WO2012082509A2 - Biomarkers for enhanced protein production - Google Patents

Abstract

The present invention provides compositions and methods for enhanced protein production. In particular, the invention provides genetically modified non-mouse cells having disrupted expression of at least one biomarker of increased protein production, kits comprising the cells having disrupted biomarker expression, and methods of using the cells having disrupted biomarker expression for the production of increased amounts of recombinant proteins.

Description

BIOMARKERS FOR ENHANCED PROTEIN PRODUCTION

FIELD OF THE INVENTION

[0001 ] The present invention generally relates to compositions and methods for enhanced protein production. In particular, the invention relates to biomarkers for enhanced protein production, cells having increased protein production capacity, and methods of using said cells for increased protein production.

BACKGROUND OF THE INVENTION

[0002] Recombinant proteins for therapeutic or diagnostic uses are a category of biopharmaceuticals that can be produced in many host organisms such as microbial, insect, plant, and mammalian cells. Many recombinant proteins have been approved by regulatory agencies in the US and Europe for the treatment of cancers, diabetes, rheumatoid arthritis, blood disorders, growth disturbances, hemophilia, or hepatitis. For example, recombinant insulin, blood factor VIII, tissue plasminogen activator, erythropoietin, interferon-a, and interleukin-based products are among the many products in the market.

[0003] The markets for biopharmaceuticals have increased significantly over the years, mainly because many recombinant proteins are used for the treatment of chronic diseases and, thus, there is a demand for increased quantities. Moreover, new and efficacious recombinant proteins are needed for the treatment of many other conditions or diseases. Thus, there is a need for increased

manufacturing capacity of recombinant proteins, and especially increased levels of expression. That is, expression levels need to be improved significantly to increase the production levels, as well as reduce the cost of the biopharmaceuticals and thus the health care costs.

[0004] During recombinant protein production, however, the

overproduction of heterologous gene products in some hosts can result in metabolic burden and physiological stress. Negative factors include the intracellular presence of multi-copy expression vectors, toxicity of gene products, protein mis-folding, extracellular accumulation of toxic wastes or metabolites, nutrient-limitation, oxygen- limitation, and the presence of inhibitors, which as a consequence, can limit recombinant protein production.

[0005] Strategies have been developed to alleviate some of these negative factors and thus restore cell physiology. For example, high-level recombinant protein expression can be achieved by co-amplifying the recombinant gene alongside with a selectable marker, such as dihydrofolate reductase (dhfr). Thus, factors or genes that regulate those negative factors can be utilized as high- producing biomarkers and may be manipulated to improve cell physiology for high- level recombinant protein production. Genetic and metabolic strategies to develop superior host/vector systems to enhance recombinant protein production have been widely explored by co-expression or knockout of certain key gene(s). Proper identification of the key gene(s) as biomarker(s) affecting cell physiology under various stressful conditions becomes critical for physiological improvement.

[0006] Due to the increasing demand for recombinant therapeutic proteins, including monoclonal antibodies (mAb), the development of stable, high- producing mammalian cell lines for therapeutic protein production has been a major challenge in the biopharmaceutical industry. The stability of these cell lines in the absence of selection pressure is important to ensure predictable high recombinant protein yields during production. Therefore, there is a need to identify key genes that play a role in regulating recombinant protein production in cells. Moreover, there is a need to manipulate the endogenous expression levels of these genes in order to create cells having enhanced production of recombinant proteins.

SUMMARY OF THE INVENTION

[0007] Briefly, therefore, one aspect of the present disclosure provides a genetically modified non-mouse cell, wherein the cell comprises disrupted expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd 0, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik.

[0008] Another additional aspect of the disclosure provides a kit for producing a recombinant protein. The kit comprises a plurality of genetically modified non-mouse cells comprising disrupted expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik.

[0009] A further aspect of the disclosure encompasses a method for preparing a cell that has the capacity to produce high levels of a recombinant protein. The method comprises disrupting expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf 12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209 M 04 Rik in the cell.

[0010] Still another aspect of the disclosure provides a method for producing a recombinant protein. The method comprises expressing a nucleic acid sequence encoding the recombinant protein in a cell comprising disrupted

expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd 0, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik, wherein the cell having disrupted expression of the biomarker produces higher levels of the recombinant protein than a comparable cell not having disrupted expression of the biomarker.

[001 1] Other aspects and iterations of the disclosure are described in more detail below.

DESCRIPTION OF THE FIGURES

[0012] FIG. 1 illustrates cell growth and cell viability in various samples.

(A) Viable cell density (VCD) is plotted on Days 0, 2, and 4 for samples: (1 ) no electroporation (non-transfected); (2) no siRNA (mock transfected); (3) HC+LC (IgG HC and LC siRNA transfected) and (4) non-targeting (non-targeting siRNA

transfected). (B) Percent of viable cells in plotted as a function of days in culture for each of the samples.

[0013] FIG. 2 presents qRT-PCR relative quantification of IgG HC mRNA (A) and IgG LC mRNA (B) on Day 2 and Day 4 samples: (1 ) no electroporation (non-transfected); (2) no siRNA (mock transfected); (3) HC+LC (IgG HC and LC siRNA transfected) and (4) non-targeting (non-targeting siRNA transfected).

[0014] FIG. 3 illustrates IgG protein production in samples on Day 2 and Day 4. The samples are: (1 ) no electroporation (non-transfected); (2) no siRNA (mock transfected); (3) HC+LC (IgG HC and LC siRNA transfected) and (4) non- targeting (non-targeting siRNA transfected).

[0015] FIG. 4 depicts the cellular and molecular functions of the differentially expressed genes between low and high producing cells on Day 2 and Day 4.

[0016] FIG. 5 depicts images from Cell Xpress™ following capture and detection of secreted antibody, fluorescence visualization of secreted protein (PE channel only). (A) CHO cells transfected with GFP siRNAs. (B) CHO cells transfected with IgG heavy chain siRNAs.

[0017] FIG. 6 depicts the scatter plot of the data extracted from Cell

Xpress™ analysis of CHO cells transfected with siRNAs targeted against IgG. siRNA conditions are indicated on the X axis, and the mean secretion area average intensities are represented by black lines.

[0018] FIG. 7 depicts scatter plot of the data extracted from Cell

Xpress™ analysis of CHO cells transfected with siRNAs targeted against CHO biomarkers. siRNA conditions are indicated on the X axis, and the mean secretion area average intensities are represented by black lines. The dotted line represents the mean level of the control condition.

[0019] FIG. 8 illustrates enhanced IgG productivity and qRT-PCR validation of Akr1 b8 gene knockdown in cell line SAFCB-A. (A) peak viable cell densities and IgG titers of SAFCB-A cell lines transduced with lentiviruses expressing shRNAs to Akr1 b8; (B) quantitative real-time PCR analysis of Akr1 b8.

[0020] FIG. 9 illustrates enhanced IgG productivity and qRT-PCR validation of Anap10 gene knockdown in cell line SAFCB-A. (A) peak viable cell densities and IgG titers of SAFCB-A cell lines transduced with lentiviruses expressing shRNAs to Anap10; (B) quantitative real-time PCR analysis of Anap10.

[0021 ] FIG. 10 illustrates enhanced IgG productivity and qRT-PCR validation of Gjb3 gene knockdown in cell line SAFCB-A. (A) peak viable cell densities and IgG titers of SAFCB-A cell lines transduced with lentiviruses expressing shRNAs to Gjb3; (B) quantitative real-time PCR analysis of Gjb3.

[0022] FIG. 11 illustrates enhanced IgG productivity and qRT-PCR validation of Sen2 gene knockdown in cell line SAFCB-B. (A) peak viable cell densities and IgG titers of SAFCB-B cell lines transduced with lentiviruses expressing shRNAs to Sen2; (B) quantitative real-time PCR analysis of Sen2.

DETAILED DESCRIPTION OF THE INVENTION

[0023] The present disclosure provides compositions and methods for enhanced production of recombinant proteins. Advantageously, it has been discovered that knockdown or knockout of certain genes in a cell improves cell growth or viability and/or enhances recombinant protein production. The genes whose disrupted expression leads to improved cell growth or viability and/or enhanced protein production are called biomarkers for enhanced protein production. The biomarkers for enhanced protein production disclosed herein consist of Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b,

0610007C21 Rik, and 2610209M04Rik.

[0024] Also provided herein are genetically modified, non-mouse cells comprising disrupted expression of at least one of the biomarkers for enhanced protein expression, as well as kits comprising the cells disclosed herein. The present disclosure also provides methods for preparing the cells disclosed herein, wherein the methods comprise disrupting expression of at least one of the biomarkers for enhanced protein expression. Also provided are methods for producing increased levels of recombinant proteins. The methods comprise expressing a recombinant protein in a cell comprising disrupted expression of at least one of the biomarkers, wherein the cell comprising disrupted expression of the biomarker produces higher levels of the recombinant protein relative to a comparable cell not having disrupted expression of the biomarker. (I) Biomarkers

[0025] Among the various aspects of the present disclosure is the provision of a set of biomarkers for enhanced protein production. As used herein, the term "biomarker" refers to a gene and its gene products (i.e., RNA and protein) whose expression is indicative of a particular phenotype or cellular condition.

Moreover, the biomarker disclosed herein is an endogenous gene, i.e., a gene located in the genome of an organism, and the products of that gene.

[0026] The biomarkers disclosed herein are indicators of increased protein production. More specifically, disrupted expression of the biomarkers disclosed herein is correlated with increased recombinant protein production.

Without being bound by any particular theory, disrupted expression of the

biomarkers disclosed herein may restore cell physiology such that production of a recombinant protein is enhanced. In general, increased protein production may alter cell physiology due to increased metabolic burdens and/or other stresses.

[0027] The set of biomarkers for enhanced protein production consist of Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, CtsI, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik. TABLE A presents the name of each biomarker, as well as the GenBank and UniProKB/Swiss-Prot Accession number for the mouse homolog of each biomarker.

TABLE A

Gene/Protein Gene/Protein Name RefSeq UniProKB/Swiss-

Annotation Prot Accession

Acsl3 acyl-CoA synthetase NM_028817 Q9CZW4

long-chain family

member 3

Akr1 b8 aldo-keto reductase NM_008012 P45377

family 1 , member B8

Anapd O anaphase promoting NM_026904 C6EQJ2

complex subunit 10

Arl6ip1 ADP-ribosylation NM_019419 Q9JKW0

factor-like 6 interacting

protein 1

Cnih2 cornichon homolog 2 NM 009920 035089

Ctsd cathepsin D NM 009983 P 18242

CtsI cathepsin L NM 009984 P06797

Tinagl tubulointerstitial NM 023476 Q99JR5

[0028] In one embodiment, the biomarker may be Acsl3 (acyl-CoA synthetase long-chain family member 3), which is an isozyme of the long-chain fatty- acid-coenzyme A ligase family that play a key role in lipid biosynthesis and fatty acid degradation by converting free long-chain fatty acids into fatty acyl-CoA esters.

[0029] In another embodiment, the biomarker may be Akr1 b8 (aldo- keto reductase family 1 , member B8), which is involved in oxidation reduction.

