Engineering, expression screening, and production cell line development of hetero Ig molecules using charge pair mutations

In recent years, there has been an increase in therapeutic indications that require bispecific targeting. Bispecific Hetero Ig antibodies that can target two antigens have long been considered as an attractive approach to drive synergistic biologic activity while maintaining the structure and stability of a traditional antibody. However, clinical development of such molecules has been hampered by CMC related challenges relating to product heterogeneity. During the development of a Hetero Ig molecule targeting the Wnt pathway antagonists Dkk-1 and SCL-1, we employed a novel strategy to drive the heterodimerization of IgG antibodies through the addition of charge pair reside mutations (CPM) at both the heavy chain and light chain surface interface. Through electrostatic interactions, these CPMs drive appropriate chain pairing, while minimizing undesired side products. During engineering and expression in transient expression systems, we identified combinations of single residue pair mutations that promoted correct chain pairing. However, the combination of antibody pairs and expression balance is important to enable reduction in undesired side products. These findings extend to stable cell line development, where vector design and appropriate analytics enable the identification of pools and then clones with desired product quality. We have expanded this strategy for the development of a platform approach toward the efficient development of HeteroIg molecules

Increasing diversity of production cell lines through miniaturization, automation, and high-throughput analytics

The development of a successful biologic therapeutic manufacturing process begins with the creation of a stable clonal cell line. Since attributes of the production cell line will significantly impact upstream and downstream processes, researchers must find ways to generate several candidate lines with diverse properties. However, a wide diversity is difficult to achieve since cultures are commonly selected, maintained, and screened as populations. In these populations, robust sub-populations can overtake the overall culture and reduce diversity. To combat this, sub-populations must be physically separated by splitting or subcloning, and maintained in individual vessels requiring intensive labor and infrastructure. As a result, researchers must balance between either increasing diversity vs. increasing resources need to maintain and screen hundreds of cultures. In order to shift this balance towards greater diversity, we have developed systems that combines miniaturization of culture vessels, targeted use of automation, and single cell analysis to allow for hundreds of cell lines to be isolated, maintained, and analyzed. We demonstrate cell lines can be easily maintained in simple low volume formats with no impact on cells. We show that we can significantly improve and maintain diversity through separation and isolation of hundreds of cultures. Additionally, higher throughputs allows to assess cell line phenotypes of multiple candidate lines early in development. Benefits achieved through this approach did not increase resources or timelines. Moving towards miniaturization combined with single cell analysis will also enable future possibilities for more precise cell engineering and gene editing

A repeated IMP-binding motif controls oskar mRNA translation and anchoring independently of Drosophila melanogaster IMP

Zip code–binding protein 1 (ZBP-1) and its Xenopus laevis homologue, Vg1 RNA and endoplasmic reticulum–associated protein (VERA)/Vg1 RNA-binding protein (RBP), bind repeated motifs in the 3′ untranslated regions (UTRs) of localized mRNAs. Although these motifs are required for RNA localization, the necessity of ZBP-1/VERA remains unresolved. We address the role of ZBP-1/VERA through analysis of the Drosophila melanogaster homologue insulin growth factor II mRNA–binding protein (IMP). Using systematic evolution of ligands by exponential enrichment, we identified the IMP-binding element (IBE) UUUAY, a motif that occurs 13 times in the oskar 3′UTR. IMP colocalizes with oskar mRNA at the oocyte posterior, and this depends on the IBEs. Furthermore, mutation of all, or subsets of, the IBEs prevents oskar mRNA translation and anchoring at the posterior. However, oocytes lacking IMP localize and translate oskar mRNA normally, illustrating that one cannot necessarily infer the function of an RBP from mutations in its binding sites. Thus, the translational activation of oskar mRNA must depend on the binding of another factor to the IBEs, and IMP may serve a different purpose, such as masking IBEs in RNAs where they occur by chance. Our findings establish a parallel requirement for IBEs in the regulation of localized maternal mRNAs in D. melanogaster and X. laevis

