References
1. Bulaklak, K. & Gersbach, C. A. (2020). The once and future gene
therapy. Nat. Commun. 11 , 11–14.
2. Kuzmin, D. A. et al. (2021). The clinical landscape for AAV
gene therapies. Nat. Rev. Drug Discov. 20 , 173–174.
3. Mendell, J. R. et al. (2017). Single-Dose Gene-Replacement
Therapy for Spinal Muscular Atrophy. N. Engl. J. Med.377 , 1713–1722.
4. Xiao, X., Li, J. & Samulski, R. J. (1998). Production of High-Titer
Recombinant Adeno-Associated Virus Vectors in the Absence of Helper
Adenovirus. J. Virol. 72 , 2224–2232.
5. Maurer, A. C. & Weitzman, M. D. (2020). Adeno-Associated Virus
Genome Interactions Important for Vector Production and Transduction.Hum. Gene Ther. 31 , 499–511.
6. Meier, A. F., Fraefel, C. & Seyffert, M. (2020). The Interplay
between Adeno-Associated Virus and Its Helper Viruses. Viruses12 , 8–12.
7. Sha, S. et al. (2021). Cellular pathways of recombinant
adeno-associated virus production for gene therapy. Biotechnol.
Adv. 49 , 107764.
8. Johari, Y. B., Estes, S. D., Alves, C. S., Sinacore, M. S. & James,
D. C. (2015). Integrated cell and process engineering for improved
transient production of a ‘difficult-to-express’ fusion protein by CHO
cells. Biotechnol. Bioeng. 112 , 2527–2542.
9. Meyer, H. J. et al. (2017). High throughput screening
identifies novel, cell cycle-arresting small molecule enhancers of
transient protein expression. Biotechnol. Prog. 33 ,
1579–1588.
10. Chang, J. et al. (2020). High-throughput screening identifies
two novel small molecule enhancers of recombinant protein expression.Molecules 25 ,.
11. Zhao, H. et al. (2020). Creation of a High-Yield AAV Vector
Production Platform in Suspension Cells Using a Design-of-Experiment
Approach. Mol. Ther. - Methods Clin. Dev. 18 , 312–320.
12. Yu, C. et al. (2021). NaCl and KCl mediate log increase in
AAV vector particles and infectious titers in a specific/timely manner
with the HSV platform. Mol. Ther. - Methods Clin. Dev.21 , 1–13.
13. Hildinger, M., Baldi, L., Stettler, M. & Wurm, F. M. (2007).
High-titer, serum-free production of adeno-associated virus vectors by
polyethyleneimine-mediated plasmid transfection in mammalian suspension
cells. Biotechnol. Lett. 29 , 1713–1721.
14. Duetz, W. A. et al. (2000). Methods for intense aeration,
growth, storage, and replication of bacterial strains in microtiter
plates. Appl. Environ. Microbiol. 66 , 2641–2646.
15. Kusaczuk, M. (2019). Tauroursodeoxycholate—bile acid with
chaperoning activity: Molecular and cellular effects and therapeutic
perspectives. Cells 8 ,.
16. Zou, Q., Bennion, B. J., Daggett, V. & Murphy, K. P. (2002). The
molecular mechanism of stabilization of proteins by TMAO and its ability
to counteract the effects of urea. J. Am. Chem. Soc.124 , 1192–1202.
17. Roth, S. D. et al. (2012). Chemical Chaperones Improve
Protein Secretion and Rescue Mutant Factor VIII in Mice with Hemophilia
A. PLoS One 7 ,.
18. Blajeski, A. L., Phan, V. A., Kottke, T. J. & Kaufmann, S. H.
(2002). G1 and G2 cell-cycle arrest following microtubule
depolymerization in human breast cancer cells. J. Clin. Invest.110 , 91–99.
19. Steegmaier, M. et al. (2007). BI 2536, a Potent and Selective
Inhibitor of Polo-like Kinase 1, Inhibits Tumor Growth In Vivo.Curr. Biol. 17 , 316–322.
20. Li, X. et al. (2019). The Caspase Inhibitor Z-VAD-FMK
Alleviates Endotoxic Shock via Inducing Macrophages Necroptosis and
Promoting MDSCs-Mediated Inhibition of Macrophages Activation.Front. Immunol. 10 , 1824.
21. Mimura, Y. et al. (2001). Butyrate increases production of
human chimeric IgG in CHO-K1 cells whilst maintaining function and
glycoform profile. J. Immunol. Methods 247 , 205–216.
22. Yang, W. C. et al. (2014). Addition of valproic acid to CHO
cell fed-batch cultures improves monoclonal antibody titers. Mol.