[0030] In an alternative embodiment, the biomarker may be Anapd O

(anaphase promoting complex subunit 10), a component of the anaphase promoting complex/cyclosome (APC/C), which is a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle.

[0031 ] In still another embodiment, the biomarker may be Arl6ip1

(ADP-ribosylation factor-like 6 interacting protein 1 ), which may be involved in protein transport, membrane trafficking, and/or cell signaling during hematopoietic maturation.

[0032] In yet another embodiment, the biomarker may be Cnih2

(cornichon homolog 2), which is involved in the transport and maturation of proteins.

[0033] In another embodiment, the biomarker may be Ctsd (cathepsin

D), a lysosomal aspartyl protease composed of a dimer of disulfide-linked heavy and light chains, which are produced from a single protein precursor. The cellular role of cathepsin D is the proteolysis of peptides and protein in lysosomes. However, cathepsin D may play a role in the pathogenesis of several diseases, including breast cancer and possibly Alzheimer's disease.

[0034] In still another embodiment, the biomarker may be Ctsl

(cathepsin L), a lysosomal cysteine proteinase that plays a major role in intracellular protein catabolism. [0035] In another alternate embodiment, the biomarker may be DerM

(Deri -like domain family, member 1 ), which is a functional component of the endoplasmic reticulum-associated degradation (ERAD) complex that forms a channel allowing the retrotranslocation of mis-folded proteins into the cytoplasm where they are ubiquitinated and degraded by the proteasome.

[0036] In a further embodiment, the biomarker may be Dse (dermatan sulfate epimerase), which is located in the endoplasmic reticulum and converts D- glucuronic acid to L-iduronic acid (IdoUA) residues.

[0037] In yet another embodiment, the biomarkers may be Ebpl

(emopamil binding protein-like), a multi-pass membrane protein that does not possess sterol isomerase activity and does not bind sigma ligands.

[0038] In still another embodiment, the biomarker may be Ecm1

(extracellular matrix protein 1 ), which is involved in epidermal differentiation.

[0039] In an alternate embodiment, the biomarker may be Elk3 (ETS domain-containing protein), which regulates transcriptional activation by signal- induced phosphorylation.

[0040] In another embodiment, the biomarker may be Fth1 (ferritin, heavy polypeptide 1 ), which encodes the heavy subunit of ferritin, the major intracellular iron storage protein in cells.

[0041 ] In still another embodiment, the biomarker may be Gjb3 (gap junction protein, beta 3), which is a protein component of gap junctions that provide intercellular channels for the diffusion of low molecular weight material from cell to cell.

[0042] In yet another embodiment, the biomarker may be Hmoxl

(heme oxygenase 1 ), which is an essential enzyme in heme catabolism. Hmoxl cleaves heme to form a heme by-product.

[0043] In a further embodiment, the biomarker may be Itgbl bp1

(integrin beta 1 binding protein 1 ), which may play a role in the recruitment of beta-1 integrins to the focal contacts during integrin-dependent cell adhesion.

[0044] In an alternative embodiment, the biomarker may be Ldha

(lactate dehydrogenase A), which catalyzes the conversion of L-lactate and NAD to pyruvate and NADH in the final step of anaerobic glycolysis. [0045] In still another embodiment, the biomarker may be Lgalsl

(lectin, galactoside-binding, soluble, 1 ), a beta-galactoside-binding protein that modulates cell-cell and cell-matrix interactions.

[0046] In a further embodiment, the biomarker may be Lgals3 (lectin, galactoside-binding, soluble, 3), which plays a role in numerous cellular functions including apoptosis, innate immunity, cell adhesion, and T-cell regulation.

[0047] In another embodiment, the biomarker may be Lrpapl (low density lipoprotein receptor-related protein associated protein 1 ), which interacts with LRP1/alpha-2-macroglobulin receptor and glycoprotein 330.

[0048] In still another embodiment, the biomarker may be Myl6b

(myosin light chain 6B), which is the regulatory light chain of myosin, a hexameric ATPase cellular motor protein.

[0049] In yet another embodiment, the biomarker may be Pit1 (POU domain, class 1 , transcription factor 1 ), which regulates expression of several genes involved in pituitary development and hormone expression. Mutations of Pit1 result in combined pituitary hormone deficiency.

[0050] In a further embodiment, the biomarker may be Pomp

(proteasome maturation protein), a molecular chaperone that binds 20S

preproteasome components and is essential for 20S proteasome formation.

[0051 ] In yet another embodiment, the biomarker may be Rps26

(ribosomal protein S26), a protein that belongs to the S26E family of ribosomal proteins.

[0052] In still another embodiment, the biomarker may be Sen2 (tRNA- splicing endonuclease subunit Sen2; also called Tsen2), which is one of the two catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA.

[0053] In an alternative embodiment, the biomarker may be SH2d3c

(SH2 domain containing 3C), an Eph receptor-binding protein which may be a positive regulator of TCR (T-cell receptor) signaling.

[0054] In another embodiment, the biomarker may be S100a4 (S100 calcium binding protein A4), which is involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100a4 may also function in motility, invasion, and tubulin polymerization. Chromosomal rearrangements and altered expression of S100a4 have been implicated in tumor metastasis.

[0055] In still another embodiment, the biomarker may be Tmedl

(transmembrane emp24 protein transport domain containing 1 ), which interacts with interleukin 1 receptor-like 1 (IL1 RL1 ).

[0056] In yet another embodiment, the biomarker may be Tnfrsf25

(tumor necrosis factor receptor superfamily, member 25), which is a member of the TNF-receptor superfamily and may play a role in regulating lymphocyte homeostasis by stimulating NF-kappa B activity and regulate cell apoptosis.

[0057] In a further embodiment, the biomarker may be Tinagl

(tubulointerstitial nephritis antigen-like 1 ), which is matricellular protein that interacts with both structural matrix proteins and cell surface receptors. Tinagl may be implicated in the adrenocortical zonation in adrenocortical cells and in mechanisms for repressing the CYP1 1 B1 gene expression

[0058] In another embodiment, the biomarker may be Tnfrsf12a (tumor necrosis factor receptor superfamily, member 12A), which is a member of the tumor necrosis factor (TNF) receptor superfamily. This receptor appears to be involved with cell adhesion and cell death.

[0059] In yet another embodiment, the biomarker may be Trappc6b

(trafficking protein particle complex 6B), which is a component of tethering complexes involved in vesicle transport.

[0060] In still another embodiment, the biomarker may be

0610007C21 Rik (RIKEN cDNA 0610007C21 gene), which was identified through differential gene expression profiling but with unknown function.

[0061 ] In an alternate embodiment, the biomarker may be

2610209 M 04 Rik (RIKEN cDNA 2610209M04 gene), which is a putative nucleic acid binding protein.

[0062] Exemplary biomarkers include Akr1 b8, Anapd 0, Gjb3, and

Sen2.

(II) Cells Comprising Disrupted Expression of a Biomarker

[0063] Another aspect of the present disclosure encompasses a genetically modified, non-mouse cell comprising disrupted expression of at least one of the biomarkers disclosed herein. Because of the disrupted expression of the biomarker, the cells disclosed herein have the ability to produce high levels of recombinant proteins.

(a) biomarker

[0064] The identity of the biomarker having disrupted expression can and will vary. As detailed in section (I), the biomarker may be Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, 2610209M04Rik, or combinations thereof.

[0065] In one embodiment, the cell may have disrupted expression of one of the biomarkers disclosed herein. In another embodiment, the cell may have disrupted expression of two of the biomarkers disclosed herein. In still another embodiment, the cell may have disrupted expression of three of the biomarkers disclosed herein. In yet another embodiment, the cell may have disrupted

expression of four of the biomarkers disclosed herein. In alternate embodiments, the cell may have disrupted expression of five, six, seven, eight, nine, ten, or more than ten of the biomarkers disclosed herein.

(b) disrupted expression

[0066] In some embodiments, the cell having disrupted expression of the biomarker(s) may have reduced expression of the biomarker relative to a comparable cell not having disrupted expression of the biomarker(s). For example, the levels of mRNA and/or protein of each disrupted biomarker may be reduced by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% relative to cells not having disrupted expression of the biomarker. Alternatively, the activity of the protein biomarker, such as, e.g., enzyme activity or binding activity, may be reduced in the cell having disrupted expression. For example, protein activity may be decreased from about 1 % to about 20%, from about 20% to about 40%, from about 40% to about 60%, from about 60% to about 80%, or from about 80% to about 99% relative to cells without disrupted expression of the biomarker. [0067] In other embodiments, expression of the biomarker(s) may be completely eliminated in the cell having disrupted expression of the biomarker(s). That is, expression of the biomarker(s) may be knocked-out, and the cell is a knockout cell. For example, the cell may comprise a chromosomal deletion or insertion such no functional biomarker gene product is produced. In one

embodiment, the genome of the cell may comprise an insertion of a short hairpin RNA (shRNA) cassette such that no biomarker gene product is made. In another embodiment, the genome of the cell may comprise a deletion and/or an insertion in the chromosomal region encoding the biomarker such that no functional biomarker gene product is produced. The chromosomal alteration may be heterozygous, homozygous, or hemizygous.

[0068] The disrupted expression of the at least one biomarker may be transient. That is, the disrupted expression may be temporary and may not be propagated during cell division. Alternatively, the disrupted expression of the at least one biomarker may be stable. In this case, the genome of the cell has been modified such that the modified genome may be propagated and stably inherited during cell division.

(c) cell types

[0069] The type of cell comprising disrupted expression of the biomarker(s) with can and will vary. In general, the cell will be a eukaryotic cell. In some instances, the cell may be a primary cell, a cultured cell, or immortal cell line cell. Non-limiting examples of suitable cells include fungi or yeast, such as Pichia, Saccharomyces, or Schizosaccharomyces; insect cells, such as SF9 cells from Spodoptera frugiperda or S2 cells from Drosophila melanogaster; and animal cells, such as frog, zebrafish, rodent, mammalian, non-human primate, or human cells. Exemplary cells are mammalian. In some embodiments, the cell is other than a mouse cell. In some embodiment, the cells may be primary cells. Examples of suitable primary cells include but are not limited to fibroblasts, myoblasts, T or B cells, macrophages, epithelial cells, hepatocytes, and so forth.

[0070] In other embodiments, the cell may be a cell line cell. When mammalian cell lines are used, the cell line may be any established cell line or a primary cell line that is not yet described. Suitable non-mouse mammalian cell lines include Chinese hamster ovary (CHO) cells, monkey kidney CVI line transformed by SV40 (COS7); human embryonic kidney line 293; baby hamster kidney cells (BHK); monkey kidney cells (CVI-76); African green monkey kidney cells (VERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK); buffalo rat liver cells (BRL 3A); human lung cells (W138); human liver cells (Hep G2); rat hepatoma cells (HTC); HIH/3T3 cells, the human U2-OS osteosarcoma cell line, the human A549 cell line, the human A-431 cell line, the human K562 cell line, the human HEK293 cell lines, the human HEK293T cell line, and TRI cells. For an extensive list of mammalian non-mouse cell lines, those of ordinary skill in the art may refer to the American Type Culture Collection catalog (ATCC^®, Mamassas, VA).

