# Patent

## Title
Complex chromosome engineering for production of human antibodies in transgenic animals

## Abstract

The invention relates to large-scale production of human antibodies by transgenic animals with high production of fully human IgG up to >10 g/L in sera with human IgG1 subclass dominancy. This invention also supports a feasibility of complex chromosome engineering for complicated genetic studies in non-murine mammalian species.

## Background
RELATED APPLICATIONS
This application is a U.S. national phase of International Application No. PCT/US2013/053618 filed on Aug. 5, 2013, which claims benefit of U.S. Provisional Application No. 61/679,288 filed Aug. 3, 2012, both of which are incorporated by reference herein in their entirety.


BACKGROUND OF THE INVENTION
Human antibodies, also known as intravenous immunoglobulin (IVIG), obtained from donated human plasma with or without immunization of specific antigens, have been used therapeutically for many years. However, human plasma-derived WIG has also entailed substantial challenges and restrictions, mainly due to the voluntary nature of donation from uncontrollable human populations. In particular, it is difficult to robustly generate human plasma-derived IVIG against human-origin antigens, such as cancer cells, due to immune tolerance in humans. Thus, improved systems for obtaining human antibodies are needed.
SUMMARY OF THE INVENTION
In a first aspect, the invention provides a human artificial chromosome (HAC) vector comprising genes encoding:
(a) one or more human antibody heavy chains, wherein each gene encoding an antibody heavy chain is operatively linked to a class switch regulatory element;
(b) one or more human antibody light chains; and
(c) one or more human antibody surrogate light chains, and/or an ungulate-derived IgM heavy chain constant region;
wherein at least one class switch regulatory element of the genes encoding the one or more human antibody heavy chains is replaced with an ungulate-derived class switch regulatory element.
In one embodiment, the one or more human antibody heavy chains comprise a human IgG antibody heavy chain. In another embodiment, the IgG heavy chain comprises an IgG1 antibody heavy chain. In a further embodiment, the one or more human antibody heavy chains comprise a human IgA antibody heavy chain. In another embodiment, the one or more human antibody heavy chains comprise a human IgM antibody heavy chain. In a still further embodiment, the one or more human antibody heavy chains comprise IgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgE and IgD human antibody heavy chains.
In one embodiment, the HAC vector comprises a gene encoding an ungulate-derived IgM heavy chain constant region, wherein the ungulate-derived IgM heavy chain constant region is expressed as a chimera with a human IgM heavy chain variable region. In another embodiment, the ungulate-derived IgM heavy chain constant region is a bovine-derived IgM heavy chain constant region.
In a further embodiment, the one or more human antibody heavy chains comprise a human IgG antibody heavy chain, wherein a transmembrane domain and an intracellular domain of a constant region of the human IgG heavy antibody chain are replaced with a transmembrane domain and an intracellular domain of an ungulate-derived IgG antibody heavy chain constant region. In another embodiment, the human IgG antibody heavy chain comprises a human IgG1 antibody heavy chain. In a further embodiment, the ungulate-derived IgG antibody heavy chain constant region comprise a bovine-derived IgG antibody heavy chain constant region.
In one embodiment, the ungulate-derived class switch regulatory element comprises an Iγ-Sγ class switch regulatory element. In another embodiment, the Iγ-Sγ class switch regulatory element comprises Iγ1-Sγ1. In a still further embodiment, each class switch regulatory element of the genes encoding the one or more human antibody heavy chains is replaced with an ungulate-derived class switch regulatory element. In another embodiment, the ungulate-derived class switch regulatory element(s) are bovine-derived class switch regulatory elements.
In one embodiment, the HAC vector comprises one or more genes encoding a human antibody surrogate light chain selected from the group consisting of VpreB1, VpreB3 and λ5 human antibody surrogate light chains.
In another embodiment, the HAC further comprises an ungulate-derived enhancer operatively linked to one or more genes encoding the one or more human antibody heavy chains. In one embodiment, the enhancer comprises a 3′Eα enhancer.
In a second aspect, the present invention provides a transgenic ungulate comprising a HAC vector according to any embodiment or combination of embodiments of the first aspect of the invention. In one embodiment, the transgenic ungulate is a transgenic bovine.
In a third aspect, the present invention provides transgenic ungulates comprising genes integrated into its genome encoding:
(a) one or more human antibody heavy chains, wherein each gene encoding an antibody heavy chain is operatively linked to a class switch regulatory element;
(b) one or more human antibody light chains; and
(c) one or more human antibody surrogate light chains, and/or an ungulate-derived IgM heavy chain constant region;
wherein at least one class switch regulatory element of the genes encoding the one or more human antibody heavy chains is replaced with an ungulate-derived class switch regulatory element.
The transgenic ungulates of this third aspect of the invention may comprise any embodiment or combination of embodiments of genes, class switch regulatory elements, and/or enhancers as described for the HACs of the first aspect of the invention, but where the genes, class switch regulatory elements, and/or enhancers are integrated into its genome.
In a fourth aspect, the present invention provides methods of producing a human antibody, comprising:
(a) administering a target antigen to the transgenic ungulate of any embodiment or combination of embodiments of the second and third aspects of the invention to produce and accumulate human antibody specific to the target antigen in the serum or plasma of the ungulate; and
(b) recovering the human antibody specific to the target antigen from the serum or plasma of the ungulate.
In one embodiment, the recovering comprises:

    
    
        (i) isolating lymphocytes from the transgenic ungulate;
        (ii) generating a human monoclonal antibody producing hybridoma from the lymphocytes; and
        (iii) recovering human monoclonal antibody specific to the target antigen from the hybridoma.
    
    


