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1.
Mol Ther ; 31(3): 676-685, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36518079

ABSTRACT

A chromosome 14 inversion was found in a patient who developed bone marrow aplasia following treatment with allogeneic chimeric antigen receptor (CAR) Tcells containing gene edits made with transcription activator-like effector nucleases (TALEN). TALEN editing sites were not involved at either breakpoint. Recombination signal sequences (RSSs) were found suggesting recombination-activating gene (RAG)-mediated activity. The inversion represented a dominant clone detected in the context of decreasing absolute CAR Tcell and overall lymphocyte counts. The inversion was not associated with clinical consequences and wasnot detected in the drug product administered to this patient or in any drug product used in this or other trials using the same manufacturing processes. Neither was the inversion detected in this patient at earlier time points or in any other patient enrolled in this or other trials treated with this or other product lots. This case illustrates that spontaneous, possibly RAG-mediated, recombination events unrelated to gene editing can occur in adoptive cell therapy studies, emphasizes the need for ruling out off-target gene editing sites, and illustrates that other processes, such as spontaneous V(D)J recombination, can lead to chromosomal alterations in infused cells independent of gene editing.


Subject(s)
Hematopoietic Stem Cell Transplantation , Receptors, Chimeric Antigen , Humans , Gene Editing , Transcription Activator-Like Effector Nucleases/genetics , T-Lymphocytes , Receptors, Chimeric Antigen/genetics , Immunotherapy, Adoptive/adverse effects
2.
J Proteome Res ; 20(6): 3150-3164, 2021 06 04.
Article in English | MEDLINE | ID: mdl-34008986

ABSTRACT

Citrullination is an important post-translational modification implicated in many diseases including rheumatoid arthritis (RA), Alzheimer's disease, and cancer. Neutrophil and mast cells have different expression profiles for protein-arginine deiminases (PADs), and ionomycin-induced activation makes them an ideal cellular model to study proteins susceptible to citrullination. We performed high-resolution mass spectrometry and stringent data filtration to identify citrullination sites in neutrophil and mast cells treated with and without ionomycin. We identified a total of 833 validated citrullination sites on 395 proteins. Several of these citrullinated proteins are important components of pathways involved in innate immune responses. Using this benchmark primary sequence data set, we developed machine learning models to predict citrullination in neutrophil and mast cell proteins. We show that our models predict citrullination likelihood with 0.735 and 0.766 AUCs (area under the receiver operating characteristic curves), respectively, on independent validation sets. In summary, this study provides the largest number of validated citrullination sites in neutrophil and mast cell proteins. The use of our novel motif analysis approach to predict citrullination sites will facilitate the discovery of novel protein substrates of protein-arginine deiminases (PADs), which may be key to understanding immunopathologies of various diseases.


Subject(s)
Citrullination , Mast Cells , Citrulline/metabolism , Ionomycin/pharmacology , Machine Learning , Mass Spectrometry , Mast Cells/metabolism , Neutrophils/metabolism , Protein-Arginine Deiminases/genetics
3.
Proc Natl Acad Sci U S A ; 114(10): 2687-2692, 2017 03 07.
Article in English | MEDLINE | ID: mdl-28209777

ABSTRACT

CD6 was established as a marker of T cells more than three decades ago, and recent studies have identified CD6 as a risk gene for multiple sclerosis (MS), a disease in which autoreactive T cells are integrally involved. Nevertheless, the precise role of CD6 in regulating T-cell responses is controversial and its significance in the pathogenesis of various diseases remains elusive, partly due to the lack of animals engineered to alter expression of the CD6 gene. In this report, we found that CD6 KO mice showed decreased pathogenic T-cell responses, reduced spinal cord T-cell infiltration, and attenuated disease severity in experimental autoimmune encephalomyelitis (EAE), an animal model of MS. CD6-deficient T cells exhibited augmented activation, but also significantly reduced survival and proliferation after activation, leading to overall decreased Th1 and Th17 polarization. Activated CD6-deficient T cells also showed impaired infiltration through brain microvascular endothelial cell monolayers. Furthermore, by developing CD6 humanized mice, we identified a mouse anti-human CD6 monoclonal antibody that is highly effective in treating established EAE without depleting T cells. These results suggest that (i) CD6 is a negative regulator of T-cell activation, (ii) at the same time, CD6 is a positive regulator of activated T-cell survival/proliferation and infiltration; and (iii) CD6 is a potential new target for treating MS and potentially other T-cell-driven autoimmune conditions.