[0071 ] In still other embodiments, the cell may be a stem cell. Suitable stem cells include without limit embryonic stem cells, ES-like stem cells, fetal stem cells, adult stem cells, pluripotent stem cells, induced pluripotent stem cells, multipotent stem cells, oligopotent stem cells, and unipotent stem cells.

[0072] In preferred embodiments, the cell is of a type that is widely used for the production of recombinant proteins, such as antibodies, glycoproteins, and the like. In an exemplary embodiment, the cell may be a CHO cell. Numerous CHO cell lines are available from American Type Culture Collection (ATCC).

Suitable CHO cell lines include, but are not limited to, CHO K1 cells, CHO 1 -15 500 cells, CHO DP-12 cells, CHO DG44 cells, CHO-S cells, CHO dhFr- cells, CHO K1 SV cells, and CHO GS- cells.

(d) optional nucleic acid

[0073] In some embodiments, the cell comprising disrupted expression of the at least one biomarker disclosed herein may further comprise a nucleic acid sequence encoding a recombinant protein. The recombinant protein may be, without limitation, an antibody, a fragment of an antibody, a monoclonal antibody, a humanized antibody, a humanized monoclonal antibody, a chimeric antibody, an IgG molecule, an IgG heavy chain, an IgG light chain, an IgA molecule, an IgD molecule, an IgE molecule, an IgM molecule, a glycoprotein, an enzyme, a therapeutic protein, a nutraceutical protein, a fusion protein, a vaccine, a blood factor, a thrombolytic agent, an anticoagulant, a hormone, a growth factor, an interferon, or an interleukin. [0074] In some embodiments, the nucleic acid sequence encoding the recombinant protein may be extrachromosomal. That is, the nucleic acid encoding the recombinant protein may be transiently expressed from a plasmid, a cosmid, an artificial chromosome, or the like. Those skilled in the art are familiar with suitable expression constructs, appropriate expression control sequences, and methods of introducing said constructs into cells.

[0075] In other embodiments, the nucleic acid sequence encoding the recombinant protein may be chromosomally integrated such the recombinant protein may be stably expressed. In some iterations, the sequence encoding the recombinant protein may be operably linked to a heterologous expression control sequence or promoter. In other iterations, the sequence encoding the recombinant protein may be placed under control of an endogenous expression control sequence or promoter. The nucleic acid sequence encoding the recombinant protein may be introduced into the cell using well known techniques. Non-limiting examples of suitable techniques include viral vectors and targeting endonuclease mediated genome editing.

(e) preferred embodiments

[0076] In preferred embodiments, the cell may be a CHO cell comprising disrupted expression of Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, 2610209M04Rik, or combinations thereof. In one embodiment, the CHO cell may comprise disrupted expression of Akr1 b8. In another embodiment, the CHO cell may comprise disrupted expression of Anapd O. In still another embodiment, the CHO cell may comprise disrupted expression of Gjb3. In yet another embodiment, the CHO cell may comprise disrupted expression of Sen2. In an alternate embodiment, the CHO cell may comprise disrupted expression of at least two biomarkers chosen from Akr1 b8, Anapd O, Gjb3, and Sen2. (III) Kits

[0077] Still another aspect of the invention encompasses kits for producing recombinant proteins. The kits comprise a plurality of non-mouse cells having disrupted expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik. Typically the cells provided in the kits will be cultured cell line cells. Suitable cell line cells are detailed above in section (ll)(c). In a preferred embodiment, the plurality of cells having disrupted expression of the biomarker(s) may be a cell line of CHO cells.

[0078] The kits may further comprise at least one agent for introducing a nucleic acid sequence encoding a recombinant protein of interest into the non- mouse cell having disrupted expression of the biomarker(s). Suitable agents include plasmid vectors, viral vectors, targeting endonuclease mediated systems, etc., which are well known in the art.

[0079] In some embodiments, the kit may further comprise at least one additional component. Suitable components include transfection reagents, agents to enhance vector delivery, culture media for growing the cells, control vectors, dilution reagents, and the like. The kits may also comprise instructions for use.

[0080] In still another embodiment, the kit may also further comprise reagents for detecting and/or purifying the recombinant protein that is produced by the cells provided in the kit. Non-limiting examples of suitable reagents include PCR primers, polyclonal antibodies, monoclonal antibodies, affinity chromatography media, immunoaffinity chromatography media, and the like.

(IV) Methods for Preparing Cells Having Disrupted Biomarker Expression

[0081 ] Yet another aspect of the present disclosure provides a method for preparing a cell having disrupted expression of a biomarker for enhanced protein production, wherein the cell has the ability to produce high levels of a recombinant protein. The method comprises disrupting expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik.

[0082] The type of cell used in the method can and will vary. Suitable cells are detailed above in section (ll)(c). The cell may be engineered to express a recombinant protein before or after disruption of the biomarker expression. Nucleic acids encoding the recombinant protein are detailed above in section (ll)(d).

Preferred cells having disrupted biomarker expression are described above in section (ll)(e).

[0083] In general, the method comprises disrupting expression of at least one of the biomarkers disclosed herein. That is, the biomarker expression is disrupted by genetic modification of the cell. The expression may be disrupted at several different steps during gene expression. For example, the DNA sequence encoding the biomarker polypeptide may be altered such that no functional messenger RNA (mRNA) (and, consequently, no functional polypeptide) is made. Alternatively, the mRNA may be altered (or degraded) such that the polypeptide is not made or reduced levels of the polypeptide are made. Suitable means for disrupting expression of the biomarker(s) include RNA interference, genome editing with targeting endonucleases, and homologous recombination, as detailed below.

(a) RNA interference

[0084] In some embodiments, the expression of the biomarker(s) may be disrupted by introducing into the cell an RNA interference (RNAi) agent that inhibits expression of a target biomarker mRNA or transcript. The RNAi agent may lead to cleavage of the target mRNA or transcript. Alternatively, the RNAi agent may prevent or disrupt translation of the target mRNA into protein.

[0085] In some instances, the RNAi agent may be a short interfering

RNA (siRNA). In general, a siRNA comprises a double-stranded RNA molecule that ranges from about 15 to about 29 nucleotides in length. The siRNA may be about 16-18, 17-19, 21 -23, 24-27, or 27-29 nucleotides in length. In a preferred

embodiment, the siRNA may be about 21 nucleotides in length. The siRNA may optionally further comprise one or two single-stranded overhangs, e.g., a 3' overhang on one or both ends. The siRNA may be formed from two RNA molecules that hybridize together or, alternatively, may be generated from a short hairpin RNA (shRNA) (see below). In some embodiments, the two strands of the siRNA may be completely complementary, such that no mismatches or bulges exist in the duplex formed between the two sequences. In other embodiments, the two strands of the siRNA may be substantially complementary, such that one or more mismatches and/or bulges may exist in the duplex formed between the two sequences. In certain embodiments, one or both of the 5' ends of the siRNA may have a phosphate group, while, in other embodiments, one or both of the 5' ends may lack a phosphate group. In other embodiments, one or both of the 3' ends of the siRNA may have a hydroxyl group, while, in other embodiments, one or both of the 5' ends may lack a hydroxyl group.

[0086] One strand of the siRNA, which is referred to as the "antisense strand" or "guide strand," includes a portion that hybridizes with the target transcript. In preferred embodiments, the antisense strand of the siRNA may be completely complementary with a region of the target transcript, i.e., it hybridizes to the target transcript without a single mismatch or bulge over a target region between about 15 and about 29 nucleotides in length, preferably at least 16 nucleotides in length, and more preferably about 18-20 nucleotides in length. In other embodiments, the antisense strand may be substantially complementary to the target region, i.e., one or more mismatches and/or bulges may exist in the duplex formed by the antisense strand and the target transcript. Typically, siRNAs are targeted to exonic sequences of the target transcript. Those of skill in the art are familiar with programs, algorithms, and/or commercial services that design siRNAs for target transcripts. An exemplary example is the Rosetta siRNA Design Algorithm (Rosetta Inpharmatics, North Seattle, WA) and MISSION^® siRNA (Sigma-Aldrich, St. Louis, MO). The siRNA may be enzymatically synthesized in vitro using methods well known to those of skill in the art. Alternatively, the siRNA may be chemically synthesized using oligonucleotide synthesis techniques that are well known in the art.

[0087] In other embodiments, the RNAi agent may be a short hairpin

RNA (shRNA). In general, a shRNA is an RNA molecule comprising at least two complementary portions that are hybridized or are capable of hybridizing to form a double-stranded structure sufficiently long to mediate RNA interference (as described above), and at least one single-stranded portion that forms a loop connecting the regions of the shRNA that form the duplex. The structure may also be called a stem-loop structure, with the stem being the duplex portion. In some embodiments, the duplex portion of the structure may be completely complementary, such that no mismatches or bulges exist in the duplex region of the shRNA. In other embodiments, the duplex portion of the structure may be substantially

complementary, such that one or more mismatches and/or bulges may exist in the duplex portion of the shRNA. The loop of the structure may be from about 1 to about 20 nucleotides in length, preferably from about 4 to about 10 about nucleotides in length, and more preferably from about 6 to about 9 nucleotides in length. The loop may be located at either the 5' or 3' end of the region that is complementary to the target transcript (i.e., the antisense portion of the shRNA).

[0088] The shRNA may further comprise an overhang on the 5' or 3' end. The optional overhang may be from about 1 to about 20 nucleotides in length, and more preferably from about 2 to about 15 nucleotides in length. In some embodiments, the overhang may comprise one or more U residues, e.g., between about 1 and about 5 U residues. In some embodiments, the 5' end of the shRNA may have a phosphate group, while in other embodiments it may not. In other embodiments, the 3' end of the shRNA may have a hydroxyl group, while in other embodiments it may not. In general, shRNAs are processed into siRNAs by the conserved cellular RNAi machinery. Thus, shRNAs are precursors of siRNAs and are similarly capable of inhibiting expression of a target transcript that is

complementary of a portion of the shRNA (i.e., the antisense portion of the shRNA). Those of skill in the art are familiar with the available resources (as detailed above) for the design and synthesis of shRNAs. An exemplary example is MISSION^® shRNA (Sigma-Aldrich).

[0089] In still other embodiments, the RNAi agent may be an RNAi expression vector. Typically, an RNAi expression vector may be used for

intracellular (in vivo) synthesis of RNAi agents, such as siRNAs or shRNAs. In one embodiment, two separate, complementary siRNA strands may be transcribed using a single vector containing two promoters, each of which directs transcription of a single siRNA strand (i.e., each promoter is operably linked to a template for the siRNA so that transcription may occur). The two promoters may be in the same orientation, in which case each is operably linked to a template for one of the complementary siRNA strands. Alternatively, the two promoters may be in opposite orientations, flanking a single template so that transcription for the promoters results in synthesis of two complementary siRNA strands. In another embodiment, the RNAi expression vector may contain a promoter that drives transcription of a single RNA molecule comprising two complementary regions, such that the transcript forms a shRNA.

[0090] Those of skill in the art will appreciate that it is preferable for siRNA and shRNA agents to be produced in vivo via the transcription of more than one transcription unit. Generally speaking, the promoters utilized to direct in vivo expression of the one or more siRNA or shRNA transcription units may be promoters for RNA polymerase II I (Pol III). Certain Pol III promoters, such as U6 or H1 promoters, do not require c/^'s-acting regulatory elements within the transcribed region, and thus, are preferred in certain embodiments. In other embodiments, promoters for Pol II may be used to drive expression of the one or more siRNA or shRNA transcription units. In some embodiments, tissue-specific, cell-specific, or inducible Pol II promoters may be used.

