Engineered cell lines for increased protein production

Abstract

The present disclosure relates to engineered cells that include genetic alterations leading to up- or down-regulation of certain genes in the cells for improved production of a recombinant protein. Also provided are methods of preparing and using such cells.

Claims

1. An isolated engineered mammalian cell comprising one or more genetic alterations resulting in increased expression or activity of hk1 (hexokinase 1), MAPK3 (mitogen-activated protein kinase 3), CAP (catabolite activator protein) and Nrf2 (nuclear factor (erythroid-derived 2)-like 2), wherein the increase is as compared to a corresponding mammalian cell without the genetic alterations.

2. The cell of claim 1, wherein the cell further comprises an exogenous polynucleotide encoding a polypeptide.

3. The cell of claim 2, wherein the polypeptide is a therapeutic protein.

4. The cell of claim 2, wherein the polypeptide is an antibody or an antibody fragment.

5. The cell of claim 1, wherein the cell is a human cell.

6. The cell of claim 1, wherein the cell is a CHO cell.

7. A composition comprising the cell of claim 2 and a cell culture medium.

8. The composition of claim 7, wherein the medium comprises a supplement selected from the group consisting of ubiquinone, aspartic acid, and rapamycin.

9. A method of producing a protein, comprising culturing the cell in the composition of claim 7 and isolating the polypeptide.

10. An isolated mammalian cell comprising one or more exogenous polynucleotides encoding hk1 (hexokinase 1), MAPK3 (mitogen-activated protein kinase 3), CAP (catabolite activator protein) and Nrf2 (nuclear factor (erythroid-derived 2)-like 2).

11. The cell of claim 10, wherein the cell is a CHO cell.

Description

DETAILED DESCRIPTION

I. Definitions

(1) All numerical designations, e.g., pH, temperature, time, concentration, and molecular weight, including ranges, are approximations which are varied (+) or () by increments of 0.1. It is to be understood, although not always explicitly stated that all numerical designations are preceded by the term about. It also is to be understood, although not always explicitly stated, that the reagents described herein are merely exemplary and that equivalents of such are known in the art.

(2) As used in the specification and claims, the singular form a, an and the include plural references unless the context clearly dictates otherwise. For example, the term a polynucleotide includes a plurality of polynucleotides, including mixtures thereof.

(3) The terms polynucleotide and oligonucleotide are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides or analogs thereof. A polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure can be imparted before or after assembly of the polynucleotide. The sequence of nucleotides can be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component. The term also refers to both double- and single-stranded molecules. Unless otherwise specified or required, any embodiment of this disclosure that is a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.

II. Cell Engineering

(4) Metabolic pathways are broken up into catabolic and anabolic pathways. Catabolic pathways deal with turning glucose into ATP and anabolic pathways deal with turning glucose into proteins. There is an overlap of enzymes between these two pathways, while some steps are unique to each.

(5) Cells generally control their own production of proteins and ATP, however through cellular engineering of the anabolic and catabolic pathways the cell machinery can be hijacked to produce more protein and the right type of protein. It is sometime not sufficient to regulate a single gene or pathway to achieve improved production of a protein.

(6) The present disclosure provides genetically engineered cells that avoid the Warburg effect which is common to many protein production systems. The Warburg effect refers to cells drowning in ATP and other metabolites if there is an overabundance of these from overexpressing the genes for enhancing metabolites. For example, by replacing the natural (slow) glucose transporter with a rapid transporter, a cell of the present disclosure can control exactly how much glucose the cells consume by controlling the amount of glucose added. In another example, by increasing highly expressed gene transcript number, the cell will have enough target to put the metabolites into.

(7) The genetic engineering employed in certain embodiments of the present disclosure helps to turn a cell into a factory, built mainly for growth and protein production. In some aspects, genetic alternations turn off some or all nonessential items for protein production or overexpress certain growth and production enzymes. In a preferred embodiment, both of these are implemented.

(8) In some aspects, in order to not require too many genetic alternations but still achieving impact on a good number of genes, the genetic alternations can trigger cascades of excess production by overexpressing the rate limiting enzymes in a pathway. As such, by slightly increasing the effect of enough individual points along the pathway, the rate of the given pathway should increase. In this aspect, an engineered cell of the present disclosure can be viewed as a cell with distinct growth and production phases with each having regulatable control.

(9) For instance, increasing the rate of the entire catabolic pathway results in an increase of byproduct metabolites which are necessary for efficiently creating proteins, so taking a holistic approach to catabolic engineering may pay off in anabolics as well.

(10) Overall, the present disclosure identifies the main rate determining steps in the main pathways that turn glucose into ATP as well as other anabolic factors that can increase the rate of protein production, cell proliferation, and cell size.

(11) Table 1 below lists a few genes that can be suitably targeted (for up- or down-regulation) for generating an engineered cell, as well as supply of nutritional factors in cell culture (Supply) for improved production of protein products.