Subject(s)
Antibodies, Monoclonal, Humanized/immunology , Antigens, CD/immunology , Antigens, Differentiation, T-Lymphocyte/immunology , Encephalomyelitis, Autoimmune, Experimental/drug therapy , Multiple Sclerosis/drug therapy , Animals , Antibodies, Monoclonal, Humanized/therapeutic use , Antigens, CD/therapeutic use , Antigens, Differentiation, T-Lymphocyte/therapeutic use , CD4-Positive T-Lymphocytes/immunology , Cell Differentiation/drug effects , Cell Differentiation/immunology , Cell Proliferation/drug effects , Disease Models, Animal , Encephalomyelitis, Autoimmune, Experimental/immunology , Encephalomyelitis, Autoimmune, Experimental/pathology , Humans , Lymphocyte Activation/drug effects , Lymphocyte Activation/immunology , Mice , Mice, Knockout , Multiple Sclerosis/immunology , Multiple Sclerosis/pathology , Spinal Cord/drug effects , Spinal Cord/immunology , Spinal Cord/pathology , Th1 Cells/immunology , Th17 Cells/immunology , Th17 Cells/pathology
4.
J Proteome Res ; 18(6): 2433-2445, 2019 06 07.
Article in English | MEDLINE | ID: mdl-31020842

ABSTRACT

A high-quality genome annotation greatly facilitates successful cell line engineering. Standard draft genome annotation pipelines are based largely on de novo gene prediction, homology, and RNA-Seq data. However, draft annotations can suffer from incorrect predictions of translated sequence, inaccurate splice isoforms, and missing genes. Here, we generated a draft annotation for the newly assembled Chinese hamster genome and used RNA-Seq, proteomics, and Ribo-Seq to experimentally annotate the genome. We identified 3529 new proteins compared to the hamster RefSeq protein annotation and 2256 novel translational events (e.g., alternative splices, mutations, and novel splices). Finally, we used this pipeline to identify the source of translated retroviruses contaminating recombinant products from Chinese hamster ovary (CHO) cell lines, including 119 type-C retroviruses, thus enabling future efforts to eliminate retroviruses to reduce the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate resource for CHO cell line engineering, by facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.


Subject(s)
Cricetulus/genetics , Genome/genetics , Proteogenomics , Proteomics/methods , Animals , CHO Cells , Cricetinae , Molecular Sequence Annotation/methods , RNA-Seq/methods , Sequence Analysis, RNA/methods
5.
Biotechnol Bioeng ; 116(4): 793-804, 2019 04.
Article in English | MEDLINE | ID: mdl-30536645

ABSTRACT

Cell line development (CLD) for biotherapeutics is a time- and resource-intensive process requiring the isolation and screening of large numbers of clones to identify high producers. Novel methods aimed at enhancing cell line screening efficiency using markers predictive of productivity early in the CLD process are needed to reliably generate high-yielding cell lines. To enable efficient and selective isolation of antibody expressing Chinese hamster ovary cells by fluorescence-activated cell sorting, we developed a strategy for the expression of antibodies containing a switchable membrane-associated domain to anchor an antibody to the membrane of the expressing cell. The switchable nature of the membrane domain is governed by the function of an orthogonal aminoacyl transfer RNA synthetase/tRNApyl pair, which directs a nonnatural amino acid (nnAA) to an amber codon encoded between the antibody and the membrane anchor. The process is "switchable" in response to nnAA in the medium, enabling a rapid transition between the surface display and secretion. We demonstrate that the level of cell surface display correlates with productivity and provides a method for enriching phenotypically stable high-producer cells. The strategy provides a means for selecting high-producing cells with potential applications to multiple biotherapeutic protein formats.


