Mitigating transcriptional bottleneck using a constitutively active transcription factor, VP16-CREB, in mammalian cells

Metabolic Engineering - Tập 80 - Trang 33-44 - 2023
Chansik Yoon1, Kyoung Eun Baek1, Dongil Kim1, Gyun Min Lee1
1Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea

Tài liệu tham khảo

Arige, 2021, CREB regulates the expression of type 1 inositol 1,4,5-trisphosphate receptors, J. Cell Sci., 134, jcs258875, 10.1242/jcs.258875 Balasubramanian, 2018, Generation of high expressing Chinese hamster ovary cell pools using the leap-in transposon system, Biotechnol. J., 13, 1700748, 10.1002/biot.201700748 Barco, 2002, Expression of constitutively active CREB protein facilitates the late phase of long-term potentiation by enhancing synaptic capture, Cell, 108, 689, 10.1016/S0092-8674(02)00657-8 Barco, 2011, Genetic approaches to investigate the role of CREB in neuronal plasticity and memory, Mol. Neurobiol., 44, 330, 10.1007/s12035-011-8209-x Barco, 2005, Gene expression profiling of facilitated L-LTP in VP16-CREB mice reveals that BDNF is critical for the maintenance of LTP and its synaptic capture, Neuron, 48, 123, 10.1016/j.neuron.2005.09.005 Bartok, 2020, Immune sensing mechanisms that discriminate self from altered self and foreign nucleic acids, Immunity, 53, 54, 10.1016/j.immuni.2020.06.014 Berger, 2020, Overexpression of transcription factor Foxa1 and target genes remediate therapeutic protein production bottlenecks in Chinese hamster ovary cells, Biotechnol. Bioeng., 117, 1101, 10.1002/bit.27274 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Boshart, 1985, A very strong enhancer is located upstream of an immediate early gene of human cytomegalovirus, Cell, 41, 521, 10.1016/S0092-8674(85)80025-8 Brewster, 2014, The transcription factor titration effect dictates level of gene expression, Cell, 156, 1312, 10.1016/j.cell.2014.02.022 Brown, 2017, In silico design of context-responsive mammalian promoters with user-defined functionality, Nucleic Acids Res., 45, 10906, 10.1093/nar/gkx768 Brown, 2013, Block decoys: transcription-factor decoys designed for in vitro gene regulation studies, Anal. Biochem., 443, 205, 10.1016/j.ab.2013.09.003 Brown, 2014, Synthetic promoters for CHO cell engineering, Biotechnol. Bioeng., 111, 1638, 10.1002/bit.25227 Brown, 2015, NF-κB, CRE and YY1 elements are key functional regulators of CMV promoter-driven transient gene expression in CHO cells, Biotechnol. J., 10, 1019, 10.1002/biot.201400744 Bullock, 1998, Phosphorylation of the cAMP response element binding protein CREB by cAMP-dependent protein kinase A and glycogen synthase kinase-3 alters DNA-binding affinity, conformation, and increases net charge, Biochemistry, 37, 3795, 10.1021/bi970982t Butler, 2014, The choice of mammalian cell host and possibilities for glycosylation engineering, Curr. Opin. Biotechnol., 30, 107, 10.1016/j.copbio.2014.06.010 Carpentier, 2007, Limiting factors governing protein expression following polyethylenimine-mediated gene transfer in HEK293-EBNA1 cells, J. Biotechnol., 128, 268, 10.1016/j.jbiotec.2006.10.014 Chu, 2015, Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells, Nat. Biotechnol., 33, 543, 10.1038/nbt.3198 Chusainow, 2009, A study of monoclonal antibody-producing CHO cell lines: what makes a stable high producer?, Biotechnol. Bioeng., 102, 1182, 10.1002/bit.22158 Crino, 1998, Presence and phosphorylation of transcription factors in developing dendrites, Proc. Natl. Acad. Sci. U.S.A., 95, 2313, 10.1073/pnas.95.5.2313 Dahodwala, 2022, Evaluation of site-specific methylation of the CMV promoter and its role in CHO cell productivity of a recombinant monoclonal antibody, Antib. Therapeutics., 5, 121, 10.1093/abt/tbac010 Dahodwala, 2019, Increased mAb production in amplified CHO cell lines is associated with increased interaction of CREB1 with transgene promoter, Curr. Res. Biotechnol., 1, 49, 10.1016/j.crbiot.2019.09.001 Deniaud, 2009, Overexpression of transcription factor Sp1 leads to gene expression perturbations and cell cycle inhibition, PLoS One, 4, 10.1371/journal.pone.0007035 Deniaud, 2006, Overexpression of Sp1 transcription factor induces apoptosis, Oncogene, 25, 7096, 