[0091 ] A construct that provides a template for the synthesis of siRNA or shRNA may be produced using standard recombinant DNA methods and inserted into any of a wide variety of different vectors suitable for expression in eukaryotic cells. Guidance may be found in Current Protocols in Molecular Biology (Ausubel et al., John Wiley & Sons, New York, 2003) or Molecular Cloning: A Laboratory Manual (Sambrook & Russell, Cold Spring Harbor Press, Cold Spring Harbor, NY, 3^rd edition, 2001 ). Those of skill in the art also appreciate that vectors may comprise additional regulatory sequences (e.g., termination sequence, translational control sequence, etc.), as well selectable marker sequences. DNA plasmids are known in the art, including those based on pBR322, PUC, and so forth. Since many expression vectors already contain a suitable promoter or promoters, it may be only necessary to insert the nucleic acid sequence that encodes the RNAi agent of interest at an appropriate location with respect to the promoter(s). Viral vectors may also be used to provide intracellular expression of RNAi agents. Suitable viral vectors include retroviral vectors, lentiviral vectors, adenoviral vectors, adeno-associated virus vectors, herpes virus vectors, and so forth. In preferred embodiment, the RNAi expression vector is a shRNA lentiviral-based vector or lentiviral particle, such as that provided in MISSION^® TRC shRNA products (Sigma-Aldrich). [0092] The RNAi agents or RNAi expression vectors may be introduced into the cell using methods well known to those of skill in the art. Guidance may be found in Ausubel et al., supra or Sambrook & Russell, supra, for example. In some embodiments, the RNAi expression vector, e.g., a viral vector, may be stably integrated into the genome of the cell, such that biomarker expression is disrupted over subsequent cell generations.

(b) genome editing using targeting endonucleases

[0093] In other embodiments, expression of the biomarker may be disrupted by targeted genome editing mediated by targeting endonucleases. A targeting endonuclease is an entity that recognizes and binds a specific double- stranded chromosomal DNA sequence and introduces a double-stranded break at a targeted cleavage site in the chromosomal sequence. As used herein, "genome editing" refers to the modification or editing of a chromosomal sequence encoding the biomarker such that reduced levels of the biomarker are made or no biomarker is made. The edited chromosomal sequence may comprise a deletion, an insertion, or a combination thereof such that expression of the biomarker is disrupted.

[0094] In general, a method for targeted genome editing comprises introducing into a cell at least one targeting endonuclease or nucleic acid encoding a targeting endonuclease that recognizes a target sequence in the chromosomal sequence and is able to cleave a site in the chromosomal sequence, and, optionally, (i) at least one donor polynucleotide comprising a sequence for integration, the sequence flanked by an upstream sequence and a downstream sequence that share substantial sequence identity with either side of the cleavage site, wherein the targeting endonuclease introduces a double-stranded break into the chromosomal sequence, and the double-stranded break is repaired by (i) a non-homologous end- joining repair process such that an inactivating mutation is introduced into the chromosomal sequence, or (ii) a homology-directed repair process such that the sequence in the donor polynucleotide is integrated into the chromosomal sequence.

[0095] The type of targeting endonuclease used in the method disclosed herein can and will vary. The targeting endonuclease may be a naturally- occurring protein or an engineered protein. In one embodiment, the targeting endonuclease may be a meganuclease. Meganucleases are endodeoxyribonucleases characterized by a large recognition site, i.e., the recognition site generally ranges from about 12 base pairs to about 40 base pairs. As a consequence of this requirement, the recognition site generally occurs only once in any given genome. Among meganucleases, the LAGLIDADG family of homing endonucleases has become a valuable tool for the study of genomes and genome engineering. Meganucleases can be targeted to specific chromosomal sequence by modifying their recognition sequence using techniques well known to those skilled in the art.

[0096] In another embodiment, the targeting endonuclease may be a transcription activator- 1 ike effector (TALE) nuclease. TALEs are transcription factors from the plant pathogen Xanthomonas that can be readily engineered to bind new DNA targets. TALEs or truncated versions thereof may be linked to the catalytic domain of endonucleases such as Fokl to create targeting endonuclease called TALE nucleases or TALENs.

[0097] In still another embodiment, the targeting endonuclease may be a site-specific nuclease. In particular, the site-specific nuclease may be a "rare- cutter" endonuclease whose recognition sequence occurs rarely in a genome.

Preferably, the recognition sequence of the site-specific nuclease occurs only once in a genome. In an alternate further embodiment, the targeting nuclease may be an artificial targeted DNA double strand break inducing agent.

[0098] In a preferred embodiment, the targeting endonuclease may be a zinc finger nuclease (ZFN). Typically, a zinc finger nuclease comprises a DNA binding domain (i.e., zinc finger) and a cleavage domain (i.e., nuclease), both of which are described below.

[0099] Zinc finger binding domain. Zinc finger binding domains may be engineered to recognize and bind to any nucleic acid sequence of choice. See, for example, Beerli et al. (2002) Nat. Biotechnol. 20:135-141 ; Pabo et al. (2001 ) Ann. Rev. Biochem. 70:313-340; Isalan et al. (2001 ) Nat. Biotechnol. 19:656-660; Segal et al. (2001 ) Curr. Opin. Biotechnol. 12:632-637; Choo et al. (2000) Curr. Opin. Struct. Biol. 10:41 1 -416; Zhang et al. (2000) J. Biol. Chem. 275(43):33850-33860; Doyon et al. (2008) Nat. Biotechnol. 26:702-708; and Santiago et al. (2008) Proc. Natl. Acad. Sci. USA 105:5809-5814. An engineered zinc finger binding domain may have a novel binding specificity compared to a naturally-occurring zinc finger protein. Engineering methods include, but are not limited to, rational design and various types of selection. Rational design includes, for example, using databases comprising doublet, triplet, and/or quadruplet nucleotide sequences and individual zinc finger amino acid sequences, in which each doublet, triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, for example, U.S. Pat. Nos. 6,453,242 and 6,534,261 , the disclosures of which are incorporated by reference herein in their entireties. As an example, the algorithm of described in US patent 6,453,242 may be used to design a zinc finger binding domain to target a preselected sequence. Alternative methods, such as rational design using a nondegenerate recognition code table may also be used to design a zinc finger binding domain to target a specific sequence (Sera et al. (2002) Biochemistry 41 :7074-7081 ). Publically available web-based tools for identifying potential target sites in DNA sequences and designing zinc finger binding domains may be found at http://www.zincfingertools.org and http://bindr.gdcb.iastate.edu/ZiFiT/, respectively (Mandell et al. (2006) Nuc. Acid Res. 34:W516-W523; Sander et al. (2007) Nuc. Acid Res. 35:W599-W605).

[0100] A zinc finger binding domain may be designed to recognize and bind a DNA sequence ranging from about 3 nucleotides to about 21 nucleotides in length, or preferably from about 9 to about 18 nucleotides in length. In general, the zinc finger binding domains of the zinc finger nucleases disclosed herein comprise at least three zinc finger recognition regions (i.e., zinc fingers). In one embodiment, the zinc finger binding domain may comprise four zinc finger recognition regions. In another embodiment, the zinc finger binding domain may comprise five zinc finger recognition regions. In still another embodiment, the zinc finger binding domain may comprise six zinc finger recognition regions. A zinc finger binding domain may be designed to bind to any suitable target DNA sequence. See for example, U.S. Pat. Nos. 6,607,882; 6,534,261 and 6,453,242, the disclosures of which are incorporated by reference herein in their entireties.

[0101 ] Exemplary methods of selecting a zinc finger recognition region may include phage display and two-hybrid systems, and are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523; 6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; as well as WO 98/37186; WO 98/53057; WO 00/27878; WO 01/88197 and GB 2,338,237, each of which is incorporated by reference herein in its entirety. In addition, enhancement of binding specificity for zinc finger binding domains has been described, for example, in WO 02/077227, the disclosure of which is incorporated herein by reference.

[0102] Zinc finger binding domains and methods for design and construction of fusion proteins (and polynucleotides encoding same) are known to those of skill in the art and are described in detail in U.S. Patent Application

Publication Nos. 20050064474 and 20060188987, each incorporated by reference herein in its entirety. Zinc finger recognition regions and/or multi-fingered zinc finger proteins may be linked together using suitable linker sequences, including for example, linkers of five or more amino acids in length. See, U.S. Pat. Nos.

6,479,626; 6,903,185; and 7, 153,949, the disclosures of which are incorporated by reference herein in their entireties, for non-limiting examples of linker sequences of six or more amino acids in length. The zinc finger binding domain described herein may include a combination of suitable linkers between the individual zinc fingers of the protein.

[0103] In some embodiments, the zinc finger nuclease may further comprise a nuclear localization signal or sequence (NLS). A NLS is an amino acid sequence which facilitates targeting the zinc finger nuclease protein into the nucleus to introduce a double stranded break at the target sequence in the chromosome. Nuclear localization signals are known in the art. See, for example, Makkerh et al. (1996) Current Biology 6:1025-1027.

[0104] Cleavage domain. A zinc finger nuclease also includes a cleavage domain. The cleavage domain portion of the zinc finger nuclease may be obtained from any endonuclease or exonuclease. Non-limiting examples of endonucleases from which a cleavage domain may be derived include, but are not limited to, restriction endonucleases and homing endonucleases. See, for example, 2002-2003 Catalog, New England Biolabs, Beverly, Mass.; and Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388 or www.neb.com. Additional enzymes that cleave DNA are known (e.g., S1 Nuclease; mung bean nuclease; pancreatic DNase I;

micrococcal nuclease; yeast HO endonuclease). See also Linn et al. (eds.)

Nucleases, Cold Spring Harbor Laboratory Press, 1993. One or more of these enzymes (or functional fragments thereof) may be used as a source of cleavage domains.

[0105] A cleavage domain also may be derived from an enzyme or portion thereof, as described above, that requires dimerization for cleavage activity. Two zinc finger nucleases may be required for cleavage, as each nuclease comprises a monomer of the active enzyme dimer. Alternatively, a single zinc finger nuclease may comprise both monomers to create an active enzyme dimer. As used herein, an "active enzyme dimer" is an enzyme dimer capable of cleaving a nucleic acid molecule. The two cleavage monomers may be derived from the same endonuclease (or functional fragments thereof), or each monomer may be derived from a different endonuclease (or functional fragments thereof).

[0106] When two cleavage monomers are used to form an active enzyme dimer, the recognition sites for the two zinc finger nucleases are preferably disposed such that binding of the two zinc finger nucleases to their respective recognition sites places the cleavage monomers in a spatial orientation to each other that allows the cleavage monomers to form an active enzyme dimer, e.g., by dimerizing. As a result, the near edges of the recognition sites may be separated by about 5 to about 18 nucleotides. For instance, the near edges may be separated by about 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 16, 17 or 18 nucleotides. It will however be understood that any integral number of nucleotides or nucleotide pairs may intervene between two recognition sites (e.g., from about 2 to about 50 nucleotide pairs or more). The near edges of the recognition sites of the zinc finger nucleases, such as for example those described in detail herein, may be separated by 6 nucleotides. In general, the site of cleavage lies between the recognition sites.

