RESUMEN
Drug resistance and relapse remain key challenges in pancreatic cancer. Here, we have used RNA sequencing (RNA-seq), chromatin immunoprecipitation (ChIP)-seq, and genome-wide CRISPR analysis to map the molecular dependencies of pancreatic cancer stem cells, highly therapy-resistant cells that preferentially drive tumorigenesis and progression. This integrated genomic approach revealed an unexpected utilization of immuno-regulatory signals by pancreatic cancer epithelial cells. In particular, the nuclear hormone receptor retinoic-acid-receptor-related orphan receptor gamma (RORγ), known to drive inflammation and T cell differentiation, was upregulated during pancreatic cancer progression, and its genetic or pharmacologic inhibition led to a striking defect in pancreatic cancer growth and a marked improvement in survival. Further, a large-scale retrospective analysis in patients revealed that RORγ expression may predict pancreatic cancer aggressiveness, as it positively correlated with advanced disease and metastasis. Collectively, these data identify an orthogonal co-option of immuno-regulatory signals by pancreatic cancer stem cells, suggesting that autoimmune drugs should be evaluated as novel treatment strategies for pancreatic cancer patients.
Asunto(s)
Adenocarcinoma/patología , Células Madre Neoplásicas/metabolismo , Neoplasias Pancreáticas/patología , Adenocarcinoma/genética , Adenocarcinoma/metabolismo , Animales , Moléculas de Adhesión Celular/genética , Moléculas de Adhesión Celular/metabolismo , Diferenciación Celular , Epigénesis Genética , Biblioteca de Genes , Humanos , Ratones , Ratones Noqueados , Ratones SCID , Células Madre Neoplásicas/citología , Miembro 3 del Grupo F de la Subfamilia 1 de Receptores Nucleares/antagonistas & inhibidores , Miembro 3 del Grupo F de la Subfamilia 1 de Receptores Nucleares/genética , Miembro 3 del Grupo F de la Subfamilia 1 de Receptores Nucleares/metabolismo , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/metabolismo , Interferencia de ARN , ARN Interferente Pequeño/metabolismo , Receptores Acoplados a Proteínas G/antagonistas & inhibidores , Receptores Acoplados a Proteínas G/genética , Receptores Acoplados a Proteínas G/metabolismo , Receptores de Interleucina-10/antagonistas & inhibidores , Receptores de Interleucina-10/genética , Receptores de Interleucina-10/metabolismo , Linfocitos T/citología , Linfocitos T/inmunología , Linfocitos T/metabolismo , Transcriptoma , Células Tumorales CultivadasRESUMEN
Heparan sulfate (HS) proteoglycans bind extracellular proteins that participate in cell signaling, attachment and endocytosis. These interactions depend on the arrangement of sulfated sugars in the HS chains generated by well-characterized biosynthetic enzymes; however, the regulation of these enzymes is largely unknown. We conducted genome-wide CRISPR-Cas9 screens with a small-molecule ligand that binds to HS. Screening of A375 melanoma cells uncovered additional genes and pathways impacting HS formation. The top hit was the epigenetic factor KDM2B, a histone demethylase. KDM2B inactivation suppressed multiple HS sulfotransferases and upregulated the sulfatase SULF1. These changes differentially affected the interaction of HS-binding proteins. KDM2B-deficient cells displayed decreased growth rates, which was rescued by SULF1 inactivation. In addition, KDM2B deficiency altered the expression of many extracellular matrix genes. Thus, KDM2B controls proliferation of A375 cells through the regulation of HS structure and serves as a master regulator of the extracellular matrix.