In a further embodiment, the lymphocytes from the transgenic ungulate are isolated from lymph nodes of the transgenic ungulate. In a further embodiment, the transgenic ungulate is hyperimmunized with the target antigen.
In a fifth aspect, the invention provides compositions comprising a human antibody produced by the methods of any embodiment or combination of embodiments of the fourth aspect of the invention.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the structure of the bovine IGLJ-IGLC gene cluster and its cluster deletion strategy. (A) Genomic organization of the bovine IGLJ-IGLC gene cluster. (B) Structure of targeting vectors and a strategy for the cluster deletion. The plasmid pCλ1CAGzeoPuroloxPDT was a first knockout (KO) vector to place a loxP site 5′ outside of the IGLJ1 gene, composed of 9.9 kb and 3.1 kb genomic DNA as a long and short arm, respectively, a loxP sequence, the CAG promoter-driven zeocin-resistant gene (zeo), DT-A and promoter-less puromycin-resistant gene (puro). The plasmid pCλ5CAGloxPneoDT was a second KO vector to place another loxP site 3′ outside of the IGLC5 gene, composed of 8.7 kb and 1.5 kb genomic DNA as a long and short arm, respectively, a loxP sequence, the chicken β-actin promoter-driven neomycin-resistant gene (neo), DT-A, SV40 polyA and CAG promoter. The second KO vector was co-transfected with a Cre-expression plasmid to bring about the cluster deletion, which reconstitutes the CAG promoter-driven puro gene.
FIG. 2 shows the generation of male and female bovine IGTINF−/−IGHML1−/−IGL−/− (triple knock out, “TKO”) cell lines. (A) Breeding pedigree to establish the TKO cell lines. The male cell line 6939 and female cell line 3427 were sequentially targeted to obtain IGHM−/+IGHML1−/− and IGHM−/− animals, respectively, for the first round of breeding, which generated both male and female IGHM−/−IGHML1−/+ cell lines. These cell lines were subjected to the cluster deletion to generate IGHM−/−IGHML1−/+IGL−/+ animals for the second round of breeding, which led to the establishment of the male and female TKO cell lines. (B) Generation of male and female IGHM−/−IGHML1−/+ cell lines. In the male cell line IGHM−/+IGHML1−/− originated from the cell line 6939, the two IGHML1 alleles, U and u, and the one IGHM allele, AY, were knocked out by the targeting vectors pBCμΔNKOneo, pBCμΔKOpuro and pbCμAYKObsr, respectively. In the female cell line IGHM−/− originated from the cell line 3427, the two IGHM alleles, 10AY and 7AYJ, were knocked out by the targeting vectors pbCμAYKObsr and pbCμ7AYJKOhyg, respectively. After breeding between the male IGHM−/+IGHML1−/− and female IGHM−/− animals, each fetus was subjected to genomic PCR (AYKObsr-F2R2, ayKOhyg-F2R2, Neo-F2R2 or Puro-F2R2) to identify the genotype IGHM−/−IGHML1−/+, leading to establishment of the male and female cell lines, J481 and H412, respectively. In the genomic PCR with AYKObsr-F2R2 for H412, sequence analysis was done to confirm that both the alleles AY and 10AY were disrupted. (C) Integration of the loxP sequence 5′ outside of the IGLJ1 gene by the targeting vector pCλ1CAGzeoPuroloxPDT in the cell line J481. The occurrence of the homologous recombination was confirmed by the genomic PCR, CL1puro-F2F2, as a positive PCR. Furthermore, the negative PCR, R-F2×R-R1, was done to double check the homologous recombination because it can be only amplified from the wild type allele; J481 amplified it both from the alleles A and D, showing the double peaks (T for the allele A and G for the allele D). Colony 27 showed only “G”, demonstrating that the allele A was specifically knocked out while Colony 22 showed only “T”, demonstrating that the allele D was specifically knocked out. From colony 27, the fetal cell line, K655-1, was established, which was positive with the CL1puro-F2R2. (D) Integration of the loxP sequence 3′ outside of the IGLC5 gene by the targeting vector pCλ5(A)CAGloxPneoDT in the cell line K655-1. The occurrence of the homologous recombination was confirmed by the genomic PCR, CL5CAG-F2F2, as positive PCR. Moreover, the reconstitution of the CAG promoter-driven puro gene caused by the cluster deletion was also confirmed by the genomic PCR, CAGpuro-F3R3. The cell line G054 was used to generate calves for breeding. (E) Generation of the male and female IGHM−/−IGHML1−/−IGL−/− (TKO) cell lines. The male and female IGHM−/−IGHML1−/+IGL−/+ animals were subjected to the second round of breeding. Each fetus was examined by a series of genomic PCR, L001-F1×L002×R2 (to amplify the IGLC genes), BCμ-f2r2 (to amplify the IGHM or IGHML1 constant region gene), the cluster deletion-specific CAGpuro-F3R3 and BCμKO-F14R14 (to amplify the targeted IGHM or IGHML1 gene). The five fetal cell lines, E024A-2, A596A-1, A332A, C970 and A114A, were genotyped as shown in the table, proving to be the IGHM−/−IGHML1−/−IGL−/−.
FIG. 3 shows the concept and construction of the KcHACΔ and cKSL-HACΔ vectors. (A) Structure of the KcHACΔ and cKSL-HACΔ vectors. The KcHACΔ vector is a derivative of the original κHAC where part of the hIGHM gene constant region, the CH1 through TM domains, is bovinized with the bovine-origin sequence. Because of this modification, the KcHACΔ vector expresses the bovinized, chimeric IgM {cIgM (CH1)} protein on pre-BB cell surface. Through the bovinized CH1 domain, the cIgM (CH1) better pair with bovine surrogate light chain (bSLC)/light chain (bLC). Furthermore, the bovinized TM1-TM2 domains more efficiently interact with bovine Ig-α/β complex (bIg-α/β) for better pre-BCR/BCR signaling. The cKSL-HACΔ vector is composed of the three different human chromosome (hChr) fragments, hChr14 (14D), hChr2 and hChr22 containing the entire human IGL and surrogate light chain (hVPREB1 and hIGLL1) loci. In this vector, part of the hIGHM gene constant region, the CH2 through TM domains, is bovinized to express the cIgM (CH2) protein. At pre-B cell stage, this cIgM (CH2) may preferentially pair with human surrogate light chain (hSLC, hVPREB1/hIGLL1) to mimic human pre-BCR but with the bovinized TM1-TM2 domain interacting better with bIg-α/β for pre-BCR signal transduction. (B) Construction of the cKSL-HACΔ vector in chicken DT40 cells. The DT40 clone, SLKH18, containing the SLKH fragment where the hChr22 fragment was translocated to the hChr2 fragment, was fused with another DT40 clone, CH2D4, retaining the cIgM (CH2)-bovinized 14D vector to generate the DT40 hybrid clone cKSLD22. The presence of the two hChr fragments was confirmed by human COT1 DNA fluorescent in-situ hybridization (FISH). By introducing a Cre-expression plasmid, chromosome translocation between the two hChr fragments was induced to generate the cKSL-HACΔ vector. Three color-FISH indicates the presence of the hIGH, hIGK and hIGL loci on the cKSL-HACΔ vector. (C) Construction of the KcHACΔ vector in chicken DT40 cells.
FIG. 4 shows the characterization of the κHAC, cKSL-HACΔ and KcHAC IGHM−/−IGHML1−/− double knockout (DKO) calves. (A) Representative flow cytometry analysis of peripheral blood monocytes (PBMCs) from a series of HAC/DKO calves at newborn stage. For IgM detection, anti-hIgM or anti-bIgM antibody was used for the κHAC and cKSL-HACΔ/DKO calves or for the KcHAC/DKO calves, respectively. From left to right panels, PBMCs were stained for IgM alone, IgM/bCD21, IgM/bIgλ, IgM/bIgκ and IgM/hIgκ. Each bold number represents percentages of cells in Q1 (IgM alone) or Q2 (IgM/bCD21, IgM/bIgλ, IgM/bIgκ and IgM/hIgκ). NA; not applicable (because, at that time, the anti-bIgκ antibody was not available). (B,C) Serum concentrations of (B) total hIgG (μg/ml) and (C) fully hIgG/hIgκ (μg/ml) in a series of HAC/DKO calves at 5-6 months of age. n, number of animals analyzed for each genotype. For each genotype, values of minimum, first quartile, median, third quartile and maximum were calculated and plotted in each graph. The values of calf 468 were indicated in dashed circle. (D,E) Serum (D) fully hIgG/hIgκ (%)/total hIgG and (E) hIgG1/hIgG2 ratio in a series of HAC/DKO calves at 5-6 months of age. n, number of animals analyzed for each genotype. For each genotype, values of minimum, first quartile, median, third quartile and maximum were calculated and plotted in the left graph.
FIG. 5 shows the construction of the isHAC (isKcHACΔ) and istHAC. On either cKSL-HACΔ or KcHACΔ vector, the hIγ1-hSγ1 class switch regulatory element was bovinized to build the isHAC or isKcHACΔ vector, respectively. The istHAC vector is a derivative of the isHAC vector where the hIGHG1 gene transmembrane/cytoplasmic domains were also bovinized.
FIG. 6 shows the characterization of the isHAC/TKO, istHAC/TKO and isKcHACΔ/TKO calves. (A) Lack of the bIGL expression in the HAC/TKO calves. PBMCs from five KcHACΔ/TKO calves (Calf 1-5) at newborn stage were subjected to RT-PCR to confirm the lack of the bIGL expression. The primer pairs, bIgL-Ld-F1×bIgL-C-R and L003-F2×L004-R2, are to amplify the VJ-rearranged bIGL and constant region IGLC (bCλ) genes, respectively. The primer pair, bIgκ-FR, is to amplify the VJ-rearranged bIGK gene. N, negative control; P, positive control. (B) Representative flow cytometry analysis of PBMCs from a series of HAC/TKO calves at newborn stage. For IgM detection, anti-hIgM or anti-bIgM antibody was used for the isHAC, istHAC and cKSL-HACΔ/TKO calves or for the isKcHACΔ and KcHACΔ/TKO calves, respectively. From left to right panels, PBMCs were stained for IgM alone, IgM/bCD21, IgM/bIgλ, IgM/bIgκ and IgM/hIgκ. Each bold number represents percentages of cells in Q1 (IgM alone) or Q2 (IgM/bCD21, IgM/bIgλ, IgM/bIgκ and IgM/hIgκ). (C) Box-whisker plots of serum concentrations of total hIgG (g/l) in a series of HAC/TKO and HAC/DKO calves at 5-6 months of age. A, cKSL-HACΔ/TKO (n=8); B, isHAC/TKO (n=12); C, istHAC/TKO (n=8); D, KcHACΔ/TKO (n=8); E, isKcHACΔ/TKO (n=12); F, cKSL-HACΔ/DKO (n=33); G, KcHAC/DKO (n=12); H, κHAC/DKO (n=8). Dots represent outliers. The value of calf 468 was indicated with an arrow. For each genotype, values of min, first quartile, median, third quartile and max were calculated and plotted in each graph. (D) Panel shows 95% family-wise confidence level in each pair comparison. (E) Box-whisker plots of serum concentrations of fully hIgG/hIgκ (g/l) in a series of HAC/TKO and HAC/DKO calves at 5-6 months of age. A, cKSL-HACΔ/TKO (n=8); B, isHAC/TKO (n=12); C, istHAC/TKO (n=8); D, KcHACΔ/TKO (n=8); E, isKcHACΔ/TKO (n=12); F, cKSL-HACΔ/DKO (n=33); G, KcHAC/DKO (n=12); H, κHAC/DKO (n=8). Dots represent outliers. The value of calf 468 was indicated with an arrow. For each genotype, values of min, first quartile, median, third quartile and max were calculated and plotted in each graph. (F) Panel shows 95% family-wise confidence level in each pair comparison. (G) Box-whisker plots of serum fully hIgG/hIgκ (%)/total hIgG in a series of HAC/TKO and HAC/DKO calves at 5-6 months of age. Dots represent outliers. The value of calf 468 was indicated with an arrow. For each genotype, values of min, first quartile, median, third quartile and max were calculated and plotted in each graph. (H) Panel shows 95% family-wise confidence level in each pair comparison. n, number of animals analyzed for each genotype. (I) Box-whisker plots of hIgG1/hIgG2 ratio in a series of HAC/TKO and HAC/DKO calves at 5-6 months of age. Dots represent outliers. A, cKSL-HACΔ/TKO (n=8); B, isHAC/TKO (n=12); C, istHAC/TKO (n=8); D, KcHACΔ/TKO (n=8); E, isKcHACΔ/TKO (n=12); F, cKSL-HACΔ/DKO (n=33); G, KcHAC/DKO (n=12); H, κHAC/DKO (n=8). For each genotype, values of min, first quartile, median, third quartile and max were calculated and plotted in the left graph. (J) Panel shows 95% family-wise confidence level in each pair comparison in difference in proportions of hIgG1-dominancy. (K) The table shows actual values for each genotype. (L) Anti-human carcinoma hIgG/hIgκ response in a series of HAC/TKO and HAC/DKO calves, following two times vaccinations (V2) of human oral squamous cell carcinoma. The percentages of bold rectangle area shows percentages of the human carcinoma cells doubly positive with hIgG and hIgκ derived from serum of each animal at day 9-10 after V2, where serum dilution factor is 1:1280. A separated panel labeled as “V1D0” is flow cytometry result of the human carcinoma cells stained with serum of the istHAC/TKO calf 2 at day 0 after V1 (V1D0), where serum dilution factor is 1:1280.
FIG. 7 shows comparative genomic hybridization (CGH) analysis on fibroblasts derived from the κHAC/IGHM−/−IGHML1−/− (DKO) fetuses and calf 468. More extensive analysis of calf 468 using CGH analysis on the κHAC vector present in the cell line that generated calf 468 showed some distinct structural alteration. A254-2 is the fetal fibroblast cell line that generated calf 468. A254-2, G827-1, K439-1 and K439-2 were generated through independent MMCT events of the κHAC vector from the CHO cell line κC1-1 to DKO cell lines. DNA from the fetal cell line K439-1 was used as a reference. Only A254-2 and the calf 468 showed the distinct CGH pattern around the 3′ Eα2 region on the hChr14 (dashed circle).
FIG. 8 shows DNA sequence alignment between the bovine IGLJ2-IGLC2 and IGLJ3-IGLC3 genes. (A) Intron DNA sequence alignment between the bovine IGLJ2-IGLC2 and IGLJ3-IGLC3 genes. “JL2-CL2” (SEQ ID NO: 147) and “JL3-CL3” (SEQ ID NO: 148) corresponds to intronic sequence of the IGLJ2-IGLC2 and IGLJ3-IGLC3 genes, respectively. (B) 3′UTR DNA sequence alignment between the bovine IGLC2 and IGLC3 genes. “bCL2” (SEQ ID NO: 149) and “bCL3” (SEQ ID NO: 150) corresponds to 3′UTR sequence of the IGLC2 and IGLC3 genes, respectively.
FIG. 9 shows the deduced structure of the bovine IGH gene cluster on the bChr21. A BAC clone 227-A16 seemed to contain part of the IGH variable region and the IGHML1 through the Cγ1 region. A BAC clone 517-B22 appeared to cover the IGHM through the Cα region. A BAC clone 382-F19 is likely to include the Cγ2 through the 3′Eα region. The size of the three BAC clones contig is estimated to be around 380 kb in length.
FIG. 10 shows genotyping of the IGHM−/−IGHML1−/−IGL−/− (TKO) cell lines. To confirm the IGHM−/−IGHML1−/− (DKO) genotype, the negative PCR, BCμ-f2r2, was performed because the presence of KO cassettes inhibits the amplification. As a positive PCR, BCμKO-F14R14, was implemented. For the IGL−/− genotype, the negative PCR, L001-F×L002-R, was done to confirm the absence of the IGLC genes. At the same time, the positive PCR, CAGpuro-F3R3, specific to the cluster deletion was carried out.
FIG. 11 shows the amino acid sequence alignment of human, bovine and mouse (A) IgM (human SEQ ID NO: 151, bovine SEQ ID NO: 152 and mouse SEQ ID NO: 153); (B) VpreB1 (human SEQ ID NO: 154, bovine SEQ ID NO: 155 and mouse SEQ ID NO: 156); (C) λ5 (human SEQ ID NO: 157, bovine SEQ ID NO: 158 and mouse SEQ ID NO: 159), (D) Ig-α (human SEQ ID NO: 160, bovine SEQ ID NO: 161 and mouse SEQ ID NO: 162) and (E) Ig-β (human SEQ ID NO: 163, bovine SEQ ID NO: 164 and mouse SEQ ID NO: 165) among human, bovine and mouse. Each percentage shows homology. h, human, b, bovine, m; mouse. Shaded amino acid depicts a different one from human.
FIG. 12 shows genotyping of the cKSL-HACΔ and KcHACΔ vector, and characterization of the cKSL-HACΔ/DKO calves. (A) Extensive genomic PCR for genotyping of the cKSL-HACΔ vector. Location of each genomic PCR primer pair is depicted in relation to the cKSL-HACΔ vector structure. (B) Extensive genomic PCR for genotyping of the KcHACΔ vector. Location of each genomic PCR primer pair is depicted in relation to the KcHACΔ vector structure. (C) CGH analysis on the CHO clones containing either the cKSL-HACΔ, KcHACΔ or KcHAC vector. In the upper panel, the cKSL-HACΔ containing CHO clones (cKSLDC6, 15, 23) were compared with the κC1-1 containing the κHAC and the KCF4 containing the KcHAC vector. There was no apparent structural difference among all the HACs, except for potential some amplification of DNA around the 3′Ea2 region (dashed circled) unique to the SC20-based HACs, κHAC and KcHAC. DNA from cKSLDC15 was used as a reference. The lower panel shows CGH pattern among three different CHO clones containing the KcHACΔ vector, where DNA from KCDC1 was used as a reference. There was no apparent structural difference of the KcHACΔ among the three cell lines. (D) Transcription of the human IGL, VPREB1 and IGLL1 genes in the cKSL-HACΔ/DKO calves. PBMCs from three cKSL-HACΔ/DKO calves (Calf 1-3) at newborn stage were subjected to RT-PCR to confirm expression of the human IGL, VPREB1 and IGLL1 genes. N, negative control; P, positive control.
FIG. 13 shows the alignment of the sequence relevant to IgG1 class switch regulation and secretion between bovine and human. (A) Alignment of DNA sequence of the Iγ1 (human Igamma1 SEQ ID NO: 166, bovine Igamma1 SEQ ID NO: 167), Iγ2 (human Igamma 2 SEQ ID NO: 168, bovine Igamma2 SEQ ID NO: 169) and Iγ3 (human Igamma 3 SEQ ID NO: 170, bovine Igamma3 SEQ ID NO: 171) ECS (evolutionary conserved sequence) elements between human and bovine. Shaded nucleotide base depicts a different one from the human Iγ1 sequence. Binding sites of KB3 (kappa B3), KB4 (kappa B4), KB5 (kappa B5), ISRE (interferon stimulated response element), C-EBP (CCAAT-enhancer binding protein), BSAP (B-cell lineage specific activator protein) and GAS (Gamma interferon activation site) are indicated by line rectangle. (B) Dot plot alignment between the human and bovine Sγ1 sequence. (C) Amino acid sequence alignment of the IgG1 transmembrane/cytoplasmic domains between human (SEQ ID NO: 172) and bovine (SEQ ID NO: 173). Shaded amino acid depicts a different one from human.
FIG. 14 shows serum concentrations of fully hIgG/hIgκ (g/L) in a series of HAC/TKO calves at 5-6 months of age. n, number of animals analyzed for each genotype. For each genotype, individual value was plotted, based on the TKO cell line used.
FIG. 15 shows serum fully hIgG/bIgκ (%)/total hIgG in a series of HAC/TKO and HAC/DKO calves at 5-6 months of age. n, number of animals analyzed for each genotype. For each genotype, values of min, first quartile, median, third quartile and max were calculated and plotted in the left graph.
FIG. 16 shows anti-human carcinoma hIgG/hIgκ response in a series of HAC/TKO and HAC/DKO calves, following two times vaccinations (V2) of human oral squamous cell carcinoma. Percentages of hIgG/hIgκ-double positive human carcinoma cells was plotted from each animal immunized, at day 9-10 after V2 at indicated serum dilution factors.
FIG. 17 shows construction of 14D vector. (A) A flow of the 14D vector construction. The first lox511 was integrated at the AL512355 on the intact hChr14 to generate I355-2. Then, the second lox511 was placed at the AL391156 to generate I156-10. Cre introduction brought about a big DNA deletion on the chromosome to generate D8. 14D1 was built by integrating the loxP at RNR2 locus. Subsequently, the cIgM (CH1) or cIgM (CH2) bovinization generated CH1D2 or CH2D4, which was used for the KcHACΔ or cKSL-HACΔ vector construction, respectively. (B) Detailed strategy of the 14D vector construction. The targeting vector pSC355CAGlox511hisDDT consists of 8.2 kb and 2.0 kb genomic DNA as a long and short arm, respectively, CAG promoter, lox511, SV40 polyA signal, the chicken β-actin promoter-driven hisD gene and DT-A gene, which was used to integrate the lox511 sequence at the AL512355,  ̃300 kb centromeric to the IGHA2 locus. Another targeting vector p14CEN(FR)hygpurolox511DT is composed of 8.2 kb and 1.8 kb genomic DNA as a long and short arm, respectively, the promoter-less puro gene, lox511, chicken β-actin promoter-driven hyg gene and DT-A gene, which was used to integrate the lox511 sequence at the AL391156. Cre introduction induced the big DNA deletion ( ̃85 Mb) between the two lox511 sites to generate the 14D. As a result of the big deletion, the CAG promoter-driven puro gene was reconstituted and selected by puromycin. Puromycin-resistant cells were subjected to genomic PCR, CAGpuro-F3R3, to confirm the deletion at molecular level. The cells were also sensitive to hygromycin B or histidinol due to the deletion. (C) The IgM bovinization for the CH1D and CH2D. The bovinization vector pCH1CAGzeo(R)DT(F) comprises 7.4 kb and 1.7 kb human genomic DNA as a long and short arm, respectively, 6 kb of the bovine IGHM constant region genomic DNA covering the CH1 through TM2 domains where the floxed, CAG promoter-driven zeo gene cassette was integrated between the CH4 and TM1 intron, and DT-A gene. After the homologous recombination, part of the hIGHM constant region, the CH1 through TM2 domains, was bovinized on the CH1D. Another bovinization vector pCH2CAGzeoDT(F) contains 7.2 kb and 1.7 kb human genomic DNA as a long and short arm, respectively, 5.4 kb of the bovine IGHM constant region genomic DNA covering the CH2 through TM2 domains where the floxed, CAG promoter-driven zeo gene cassette was integrated between the CH4 and TM1 intron, and DT-A gene. After the homologous recombination, part of hIGHM constant region, the CH2 through TM2 domains, was bovinized on the CH2D. (D) Genotyping of each targeting event. At the AL512355, SC355KO-F2R2 was used as a positive PCR specific to the homologous recombination along with the negative PCR, 355N-FR, which was prohibited by the presence of KO cassette. At the AL391156, 14CENKO-F3R3 was used as a positive PCR specific to the homologous recombination along with the negative PCR, 14CEN(N)-F2R2, which was prohibited by the presence of KO cassette. For the CH1D modification {e.g., cIgM (CH1) bovinization}, cHAC-F3F3 was used as a positive PCR specific to the homologous recombination along with CH1 5′-FR and cHAC 3′-FR to check the junction sequences between the human and bovine sequence. Similarly, for the CH2D modification {e.g., cIgM (CH2) bovinization}, cHAC-F3F3 was used as a positive PCR specific to the homologous recombination along with CH2 5′-FR and cHAC 3′-FR to check the junction sequences between the human and bovine sequence. (E) Human COT-1 FISH between the intact hChr14 and the shortened hChr14 fragment.
FIG. 18 shows modification of the hChr2 fragment. (A) Generation of clone κZ7. The clone κTL1 was transfected with the targeting vector pTELCAGzeoCD8A to replace the puro cassette with zeo cassette. The targeted event was confirmed by genomic PCR, CD8AKO-F2R2. (B) Truncation of the hChr2 fragment to generate clone K53. The clone κTL1 was transfected with the targeting vector pTEL′hisDpurolox2272F9R9, composed of 7.4 kb of genomic DNA as a homologous arm, promoter-less puro gene, lox2272, the chicken β-actin promoter-driven hisD gene and human telomeric repeat sequence (TEL), to truncate the hChr2 fragment and to integrate the lox2272 at the AC104134.
FIG. 19 shows modification of the hChr22 fragment. (A) Generation of clone STL54. The intact hChr22 retained in a clone 52-18 was truncated at the AP000350 by the targeted truncating vector pTELCAGzeoSLFR to generate ST13. Subsequently, the lox2272 sequence was integrated at the AP000553 by the targeting vector p553CAGlox2272bsrDT to generate STL54. (B) Truncation of the hChr22 at the AP000350. The locus AP000350 is located  ̃70 kb telomeric to the hVPREB3 locus. The truncating vector pTELCAGzeoSLFR consists of 7.4 kb genomic DNA as a homologous arm, the CAG promoter-driven zeo gene and human telomeric repeat sequence (TEL). After the homologous recombination, the hChr22 was truncated at the AP000350. (C) Integration of the lox2272 site at the AP000553. The targeting vector p553CAGlox2272bsrDT comprises 6.9 kb and 2.8 kb genomic DNA as a long and short arm, CAG promoter, lox2272, SV40 polyA signal, the chicken β-actin promoter-driven bsr gene and DT-A gene. 553KO-F3R3 was used as a positive PCR specific to the homologous recombination along with the negative PCR, 553-F4R4, which was prohibited by the presence of KO cassette.
FIG. 20 shows construction of the SLKH fragment. (A) A flow of generation of the SLKH fragment. The two DT40 clones K53 and STL54 were subjected to whole cell fusion to generate a DT40 hybrid clone SLK2. Then, the Cre recombinase was introduced to induce the chromosome translocation between the two hChr fragments that built the SLKH fragment. As a result of the chromosome translocation, the CAG promoter-driven puro gene was reconstituted and selected by puromycin. Furthermore, the occurrence of translocation was confirmed by genomic PCR, CAGpuro-F3R3. From the DT40 hybrid clone SLKH6, the SLKH fragment was transferred to a plane DT40 cell by MMCT to generate SLKD18. (B) Multi-color FISH on the SLK2, SLKH6 and SLKD18. The SLK2 was simply stained with human COT-1 probe, confirming the presence of the longer hChr2 fragment and shorter hChr22 fragment. For the SLKH6 and SLKD18, two-color FISH was implemented. In the SLKH6, the two reciprocally translocated hChr fragments were seen; the longer one was the SLKH fragment. In the SLKD18, just the single SLKH fragment was present.
FIG. 21 shows occurrence of the chromosome inversion on the CH2D. A leaky recombination between the loxP at the RNR2 locus and the lox511 at the deletion junction site AP391156/AP512355 caused the inversion that also reconstituted the CAG promoter-driven GFP gene, leading to the higher GFP expression than the PGK promoter-driven GFP gene from the cKSL-HACΔ vector. The inversion was confirmed by genomic PCR, STOPpuro-F2R2 and GFP2×CAGpuro-F3.
FIG. 22 shows construction of the isHAC and isKcHACΔ vectors. (A) A flow of the isHAC and isKcHACΔ vector construction. The bovinizing vector pCC1BAC-isHAC is a BAC-based one (backbone is pCC1BAC vector), consisting of 10.5 kb and 2 kb of genomic DNA as a long and short arm, respectively, 9.7 kb of the bovine genomic DNA covering the bovine Iγ1-Sγ1 and its surrounding region to replace the human corresponding 6.8 kb of Iγ1-Sγ1 region, the chicken β-actin promoter-driven neo gene flanked by FRT sequence and DT-A gene. After the targeted bovinization, the neo cassette is removed by FLP introduction. (B) Detailed information of the targeting vector pCC1BAC-isHAC. The 2 kb of Afe I-Bam HI fragment and 10.5 kb of Apa I-Hpa I fragment for a short arm and long arm were obtained from clone h10 and clone h18/h20, respectively, derived from λ, phage genomic library constructed from CHO cells containing the κHAC by screening using a probe around the human Iγ1-Sγ1 region. The 9.7 kb fragment (5′ end through Bsu36 I) was obtained from clone b42 derived from the λ phage bovine genomic library. (C) Genotyping of the bovinized Iγ1-Sγ1 region. Basically, five sets of genomic PCR were implemented, as indicated. iscont1-F1/R1 is a positive PCR specific to the homologous recombination. iscont1-F1×hIgG1-R10 is a negative PCR that is prohibited by the presence of the neo cassette. isHAC-Sw-dig-F5/R3 and isHAC-TM-dig-F3/R2 are for structural integrity check of their corresponding region, digested by Bam HI+Pvu II and Age I, Sma I or Pvu II, respectively. bNeo 5′-R×bIgG1-5′-seq-R6 is to confirm the presence of FRT sequence. (D) Genotyping after the FLP-FRT deletion of the neo cassette. (E) Extensive genomic PCR for genotyping of the isHAC vector. Location of each genomic PCR primer pair is depicted in relation to the isHAC vector structure. (F) CGH analysis among three different CHO clones containing the isHAC vector. DNA from isC1-133 was used as a reference. There was no apparent structural difference of the isHAC among the three cell lines. (G) Extensive genomic PCR for genotyping of the isKcHACΔ vector. Location of each genomic PCR primer pair is depicted in relation to the isKcHACΔ vector structure. (H) CGH analysis among three different CHO clones containing the isKcHACΔ vector. DNA from isKCDC15-8 was used as a reference. There was no apparent structural difference of the isKcHACΔ among the three cell lines.
FIG. 23 shows construction of the istHAC vector. (A) A flow of the istHAC vector construction. The attP sequence is integrated at 5′ side of the hIγ1 exon 1 and 3′ side of the hIGHG1 TM2 by the targeting vectors phIγ1FRTCAGattPhisDDT and phγ1TMNeoattPDT, respectively. Then, the replacement vector pBAC-istHAC is introduced with the φC31 recombinase to bring about the attP/attB recombination to replace the flanked region. The successful replacement causes the CAG promoter-driven DsRed gene to be reconstituted to provide red fluorescence for sorting. Finally, the DsRed cassette is removed by the FLP expression. (B) Integration of the attP sequence at 3′ side of the hIGHG1 TM2. The targeting vector phγ1TMNeoattPDT consists of 6.3 kb and 1.2 kb of genomic DNA as a long and short arm, the chicken β-actin promoter-driven neo gene, attP and DT-A gene. hg1TMneoattP-F1/R1 was used as a positive PCR specific to the homologous recombination along with the negative PCRs, hIgG1-F25/R23 and hg1TMneg-F3/R3, which were prohibited by the presence of KO cassette. hIgG1TM-dig-F1/R2, followed by Sma I or Age I digestion, was employed to check structural integrity of the corresponding region. (C) Integration of the attP sequence at 5′ side of the hIγ1 exon 1. The targeting vector phIγ1FRTCAGattPhisDDT comprises 9.6 kb and 1.8 kb of genomic DNA as a long and short arm, the chicken β-actin promoter-driven hisD gene, attP, CAG promoter, FRT and DT-A gene. hg1FRTCAGattPhisD-F1/R1 was used as a positive PCR specific to the homologous recombination along with the negative PCR, iscont1-F1×hIgG1-R10, which was prohibited by the presence of KO cassette. (D) The big DNA replacement mediated by attP-attB recombination. The replacement vector pBACistHAC is made of 18.1 kb of the chimeric genomic DNA (the bIγ1-bSγ1+the hIGHG1 CH1 through CH3+bIGHG1 TM1-TM2), the promoter-less DsRed, FRT and two flanking attB sequences. The DNA replacement by the φC31 expression was confirmed by DsRed expression and genomic PCR, CAGDsRed-F2/R2 and bIgG1-3′-SeqF3×hIgG1-R15, to check generation of the attR and attL, respectively. (E) Genotyping after the FLP-FRT deletion of the DsRed cassette. (F) Extensive genomic PCR for genotyping of the istHAC vector. Location of each genomic PCR primer pair is depicted in relation to the istHAC vector structure. (G) CGH analysis among three different CHO clones containing the istHAC vector. DNA from istC1-6 was used as a reference. There was no apparent structural difference of the istHAC among the three cell lines.
FIG. 24 shows probe design for CGH, based on the deduced cKSL-HACΔ vector sequence. For the hChr14, hChr2 and hChr22 fragment sequence, the AB019437 to AL512355, the AC113612 to AC104134, and the AP000553 to AP000350, respectively, were assembled and linked with artificial “NNN . . . N” to create the 4,932,030 by DNA sequence as the deduced cKSL-HACΔ vector sequence.
FIG. 25 shows model of interspecies-incompatibilities at two levels in Tc bovine B cells. One is at protein-protein interaction, such as pre-BCR/BCR structure (e.g. pairing between human IgM and bovine surrogate/orthodox light chain, interaction between human IgM/IgG1 and bovine Ig-α/β). Another one is at DNA-protein interaction, such as between human Iγ1-Sγ1 DNA sequence and bovine cytokine/activator-induced bovine DNA binding proteins. The former is addressed by KcHAC(Δ) and cKSL-HACΔ (also by isHAC, istHAC and isKcHACΔ). The latter is addressed by isHAC, istHAC and isKcHACΔ.
FIG. 26 shows an analysis of Iγ1-Sγ1 region of bovine (SEQ ID NO: 182), horse (SEQ ID NO: 185) and porcine (SEQ ID NO: 186). (A) Comparison between bovine and porcine Iγ1-Sγ1 indicates some homology between bovine and porcine Iγ1 regions (oval), with a potential ECS circled in (B). (C) Comparison between bovine and horse Iγ1-Sγ1 indicates some homology between bovine and horse Iγ1 regions (oval). (D) Comparison between horse and porcine Iγ1-Sγ1 indicates some homology between horse and porcine Iγ1 regions (oval).
FIG. 27 shows that ECS of the Iγ1 region is well conserved. (A) Multiple sequence alignment of ECS of Iγ1 in human (SEQ ID NO: 166), bovine (SEQ ID NO: 187), pig (SEQ ID NO: 189) and horse (SEQ ID NO: 188). (B) Multiple sequence alignment of ECS of Iγ1 in ungulates.
FIG. 28 shows a multiple sequence alignment of IgM in ungulates. Sheep (SEQ ID NO: 174), bovine (SEQ ID NO: 152), pig (SEQ ID NO: 175) and horse (SEQ ID NO: 176).
FIG. 29 shows the bovinization of HAC with bovine Ig heavy chain 3′ enhancer. (A) Conservation of structure among human, bovine and mouse 3′ E-alpha enhancers. (B) Indicates region containing bovine 3′E that was used for bovinization of 3′Ealpha1 on HAC. (C) Bovine genomic fragment used for bovinization of 3′alpha1 on HAC. (D) Demonstrates the construction of mu-HAC. (E) Structural integrity of HAC was confirmed after attP/attB recombination.
FIG. 30 shows a multiple sequence alignment of IgG1 amino acid sequences in ungulates and human. Bovine (SEQ ID NO: 196), horse (SEQ ID NO: 197), pig (SEQ ID NO: 198) and human (SEQ ID NO: 199).
FIG. 31 shows the human-bovine chimeric IgM (CH2-TM2 bovinized IgM)-cIgM(CH2) sequence (SEQ ID NO: 200).