Subject(s)
Codon, Terminator , Genetic Vectors/genetics , Immunoglobulin G/genetics , Recombinant Proteins/genetics , Animals , Batch Cell Culture Techniques/methods , CHO Cells , Cricetulus , Humans , Transfection/methods
6.
J Immunol ; 198(1): 528-537, 2017 01 01.
Article in English | MEDLINE | ID: mdl-27881707

ABSTRACT

Affinity- and stability-engineered variants of CTLA4-Ig fusion molecules with enhanced pharmacokinetic profiles could yield improved therapies with the potential of higher efficacy and greater convenience to patients. In this study, to our knowledge, we have, for the first time, used in vitro evolution to simultaneously optimize CTLA4 affinity and stability. We selected for improved binding to both ligands, CD80 and CD86, and screened as dimeric Fc fusions directly in functional assays to identify variants with stronger suppression of in vitro T cell activation. The majority of CTLA4 molecules showing the largest potency gains in primary in vitro and ex vivo human cell assays, using PBMCs from type 1 diabetes patients, had significant improvements in CD80, but only modest gains in CD86 binding. We furthermore observed different potency rankings between our lead molecule MEDI5265, abatacept, and belatacept, depending on which type of APC was used, with MEDI5265 consistently being the most potent. We then created fusions of both stability- and potency-optimized CTLA4 moieties with human Fc variants conferring extended plasma t1/2 In a cynomolgus model of T cell-dependent Ab response, the CTLA4-Ig variant MEDI5265 could be formulated at >100 mg/ml for s.c. administration and showed superior efficacy and significantly prolonged serum t1/2 The combination of higher stability and potency with prolonged pharmacokinetics could be compatible with very infrequent, s.c. dosing while maintaining a similar level of immune suppression to more frequently and i.v. administered licensed therapies.


Subject(s)
Abatacept/pharmacology , Drug Design , Immunosuppressive Agents/pharmacology , Abatacept/chemistry , Animals , B7-1 Antigen/immunology , B7-2 Antigen , Drug Stability , Humans , Immunosuppressive Agents/chemistry , Protein Binding/immunology
7.
J Proteome Res ; 16(9): 3124-3136, 2017 09 01.
Article in English | MEDLINE | ID: mdl-28745510

ABSTRACT

Mass spectrometry is being used to identify protein biomarkers that can facilitate development of drug treatment. Mass spectrometry-based labeling proteomic experiments result in complex proteomic data that is hierarchical in nature often with small sample size studies. The generalized linear model (GLM) is the most popular approach in proteomics to compare protein abundances between groups. However, GLM does not address all the complexities of proteomics data such as repeated measures and variance heterogeneity. Linear models for microarray data (LIMMA) and mixed models are two approaches that can address some of these data complexities to provide better statistical estimates. We compared these three statistical models (GLM, LIMMA, and mixed models) under two different normalization approaches (quantile normalization and median sweeping) to demonstrate when each approach is the best for tagged proteins. We evaluated these methods using a spiked-in data set of known protein abundances, a systemic lupus erythematosus (SLE) data set, and simulated data from multiplexed labeling experiments that use tandem mass tags (TMT). Data are available via ProteomeXchange with identifier PXD005486. We found median sweeping to be a preferred approach of data normalization, and with this normalization approach there was overlap with findings across all methods with GLM being a subset of mixed models. The conclusion is that the mixed model had the best type I error with median sweeping, whereas LIMMA had the better overall statistical properties regardless of normalization approaches.


Subject(s)
Blood Proteins/isolation & purification , Escherichia coli Proteins/isolation & purification , Lupus Erythematosus, Systemic/genetics , Models, Statistical , Protein Array Analysis/statistics & numerical data , Blood Proteins/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Humans , Lupus Erythematosus, Systemic/blood , Lupus Erythematosus, Systemic/diagnosis , Lupus Erythematosus, Systemic/pathology , Proteomics/methods , Proteomics/statistics & numerical data , Staining and Labeling/methods
8.
J Proteome Res ; 16(10): 3672-3687, 2017 10 06.
Article in English | MEDLINE | ID: mdl-28876938

ABSTRACT

Chinese hamster ovary cells represent the dominant host for therapeutic recombinant protein production. However, few large-scale data sets have been generated to characterize this host organism and derived CHO cell lines at the proteomics level. Consequently, an extensive label-free quantitative proteomics analysis of two cell lines (CHO-S and CHO DG44) and two Chinese hamster tissues (liver and ovary) was used to identify a total of 11 801 unique proteins containing at least two unique peptides. 9359 unique proteins were identified specifically in the cell lines, representing a 56% increase over previous work. Additionally, 6663 unique proteins were identified across liver and ovary tissues, providing the first Chinese hamster tissue proteome. Protein expression was more conserved within cell lines during both growth phases than across cell lines, suggesting large genetic differences across cell lines. Overall, both gene ontology and KEGG pathway analysis revealed enrichment of cell-cycle activity in cells. In contrast, upregulated molecular functions in tissue include glycosylation and lipid transporter activity. Furthermore, cellular components including Golgi apparatus are upregulated in both tissues. In conclusion, this large-scale proteomics analysis enables us to delineate specific changes between tissues and cells derived from these tissues, which can help explain specific tissue function and the adaptations cells incur for applications in biopharmaceutical productions.