(12) TABLE-US-00002 TABLE 1 No. Gene(s)/Supplement(s) Regulation Function Catabolics C1 PDP Up rate control over ATP production through phosphorylation of the PDHc C2 CS and isocitrate dehydrogenase Up rate determining steps of the Kreb's Cycle C3 hk1, pfk1, or pkm Up Rate limiting steps of glucose oxidation into pyruvate Anabolics A1 Nrf2 Up Nrf2 redirects glucose and glutamine into anabolic pathways, especially under the sustained activation of PI3K-Akt signaling A2 Hk2 Up cytoplasmic HKII channel G-6-P towards regulating glycogen formation (anabolic use) A3 PFKB2, AS160, or PIP5K Up some of the various enzymes that are upregulated with Akt signaling, results in higher energy production and vesicle based transport Secretion S1 Unc18b Up protein regulating the fusion of secretory vesicles to the plasma membrane S2 SRP14 Up CHO cells engineered to express SRP proteins such as SRP14 gained the ability to properly process and secrete the difficult-to-express immunoglobulin, and they also displayed improved secretion of an easy-to-express antibody. S3 BiP Up increases Igg solubility resulting in a 90% increase in secretion S4 Calnexin Up fends off ER stress induced apoptosis by ensuring proper protein folding Protein Folding F1 XBP1S Up Regulator of protein folding and secretion, generally responsive to ER stress Growth Factors G1 Akt1, Akt 2, or Akt 3 Up Akt pathways results in increased glucose uptake through increased glut1 expression, cell cycle progression, and cell survival pathways G2 p21, or p27 Up arrests the cell cycle at G1 allowing for more glucose to be channeled towards protein production G3 c-jun Up overexpression of c-Jun represses p53 and p21 expression and accelerates cell proliferation Cytotoxicity T1 LDHA Down inhibit lactate production T2 carbamoyl phosphate synthetase I Up To reduce the level of the accumulated ammonium ion, carbamoyl phosphate synthetase I (CPS I) and ornithine transcarbamoylase (OTC) were used, which catalyze the first and second steps of the urea cycle in the liver. T3 transcarbamoylase Up To reduce the level of the accumulated ammonium ion, carbamoyl phosphate synthetase I (CPS I) and ornithine transcarbamoylase (OTC) were used, which catalyze the first and second steps of the urea cycle in the liver. T4 CAP Up transcription factor that regulates transcription of many catabolic operons involved in lactate metabolism Anti-Apoptosis P1 Caspase 3 and/or 8 and/or 9 Down increase cell viability by knocking out cell death signaling proteins P2 Bcl2 or Bcl-xl Up antiapoptotic gene P3 XIAP Up XIAP is the most potent caspase inhibitor encoded in the mammalian genome. protein engineering of the XIAP protein can be used to alter the intracellular distribution pattern and improve the ability of this caspase inhibitor to protect against apoptosis for two mammalian cell lines. Gene Expression E1 TBP Up first transcription factor in the transcription unit. Only TBP is necessary for transcription at promoters that contain a TATA box E2 Prdm1 or Blimp1 Up changes B-cells to resemble high producing plasma cells, this system may change the shape and function of CHO cells E3 IL3 Up activates various transcription factors such as JUN and FOS which are involved in the regulation of cell growth and differentiation. also inhibits apoptosis

(13) The following table (Table 2) lists additional genes in each category that can also be considered for targeted regulation when preparing an engineered cell of the present disclosure.

(14) TABLE-US-00003 TABLE 2 No. Gene(s)/Supplement(s) Regulation Function Catabolics C4 PDK1 and/or PDK4 Down turns off the PDHc C5 PDH, DLAT, DLD Up turns pyruvate into acetyl coA C6 Ubiquinone Supply increase NADH production C7 Aspartatic Acid Supply increase cellular ability to manage electrons C8 ATP synthase subunits Up increase number of ATP synthases to increase ATP generation Anabolics A4 IL2 Up Involved in p13-Akt and TGF-beta pathways A5 IL5 Up Involved in p13-Akt and TGF-beta pathways A6 Glycogen Synthase Up Upregulated by the Akt pathway, converts glucose into glycogen sending the glucose to the protein production path Protein Folding F2 Ero1la Up Protein folding enzyme F3 PDI Up Protein folding enzyme F4 Ero1lb Up Protein folding enzyme F5 ERp57 Up ERp57 is a disulfide isomerase involved in the folding of a subset of glycoproteins in the ER as part of the calnexin/calreticulin cycle F6 GRP94 Up Embryonic stem (ES) cells that lack GRP94 are hypersensitive to stress conditions such as serum deprivation and die by apoptosis because they cannot respond to the stress by producing active IGF-II. This chaperone- client interaction may explain the previously documented antiapoptotic activity of GRP94 in a number of stress responses. F7 Endoplasmin Up a member of a family of adenosine triphosphate(ATP)-metabolizing molecular chaperones with roles in stabilizing and folding other proteins. The encoded protein is localized to melanosomes and the endoplasmic reticulum. F8 Calnexin Up also fends off ER stress induced apoptosis by ensuring proper protein folding F9 Calreticulin Up transcriptional regulation properties as well as calcium binding and protein folding Growth Factors G4 MAPK1 and/or MAPK3 Up Integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development G5 Rapamycin Supply inhibits mTOR based autophagy G6 Smad2 and/or Smad3 Up The broad range of biological responses elicited by transforming growth factor- (TGF-) in various types of tissues and cells is mainly determined by the expression level and activity of the effector proteins Smad2 and Smad3. Anti-Apoptosis P4 Caspase 7 and/or 6 Down knockout of cell death signaling molecules extends viability of cells P5 Fas-l Down Engagement of the cell death surface receptor Fas by Fas ligand (FasL) results in apoptotic cell death, mediated by caspase activation. P6 Gsk-3 Up Smad3 physically interacts with Axin and GSK3- only in the absence of TGF-. Reduction in the expression or activity of Axin/GSK3- leads to increased Smad3 stability. The broad range of biological responses elicited by transforming growth factor- (TGF-) in various types of tissues and cells is mainly determined by the expression level and activity of the effector proteins Smad2 and Smad3. P7 Aven Up Aven appeared to act synergistically to enhance the protective function of Bcl-xL P8 Crma Up another caspase inhibitor, each inhibitor has varying degrees of effectiveness in different cases P9 E1b-19k Up The E1B 19K protein is a potent apoptosis inhibitor and the putative adenovirus Bcl-2 homolog. Gene Expression E4 Subunits of the TFIID complex Up TFIID is the transcription initiation complex, although TBP upregulation should be enough to affect the gene of interest, other individual subunits of the TFIID could similarly be upregulated to increase transcript initiation E5 Xbp1 Up activated by Blimp1 to increase gene expression

(15) In summary, the present disclosure contemplates genetic alternations resulting in up- or down-regulations (collectively targeted modulation) of one or more genes as listed in Tables 1-2, which are summarized below. The up- or down-regulation is annotated in Tables 1-2 for each gene and is implied for the concerned gene throughout the disclosure.