DETAILED DESCRIPTION OF THE INVENTION
All references cited are herein incorporated by reference in their entirety. Within this application, unless otherwise stated, the techniques utilized may be found in any of several well-known references such as: Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press, Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney. 1987. Liss, Inc. New York, N.Y.), Gene Transfer and Expression Protocols, pp. 109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.).
As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. “And” as used herein is interchangeably used with “or” unless expressly stated otherwise.
All embodiments of any aspect of the invention can be used in combination, unless the context clearly dictates otherwise.
Unless the context clearly requires otherwise, throughout the description and the claims, the words ‘comprise’, ‘comprising’, and the like are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense; that is to say, in the sense of “including, but not limited to”. Words using the singular or plural number also include the plural and singular number, respectively. Additionally, the words “herein,” “above,” “below,” and words of similar import, when used in this application, shall refer to this application as a whole and not to any particular portions of the application.
The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While the specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize.
In a first aspect, the invention provides a human artificial chromosome (HAC) vector comprising genes encoding:
(a) one or more human antibody heavy chains, wherein each gene encoding an antibody heavy chain is operatively linked to a class switch regulatory element;
(b) one or more human antibody light chains; and
(c) one or more human antibody surrogate light chains, and/or an ungulate-derived IgM heavy chain constant region;
wherein at least one class switch regulatory element of the genes encoding the one or more human antibody heavy chains is replaced with an ungulate-derived class switch regulatory element.
The HAC vectors of the invention can be used, for example, for large-scale production of fully human antibodies by transgenic animals, as described for the methods of the invention. As shown in the examples that follow, the HAC vectors can be used to produce unexpectedly high levels of antigen-specific polyclonal antibodies in ungulates, relative to previous HACs.
In the present invention, the term “HAC vector” means a vector which comprises at least a human chromosome-derived centromere sequence, a telomere sequence, and a replication origin, and may contain any other sequences as desired for a given application. When present in a host cell, the HAC vector exists independently from a host cell chromosome the nucleus. Any suitable methods can be used to prepare HAC vectors and to insert nucleic acids of interest into the HAC, including but not limited to those described in the examples that follow. The HAC vector is a double stranded DNA vector, as is known to those of skill in the art.
The HAC vector of the present invention comprises one or more genes encoding a human antibody heavy chain. Any human antibody heavy chain or combinations of human antibody heavy chains in combination may be encoded by one or more nucleic acids on the HAC. In various embodiments, 1, 2, 3, 4, 5, 6, 7, 8, or all 9 of human antibody heavy chains IgM, IgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgE and IgD may be encoded on the HAC in one or more copies. In one embodiment, the HAC comprises a human IgM antibody heavy chain encoding gene, alone or in combinations with 1, 2, 3, 4, 5, 6, 7, or the other 8 human antibody chain encoding genes. In one preferred embodiment, the HAC comprises a gene encoding at least a human IgG1 antibody heavy chain; in this embodiment, it is further preferred that the HAC comprises a gene encoding a human IgM antibody heavy chain or a gene encoding a human IgM antibody heavy chain that has been chimerized to encode an ungulate-derived IgM heavy chain constant region (such as a bovine heavy chain constant region). In another embodiment, the HAC comprises a gene encoding at least a human IgA antibody heavy chain; in this embodiment, it is further preferred that the HAC comprises a gene encoding a human IgM antibody heavy chain or a gene encoding a human IgM antibody heavy chain that has been chimerized to encode an ungulate-derived IgM heavy chain constant region (such as a bovine heavy chain constant region). In another preferred embodiment, the HAC comprises genes encoding all 9 antibody heavy chains, and more preferably where the gene encoding a human IgM antibody heavy chain has been chimerized to encode an ungulate-derived IgM heavy chain constant region. In another embodiment, the HAC may comprise a portion of human chromosome 14 that encodes the human antibody heavy chains. The variable region genes and the constant region genes of the human antibody heavy chain form a cluster and the human heavy chain locus is positioned at 14q32 on human chromosome 14. In one embodiment, the region of human chromosome 14 inserted in the HAC comprises the variable region and the constant region of the human antibody heavy chains from the 14q32 region of human chromosome 14.
In the HAC vectors of the present invention, at least one class switch regulatory element of the human antibody heavy chain encoding nucleic acid is replaced with an ungulate-derived class switch regulatory element. The class switch regulatory element refers to nucleic acid which is 5′ to an antibody heavy chain constant region. Each heavy chain constant region gene is operatively linked with (i.e.: under control of) its own switch region, which is also associated with its own I-exons. Class switch regulatory elements regulate class switch recombination and determine Ig heavy chain isotype. Germline transcription of each heavy chain isotype is driven by the promoter/enhancer elements located just 5′ of the I-exons and those elements are cytokine or other activator-responsive. In a simple model of class switch, the specific activators and/or cytokines induce each heavy chain isotype germline transcription from its class switch regulatory element (i.e., activator/cytokine-responsive promoter and/or enhancer). Class switch is preceded by transcription of I-exons from each Ig heavy (IGH) locus-associated switch region. As each heavy chain constant region gene is linked with its own switch region.
Any suitable ungulate-derived class switch regulatory element can be used. As used herein, “ungulates” may be any suitable ungulate, including but not limited to bovine, pig, horse, donkey, zebra, deer, oxen, goats, sheep, and antelope. For example, the human heavy chain gene isotypes listed below has the following class switch regulatory elements:
IgM: Iμ-Sμ,
IgG1: Iγ1-Sγ1,
IgG2: Iγ2-Sγ2,
IgG3: Iγ3-Sγ3,
IgG4: Iγ4-Sγ4,
IgA1: Iα1-Sα1,
IgA2: Iα2-Sα2, and
IgE: Iε-Sε.
In various embodiments, 1, more than 1, or all of the human antibody heavy chain genes on the HAC have their class switch regulatory element replaced with an ungulate-derived class switch regulatory element, including but not limited to ungulate Iμ-Sμ, Iγ-Sγ, Iα-Sα, or Iε-Sε, class switch regulatory elements. In one embodiment, an Iγ1-Sγ1 human class switch regulatory element for human IgG1 heavy chain encoding nucleic acid on the HAC (such as that in SEQ ID NO: 183) is replaced with an ungulate Iγ1-Sγ1 class switch regulatory element. Exemplary ungulate Iγ1-Sγ1 class regulatory switch elements include a bovine IgG1 Iγ1-Sγ1 class switch regulatory element (SEQ ID NO: 182), a horse Iγ1-Sγ1 class switch regulatory element (SEQ ID NO: 185), and a pig Iγ1-Sγ1 class switch regulatory element (SEQ ID: 186). However, it is not necessary to replace the human class switch regulatory element with an ungulate class switch regulatory element from the corresponding heavy chain isotype. Thus, for example, an Iγ3-Sγ3 human class switch regulatory element for human IgG3 heavy chain encoding nucleic acid on the HAC can be replaced with an ungulate Iγ1-Sγ1 class switch regulatory element. As will be apparent to those of skill in the art based on the teachings herein, any such combination can be used in the HACs of the invention.
In another embodiment, the HAC comprises at least one ungulate enhancer element to replace an enhancer element associated with one or more human antibody heavy chain constant region encoding nucleic acids on the HAC. There are two 3′ enhancer regions (Alpha 1 and Alpha 2) associated with human antibody heavy chain genes. Enhancer elements are 3′ to the heavy chain constant region and also help regulate class switch. Any suitable ungulate enhancer can be used, including but not limited to 3′Eα enhancers. Non-limiting examples of 3′ Eα enhancers that can be used include 3′Eα, 3′Eα1, and 3′Eα2. Exemplary 3′Eα enhancer elements from bovine that can be used in the HACs and replace the human enhancer include, but are not limited to bovine HS3 enhancer (SEQ ID NO: 190), bovine HS12 enhancer (SEQ ID NO: 191), and bovine enhancer HS4. This embodiment is particularly preferred in embodiments wherein the HAC comprises the variable region and the constant region of the human antibody heavy chains from the 14q32 region of human chromosome 14.
The HAC vectors of the present invention may comprise one or more genes encoding a human antibody light chain. Any suitable human antibody light chain-encoding genes can be used in the HAC vectors of the invention. The human antibody light chain includes two types of genes, i.e., the kappa/K chain gene and the lambda/chain gene. In one embodiment, the HAC comprises genes encoding both kappa and lambda, in one or more copies. The variable region and constant region of the kappa chain are positioned at 2p11.2-2p12 of the human chromosome 2, and the lambda chain forms a cluster positioned at 22q11.2 of the human chromosome 22. Therefore, in one embodiment, the HAC vectors of the invention comprise a human chromosome 2 fragment containing the kappa chain gene cluster of the 2p11.2-2p12 region. In another embodiment, the HAC vectors of the present invention comprise a human chromosome 22 fragment containing the lambda chain gene cluster of the 22q11.2 region.
In another embodiment, the HAC vector comprises at least one gene encoding a human antibody surrogate light chain. The gene encoding a human antibody surrogate light chain refers to a gene encoding an imaginary antibody light chain which is associated with an antibody heavy chain produced by a gene reconstitution in the human pro-B cell to constitute the pre-B cell receptor (preBCR). Any suitable human antibody surrogate light chain encoding gene can be used, including but not limited to the VpreB1 (SEQ ID NO: 154), VpreB3 (SEQ ID NO: 178) and λ5 (also known as IgLL1, SEQ ID NO: 157) human antibody surrogate light chains, and combinations thereof. The VpreB gene and the λ5 gene are positioned within the human antibody lambda chain gene locus at 22q11.2 of the human chromosome 22. Therefore, in one embodiment the HAC may comprise the 22q11.2 region of human chromosome 22 containing the VpreB gene and the λ5 gene. The human VpreB gene of the present invention provides either or both of the VpreB1 gene (SEQ ID NO: 154) and the VpreB3 (SEQ ID NO: 178) gene and in one embodiment provides both of the VpreB1 gene and the VpreB3 gene.
In yet another embodiment, the HAC vector comprises a gene encoding an ungulate-derived IgM heavy chain constant region. In this embodiment, the IgM heavy chain constant region is expressed as a chimera with the human IgM antibody heavy chain variable region. Any suitable ungulate IgM heavy chain antibody constant region encoding nucleic acid can be used, including but not limited to bovine IgM, (SEQ ID NO: 152), horse IgM, (SEQ ID NO: 176), sheep IgM, (SEQ ID NO: 174), and pig IgM, (SEQ ID NO: 175). In one embodiment, the chimeric IgM comprises the sequence in SEQ ID NO: 200. Pre-BCR/BCR signaling through the IgM heavy chain molecule promotes proliferation and development of the B cell by interacting with the B cell membrane molecule Ig-alpha/Ig-beta to cause a signal transduction in cells. Transmembrane region and/or other constant region of IgM are considered to have important roles in the interaction with Ig-alpha/Ig-beta for signal transduction. Examples of the IgM heavy chain constant regions include nucleic acids encoding constant region domains such as CH1, CH2, CH3, and CH4, and the B-cell transmembrane and cytoplasmic domains such as TM1 and TM2. The nucleic acid encoding an ungulate-derived IgM heavy chain constant region which is comprised in the human artificial chromosome vector of the invention is not particularly limited so long as the region is in a range which may sufficiently induce the signal of the B-cell receptor or B-cell proliferation/development in the above-described IgM heavy chain constant region. In one embodiment, the nucleic acid encoding an ungulate-derived IgM heavy chain constant region provides a transmembrane and cytoplasmic TM1 domain and TM2 domain derived from an ungulate, and in other embodiments encodes the ungulate-derived CH2 domain, CH3 domain, CH4 domain, TM1 domain, and TM2 domain or the ungulate-derived CH1 domain, CH2 domain, CH3 domain, CH4 domain, TM1 domain, and TM2 domain.
In one embodiment, the gene encoding the IgM heavy chain constant region of the bovine is a gene encoding a bovine IgM heavy chain constant region which is included in an IGHM region at which a bovine endogenous IgM heavy chain gene is positioned (derived from IGHM) or a gene encoding a bovine IgM heavy chain constant region in an IGHML1 region (derived from IGHML1). In another embodiment, the gene encoding a bovine IgM heavy chain constant region is included in the IGHM region.
In a further embodiment, the HAC comprises a gene encoding a human antibody heavy chain comprises a gene encoding a human heavy chain (for example, a human IgG heavy chain, such as an IgG1 heavy chain), and wherein a transmembrane domain and an intracellular domain of a constant region of the human heavy chain gene are replaced with a transmembrane domain and an intracellular domain of an ungulate-derived heavy chain (for example, an ungulate IgG heavy chain, such as an IgG1 heavy chain), constant region gene. In one embodiment, gene encoding the transmembrane domain and the intracellular domain of an ungulate-derived (such as bovine) IgG (such as IgG1) heavy chain constant region are used to replace the corresponding regions of the human IgG heavy chain gene. In another embodiment, the gene encoding the TM1 and TM2 domains of an ungulate-derived (such as bovine) IgG (such as IgG1) heavy chain constant region are used to replace the corresponding regions of the human IgG heavy chain gene. In another embodiment, the gene encoding the one or more of the CH1-CH4 domains and/or the TM1 and TM2 domains of an ungulate-derived (such as bovine) IgG (such as IgG1) heavy chain constant region are used to replace the corresponding regions of the human IgG heavy chain gene.
In a second aspect, the invention provides transgenic ungulates comprising a HAC vector according to any embodiment or combination of embodiments of the first aspect of the invention. The transgenic ungulate comprising the HAC vector of the present invention refers to an animal into which the human artificial chromosome vector of the present invention is introduced. The transgenic ungulate having the HAC of the present invention is not particularly limited so long as the animal is a transgenic ungulate in which the human artificial chromosome fragment may be introduced into a cell thereof, and any non-human animals, for example, ungulates such as cows, horses, goats, sheep, and pigs; and the like may be used. In one aspect, the transgenic ungulate is a bovine. A transgenic ungulate having the HAC vector of the present invention may be constructed, for example, by introducing the HAC vector of the present invention into an oocyte of a host animal using any suitable technique, such as those described herein. The HAC vector of the present invention may, for example, be introduced into a somatic cell derived from a host ungulate by a microcell fusion method. Thereafter, the animal having the HAC vector may be constructed by transplanting a nucleus or chromatin agglomerate of the cell into an oocyte and transplanting the oocyte or an embryo to be formed from the oocyte into the uterus of a host animal to give birth. It may be confirmed by a method of Kuroiwa et al. (Kuroiwa et al., Nature Biotechnology, 18, 1086-1090, 2000 and Kuroiwa et al., Nature Biotechnology, 20, 889-894) whether an animal constructed by the above method has the human artificial chromosome vector of the present invention.
In a third aspect, the invention provides transgenic ungulates comprising genes integrated into its genome encoding:

    
    
        (a) one or more human antibody heavy chains, wherein each gene encoding an antibody heavy chain is operatively linked to a class switch regulatory element;
        (b) one or more human antibody light chains; and
        (c) one or more human antibody surrogate light chains, and/or an ungulate-derived IgM heavy chain constant region;
    
    


wherein at least one class switch regulatory element of the genes encoding the one or more human antibody heavy chains is replaced with an ungulate-derived class switch regulatory element.
In this third aspect, the transgenic ungulate may comprise any embodiment or combination of embodiments of the nucleic acids as described herein for the HAC, but rather than being present in a HAC, they are integrated into a chromosome of the ungulate.
In a fourth aspect, the invention provides a method of producing a human antibody, comprising: (a) administering a target antigen to the transgenic ungulate of any embodiment or combination of embodiments of the invention to produce and accumulate human antibody specific to the target antigen in the serum or plasma of the ungulate; and (b) recovering the human antibody specific to the target antigen from the serum or plasma of the ungulate. In one embodiment, recovering the antibody comprises: (i) isolating lymphocytes from the transgenic ungulate; (ii) generating a human monoclonal antibody producing hybridoma from the lymphocytes; and (iii) recovering human monoclonal antibody specific to the target antigen from the hybridoma. In another embodiment, the lymphocytes from the transgenic ungulate are isolated from lymph nodes of the transgenic ungulate. In a further embodiment the transgenic ungulate is hyperimmunized with the target antigen.
A target antigen-specific human antibody may be produced by immunizing the transgenic ungulate having the HAC vector of the present invention with a desired target antigen to produce the target antigen-specific human antibody in the serum of the transgenic ungulate and recovering the target antigen-specific human antibody from the serum of the transgenic ungulate. The target antigens for immunizing the transgenic ungulate having the HAC vector of the present invention are not particularly limited and examples include a tumor-associated antigen, an antigen associated with allergy or inflammation, an antigen associated with cardiovascular disease, an antigen associated with autoimmune disease, an antigen associated with neurodegenerative disease, and an antigen associated with viral or bacterial infections.
Examples of tumor-associated antigens include CD1a, CD2, CD3, CD4, CD5, CD6, CD7, CD9, CD10, CD13, CD19, CD20, CD21, CD22, CD25, CD28, CD30, CD32, CD33, CD38, CD40, CD40 ligand (CD40L), CD44, CD45, CD46, CD47, CD52, CD54, CD55, CD55, CD59, CD63, CD64, CD66b, CD69, CD70, CD74, CD80, CD89, CD95, CD98, CD105, CD134, CD137, CD138, CD147, CD158, CD160, CD162, CD164, CD200, CD227, adrenomedullin, angiopoietin related protein 4 (ARP4), aurora, B7-H1, B7-DC, integlin, bone marrow stromal antigen 2 (BST2), CA125, CA19.9, carbonic anhydrase 9 (CA9), cadherin, cc-chemokine receptor (CCR) 4, CCR7, carcinoembryonic antigen (CEA), cysteine-rich fibroblast growth factor receptor-1 (CFR-1), c-Met, c-Myc, collagen, CTA, connective tissue growth factor (CTGF), CTLA-4, cytokeratin-18, DF3, E-catherin, epidermal growth facter receptor (EGFR), EGFRvIII, EGFR2 (HER2), EGFR3 (HERS), EGFR4 (HER4), endoglin, epithelial cell adhesion molecule (EpCAM), endothelial protein C receptor (EPCR), ephrin, ephrin receptor (Eph), EphA2, endotheliase-2 (ET2), FAM3D, fibroblast activating protein (FAP), Fc receptor homolog 1 (FcRH1), ferritin, fibroblast growth factor-8 (FGF-8), FGF8 receptor, basic FGF (bFGF), bFGF receptor, FGF receptor (FGFR)3, FGFR4, FLT1, FLT3, folate receptor, Frizzled homologue 10 (FZD10), frizzled receptor 4 (FZD-4), G250, G-CSF receptor, ganglioside (GD2, GD3, GM2, GM3, and the like), globo H, gp75, gp88, GPR-9-6, heparanase I, hepatocyte growth factor (HGF), HGF receptor, HLA antigen (HLA-DR, and the like), HM1.24, human milk fat globule (HMFG), hRS7, heat shock protein 90 (hsp90), idiotype epitope, insulin-like growth factor (IGF), IGF receptor (IGFR), interleukin (IL-6, IL-15, and the like), interleukin receptor (IL-6R, IL-15R, and the like), integrin, immune receptor translocation associated-4 (IRTA-4), kallikrein 1, KDR, KIR2DL1, KIR2DL2/3, KS1/4, lamp-1, lamp-2, laminin-5, Lewis y, sialyl Lewis x, lymphotoxin-beta receptor (LTBR), LUNX, melanoma-associated chondroitin sulfate proteoglycan (MCSP), mesothelin, MICA, Mullerian inhibiting substance type II receptor (MISIIR), mucin, neural cell adhesion molecule (NCAM), Nec1-5, Notch1, osteopontin, platelet-derived growth factor (PDGF), PDGF receptor, platelet factor-4 (PF-4), phosphatidylserine, Prostate Specific Antigen (PSA), prostate stem cell antigen (PSCA), prostate specific membrane antigen (PSMA), Parathyroid hormone related protein/peptide (PTHrP), receptor activator of NF-kappaB ligand (RANKL), receptor for hyaluronic acid mediated motility (RHAMM), ROBO1, SART3, semaphorin 4B (SEMA4B), secretory leukocyte protease inhibitor (SLPI), SM5-1, sphingosine-1-phosphate, tumor-associated glycoprotein-72 (TAG-72), transferrin receptor (TfR), TGF-beta, Thy-1, Tie-1, Tie2 receptor, T cell immunoglobulin domain and mucin domain 1 (TIM-1), human tissue factor (hTF), Tn antigen, tumor necrosis factor (TNF), Thomsen-Friedenreich antigen (TF antigen), TNF receptor, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), TRAIL receptor (DR4, DRS, and the like), system ASC amino acid transporter 2 (ASCT2), trkC, TROP-2, TWEAK receptor Fn14, type IV collagenase, urokinase receptor, vascular endothelial growth factor (VEGF), VEGF receptor (VEGFR1, VEGFR2, VEGFR3, and the like), vimentin, VLA-4, and the like.
Examples of antigens associated with allergy or flare include IL-6, IL-6R, IL-5, IL-5R, IL-4, IL-4R, TNF, TNF receptor, CCR4, chemokine, chemokine receptor, and the like. Examples of antigens associated with cardiovascular disease include GPIIb/IIIa, PDGF, PDGF receptor, blood coagulation factor, IgE, and the like. Examples of antigens associated with viral or bacterial infections include gp120, CD4, CCR5, a verotoxin, an anthrax protective antigen, a methicillin-resistant Staphylococcus aureus (MRSA) antigen, a hepatitis type B virus (HBV) antigen, a cytomegalovirus (CMV) antigen, a Rabies antigen, a Varicella zoster antigen, and the like. Other examples thereof include a T cell surface membrane protein mixtures, a Rh (D) antigen, crotalid venom, digoxin, and the like.
The immunization is carried out by administering the target antigen with, for example, a complete Freund's adjuvant or an appropriate adjuvant such as an aluminum hydroxide gel, and pertussis bacteria vaccine, subcutaneously, intravenously, or intraperitoneally into a transgenic ungulate. In one embodiment, the immunization comprises hyper-immunization, which refers to immunization that goes beyond just giving the animals protective titers to an antigen. For example, if a protective titer is 1:120, we may hyperimmunize an animal to 1:10,240 so that these titers may be diluted in the production of a biotherapeutic in order to give protective titers in a passive transfer of immunity. Examples of the form of administering the target antigen into an transgenic ungulate having the HAC vector of the present invention include peptides, protein, bacteria, viruses, cells, biological tissue pieces, and the like. When the target antigen is a partial peptide, a conjugate is produced with a carrier protein such as bovine serum albumin (BSA), keyhole Limpet hemocyanin (KLH) or the like, and is used as the immunogen. The target antigen is administered once to 10 times every 1 to 4 weeks after the first administration. After 1 to 14 days from each administration, blood is collected from the animal to measure the antibody value of the serum.
Examples of the method for detecting and measuring the target antigen-specific human antibody included in the serum include a binding assay by an enzyme-linked immunosorbent assay, and the like. The binding amount of a human antibody in the serum may be measured by incubating the serum comprising the human antibody with antigen expressing cells, and then using an antibody specifically recognizing a human antibody.
Further, in addition to these methods, the antibody may be selected by identifying a target antigen of the antibody according to a method known in the art. Examples of the method for recovering human antibodies from the serum include a method of purifying by adsorbing the human antibody on a protein A carrier, a protein G carrier, or a carrier on which the human immunoglobulin specific antibody is supported. Methods used in purification of proteins, such as gel filtration, ion exchange chromatography, and ultrafiltration, may be combined.
A human antibody produced by the above method may be a polyclonal antibody or a monoclonal antibody. Methods of preparing and utilizing various types of antibodies are well-known to those of skill in the art and would be suitable in practicing the present invention (see, for example, Harlow, et al. Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; Kohler and Milstein, Nature, 256:495 (1975)). An example of a preparation method for hybridomas comprises the following steps of: (1) immunizing a transgenic ungulate with a target antigen; (2) collecting antibody-producing cells from the transgenic ungulate (i.e. from lymph nodes); (3) fusing the antibody-producing cells with myeloma cells; (4) selecting hybridomas that produce a monoclonal antibody reacting target antigen from the fused cells obtained in the above step; and (5) selecting a hybridoma that produces a monoclonal antibody reacting with target antigen from the selected hybridomas.
EXAMPLES
Methods
All animal procedures were performed in compliance with Hematech's guidelines, and protocols were approved by the Institutional Animal Care and Use Committee.
Genomic Library.
Genomic DNA was extracted either from CHO cells containing the κHAC vector (κC1-1) or the bovine fibroblast cell lines, 6939 and 3427, to construct the κHAC or bovine genomic libraries, respectively. Each λ phage-based genomic library was constructed using λFIX II vector through a custom library construction service (Lofstrand Labs Ltd.). Library screening and λ phage DNA extraction/purification was done as described previously5. The bovine genomic BAC library (CHORI-240) was purchased from Children's Hospital Oakland Research Institute and screening was performed, according to their instruction.
Construction of Targeting Vectors.
Each vector construction was performed as previously described5, 12, 20, 21 with some modification as described below. pTEL′hisDpurolox2272F9R9; a genomic DNA fragment for a homologous arm was amplified by using a PCR primer pair, kD-F9 and kD-R9, in 40 cycles of 98° C. for 10 s and 68° C. for 9 min. This PCR product was subcloned into Bam HI site of a plasmid pTEL′hisDpurolox2272, which was constructed as follows. The modified lox2272-containing oligo DNAs (Oligo DNA pair 1; see Table 1 below) were, after annealing, cloned into Hin dIII site of a plasmid pPUR (BD Bioscience Clontech), generating a plasmid pPURlox2272. On the other hand, another plasmid pTEL′hisDPm was constructed by modifying the previous plasmid pTELpuro, where the puro gene was replaced with hisD gene, Eco RI site was replaced with Srf I and Spe I site was converted to Pme I site. The Bam HI fragment from the pPURlox2272 was then cloned, after blunting, to Pme I site of the pTEL′hisDPm, which generated pTEL′hisDpurolox2272F9R9.
pTELCAGzeoSLF2R2;
the plasmid pTELpuro was further modified by converting the Eco RI site to Srf I and then to Pme I and by replacing the puro gene to CAGzeo gene {pTELCAGzeo(Sr)Pm}. On the other hand, a genomic DNA fragment for a homologous arm was amplified by using a PCR primer pair, SL-F2 and SL-R2, in 40 cycles of 98° C. for 10 s and 68° C. for 9 min. This PCR product was subcloned into Bam HI site of the plasmid pTELCAGzeo(Sr)Pm, which generated pTELCAGzeoSLF2R2.
p553CAGlox2272BsrDT;
The previous targeting vector pHCF2loxPHyg was modified where the homology arm sequence of the HCF2 gene was replaced with that of the AP000553, which was amplified by using a PCR primer pair, 553-F3 and 553-R3, in 40 cycles of 98° C. for 10 seconds and 68° C. for 15 min, generating p553loxPHyg(F). This plasmid was Not I-digested and self-ligated, followed by cloning of DT-A fragment into Srf I site. On the other hand, pDRIVE-CAG (InvivoGen) was modified as below. The lacZ fragment (Bsr GI-Eco RI) was replaced with the loxP-containing oligo DNAs (Oligo DNA pair 2; see Table 1 below) after annealing and then Sda I-Swa I fragment was cloned into Pst I/Sma I-digested pBluescript SK—(Stratagene), generating pCAGloxP. The loxP sequence was further replaced with the lox2272-containing sequence that was generated after annealing two oligo DNAs (Oligo DNA pair 3; see Table 1 below). And then, the bsr gene was added to Spe I site, generating pcAGloxP2272bsr. Finally, the Not I-Kpn I fragment (CAG-lox2272-polyA-bsr) was cloned into the Not I site to complete p553CAGlox2272BsrDT.
pSC355CAGlox511hisDDT; a genomic DNA fragment for a homologous arm was amplified by using a PCR primer pair, SC355-F3 and SC355-R3, in 40 cycles of 98° C. for 10 seconds and 68° C. for 15 min. This PCR product was subcloned into Spe I site of a plasmid pBluescript where the Kpn I site was converted to Srf I site, generating pSC355F3R3. The pCAGloxP plasmid was similarly modified where the loxP sequence was further replaced with the lox511-containing sequence that was generated after annealing two oligo DNAs (Oligo DNA pair 4; see Table 1 below). And then, the hisD gene was added to Spe I site, generating pCAGlox511hisD. The Not I-Kpn I fragment (CAG-lox511-polyA-hisD) was cloned into the Eco RV site of pSC355F3R3. Finally, the DT-A cassette was subcloned into Not I to complete pSC355CAGlox511hisDDT.
p14CEN(FR)hygpurolox511DT;
a genomic DNA fragment for a homologous arm was amplified by using a PCR primer pair, 14CEN-F and 14CEN-R, in 40 cycles of 98° C. for 10 seconds and 68° C. for 15 min. This PCR product was subcloned into Bam HI site of a plasmid pBluescript where the Kpn I site was converted to Pme I site, generating p14CEN(FR). The modified lox511-containing oligoDNAs (Oligo DNA pair 5; see Table 1 below) were, after annealing, cloned into Hind III site of a plasmid pPUR (BD Bioscience Clontech), generating a plasmid pPURlox511. The Bam HI fragment from the pPURlox511 was cloned to Bam HI site of pBluescript SK (Stratagene), followed by cloning of the hyg gene to Eco RV, generating pHygPurolox511. The Not I-Kpn I fragment (puro-lox511-hyg) was cloned into the Hpa I site of p14CEN(FR). Finally, the DT-A cassette was subcloned into Pme I to complete p14CEN(FR)hygpurolox511DT.
pRNR2loxPbsrDT;
the previous vector pRNR2loxPbsr (Ref 20) was modified to construct the pRNR2loxPbsrDT by simply adding the DT-A cassette.
pCH1CAGzeo(R)DT(F);
a genomic λ phage library was constructed from CHO cells containing the κHAC using λ FIX II vector through a custom library construction service (Lofstrand). The genomic library was screened for hIGHM constant region by using a probe that was a PCR product by amplified a PCR pair, hCμ-FR, and then clones #1, #4 and #7 were isolated. From the clone #4, 1.7 kb of Pml I fragment was subcloned into Sma I site of pBluescript, generating pCH1S (F). 1 kb of Sac I-Pml I fragment from the plasmid pBCμAY37-95 where Sal I-bovine IGHM genomic fragment was cloned into pBluescript was subcloned into Pst I site of the pCH1S (F), generating pCH1SSP (F). 7.4 kb of the Sma I-Eco RI fragment from the above clone #1 was cloned into Eco RV/Eco RI-digested pCH1SSP (F), generating pCH1SL. On the other hand, from the plasmid pBCμAY37-95, 3.5 kb of Sac I fragment was subcloned into pBluescript and then the Xho I fragment of floxed CAGzeo {CAGzeo fragment was subcloned into Eco RV site of pBS246 (Gibco)} was cloned into Van91 I site, generating pmAYSazeo (F). The Sac I fragment from the pmAYSazeo (F) was further subcloned into blunted Eco RI site of pCH1SL, generating pCH1zeo (F). As a final step, the DT-A cassette was subcloned into Not I site of the pCH1zeo (F) to complete the pCH1CAGzeo(R)DT(F).
pCH2CAGzeoDT;
an annealed oligo DNA pair, SeSp, was cloned into blunted Pst I site of pBluescript. From the pBCμAY37-95, 2 kb of Sph I-Bam HI fragment was subcloned into Sph I-Bam HI site, generating pmAYSpB. Similarly, 2 kb of Bam HI-Pml I fragment from the pBCμAY37-95 was subcloned into Bam HI-Pme I site (converting the original Spe I site), generating pmAYSpBPml. 0.6 kb of Eco RI-Sex AI fragment from the above clone #1 was subcloned into Eco RI-Sex AI site of the pmAYSpBPml, generating pRISe. Then, the floxed CAGzeo was subcloned into Van91 I site of the pRISe, generating pRISeCAGzeo (R), of which Not I site was converted to Eco RI site, generating pRISeCAGzeoE. Meanwhile, 1.7 kb of Pml I fragment from the above clone #4 was subcloned into Sma I site of pBluescript of which Eco RV site was converted to Mlu I site, generating pCH2S (F). 6.6 kb of Mlu I-Eco RI fragment from the above clone #1 was cloned into Mlu I-Eco RI of the pCH2S (F), generating pCH2LS. Then, the Eco RI fragment from the pRISeCAGzeoE was subcloned into Eco RI site of the pCH2LS, generating pCH2CAGzeo (F). As a final step, the DT-A cassette was subcloned into Not I site of the pCH2CAGzeo (F) to complete the pCH2CAGzeoDT.
pCC1BAC-isHAC;
the genomic λ phage library constructed from CHO cells containing the κHAC was screened to isolate genomic DNA fragments covering the human Iγ1-Sγ1 region followed by the hIGHG1 constant region by using a probe that was a PCR product by amplified with a PCR pair, g1(g2)-FR, and then we identified clones #h10 and #h18/h20. From the clone #h10, 2 kb of Afe I-Bam HI fragment was rescued to be used as a short arm while 10.5 kb of Apa I-Hpa I fragment was obtained from the clone #h18/h20 for a long arm. On the other hand, a bovine genomic λ phage library was screened to isolate genomic DNA fragments covering the bovine Iγ1-Sγ1 region followed by the bIGHG1 constant region by using a probe that was a PCR product by amplified with a PCR pair, bIgG1-FR, and then we identified a clone #b42, from which a 9.7 kb fragment (5′ end through Bsu36 I) was assembled to replace a 6.8 kb of the human Iγ1-Sγ1 region. A Bsu36 I-Apa I linker was used to join 3′ end of the bovine Iγ1-Sγ1 region and 5′ end of the hIGHG1 constant region. The neo gene flanked by FRT and DT-A gene were inserted as shown in FIG. 22B. All the above assembles were done on a BAC-based backbone vector pCC1BAC (EPICENTRE).