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Proteínas F-Box/antagonistas & inhibidores , Estudio de Asociación del Genoma Completo , Heparitina Sulfato/metabolismo , Histona Demetilasas con Dominio de Jumonji/antagonistas & inhibidores , Algoritmos , Sistemas CRISPR-Cas , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Descubrimiento de Drogas , Matriz Extracelular/genética , Ensayos Analíticos de Alto Rendimiento , Humanos , Unión Proteica/genética , RNA-Seq , Sulfotransferasas/antagonistas & inhibidoresRESUMEN
Heparin is the most widely prescribed biopharmaceutical in production globally. Its potent anticoagulant activity and safety makes it the drug of choice for preventing deep vein thrombosis and pulmonary embolism. In 2008, adulterated material was introduced into the heparin supply chain, resulting in several hundred deaths and demonstrating the need for alternate sources of heparin. Heparin is a fractionated form of heparan sulfate derived from animal sources, predominantly from connective tissue mast cells in pig mucosa. While the enzymes involved in heparin biosynthesis are identical to those for heparan sulfate, the factors regulating these enzymes are not understood. Examination of the promoter regions of all genes involved in heparin/heparan sulfate assembly uncovered a transcription factor-binding motif for ZNF263, a C2H2 zinc finger protein. CRISPR-mediated targeting and siRNA knockdown of ZNF263 in mammalian cell lines and human primary cells led to dramatically increased expression levels of HS3ST1, a key enzyme involved in imparting anticoagulant activity to heparin, and HS3ST3A1, another glucosaminyl 3-O-sulfotransferase expressed in cells. Enhanced 3-O-sulfation increased binding to antithrombin, which enhanced Factor Xa inhibition, and binding of neuropilin-1. Analysis of transcriptomics data showed distinctively low expression of ZNF263 in mast cells compared with other (non-heparin-producing) immune cells. These findings demonstrate a novel regulatory factor in heparan sulfate modification that could further advance the possibility of bioengineering anticoagulant heparin in cultured cells.
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Proteínas de Unión al ADN/metabolismo , Heparina/metabolismo , Heparitina Sulfato/biosíntesis , Animales , Anticoagulantes , Línea Celular , Células Cultivadas , Cromatografía Líquida de Alta Presión , Regulación de la Expresión Génica/genética , Células HeLa , Heparina/biosíntesis , Heparina/genética , Heparitina Sulfato/genética , Heparitina Sulfato/metabolismo , Humanos , Mastocitos/metabolismo , Sulfotransferasas/metabolismo , Porcinos , Factores de TranscripciónRESUMEN
Chinese hamster ovary (CHO) cells are the primary host for manufacturing of therapeutic proteins. However, productivity loss is a major problem and is associated with genome instability, as chromosomal aberrations reduce transgene copy number and decrease protein expression. We analyzed whole-genome sequencing data from 11 CHO cell lines and found deleterious single-nucleotide variants in DNA repair genes. Comparison with primary Chinese hamster cells confirmed DNA repair to be compromised in CHO. Correction of key DNA repair genes by single-nucleotide variant reversal or expression of intact complementary DNAs successfully improved DNA repair and mitigated karyotypic instability. Moreover, overexpression of intact copies of LIG4 and XRCC6 in a CHO cell line expressing secreted alkaline phosphatase mitigated transgene copy loss and improved protein titer retention. These results show that correction of DNA repair genes yields improvements in genome stability in CHO, and provide new opportunities for cell line development for sustainable protein expression.
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Reparación del ADN , Inestabilidad Genómica , Animales , Células CHO , Cricetinae , Cricetulus , Reparación del ADN/genética , Inestabilidad Genómica/genética , CariotipificaciónRESUMEN
Media and feed optimization have fueled many-fold improvements in mammalian biopharmaceutical production, but genome editing offers an emerging avenue for further enhancing cell metabolism and bioproduction. However, the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we present a comprehensive pooled CRISPR screen for CHO cell metabolism, including ~16,000 gRNAs against ~2500 metabolic enzymes and regulators. Using this screen, we identified a glutamine response network in CHO cells. Glutamine is particularly important since it is often over-fed to drive increased TCA cycle flux, but toxic ammonia may accumulate. With the screen we found one orphan glutamine-responsive gene with no clear connection to our network. Knockout of this novel and poorly characterized lipase, Abhd11, substantially increased growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait, and elucidate novel regulators of metabolism.
