Table 8.
Whole genome analyses and engineering strategies for the identification of engineering gene targets for improved recombinant protein expression in the HEK293 cell line.
| Type of Screen/Analysis | Genes/Genomic Elements/ Pathways Identified | Recombinant Protein(s) | Ref. | Genes/Genomic Elements Identified or Confirmed in Follow-up Study(ies) | Modification | Outcome | Ref. |
|---|---|---|---|---|---|---|---|
| miRNA | hsa-miR-22-5p, hsa-miR-18a-5p, hsa-miR-22-3p, hsa-miR-429 and hsa miR-2110 | Neurotensin receptor, cytoplasmic luciferase and secreted glypican −3 hFc-fusion protein (GPC3) | [111] | HIPK1 | Knockdown | 3.2-fold higher Luciferase and 2.3-fold higher GPC3 expression | [112] |
| miRNA-22-3b | Stable overexpression | 2.4-fold higher luciferase activity | [113] | ||||
| HIPK1 | Knockout | 4.7-fold higher luciferase expression | |||||
| siRNA | CCAAT/enhancer binding protein gamma (CEBPG) | Recombinant EPO, interferon γ and monoclonal antibody | [114] | ||||
| siRNA | INTS1, HNRHPC, CASP8AP2, OAZ1 and PPP2R1A | Luciferase, GPC3, neurotensin receptor type I and serotonin transporter | [115] | OAZ1 | Knockout | 5-fold higher specific luciferase and 2.5-fold higher specific SEAP production |
[116] |
| CASP8AP2 | Knockout | 7-fold increase in specific luciferase and 2.5-fold increase in specific SEAP expression | [117] | ||||
| Multi-omics analysis (transcriptomic, fluxomic, metabolomic) |
FABP5, RETNLB, pyruvate carboxylase (PC) X-box binding protein (XBP1), HSPA5 and HERPUD1 |
A heavy chain variable region fused to the Fc region of a human IgG (dAb-Fc) | [118] | ||||
| Transcriptomic analysis | Amino acid metabolism, carbohydrate metabolism, polyamine metabolism, glutathione metabolism, nucleotide metabolism, the pentose phosphate pathway and lipid metabolism | A murine leukemia virus-based vector. | [119] | ||||
| Proteomic analysis | NEDD8, NEDD4L, ESCRT1, lipid biosynthesis, glycosphingolipids metabolism, calcium regulation, oxidant detoxification, xenobiotic metabolism, peptidase activity, DNA detoxification, endocytosis and late endosomal-related pathways | HIV-gag VLP | [120] | NEDD8 | Overexpression | 1.5-fold increase in VLP production. | [121] |
| NEDD4L | Overexpression | 3.3- fold increase in VLP production. | |||||
| UGCG | Overexpression | 2.9- fold increase in VLP production. | |||||
| CIT | Overexpression | 2.4-fold increase in VLP production. | |||||
| CNP | ShRNA knockdown | 2.7-fold increase in VLP production |