phIγ1FRTCAGattPhisDDT;
11.4 kb of Kpn I-Not I genomic fragment from clone h10 was isolated from the clone #h10 and subcloned into pBluescript SK(−) vector. Then, the FRT-CAG promoter-attP-polyA-hisD cassette was inserted into the 5′ Bam HI site which is 1.8 kb downstream from the Kpn I site. Finally, DT-A gene was cloned into Not I site.
phγ1TMNoeattPDT;
7.5 kb of Sac II genomic fragment from clone h20 was subcloned into pBluescript SK (−) vector. Next, the neo-attP cassette was inserted into Hin dill site, followed by cloning of DT-A gene into Not I site.
pBAC-istHAC;
7.3 kb of Bmg BI-Sph I bovine genomic fragment containing the bovine TM1/TM2 domain was obtained from the clone #b66, of which 5′ part was joined with 3′ part of the 9.5 kb of the bovine Iγ1-Sγ1 fragment (from #b42) and 1.6 kb of hIGHG1 gene (from #h10) from the isHAC by a linker, pNsiI-bG1-hG1-BmgBI. The attB-DsRed-FRT cassette was inserted at 5′ side of the 9.5 kb of the bovine Iγ1-Sγ1 fragment (from #b42) and another attB sequence was placed at 3′ side of 7.3 kb of Bmg BI-Sph I bovine genomic fragment containing the bovine TM1/TM2 domain that was obtained from the clone #b66. All the above assembles were done on a BAC-based backbone vector pCC1BAC (EPICENTRE).
pCλ1CAGzeoPuroloxPDT;
a probe amplified by a primer pair, bCLR-FR, identified several λ phage clones covering the 5′ side of the IGLJ1-IGLC1 gene. The 13 kb Nde I-Hin dIII genomic fragment was subcloned into pBluescript SK(−) vector and the CAGzeo/loxP/promoter-less puro cassette was inserted at Afe I site present in the genomic fragment. Finally, DT-A gene was inserted at Not I site. This vector was constructed from the alleles A and B.
pCλ5CAGloxPneoDT;
a probe amplified by a primer pair, bCLL-FR, identified several λ phage clones covering the 3′ side of the IGLJ5-IGLC5 gene. The 10 kb Sac II-Nsi I genomic fragment was subcloned into pBluescript SK(−) vector and the CAG promoter/loxP/poly A/neo cassette was inserted at Hin dIII site present in the genomic fragment. Finally, DT-A gene was inserted at Not I site. This vector was constructed from the alleles A and B.
Modification of the Human Chromosome 14 Fragments in Chicken DT40 Cells.
For the purpose of using structure-defined hChr14 vector and of removing as many irrelevant human genes as possible, the intact hChr14 was modified, followed by the IgM bovinization (FIG. 17A). Chicken DT40 cells retaining the intact hChr14 was electroporated with the targeting vector pSC355CAGlox511hisDDT to integrate the lox511 and the CAG promoter at the locus AL512355, which is about 300 kb centromeric to the hIGH locus. Colonies were selected with histidinol and subjected to genomic PCR screening to confirm the occurrence of the homologous recombination with primers, SC355KO-F2/R2, as a positive PCR and also with primers, 355N-F/R, as a negative PCR (FIG. 17D). Clone I355-2 was identified as a successfully targeted clone.
I355-2 was further transfected with the targeting vector p14CEN(FR)hygpurolox511DT to integrate another lox511 and the promoter-less puro gene at the locus AL391156, which is about the 85 Mb centromeric to the AL512355. Colonies were selected with hygromycin B and subjected to PCR screening to confirm the occurrence of the homologous recombination with primers, 14CENKO-F3/R3(see Table 1 below), as a positive PCR and also with primers, 14CEN(N)-F2/R2 (see Table 1 below), as a negative PCR (FIG. 17D). Clone I156-10 was identified as a successfully targeted clone.
I156-10 was transfected with the Cre expression plasmid to mediate site-specific recombination between the two lox511 sites, one on the locus AL512355 and another on the AL391156, to delete about 85 Mb of sequence between them to shorten the hChr14 from 106 Mb down to about 21 Mb. Cells where the big deletion took place were selected with puromycin as puromycin resistance is conferred by the CAG promoter-lox511-puro cassette reconstituted at the recombination site. This cassette reconstitution was confirmed by PCR with primers, CAGpuro-F3/R3 (see Table 1 below), as described in the bIGL cluster deletion section. Also, histidinol and hygromycin B sensitivity was confirmed as both hisD and hyg cassettes are to be removed as a result of this 85 Mb deletion (FIG. 17B). Finally, fluorescent in-situ hybridization (FISH) with human COT-1 DNA as a probe confirmed the shortening of the hChr14 (FIG. 17E). Clone D8 was identified as a successfully shortened clone. Clone D8 was sequentially modified with the targeting vector pRNR2loxPbsrDT to integrate the loxP sequence and the GFP gene at the RNR2 locus, as described previously20, 21. Clones 14D1 was selected for the final IgM bovinization step (CH1D and CH2D).
Clone 14D1 was finally bovinized with the targeting vector pCH1CAGzeo(R)DT(F) to replace the CH1 domain through the TM2 domain of the hIGHM gene with that of bovine to generate the cIgM (CH1) protein. Colonies were selected with zeocin and subjected to genomic PCR screening to confirm the occurrence of the homologous recombination with primers (see Table 1 below), cHAC-F3/R3, as a positive PCR and also with primers, CH1 5′-F/R and cHAC 3′-F/R, to make sure that the junction sequences between human and bovine are accurate (FIG. 17D). Clone CH1D2 was identified as a positive clone retaining the CH1D fragment for the KcHACΔ construction. Similarly, clone 14D1 was bovinized with the targeting vector pCH2CAGzeoDT(F) to replace the CH2 domain through the TM2 domain of the hIGHM gene with that of bovine to generate the cIgM (CH2) protein and then clone CH2D4 was selected for the cKSL-HACΔ construction.
Modification of the Human Chromosome 2 Fragments in Chicken DT40 Cells.
κTL1 is a DT40 clone containing the hChr2 fragment covering the hIGK locus. This cell line was transfected with the vector pTELCAGzeoCD8A to simply replace the PGKpuro cassette with the CAGzeo because zeocin selection usually works better in bovine fibroblasts at later steps. After zeocin selection, genomic PCR, CD8AKO-F2R2 (FIG. 18A) specific to the homologous recombination, identified clone κZ7, for which puromycin sensitivity was confirmed, and then used for the KcHACΔ construction with the CH1D2.
On the other hand, the κTL1 was also electroporated with the targeting vector pTEL′hisDpurolox2272F9R9 to both truncate the hChr2 fragment and integrate the lox2272 and the promoter-less puro gene at the locus AC104134, which is about 300 kb telomeric to the hIGK constant region Cκ gene, IGKC. Colonies were selected with histidinol, and then puromycin sensitivity was confirmed since the successful truncation results in the loss of the puro cassette at the CD8A locus. Genomic DNA was extracted from puromycin sensitive colonies and subjected to PCR screening with primers, FABP1-F, which amplifies the FABP1 locus present in κTL1 but absent in the targeted clones (FIG. 18B). Clone K53 was identified and used for the cKSL-HACΔ construction.
Modification of the Human Chromosome 22 Fragment in Chicken DT40 Cells.
The outline is depicted in FIG. 19A. 52-18, a DT40 cell line retaining the intact hChr22, was electroporated with the targeting vector pTELCAGzeoSLFR to truncate the hChr22 at the AP000350 locus, which is about 450 kb telomeric to the AP000344 locus at which the hChr22 was truncated for the ΔΔHAC vector (FIG. 19B). Colonies were selected with zeocin and their genomic DNA was subjected to PCR screening with primers (see Table 1 below), 350T-FR, which amplifies the AP000350 locus present in 52-18 but absent in the targeted clones. Clone ST13 was identified as a successfully truncated clone.
ST13 was modified with the targeting vector p553CAGlox2272bsrDT to integrate the lox2272 and the CAG promoter at the locus AP000553. Colonies were selected with blasticidin S and subjected to PCR screening to confirm the occurrence of homologous recombination with primers, 553KO-FR, as a positive PCR and also with primers, 553-F4R4, as a negative PCR (FIG. 19C). Clone STL54 was identified as a successfully targeted clone.
Translocation of the Human Chromosome 22 Fragment to the Human Chromosome 2 Fragment to Generate the SLKH Fragment in Chicken DT40 Cells.
The SLKH fragment was constructed in DT40 hybrid cells using the chromosome cloning system (FIG. 20A). Clone K53 retaining the hChr2 fragment with the hyg cassette and clone STL54 retaining the hChr22 fragment with the bsr cassette were fused (whole cell fusion, WCF) to generate DT40 hybrid cells. Colonies were maintained in hygromycin B and blasticidin S to select for cells retaining both hChr fragments, which was confirmed by genomic PCR with the following primers (see Table 1 below), IGKC-F/R, IGKV-F/R, RPIA-F/R, EIF2AK3-F/R and cos138KO-F/R for the hChr2 fragment, and another set of primers, 553P-F/R, hVpreB1-F/R, hVpreB3-F/R, IgL-F/R, 344-F/R, hL5-F/R, 350P-F/R and 553KO-F/R for the hChr22 fragment. FISH using Human COT-1 DNA as a probe confirmed the presence of the two human chromosome fragments (FIG. 20B). Clone SLK2 was identified as a positive clone. SLK2 was transfected with the Cre expression plasmid to mediate site-specific recombination between the two lox2272 sites, one at the locus AC104134 on the hChr2 fragment and another at the locus AP000553 on the hChr22 fragment. Recombinants were selected by puromycin as puromycin resistance is conferred by reconstitution of the CAG promoter-lox2272-puro cassette at the translocation site. This was also confirmed by the genomic PCR, CAGpuro-F3R3, followed by direct sequencing of the PCR product. SLKH6 was identified as a successfully translocated clone retaining the SLKH fragment (FIG. 20A, 20B).
The SLKH fragment was transferred from DT40 hybrid cell line SLKH6 to plain DT40 cells by MMCT. Selection was done with puromycin and then colonies were investigated for blasticidin S sensitivity as the successful transfer of the SLKH fragment into DT40 cells should result in the loss of the bsr cassette (FIG. 20A). Genomic DNA from blasticidin S-sensitive and puromycin-resistant colonies was extracted and the SLKH fragment retention was confirmed by PCR primers (see Table 1 below), IGKC-F/R, IGKV-F/R, RPIA-F/R, EIF2AK3-F/R, cos138KO-F/R, CAGpuro-F3/R3, 553P-F/R, hVpreB1-F/R, hVpreB3-F/R, IgL-F/R, 344-F/R, hL5-F/R, 350P-F/R, and 553KO-F/R. Two-color FISH using the hChr2 painting probe directly labeled with Rhodamine and the hChr22 painting probe directly labeled with Fluorescein confirmed the presence of the SLKH fragment (FIG. 20B). SLKD18 was identified as a positive clone.
Construction of cKSL-HACΔ and KcHACΔ Vectors in Chicken DT40 Cells.
The cKSL-HACΔ vector was constructed in DT40 hybrid cells as outlined in FIG. 3B, using the chromosome cloning system. SLKD18 which contains the hChr2 fragment translocated with the hChr22 fragment, bearing the hyg cassette, and CH2D4 which contains the hChr14 fragment (14D) with the bsr cassette and the cIgM (CH2)-bovinized hIGH locus, were fused to generate DT40 hybrid clone cKSLD22, selected by hygromycin B and blasticidin S. Extensive genomic PCR was done with a first set of PCR primers (see Table 1 below) for the hChr22, 553P-F/R, hVpreB1-F/R, hVpreB3-F/R, IgL-F/R, 344-F/R, hL5-F/R, 350P-F/R, and 553KO-F/R, a second set of primers for the hChr2, IGKC-F/R, IGKV-F/R, RPIA-F/R, EIF2AK3-F/R, cos138KO-F/R, CAGpuro-F3/R3 (junction between the hChr2 and hChr22), and a third set of primers (see Table 1 below) for the hChr14, RNR2-1×STOP-3, VH3-F/R, g1(g2)-F/R, 14CENKO-F3/R3, CH2 5′-F/R, cHAC-F3/R3 and SC355F3R3KO-F/2R2. Furthermore, FISH using Human COT-1 DNA also confirmed the presence of the two human chromosome fragments.
cKSLD22 was electroporated with the Cre expression plasmid to mediate site-specific recombination between the two loxP sites, one at the cos138 locus on the SLKH fragment and another at the RNR2 locus on the CH2D fragment, and also to delete the floxed CAG promoter-zeo cassette within the cIgM (CH2) domain. Recombinants were enriched by sorting of GFP positive cells as GFP expression is conferred by reconstitution of the PGK promoter-loxP-GFP cassette at the translocation site. Sorting was conducted twice which resulted in two distinct GFP positive populations with different expression levels. The lower GFP population contained the successfully translocated cKSL-HACΔ determined by PCR primers (see Table 1 below), PGK2×GFP2, and PCR primers, CreCAGzeo-F3/R3, confirmed the CAG promoter-zeo cassette deletion in the cIgM (CH2) site. The higher GFP population contained an inverted CH2D fragment between the loxP at the RNR2 locus and the lox511 at the locus AL512355/AL391156 by a leaky Cre-mediated recombination which was confirmed by PCR primers (see Table 1 below), CAGpuro-F3×GFP2 and STOPpuro-F2×STOPpuro-R, followed by direct sequencing (FIG. 21). cKSLDH22 (2L) was finally identified as a DT40 hybrid cell line retaining the cKSL-HACΔ, subjected to extensive genomic PCR and three color-FISH (FIG. 12A). The KcHACΔ vector was similarly constructed in DT40 cells as outlined in FIG. 3C. The clone KCDH1 was subjected to extensive genomic PCR and two color-FISH (FIG. 12B). Likewise, we also constructed the KcHAC where the hChr2 fragment (KTL1) was translocated to the SC20 fragment bearing the bovinized cIgM (CH1).
Construction of the isHAC and isKcHACΔ Vectors in Chicken DT40 Cells.
Outline of the isHAC (isKcHACΔ) construction is depicted in FIG. 22A. The targeting vector pCC1BAC-isHAC was constructed (FIG. 22B) and used to bovinize the Iγ1-Sγ1 region on the cKSL-HACΔ or KcHACΔ. Clone cKSLDD1, a chicken DT40 cell line retaining the cKSL-HACΔ obtained by MMCT from cKSLDH22 (2L), was electroporated with the targeting vector pCC1BAC-isHAC. Colonies were selected with G418 and their genomic DNA was subjected to PCR screening with primers, iscont1-F1R1, to identify the occurrence of the homologous recombination. Furthermore, additional diagnostic PCRs were also performed to check structural integrity (FIG. 22C). One clone is 1-11 was selected for the subsequent neo cassette deletion by introduction of the FLP-expression plasmid. The is 1-11 was co-transfected with the FLP-expressing plasmid and the DsRed-expressing plasmid. DsRed-positive cells were sorted and subjected to single colony isolation. G418-sensitive colonies where the neo cassette was deleted by the FRT-FLP recombination were tested for the genomic PCRs including iscont1-F3/R6 (see Table 1 below) (FIG. 22D). Finally, we selected isH11-S2 and isH9-3, and then they were transferred to CHO cells to establish master cell banks, isC1-133, isC10-2 and isC10-18, respectively, for which the extensive genomic PCR and CGH were performed to check structural integrity (FIG. 22E, 22F). The isKcHACΔ was constructed in DT40 cells, similarly to the isHAC, and two clones, isKCDH17, isKCDH30, were selected and then were transferred to CHO cells to establish master cell banks, isKCDC8 and isKCDC38, respectively, for which the extensive genomic PCR and CGH were performed to check structural integrity (FIG. 22G, 22H).
Construction of the istHAC Vector in Chicken DT40 Cells.
A scheme of construction of the istHAC is depicted in FIG. 23A. Clone cKSLDD1 was sequentially targeted with the two targeting vectors phγ1TMNeoattPDT (FIG. 23B) and phIγ1FRTCAGattPhisDDT (FIG. 23C) to integrate the attP sequence at 3′ side of the hIGHG1 TM2 domain and at 5′ side of the human Iγ1 region, respectively, which generated two clones ist1-5 and ist1-21. They were co-electroporated with the pBAC-istHAC and φC31-expression vectors together to bring about the big DNA replacement. As shown in FIG. 23D, the expected recombination between the attP and attB should result in reconstitution of the CAG promoter-DsRed gene expression, which can be detected by flow cytometry. DsRed-positive cells were accordingly sorted. This sorting process was repeated 2-3 times until purity of DsRed-positive cells reached >95%. And then, cells were subjected to single colony isolation and examined by three diagnostic genomic PCRs (see Table 1 below), CAGDsRed-F2/R2 (positive), bIgG1-3′-SeqF3×hIgG1-R15 (positive) and bIgG1-3′-SeqF3×attPPuro-R3 (negative). As a result, istH5-S16 from ist1-5 and istH21H-S10 from ist1-21 were selected.
The two clones, istH5-S16 and istH21H-S10, were finally transfected with the FLP-expression vector. As shown in FIG. 23E, FLP expression should cause the removal of the CAG-DsRed gene expression, which can be detected by flow cytometry. DsRed-negative cells were accordingly sorted, resulting in >95% purity of DsRed-negative cells. And then, cells were subjected to single colony isolation and examined by three diagnostic genomic PCRs (see Table 1 below), CAGDsRed-F2/R2 (negative), bIgG1-3′-SeqF3×hIgG1-R15 (positive) and hIgG1-F10×bIgG1-5′-Seq-R10 (positive). Consequently, istHD16L from istH5-S16 and istHD10L from istH21H-S10 were selected and then were transferred to CHO cells to establish master cell banks, istC1-49 and istC1-6, respectively, for which the extensive genomic PCR and CGH were performed to check structural integrity (FIG. 23F, 23G).
Transfection of Chicken DT40 Cells for HAC Vector Construction.
HAC vector construction was carried out as previously described5, 20, 21. Briefly, DT40 cells containing each hChr fragment were electroporated (550 V, 25 μF) with  ̃25 μg of each targeting vector. Colonies were selected by each drug; G418 (2 mg/ml), puromycin (0.5 μg/ml), hygromycin B (1.5 mg/ml), blasticidin S (15 μg/ml), histidinol (0.5 mg/ml) or zeocin (1 mg/ml) for two weeks and their DNAs were subjected to PCR screening as indicated.
Transfection of Bovine Fibroblasts for the Bovine IGLJ-IGLC Gene Cluster Deletion and Microcell-Mediated Chromosome Transfer (MMCT).
Bovine fetal fibroblasts were cultured and transfected as previously described5, 12, 21. Briefly, fibroblasts were electroporated with 30 pg of each targeting vector at 550 V and 50 μF. After 48 hours, the cells were selected under an appropriate drug; zeocin (0.4 mg/ml) or puromycin (1 μg/ml) for two weeks and resistant colonies were picked up and transferred to replica plates; one was for genomic DNA extraction and the other was for embryonic cloning. MMCT was done with each HAC vector as described previously5, 20, 21.
Genomic PCR and RT-PCR Analyses.
These analyses were implemented as previously described5, 12, 20, 21. All the PCR products were run on 0.8% agarose gels. Primer sequences are available in Table 1 below.