10.1038/sj.onc.1209696 Du, 2000, Characterization of a CREB gain-of-function mutant with constitutive transcriptional activity in vivo, Mol. Cell Biol., 20, 4320, 10.1128/MCB.20.12.4320-4327.2000 Gao, 2021, A balancing act in transcription regulation by response regulators: titration of transcription factor activity by decoy DNA binding sites, Nucleic Acids Res., 49, 11537, 10.1093/nar/gkab935 Gersbach, 2014, Synthetic zinc finger proteins: the advent of targeted gene regulation and genome modification technologies, Acc. Chem. Res., 47, 2309, 10.1021/ar500039w Grav, 2018, Minimizing clonal variation during mammalian cell line engineering for improved systems biology data generation, ACS Synth. Biol., 7, 2148, 10.1021/acssynbio.8b00140 Gutiérrez-González, 2019, Transcription factor engineering in CHO cells for recombinant protein production, Crit. Rev. Biotechnol., 39, 665, 10.1080/07388551.2019.1605496 Hagiwara, 1992, Transcriptional attenuation following cAMP induction requires PP-1-mediated dephosphorylation of CREB, Cell, 70, 105, 10.1016/0092-8674(92)90537-M Hong, 2020, Runt-related transcription factor 1 promotes apoptosis and inhibits neuroblastoma progression in vitro and in vivo, J. Exp. Clin. Cancer Res., 39, 52, 10.1186/s13046-020-01558-2 Iglesias-Ara, 2018, Detection of E2F-induced transcriptional activity using a dual luciferase reporter assay, 153 Jang, 2021, Enhancement of transgene expression by mild hypothermia is promoter dependent in HEK293 cells, Life, 11, 901, 10.3390/life11090901 Karreth, 2014, Target competition: transcription factors enter the limelight, Genome Biol., 15, 114, 10.1186/gb4174 Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317 Kim, 2022, Small molecule epigenetic modulators for enhancing recombinant antibody production in CHO cell cultures, Biotechnol. Bioeng., 119, 820, 10.1002/bit.28013 Kim, 2022, Improving the secretory capacity of CHO producer cells: the effect of controlled Blimp1 expression, a master transcription factor for plasma cells, Metab. Eng., 69, 73, 10.1016/j.ymben.2021.11.001 Kim, 1998, Characterization of chimeric antibody producing CHO cells in the course of dihydrofolate reductase-mediated gene amplification and their stability in the absence of selective pressure, Biotechnol. Bioeng., 58, 73, 10.1002/(SICI)1097-0290(19980405)58:1<73::AID-BIT8>3.0.CO;2-R King, 2012, Environmental parameters influence non-viral transfection of human mesenchymal stem cells for tissue engineering applications, Cell Tissue Res., 347, 689, 10.1007/s00441-011-1297-0 Kuleshov, 2016, Enrichr: a comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Res., 44, W90, 10.1093/nar/gkw377 Lambert, 2018, The human transcription factors, Cell, 172, 650, 10.1016/j.cell.2018.01.029 Lee, 2013, Bcl-2 overexpression in CHO cells improves polyethylenimine-mediated gene transfection, Process Biochem., 48, 1436, 10.1016/j.procbio.2013.03.021 Lee, 2021, Comprehensive characterization of dihydrofolate reductase-mediated gene amplification for the establishment of recombinant human embryonic kidney 293 cells producing monoclonal antibodies, Biotechnol. J., 16, 2000351, 10.1002/biot.202000351 Liao, 2013, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656 Lopez de Armentia, 2007, cAMP response element-binding protein-mediated gene expression increases the intrinsic excitability of CA1 pyramidal neurons, J. Neurosci., 27, 13909, 10.1523/JNEUROSCI.3850-07.2007 Macaraeg, 2013, Use of an anti-apoptotic CHO cell line for transient gene expression, Biotechnol. Prog., 29, 1050, 10.1002/btpr.1763 Maelfait, 2020, Nucleic acid sensors and programmed cell death, J. Mol. Biol., 432, 552, 10.1016/j.jmb.2019.11.016 Mayr, 2001, Transcriptional regulation by the phosphorylation-dependent factor CREB, Nat. Rev. Mol. Cell Biol., 2, 599, 10.1038/35085068 Meyer, 2021, Monitoring cell productivity for the production of recombinant proteins by flow cytometry: an effective application using the cold capture assay, Eng. Life Sci., 21, 288, 10.1002/elsc.202000049 Murthy, 2020, Crosstalk between cGAS–STING signaling and cell death, Cell Death Differ., 27, 2989, 10.1038/s41418-020-00624-8 Naqvi, 2014, CREB phosphorylation at Ser133 regulates