[0107] Restriction endonucleases (restriction enzymes) are present in many species and are capable of sequence-specific binding to DNA (at a recognition site), and cleaving DNA at or near the site of binding. Certain restriction enzymes (e.g., Type I IS) cleave DNA at sites removed from the recognition site and have separable binding and cleavage domains. For example, the Type IIS enzyme Fokl catalyzes double-stranded cleavage of DNA, at 9 nucleotides from its recognition site on one strand and 13 nucleotides from its recognition site on the other. See, for example, U.S. Pat. Nos. 5,356,802; 5,436,150 and 5,487,994; as well as Li et al. (1992) Proc. Natl. Acad. Sci. USA 89:4275-4279; Li et al. (1993) Proc. Natl. Acad. Sci. USA 90:2764-2768; Kim et al. (1994a) Proc. Natl. Acad. Sci. USA 91 :883-887; Kim et al. (1994b) J. Biol. Chem. 269:31 , 978-31 , 982. Thus, a zinc finger nuclease may comprise the cleavage domain from at least one Type IIS restriction enzyme and one or more zinc finger binding domains, which may or may not be engineered. Exemplary Type IIS restriction enzymes are described for example in International Publication WO 07/014,275, the disclosure of which is incorporated by reference herein in its entirety. Additional restriction enzymes also contain separable binding and cleavage domains, and these also are contemplated by the present disclosure. See, for example, Roberts et al. (2003) Nucleic Acids Res. 31 :418-420.

[0108] An exemplary Type IIS restriction enzyme, whose cleavage domain is separable from the binding domain, is Fokl. This particular enzyme is active as a dimer (Bitinaite et al. (1998) Proc. Natl. Acad. Sci. USA 95: 10, 570-10, 575). Accordingly, for the purposes of the present disclosure, the portion of the Fokl enzyme used in a zinc finger nuclease is considered a cleavage monomer. Thus, for targeted double-stranded cleavage using a Fokl cleavage domain, two zinc finger nucleases, each comprising a Fokl cleavage monomer, may be used to reconstitute an active enzyme dimer. Alternatively, a single polypeptide molecule containing a zinc finger binding domain and two Fokl cleavage monomers may also be used.

[0109] In certain embodiments, the cleavage domain may comprise one or more engineered cleavage monomers that minimize or prevent

homodimerization, as described, for example, in U.S. Patent Publication Nos.

20050064474, 20060188987, and 20080131962, each of which is incorporated by reference herein in its entirety. By way of non-limiting example, amino acid residues at positions 446, 447, 479, 483, 484, 486, 487, 490, 491 , 496, 498, 499, 500, 531 , 534, 537, and 538 of Fokl are all targets for influencing dimerization of the Fokl cleavage half-domains. Exemplary engineered cleavage monomers of Fokl that form obligate heterodimers include a pair in which a first cleavage monomer includes mutations at amino acid residue positions 490 and 538 of Fokl and a second cleavage monomer that includes mutations at amino-acid residue positions 486 and 499.

[01 10] Thus, in one embodiment, a mutation at amino acid position 490 replaces Glu (E) with Lys (K); a mutation at amino acid residue 538 replaces Iso (I) with Lys (K); a mutation at amino acid residue 486 replaces Gin (Q) with Glu (E); and a mutation at position 499 replaces Iso (I) with Lys (K). Specifically, the engineered cleavage monomers may be prepared by mutating positions 490 from E to K and 538 from I to K in one cleavage monomer to produce an engineered cleavage monomer designated "E490K:I538K" and by mutating positions 486 from Q to E and 499 from I to L in another cleavage monomer to produce an engineered cleavage monomer designated "Q486E:I499L." The above described engineered cleavage monomers are obligate heterodimer mutants in which aberrant cleavage is minimized or abolished. Engineered cleavage monomers may be prepared using a suitable method, for example, by site-directed mutagenesis of wild-type cleavage monomers (Fokl) as described in U.S. Patent Publication No. 20050064474.

[01 1 1 ] The targeting endonuclease may be introduced into the cell as a nucleic acid that encodes the targeting endonuclease. The nucleic acid may be DNA or RNA. In embodiments in which the encoding nucleic acid is mRNA, the mRNA may be 5' capped and/or 3' polyadenylated. In embodiments in which the encoding nucleic acid is DNA, the DNA may be linear or circular. The DNA may be part of a vector, wherein the encoding DNA may be operably linked to a suitable promoter. Those skilled in the art are familiar with appropriate vectors, promoters, other control elements, and means of introducing the vector into the cell of interest.

[01 12] Optional donor polynucleotide. The method for targeted genome editing may further comprise introducing into the cell at least one donor polynucleotide comprising a sequence to be integrated into the chromosomal sequence. A donor polynucleotide comprises at least three components: the sequence of interest, a sequence that is substantially identical to a sequence upstream of the site of integration, and a sequence that is substantially identical to a sequence downstream of the site of integration. Thus, within the donor

polynucleotide, the sequence of interest is flanked by the upstream and downstream sequences, wherein the upstream and downstream sequences share sequence similarity with either side of the site of integration in the chromosome.

[01 13] Typically, the donor polynucleotide will be DNA. The DNA may be single-stranded or double-stranded. The donor polynucleotide may be a DNA plasmid, a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC), a viral vector, a linear piece of DNA, a PCR fragment, a naked nucleic acid, or a nucleic acid complexed with a delivery vehicle such as a liposome or poloxamer. [01 14] The upstream and downstream sequences in the donor polynucleotide are selected to promote recombination between the chromosomal sequence of interest and the donor polynucleotide. The upstream sequence, as used herein, refers to a nucleic acid sequence that shares sequence similarity with the chromosomal sequence upstream of the targeted site of integration. Similarly, the downstream sequence refers to a nucleic acid sequence that shares sequence similarity with the chromosomal sequence downstream of the targeted site of integration. The upstream and downstream sequences in the donor polynucleotide may share about 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, or 94% sequence identity with the targeted chromosomal sequence. In other embodiments, the upstream and downstream sequences in the donor polynucleotide may share about 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with the targeted chromosomal sequence. In an exemplary embodiment, the upstream and downstream sequences in the donor polynucleotide may share about 99% or 100% sequence identity with the targeted chromosomal sequence.

[01 15] An upstream or downstream sequence may comprise from about 20 bp to about 2500 bp. In one embodiment, an upstream or downstream sequence may comprise about 20, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1 100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, or 2500 bp. A preferred upstream or downstream sequence may comprise about 200 bp to about 2000 bp, about 600 bp to about 1000 bp, or more particularly about 700 bp to about 1000 bp.

[01 16] In some embodiments, the donor polynucleotide may further comprise a marker. Such a marker may make it easy to screen for targeted integrations. Non-limiting examples of suitable markers include restriction sites, fluorescent proteins, or selectable markers.

[01 17] One of skill in the art would be able to construct a donor polynucleotide as described herein using well-known standard recombinant techniques (see, for example, Sambrook and Russell, supra and Ausubel et al., supra). (c) homologous recombination

[01 18] In other embodiments, homologous recombination techniques may be used to disrupt biomarker expression at the level of the genomic DNA.

Accordingly, these techniques may be used to delete a nucleic acid sequence, delete a portion of a nucleic acid sequence, or introduce point mutations in the nucleic acid sequence, such that no functional biomarker may be made. In one embodiment, the nucleic acid sequence may be targeted by homologous

recombination using the techniques of Capecchi (Cell 22:4779-488, 1980) and Smithies (Proc Natl Acad Sci USA 91 :3612-3615, 1994). In other embodiments, the nucleic acid sequence may be targeted using a Cre-loxP site-specific recombination system, a Flp-FRT site-specific recombination system, or variants thereof. Such recombination systems are commercially available, and additional guidance may be found in Ausubel et al., supra.

(V) Methods for Producing a Recombinant Protein

[01 19] A further aspect of the present disclosure encompasses a method for producing high levels of a recombinant protein. The method comprises expressing a nucleic acid sequence encoding the recombinant protein in a cell having disrupted expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik, wherein the cell having disrupted expression of the biomarker produces higher levels of the recombinant protein than a comparable cell not having disrupted expression of the biomarker.

[0120] Cells having disrupted expression of the biomarker(s) are detailed above in section (II). Means of introducing nucleic acids encoding recombinant proteins are well known in the art. As mentioned previously, the nucleic acid encoding the recombinant protein may be chromosomally integrated or extrachromosomal. The recombinant protein may be any protein of interest. Non- limiting examples of a suitable protein include an antibody, a fragment of an antibody, a monoclonal antibody, a humanized antibody, a humanized monoclonal antibody, a chimeric antibody, an IgG molecule, an IgG heavy chain, an IgG light chain, an IgA molecule, an IgD molecule, an IgE molecule, an IgM molecule, a glycoprotein, an enzyme, a therapeutic protein, a nutraceutical protein, a fusion protein, a vaccine, a blood factor, a thrombolytic agent, an anticoagulant, a hormone, a growth factor, an interferon, an interleukin, and so forth. In preferred

embodiments, the recombinant protein may be a monoclonal antibody.

[0121 ] In some embodiments, the amount of recombinant protein produced by the cell having disrupted expression of the biomarker(s) may be at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 125%, 150%, 175%, or 200% more than the amount of recombinant protein produced by a comparable cell not having disrupted expression of the biomarker(s). In other embodiments, the amount of recombinant protein produced by the cell having disrupted expression of the biomarker(s) may be increased by at least about 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 12-fold, 15-fold, 20-fold, 25-fold, 30-fold, 40-fold, 50-fold, 60-fold, 80-fold, 100-fold, or more than 100-fold of the amount of protein produced by a comparable cell not having disrupted expression of the biomarker(s).

DEFINITIONS

[0122] Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991 ); and Hale & Marham, The Harper Collins Dictionary of Biology (1991 ). As used herein, the following terms have the meanings ascribed to them unless specified otherwise.

[0123] When introducing elements of the present disclosure or the preferred embodiments(s) thereof, the articles "a", "an", "the" and "said" are intended to mean that there are one or more of the elements. The terms "comprising", "including" and "having" are intended to be inclusive and mean that there may be additional elements other than the listed elements. [0124] A "biomarker" as used herein is an indicator of increased protein production. More specifically, disrupted expression of the biomarkers disclosed herein is correlated with increased recombinant protein production.

[0125] As used herein, the term "endogenous" refers to a chromosomal sequence that is native to the cell.

[0126] The terms "editing," "genome editing," or "chromosomal editing" refer to a process by which a specific chromosomal sequence is changed. The edited chromosomal sequence may comprise an insertion of at least one nucleotide, a deletion of at least one nucleotide, and/or a substitution of at least one nucleotide.

[0127] A "gene," as used herein, refers to a DNA region (including exons and introns) encoding a gene product, as well as all DNA regions which regulate the production of the gene product, whether or not such regulatory sequences are adjacent to coding and/or transcribed sequences. Accordingly, a gene includes, but is not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites, and locus control regions.