(16) TABLE-US-00004 Category Abbv Primary Secondary Catabolics C C1-C3 C4-C8 Anabolics A A1-A3 A4-A6 Secretion S S1-S4 Protein Folding F F1 F2-F9 Growth Factors G G1-G3 G4-G6 Cytotoxicity T T1-T4 Anti-Apoptosis P P1-P3 P4-P9 Gene Expression E E1-E3 E4-E5

(17) Up- or down-regulation of a gene refers to a genetic or non-genetic change of the gene that leads to increased or decreased biological activity of the expression product (e.g., protein or RNA) in a cell. In one aspect, the regulation is at genetic level, such as mutation or deletion of either or both alleles of the gene. In one aspect, the regulation is at transcription level, e.g., through modulation of relevant transcription factors or elements, resulting in increased or decreased level of transcription. In one aspect, the regulation is at translation level, e.g., through codon optimization, leading to increased or decreased protein production. In one aspect, the regulation is at post-translational level, e.g., through post-translational modification. In one aspect, the regulation is at protein activity level, e.g., through generation of co-factors and inhibitors. In a preferred embodiment, down-regulation of a gene can be achieved by knocking out the gene (e.g., deletion of at least part of the gene). In a preferred embodiment, up-regulation of a gene can be achieved by duplicating the gene or replacing the promotor or another cis-transcription regulatory element with a stronger one.

(18) In one embodiment, up- or down-regulation is as compared to a cell before the targeted modulation is made to the cell, such as an established cell line, a primary cell, or a cell that has been engineered otherwise.

(19) In one embodiment, the engineered cell has targeted modulation of at least one gene of Table 1, or at least one gene of Table 2. In one embodiment, the engineered cell has targeted modulation of at least one gene in the catabolics category (e.g., C1-C8). In one embodiment, the engineered cell has targeted modulation of at least one gene in the anabolics category (e.g., A1-A6). In one embodiment, the engineered cell has targeted modulation of at least one gene in the secretion category (e.g., S1-S4). In one embodiment, the engineered cell has targeted modulation of at least one gene in the protein folding category (e.g., F1-F9). In one embodiment, the engineered cell has targeted modulation of at least one gene in the growth factors category (e.g., G1-G6). In one embodiment, the engineered cell has targeted modulation of at least one gene in the cytotoxicity category (e.g., T1-T4). In one embodiment, the engineered cell has targeted modulation of at least one gene in the anti-apoptosis category (e.g., P1-P9). In one embodiment, the engineered cell has targeted modulation of at least one gene in the gene expression category (e.g., E1-E5).

(20) In one embodiment, the engineered cell has targeted modulation of at least one gene from a first category and another gene from a second category, as illustrated below. In one embodiment, the engineered cell further has targeted modulation of at least one gene from a third category, also illustrated below. In one aspect, each of the genes is selected from Table 1 only. In one aspect, the genes can be selected from Table 1 or Table 2.

(21) TABLE-US-00005 First category Second category Third category Catabolics Anabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Catabolics Secretion Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Catabolics Protein Folding Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Catabolics Growth Factors Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Catabolics Cytotoxicity Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Catabolics Anti-Apoptosis Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Catabolics Gene Expression Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anabolics Catabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anabolics Secretion Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anabolics Protein Folding Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anabolics Growth Factors Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anabolics Cytotoxicity Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anabolics Anti-Apoptosis Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anabolics Gene Expression Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Secretion Catabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Secretion Anabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Secretion Protein Folding Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Secretion Growth Factors Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Secretion Cytotoxicity Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Secretion Anti-Apoptosis Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Secretion Gene Expression Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Protein Folding Catabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Protein Folding Anabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Protein Folding Secretion Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Protein Folding Growth Factors Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Protein Folding Cytotoxicity Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Protein Folding Anti-Apoptosis Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Protein Folding Gene Expression Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Growth Factors Catabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Growth Factors Anabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Growth Factors Secretion Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Growth Factors Protein Folding Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Growth Factors Cytotoxicity Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Growth Factors Anti-Apoptosis Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Growth Factors Gene Expression Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Cytotoxicity Catabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Cytotoxicity Anabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Cytotoxicity Secretion Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Cytotoxicity Protein Folding Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Cytotoxicity Growth Factors Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Cytotoxicity Anti-Apoptosis Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Cytotoxicity Gene Expression Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anti-Apoptosis Catabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anti-Apoptosis Anabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anti-Apoptosis Secretion Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anti-Apoptosis Protein Folding Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anti-Apoptosis Growth Factors Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anti-Apoptosis Cytotoxicity Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Anti-Apoptosis Gene Expression Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Gene Expression Catabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Gene Expression Anabolics Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Gene Expression Secretion Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Gene Expression Protein Folding Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Gene Expression Growth Factors Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Gene Expression Cytotoxicity Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression Gene Expression Anti-Apoptosis Catabolics, Anabolics, Secretion, Protein Folding, Growth Factors, Cytotoxicity, Anti-Apoptosis, or Gene Expression

(22) In one aspect, the engineered cell has targeted modulation of at least two genes, as indicated by any of the X's in the following table (Table 3) (row headers: gene one; column header: gene two).

