<85> Endotoxin, post-gamma >40kGy USP<788> Particulates, post-gamma >40kGy USP<661> Physicochemical, post-gamma >40kGy Shelf life >2.5 years, post-gamma>40kGy Total Bioburden pre gamma Bacteriastatis/Fungistasis, Post-gamma >40kGy Configurable Assembly Component Library All available Components
  • 42. Solutions from Merck for AAV vector production and Purification Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201642 Pellicon 2 Biomax 100 kD Benzonase ELISA Kit II Mobius Mix Fractogel TMAE Express HPF > SHR Mobius Bioreactor NovAseptum Sampling Aervent (vent filter) Mobius Mix Polygard CR 5µm Clarisolve 60HX Pellicon 2 Biomax 300 kD Durapore 0.22µm Polysep II 2.0/1.2 Fractogel DMAE Mobius Integrated Fill Finish Solutions Thaw and Expand Cells and Seeds Optional Benzonase Treatment
  • 43. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201643 Benzonase® Treatment Clarification Intermediate TFF Tangential Flow Filtration Last Step Drug Substance First step Cell thawing Cell culture (perfusion) – 5 weeks Virus infection – 2 days 3-6weeks USP week 1 to 5 DSP week 5 DSP week 6 Final Filtration 2 stage Ion Exchange Chromatography Virus vector– Single Use Process manufacturing overview
  • 44. Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201644 Quality-control assays for clinical-grade AAV vectors SOURCE: Arie van Oorschot (UniQure) Setting up a market scale manufacturing platform from scratch. Cell Culture World Conference. 23 February 2016
  • 45. 45 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Schematic of the manufacturing steps associated testing regimes for a cell therapy production process Source: Alison Armstrong (2016) Advances in Assay Technologies for CAR T-Cell Therapies. BioPahrm International, 28(2): 32-37. Quality, Science and Services You Can Trust
  • 46.  Merck Life Science (SAFC and BioReliance) provide the greatest array of process development, manufacturing and testing support services for our clients.  Viral Based Gene Therapy products (Adenovirus, AAV, Retrovirus, Lentivirus, others)  Cell Banking  Viral Banking  Bulk Drug Substance  Bulk Drug Product  Custom Assay Development  BioSafety Testing Viral Vector Production at SAFC Carlsbad Facility Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 201646
  • 47. 47 Production and Purification of Virus Vectors | Priyabrata Pattnaik | October 2016 Merck offers wide range of technology, tools and services for Production and purification of Viral vectors for gene and cell therapy
  • 48. Thank You Priyabrata Pattnaik, PhD priyabrata.pattnaik@merckgroup.com @pattnaik_p https://sg.linkedin.com/in/priyabratapattnaik https://plus.google.com/109816383630328905377