Cells having gene duplications and uses thereof
Host cells having improved growth characteristics are provided. Also provided are methods of selecting, using, and making the cells.
1 . A Chinese Hamster Ovary (CHO) mammalian host cell comprising an exogenous nucleic acid and a duplication of at least one gene selected from the group consisting of: Spire1, Nars, Rps14, Smim3, Fem1c, Ppic, Lmnb1, Me2, Pias2, Sh3rf2, Rnmt, and Sehl1,
wherein the Spirel gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1; wherein the Nars gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 2; wherein the Rps14 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 3; wherein the Smim3 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 4; wherein the Fem 1c gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 5; wherein the Ppic gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 6; wherein the Lmnb 1 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 7; wherein the Me2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 8; wherein the Pias2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 9; wherein the Sh3rf2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 10; and
wherein the host cell has an improved growth characteristic as compared to an otherwise identical host cell lacking duplication of the at least one gene.
2 . The CHO host cell of claim 1 , comprising a duplication of at least two genes, wherein one of the at least two gens is selected from the group consisting of: Spire1, Nars, Rps14, and Smim3, and one of the at least two genes is selected from the group consisting of: Fem1c, Ppic, Lmnb1, Me2, Pias2, and Sh3rf2.
3 . The CHO host cell of claim 1 , comprising a duplication of at least four genes:
wherein one of the at least four genes is selected from the group consisting of: Spire1, Nars, Rps14, and Smim3;
wherein one of the at least four genes is selected from the group consisting of: Fem1c, Ppic, and Lmnb1;
wherein one of the at least four genes is selected from the group consisting of: Me2 and Pias2; and
wherein one of the at least four genes is Sh3rf2.
4 . A method of selecting a Chinese Hamster Ovary (CHO) host cell having an improved growth characteristic, the method comprising:
(a) assaying a CHO host cell comprising an exogenous nucleic acid for duplication of at least one gene selected from the group consisting of: Spire1, Nars, Rps14, Smim3, Fem1c, Ppic, Lmnb1, Me2, Pias2, Sh3rf2, Rnmt, and Sehl1,
wherein the Spirel gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1; wherein the Nars gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 2; wherein the Rps14 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 3; wherein the Smim3 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 4; wherein the Fem 1c gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 5; wherein the Ppic gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 6; wherein the Lmnb 1 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 7; wherein the Me2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 8; wherein the Pias2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 9; wherein the Sh3rf2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 10; and
(b) selecting the CHO host cell comprising duplication of the at least one gene,
wherein the assaying step (a) comprises fluorescent in situ hybridization (FISH), comparative genomic hybridization, microarray based systems, whole genome sequencing or a combination thereof, and
wherein the CHO host cell comprising duplication of the at least one gene has an improved growth characteristic as compared to an otherwise identical CHO host cell lacking duplication of the at least one gene.
5 . The method of claim 4 , wherein the CHO host cell is assayed for duplication of at least two genes and wherein one of the at least two genes is selected from the group consisting of: Spire1, Nars, Rps14, Smim3, and one of the at least two genes is selected from the group consisting of: Fem1c, Ppic, Lmnb1, Me2, Pias2, and Sh3rf2.
6 . A method for producing a recombinant protein, the method comprising:
(a) providing the CHO host cell of claim 1 , wherein the exogenous nucleic acid of the host cell encodes a recombinant protein;
(b) culturing the CHO host cell under conditions sufficient to express the recombinant protein.
7 . A method for producing a recombinant protein, the method comprising:
(a) providing a CHO host cell selected according to the method of claim 4 , wherein the exogenous nucleic acid of the host cell encodes a recombinant protein;
(b) culturing the CHO host cell under conditions sufficient to express the recombinant protein.
8 . The method of claim 6 , further comprising recovering the expressed recombinant protein.
9 . The CHO host cell of claim 1 , wherein the exogenous nucleic acid encodes a protein.
10 . The CHO host cell of claim 9 , wherein the protein is an antibody or a cytokine.
11 . A method of preparing a Chinese Hamster Ovary (CHO) host cell having an improved growth characteristic, the method comprising:
introducing an exogenous nucleic acid molecule comprising the sequence of at least one gene selected from the group consisting of: Spire1, Nars, Rps14, Smim3, Fem1c, Ppic, Lmnb1, Me2, Pias2, Sh3rf2, Rnmt, and Sehl1l into the CHO host cell,
wherein the Spirel gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1; wherein the Nars gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 2; wherein the Rps14 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 3; wherein the Smim3 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 4; wherein the Fem 1c gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 5; wherein the Ppic gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 6; wherein the Lmnb 1 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 7; wherein the Me2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 8; wherein the Pias2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 9; wherein the Sh3rf2 gene encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 10; and
wherein the host cell comprising the exogenous nucleic acid molecule has an improved growth characteristic as compared to an otherwise identical CHO host cell that does not contain the exogenous nucleic acid molecule.
12 . The method of claim 11 , wherein one or more exogenous nucleic acid molecules comprising the sequence of at least two of the at least one genes are introduced into the host cell.
13 . The method of claim 12 , wherein one of the at least two genes is selected from the group consisting of: Spire1, Nars, Rps14, Smim3, and one of the at least two genes is selected from the group consisting of: Fem1c, Ppic, Lmnb1, Me2, Pias2, and Sh3rf2.
14 . The CHO host cell of claim 1 , wherein the exogenous nucleic acid is chromosomally-integrated in a host cell chromosome.
15 . The CHO host cell of claim 1 , wherein the improved growth characteristic is greater cell count, greater viable cell count, greater cell density, or greater viable cell density of a first cell culture comprising the cell having an improved growth characteristic as compared to a second cell culture comprising the otherwise identical CHO host cell lacking duplication of the gene(s), wherein the first and second cell cultures are grown under the same conditions and for the same time period.
16 . The method of claim 7 , further comprising recovering the recombinant protein.
17 . The method of claim 7 , wherein the exogenous nucleic acid encodes a protein and wherein the protein is an antibody or a cytokine.