(23) TABLE-US-00006 TABLE 3 C1 C2 C3 A1 A2 A3 S1 S2 S3 S4 F1 G1 G2 G3 T1 T2 T3 T4 P1 P2 P3 E1 E2 E3 C1 C2 X C3 X X A1 X X X A2 X X X X A3 X X X X X S1 X X X X X X S2 X X X X X X X S3 X X X X X X X X S4 X X X X X X X X X F1 X X X X X X X X X X G1 X X X X X X X X X X X G2 X X X X X X X X X X X X G3 X X X X X X X X X X X X X T1 X X X X X X X X X X X X X X T2 X X X X X X X X X X X X X X X T3 X X X X X X X X X X X X X X X X T4 X X X X X X X X X X X X X X X X X P1 X X X X X X X X X X X X X X X X X X P2 X X X X X X X X X X X X X X X X X X X P3 X X X X X X X X X X X X X X X X X X X X E1 X X X X X X X X X X X X X X X X X X X X X E2 X X X X X X X X X X X X X X X X X X X X X X E3 X X X X X X X X X X X X X X X X X X X X X X X

(24) In one aspect, the engineered cell has targeted modulation of at least three genes, as indicated by any of the X's in the following table (Table 4) (columns 1 and 2 for each row: genes 1 and 2; other column heads: gene 3).

(25) TABLE-US-00007 TABLE 4 Gene Gene Gene 3 1 2 C1 C2 C3 A1 A2 A3 S1 S2 S3 S4 F1 G1 G2 G3 T1 T2 T3 T4 P1 P2 P3 E1 E2 E3 C1 C2 X X X X X X X X X X X X X X X X X X X X X X X X C1 C3 X X X X X X X X X X X X X X X X X X X X X X X X C1 A1 X X X X X X X X X X X X X X X X X X X X X X X X C1 A2 X X X X X X X X X X X X X X X X X X X X X X X X C1 A3 X X X X X X X X X X X X X X X X X X X X X X X X C1 S1 X X X X X X X X X X X X X X X X X X X X X X X X C1 S2 X X X X X X X X X X X X X X X X X X X X X X X X C1 S3 X X X X X X X X X X X X X X X X X X X X X X X X C1 S4 X X X X X X X X X X X X X X X X X X X X X X X X C1 F1 X X X X X X X X X X X X X X X X X X X X X X X X C1 G1 X X X X X X X X X X X X X X X X X X X X X X X X C1 G2 X X X X X X X X X X X X X X X X X X X X X X X X C1 G3 X X X X X X X X X X X X X X X X X X X X X X X X C1 T1 X X X X X X X X X X X X X X X X X X X X X X X X C1 T2 X X X X X X X X X X X X X X X X X X X X X X X X C1 T3 X X X X X X X X X X X X X X X X X X X X X X X X C1 T4 X X X X X X X X X X X X X X X X X X X X X X X X C1 P1 X X X X X X X X X X X X X X X X X X X X X X X X C1 P2 X X X X X X X X X X X X X X X X X X X X X X X X C1 P3 X X X X X X X X X X X X X X X X X X X X X X X X C1 E1 X X X X X X X X X X X X X X X X X X X X X X X X C1 E2 X X X X X X X X X X X X X X X X X X X X X X X X C1 E3 X X X X X X X X X X X X X X X X X X X X X X X X C2 C1 X X X X X X X X X X X X X X X X X X X X X X X X C2 C3 X X X X X X X X X X X X X X X X X X X X X X X X C2 A1 X X X X X X X X X X X X X X X X X X X X X X X X C2 A2 X X X X X X X X X X X X X X X X X X X X X X X X C2 A3 X X X X X X X X X X X X X X X X X X X X X X X X C2 S1 X X X X X X X X X X X X X X X X X X X X X X X X C2 S2 X X X X X X X X X X X X X X X X X X X X X X X X C2 S3 X X X X X X X X X X X X X X X X X X X X X X X X C2 S4 X X X X X X X X X X X X X X X X X X X X X X X X C2 F1 X X X X X X X X X X X X X X X X X X X X X X X X C2 G1 X X X X X X X X X X X X X X X X X X X X X X X X C2 G2 X X X X X X X X X X X X X X X X X X X X X X X X C2 G3 X X X X X X X X X X X X X X X X X X X X X X X X C2 T1 X X X X X X X X X X X X X X X X X X X X X X X X C2 T2 X X X X X X X X X X X X X X X X X X X X X X X X C2 T3 X X X X X X X X X X X X X X X X X X X X X X X X C2 T4 X X X X X X X X X X X X X X X X X X X X X X X X C2 P1 X X X X X X X X X X X X X X X X X X X X X X X X C2 P2 X X X X X X X X X X X X X X X X X X X X X X X X C2 P3 X X X X X X X X X X X X X X X X X X X X X X X X C2 E1 X X X X X X X X X X X X X X X X X X X X X X X X C2 E2 X X X X X X X X X X X X X X X X X X X X X X X X C2 E3 X X X X X X X X X X X X X X X X X X X X X X X X C3 C1 X X X X X X X X X X X X X X X X X X X X X X X X C3 C2 X X X X X X X X X X X X X X X X X X X X X X X X C3 A1 X X X X X X X X X X X X X X X X X X X X X X X X C3 A2 X X X X X X X X X X X X X X X X X X X X X X X X C3 A3 X X X X X X X X X X X X X X X X X X X X X X X X C3 S1 X X X X X X X X X X X X X X X X X X X X X X X X C3 S2 X X X X X X X X X X X X X X X X X X X X X X X X C3 S3 X X X X X X 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X X X X X E1 T1 X X X X X X X X X X X X X X X X X X X X X X X X E1 T2 X X X X X X X X X X X X X X X X X X X X X X X X E1 T3 X X X X X X X X X X X X X X X X X X X X X X X X E1 T4 X X X X X X X X X X X X X X X X X X X X X X X X E1 P1 X X X X X X X X X X X X X X X X X X X X X X X X E1 P2 X X X X X X X X X X X X X X X X X X X X X X X X E1 P3 X X X X X X X X X X X X X X X X X X X X X X X X E1 E2 X X X X X X X X X X X X X X X X X X X X X X X X E1 E3 X X X X X X X X X X X X X X X X X X X X X X X X E2 C1 X X X X X X X X X X X X X X X X X X X X X X X X E2 C2 X X X X X X X X X X X X X X X X X X X X X X X X E2 C3 X X X X X X X X X X X X X X X X X X X X X X X X E2 A1 X X X X X X X X X X X X X X X X X X X X X X X X E2 A2 X X X X X X X X X X X X X X X X X X X X X X X X E2 A3 X X X X X X X X X X X X X X X X X X X X X X X X E2 S1 X X X X X X X X X X X X X X X X X X X X X X X X E2 S2 X X X X X X X X X X X X X X X X X X X X X X X X E2 S3 X X X X X X X X X X X X X X X X X X X X X X X X E2 S4 X X X X X X 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X X X X E3 A3 X X X X X X X X X X X X X X X X X X X X X X X X E3 S1 X X X X X X X X X X X X X X X X X X X X X X X X E3 S2 X X X X X X X X X X X X X X X X X X X X X X X X E3 S3 X X X X X X X X X X X X X X X X X X X X X X X X E3 S4 X X X X X X X X X X X X X X X X X X X X X X X X E3 F1 X X X X X X X X X X X X X X X X X X X X X X X X E3 G1 X X X X X X X X X X X X X X X X X X X X X X X X E3 G2 X X X X X X X X X X X X X X X X X X X X X X X X E3 G3 X X X X X X X X X X X X X X X X X X X X X X X X E3 T1 X X X X X X X X X X X X X X X X X X X X X X X X E3 T2 X X X X X X X X X X X X X X X X X X X X X X X X E3 T3 X X X X X X X X X X X X X X X X X X X X X X X X E3 T4 X X X X X X X X X X X X X X X X X X X X X X X X E3 P1 X X X X X X X X X X X X X X X X X X X X X X X X E3 P2 X X X X X X X X X X X X X X X X X X X X X X X X E3 P3 X X X X X X X X X X X X X X X X X X X X X X X X E3 E1 X X X X X X X X X X X X X X X X X X X X X X X X E3 E2 X X X X X X X X X X X X X X X X X X X X X X X X