[0128] The terms "nucleic acid" and "polynucleotide" refer to a deoxyribonucleotide or ribonucleotide polymer, in linear or circular conformation. For the purposes of the present disclosure, these terms are not to be construed as limiting with respect to the length of a polymer. The terms can encompass known analogs of natural nucleotides, as well as nucleotides that are modified in the base, sugar and/or phosphate moieties (e.g., phosphorothioate backbones). In general, an analog of a particular nucleotide has the same base-pairing specificity; i.e., an analog of A will base-pair with T.

[0129] The terms "polypeptide" and "protein" are used interchangeably to refer to a polymer of amino acid residues.

[0130] As used herein, the terms "target site" or "target sequence" refer to a nucleic acid sequence that defines a portion of a chromosomal sequence to be edited and to which a targeting endonuclease is engineered to recognize and bind, provided sufficient conditions for binding exist.

[0131 ] The terms "upstream" and "downstream" refer to locations in a nucleic acid sequence relative to a fixed position. Upstream refers to the region that is 5' (i.e., near the 5' end of the strand) to the position and downstream refers to the region that is 3' (i.e., near the 3' end of the strand) to the position.

[0132] Techniques for determining nucleic acid and amino acid sequence identity are known in the art. Typically, such techniques include determining the nucleotide sequence of the mRNA for a gene and/or determining the amino acid sequence encoded thereby, and comparing these sequences to a second nucleotide or amino acid sequence. Genomic sequences can also be determined and compared in this fashion. In general, identity refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Two or more sequences (polynucleotide or amino acid) can be compared by determining their percent identity. The percent identity of two sequences, whether nucleic acid or amino acid sequences, is the number of exact matches between two aligned sequences divided by the length of the shorter sequences and multiplied by 100. An approximate alignment for nucleic acid sequences is provided by the local homology algorithm of Smith and Waterman, Advances in Applied Mathematics 2:482-489 (1981 ). This algorithm can be applied to amino acid sequences by using the scoring matrix developed by Dayhoff, Atlas of Protein Sequences and Structure, M. O. Dayhoff ed., 5 suppl. 3:353-358, National Biomedical Research Foundation, Washington, D.C., USA, and normalized by Gribskov, Nucl. Acids Res. 14(6):6745-6763 (1986). An exemplary implementation of this algorithm to determine percent identity of a sequence is provided by the Genetics Computer Group (Madison, Wis.) in the "BestFit" utility application. Other suitable programs for calculating the percent identity or similarity between sequences are generally known in the art, for example, another alignment program is BLAST, used with default parameters. For example, BLASTN and BLASTP can be used using the following default parameters: genetic code=standard; filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+Swiss

protein+Spupdate+PIR. Details of these programs can be found on the GenBank website. With respect to sequences described herein, the range of desired degrees of sequence identity is approximately 80% to 100% and any integer value

therebetween. Typically the percent identities between sequences are at least 70- 75%, preferably 80-82%, more preferably 85-90%, even more preferably 92%, still more preferably 95%, and most preferably 98% sequence identity.

[0133] Alternatively, the degree of sequence similarity between polynucleotides can be determined by hybridization of polynucleotides under conditions that allow formation of stable duplexes between regions that share a degree of sequence identity, followed by digestion with single-stranded-specific nuclease(s), and size determination of the digested fragments. Two nucleic acid, or two polypeptide sequences are substantially similar to each other when the sequences exhibit at least about 70%-75%, preferably 80%-82%, more-preferably 85%-90%, even more preferably 92%, still more preferably 95%, and most preferably 98% sequence identity over a defined length of the molecules, as determined using the methods above. As used herein, substantially similar also refers to sequences showing complete identity to a specified DNA or polypeptide sequence. DNA sequences that are substantially similar can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al., supra; Nucleic Acid Hybridization: A Practical Approach, editors B. D. Hames and S. J. Higgins, (1985) Oxford; Washington, D.C.; IRL Press).

[0134] Selective hybridization of two nucleic acid fragments can be determined as follows. The degree of sequence identity between two nucleic acid molecules affects the efficiency and strength of hybridization events between such molecules. A partially identical nucleic acid sequence will at least partially inhibit the hybridization of a completely identical sequence to a target molecule. Inhibition of hybridization of the completely identical sequence can be assessed using

hybridization assays that are well known in the art (e.g., Southern (DNA) blot, Northern (RNA) blot, solution hybridization, or the like, see Sambrook, et al.,

Molecular Cloning: A Laboratory Manual, Second Edition, (1989) Cold Spring Harbor, N.Y.). Such assays can be conducted using varying degrees of selectivity, for example, using conditions varying from low to high stringency. If conditions of low stringency are employed, the absence of non-specific binding can be assessed using a secondary probe that lacks even a partial degree of sequence identity (for example, a probe having less than about 30% sequence identity with the target molecule), such that, in the absence of non-specific binding events, the secondary probe will not hybridize to the target.

[0135] When utilizing a hybridization-based detection system, a nucleic acid probe is chosen that is complementary to a reference nucleic acid sequence, and then by selection of appropriate conditions the probe and the reference sequence selectively hybridize, or bind, to each other to form a duplex molecule. A nucleic acid molecule that is capable of hybridizing selectively to a reference sequence under moderately stringent hybridization conditions typically hybridizes under conditions that allow detection of a target nucleic acid sequence of at least about 10-14 nucleotides in length having at least approximately 70% sequence identity with the sequence of the selected nucleic acid probe. Stringent hybridization conditions typically allow detection of target nucleic acid sequences of at least about 10-14 nucleotides in length having a sequence identity of greater than about 90-95% with the sequence of the selected nucleic acid probe. Hybridization conditions useful for probe/reference sequence hybridization, where the probe and reference sequence have a specific degree of sequence identity, can be determined as is known in the art (see, for example, Nucleic Acid Hybridization: A Practical Approach, editors B. D. Hames and S. J. Higgins, (1985) Oxford; Washington, D.C.; IRL Press). Conditions for hybridization are well-known to those of skill in the art.

[0136] Hybridization stringency refers to the degree to which

hybridization conditions disfavor the formation of hybrids containing mismatched nucleotides, with higher stringency correlated with a lower tolerance for mismatched hybrids. Factors that affect the stringency of hybridization are well-known to those of skill in the art and include, but are not limited to, temperature, pH, ionic strength, and concentration of organic solvents such as, for example, formamide and

dimethylsulfoxide. As is known to those of skill in the art, hybridization stringency is increased by higher temperatures, lower ionic strength and lower solvent

concentrations. With respect to stringency conditions for hybridization, it is well known in the art that numerous equivalent conditions can be employed to establish a particular stringency by varying, for example, the following factors: the length and nature of the sequences, base composition of the various sequences, concentrations of salts and other hybridization solution components, the presence or absence of blocking agents in the hybridization solutions (e.g., dextran sulfate, and polyethylene glycol), hybridization reaction temperature and time parameters, as well as, varying wash conditions. A particular set of hybridization conditions may be selected following standard methods in the art (see, for example, Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, (1989) Cold Spring Harbor, N.Y.).

[0137] As various changes could be made in the above cells, kits, and methods without departing from the scope of the invention, it is intended that all matter contained in the above description and in the examples given below, shall be interpreted as illustrative and not in a limiting sense.

EXAMPLES

[0138] The following examples illustrate certain aspects of the invention.

Example 1: Identify Biomarkers Using Microarray Analysis

[0139] A 4x44K custom CHO microarray platform (Agilent

Technologies, Santa Clara, CA) designed with sequences from SAFC Biosciences proprietary CHO Database was used in all microarray studies in the following examples. The total number of features on the 4x44 microarray platform was over 45,000, which include more than 30,000 SAFC CHO probes, 1400 Agilent control probes, and 168 SAFC control probes. SAFC control probes further comprised CHO housekeeping probes (β2Μ, β-act, PGKs), IgG H and L subunit genes, marker genes such as DHFR and GS, and pathway specific probe sets. Agilent control probes included spike-in probes for quality control and darkspot probes as negative control.

[0140] Sample preparation. Cells of parental versus high producer

CHO cell lines that produced 1 .5 g/L human IgG were collected during the mid- logarithmic growth phase for RNA extraction (Day 4-5). Dye swap, biological triplicates, technical duplicates, direct comparison and reference poo! comparison were adopted for quality control. Sample labeling, amplification and hybridization were performed with Agilent's 2-Color Low RNA Input Linear Amplification Kit according to manufacturer's instructions. Samples are labeled in 2-co!or technical duplicates and hybridized against a CHO common reference RNA Pool created from an assortment of CHO lines and conditions. Agilent's Feature extraction software 9.5 was used to perform dye normalization and QC statistics for overall array quality. Outliers and low quality probes were removed based on the software's

recommendations. Expression levels between experiments were normalized using the intensity of the replicated control probes representing ail control genes in the reference pool on each array. Based on relative expression level variability across all arrays, a novel panel of genes were selected in which they were observed over- expressed or under-expressed in CHO high producer cell line in comparison to their expression in the parental CHO ceil line (Table 1 ). The gene expression and pathway analysis can be done using a variety of software and tools known in the art, such as Genesifter and Ingenuity software.

[0141 ] RT-PCR validation . Gene validation after microarray screening may be performed in variable ways known in the art. in the present disclosure, quantitative RT-PCR (qRT-PCR) was used for biomarker validation. Primers were designed against sequences from SAFC Bioscience's CHO Sequence Database using Primer3 software and ordered from Sigma Genosys. The RNA samples from the microarray studies were DNasel (New England Biolabs, Ipswich, MA) treated followed by Oligo-dT (Sigma Genosys) primed Reverse Transcription. Biological duplicates from the array experiments were pooled for RT reactions. Samples were run in triplicate for each experimental condition and the threshold values (Ct) were averaged. qRT-PCR was performed on a Stratagene MX3000P (Stratagene, La Jolia, CA). Reactions were run with SYBR® Green Jumpstart™ Taq Ready ix™ (#34438, Sigma-Aldrich®) mixed with 25 ng of cDNA and primers at 500 nM in a final volume of 20 μ!. Dissociation curve analysis was performed to ensure primer specificity.

Table 1. CHO genes targeted by shRNAs

Example 2: RNAi Facilitated High-Throughput Biomarker Screening

[0142] Microarray screening using parental or low producer versus high producer sometimes runs into the risk of chasing artifacts. There are a range of potential confounding factors that lead to false positive results. These factors include, but are not limited to, differential gene expression due to genetic

background of the cell lines originated from transfection or integration site variance of the recombinant protein gene, or originated from CHO genomic instability. The artificial gene differential expression can be minimized through reducing the metabolic burden of recombinant IgG production, and one of the methods is knockdown or knockout the recombinant IgG through siRNA.

[0143] CHO K1 cell line that produces a recombinant humanized IgG (2.2 g/L in optimized bioreactor system) underwent different siRNA treatment on Day 0, and generated sample (1 ) non-transfected; (2) mock transfected; (3) IgG heavy chain (HC) and light chain (LC) siRNA transfected; (4) non-targeting siRNA transfected. On Day 2 and Day 4, post-transfection analyses were conducted, which included cell counts and viability quantification, see FIG. 1. FIG. 1A illustrates cell growth on Day 0, 2 and 4 for each sample. Cells with IgG HC and LC siRNA transfected had the largest growth increase between Day 0 and Day 2 FIG. 1 B shows that except the non-transfected sample, the other three samples: (2) no siRNA (mock transfected); (3) HC+LC (IgG HC and LC siRNA transfected) and (4) non-targeting (non-targeting siRNA transfected) had increased cell viability when comparing Day 0 and Day 2.

