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Файл:Ординатура / Хирургия / Библиотека им академика М.И. Перельмана / Книга_5886_Библиотеки_им_академика_М_И_Перельмана.pdf
X
- •Foreword
- •Preface
- •Acknowledgements
- •Contents
- •Contributors
- •About the Editors
- •1.2.2.3 Progeria
- •1. Bioprocessing, Bioengineering and Process Chemistry in the Biopharmaceutical Industry: Using Chemistry and Bioengineering to Improve the Performance of Biologics
- •1.1 Introduction
- •1.2.2.2 Cystic Fibrosis
- •1.3.2.1 ADC Drugs
- •1.4 Top 25 Best-Selling Drugs
- •1.5.1 An Overview
- •1.5.2 Synthetic Biology
- •1.5.8 Biopharmaceutical Regulatory CMC
- •1.5.9 Technology Transfer
- •References
- •2.1 What Is Synthetic Biology?
- •2.6 CAR-T Cell Therapies
- •2.7 Conclusion
- •References
- •3.1 Introduction
- •3.2.1 Oligonucleotide Synthesis
- •3.2.1.1 Early Synthetic Chemistries
- •3.2.2 Solid Supports
- •3.2.3 Modern Oligo Synthesis Platforms
- •3.3 Gene Synthesis
- •3.3.1 Early DNA Assembly Methods
- •3.3.2 Array-Based Gene Synthesis
- •3.4 New Discovery Bottleneck
- •3.4.1.1 Hybridoma Technology
- •3.4.1.2 Phage Display Technology
- •3.4.1.3 Synthetic Antibody Library Construction
- •Semi-Synthetic Libraries
- •Fully Synthetic Libraries
- •3.5 Perspectives
- •References
- •4.1 Introduction
- •4.2.1 Batch
- •4.2.2 Fed-Batch
- •4.2.4 Hybrid Processes
- •4.2.7 Dynamic Perfusion Processes
- •4.3.2 Glucose Limitation
- •4.4.1 N-1 Perfusion
- •4.4.3 Linked Bioreactors
- •4.5 Process Analytical Technology
- •4.6 Single-Use Bioreactors (SUBs)
- •4.7 Conclusions
- •References
- •5.1 Introduction
- •5.2.1 Molecular Format Considerations
- •5.2.1.1 The Charge-Based Electrostatic Approach
- •5.2.1.2 The Knob into Hole Approach
- •5.2.2.1 Stable CHO Host Cell Integration System—Random or Targeted?
- •5.2.2.2 Expression Vector Considerations
- •5.2.2.3 Cell Line Screening Strategy Considerations
- •5.3.1 Upstream Process Development
- •5.3.2 Downstream Process Development Considerations
- •5.3.2.1 Unique Impurity Challenges
- •5.3.2.2 Stability Concerns
- •5.5.2.1 H/H Removal
- •5.5.2.2 HMMS Removal
- •References
- •6.1 Introduction
- •6.2.1 N-Linked Glycosylation
- •6.2.2 O-Linked Glycosylation
- •6.2.3 Glycosaminoglycan Synthesis
- •6.3.1 Mannosylation
- •6.3.2 Fucosylation
- •6.3.3 Galactosylation
- •6.3.4 Sialylation
- •6.5 Glycoengineering
- •6.5.1 Manipulating Heterogeneity
- •6.5.2 Manipulating Sialylation
- •6.5.2.1 Increasing α-2,6 Sialylation
- •6.5.3 Manipulating Fucosylation
- •6.5.4 Manipulating Branching
- •6.6.1 Temperature
- •6.6.2 pH
- •6.6.3.2 Amino Acids
- •6.6.3.3 Glycosaminoglycan Production
- •6.6.4 Culture Additives
- •References
- •7.1 Introduction
- •7.1.1 AAV Gene Therapy
- •7.3.1 Humoral Immunity
- •7.3.2 Cell-Mediated Immunity
- •7.4 Conclusion
- •References
- •8.1 Introduction
- •8.2 mRNA Vaccines
- •8.2.1 Background
- •8.2.2 Production Process
- •8.2.2.2 Production
- •8.4.1 Background
- •8.4.2 Production Process
- •8.4.2.2 Production
- •8.4.2.3 Viral Inactivation
- •8.5 Protein-Based Vaccines
- •8.5.1 Background
- •8.5.2 Production Processes
- •8.5.2.1 NVX-CoV2373 (Novavax)
- •8.3 Viral Vectors
- •8.3.1 Background
- •8.3.2 Production Process
- •8.3.2.2 Production
- •8.4 Whole Inactivated Virus Vaccines
- •8.5.2.2 CoVLP (Medicago)
- •8.5.2.3 EpiVacCorona (Vector Institute)
- •8.7 Conclusions
- •References
- •9. CAR-T Bioprocessing
- •9.1 Introduction
- •9.2.1 Introduction
- •9.2.2 Lentiviral Vector Design
- •9.2.5 Upstream Bioprocessing
- •9.2.6 Downstream Bioprocessing
- •9.3 Cell Product Bioprocessing
- •9.3.1 End-to-End Systems
- •9.3.4 Activation
- •9.3.6 Cell Expansion
- •9.3.8 T-Cell Cryopreservation
- •References
- •10.1.1 What Is CRISPR?