(26) In one aspect of the above embodiment, the engineered cell that has targeted modulation of three genes further has targeted modulation of a fourth gene. In one aspect, the fourth gene is selected from the group consisting of C1, C2, C3, A1, A2, A3, S1, S2, S3, S4, F1, G1, G2, G3, T1, T2, T3, T4, P1, P2, P3, E1, E2, and E3.

(27) In one aspect of the above embodiment, the engineered cell that has targeted modulation of four genes further has targeted modulation of a fifth gene. In one aspect, the fifth gene is selected from the group consisting of C1, C2, C3, A1, A2, A3, S1, S2, S3, S4, F1, G1, G2, G3, T1, T2, T3, T4, P1, P2, P3, E1, E2, and E3.

(28) In one aspect of the above embodiment, the engineered cell that has targeted modulation of five genes further has targeted modulation of a sixth gene. In one aspect, the sixth gene is selected from the group consisting of C1, C2, C3, A1, A2, A3, S1, S2, S3, S4, F1, G1, G2, G3, T1, T2, T3, T4, P1, P2, P3, E1, E2, and E3.

(29) In one aspect of the above embodiment, the engineered cell that has targeted modulation of six genes further has targeted modulation of a seventh gene. In one aspect, the seventh gene is selected from the group consisting of C1, C2, C3, A1, A2, A3, S1, S2, S3, S4, F1, G1, G2, G3, T1, T2, T3, T4, P1, P2, P3, E1, E2, and E3.

(30) In any of the above embodiments, the engineered cell can optionally have targeted modulation of one or more genes selected from the group consisting of C4-C8, A4-A6, F2-F9, G4-G6, P4-P9 and E4-E5.

(31) In one embodiment, the engineered cell has targeted modulation of one, two, three, four, five, six, seven or eight genes selected from the group consisting of C1-C8, A1-A6, S1-S4, F1-F9, G1-G6, T1-T4, P1-P9, and E1-E5.

(32) In one embodiment, the engineered cell has targeted modulation of either or both of U1 and U2 (as shown in the table below), U1 and one of U2-U4, or any of U1-U4. In one embodiment, the engineered has modulation of one, two, three, four, five, six, seven or eight genes selected from the group consisting of C1-C8, A1-A6, S1-S4, F1-F9, G1-G6, T1-T4, P1-P9, E1-E5, and U1-U4.