transcription via distinct mechanisms downstream of cAMP and MAPK signalling, Biochem. J., 458, 469, 10.1042/BJ20131115 Ng, 2021, Development of a targeted integration Chinese hamster ovary host directly targeting either one or two vectors simultaneously to a single locus using the Cre/Lox recombinase-mediated cassette exchange system, Biotechnol. Prog., 37 Nguyen, 2019, Novel promoters derived from Chinese hamster ovary cells via in silico and in vitro analysis, Biotechnol. J., 14, 1900125, 10.1002/biot.201900125 Noh, 2018, Comprehensive characterization of glutamine synthetase-mediated selection for the establishment of recombinant CHO cells producing monoclonal antibodies, Sci. Rep., 8, 5361, 10.1038/s41598-018-23720-9 Orellana, 2018, RNA-seq highlights high clonal variation in monoclonal antibody producing CHO cells, Biotechnol. J., 13, 1700231, 10.1002/biot.201700231 Park, 2022, Development of an in vitro screening system for synthetic signal peptide in mammalian cell-based protein production, Appl. Microbiol. Biotechnol., 106, 3571, 10.1007/s00253-022-11955-6 Petersen, 2018, Modular 5′-UTR hexamers for context-independent tuning of protein expression in eukaryotes, Nucleic Acids Res., 46, e127 Pristovšek, 2018, Using titer and titer normalized to confluence are complementary strategies for obtaining Chinese hamster ovary cell lines with high volumetric productivity of etanercept, Biotechnol. J., 13, 1700216, 10.1002/biot.201700216 Pristovšek, 2019, Systematic evaluation of site-specific recombinant gene expression for programmable mammalian cell engineering, ACS Synth. Biol., 8, 758, 10.1021/acssynbio.8b00453 Rajendra, 2015, Transcriptional and post-transcriptional limitations of high-yielding, PEI-mediated transient transfection with CHO and HEK-293E cells, Biotechnol. Prog., 31, 541, 10.1002/btpr.2064 Reusch Jane, 2000, CREB activation induces adipogenesis in 3T3-L1 cells, Mol. Cell Biol., 20, 1008, 10.1128/MCB.20.3.1008-1020.2000 Rita Costa, 2010, Guidelines to cell engineering for monoclonal antibody production, Eur. J. Pharm. Biopharm., 74, 127, 10.1016/j.ejpb.2009.10.002 Robinson, 2009, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Sanjana, 2012, A transcription activator-like effector toolbox for genome engineering, Nat. Protoc., 7, 171, 10.1038/nprot.2011.431 Sarvagalla, 2019, vol. 9, 1230 Semenova, 2019, Multiple cytosolic DNA sensors bind plasmid DNA after transfection, Nucleic Acids Res., 47, 10235, 10.1093/nar/gkz768 Sergeeva, 2020, Multicopy targeted integration for accelerated development of high-producing Chinese hamster ovary cells, ACS Synth. Biol., 9, 2546, 10.1021/acssynbio.0c00322 Tastanova, 2016, Overexpression of YY1 increases the protein production in mammalian cells, J. Biotechnol., 219, 72, 10.1016/j.jbiotec.2015.12.005 Tossolini, 2022, Screening of CHO-K1 endogenous promoters for expressing recombinant proteins in mammalian cell cultures, Plasmid, 119–120, 102620, 10.1016/j.plasmid.2022.102620 Valor, 2010, Ultrastructural and transcriptional profiling of neuropathological misregulation of CREB function, Cell Death Differ., 17, 1636, 10.1038/cdd.2010.40 Viosca, 2009, Chronic enhancement of CREB activity in the hippocampus interferes with the retrieval of spatial information, Learn. Mem., 16, 198, 10.1101/lm.1220309 Walsh, 2018, Biopharmaceutical benchmarks 2018, Nat. Biotechnol., 36, 1136, 10.1038/nbt.4305 Wang, 2018, cAMP response element-binding protein (CREB): a possible signaling molecule link in the pathophysiology of schizophrenia, Front. Mol. Neurosci., 11, 255, 10.3389/fnmol.2018.00255 Yoon, 2020, Forskolin increases cAMP levels and enhances recombinant antibody production in CHO cell cultures, Biotechnol. J., 15, 2000264, 10.1002/biot.202000264 Zahid, 2020, Molecular and structural basis of DNA sensors in antiviral innate immunity, Front. Immunol., 11, 613039, 10.3389/fimmu.2020.613039 Zboray, 2015, Heterologous protein production using euchromatin-containing expression vectors in mammalian cells, Nucleic Acids Res., 43, e102, 10.1093/nar/gkv475 Zhu, 2012, Mammalian cell protein expression for biopharmaceutical production, Biotechnol. Adv., 30, 1158, 10.1016/j.biotechadv.2011.08.022