Asunto(s)
Sistemas CRISPR-Cas , Glutamina , Animales , Células CHO , Cricetinae , Cricetulus , Edición Génica , Glutamina/genética , Glutamina/metabolismoRESUMEN
Glycosylation is a critical quality attribute of most recombinant biotherapeutics. Consequently, drug development requires careful control of glycoforms to meet bioactivity and biosafety requirements. However, glycoengineering can be extraordinarily difficult given the complex reaction networks underlying glycosylation and the vast number of different glycans that can be synthesized in a host cell. Computational modeling offers an intriguing option to rationally guide glycoengineering, but the high parametric demands of current modeling approaches pose challenges to their application. Here we present a novel low-parameter approach to describe glycosylation using flux-balance and Markov chain modeling. The model recapitulates the biological complexity of glycosylation, but does not require user-provided kinetic information. We use this method to predict and experimentally validate glycoprofiles on EPO, IgG as well as the endogenous secretome following glycosyltransferase knock-out in different Chinese hamster ovary (CHO) cell lines. Our approach offers a flexible and user-friendly platform that can serve as a basis for powerful computational engineering efforts in mammalian cell factories for biopharmaceutical production.
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Glicoproteínas/metabolismo , Cadenas de Markov , Ingeniería Metabólica/métodos , Análisis de Flujos Metabólicos/métodos , Modelos Estadísticos , Polisacáridos/metabolismo , Animales , Células CHO , Simulación por Computador , Cricetulus , Glicoproteínas/química , Glicoproteínas/genética , Glicosilación , Modelos Biológicos , Polisacáridos/química , Polisacáridos/genéticaRESUMEN
serpent (srp) encodes a GATA-factor that controls various aspects of embryogenesis in Drosophila, such as fatbody development, gut differentiation and hematopoiesis. During hematopoiesis, srp expression is required in the embryonic head mesoderm and the larval lymph gland, the two known hematopoietic tissues of Drosophila, to obtain mature hemocytes. srp expression in the hemocyte primordium is known to depend on snail and buttonhead, but the regulatory complexity that defines the primordium has not been addressed yet. Here, we find that srp is sufficient to transform trunk mesoderm into hemocytes. We identify two disjoint cis-regulatory modules that direct the early expression in the hemocyte primordium and the late expression in mature hemocytes and lymph gland, respectively. During embryonic hematopoiesis, a combination of snail, buttonhead, empty spiracles and even-skipped confines the mesodermal srp expression to the head region. This restriction to the head mesoderm is crucial as ectopic srp in mesodermal precursors interferes with the development of mesodermal derivates and promotes hemocytes and fatbody development. Thus, several genes work in a combined fashion to restrain early srp expression to the head mesoderm in order to prevent expansion of the hemocyte primordium.
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Proteínas de Drosophila/metabolismo , Drosophila/embriología , Factores de Transcripción GATA/metabolismo , Regulación del Desarrollo de la Expresión Génica , Hemocitos/metabolismo , Animales , Animales Modificados Genéticamente , Secuencia de Bases , Elementos de Facilitación Genéticos , Mesodermo/metabolismo , Datos de Secuencia Molecular , Mutación , Filogenia , Plásmidos/metabolismo , Especificidad de la Especie , Transcripción GenéticaRESUMEN
The PDZ-GEF protein Dizzy (Dzy) and its downstream GTPase Rap1 have pleiotropic roles during development of the Drosophila embryo. Here, we show that maternally provided Dzy and Rap1 first function during ventral furrow formation (VFF) where they are critical to guarantee rapid apical cell constrictions. Contraction of the apical actomyosin filament system occurs independently of Dzy and Rap1, but loss of Dzy results in a delayed establishment of the apical adherens junction (AJ) belt, whereas in the absence of Rap1 only a fragmentary apical AJ belt is formed in the epithelium. The timely establishment of apical AJs appears to be essential for coupling actomyosin contractions to cell shape change and to assure completion of the ventral furrow. Immediately after VFF, the downregulation of Dzy and Rap1 is necessary to allow normal mesodermal development to continue after the epithelial-to-mesenchymal transition, as overexpression of Dzy or of constitutively active Rap1 compromises mesodermal migration and monolayer formation. We propose that Dzy and Rap1 are crucial factors regulating the dynamics of AJs during gastrulation.