(33) TABLE-US-00008 No. Gene(s) Regulation Function U1 GLUT1 Down also known as solute carrier family 2, facilitated glucose transporter member 1 (SLC2A1) U2 GLUT2 Up also known as solute carrier family 2 (facilitated glucose transporter), member 2 (SLC2A2) is a transmembrane carrier protein that enables protein facilitated glucose movement across cell membranes U3 GLUT3 Up encoded by the SLC2A3 gene and facilitates the transport of glucose across the plasma membranes of mammalian cells U4 GLUT4 Up Encoded by the GLUT4 gene and is the insulin-regulated glucose transporter found primarily in adipose tissues and striated muscle

(34) In some embodiments, the engineered cell is cultured in a medium that includes supplements suitable for its growth and protein production. Non-limiting examples of such supplements include:

(35) TABLE-US-00009 No. Supplement Description M1 Ubiquinone increases NADH production M2 Aspartic acid Increases cellular ability to manage electrons M3 Rapamycin Delays the viability drop and apoptosis induction. In particular, the improved cell viability of an antibody-producing rCHO cell line resulting from the rapamycin treatment leads to increased antibody concentration

(36) In one embodiment, the engineered cell has targeted modulation of genes of any of the following lists:

(37) TABLE-US-00010 Engineered Optional Supplement cell Modulation of genes in Medium 1 C3, C5, U2, C2, E2, G2, A2, M1, and M2 A1, S1, S3, U1, P1, and T1 2 P1, and T1 M2 3 U2, E2, A2, A1, and S1 4 C3, C5, U2, G2, A1, and S3 M1, and M2 5 U2, E2, and S1 M1

(38) In a preferred aspect of any of the above embodiments, the modulation is achieved by mutating or deleting at least part of the gene for down-regulation or introducing one or more copies of the gene or its coding sequence for up-regulation.

(39) In one embodiment, the engineered cell further includes an exogenous coding sequence (gene of interest or GOI). The GOI can be included on a separate vector (e.g., plasmid) or integrated to one of the chromosomes of the cell. In one embodiment, the GOI encodes a polypeptide which can be a therapeutic protein. In one embodiment, the GOI encodes an antibody or an antibody fragment.

(40) In one embodiment, the engineered cell is a mammalian cell and preferably a human cell. In one embodiment, the cell is a CHO cell, such as CHO lineage-DG44, DxB11, CHOM (Selexis), CHOs (Life Tech), CHOK1SV (Lonza), or CHOZN (Sigma). In one embodiment, the cell is NSO-mouse, BHK, PerC6, K562, or Cos1&7 cells.

(41) Methods of using any cell of the present disclosure for expressing or producing a product of the GOI are also provided.

III. Methods for Up- or Down-Regulating a Gene in a Cell

(42) Methods for up-regulating a gene (e.g., increasing the biological activity of the gene) in a cell is known in the art. In one aspect, the gene level is increased by increasing the amount of a polynucleotide encoding gene, as provided above, wherein that polynucleotide is expressed such that new gene is produced. In another aspect, increasing the gene level is increased by increasing the transcription of a polynucleotide encoding gene, or alternatively translation of gene, or alternatively post-translational modification, activation or appropriate folding of gene. In yet another aspect, increasing gene level is increased by increasing the binding of the protein to appropriate cofactor, receptor, activator, ligand, or any molecule that is involved in the protein's biological functioning. In some embodiments, increasing the binding of gene to the appropriate molecule is increasing the amount of the molecule. In one aspect of the embodiments, the molecule is the gene protein. In another aspect of the embodiments, the molecule is a small molecule. In a further aspect of the embodiments, the molecule is a polynucleotide.

(43) Methods of increasing the amount of polynucleotide in a cell are known in the art and can be modified for increasing the amount of a polynucleotide encoding gene. In one aspect, the polynucleotide can be introduced to the cell and expressed by a gene delivery vehicle that can include a suitable expression vector.

(44) Suitable expression vectors are well-known in the art, and include vectors capable of expressing a polynucleotide operatively linked to a regulatory element, such as a promoter region and/or an enhancer that is capable of regulating expression of such DNA. Thus, an expression vector refers to a recombinant DNA or RNA construct, such as a plasmid, a phage, recombinant virus or other vector that, upon introduction into an appropriate host cell, results in expression of the inserted DNA. Appropriate expression vectors include those that are replicable in eukaryotic cells and/or prokaryotic cells and those that remain episomal or those which integrate into the host cell genome.

(45) As used herein, the term vector refers to a non-chromosomal nucleic acid comprising an intact replicon such that the vector may be replicated when placed within a cell, for example by a process of transformation. Vectors may be viral or non-viral. Viral vectors include retroviruses, adenoviruses, herpesvirus, papovirus, or otherwise modified naturally occurring viruses. Exemplary non-viral vectors for delivering nucleic acid include naked DNA; DNA complexed with cationic lipids, alone or in combination with cationic polymers; anionic and cationic liposomes; DNA-protein complexes and particles comprising DNA condensed with cationic polymers such as heterogeneous polylysine, defined-length oligopeptides, and polyethylene imine, in some cases contained in liposomes; and the use of ternary complexes comprising a virus and polylysine-DNA.

(46) Non-viral vector may include plasmid that comprises a heterologous polynucleotide capable of being delivered to a target cell, either in vitro, in vivo or ex-vivo. The heterologous polynucleotide can comprise a sequence of interest and can be operably linked to one or more regulatory elements and may control the transcription of the nucleic acid sequence of interest. As used herein, a vector need not be capable of replication in the ultimate target cell or subject. The term vector may include expression vector and cloning vector.

(47) Methods of down-regulating a gene (e.g., decreasing the biological activity or inhibiting a gene product) are known in the art. Non-limiting examples include mutating the gene, deleting part or whole of the sequence of the gene, or inhibiting the gene with siRNA, dsRNA, miRNA, antisense polynucleotide, ribozymes, triplex polynecleotide, antibody, or an antibody variant.