Subject(s)
CHO Cells/metabolism , Proteome/genetics , Proteomics , Recombinant Proteins/genetics , Animals , Cricetinae , Cricetulus/genetics , Cricetulus/metabolism , Recombinant Proteins/metabolism , Tandem Mass Spectrometry
9.
Anal Chem ; 89(3): 1477-1485, 2017 02 07.
Article in English | MEDLINE | ID: mdl-27991764

ABSTRACT

A combined lipidomics and transcriptomics analysis was performed on mouse myeloma SP2/0, Chinese hamster ovary (CHO), and human embryonic kidney (HEK) cells in order to compare widely used mammalian expression systems. Initial thin layer chromatography (TLC) analysis indicated that phosphatidylethanolamine (PE) and phosphatidylcholine (PC) were the major lipid components in all cell lines with lower amounts of sphingomyelin (SM) in SP2/0 compared to CHO and HEK, which was subsequently confirmed and expanded upon following mass spectrometry (MS) analysis. HEK contained 4-10-fold higher amounts of lyso phosphatidylethanolamine (LPE) and 2-4-fold higher amounts of lyso phosphatidylcholine (LPC) compared to SP2/0 and CHO cell lines. C18:1 followed by C16:1 were the main contributors to the difference in both LPE and LPC levels. Alternatively, the SP2/0 cell line exhibited 30-65-fold lower amounts of SM principally in the amount of 16:0. By mapping the transcriptomics data to KEGG pathways, we found expression levels of secretory phospholipase A2 (sPLA2), lysophospholipid acyltransferase (LPEAT), lysophosphatidylcholine acyltransferase (LPCAT), and lysophospholipase (LYPLA) can contribute to the differences in LPE and LPC. Sphingomyelin synthases (SMS) and sphingomyelin phosphodiesterase (SMase) enzymes may play roles in SM differences across the three cell lines. The results of this study provide insights that will aid the understanding of the physiological and secretory differences across recombinant protein production systems.


Subject(s)
Chromatography, Thin Layer , Lysophosphatidylcholines/analysis , Lysophospholipids/analysis , Sphingomyelins/analysis , Transcriptome , Animals , CHO Cells , Cell Line , Cricetinae , Cricetulus , HEK293 Cells , Humans , Mass Spectrometry , Mice , Phosphoric Diester Hydrolases/genetics , Principal Component Analysis , RNA, Messenger/metabolism , Transferases (Other Substituted Phosphate Groups)/genetics
10.
J Proteome Res ; 15(9): 3180-7, 2016 09 02.
Article in English | MEDLINE | ID: mdl-27386737

ABSTRACT

Derivitization of peptides with isobaric tags such as iTRAQ and TMT is widely employed in proteomics due to their compatibility with multiplex quantitative measurements. We recently made publicly available a large peptide library derived from iTRAQ 4-plex labeled spectra. This resource has not been used for identifying peptides labeled with related tags with different masses, because values for virtually all masses of precursor and most product ions would differ for ions containing the different tags as well as containing different tag-specific peaks. We describe a method for interconverting spectra from iTRAQ 4-plex to TMT (6- and 10-plex) and to iTRAQ 8-plex. We interconvert spectra by appropriately mass shifting sequence ions and discarding derivative-specific peaks. After this "cleaning" of search spectra, we demonstrate that the converted libraries perform well in terms of peptide spectral matches. This is demonstrated by comparing results using sequence database searches as well as by comparing search effectiveness using original and converted libraries. At 1% FDR TMT labeled query spectra match 97% as many spectra against a converted iTRAQ library as compared to an original TMT library. Overall this interconversion strategy provides a practical way to extend results from one derivatization method to others that share related chemistry and do not significantly alter fragmentation profiles.