Biotechnol. 56 , 421–428.
23. Riessland, M., Brichta, L., Hahnen, E. & Wirth, B. (2006). The
benzamide M344, a novel histone deacetylase inhibitor, significantly
increases SMN2 RNA/protein levels in spinal muscular atrophy cells.Hum. Genet. 120 , 101–110.
24. Wong, V. V. T., Ho, K. W. & Yap, M. G. S. (2004). Evaluation of
insulin-mimetic trace metals as insulin replacements in mammalian cell
cultures. Cytotechnology 45 , 107–115.
25. Mitchell, A. M. & Samulski, R. J. (2013). Mechanistic Insights into
the Enhancement of Adeno-Associated Virus Transduction by Proteasome
Inhibitors. J. Virol. 87 , 13035–13041.
26. Jennings, K. et al. (2005). Proteasome inhibition enhances
AAV-mediated transgene expression in human synoviocytes in vitro and in
vivo. Mol. Ther. 11 , 600–607.
27. Wu, M. et al. (2021). ONX0912, a selective oral proteasome
inhibitor, triggering mitochondrial apoptosis and mitophagy in liver
cancer. Biochem. Biophys. Res. Commun. 547 , 102–110.
28. Fernandez-Martell, A., Johari, Y. B. & James, D. C. (2018).
Metabolic phenotyping of CHO cells varying in cellular biomass
accumulation and maintenance during fed-batch culture. Biotechnol.
Bioeng. 115 , 645–660.
29. Lloyd, D. R., Holmes, P., Jackson, L. P., Emery, A. N. & Al-Rubeai,
M. (2000). Relationship between cell size, cell cycle and specific
recombinant protein productivity. Cytotechnology 34 ,
59–70.
30. Pan, X., Dalm, C., Wijffels, R. H. & Martens, D. E. (2017).
Metabolic characterization of a CHO cell size increase phase in
fed-batch cultures. Appl. Microbiol. Biotechnol. 101 ,
8101–8113.
31. Nguyen, T. N. T. et al. (2021). Mechanistic model for
production of recombinant adeno-associated virus via triple transfection
of HEK293 cells. Mol. Ther. - Methods Clin. Dev. 21 ,
642–655.
32. Trempe, J. P. & Carter, B. J. (1988). Regulation of
adeno-associated virus gene expression in 293 cells: control of mRNA
abundance and translation. J. Virol. 62 , 68–74.
33. Beswick, R. W., Ambrose, H. E. & Wagner, S. D. (2006). Nocodazole,
a microtubule depolymerising agent, induces apoptosis of chronic
lymphocytic leukaemia cells associated with changes in Bcl-2
phosphorylation and expression. Leuk. Res. 30 , 427–436.
34. Bernard, D., Mondesert, O., Gomes, A., Duthen, Y. & Lobjois, V.
(2019). A checkpoint-oriented cell cycle simulation model. Cell
Cycle 18 , 795–808.
35. Uetake, Y. & Sluder, G. (2007). Cell-Cycle Progression without an
Intact Microtubule Cytoskeleton. Curr. Biol. 17 ,
2081–2086.
36. Vasquez, R. J., Howell, B., Yvon, A. M. C., Wadsworth, P. &
Cassimeris, L. (1997). Nanomolar concentrations of nocodazole alter
microtubule dynamic instability in vivo and in vitro. Mol. Biol.
Cell 8 , 973–985.
37. Rieder, C. L. & Maiato, H. (2004). Stuck in division or passing
through: What happens when cells cannot satisfy the spindle assembly
checkpoint. Dev. Cell 7 , 637–651.
38. Quignon, F. et al. (2007). Sustained mitotic block elicits
DNA breaks: One-step alteration of ploidy and chromosome integrity in
mammalian cells. Oncogene 26 , 165–172.
39. Tait, A. S. et al. (2004). Transient production of
recombinant proteins by Chinese hamster ovary cells using
polyethyleneimine/DNA complexes in combination with microtubule
disrupting anti-mitotic agents. Biotechnol. Bioeng. 88 ,
707–721.
40. Hernandez-Verdun, D. (2011). Assembly and disassembly of the
nucleolus during the cell cycle. Nucleus 2 , 189–194.
41. Ma, N. et al. (2007). Nucleolin functions in nucleolus
formation and chromosome congression. J. Cell Sci. 120 ,
2091–2105.
42. Amin, M. A. et al. (2007). Fibrillarin, a nucleolar protein,
is required for normal nuclear morphology and cellular growth in HeLa
cells. Biochem. Biophys. Res. Commun. 360 , 320–326.