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Uniones Adherentes/fisiología , Proteínas de Drosophila/fisiología , Drosophila melanogaster/embriología , Factores de Intercambio de Guanina Nucleótido/fisiología , Uniones Adherentes/metabolismo , Animales , Movimiento Celular/fisiología , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/ultraestructura , Embrión no Mamífero , Desarrollo Embrionario , Activación Enzimática , Gastrulación , Factores de Intercambio de Guanina Nucleótido/genética , Factores de Intercambio de Guanina Nucleótido/metabolismo , Transducción de SeñalRESUMEN
The estimation of the minimum postmortem interval can be implemented by age estimation of corpse-associated primary colonizers such as the blow flies (Diptera: Calliphoridae). In cases where pupae represent the oldest stages found on a body, their age must be added to the duration of prepupal development to estimate the minimum postmortem interval. Although methods to age blow fly larvae have been well established using morphology, length or weight and age estimation of pupae has proved challenging. In a previous work, we quantified the changes in mRNA levels of four differentially expressed genes during the metamorphosis of Calliphora vicina pupae, hence representing molecular markers for pupal age (i.e., time elapsed since pupariation). Here, we demonstrate how these data can be used to estimate pupal age with inverse prediction. We present three blind studies conducted under various conditions and show that age of C. vicina pupae can be well estimated based on gene expression data. As these data are quantitative and can be processed automatically, gene expression has the potential to outperform morphological analysis in age estimation of forensically relevant blow fly pupae.
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Dípteros/crecimiento & desarrollo , Dípteros/genética , Expresión Génica , Metamorfosis Biológica/genética , Actinas/genética , Animales , Proteínas Portadoras/genética , Entomología , Patologia Forense , Proteínas de Insectos/genética , Análisis de los Mínimos Cuadrados , Pupa/crecimiento & desarrollo , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Manejo de Especímenes , TemperaturaRESUMEN
Necrophagous blow fly larvae can provide accurate estimates of the minimum postmortem interval in death investigations. During larval development, predictable morphological changes occur and measurements of weight, length, and width are compared to species-specific growth curves for reliable age estimates. However, aging blow fly pupae is more challenging because morphological and anatomical changes are not visible with the naked eye. Thus, delicate preparation of the pupae or rearing to the adult stage seems unavoidable. Conversely, metamorphosis evokes a remodelling of the larval shape to adult structures, and gene expression analysis potentially serves as a molecular tool to mirror the ageing process of a pupa. The present study focuses on the differential expression of two newly described, arbitrarily named genes (15_2, 2014192) and two previously identified genes (actin, arylphorin receptor) during Calliphora vicina (Diptera: Calliphoridae) metamorphosis. Quantification through real-time PCR revealed significant up- and downregulation of these transcripts found to be temperature dependent and age specific, hence, a new possibility to age forensically important blow fly pupae.