[0144] FIG. 2 presents qRT-PCR relative quantification of IgG HC mRNA (A) and IgG LC mRNA (B) on Day 2 and Day 4 samples. IgG HC and LC expression were the lowest in sample (3) with IgG HC and LC siRNA transfected, although mock transfection and non-targeted transfection also caused lowered expression of IgG HC and LC in comparison to non-transfected sample.

[0145] FIG. 3 illustrates IgG protein production in samples on Day 2 and Day 4. The samples with IgG HC and LC siRNA transfected had the lowest protein production on both Day 2 and Day 4. Samples with non-targeted siRNA transfection had increased production mostly seen on Day 4, despite the lower IgG HC and LC expression on Day 4 in FIG. 2.

[0146] Using RNAi to alleviate the metabolic burden of recombination

IgG protein production from CHO cells provides a system with less background noise. Differentially expressed genes were selected by expression profiling between IgG siRNA sample (low productivity) versus non-targeting siRNA sample (high productivity). The pair wise statistical analysis was performed under Welch's f-test, and the cut-off parameters for selection were: Benjamini-Hochberg adjusted p-value < 0.05; quality score > 0.99; and Fold change > 1 .4. Day 4 and Day 2 uniquely expressed or commonly expressed genes were counted and categorized according to their functions. An approximately 80% reduction in IgG productivity led to the differential expression of 550 genes. Among these 550 genes, 274 were unique to D2, and were primarily down-regulated; 228 genes were unique to D4, and were primarily up-regulated. [0147] As shown in FIG. 4, the genes that were differentially expressed had functions ranging from RNA-post transcriptional modification, drug metabolism, gene expression, cell cycle, cellular movement, cell death, cellular growth and proliferation. Table 2 presented the number of genes in each class that were differentially expressed at Day 2 and Day 4..

Table 2.

[0148] Other differentially expressed genes were found to be involved in RNA post-transcriptional modifications, post-translational modifications, molecular transport and protein trafficking. The differentially expressed genes for RNA post- transcriptional modifications included: PRPF4B, a pre-mRNA processing factor 4 homologue B, SFRS5, a splicing factor, arginine/serine-rich 5; SFRS9, a splicing factor, arginine/serine-rich 9. PRPF4B is a transferase responsible for nucleotide binding, protein serine/threonine kinase activity, protein binding, ATP binding, mRNA processing, protein amino acid phosphorylation and RNA splicing. Both SFRS5 and SFRS9 are involved in nucleotide binding, RNA binding, protein binding during nuclear mRNA splicing, mRNA splice site selection and RNA splicing. Some molecular transporter genes are differentially expressed between low productivity versus high productivity samples. SLC5A2 (solute carrier family 5, member 2) is a sodium/glucose co-transporter. SLC46A1 (solute carrier family 46, member 1 ) is a folate transporter. And SLC6A4 (solute carrier family 6, member 4) is a

neurotransmitter, serotoin, transporter.

Example 3: Biomarker Validation Using Cell Xpress™

[0149] Cell Culture Maintenance and siRNA Transfection Assays.

Parental and recombinant IgG producing CHO cells were maintained as suspension cultures grown in a proprietary serum-free formulation. siRNAs were delivered to the cells by electroporation, and the cells were seeded in six-well tissue culture plates. Transfected cells were then maintained for three days. Cell growth and viability were monitored using the Vi-CELL (Beckman Coulter). IgG quantities were measured by standard HPLC analysis.

[0150] Cell Xpress™ Analysis. RNAi knockdown techniques combined with single cell imaging capabilities of LEAP™ and Cell Xpress™ platform provide a high throughput method to screen the productivity effects of potential biomarkers. Two days post-siRNA transfection, cells were seeded in the growth medium at a density of 150-300 cells per well in 384-well C-Lect™ plates (Cyntellect) in the presence of a protein G capture matrix. Secreted IgG molecules were captured by the matrix during incubation. The following day, secreted IgG was detected by incubation with a donkey anti-human IgG F(ab')² fragment with a recombinant phycoerythrin (PE) conjugate. Live cells were stained concurrently with Cell Tracker Green (CTG) (Molecular Probes). The fluorescent signal from each secreting cell was imaged and quantitated using the LEAP instrument and Cell Xpress™ software. Relative changes in IgG secretion were then represented by changes in the PE fluorescent signals associated with individual live cells.

[0151 ] siRNA Design and Validation. To validate the RNAi and Cell Xpress™ assay, siRNAs were designed in triplicate against the IgG heavy and light chain constant regions. siRNAs designed against the GFP messenger RNA (mRNA) were used as negative control siRNAs. These siRNA pools were then transfected into a recombinant CHO cell line that secretes 1 .5 grams per liter of IgG in a fed batch shake flask culture. The growth and viability of the siRNA transfected cells were then monitored for three days using the Vi-CELL. Electroporation of the siRNAs into the CHO cells did not have any significant negative impact on the growth or viability of the cells. For all conditions, the cell densities were greater than 1 .0 x 10⁶ cells/ml, and the cells were greater than 80% viable on day 3 of the assay (data not shown).

[0152] Knockdown ability of the siRNAs was verified by quantitative

RT-PCR (qRT-PCR) of the IgG heavy chain and light chain messages from day 3 samples of the assay. For both targets, the mRNA levels were significantly decreased when compared to the no siRNA or GFP siRNA controls (data not shown). HPLC analysis confirmed that the decrease in IgG mRNA levels resulted in a corresponding decrease in IgG protein secreted into the cell culture supernantant (data not shown).

[0153] Cell Xpress™ Analysis of CHO Cells Transfected with IgG siRNAs. In order to develop a high throughput screening assay to observe differences in IgG secretion, the Cell Xpress™ analysis platform of the LEAP™ instrument was used. Briefly, this assay was used to detect phenotypic changes in the amount of IgG secreted from individual live cells by measuring cell-associated fluorescent intensity resulting from the binding of PE-conjugated anti-human IgG to secreted recombinant IgG in the capture medium. Cell Xpress™ images acquired from IgG producing recombinant CHO cells transfected with either GFP (A) or IgG heavy chain siRNAs (B) are shown in FIG. 5. There was a substantial reduction in the amount of PE fluorescence observed in the IgG siRNA transfected cells. IgG secretion was quantitated using Cell Xpress™ by calculating the secretion area average fluorescence intensity associated with each individual cell for a particular condition. A scatter plot of the data obtained in this assay is shown in FIG. 6. When compared to the control conditions (no electroporation, no siRNA, and GFP siRNA), the cells transfected with the IgG heavy chain and light chain siRNAs displayed a significant decrease in their mean secretion area intensities, indicating a reduction in IgG secretion. To validate the Cell Xpress™ data, the mean fluorescence intensities were compared for each electroporation condition to the IgG secretion data obtained by HPLC. When these two data sets were plotted against each other, a correlation coefficient of 0.996 was obtained (data not shown). The relative changes in IgG secretion as measured by Cell Xpress™ and HPLC methods were in very good concordance.

[0154] Cell Xpress™ Analysis of CHO Cells Transfected with

Biomarker siRNAs. To determine if the Cell Xpress™ assay could be used to observe indirect effects on productivity resulting from siRNA knockdown of genes that may play a role in regulating recombinant protein production in CHO cells, siRNAs were designed to specific gene targets of interest that were discovered as being differentially expressed in a CHO parental cell line versus a high producing recombinant IgG CHO cell line (data not shown). These siRNAs were transfected into recombinant IgG producing CHO line and Cell Xpress™ analysis was

performed. A scatter plot of the data obtained is shown in FIG. 7. Electroporation of the cells with siRNAs designed against several gene targets resulted in differences in the mean secretion fluorescence intensities, indicating that this assay can be used as a high throughput method to screen the effects of various gene knockdowns on recombinant IgG secretion from CHO.

[0155] Therefore, Cell Xpress™ provided detailed, real time, single cell analysis of each cellular population, thus allowing for the measurement of the biological variation that is intrinsic to a population of heterogeneous secreting cells. Accounting for this variation provides one with an extremely sensitive approach for detecting subtle changes in IgG secretion. This method was as sensitive as HPLC analysis for measuring relative changes in IgG secretion and provided a high- throughput method for rapidly screening conditions that increase or decrease cellular IgG productivity. The Cell Xpress™ platform was used in combination with siRNA knockdown and vector based over-expression methods to validate microarray identified targets and to examine common biological pathways that are suspected to be involved with improved IgG secretion in CHO cells.

Example 4: Akr1b8 Marker Validation

[0156] SAFCB-A cell line expressing IgG was transduced with lentiviruses expressing shRNAs to Akr1 b8. Peak viable cell densities and IgG titers of shRNA transfected cell were measured. For the growth and productivity assays, 30 ml shake flask cell cultures were inoculated at a viable cell density of 1 x 10⁵ cells/ml. The viable cells densities and percent viabilities of the cultures were monitored daily. Starting near the mid-exponential growth phase, spent media samples were collected for IgG productivity analysis. The peak viable cell densities (Peak VCD) of SAFCB with and without Akr1 b8 knockdown are shown in FIG. 8A. As represented by the diamond label, both SAFCB with and without Akr1 b8 knockdown had a peak viable cell densities at about 4.0x10⁶ cells/ml. However, the IgG titers represented by peak volumetric productivity for SAFCB with Akr1 b8 knockdown, as shown in FIG. 8A, was at about 245 μg/ml, as compared to about 80 μg/ml by the non-targeted cell. The difference was nearly 3 fold.

[0157] Quantitative Real-Time PCR analysis of Akr1 b8 was performed as well. RNA was purified from mid-exponential growth phase cultures of cells expressing shRNAs to the target genes and then reverse-transcribed using Oligo-dT priming. Quantitative RT-PCR (qRT-PCR) reactions were run with SYBR Green Jumpstart Taq ReadyMix. Dissociation curve analysis was performed to ensure primer specificity. The relative quantities of mRNA were normalized to Actr5, and the mRNA levels of Akr1 b8 in Akr1 b8 knockdown cells and non-targeting cells were shown in FIG. 8B. The expression level of Akr1 b8 in the non-targeted cell was 3 times of that in the Akr1 b8 knockdown cells. Therefore, it can be concluded that the enhanced IgG productivity was due to the Akr1 b8 gene knockdown in the cells, and Akr1 b8 is a valid biomarker for the high-producing trait.