- •10.1.4 Mechanism Behind CRISPR Gene Editing
- •10.2.1 Creating Gene Knockouts
- •10.2.2 Creating Gene Knock-Ins
- •10.2.4 CRISPR Screens
- •10.3.1 Derivative Technologies
- •10.4.2 Delivery Methods
- •10.6.2 TCR Engineered T Cell Therapy
- •10.6.3 Chimeric Antigen Receptor T Cell Therapy
- •10.9.2 Safety Considerations
- •References
- •11.1 Introduction
- •11.1.2 Categories
- •11.2 Current Status
- •11.2.1 Approved Products
- •11.2.2 Market
- •11.3 Design
- •11.3.1 Building Blocks
- •11.3.2 Linkers
- •11.3.3 Oligomerization
- •11.3.3.1 Monomer
- •11.3.3.2 Dimer
- •11.3.3.3 Trimer
- •11.3.3.4 Tetramer
- •11.3.3.5 Pentamer
- •11.3.3.6 Hexamer
- •11.3.3.7 Octamer
- •11.3.4 Orientation
- •11.3.5 Protein Engineering
- •11.3.6 Immunogenicity
- •11.4 Manufacturing
- •11.4.1 Upstream
- •11.4.2 Downstream
- •11.4.3 Glycosylation
- •11.4.4 Aggregation
- •11.4.5 Analytics
- •11.5 Therapeutic Concepts
- •11.5.1 Half-Life Extension
- •Albumin Fusions
- •Fc Fusions
- •Transferrin Fusions
- •Repetitive Peptide Fusions
- •Glycosylated Peptides
- •11.5.1.3 Aggregate Forming Peptides
- •11.5.2 Targeting Functions
- •11.5.3.1 Fc Domain Receptor-Mediated Toxicity
- •11.5.3.2 Toxins
- •11.5.3.3 Immunocytokines
- •11.5.3.4 Human Enzymes
- •11.5.3.5 Apoptosis Induction
- •11.6 Summary
- •11.7 Future Perspectives
- •References
- •12.1 Introduction
- •12.2 ADC History
- •12.3 Target Selection
- •12.4 Antibody Selection
- •12.6 ADC Technology
- •12.7 ADC Clinical Development
- •12.8.1 Mylotarg
- •12.8.2 Adcetris
- •12.8.3 Kadcyla
- •12.8.4 Besponsa
- •12.8.5 Polivy
- •12.8.6 Padcev
- •12.8.7 Enhertu
- •12.8.8 Trodelvy
- •12.8.9 Blenrep
- •12.8.10 Zynlonta
- •12.8.11 Tivdak
- •12.9 Concluding Remarks
- •References
- •13.1 Introduction
- •13.2 Gemtuzumab Ozogamicin
- •13.3 Gemtuzumab Antibody
- •13.4 Calicheamicin
- •13.7.3 Isolation of N-Acetyl Calicheamicin
- •13.10 Conclusions
- •References
- •14.1 Introduction
- •14.2.1 Antibody Generation
- •14.3.1 Structure Prediction
- •14.3.2 Biophysical Properties
- •14.3.3 Hydrophobicity
- •14.3.5 Isoelectric Point (pI)
- •References
- •15.1 Introduction
- •15.2 ADA Program Development
- •15.2.3 Project Approach
- •15.2.4 Model Library
- •15.3 Case Study
- •15.3.3 Hypothesis Generation
- •15.3.5 Feature Engineering Example
- •15.3.7 Model Insights
- •References
- •16.1 Introduction
- •16.1.1.1 United States
- •16.1.1.2 European Union
- •16.1.2 Global Markets
- •16.4.1 United States FDA
- •16.4.2 European Medicines Agency (EMA)
- •16.4.3 The World Health Organization
- •References
- •17.1 Introduction
- •17.3.1.2 Clone Selection

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J. Bauer et al.