TABLE 1







Primer sequences.









Name of oligo

SEQ ID


DNA
Sequence (5′ → 3′)
NO












kD-F9
TCGAGGATCCGCCAGGGAGACAGATGCCAAGTACGGTTTAG
1


 


kD-R9
TCGAGGATCCAGGATCTTTGGGGGACTGAATGGGGTGTGCT
2


 


Oligo DNA pair
AGCTTGGATCCATAACTTCGTATAGGATACTTTATACGAAGTTATA
3


1-F




 


Oligo DNA pair
AGCTTATAACTTCGTATAAAGTATCCTATACGAAGTTATGGATCCA
4


1-R




 


SL-F2
TCGAGGATCCGGCCTCCCAAAGGATTATAGACGTGAGCCACTGT
5


 


SL-R2
TCGAGGATCCAAAGAAGGGGCCCGCCTCTGCCTCTAAATCCTGAC
6


 


553-F3
TGTAGCTGACTTTAGCCACCCACAAGTAC
7


 


553-R3
CTTGCTGATTATACCTCATCTCCTTCCCTC
8


 


Oligo DNA pair
GTACAATAACTTCGTATAGCATACATTATACGAAGTTATAGATCTG
9


2-F




 


Oligo DNA pair
AATTCAGATCTATAACTTCGTATAATGTATGCTATACGAAGTTATT
10


2-R




 


Oligo DNA pair
GATCTATAACTTCGTATAGGATACTTTATACGAAGTTATG
11


3-F




 


Oligo DNA pair
CTAGCATAACTTCGTATAAAGTATCCTATACGAAGTTATA
12


3-R




 


SC355-F3
GTACAATCTTGGATCACTACAACCTCTGCCTACCA
13


 


SC355-R3
TGCTGTGTCTAATCAGGTGTTGAACCCATCTACTA
14


 


Oligo DNA pair
GATCTATAACTTCGTATAGTATACATTATACGAAGTTATG
15


4-F




 


Oligo DNA pair
CTAGCATAACTTCGTATAATGTATACTATACGAAGTTATA
16


4-R




 


14CEN-F
TCGAGGATCCTTCGCCACCCCAAAGATGATTACAGATTAC
17


 


14CEN-R
TCGAGGATCCTACACTAGAAGCACAAACCCCACCATTACACAT
18


 


Oligo DNA pair
AGCTTGGATCCATAACTTCGTATAGTATACATTATACGAAGTTATA
19


5-F




 


Oligo DNA pair
AGCTTATAACTTCGTATAATGTATACTATACGAAGTTATGGATCCA
20


5-R




 


hCm-F
CAGTCCCCGGCAGATTCAGGTGTCC
21


 


hCm-R
GAAAGTGGCATTGGGGTGGCTCTCG
22


 


SeSp-F
GGACCAGGTGGAGACTGTGCAGTCCTCACCCATAACTTTCAGGGCCTA
23



CAGCATGCTG



 


SeSp-R
CAGCATGCTGTAGGCCCTGAAAGTTATGGGTGAGGACTGCACAGTCTC
24



CACCTGGTCC



 


g1(g2)-F
ACCCCAAAGGCCAAACTCTCCACTC
25


 


g1(g2)-R
CACTTGTACTCCTTGCCATTCAGC
26


 


bIgG1-F
TCAACAGCACCTACCGCGTGGTCAG
27


 


bIgG1-R
GCGGGGTCGTGCCGTACTTGTCCTC
28


 


pNsiI-bG1-hG1-
ATGCATGAGGCTCTGCACAACCACTACACACAGAAGAGCCTCTCCCTG
29


BmgBI-F
TCTCCGGGTAAATGAGCCTCACGTC



 


pNsiI-bGl-hG1-
GACGTGAGGCTCATTTACCCGGAGACAGGGAGAGGCTCTTCTGTGTGT
30


BmgBI-R
AGTGGTTGTGCAGAGCCTCATGCAT



 


bCLR-F
TCTGTCTGTCCAACAGTGGC
31


 


bCLR-R
ATTATGGGATGAGTCCAGGC
32


 


bCLL-F
TTAACTGCGGTACAAGGTGC
33


 


bCLL-R
CAACCTCTCCAGGATTCTGG
34


 


R-F2
GACAAGCGTGCTAGGGTCATG
35


 


R-R1
GGGATGGGACCTTGTTAGACTTG
36


 


CL1puro-F2
CGCGCATGGCCGAGTTGAGCGGTTCC
37


 


CL1puro-R2
CAGGCTCCCGGCTGGCGCTGGTAAGTCC
38


 


CL5CAG-F2
GCCCGGCCCCAGATGGAACCCGAGACAGG
39


 


CL5CAG-R2
ATGCCAGGCGGGCCATTTACCGTCATTGA
40


 


CAGpuro-F3
GCGGCGCCGGCAGGAAGGAAATG
41


 


CAGpuro-R3
CGAGGCGCACCGTGGGCTTGTA
42


 


L001-F1
ACCCTCGGTCACCCTGTT
43


 


L002-R2
TGAGAAGGTCTTTATTCAGGAG
44


 


BCm-f2
TCTCTGGTGACGGCAATAG
45


 


BCm-r2
CTTCGTGAGGAAGATGTCGG
46


 


BCmKO-F14
CCACAAAGGAAAAAGCTGCACTGCTATAC
47


 


BCmKO-R14
TGTGGGATCAGGAGGTCAGATAGACATC
48


 


bIgL-Ld-F1
GTGGGGCCACAGAAGGCAGGAC
49


 


bIgL-C-R
ACCCGGGTAGAAGTCGCTGATGAGA
50


 


L003-F2
CCCTCGGTCACCCTGTTCCC
51


 


L004-R2
CTGGTGTGAGGCGACCTGGG
52


 


bIgk-F
CAGCTCCTGGGGCTCCTCCTG
53


 


bIgk-R
TGCAATAGGGGTTGATCTGTGGACA
54


 


335N-F
GGGCAACATAGCAAGACACCATTC
55


 


335N-R
TCCTCTCACCTCAGCCTCCATAGTA
56


 


SC335KO-F2
ACGGCG TGAGGACCAAGGAGCGAAACC
57


 


SC335KO-R2
TGAGCGACGAATTAAAAC AGGCGATGAC
58


 


14CEN(N)-F2
AACAGTTGAATTTATGGGGAGTC
59


 


14CEN(N)-R2
TCAGGCTTTAAACACAGTATCACAG
60


 


14CENKO-F3
ACTGAAATATTTTAAATGTTTGCCCTTCCCACTCC
61


 


14CENKO-R3
AGACCTCCGCGCCCCGCAACCTCCCCTTCTAC
62


 


cHAC 3′-F
CAAGCATGGAGCCCGCAGTAATAG
63


 


cHAC 3′-R
AAGGTGACCCGGGCAGTTGTAGG
64


 


CH1 5′-F
CCGACAGGCAGGGCACGAGGAG
65


 


CH1 5′-R
TGCGAGGCGGGACAAAGACAC
66


 


cHAC-F3
TGCAGGTGAAGTGACGGCCAGCCAAGAACA
67


 


cHAC-R3
TGGCAGCAGGGTGACAGGGAAGGCAGGGAAAAG
68


 


CH2 5′-F
CAGCACCCCAACGGCAACAAAGAAA
69


 


CH2 5′-R
CCCCAGGGCTGCACTCACCAACAT
70


 


CD8AKO-F2
AAGGCCCCCAAGCTGATTTCCGTGAGACTAAG
71


 


CD8AKO-R2
GCCTGGACGAGCTGTACGCCGAGTGGT
72


 


553-F4
GCTAAGGCACTTCGGTTCTCTTTGTGTTC
73


 


553-R4
GGTTGTCTTTAAAAGCAGGGATAAGGATG
74


 


553KO-F
GTCAGCCAGGCGGGCCATTTACCGTAAGTTATGTA
75


 


553KO-R
AGGGCTGGGTTAGATGGCACCAAATGAAAGGAGAA
76


 


STOPpuro-F2
ACTCCACACAGGCATAGAGTGTC
77


 


STOPpuro-R
GTGGGCTTGTACTCGGTCAT
78


 


GFP2
TGAAGGTAGTGACCAGTGTTGG
79


 


350P-F
ACCAGCGCGTCATCATCAAG
80


 


350P-R
ATCGCCAGCCTCACCATTTC
81


 


hVpreB3-F
CACTGCCTGCCCGCTGCTGGTA
82


 


hVpreB3-R
GGGCGGGGAAGTGGGGGAGAG
83


 


h15-F
AGCCCCAAGAACCCAGCCGATGTGA
84


 


h15-R
GGCAGAGGGAGTGTGGGGTGTTGTG
85


 


344-F
ATCATCTGCTCGCTCTCTCC
86


 


344-R
CACATCTGTAGTGGCTGTGG
87


 


IgL-F
GGAGACCACCAAACCCTCCAAA
88


 


IgL-R
GAGAGTTGCAGAAGGGGTGACT
89


 


hVpreB1-F
TGTCCTGGGCTCCTGTCCTGCTCAT
90


 


hVpreB1-R
GGCGGCGGCTCCACCCTCTT
91


 


553P-F
AGATCTCTTGAGCCCAGCAGTTTGA
92


 


553P-R
TGAAGTTAGCCGGGGATACAGACG
93


 


FABP1-F
TATCAAGGGGGTGTCGGAAATCGTG
94


 


FABP1-R
ACTGGGCCTGGGAGAACCTGAGACT
95


 


EIF2AK3-F
AGGTGCTGCTGGGTGGTCAAGT
96


 


EIF2AK3-R
GCTCCTGCAAATGTCTCCTGTCA
97


 


RPIA-F
CTTACCCAGGCTCCAGGCTCTATT
98


 


RPIA-R
CTCTACCTCCCTACCCCATCATCAC
99


 


IGKC-F
TGGAAGGTGGATAACGCCCT
100


 


IGKC-R
TCATTCTCCTCCAACATTAGCA
101


 


IGKV-F
AGTCAGGGCATTAGCAGTGC
102


 


IGKV-R
GCTGCTGATGGTGAGAGTGA
103


 


cos138KO-F
TCTTTCTCTCACCTAATTGTCCTGGC
104


 


cos138KO-R
AGGACTGGCACTCTTGTCGATACC
105


 


SC355F3R3KO-
GCCATTGTCGAGCAGGTAGT
106


F2




 


SC355F3R3KO-
TCCCTCATCAGCCATCCTAA
107


R2




 


MTA1-F3
AGCACTTTACGCATCCCAGCATGT
108


 


MTA1-R3
CCAAGAGAGTAGTCGTGCCCCTCA
109


 


ELK2P2-F
CCCACTTTACCGTGCTCATT
110


 


ELK2P2-R
ATGAAGGTCCGTGACTTTGG
111


 


CreCAGzeo-F3
GCCCTCACCTTGCAGACCACCTCCATCAT
112


 


CreCAGzeo-R3
CCTCTCCTGCTCAGTCCCCTTCCTTCCATC
113


 


VH3-F
AGTGAGATAAGCAGTGGATG
114


 


VH3-R
CTTGTGCTACTCCCATCACT
115


 


iscont1-F1
TTGCAAAGGGGCCTGGTGGAATA
116


 


hIgG1-R10
GCAGGGAACGGGATGAGGATAGAGG
117


 


bNeo 5′-R
GGGAGAGTGAAGCAGAACGT
118


 


bIgG1-5′-seq-R6
TTGCTGACAAAGGTCCGTCTA
119


 


iscont1-R1
GCTTGGCGGCGAATGGGCTGAC
120


 


isHAC-TM-dig-
AGAGAAGATGGGGCCCAAGAGCGCAGCTGTCCAGA
121


F3




 


isHAC-TM-dig-
GTTCACGCTGTTCTCCTGCCGCACTCCCCGTATGG
122


R2




 


isHAC-Sw-dig-
TTTCTCAGGAGGCAGTTAATGTGGTCTGGTATTCC
123


F5




 


isHAC-Sw-dig-
GCAGGGCTGCCAGGGGTTAGTGCCGTGGGGGTAGAT
124


R3




 


hIgG1-F10
CCAGGGCCACAGTTAACGGATACGA
125


 


bIgG1-5′-Seq-
GGGTCACTTTCTCGGTCCTGGTCT
126


R10




 


iscont1-F3
GGCCCCTCCATTTGTACTTTCTAT
127


 


iscont1-R6
GGGGCAGGAGGAGAAGGGGACGAC
128


 


hIgG1-F25
CCTGGTCCTCACATGGCCATACCTC
129


 


hIgG1-R23
GGTCCGGGCTCTGGGGATTTCAT
130


 


hg1TMneg-F3
CCTCCCTGGTCCTCACATGGCCATA
131


 


hg1TMneg-R3
CATGGCACGGCAGGGTCCGGGC
132


 


hIgG1TM-dig-F1
CTCTGCAGAGCCCAAATCTTGTGACAAAACTCA
133


 


hIgG1TM-dig-R2
CCCCCGGGCTGCAGGAATTCGATATCAAGCTTAGGAC
134


 


hg1TMneoattP-
AAGCGGGAAGGGACTGGCTGCTATTGGGCGAAGTG
135


F1




 


hg1TMneoattP-
GGAGCCCGGCACCGTCCTGGGTTTCCTTTCCTTAT
136


R1




 


hg1FRTCAGattP
ATGGACGGGATGACCTGGGAGATCGTGGCAAGTTT
137


hisD-F1




 


hg1FRTCAGattP
GGGGGCCCGGTACCGAAGTTCCTATTCCGAAGTTC
138


hisD-R1




 


bIgG1-3′-SeqF3
CACTGGTCAGTGAGAAGGAC
139


 


attPpuro-R3
CACCCCAGGCTTTACACTTTATGCTTCC
140


 


hIgG1-R15
GCTCCCCCTACCACCTCCCTTTAC
141


 