Example 5: AnapdO Biomarker Validation

[0158] SAFCB-A cell line expressing IgG was transduced with lentiviruses expressing shRNAs to Anapd O. Peak viable cell densities and IgG titers of shRNA transfected cell were measured. For the growth and productivity assays, 30 ml shake flask cell cultures were inoculated at a viable cell density of 1 x 10⁵ cells/ml. The viable cells densities and percent viabilities of the cultures were monitored daily. Starting near the mid-exponential growth phase, spent media samples were collected for IgG productivity analysis. The peak viable cell densities of SAFCB with Anapd O knockdown is shown in FIG. 9A. As represented by the diamond label, both SAFCB with and without Anapd O knockdown had a peak viable cell density of about 2.7 x 10⁶ cells/ml. However, the IgG titers represented by peak volumetric productivity for SAFCB with Anapd O knockdown, as shown in FIG. 9A, was at about 95 μg/ml, as compared to about 25 μg/ml by the non-targeted cell. The difference is nearly 4 fold. [0159] Quantitative Real-Time PCR analysis of Anapd 0 was performed as well. RNA was purified from mid-exponential growth phase cultures of cells expressing shRNAs to the target genes and then reverse transcribed using Oligo-dT priming. Quantitative RT-PCR (qRT-PCR) reactions were run with SYBR Green Jumpstart Taq ReadyMix. Dissociation curve analysis was performed to ensure primer specificity. The relative quantities of mRNA were normalized to Actr5, and the mRNA levels of Anapd 0 in Anapd 0 knockout cells and non-targeting cells were shown in FIG. 9B. The expression level of Anapd 0 in the non-targeted cell was nearly 7 times of that in the Anapd 0 knockdown cells. Therefore, it can be concluded that the enhanced IgG productivity is due to the Anapd 0 gene

knockdown in the cells, and Anapd 0 is a valid biomarker for high-producing trait.

Example 6: Gjb3 Bio marker Validation

[0160] SAFCB-A cell line expressing IgG was transduced with lentiviruses expressing shRNAs to Gjb3. Peak viable cell densities and IgG titers of shRNA transfected cell were measured. For the growth and productivity assays, 30 ml shake flask cell cultures were inoculated at a viable cell density of 1 x 10⁵ cells/ml. The viable cells densities and percent viabilities of the cultures were monitored daily. Starting near the mid-exponential growth phase, spent media samples were collected for IgG productivity analysis. The peak viable cell densities of SAFCB with Gjb3 knockdown is shown in FIG. 10A. As represented by the diamond label, both SAFCB with Gjb3 knockdown had a peak viable cell densities of about 3.7 x 10⁶ cells/ml. In comparison, SAFCB without Gjb3 knockdown had a peak viable cell density of about 0.5 x10⁶ cells/ml. Therefore, Gjb3 knockdown had an effect on the cells growth properties. Further, the IgG titers represented by peak volumetric productivity for SAFCB with Gjb3 knockdown, as shown in FIG. 10A, was at about 195 μg/ml, as compared to about 25 μg/ml by the non-targeted cell. The difference is nearly 8 fold.

[0161 ] Quantitative Real-Time PCR analysis of Gjb3 was performed as well. RNA was purified from mid-exponential growth phase cultures of cells expressing shRNAs to the target genes and then reverse-transcribed using Oligo-dT priming. Quantitative RT-PCR (qRT-PCR) reactions were run with SYBR Green Jumpstart Taq ReadyMix. Dissociation curve analysis was performed to ensure primer specificity. The relative quantities of mRNA were normalized to Actr5, and the mRNA levels of Gjb3 in Gjb3 knockout cells and non-targeting cells were shown in FIG. 10B. The expression level of Gjb3 in the non-targeted cell was nearly 4 times of that in the Gjb3 knockdown cells. Therefore, it can be concluded that the enhanced IgG productivity is due to the Gjb3 gene knockdown in the cells and the improved cell growth properties, and Gjb3 is a valid biomarker for high-producing trait.

Example 7: Sen2 Biomarker Validation

[0162] SAFCB-B cell line expressing IgG was transduced with lentiviruses expressing shRNAs to Sen2. Peak viable cell densities and IgG titers of shRNA transfected cell were measured. For the growth and productivity assays, 30 ml shake flask cell cultures were inoculated at a viable cell density of 1 x 10⁵ cells/ml. The viable cells densities and percent viabilities of the cultures were monitored daily. Starting near the mid-exponential growth phase, spent media samples were collected for IgG productivity analysis. The peak viable cell densities of SAFCB with Sen2 knockdown is shown in FIG. 11 A. As represented by the diamond label, both SAFCB with and without Sen2 knockdown had a peak viable cell densities of about 3.6 x 10⁶ cells/ml. However, the IgG titers represented by peak volumetric productivity for SAFCB with Sen2 knockdown, as shown in FIG. 11 A, was at about 410 μg/ml, as compared to about 320 μg/ml by the non-targeted cell. The difference was about 1 .3 fold.

[0163] Quantitative Real-Time PCR analysis of Sen2 was performed as well. RNA was purified from mid-exponential growth phase cultures of cells expressing shRNAs to the target genes and then reverse-transcribed using Oligo-dT priming. Quantitative RT-PCR (qRT-PCR) reactions were run with SYBR Green Jumpstart Tag ReadyMix. Dissociation curve analysis was performed to ensure primer specificity. The relative quantities of mRNA were normalized to Actr5, and the mRNA levels of Sen2 in Sen2 knockout cells and non-targeting cells were shown in FIG. 1 1 B. The expression level of Sen2 in the non-targeted cell was over 3 times of that in the Sen2 knockdown cells. Therefore, it can be concluded that the enhanced IgG productivity is due to the Sen2 gene knockdown in the cells, and Sen2 is a valid biomarker for high-producing trait.

Claims

CLAIMS What is claimed is:

1 . A genetically modified non-mouse cell, the cell comprising disrupted

expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik.

2. The genetically modified non-mouse cell of claim 1 , wherein disrupted expression of the biomarker is such that a reduced level of the biomarker is produced.

3. The genetically modified non-mouse cell of claim 1 , wherein disrupted expression of the biomarker is such that none of the biomarker is produced.

4. The genetically modified non-mouse cell of claim 1 , wherein expression of the biomarker is disrupted by a technique chosen from RNA interference, targeting endonuclease-mediated genome editing, and homologous recombination.

5. The genetically modified non-mouse cell of claim 4, wherein the targeting endonuclease is a zinc finger nuclease.

6. The genetically modified non-mouse cell of claim 1 , wherein the cell is chosen from a human cell, a mammalian cell, a vertebrate cell, and an invertebrate cell.

7. The genetically modified non-mouse cell of claim 6, wherein the cell is a Chinese hamster ovary (CHO) cell.

8. The genetically modified non-mouse cell of claim 7, wherein the biomarker is chosen from Sen2, Akr1 b8, Anapd O, and Gjb3.

9. The genetically modified non-mouse cell of claim 1 , further comprising a nucleic acid sequence encoding a recombinant protein, the nucleic acid sequence being extrachromosomal or chromosomally integrated.

10. A kit for producing a recombinant protein, the kit comprising a plurality of genetically modified non-mouse cells comprising disrupted expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd 0, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b,

0610007C21 Rik, and 2610209M04Rik.

1 1 . The kit of claim 10, wherein the plurality of cells having disrupted

expression of the biomarker produces higher levels of the recombinant protein that a plurality of comparable cells not having disrupted expression of the biomarker.

12. The kit of claim 10, wherein disrupted expression is such that a reduced level of the biomarker is produced.

13. The kit of claim 10, wherein disrupted expression is such that none of the biomarker is produced.

14. The kit of claim 10, wherein expression of the biomarker is disrupted by a technique chosen from RNA interference, targeting endonuclease- mediated genome editing, and homologous recombination.

15. The kit of claim 14, wherein the targeting endonuclease is a zinc finger nuclease.

16. The kit of claim 10, wherein the plurality of cells is chosen from human cells, mammalian cells, vertebrate cells, and invertebrate cells.

17. The kit of claim 10, wherein the plurality of cells is Chinese hamster ovary (CHO) cells.

18. The kit of claim 17, wherein the biomarker is chosen from Sen2, Akr1 b8, Anapd O, and Gjb3.

19. The kit of claim 10, further comprising at least one agent to introduce a nucleic acid sequence encoding the recombinant protein to the non-mouse cell.

20. A method for preparing a cell that has the capacity to produce high levels of a recombinant protein, the method comprising disrupting expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b,

0610007C21 Rik, and 2610209M04Rik in the cell.

21 . The method of claim 20, wherein disprupting expression comprises

introducing into the cell an RNA interference agent chosen from a short interfering RNA, a short hairpin RNA, and an RNAi expression vector.

22. The method of claim 20, wherein disprupting expression comprises

introducing into the cell a targeting endonuclease that binds to and is able to cleave a targeted site in a chromosomal sequence that codes the biomarker.

23. The method of claim 22, wherein the targeting endonuclease is a zinc finger nuclease.

24. The method of claim 22, further comprising introducing a donor

polynucleotide comprising an upstream sequence and a downstream sequence that have substantial sequence identity with either side of the targeted site of cleavage.

25. The method of claim 20, wherein expression of the biomarker is disrupted such that a reduced level of the biomarker is produced.

26. The method of claim 20, wherein expression of the biomarker is disrupted such that none of the biomarker is produced.

27. The method of claim 20, wherein the cell is chosen form a human cell, a mammalian cell, a vertebrate cell, and an invertebrate cell.

28. The method of claim 20, wherein the cell is a Chinese hamster ovary

(CHO) cell.

29. The method of claim 28, wherein the biomarker is chosen from Sen2, Akr1 b8, Anapd O, and Gjb3.

30. The method of claim 20, wherein the cell further comprises a nucleic acid sequence encoding a recombinant protein, the nucleic acid sequence being extrachromosomal or chromosomally integrated.

31 . A method for producing a recombinant protein, the method comprising expressing a nucleic acid sequence encoding the recombinant protein in a cell comprising disrupted expression of at least one biomarker chosen from Acsl3, Akr1 b8, Anapd O, Arl6ip1 , Cnih2, Ctsd, Ctsl, DerM , Dse, Ebpl, Ecm1 , Elk3, Fth1 , Gjb3, Hmoxl , Itgb1 bp1 , Ldha, Lgalsl , Lgals3, Lrpapl , Myl6b, Pit1 , Pomp, Rps26, Sen2, Sh2d3c, S100a4, Tmedl , Tnfrsf12a, Tinagl, Tnfrsf25, Trappc6b, 0610007C21 Rik, and 2610209M04Rik, wherein the cell having disrupted expression of the biomarker produces higher levels of the recombinant protein than a comparable cell not having disrupted expression of the biomarker.

32. The method of claim 31 , wherein disrupted expression of the biomarker is such that a reduced level of the biomarker is produced.

33. The method of claim 31 , wherein disrupted expression of the biomarker is such that none of the biomarker is produced.

34. The method of claim 31 , wherein expression of the biomarker is disrupted by a technique chosen from RNA interference, targeting endonuclease- mediated genome editing, and homologous recombination.

35. The method of claim 34, wherein the targeting endonuclease is a zinc finger nuclease.

36. The method of claim 31 , wherein the cell is chosen from a human cell, a mammalian cell, a vertebrate cell, and an invertebrate cell.

37. The method of claim 36, wherein the cell is a Chinese hamster ovary (CHO) cell.

38. The method of claim 38, wherein the biomarker is chosen from Sen2, Akr1 b8, Anapd O, and Gjb3.

39. The method of claim 31 , wherein the nucleic acid sequence encoding the recombinant protein is extrachromosomal or chromosomally integrated.

40. The method of claim 31 , wherein the recombinant protein is a monoclonal antibody.