Subject(s)
Peptide Library , Proteomics/methods , Databases, Protein , Mass Spectrometry , Molecular Weight , Staining and Labeling
11.
J Proteome Res ; 14(11): 4687-703, 2015 Nov 06.
Article in English | MEDLINE | ID: mdl-26418914

ABSTRACT

Chinese hamster ovary (CHO) cells are the preferred host cell line for manufacturing a variety of complex biotherapeutic drugs including monoclonal antibodies. We performed a proteomics and bioinformatics analysis on the spent medium from adherent CHO cells. Supernatant from CHO-K1 culture was collected and subjected to in-solution digestion followed by LC/LC-MS/MS analysis, which allowed the identification of 3281 different host cell proteins (HCPs). To functionally categorize them, we applied multiple bioinformatics tools to the proteins identified in our study including SignalP, TargetP, SecretomeP, TMHMM, WoLF PSORT, and Phobius. This analysis provided information on the presence of signal peptides, transmembrane domains, and cellular localization and showed that both secreted and intracellular proteins were constituents of the supernatant. Identified proteins were shown to be localized to the secretory pathway including ones playing roles in cell growth, proliferation, and folding as well as those involved in protein degradation and removal. After combining proteins predicted to be secreted or having a signal peptide, we identified 1015 proteins, which we termed as CHO supernatant-ome (CHO-SO), or superome. As a part of this effort, we created a publically accessible web-based tool called GO-CHO to functionally categorize proteins found in CHO-SO and identify enriched molecular functions, biological processes, and cellular components. We also used a tool to evaluate the immunogenicity potential of high-abundance HCPs. Among enriched functions were catalytic activity and structural constituents of the cytoskeleton. Various transport related biological processes, such as vesicle mediated transport, were found to be highly enriched. Extracellular space and vesicular exosome associated proteins were found to be the most enriched cellular components. The superome also contained proteins secreted from both classical and nonclassical secretory pathways. The work and database described in our study will enable the CHO community to rapidly identify high-abundance HCPs in their cultures and therefore help assess process and purification methods used in the production of biologic drugs.


Subject(s)
CHO Cells/metabolism , Computational Biology/methods , Proteome/genetics , Animals , Antibodies, Monoclonal/biosynthesis , Antibodies, Monoclonal/genetics , Biological Transport , CHO Cells/cytology , Cell Proliferation , Chromatography, Liquid , Cricetulus , Culture Media, Conditioned/chemistry , Cytoplasm/chemistry , Cytoskeleton/chemistry , Gene Expression , Molecular Sequence Annotation , Protein Interaction Mapping , Protein Sorting Signals/genetics , Proteolysis , Proteome/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/genetics , Secretory Pathway/genetics , Tandem Mass Spectrometry
12.
Acta Crystallogr D Biol Crystallogr ; 71(Pt 11): 2354-61, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26527150

ABSTRACT

The three-dimensional structure of a human IgG1 Fc fragment bound to wild-type human FcγRI is reported. The structure of the corresponding complex was solved at a resolution of 2.4 Šusing molecular replacement; this is the highest resolution achieved for an unmutated FcγRI molecule. This study highlights the critical structural and functional role played by the second extracellular subdomain of FcγRI. It also explains the long-known major energetic contribution of the Fc `LLGG' motif at positions 234-237, and particularly of Leu235, via a `lock-and-key' mechanism. Finally, a previously held belief is corrected and a differing view is offered on the recently proposed direct role of Fc carbohydrates in the corresponding interaction. Structural evidence is provided that such glycan-related effects are strictly indirect.


Subject(s)
Immunoglobulin G/chemistry , Immunoglobulin G/metabolism , Receptors, IgG/chemistry , Receptors, IgG/metabolism , Cell Line , Crystallography, X-Ray , Humans , Models, Molecular , Polysaccharides/metabolism , Protein Binding , Protein Interaction Domains and Motifs
13.
Bioconjug Chem ; 26(11): 2249-60, 2015 Nov 18.
Article in English | MEDLINE | ID: mdl-26332743