(48) Short interfering RNAs (siRNA) refer to double-stranded RNA molecules (dsRNA), generally, from about 10 to about 30 nucleotides in length that are capable of mediating RNA interference (RNAi). RNA interference (RNAi) refers to sequence-specific or gene specific suppression of gene expression (protein synthesis) that is mediated by short interfering RNA (siRNA). As used herein, the term siRNA includes short hairpin RNAs (shRNAs). A siRNA directed to a gene or the mRNA of a gene may be a siRNA that recognizes the mRNA of the gene and directs a RNA-induced silencing complex (RISC) to the mRNA, leading to degradation of the mRNA. A siRNA directed to a gene or the mRNA of a gene may also be a siRNA that recognizes the mRNA and inhibits translation of the mRNA. A siRNA may be chemically modified to increase its stability and safety.

(49) Double stranded RNAs (dsRNA) refer to double stranded RNA molecules that may be of any length and may be cleaved intracellularly into smaller RNA molecules, such as siRNA. In cells that have a competent interferon response, longer dsRNA, such as those longer than about 30 base pair in length, may trigger the interferon response. In other cells that do not have a competent interferon response, dsRNA may be used to trigger specific RNAi.

(50) MicroRNAs (miRNA) refer to single-stranded RNA molecules of 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (non-coding RNA); instead each primary transcript (a pri-miRNA) is processed into a short stem-loop structure called a pre-miRNA and finally into a functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression.

EXAMPLES

(51) The disclosure is further understood by reference to the following examples, which are intended to be purely exemplary of the invention. The present invention is not limited in scope by the exemplified embodiments, which are intended as illustrations of single aspects of the invention only. Any methods that are functionally equivalent are within the scope of the invention. Various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description and accompanying figures. Such modifications fall within the scope of the appended claims.

Example 1. Methods for Testing Engineered Cells

(52) This example provides materials and methods for evaluating the genes in protein expression as shown in Example 2. 21 genes used in the experiments were cloned into pCT Mnd 4, 5, and 6. Each of the vectors was SV40 based gene expression system with a DHFR gene followed by a primary selection marker that differs for each of the vectors. Mnd4 had neomycin resistance, Mnd5 had hygromycin resistance, and Mnd6 had zeocin resistance. The Av1 gene was removed in the vectors that were used in the control (MND) experiments. The genes were cloned into each of the vectors to replace the Av1 gene denoted on the sequence maps as shown in Table 5. To quantify the presence or absence of the genes, mRNA and cDNA isolation methods were used followed by PCR.

(53) TABLE-US-00011 TABLE 5 Vector Name of Candidate Gene Gene Code Mnd4 IDH3G M09 Mnd5 PDP M12 Mnd6 PKM M17 Mnd4 PRDM1 M18 Mnd4 AKT1 M21 Mnd4 AKT2 M22 Mnd6 UNC18B M27 Mnd6 Transcarbamoylase M280 Mnd5 Calnexin M300 Mnd6 Carbamoyl phosphate synthetase M310 Mnd6 Endoplasmin M320 Mnd4 PDIA3/GRP58 M37 Mnd6 MAPK3 M38 Mnd4 HK1 M07 Mnd5 Citrate Synthase M10 Mnd5 Cdkn1b M03 Mnd6 IL3 M24 Mnd4 Bcl2 M290 Mnd5 XIAP M39 Mnd5 HK2 M08 Mnd4 SRP14 M25 Mnd4 Cdkn1a M02 Mnd5 AKT3 M23 Mnd5 Nrf2 M13 Mnd5 Tbp M19 Mnd6 Pfk1 M16 Mnd6 Bip M26
mRNA Isolation

(54) mRNA was isolate using mRNA Catcher (Invitrogen, Catalog No. K1570-02). For each clone, 500 l cell suspension containing 17,000-30,000 cells was collected from a well of 24-well plate and was spin down at 3,000 rpm in a micro centrifuge. The media removed. The cell pellet was re-suspended into 40 l PBS. The cell suspension was transferred to a well of the mRNA Catcher plate. 40 l of 2Lysis Buffer containing 5 mM DTT was add to the well, and was mixed by pipetting up and down. After incubation at room temperature for 60 minutes, the lysates were aspirated from the well. 100 l Wash Buffer was add to the wells followed by incubation at room temperature for 1 minute. The Wash Buffer was aspirated. The washing steps were repeated twice. Then 80 l Elution Buffer was added into the well. The plate was incubated at 68 C. for 5 minutes and then cooled to 4 C. using a thermocycler. The eluted mRNA was transferred into a tube and stored at 80 C. until use.

(55) cDNA Synthesis

(56) cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen Cat. No. 18064-022). For each sample, the following components were mixed: 1 l of 300 ng/l random primers (Invitrogen Cat. No. 48190-011); 5 l of mRNA obtained in the above-mentioned methods; 1 l of 10 mM dNTP Mix; and sterile, distilled water was added to a final volume of 12 l. The mixture was heated to 65 C. for 5 min followed by quick chill on ice. Then the following components were added: 4 l of 5First-Strand Buffer; 2 l of 0.1 M DTT; 1 l of RNaseOUT (Invitrogen Cat. No. 40 units/l). The mixture was then incubate at 25 C. for 2 min. 1 l of SuperScript II RT was added and the tub was incubated at 25 C. for 10 min, 42 C. for 50 min, and then 70 C. for 15 min.