Chapter 15
Advanced Data Analytics Application
inBiomanufacturing Processes
JunLuo, LinQiu, YangTang, GrantSumida, SidKundu, andYimingPeng
Abstract Biomanufacturing drug substance processes include cell culture (thaw,
seed train, inoculum, and protein production), harvest, and purication steps. Due
to the living nature, the bioprocess inherently has higher variability when compared
to chemical reactions. Ensuring consistent process performance and continuous
process improvement are ongoing challenges for bioprocess.
Thorough characterization of process and product attributes using statistical
design of experiments (DoE) during the process design (PD) stage is a proven
means to establish the process and product knowledge. Recent accelerated development timelines are putting pressure and limitations on the extent of characterization
during the PD stage, and, therefore, increasing the importance of a lifecycle
approach to accumulate process and product knowledge during the post-approval
stage of process validation (i.e., continued process verication).
Following telecoms, advertising, and insurance, the biopharma industry has
started to embrace methods like Bayesian statistics and advanced data analytics
(ADA) to gain additional process and product understanding, improved process
control, and process performance. Using ADA may elucidate previously undetected
relationships between process inputs and outputs, which hold promise as an additional tool to augment traditional DoE as a means to gain actionable insights, process and product knowledge.
An internal multidisciplinary team (e.g., ADA) comprising data engineers, data
scientists, bioprocess experts, and a translator /project manager is formed.
J. Luo (*) · G. Sumida
Manufacturing Sciences, Genentech, Vacaville, CA, USA
e-mail: luo.jun@gene.com
L. Qiu · Y. Peng
Nonclinical Biostatistics, Genentech, South San Francisco, CA, USA
Y. Tang
Nonclinical Biostatistics, Roche, Mississauga, ON, Canada
S. Kundu
Cell Culture and Bioprocess Operations, Genentech, South San Francisco, CA, USA
K. Gadamasetti, S. A. Kolodziej (eds.), Bioprocessing, Bioengineering
and Process Chemistry in the Biopharmaceutical Industry,
https://doi.org/10.1007/978-3-031-62007-2_15
437© The Author(s), under exclusive license to Springer Nature Switzerland AG 2024

438
J. Luo et al.
IT infrastructure to support ADA projects is established, the standard approaches to
run the case studies are developed, and a library of models for bioprocess is built.
An upstream process case study to improve upstream productivity and process
robustness is discussed. The team is able to extract, cleanse, ingest, and process
800GB of data from 11 disparate data sources into a cloud environment to evaluate
more than 100 hypotheses. Implementing the insights leads to improved process
performance. Through the case study, the strategy to sustain the internal capability
is developed. The importance of building ADA capabilities to enable more efcient
and reliable bioprocesses is discussed.
Keywords Advanced data analytics · Machine learning · Cell culture · Process
performance variation
15.1 Introduction
Biomanufacturing drug substance processes include cell culture (thaw, seed train,
inoculum and protein production), harvest, and purication (chromatography, viral
ltration, ultraltration dialtration, and freeze) steps. Due to the living nature, the
bioprocess inherently has higher variability when compared to chemical reaction.