ABSTRACT

Antibody-drug conjugates (ADC) have emerged as potent antitumor drugs that provide increased efficacy, specificity, and tolerability over chemotherapy for the treatment of cancer. ADCs generated by targeting cysteines and lysines on the antibody have shown efficacy, but these products are heterogeneous, and instability may limit their dosing. Here, a novel technology is described that enables site-specific conjugation of toxins to antibodies using chemistry to produce homogeneous, potent, and highly stable conjugates. We have developed a cell-based mammalian expression system capable of site-specific integration of a non-natural amino acid containing an azide moiety. The azide group enables click cycloaddition chemistry that generates a stable heterocyclic triazole linkage. Antibodies to Her2/neu were expressed to contain N6-((2-azidoethoxy)carbonyl)-l-lysine at four different positions. Each site allowed over 95% conjugation efficacy with the toxins auristatin F or a pyrrolobenzodiazepine (PBD) dimer to generate ADCs with a drug to antibody ratio of >1.9. The ADCs were potent and specific in in vitro cytotoxicity assays. An anti Her2/neu conjugate demonstrated stability in vivo and a PBD containing ADC showed potent efficacy in a mouse tumor xenograph model. This technology was extended to generate fully functional ADCs with four toxins per antibody. The high stability of the azide-alkyne linkage, combined with the site-specific nature of the expression system, provides a means for the generation of ADCs with optimized pharmacokinetic, biological, and biophysical properties.


Subject(s)
Amino Acids/chemistry , Azides/chemistry , Click Chemistry , Cycloaddition Reaction , Immunoconjugates/chemistry , Amino Acids/genetics , Animals , Antibodies, Monoclonal/chemistry , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/therapeutic use , Azides/metabolism , Humans , Immunoconjugates/genetics , Immunoconjugates/immunology , Immunoconjugates/therapeutic use , Male , Mice , Neoplasms/drug therapy , Protein Engineering , Rats, Sprague-Dawley , Receptor, ErbB-2/immunology
15.
J Rheumatol ; 49(1): 26-35, 2022 01.
Article in English | MEDLINE | ID: mdl-34334364

ABSTRACT

OBJECTIVE: Autoantibodies against proteins encoded by human endogenous retrovirus K (HERV-K) have been reported in patients with rheumatoid arthritis (RA), but their relevance, if any, has remained unresolved. We revisited this question and tested if such autoantibodies may react with citrullinated epitopes on the envelope (Env) protein of HERV-K. METHODS: Immunoblotting and ELISAs were conducted with unmodified Env protein and with Env citrullinated by protein arginine deiminase 4 (PAD4). Sera from 100 patients with RA, plasma from 32 patients with juvenile idiopathic arthritis (JIA), and healthy adult and pediatric controls were included. Antibody reactivity was evaluated for correlations with clinical and laboratory variables of the patients. RESULTS: We replicated and expanded upon published data suggesting that patients with RA or JIA have autoantibodies against HERV-K Env, some with high titers. Anti-HERV-K antibodies correlated with cigarette smoking and with circulating myeloperoxidase-DNA complexes indicative of nonapoptotic neutrophil cell death. Further, most of the patients with RA, but not those with JIA, had autoantibodies that reacted more strongly with Env that was citrullinated by PAD4. These anticitrullinated Env autoantibodies correlated with seropositivity and tended to be higher in patients with erosive disease. CONCLUSION: Our data suggest that anti-HERV-K immunity is elevated in RA and JIA and may have a connection with pathogenic protein citrullination in RA.


Subject(s)
Arthritis, Rheumatoid , Endogenous Retroviruses , Autoantibodies , Child , Gene Products, env , Humans , Protein-Arginine Deiminase Type 4
16.
Sci Rep ; 12(1): 3280, 2022 02 28.
Article in English | MEDLINE | ID: mdl-35228567

