Protein Expression System Engineering

CHI’s 6th Annual Protein Expression System Engineering conference examines the functioning of the cellular machinery harnessed during protein biosynthesis, and how to engineer hosts to efficiently express a protein of interest. The intricate steps required to achieve properly folded protein will be discussed, including verification and sequence analysis of the gene, codon optimization, vector construction, selecting and optimizing a clone, and selecting a host system. In addition, engineering host cells to sustain expression for longer time periods will be discussed, along with overcoming cellular stress response to produce and secrete functionally active recombinant proteins.

Final Agenda


12:00 pm Registration

12:35 Luncheon in the Exhibit Hall with Poster Viewing


1:40 Chairperson’s Opening Remarks

Stefan Schmidt, PhD, MBA, COO and Head, Operations, BioAtrium AG

1:50 KEYNOTE PRESENTATION: New Methods for Cell Free Presentation of Proteins for Functional Analysis

Joshua LaBaer, MD, PhD, Executive Director & Professor, Molecular Sciences, BioDesign Institute, Arizona State University

Self-assembling protein microarrays made through cell-free synthesis have been used widely to study protein interactions with drugs and other proteins, to search for enzyme substrates, and to find disease biomarkers, including some that are in clinical use for the detection of cancer in blood. Recent methodological advances now enable new types of studies including highly multiplexed analysis, testing the effects of post-translational changes on protein interactions and providing highly quantitative readouts with significantly reduced background noise.

2:20 Cell-Free Based Approach for Genetic Encoding of Unnatural Chemistries

Zhenling Cui, PhD, CTCB, Research Associate, Science and Engineering, Chemistry, Physics, Mechanical Engineering, Energy and Process Engineering, Queensland University of Technology (QUT)

Genetic code expansion holds the promise to revolutionize the life science and biomedicine through expanding macromolecular chemical diversity outside the natural space. We developed an engineered Escherichia coli cell-free system which allows rapid sequestration of selected native tRNA isoacceptors and subsequent reassignment of the liberated sense codons to unnatural amino acids. This represents a powerful tool for numerous practical applications including production of constrained peptides, antibody-drug conjugates and novel enzymes.

2:50 Co-Translational Insertion of Challenging Membrane Proteins into Nanomembranes by Cell-Free Expression

Julija Mezhyrova, MSc, Scientist, Institute of Biophysical Chemistry, Goethe University

Cell-free expression systems became key tools for the production of membrane proteins and other challenging targets. We have developed protocols to insert membrane proteins already co-translationally into supplied nanomembranes of defined composition. The generated protein/nanoparticles are suitable for biochemical and structural studies and contacts with detergents or other artificial environments are avoided. The strategy is exemplified with membrane-inserted phage toxins currently being explored as potential inhibitors of bacterial cell-wall formation.

LakePharma3:20 Presentation to be Announced

Hua Tu, PhD, President & CEO, LakePharma

3:50 Networking Refreshment Break


4:20 FEATURED PRESENTATION: Product Quality Control Strategy Development for Non-mAb Complex Modalities by Using Combinatorial Cell Engineering and OMICS Screening Tools

Zhimei Du, PhD, Director, Process Development, Merck and Co., Inc.

To improve understanding and increase options in developing a successful production cell line with desired product quality profile, it is important to develop diversified CHO host lineages with differences in cell growth and protein production in responding to medium and process conditions. In addition, developing predictive OMICS tools and integrating into quality control strategy are highly useful in selecting highly productive recombinant cell lines with the desired protein quality profile.

4:50 Application of Multi-Omics Analyses to Guide Rational Process Development for Recombinant Protein Expression

Yalamanchili_HimaHima Yalamanchili, PhD, Postdoctoral Fellow, Cell Line Development, Biogen

In biologics manufacturing, cell culture process development is conventionally driven by empirical studies and thus requires significant resources. We established a cross-program multi-omics platform that enables cross-dataset comparisons and integrated computational analyses. By incorporating multi-omics analyses into routine bioprocess development proactively, we established biological understandings of Biogen’s platform cell lines and processes, and further applied the knowledge to monitor process trends, identify cell engineering targets, and guide process optimizations.

5:20 End of Day

5:15 Registration for Dinner Short Courses

5:45-8:15 pm Recommended Dinner Short Course*

SC16: Assembling an Effective Toolbox of Expression Systems to Support your Research Efforts

*Separate registration required.


8:00 am Registration and Morning Coffee


8:30 Chairperson’s Remarks

William Chen, MD, PhD, Research Scientist, Electronics and Biological Engineering, Massachusetts Institute of Technology (MIT)

8:35 Elevating the Science via a Novel Pipetting Algorithm, 3D-Printing Technology and a Next-Generation Advanced Control Machine

Idris Mustafa, MS, Lead Automation Scientist, BioMolecular Resources, Genentech, Inc.

TipSort technology (an advanced, in-house robot pipetting algorithm) optimizes pipetting throughout a dynamic 96-position plate or tip tray. In-house CAD design married to 3D-printing fuels the crafting of custom lab inventions, spawning innovation and saving dollars. A fully-loaded Hamilton Vantage Robot enhanced with custom configuration/integrations and a built-in machine learning driven scheduler will support the future of small-scale protein expression analysis in the laboratory.