(57) PCR

(58) PCR was performed using Taq 2 Master Mix (NEB M0270). For each sample, the following components were mixed: 0.5 l of 10 M Forward primer; 0.5 l of 10 M Reverse primer; 5 l of cDNA obtained in the above-mentioned methods; 12.5 l of Taq 2master mix; and Nucleae-free water was added to a final volume of 25 l. Thermocycling conditions were as follows: Step 1: 95 C. 30 seconds; Step 2: 95 C. 30 seconds; 58 C. 30 seconds; 68 C. 1 minute; step 2 repeated for 35 cycles; Step 3: 68 C. 5 minute. PCR products were tested by electrophoresis on 1% TAE agarose gel at 100 voltage for 40 minutes. PCR primers were listed in the following table. Sgene-r was located at the 5 end of WPRE, and the forward primers were located at the 3 end of each candidate gene and were 300 bp upstream of the 5 end of WPRE.

(59) TABLE-US-00012 Gene Code Forwardprimer Reverseprimer M2 m2-f:CTTCGACTTCGTCACCGA sgene-r:CCACATAGCGTAAAA GACG(SEQIDNO:1) GGAGCAAC(SEQIDNO:24) M3 m3-f:CCTGATCCGACGGACAGT Sameasabove CCAGC(SEQIDNO:2) M7 m7-f:AGAACAGAGGACTAGACC Sameasabove ATCTG(SEQIDNO:3) M8 m8-f:CTGGACAGCCTCAAAGTG Sameasabove ACAGTG(SEQIDNO:4) M9 m9-f:GCTAGCAAGTTGCATGAT Sameasabove GCTAG(SEQIDNO:5) M10 m10-f:TATCCTCTTAGAGCAAGG Sameasabove GAAGG(SEQIDNO:6) M13 m13-f:GAACTGGAGCAAGACTTA Sameasabove GGCCAC(SEQIDNO:7) M17 m17-f:GCTGAGGATGTAGACCTC Sameasabove CGTGTG(SEQIDNO:8) M18 m18-f:GAAGGAGATTCTAGCTGT Sameasabove GGTCAG(SEQIDNO:9) M19 m19-f:CAGCAGGGATTAGTCTAT Sameasabove GAGCCAG(SEQIDNO:10) M21 m21-f:CAGGATGTGTATGAGAAG Sameasabove AAGC(SEQIDNO:11) M22 m22-f:GAAGTGGACACAAGGTAC Sameasabove TTCG(SEQIDNO:12) M24 m24-f:CTGTGAGCACCTCCGAGA Sameasabove TGAGAG(SEQIDNO:13) M25 m25-f:AGAAAACAAGTGTCTGTT Sameasabove GAGAGC(SEQIDNO:14) M26 m26-f:GAAACCATGGAGAAAGCT Sameasabove GTAGAG(SEQIDNO:15) M27 m27-f:CCAGGCTCATTGTGTACA Sameasabove TTGTGG(SEQIDNO:16) M37 m37-f:TCCTACCATCTACTTTTC Sameasabove ACCAGC(SEQIDNO:17) M38 m38-f:CCGTACCTGGAACAGTAC Sameasabove TATGAC(SEQIDNO:18) M39 m39-f:ATCAGTACGGAAGAGCAG Sameasabove CTGAGG(SEQIDNO:19) M290 m290-f:GTGGAGGAACTCTTCAGG Sameasabove GATGG(SEQIDNO:20) M320 m320-f:CAGCTTAAACATTGACCC Sameasabove TGAAGC(SEQIDNO:21) GAPDH GAPDH-f:GTCATCATCTCCGCC GAPDH-r:GCGACATGTCAG CCTTO(SEQIDNO:22) ATCCACAAC(SEQIDNO:25) RTXLC RTXLC-co-f:CCATGTCTGTCCCAA RTXLC-co-r:TGAGGGAATAAGATG CACAGGTC(SEQIDNO:23) TACCAGAGC(SEQIDNO:26)

Example 2. Testing Engineered Cells

(60) The engineered clones were tested and the results are shown in the following table (Table 6).

(61) TABLE-US-00013 TABLE 6 Gene Hk1 Akt1 Akt2 II3 MAPK3 XIAP GAPDH D12 titer/confluency 24 well confluency Clone 54 .2 .7 .7 1 .5 1 1 3.6478 5-10% Clone 76 1.3 1.5 1.5 1.2 0 .3 1 4.66 100% Clone 73 .5 0 0 0 0 .33 1 2.7 70-80% Average 0 0 0 0 0 0 1 1.925 MND

(62) Clone 54 and clone 76 had similar set of integrated candidate genes yet had wildly different growth rates. Clone 54 that included Hk1, Akt1, Akt2, IL3, MAPK3, and XIAP had a confluency of 5-10% in 24 well plates (slowest growing clone). Clone 76, which included the similar set of genes except for MAPK3, had a 100% confluency in 24 well plates (fastest growing clone). It is contemplated that this 10-20 fold difference in growth rate between the two clones was not due to the expression of MAPK3 in clone 54, since MAPK3 was known to enhance, not hinder growth. Instead, the slow growth in clone 54 may be attributed to some characteristics specific to the cells of clone 54. For example, the cells of clone 54 may not have enough energy to grow properly while maintaining enhanced protein expression.

(63) Both clones 54 and 76 had Hk1, which would result in higher energy production. Expression of Hk1, however, is about 6 times higher in clone 76 than in clone 54. It is contemplated that expression of Hk1 may not be high enough to make a difference in energy production in clone 54. In this context, the growth enhancers (e.g., Akt1, Akt2, and 113) that are in common between the two clones had a bigger impact on the cells of clone 76 with higher energy production. Clone 73, which had a catabolic enhancement (e.g., Hk1) and a secondary enhancement (e.g., XIAP for enhancing cell survival), also had high titer.

(64) It is to be understood that while the invention has been described in conjunction with the above embodiments, that the foregoing description and examples are intended to illustrate and not limit the scope of the invention. Other aspects, advantages and modifications within the scope of the invention will be apparent to those skilled in the art to which the invention pertains.