ABSTRACT

Omics-based tools were coupled with bioinformatics for a systeomics analysis of two biopharma cell types: Chinese hamster ovary (M-CHO and CHO-K1) and SP2/0. Exponential and stationary phase samples revealed more than 10,000 transcripts and 6000 proteins across these two manufacturing cell lines. A statistical comparison of transcriptomics and proteomics data identified downregulated genes involved in protein folding, protein synthesis and protein metabolism, including PPIA-cyclophilin A, HSPD1, and EIF3K, in M-CHO compared to SP2/0 while cell cycle and actin cytoskeleton genes were reduced in SP2/0. KEGG pathway comparisons revealed glycerolipids, glycosphingolipids, ABC transporters, calcium signaling, cell adhesion, and secretion pathways depleted in M-CHO while retinol metabolism was upregulated. KEGG and IPA also indicated apoptosis, RNA degradation, and proteosomes enriched in CHO stationary phase. Alternatively, gene ontology analysis revealed an underrepresentation in ion and potassium channel activities, membrane proteins, and secretory granules including Stxbpt2, Syt1, Syt9, and Cma1 proteins in M-CHO. Additional enrichment strategies involving ultracentrifugation, biotinylation, and hydrazide chemistry identified over 4000 potential CHO membrane and secretory proteins, yet many secretory and membrane proteins were still depleted. This systeomics pipeline has revealed bottlenecks and potential opportunities for cell line engineering in CHO and SP2/0 to improve their production capabilities.


Subject(s)
Proteomics , Secretory Pathway , Animals , CHO Cells , Cricetinae , Cricetulus , Membrane Proteins/metabolism , Secretory Pathway/genetics
17.
Br J Haematol ; 155(4): 426-37, 2011 Nov.
Article in English | MEDLINE | ID: mdl-21902688

ABSTRACT

Human cluster of differentiation (CD) antigen 19 is a B cell-specific surface antigen and an attractive target for therapeutic monoclonal antibody (mAb) approaches to treat malignancies of B cell origin. MEDI-551 is an affinity-optimized and afucosylated CD19 mAb with enhanced antibody-dependent cellular cytotoxicity (ADCC). The results from in vitro ADCC assays with Natural Killer cells as effector cells, demonstrate that MEDI-551 is effective at lower mAb doses than rituximab with multiple cell lines as well as primary chronic lymphocytic leukaemia and acute lymphoblastic leukaemia samples. Targeting CD19 with MEDI-551 was also effective in several severe combined immunodeficiency lymphoma models. Furthermore, the combination of MEDI-551 with rituximab resulted in prolonged suppression of tumour growth, demonstrating that therapeutic mAbs with overlapping effector function can be combined for greater tumour growth inhibition. Together, the data demonstrate that MEDI-551 has potent antitumour activity in preclinical models of B cell malignancies. The results also suggest that the combination of the ADCC-enhanced CD19 mAb with an anti-CD20 mAb could be a novel approach for the treatment of B cell lymphomas.


Subject(s)
Antibodies, Monoclonal/pharmacology , Antigens, CD19/immunology , Leukemia, B-Cell/immunology , Leukemia, B-Cell/therapy , Lymphoma, B-Cell/immunology , Lymphoma, B-Cell/therapy , Animals , Antibodies, Monoclonal/administration & dosage , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal, Murine-Derived/administration & dosage , Antibody-Dependent Cell Cytotoxicity/drug effects , Antineoplastic Combined Chemotherapy Protocols/pharmacology , B-Lymphocytes/drug effects , B-Lymphocytes/immunology , Cell Line, Tumor , Female , Humans , Mice , Mice, SCID , Protein Engineering/methods , Receptors, Fc/immunology , Rituximab , Xenograft Model Antitumor Assays
18.
J Pharmacol Exp Ther ; 335(1): 213-22, 2010 Oct.
Article in English | MEDLINE | ID: mdl-20605905

ABSTRACT

The pan B-cell surface antigen CD19 is an attractive target for therapeutic monoclonal antibody (mAb) approaches. We have generated a new afucosylated anti-human (hu)CD19 mAb, MEDI-551, with increased affinity to human FcγRIIIA and mouse FcγRIV and enhanced antibody-dependent cellular cytotoxicity (ADCC). During in vitro ADCC assays with B-cell lines, MEDI-551 is effective at much lower mAb concentrations than the fucosylated parental mAb anti-CD19-2. Furthermore, the afucosylated CD19 mAb MEDI-551 depleted B cells from normal donor peripheral blood mononuclear cell samples in an autologous ADCC assay, as well as blood and tissue B cells in human CD19/CD20 double transgenic (Tg) mice at lower concentrations than that of the positive control mAb rituximab. In huCD19/CD20 Tg mice, both macrophage-mediated phagocytosis and complement-dependent cytotoxicity contribute to depletion with rituximab; MEDI-551 did not require complement for maximal B-cell depletion. Furthermore, extended B-cell depletion from the blood and spleen was achieved with MEDI-551, which is probably explained by bone marrow B-cell depletion in huCD19/CD20 Tg mice relative to the control mAb rituximab. In summary, MEDI-551 has potent B-cell-depleting activity in vitro and in vivo and may be a promising new approach for the treatment of B-cell malignancies and autoimmune diseases.