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Dípteros/crecimiento & desarrollo , Dípteros/genética , Expresión Génica , Metamorfosis Biológica/genética , Actinas/genética , Análisis de Varianza , Animales , Proteínas Portadoras/genética , Entomología , Patologia Forense , Proteínas de Insectos/genética , Larva/crecimiento & desarrollo , Pupa/crecimiento & desarrollo , Reacción en Cadena en Tiempo Real de la Polimerasa , TemperaturaRESUMEN
BACKGROUND: Cortinarius species in section Calochroi display local, clinal and circumboreal patterns of distribution across the Northern Hemisphere where these ectomycorrhizal fungi occur with host trees throughout their geographical range within a continent, or have disjunct intercontinental distributions, the origins of which are not understood. We inferred evolutionary histories of four species, 1) C. arcuatorum, 2) C. aureofulvus, 3) C. elegantior and 4) C. napus, from populations distributed throughout the Old World, and portions of the New World (Central- and North America) based on genetic variation of 154 haplotype internal transcribed spacer (ITS) sequences from 83 population samples. By describing the population structure of these species across their geographical distribution, we attempt to identify their historical migration and patterns of diversification. RESULTS: Models of population structure from nested clade, demographic and coalescent-based analyses revealed genetically differentiated and geographically structured haplotypes in C. arcuatorum and C. elegantior, while C. aureofulvus showed considerably less population structure and C. napus lacked sufficient genetic differentiation to resolve any population structure. Disjunct populations within C. arcuatorum, C. aureofulvus and C. elegantior show little or no morphological differentiation, whereas in C. napus there is a high level of homoplasy and phenotypic plasticity for veil and lamellae colour. The ITS sequences of the type specimens of C. albobrunnoides and C. albobrunnoides var. violaceovelatus were identical to one another and are treated as one species with a wider range of geographic distribution under C. napus. CONCLUSIONS: Our results indicate that each of the Calochroi species has undergone a relatively independent evolutionary history, hypothesised as follows: 1) a widely distributed ancestral population of C. arcuatorum diverged into distinctive sympatric populations in the New World; 2) two divergent lineages in C. elegantior gave rise to the New World and Old World haplotypes, respectively; and 3) the low levels of genetic divergence within C. aureofulvus and C. napus may be the result of more recent demographic population expansions. The scenario of migration via the Bering Land Bridge provides the most probable explanation for contemporaneous disjunct geographic distributions of these species, but it does not offer an explanation for the low degree of genetic divergence between populations of C. aureofulvus and C. napus. Our findings are mostly consistent with the designation of New World allopatric populations as separate species from the European counterpart species C. arcuatorum and C. elegantior. We propose the synonymy of C. albobrunnoides, C. albobrunnoides var. violaceovelatus and C. subpurpureophyllus var. sulphureovelatus with C. napus. The results also reinforce previous observations that linked C. arcuatorum and C. aureofulvus displaying distributions in parts of North America and Europe. Interpretations of the population structure of these fungi suggest that host tree history has heavily influenced their modern distributions; however, the complex issues related to co-migration of these fungi with their tree hosts remain unclear at this time.
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Cortinarius/clasificación , Cortinarius/genética , Evolución Molecular , Secuencia de Bases , Cortinarius/crecimiento & desarrollo , ADN de Hongos/genética , ADN Intergénico/genética , Variación Genética , Haplotipos , Datos de Secuencia Molecular , FilogeniaRESUMEN
[This corrects the article DOI: 10.1016/j.crmeth.2021.100062.].
RESUMEN
Pooled CRISPR screens have been widely applied to mammalian and other organisms to elucidate the interplay between genes and phenotypes of interest. The most popular method for delivering the CRISPR components into mammalian cells is lentivirus based. However, because lentivirus is not always an option, virus-free protocols are starting to emerge. Here, we demonstrate an improved virus-free, genome-wide CRISPR screening platform for Chinese hamster ovary cells with 75,488 gRNAs targeting 15,028 genes. Each gRNA expression cassette in the library is precisely integrated into a genomic landing pad, resulting in a very high percentage of single gRNA insertions and minimal clonal variation. Using this platform, we perform a negative selection screen on cell proliferation that identifies 1,980 genes that affect proliferation and a positive selection screen on the toxic endoplasmic reticulum stress inducer, tunicamycin, that identifies 77 gene knockouts that improve survivability.
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Sistemas CRISPR-Cas , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Animales , Cricetinae , Sistemas CRISPR-Cas/genética , Células CHO , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Cricetulus , Genoma , Lentivirus/genéticaRESUMEN
The Ampulicidae are one of the most basal groups within the apoid wasps, the paraphyletic assemblage of wasps previously known as Sphecidae. The morphology and taxonomy of the Ampulicidae are poorly studied, and there is no strict cladistic approach on their phylogeny yet. Here we assemble morphological characters of phylogenetic significance and submit them to parsimony analyses using modern cladistic methods. This produces a well-resolved and firmly supported phylogenetic hypothesis on the generic relationships within the group. Based on our phylogenetic results a revised classification is provided, subdividing the Ampulicidae into two monophyletic subfamilies, Ampulicinae (Ampulex and Trirogma) and Dolichurinae, the latter comprising two monophyletic tribes, Dolichurini (Dolichurus and Paradolichurus) and Aphelotomini, new tribe (Aphelotoma and Riekefella). Based on the resulting cladogram, the historical biogeography and the fossil record of Ampulicidae are briefly discussed. © The Willi Hennig Society 2009.