9:05 Driving Biological Discovery: An Expanding Toolkit for Affinity Proteomics

John LaCava, PhD, Group Leader, Laboratory of Macromolecules and Interactomes, European Research Institute for the Biology of Aging, University Medical Center Groningen

It remains challenging to transfer intact physiological macromolecules from their native sources into suitably stabilizing in vitro environments. To address this, we developed an interactome capture platform that is akin to a crystallographic screen. The approach will be summarized in this talk, leveraging research vignettes. Our long-term objective is to enable robust, tunable transfer of target endogenous macromolecules from their in vivo milieus into test tubes, for biochemical, structural, and mechanistic studies.

Lonza-tagline-stacked9:35 Presentation to be Announced


10:05 Networking Coffee Break


10:35 The Predictive Cellular and Protein Effects of Glycoengineering

Nathan Lewis, PhD, Associate Professor, Pediatrics, University of California, San Diego (UCSD)

With most top blockbuster drugs therapeutics being glycoproteins, there is a growing interest in engineering their glycan structures for improved safety, efficacy, and manufacturing. Using our systems biology approaches, we can predict the modifications needed to effectively glycoengineer proteins. We further have explored the more global impacts glycoengineering has on the host cell, thus helping to define the design space of CHO-produced glycoproteins.

11:05 Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design

Chava Kimchi-Sarfaty, PhD, Deputy Associate Director for Research, Office of Tissues and Advanced Therapies, CBER, FDA

A novel public resource that presents all codon usage, codon-pair usage and human tissue specific codon usage and codon-pair usage will be discussed. Examples of investigation areas which could greatly benefit from this resource will be provided, such as biotherapeutic development, tissue-specific genetic engineering and genetic disease prediction.

11:35 Transposon-Encoded CRISPR–Cas Systems Direct RNA Guided DNA Integration

Samuel Sternberg, PhD, Assistant Professor, Biochemistry and Molecular Biophysics, Columbia University

Conventional CRISPR–Cas systems leverage guide RNAs for the nuclease-dependent degradation of mobile genetic elements. Here we describe a notable inversion of this paradigm, in which bacterial Tn7-like transposons have co-opted nuclease-deficient CRISPR–Cas systems to catalyze RNA-guided DNA integration of mobile genetic elements into the genome. Deep-sequencing experiments reveal highly specific, genome-wide DNA insertion across dozens of unique target sites. This discovery of a fully programmable, RNA-guided integrase lays the foundation for genomic manipulations that obviate the requirements for double-strand breaks and homology-directed repair.

12:05 pm A General Approach to in vitro Protein Folding Using Nanoencapsulation

Chester Drum, MD, PhD, Assistant Professor, Translational Innovation, National University of Singapore

A novel nanoparticle can encapsulate, fold and release proteins of a wide range of sizes, charges, and disulfide content to produce improved yields and improved specific activity. Our index manuscript (Nature Communications | 8: 1442) described the concept and we have a much larger manuscript under review now which we fully expect to be published by May 2020.

GenScript-CRO 12:35 Luncheon Presentation to be Announced


1:05 Networking Refreshment Break


1:35 Chairperson’s Remarks

Amr Ali, PhD, Scientist, Technical Development, Biogen

1:40 Advanced Synthetic Biology Tools to Accelerate Mammalian Protein Expression System Engineering

William Chen, MD, PhD, Research Scientist, Electronics and Biological Engineering, Massachusetts Institute of Technology (MIT)

Conventional mammalian protein expression strategies using transient expression or random genome integration with gene of interest, followed by high-throughput colony screening and expansion, are laborious and/or time-consuming. To address those issues, we have developed a series of synthetic biology toolkits to transform mammalian protein expression system engineering. Our powerful platform technologies are versatile and can be adapted to different mammalian cell types and biomanufacturing settings to optimize complex therapeutic protein production.

2:10 Applying Omics/NGS Tools to Characterize CHO Cell Line Clonality, Transcript Variants and Stability

Fides Lay, PhD, Scientist, Cell Line Development & Genetic Characterization, Amgen, Inc.

2:40 Multi-Omics Analysis of CHO Cell Lines Reveals Differences in Energy Metabolism and ER Stress

Amr Ali, PhD, Scientist, Technical Development, Biogen

Chinese hamster ovary cells are widely used host cell lines in biotherapeutic manufacturing of monoclonal antibodies (mAbs). Cellular energy metabolism and endoplasmic reticulum stress are known to greatly impact cell growth, productivity, and structure of the biotherapeutics. However, molecular mechanisms responsible for these changes are not fully understood. Here, we use multi-omics analysis to investigate differences between cell lines and gain an in-depth understanding of the biological differences that can be exploited to improve the bioprocess.

3:10 Exploitation of a Ribosomal Protein Mutation to Enhance Recombinant Protein Production

Kim De Keersmaecker, PhD, Research Professor, Oncology – Laboratory for Disease Mechanisms in Cancer, Katholieke Universiteit Leuven

A mutation in a ribosomal protein that we discovered in cancer cells enhances the levels of ribosomal protein translation and its fidelity and reduces cellular proteasome activity in lymphoid cell models. To validate these findings in mammalian cell lines that are commonly used in the recombinant protein production industry, we engineered the ribosomal mutation into CHO and HEK293 cells. A 69-155% increase in production of 3 recombinant proteins was confirmed in HEK293 cells.

3:40 End of Conference

* The program is subject to change without notice, due to unforeseen reason.

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