Subject(s)
Antigens, CD19/immunology , B-Lymphocytes/physiology , Animals , Antibodies, Blocking/pharmacology , Antibodies, Monoclonal/pharmacology , Antibodies, Monoclonal, Murine-Derived , Antibody-Dependent Cell Cytotoxicity , Antigens, CD19/genetics , Cell Proliferation/drug effects , Fucose/chemistry , Humans , Immunoglobulin G/immunology , Mice , Mice, Transgenic , Protein Engineering , Rituximab
19.
MAbs ; 12(1): 1684749, 2020.
Article in English | MEDLINE | ID: mdl-31775561

ABSTRACT

The ability to genetically encode non-natural amino acids (nnAAs) into proteins offers an expanded tool set for protein engineering. nnAAs containing unique functional moieties have enabled the study of post-translational modifications, protein interactions, and protein folding. In addition, nnAAs have been developed that enable a variety of biorthogonal conjugation chemistries that allow precise and efficient protein conjugations. These are being studied to create the next generation of antibody-drug conjugates with improved efficacy, potency, and stability for the treatment of cancer. However, the efficiency of nnAA incorporation, and the productive yields of cell-based expression systems, have limited the utility and widespread use of this technology. We developed a process to isolate stable cell lines expressing a pyrrolysyl-tRNA synthetase/tRNApyl pair capable of efficient nnAA incorporation. Two different platform cell lines generated by these methods were used to produce IgG-expressing cell lines with normalized antibody titers of 3 g/L using continuous perfusion. We show that the antibodies produced by these platform cells contain the nnAA functionality that enables facile conjugations. Characterization of these highly active and robust platform hosts identified key parameters that affect nnAA incorporation efficiency. These highly efficient host platforms may help overcome the expression challenges that have impeded the developability of this technology for manufacturing proteins with nnAAs and represents an important step in expanding its utility.


Subject(s)
Amino Acids/genetics , Amino Acyl-tRNA Synthetases/genetics , Antineoplastic Agents/chemistry , Immunoconjugates/genetics , Immunoglobulin G/genetics , Protein Engineering/methods , Amino Acid Sequence , Amino Acids/chemistry , Animals , CHO Cells , Cricetulus , Gene Expression , High-Throughput Screening Assays , Humans , Immunoconjugates/chemistry , Immunoglobulin G/chemistry , Lysine/analogs & derivatives , Lysine/chemistry , Protein Processing, Post-Translational
20.
Protein Eng Des Sel ; 31(10): 389-398, 2018 10 01.
Article in English | MEDLINE | ID: mdl-30753634

ABSTRACT

Membrane proteins play key roles in the evolution of numerous diseases and as a result have become the most dominant class of targets for therapeutic intervention. However, their poor expression and detection oftentimes prohibit drug discovery and screening efforts. Herein, we have developed an approach, named 'Tag-on-Demand' that exploits amber suppression to control the expression of 'tagged' membrane proteins for detection and selections, yet can be turned off for expression of the protein in its native form. Utilizing an engineered Chinese hamster ovary cell line capable of efficient amber suppression, we evaluated the expression of a diverse panel of model membrane proteins and demonstrated the enrichment of cells with improved expression profiles, where ~200-800% improvement in total protein expression levels were observed over pre-sorted populations after a single round of fluorescence-activated cell sorting. Furthermore, results were most striking for the typically difficult-to-express G protein-coupled receptor, CXCR2, where ~2.5-fold improvement in surface expression was observed. We anticipate that the Tag-on-Demand approach will be suitable not only for membrane protein cell line development but also for the development of intracellular and secreted protein cell lines in expression systems for which amber suppression technology exists, including bacterial, yeast, insect and cell-free expression systems.


Subject(s)
Codon, Terminator/genetics , Genetic Engineering/methods , Membrane Proteins/genetics , Animals , CHO Cells , Cricetulus , Drug Evaluation, Preclinical , Gene Expression , HEK293 Cells , Humans
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