CAGDsRed-F2
GGCGGGGTTCGGCTTCTGGCGTGTGAC
142


 


CAGDsRed-R2
CTTGGCCATGTAGATTGACTTGAACTCC
143


 


bIgG1-dig-F1
GGCGCCGCTTAAACCACCCCACCAACCCACAA
144


 


hIgG1-dig-R1
ACCTGGGCACGGTGGGCATGTGTGAGTTTTGTC
145


 


bIgG1TM-R4
AGACAGCAAAGAGAAAGAACAGGCCCCCACATTAG
146









CGH Analysis.
Array probes for CGH analysis were designed by Roche NimbleGen, based on estimated sequence of the cKSL-HACΔ vector (see FIG. 24). Experiments and data analysis were performed by Roche NIMBLEGENTM.
FISH Analysis.
Human COT-1 FISH and hChr-specific multi-color FISH were performed as previously described5, 20, 21. To specifically stain the hIGH, hIGK and hIGL loci, probes were synthesized from DNA derived from BAC clones RP11-417P24, RP11-316G9 and RP11-22M5, respectively.
Flow Cytometry Analysis.
Flow cytometry analysis on B cell development in newborn transgenic (Tc) calves were performed as previously described5 with the following modifications. To detect surface hIgG on Tc bovine B cells, goat anti-hIgG (Life Technologies) directly labeled with AF 488 was used. To label surface hIgκ or hIgλ on Tc bovine B cells, mouse anti-hIgκ antibody directly labeled with PE (Biolegend) or mouse anti-hIgλ antibody directly labeled with PE (Southern Biotech) was used. To label surface bIgλ or bIgκ on the B cells, mouse monoclonal anti-bIg (in-house clone 132D7) or mouse monoclonal anti-bIgκ (in-house clone 132B10) followed by Zenon mouse IgG1PE labeling (Life Technologies) were used. Staining was done by a standard protocol and then analyzed by FACSARIATM flow cytometer (BD Biosciences).
ELISA.
Total hIgG ELISA assay was performed as previously described5. For fully hIgG/hIgκ or hIgG/hIgλ detection, goat anti-hIgκ affinity-purified or goat anti-hIgλ affinity-purified (Bethyl) as a capture and goat anti-hIgG Fc-HRP (Bethyl) as a detection antibody were used. For hIgG/bIgκ detection, mouse monoclonal anti-bIgκ (in-house clone 132B10) as a capture and mouse anti-hIgG Fcγ-HRP (Jackson) as a detection antibody were used. For detection of hIgG1 or hIgG2, mouse anti-hIgG1 Fc or mouse anti-hIgG2 Fc (Hybridoma Reagent Laboratory) as a capture and mouse anti-hIgG HRP (Southern Biotech) as a detection antibody were used.
Immunization of Human Oral Squamous Cell Carcinoma to the HAC/TKO and HAC/DKO Calves.
The HAC/TKO and HAC/DKO calves were immunized with X-ray-irradiated human oral squamous cell carcinoma (DSMZ) antigen at 2×108 cells/dose formulated with Montanide ISA 25 adjuvant (Seppic) as water-in-oil emulsion plus Quil A (Accurate Chemical & Scientific Corp) as immune stimulant. The Tc calves were immunized two times at 3-week intervals (primary immunization followed by the booster after 3 weeks). Vaccine was administered by intramuscular injection in the neck region. Serum samples were collected as previously described5 before each immunization (V1 and V2) and 10 days and 14 days after each immunization for antibody titer analysis. Anti-human oral squamous cell carcinoma antibody titers were determined by flow cytometry analysis.
Measurement of Anti-Human Carcinoma Cell hIgG/hIgκ Titer in Tc Animal Sera by Flow Cytometry.
Sera collected from Tc calves immunized with human carcinoma cells were used as the primary antibody to stain the human carcinoma cells. Pre-immune Tc calf serum (V1D0) was used as the negative controls. AF488-conjugated goat anti-hIgG Fc (Invitrogen) at 1:80 dilution and PE-conjugated mouse anti-hIgκ (BioLegend) at 1:8 dilution were used to detect bound hIgG/hIgκ antibody. The assay was performed in PBS supplemented with 4% horse serum, 0.1% sodium azide and 2 mM EDTA. The results were expressed as % of the human carcinoma cells stained and mean fluorescence intensity (MFI) as measured by FACSARIATM flow cytometer (BD Biosciences).
Somatic Cell Nuclear Transfer.
Cloned fetuses and calves were produced using chromatin transfer procedure as described previously5, 12, 20, 21.
Results
Example 1. Bovine IGL Gene Cluster Deletion
One hypothesis is that inactivation of the bovine Ig light chain, in addition to the bIgH disruption, would support high productivity of fully human IgG in cattle. Because, unlike the human and mouse, cattle predominantly express Igλ light chain over Igκ, the bIGL gene was inactivated. However, there was little information published about the bIGL gene structure in the bovine genome when the inventors started this study, thus the bIGL gene sequence including its surrounding region was determined. For that purpose, a bovine BAC (bacterial artificial chromosome) genomic library was screened and then one BAC clone was subjected to full sequencing by a shotgun approach. A gene cluster composed of the five IGLJ-IGLC genes (IGLJ1-IGLC1 through IGLJ5-IGLC5) was identified, three of which (IGLJ2-IGLC2 through IGLJ4-IGLC4) appeared to be functional, judged from its deduced amino acid sequence (FIG. 1A). Both the IGLJ1-IGLC1 and IGLJ5-IGLC5 genes contain immature stop codon mutations, indicating possible pseudo genes. Around 13 kb downstream of the IGLJ5-IGLC5 gene, a potential enhancer element was found, 3′Eλ, which showed 60% DNA sequence homology with the human 3′Eλ (HSS-3) enhancer sequence. Chen, L et al., reported that four IGLJ-IGLC genes were identified in the bovine. In the inventors' analysis, the IGLJ2-IGLC2 and IGLJ3-IGLC3 exon sequences were identical, however their surrounding sequences, such as intron and 3′ untranslated region (UTR), were slightly but different, which led to the conclusion that the IGLJ2-IGLC2 and IGLJ3-IGLC3 are distinct genes (FIG. 8A, 8B).
Since the bIGL gene forms the gene cluster, instead of a single gene structure, the strategy was to develop a novel system in somatic cells for deleting the entire IGLJ-IGLC gene cluster by using Cre/loxP-mediated site-specific recombination (FIG. 1b). By means of homologous recombination, each loxP sequence was integrated 5′ outside of the IGLJ1 gene by a targeting vector pCλ1CAGzeoPuroloxPDT and 3′ outside of the IGLC5 gene by another targeting vector pCλ5CAGloxPneoDT, respectively, followed by Cre introduction. This step required three rounds of transfection and somatic cell nuclear transfer (SCNT) just for the hemizygous cluster deletion, which could compromise animal development due to accumulated epigenetic errors. Thus, the strategy was to reduce the number of transfection and SCNT by implementing co-transfection of the Cre expression and second knockout (KO) vectors together; two rounds of transfections (1st KO and then 2nd KO+Cre) could complete the cluster deletion. To the inventors' knowledge, such a big DNA deletion (27 kb deletion in length) had never been achieved in somatic cells, and its feasibility was uncertain. Therefore, a powerful positive selection for the deletion was used in such a way that the puromycin-resistant gene (puro) can be reconstituted only when the cluster deletion takes place, which could allow for selection under the presence of puromycin in cell culture. This cluster deletion can take place at two steps at a practical efficiency; twenty-one colonies out of 5×106 somatic cells transfected, all of which showed the expected deletion, indicating, unexpectedly, a high efficiency of Cre/loxP-mediated big DNA deletion (27 kb in this work) together with the second event of homologous recombination (the 2nd KO) in bovine fibroblasts. Importantly, the implementation of the two-step big DNA deletion in somatic cells supported the ability of the cells to give rise to healthy cloned animals that are fertile. To the inventors' knowledge, this is the first report of a site-specific big DNA deletion of multiple genes in somatic cells without using ES cells, therefore, it supports a feasibility of more dynamic genome engineering, than just one-to-one single gene modification, in non-murine species where somatic fibroblast cells are available.
Example 2. Establishment of Male and Female Bovine IGHM−/−IGHML1−/−IGL−/− Cell Lines
Multiple rounds of genetic modifications followed by SCNT in somatic cells could compromise animal development due to potentially accumulated, irreversible epigenetic errors. In order to reduce the round number of SCNT, sequential gene targeting was combined with animal breeding, as summarized in FIG. 2A.
It was previously reported that the IGHML1 locus mapped to the bChr11, the data here indicated that both the IGHM and IGHML1 loci are unexpectedly located on the bovine Chr21 (FIG. 9). So, this study was implemented on the basis of this new and surprising indication. Starting with the male primary Holstein fibroblast line 6939 for which the IGHM and IGHML1 alleles are designated as AY/ay and U/u, respectively (FIG. 2B), IGHM and IGHML1 loci were sequentially knocked out in an allele-specific manner to establish IGHM−/+IGHML1−/− cell lines by using the targeting vectors, pBCμΔNKOneo, pBCμΔKOpuro and pbCμAYKObsr, for the alleles U, u and AY, respectively. A female primary Holstein×Jersey cross-breed (HoJo) fibroblast line 3427, for which the IGHM and IGHML1 alleles are designated as 10AY/7AYJ and 8U/5u, respectively (FIG. 2B), was used to generate IGHM−/− cell lines by using the targeting vectors, pbCμAYKObsr and pbCμ7AYJKOhyg, for the alleles 10AY and 7AYJ, respectively. From each of the male IGHM−/+IGHML1−/− and female IGHM−− cell lines, cloned bovines were generated and then they were bred each other around 18-20 months of age. Around 40 days of gestation, 18 fetuses were collected and genotyped. Seven fetuses (39%) were of the IGHM−/−IGHML1−/+ genotype. In all the seven fetuses, the neo KO cassette at U and the bsr one at AY were always linked, supporting that data that both the IGHM and IGHML1 loci are unexpectedly located on the bovine Chr21. One male and female cell line, J481 and H412, respectively, were selected for the bIGL gene cluster deletion (FIG. 2B).
The male cell line J481 (IGHM−/−IGHML1−/+), in which the inventors designated the bIGL alleles as A and D, was transfected with the pCλ1(A)CAGzeoPuroloxPDT vector specific to the allele A, selected under zeocin and then screened for the occurrence of homologous recombination by a genomic PCR using a primer pair, CL1puro-F2R2, as shown in FIG. 2C. Positive colonies (18%) were identified by sequencing the PCR product, some of which were further subjected to another genomic PCR using a PCR pair, R-R1×R-F2, followed by sequencing (FIG. 2C). The cell line J481 contains the alleles A and D for the bIGL locus and this PCR amplifies one polymorphic site between the two alleles; T for the allele A and G for the allele D. For example, in colony 27, only G was detected, demonstrating that the allele A was disrupted due to the insertion of the CAGzeo/loxP/promoter-less puro cassette between the R-R1 and R-F2 primer annealing sites. Colony 27 was used for SCNT to generate 40 day fetuses from which a cell line K655-1 IGHM−/−IGHML1−/+IGL1−/+ was established.
Subsequently, the cell line K655-1 was co-transfected with the pCλ5(A)CAGloxPneoDT vector specific to the allele A and the Cre-expression plasmid to bring about the cluster deletion, which was selected by puromycin. Twenty-one puromycin-resistant colonies were obtained and subjected to two kinds of genomic PCRs, CL5CAG-F2R2 and CAGpuro-F3R3, as shown in FIG. 2D. The former was to identify the occurrence of the homologous recombination at the 3′ side of the IGLC5 gene and the latter was to detect the incidence of the cluster deletion. All the PCR products were confirmed to be correct by sequencing analysis. The double positive colonies were used for cloning to establish a cell line G054 IGHM−/−IGHML1−/+IGL−/+, which was further used to generate calves. Similarly, the female cell line H412 (IGHM−/−IGHML1−/+), in which the inventors designated the bIGL alleles as B and C, was subjected to the two-step cluster deletion on the allele B to generate calves. Finally, the male and female IGHM−/−IGHML1−/+IGL−/+ animals were bred each other around 18-20 months of age. Around 40 days of gestation, 58 fetuses were collected and genotyped. Five fetuses (8.62%) were of the IGHM−/−IGHML1−/−IGL−/− genotype, and then five IGHM−/−IGHML1−/−IGL−/− triple knock out (TKO) cell lines were established (FIG. 2E and FIG. 10).
Example 3. cKSL-HACΔ and KcHACΔ Vector Construction
It is possible that there could be some species-incompatibilities between human and bovine that could hamper high production of fully hIgG in the bovine. As one of such species-incompatibilities, the IgM-based pre-BCR/BCR function was addressed. Among immunoglobulin heavy (IgH) chain classes, the IgM heavy chain is the first to be expressed, and is important for B cell development to eventually lead to secretion of IgG. In the Tc bovine condition, hIgM is expressed on the bovine B cell surface to interact with bovine surrogate light chain, followed by orthodox bovine light chain, and with bovine Ig-α/Ig-β molecules for the pre-BCR/BCR-mediated signaling, which is crucial for the subsequent B cell development. There may be species-incompatibilities in the hIgM protein interacting with bovine surrogate light chain, orthodox light chain and Ig-α/Ig-β molecules, due to the species-specific sequence differences (FIG. 11A-11D). To address this hypothesis, two HAC vectors were constructed, KcHACΔ and cKSL-HACΔ (FIG. 3A). In the KcHACΔ, part of the hIGHM constant region gene (the CH1 through TM2 domains) was bovinized so that such a chimeric IgM {cIgM (CH1)} protein could interact with bovine surrogate light chain, orthodox light chain and Ig-α/Ig-β molecules for better pre-BCR/BCR signaling. In the cKSL-HACΔ, part of the hIGHM constant region gene (the CH2 through TM2 domains) was differently bovinized and, additionally, the human surrogate light chain hVPREB1 and hIGLL1 (λ5 in the mouse) genes were introduced with the hChr22 fragment so that such a chimeric IgM (‘cIgM (CH2)’; SEQ ID NO: 200) protein could pair with human surrogate light chain and could also interact with bovine Ig-α/Ig-β molecules for better pre-BCR/BCR signaling. Due to the species-specific distinct sequences of the variable region and constant region of hIgM, cIgM (CH1) and cIgM (CH2) proteins, pre-BCR/BCR function/signaling in each HAC vector (e.g., κHAC, KcHACΔ, cKSL-HACΔ, respectively) could affect B cell developmental fate, and eventually hIgG production profile, differently.
As a starting HAC vector onto which a defined human chromosome region can be cloned (chromosome cloning) by means of site-specific chromosome translocation, the hChr14 fragment SC20 was used. SC20 was a naturally occurring fragment during microcell-mediated chromosome transfer (MMCT), thus its structure was not defined. For the purpose of using a structure-defined hChr14 vector and of removing as many irrelevant human genes as possible, the intact hChr14 was modified, followed by the IgM bovinizations, which generated new hChr14-based vectors, CH1D2 and CH2D4, for the KcHACΔ and cKSL-HACΔ vector construction, respectively.
The cKSL-HACΔ vector was constructed in chicken DT40 cells as outlined in FIG. 3B (see also Methods). Clone SLKD18 which contains the SLKH fragment was created by translocating the hChr22 fragment, covering the entire hIGL and surrogate light chain hVPREB1/hIGLL1 loci, to the hChr2 fragment having the hIGK locus, and clone CH2D4 which contains the hChr14 fragment (14D) with the cIgM (CH2)-bovinized hIGH locus, were fused to generate DT40 hybrid clone cKSLD22. The Cre expression plasmid was introduced to mediate site-specific recombination between the two loxP sites, one at the cos138 locus on the SLKH fragment and another at the RNR2 locus on the CH2D fragment, and also to delete the floxed CAG promoter-zeo cassette within the cIgM (CH2) domain. Recombinants were enriched by sorting of GFP positive cells as GFP expression was conferred by reconstitution of the PGK promoter-loxP-GFP cassette at the translocation site. This is the first report of construction of an artificial chromosome composed of structurally defined, three different chromosome fragments (e.g., hChr2, hChr14 and hChr22).
The KcHACΔ vector was similarly constructed in DT40 cells as outlined in FIG. 3C (see also Methods). Likewise, the KcHAC vector was constructed in which the hChr2 fragment (KTL1) was translocated to the SC20 fragment bearing the bovinized IgM {cIgM (CH1)} sequence.
Example 4. Human IgG Production in a Series of HAC/IGHM−/−IGHML1−/− (DKO) Cattle
The cKSL-HACΔ, KcHACΔ and KcHAC vectors were transferred to Chinese hamster ovary (CHO) cells by means of MMCT to establish CHO-based master cell banks, cKSLDC6, 15, 23, KCDC15 and CKF4, respectively, which were confirmed by the extensive genomic PCR and CGH (FIG. 12A-12C). Three HAC vectors, cKSL-HACΔ, KcHAC and κHAC, were then transferred from the CHO cell lines to IGHM−/−IGHML1−/− (DKO) cell lines obtained from breeding to generate cKSL-HACΔ/DKO, KcHAC/DKO and κHAC/DKO calves. An aim of the cKSL-HACΔ and KcHAC vectors was to address the species-incompatibility between human and bovine in the IgM-mediated pre-BCR/BCR function for B cell development, therefore B cell development profile was investigated in peripheral blood mononuclear cells (PBMCs) of these animals at newborn stage (FIG. 4A). For IgM detection in the KcHAC/DKO animals, anti-bIgM antibody was used because of its bovinized CH1 domain while anti-hIgM antibody can still recognize the cIgM (CH2) protein from the cKSL-HACΔ vector. In comparison with the κHAC/DKO animals, both the cKSL-HACΔ/DKO and KcHAC/DKO calves indicated higher percentages of IgM-single positive and IgM/CD21-double positive B cells. Surprisingly, IgM/bIgλ, IgM/bIgκ and even IgM/hIgκ-double positive B cells were only detected in the KcHAC/DKO animals. In the cKSL-HACΔ/DKO calves, either hIgM/bIgλ, hIgM/bIgκ, hIgM/hIgκ or hIgM/hIgλ-double positive B cells were undetectable by flow cytometry, despite the increased percentage of hIgM/CD21-double positive B cells, although these transcripts were detected by RT-PCR (FIG. 12D).
Around 5-6 months of age, concentrations of serum total hIgG, pairing either with hIgκ/λ or bIgλ/κ, and fully hIgG/hIgκ were measured (FIG. 4B). Compared with the κHAC/DKO animals excluding calf 468, serum concentrations of total hIgG drastically increased particularly with the cKSL-HACΔ vector with mostly hIgG1-dominance (hIgG1/hIgG2 ratio >1) while the KcHAC/DKO animals showed considerably high hIgG2 dominancy (FIG. 4C). Although the cKSL-HACΔ/DKO calves produced substantially higher amounts of total hIgG than the KcHAC/DKO ones, percentages of fully hIgG/hIgκ appeared to be lower (FIG. 4B, 4C), with fully hIgG/hIgλ being 5-10% of fully hIgG/hIgκ.
These data suggest potential species-incompatibilities in the IgM pre-BCR/BCR function, leading to the considerable differences in the B cell development and hIgG production profile between the differently bovinized cIgM (CH1) and cIgM (CH2) proteins without or with human surrogate light chain. This is novel evidence of the species-incompatibility in IgM pre-BCR/BCR function that eventually affects fully hIgG production profile.
Example 5. isHAC, istHAC and isKcHACΔ Vector Construction
The next strategy was to directly alter the efficiency of class switch to hIgG, especially to hIgG1, by direct bovinization of the hIGHG1 gene class switch regulatory element on the cKSL-HACΔ and KcHACΔ vectors. The transmembrane and cytoplasmic domains of the hIGHG1 gene were also bovinized for potentially better hIgG1 BCR-mediated signaling under the bovine environment.
The determination on IgG subclass class switch recombination is preceded by transcription from each immunoglobulin heavy chain (IGH) locus-associated switch region (SH), called germline transcript. Each IGH constant region (CH) gene is linked with its own SH region which is also associated with its own IH exons. The germline transcript IH-SH-CH (eventually spliced to mature IH-CH) is driven by the promoter/enhancer elements located just 5′ of the IH exons and those elements are cytokine or other activator-responsive. In a simple model of class switch, the specific activators and/or cytokines induce the germline transcript from its activator/cytokine-responsive IH promoter/enhancer. The 3′Eα element further enhances the transcription of IH-SH-CH sequence. This transcription causes the switch region to be relaxed so that it can be targeted by the enzyme, activation-induced cytidine deaminase (AID), which causes fusion with another SH region, leading to class switch. A hypothesis was that, for example, the hIγ1-hSγ1 regulatory element (from human IgG1) linked with the hIGHG1 gene was somehow incompatible with such bovine activators/cytokines-induced proteins to efficiently induce class switch to hIgG1, due to the species-specific sequence differences (FIG. 13A, 13B). This may be why many Tc bovines showed hIgG2-dominancy while hIgG1 is a major subclass in humans.
Based on the above hypothesis, the hIγ1-hSγ1 class switch regulatory element was bovinized with the class switch regulatory element of the bIGHG1 gene to construct the isHAC vector having the bIγ1-bSγ1 sequence upstream of the hCγ1 (human heavy chain IgG1) region on the cKSL-HACΔ vector (FIG. 5, see also Methods). Moreover, the transmembrane and cytoplasmic domains of the hIGHG1 gene on the isHAC was further bovinized with the bIGHG1 gene transmembrane and cytoplasmic domains to generate the istHAC (FIG. 5, see also Methods), considering the species-specific sequence differences (FIG. 13C). Since the cKSL-HACΔ and KcHACΔ vectors might potentially have functional differences, as seen in the DKO background, and it was uncertain how these two HACs would behave in the TKO background lacking the bIGL expression, the KcHACΔ vector was also bovinized to build the isKcHACΔ vector having the bIγ1-bSγ1 sequence upstream of the hCγ1 region on the KcHACΔ (FIG. 5, see also Methods).
Example 6. Human IgG Production in a Series of HAC/IGHM−/−IGHML1−/−IGL−/− (TKO) Cattle
The isHAC, istHAC, isKcHACΔ, KcHACΔ and cKSL-HACΔ vectors were transferred from the CHO master cell banks to the IGHM−/−IGHML1−/−IGL−/− (TKO) cell lines by MMCT to generate a series of HAC/TKO calves. Calving efficiency at 270 days of gestation was around 7% out of recipients implanted, 60-70% of which survived at least up to 5-6 months after birth (Table 2). First of all, the lack of the bIGL expression was confirmed by RT-PCR at newborn stage (FIG. 6A). Then, in order to address an impact of the ablation of the bIGL expression on B cell development, flow cytometry was performed on the five genotypes of HAC/TKO calves at newborn stage (FIG. 6B). In comparison with the DKO background, percentages of hIgM-single positive and hIgM/CD21-double positive B cells seemed lower, except that percentages of hIgM/hIgκ (or hIgM/bIgκ)-double positive B cells increased, in the cKSL-HACΔ series (e.g., isHAC, istHAC and cKSL-HACΔ itself) with hIgG/hIgλ-double positive B cells undetectable. On the contrary, percentages of bIgM-single positive and bIgM/CD21-double positive B cells appear to be considerably similar to that of the DKO background in the KcHACΔ series (e.g., isKcHACΔ and KcHACΔ itself), with percentages of bIgM/hIgκ (or bIgM/bIgκ)-double positive B cells substantially increased.