RESUMEN
Biosimilar drugs must closely resemble the pharmacological attributes of innovator products to ensure safety and efficacy to obtain regulatory approval. Glycosylation is one critical quality attribute that must be matched, but it is inherently difficult to control due to the complexity of its biogenesis. This usually implies that costly and time-consuming experimentation is required for clone identification and optimization of biosimilar glycosylation. Here, a computational method that utilizes a Markov model of glycosylation to predict optimal glycoengineering strategies to obtain a specific glycosylation profile with desired properties is described. The approach uses a genetic algorithm to find the required quantities to perturb glycosylation reaction rates that lead to the best possible match with a given glycosylation profile. Furthermore, the approach can be used to identify cell lines and clones that will require minimal intervention while achieving a glycoprofile that is most similar to the desired profile. Thus, this approach can facilitate biosimilar design by providing computational glycoengineering guidelines that can be generated with a minimal time and cost.
Asunto(s)
Biotecnología/métodos , Cadenas de Markov , Animales , Biosimilares Farmacéuticos/metabolismo , Células CHO , Cricetulus , GlicosilaciónRESUMEN
Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets.
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Sistemas CRISPR-Cas/genética , Biología Computacional/instrumentación , Pruebas Genéticas/instrumentación , Programas Informáticos , Genómica/instrumentación , InternetRESUMEN
Diverse glycans on proteins impact cell and organism physiology, along with drug activity. Since many protein-based biotherapeutics are glycosylated and these glycans have biological activity, there is a desire to engineer glycosylation for recombinant protein-based biotherapeutics. Engineered glycosylation can impact the recombinant protein efficacy and also influence many cell pathways by first changing glycan-protein interactions and consequently modulating disease physiologies. However, its complexity is enormous. Recent advances in glycoengineering now make it easier to modulate protein-glycan interactions. Here, we discuss how engineered glycans contribute to therapeutic monoclonal antibodies (mAbs) in the treatment of cancers, how these glycoengineered therapeutic mAbs affect the transformed phenotypes and downstream cell pathways. Furthermore, we suggest how systems biology can help in the next generation mAb glycoengineering process by aiding in data analysis and guiding engineering efforts to tailor mAb glycan and ultimately drug efficacy, safety and affordability.
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Anticuerpos Monoclonales/genética , Anticuerpos Monoclonales/metabolismo , Neoplasias/fisiopatología , Polisacáridos/metabolismo , Ingeniería de Proteínas/métodos , Animales , Anticuerpos Monoclonales/uso terapéutico , Humanos , Neoplasias/metabolismo , Neoplasias/terapiaRESUMEN
Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.
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Genoma , Animales , Células CHO , Consenso , Cricetinae , Cricetulus , Humanos , Redes y Vías Metabólicas , Proteínas RecombinantesRESUMEN
Glycosylation serves essential functions on many proteins produced in biopharmaceutical manufacturing, making it mandatory to thoroughly consider its biogenesis during the production process. Glycoengineering efforts involve the rational design of glycosylation through adjustments in culturing conditions or genetic modifications. Computational models have been developed to aid this process, aiming to offer cheaper and faster alternatives to costly screening strategies. Recently, these models have been successfully utilized to predict glycosylation of products of industrial relevance. Furthermore, systems-level analyses of glycan diversity are elucidating deeper insights into the mechanisms underlying glycosylation. As computational models of glycosylation continue to be expanded, refined, and leveraged for detailed analysis of glycomics data, they will become invaluable resources for cell line development and glycoengineering.