To ensure consistent process performance and product quality, a bioprocess validation lifecycle program is needed. The lifecycle includes three stages: PD (Stage 1),
process qualication (PQ, Stage 2), and continued process verication (CPV, Stage
3) [1]. The data are collected and evaluated through all three stages of the lifecycle
to generate process knowledge and establish scientic evidence that a process is
capable of consistently delivering quality products.
Information used to characterize the process can be split as inputs and outputs of
the process. For a specic step of mammalian cell culture processes, process inputs
could be raw material, equipment, operational parameters (e.g., operator, operation
sequence, operating parameters), and any measurements of the initial state, etc.
Process outputs could be process performance indicators (PI, or KPI: key performance indicator) from the specic process step or any downstream steps, and product quality attributes (PQA or CQA: critical quality attributes). Process knowledge
could be summarized in an equation or model to describe the correlation between
inputs and output. Quantitative models for optimization commercial drug substance
manufacturing processes have recently attracted increasing attention. Different data
analysis methods may be used to build process knowledge during different process
validation stages.
Per International Council for Harmonisation of Technical Requirements for
Pharmaceuticals for Human Use (ICH) quality guidelines ICH Q8 (R2), ICH Q9,
and ICH Q10, the concept of quality by design is introduced. This concept includes
quality-risk management systems and the implementation of Pharmaceutical
Quality Systems. Key elements are critical process parameters (CPP), which affect
CQAs, and DoE [2]. Thorough characterization of process and product attributes

15 Advanced Data Analytics Application inBiomanufacturing Processes
439
using statistical DoE during the PD stage is a proven means to establish process/
product knowledge. DoE-based approaches can provide a deeper understanding of
how product quality attributes and process-related impurities change when several
process operating parameters vary simultaneously for a given unit operation, and
thus lead to increased process knowledge with respect to the robustness of a culture
step or combination of culture steps. Prior to designing a DoE study, a risk assessment is typically conducted to rank the risk of process parameters regarding the
impact on process performance and product quality. This is based on the previous
knowledge from the platform process, rst principles, early development data, and
literature review, etc. Based on the outcome of risk assessment, follow-up studies
will be executed to identify the acceptable range for process parameters [3]. Since
most bioprocess unit steps easily have more than four factors, the rst round of
experiments typically uses the screening design (e.g., Plackett-Burman method) to
identify the most important factors early in the experimentation phase when complete knowledge about the system is usually unavailable [4]. Once the important
factors are identied, a follow-up DoE study (e.g., response surface designs or factorial design) to understand the interaction, and to rene the model. Note: Response
surface design is recommended especially if there is suspected curvature in the
response surface. Once the model is rened, the model could be used to predict
worst-case conditions for certain process output, and the predicted worst-case conditions could be further tested in experiments. Separately, certain univariate studies
could be performed to provide knowledge for ongoing manufacturing support. For
example, a pH excursion study (effect of the short-term high/low pH) is typically
executed to understand the effect of the pH probe spike issue occasionally observed
in commercial manufacturing.
Many bioprocess companies have a CPV program that involves univariate trending of quality attributes and process performance indicators, which are used to
establish the evidence for process in control or identify process change/shift/excursion for further investigation. If process performance or capability is trending unfavorably, the ability to adaptively respond and adjust controls is contingent on the
availability of documented causal relationships (i.e., models) between controllable
inputs and important process/product outputs. With accelerating development timelines, the accumulation of process knowledge during the CPV stage of process validation is becoming increasingly important. Different statistical methods/models
could be used to collect knowledge during the CPV phase in addition to performing
experiments. For example, when the sample size is small, Bayesian statistics is a
preferred method. With the increase of sample size, advanced data analytics (ADA)
can be used.
Sample sizes of data in biomanufacturing drug substance processes are frequently quite small due to time, economic, and physical constraints. The effect of
sample size on the interpretation of classical signicance tests has been emphasized
[5]. The predictive model built upon a small number of samples may highly rely on
the particular method for parameter estimation [6]. Under such circumstances, to
enable meaningful model prediction and results interpretation, Bayesian statistics is
usually preferred [7] because Bayesian methods incorporate both the observed data
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