A molecular mechanism for mRNA trafficking in neuronal dendrites

Specific neuronal mRNAs are localized in dendrites, often concentrated in dendritic spines and spine synapses, where they are translated. The molecular mechanism of localization is mostly unknown. Here we have explored the roles of A2 response element (A2RE), a cis-acting signal for oligodendrocyte RNA trafficking, and its cognate trans-acting factor, heterogeneous nuclear ribonucleoprotein ( hnRNP) A2, in neurons. Fluorescently labeled chimeric RNAs containing A2RE were microinjected into hippocampal neurons, and RNA transport followed using confocal laser scanning microscopy. These RNA molecules, but not RNA lacking the A2RE sequence, were transported in granules to the distal neurites. hnRNP A2 protein was implicated as the cognate trans-acting factor: it was colocalized with RNA in cytoplasmic granules, and RNA trafficking in neurites was compromised by A2RE mutations that abrogate hnRNP A2 binding. Coinjection of antibodies to hnRNP A2 halved the number of trafficking cells, and treatment of neurons with antisense oligonucleotides also disrupted A2RE - RNA transport. Colchicine inhibited trafficking, whereas cells treated with cytochalasin were unaffected, implicating involvement of microtubules rather than microfilaments. A2RE-like sequences are found in a subset of dendritically localized mRNAs, which, together with these results, suggests that a molecular mechanism based on this cis-acting sequence may contribute to dendritic RNA localization

Enabling next-generation cell line development using continuous perfusion and nanofluidic technologies

The manufacturing process for a biologic begins with establishing a clonally derived, stable production cell line. Generating a highly productive cell line is time and resource intensive and involves screening of a large number of candidates. While miniaturization and automation strategies can reduce resources and increase throughput, they have matured and recent advances have been incremental. With increasing pressure on time to commercialization and the increasing diversity and complexity of therapies in discovery research, there is a need to transform cell line development to accelerate patient access to novel therapies and nanofluidic technology are on potential solution. In this study, we present cell line development data on the Berkeley Lights integrated platform. Cells are manipulated at a single cell level though use of OptoElectronic Positioning (OEP) technology which utilizes projected light patterns to activate photoconductors that gently moves cells. Common cell culture tasks can be programmed though software allowing thousands of cell lines to cultured simultaneously. Cultures can be interrogated for productivity and growth characteristics while on the chip at ~100-fold miniaturization and continuous perfusion of cell culture medium enables effective and robust cell growth and product concentration despite starting from a single cell. Concepts from perfusion culture are also applied to measure productivity and product quality. We demonstrate that commercial production CHO cell lines can be cultured in this nanofluidic environment and show that sub clone isolation, recovery, and selection are achieved with high efficiency. Overall, this technology has the potential to transform cell line development workflows through the replacement of laborious manual processes with nanofluidics and automation, and can ultimately enable the rapid selection of high performing cell lines

Rethinking clonality using modeling approaches

A combination of experimental procedures, imaging, and probability estimation are typically used as evidence of clonality for the manufacture of a biotherapeutic product. In situations where the totality of evidence is unavailable, establishing a high statistical probability for monoclonality can help strengthen the argument for clonality. In this study, the probability of clonality was re-examined for the limiting dilution method using a combination of experimental and modeling approaches. A limiting dilution experiment was performed using a 50:50 mixed population of GFP-and RFP-expressing cells and the plates were imaged over a span of two weeks. The imaged cells were scored for clonality and double checked with fluorescence imager. Among all wells that had single colony-like growth on day 14 and a single cell-like image on day 0, a fraction of the wells were confirmed to have two colors on day 14 by fluorescence imaging, indicating the singe cell-like day 0 images for these wells were false reads. Considering the possibility of having 2 or more cells with the same color in a particular well, we estimated the worst case total possible number of wells with 2 or more cells on day 0. Moreover, assuming a Poisson distribution for limiting dilution, the recovery rate of any single cell that grew into a visible colony by day 14 was estimated. Our modeling analysis indicated that only a fraction of the wells with \u3e2 cells on day 0 could grow into non-monoclonal colonies. If cells from any of the wells with single colony-like growth on day 14 and single cell-like image on day 0 were chosen as the final clone, the probability of monoclonality was estimated to be \u3e 95% with a 95% upper confidence limit