43. Stenström, L. et al. (2020). Mapping the nucleolar proteome
reveals a spatiotemporal organization related to intrinsic protein
disorder. Mol. Syst. Biol. 16 , 1–16.
44. Wistuba, A., Kern, A., Weger, S., Grimm, D. & Kleinschmidt, J. A.
(1997). Subcellular compartmentalization of adeno-associated virus type
2 assembly. J. Virol. 71 , 1341–1352.
45. Qiu, J. & Brown, K. E. (1999). A 110-kDa nuclear shuttle protein,
nucleolin, specifically binds to adeno-associated virus type 2 (AAV-2)
capsid. Virology 257 , 373–382.
46. Bevington, J. M. et al. (2007). Adeno-associated virus
interactions with B23/Nucleophosmin: Identification of sub-nucleolar
virion regions. Virology 357 , 102–113.
47. Sonntag, F., Schmidt, K. & Kleinschmidt, J. A. (2010). A viral
assembly factor promotes AAV2 capsid formation in the nucleolus.Proc. Natl. Acad. Sci. U. S. A. 107 , 10220–10225.
48. Greco, A. (2009). Involvement of the nucleolus in replication of
human viruses. Rev. Med. Virol. 19 , 201–214.
49. Saudan, P., Vlach, J. & Beard, P. (2000). Inhibition of S-phase
progression by adenoassociated virus Rep78 protein is mediated by
hypophosphorylated pRb. EMBO J. 19 , 4351–4361.
50. Berthet, C., Raj, K., Saudan, P. & Beard, P. (2005). How
adeno-associated virus Rep78 protein arrests cells completely in S
phase. Proc. Natl. Acad. Sci. U. S. A. 102 ,
13634–13639.
51. Needs, S. H., Bootman, M. D., Grotzke, J. E., Kramer, H. B. &
Allman, S. A. (2022). Off‐target inhibition of NGLY1 by the poly‐caspase
inhibitor Z‐VAD‐fmk induces cellular autophagy. FEBS J. 1–17
doi:10.1111/febs.16345.
52. Jardon, M. A. et al. (2012). Inhibition of
glutamine-dependent autophagy increases t-PA production in CHO Cell
fed-batch processes. Biotechnol. Bioeng. 109 ,
1228–1238.
53. Nasseri, S. S. et al. (2014). Increased CHO cell fed-batch
monoclonal antibody production using the autophagy inhibitor 3-MA or
gradually increasing osmolality. Biochem. Eng. J. 91 ,
37–45.
54. Mietzsch, M. et al. (2021). Improved Genome Packaging
Efficiency of Adeno-associated Virus Vectors Using Rep Hybrids. J.
Virol. 95 , 1–19.
55. Allen, M. J. et al. (2008). Identification of novel small
molecule enhancers of protein production by cultured mammalian cells.Biotechnol. Bioeng. 100 , 1193–1204.
56. Johari, Y. B. et al. (2021). Production of trimeric
SARS‐CoV‐2 spike protein by CHO cells for serological COVID‐19 testing.Biotechnol. Bioeng. 118 , 1013–1021.
57. Franzoso, F. D. et al. (2017). Cell Cycle-Dependent
Expression of Adeno-Associated Virus 2 (AAV2) Rep in Coinfections with
Herpes Simplex Virus 1 (HSV-1) Gives Rise to a Mosaic of Cells
Replicating either AAV2 or HSV-1. J. Virol. 91 , 1–19.
58. Raj, K., Ogston, P. & Beard, P. (2001). Virus-mediated killing of
cells that lack p53 activity [2]. Nature 412 ,
914–917.
59. Barnes, C. R. et al. (2021). Genome-wide activation screens
to increase adeno-associated virus production. Mol. Ther. -
Nucleic Acids 26 , 94–103.
60. Strasser, L. et al. (2021). Proteomic landscape of
adeno‐associated virus (AAV)‐producing HEK293 cells. Int. J. Mol.
Sci. 22 ,.
61. Matthews, D., Emmott, E. & Hiscox, J. (2011). Viruses and the
nucleolus. Protein Rev. 15 , 321–345.
62. Boyault, C. et al. (2007). HDAC6 controls major cell response
pathways to cytotoxic accumulation of protein aggregates. Genes
Dev. 21 , 2172–2181.
63. Yan, Z. et al. (2002). Ubiquitination of both
Adeno-Associated Virus Type 2 and 5 Capsid Proteins Affects the
Transduction Efficiency of Recombinant Vectors. J. Virol.76 , 2043–2053.
64. Maurer, A. C. et al. (2018). The Assembly-Activating Protein
Promotes Stability and Interactions between AAV’s Viral Proteins to
Nucleate Capsid Assembly. Cell Rep. 23 , 1817–1830.