Thermoresponsive worms for expansion and release of human embryonic stem cells

The development of robust suspension cultures of human embryonic stem cells (hESCs) without the use of cell membrane disrupting enzymes or inhibitors is critical for future clinical applications in regenerative medicine. We have achieved this by using long, flexible, and thermoresponsive polymer worms decorated with a recombinant vitronectin subdomain that bridge hESCs, aiding in hESC's natural ability to form embryoid bodies (EBs) and satisfying their inherent requirement for cell-cell and cell-extracellular matrix contact. When the EBs reached an optimal upper size where cytokine and nutrient penetration becomes limiting, these long and flexible polymer worms facilitated EB breakdown via a temperature shift from 37 to 25 C. The thermoresponsive nature of the worms enabled a cyclical dissociation and propagation of the cells. Repeating the process for three cycles (over eighteen days) provided a >30-fold expansion in cell number while maintaining pluripotency, thereby providing a simple, nondestructive process for the 3D expansion of hESC

Limitations of subcloning as a tool to characterize homogeneity of a cell population

Cloning, or the derivation of a cell line from a single cell is a critical step in the generation of a manufacturing cell line. The expectation is that the process of cloning will result in a uniform and homogeneous cell line that will ensure robust product quality over the lifetime of the product. Regulatory guidelines require the sponsors provide assurance of clonality of the production cell line and when such evidence is not available, additional studies are required to further ensure consistent long-term manufacturing of the product. One approach to characterize homogeneity of a cell line is subclone analysis where clones are generated from the original cell line and an evaluation of their similarity is performed lines. To study the suitability of subclone analysis to provide additional assurance that a production cell line is clonally derived, an antibody producing CHO Master Cell Bank (MCB), which was cloned by a validated FACS method and with a clear documented day 0 image was characterized. Specifically, this MCB was subcloned and imaged to assure each of the subclones were derived from a single cell. A total of 46 subclones were analyzed for growth, productivity, product quality, as well as copy number and integration site analysis. Despite demonstration of clonality for both the MCB and the subclones, significant diversity in cell growth, protein productivity, and product quality attributes was observed between the 46 subclones. The diversity in protein productivity and quality were reproduced across bioreactor scales, suggesting that albeit different, the subclones were stable populations that varied from the parental clonal cell line. Additionally, while ~2-fold shifts in copy number were seen, no significant integration site changes were observed. Our data suggest subcloning induces changes (genetic or epigenetic) outside the region of the transgene which result in the subclones exhibiting a wide diversity in cell growth protein productivity, and product quality. Transcriptomic and genomic characterization studies are underway to further characterize the differences between subclones and the MCB. Importantly, the subclones do keep their individual characteristics as they mature and stabilize, suggesting that the resulting population that grows out of a single cell is stable but with unique properties. Overall, this work adds to the growing body of work on CHO cell plasticity and suggests that subcloning is not an effective approach to demonstrate homogeneity of a cell bank

Nanoscale integration of single cell biologics discovery processes using optofluidic manipulation and monitoring.

The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high-paced workflows necessary to support modern large molecule drug discovery. A high-level aspiration is a true integration of "lab-on-a-chip" methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light-induced electrokinetics with micro- and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single-cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low-throughput bioprocess workflows in biopharma and life science research

Amino acid degradation pathway inhibitors trigger apoptosis in Chinese Hamster Ovary cells

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