TABLE 2







Production of cloned calves from genetically modified fibroblast cell lines














TKO






Calves survived











cell line 


Pregnant at (%)a
up to 5-6 months














ID
Genotype
Recipients
40 d
120 d
180 d
270 d
(%)a

















E024A-2
KcHACΔ/
85
36 (42)
17 (20)
17 (20)
6 (7)
5 (6)


A596A-
TKO
85
22 (26)
11 (13)
10 (12)
5 (6)
1 (1)


1









A332A

80
28 (35)
 9 (11)
 9 (11)
4 (5)
2 (3)


Subtotal

250
86 (34)
37 (15)
36 (14)
15 (6) 
  8 (3.2)


E024A-2
cKSL-
139
52 (37)
27 (19)
25 (18)
13 (9) 
8 (6)



HACΔ/TKO








E024A-2
isHAC/TKO
81
19 (23)
4 (5)
4 (5)
3 (4)
3 (4)


A596A-

80
24 (30)
10 (13)
9 (11)
3 (4)
2 (3)


1









A332A

68
21 (31)
13 (19)
12 (18) 
6 (9)
6 (9)


A114A

48
18 (38)
 8 (17)
 7 (15)
2 (4)
1 (2)


Subtotal

277
82 (30)
35 (13)
32 (12)
14
 12 (4.3)








(5.1)



E024A-2
istHAC/TKO
80
29 (36)
18 (23)
16 (20)
 8 (10)
5 (6)


C970

46
20 (43)
11 (24)
 9 (20)
3 (7)
3 (7)


Subtotal

126
49 (39)
29 (23)
25 (20)
11
  8 (6.3)








(8.7)



E024A-2
isKcHACΔ/
80
33 (41)
24 (30)
24 (30)
11 (14)
 9 (11)


A596A-
TKO
80
41 (51)
21 (26)
19 (24)
6 (8)
3 (4)


1









Subtotal

160
74 (46)
45 (28)
43 (27)
17 (11)
 12 (7.5)


Total

952
343
173
161
70
48 (5) 





(36)
(18)
(17)
(7.4)






aPercentages were calculated by dividing the number of fetuses or calves by that of recipients implanted.













TABLE 3







p values for the comparison in serum concentration


of total hlgG among the genotypes














A
B
C
D
E
F
G
H

















A
0.8096
0.1742
0.5559
0.9495
0.9818
0.0832
0.0205*


B

0.6456
<0.001*
1.0000
0.0013*
<0.001*
<0.001*


C


<0.001*
0.8141
0.0018*
<0.001*
<0.001*


D



0.0328*
0.0039*
<0.001*
<0.001*


E




0.2741
0.0018*
<0.001*


F





<0.001*
<0.001*


G






0.1111





A, cKSL-HACΔ/TKO (n = 8);


B, isHAC/TKO (n = 12);


C, istHAC/TKO (n = 8);


D, KcHACΔ/TKO (n = 8);


E, isKcHACΔ/TKO (n = 12);


F, cKSL-HACΔ/DKO (n = 33);


G, KcHAC/DKO (n = 12);


H, κHAC/DKO (n = 8)


*shows a significant difference (p < 0.05).













TABLE 4







p values for the comparison in serum concentration


of fully hlgG/hlgκ among the genotypes














A
B
C
D
E
F
G
H

















A
0.5011
0.0369*
0.9092
0.2341
0.0438*
0.0241*
0.0170*


B

0.4092
<0.001*
0.9202
<0.001*
<0.001*
<0.001*


C


<0.001*
0.9974
<0.001*
<0.001*
<0.001*


D



0.0055*
<0.001*
<0.001*
<0.001*


E




<0.001*
<0.001*
<0.001*


F





0.0039*
<0.001*


G






0.5162





A, cKSL-HACΔ/TKO (n = 8);


B, isHAC/TKO (n = 12);


C, istHAC/TKO (n = 8);


D, KcHACΔ/TKO (n = 8);


E, isKcHACΔ/TKO (n = 12);


F, cKSL-HACΔ/DKO (n = 33);


G, KcHAC/DKO (n = 12);


H, κHAC/DKO (n = 8)


*shows a significant difference (p < 0.05).













TABLE 5







p values for the comparison in serum fully hlgG/hlgκ


(%)/total hlgG among the genotypes















A
B
C
D
E
F
G

















A

0.5344
0.0914
<0.001*
<0.001*
<0.001*
<0.001*


B


0.9248
0.0074*
<0.001*
<0.001*
<0.001*


C



0.2155
<0.001*
<0.001*
<0.001*


D




<0.0938*
<0.001*
<0.001*


E





<0.001*
<0.001*


F






<0.001*





A, cKSL-HACΔ/TKO (n = 8);


B, isHAC/TKO (n = 12);


C, istHAC/TKO (n = 8);


D, KcHACΔ/TKO (n = 8);


E, isKcHACΔ/TKO (n = 12);


F, cKSL-HACΔ/DKO (n = 33);


G, KcHAC/DKO (n = 12)


*shows a significant difference (p < 0.05).






Since the rationale for the isHAC, istHAC and isKcHACΔ vector construction was to directly alter the efficiency of class switch to hIgG, especially to hIgG1, under the bovine physiological condition, by bovinizing the hIGHG1 gene class switch regulatory element, serum concentrations of fully hIgG/hIgκ and hIgG subclass distribution were measured around 5-6 months of age in a series of HAC/TKO calves (FIG. 6C-6H, FIG. 14). Overall, in the five HAC/TKO genotypes, both concentrations and percentages of fully hIgG/hIgκ drastically increased when compared with those of the HAC/DKO animals including the previous unique calf 468, so the bIGL cluster deletion proved to be surprisingly effective for high productivity of fully hIgG/hIgκ. Fully hIgG/hIgλ was  ̃5% of hIgG/hIgκ and the rest was chimeric hIgG/bIgκ (FIG. 15). Surprisingly, the isHAC/TKO, particularly the istHAC/TKO calves, considerably raised both total hIgG and fully hIgG/hIgκ production when compared with their original cKSL-HACΔ/DKO and even cKSL-HACΔ/TKO animals (FIG. 6E and Table 4). Of particular note, hIgG1/hIgG2 ratio drastically arose both in the isHAC/TKO and istHAC/TKO calves while the cKSL-HACΔ/TKO animals turned hIgG2-dominant from hIgG1-dominancy in the cKSL-HACΔ/DKO ones (FIG. 6I). This observation was consistently seen also in comparison between the isKcHACΔ/TKO, KcHACΔ/TKO and KcHAC/DKO calves (FIG. 6C-6F), where fully hIgG/hIgκ production substantially increased with the switch to hIgG1-dominancy in the isKcHACΔ/TKO animals from hIgG2-dominancy in the original KcHACΔ/TKO and KcHAC/DKO calves.
These data demonstrated that the Iγ1-Sγ1 class switch regulatory element is controlled in a species-specific manner. The effect of the bovinized Iγ1-Sγ1 sequence is of a particular interest. It is reported that virtually all transcription factor-binding locations, landmarks of transcription initiation, and the resulting gene expression observed from the hChr21 in the human hepatocytes were recapitulated across the entire hChr21 in the mouse hepatocyte nucleus. This implies that the human-specific gene expression profile could be simply provided by the human DNA primary sequence even under the non-human species environment. Applying this view to the Tc bovine situation, the non-bovinized HAC would have been sufficient for providing the human-like hIgG expression profile, such as hIgG1-dominancy, in the bovine condition, which, however, was not the case. Thus, the finding that bovinization of the hIγ1-hSγ1 sequence surprisingly caused the sufficient switch from hIgG2-dominancy to hIgG1-dominancy in the Tc bovine condition strongly suggests the species-incompatibility in IgG1 class switch regulation between the two species. Since immunoglobulin gene organization and diversification including class switch are thought to be evolved distinctly among species, addressing such species-incompatibilities will be generally useful to express human antibodies in non-human species. The species-specific effect on fully hIgG serum concentration seems to be different between the differently bovinized cIgM proteins {cIgM (CH1) vs. cIgM (CH2)}; the bovinization of the Iγ1-Sγ1 element in the cIgM (CH1) background significantly improved it (i.e. isKcHACΔ vs KcHACΔ) while it did not in the cIgM (CH2) background (i.e. isHAC vs cKSL-HACΔ). In the cIgM (CH2) background, the bovinization of IgG1 transmembrane/cytoplasmic domains was additionally necessary to significantly improve fully hIgG/hIgκ production (i.e. istHAC vs cKSL-HACΔ). Both in the cIgM (CH1) and cIgM (CH2) backgrounds, the bovinized Iγ1-Sγ1 sequence drastically altered hIgG1 subclass-dominancy.
Finally, to show that the HAC/TKO calves that underwent such complex chromosome engineering functionally generate fully hIgG/hIgκ polyclonal antibodies in response to antigen immunization, several HAC/TKO animals were hyperimmunized with human oral squamous cell carcinoma to see antigen-specific fully hIgG/hIgκ immune response in comparison with the HAC/DKO genotype, cKSL-HACΔ/DKO. All the HAC/TKO calves immunized mounted robust anti-human carcinoma fully hIgG/hIgκ response (28.45-80.36% positive for both hIgG and hIgκ), whereas the two cKSL-HACΔ/DKO animals had only 0.73-1.54% positive for both hIgG and hIgκ, and only showed hIgG-response (FIG. 6L, FIG. 16). The data indicates that HAC/TKO genotype is important for high productivity of antigen-specific fully hIgG/hIgκ polyclonal antibodies, which was further enhanced by the bovinized HAC vectors, istHAC and isKcHACΔ.
The invention is capable of producing a large quantity of fully hIgG/hIgκ (>5 g/1 on average/median in the novel genotypes, i.e. isHAC/TKO, istHAC/TKO and isKcHACΔ/TKO) in sera of a large farm animal species. This serum concentration of fully hIgG/hIgκ is, to the inventors' knowledge, the highest of any other transgenic mouse systems producing fully hIgG (typically around 0.5 g/l) and is the closest to that in healthy humans. Moreover, hIgG subclass produced in the isHAC/TKO, istHAC/TKO and isKcHACΔ/TKO calves can be controlled to be hIgG I-dominant, which is the major subclass in healthy humans and is also that of therapeutic hIgG recombinant antibodies in development and on the market. Importantly, all the HAC/TKO calves tested functionally generated fully hIgG/hIgκ polyclonal antibodies against human-origin antigens immunized, which would be difficult to achieve by conventional human plasma-derived WIG, due to immune tolerance in humans. This was accomplished using a novel strategy of addressing potential species-incompatibilities in some key components (pre-BCR/BCR machinery and Iγ1—Sγ1 regulatory element) through complex human chromosome engineering, as well as endogenous bovine chromosome engineering (a site-specific, big DNA deletion). This new concept of species-incompatibilities may be also taken into consideration for high expression of complicatedly regulated human genes in transgenic animals if DNA sequences of some regulatory elements are considerably different from humans. Significantly, this complex chromosome engineering was done in somatic cells to alleviate a necessity of using ES cells.
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## Claims

1. A human artificial chromosome (HAC) vector comprising one or more human immunoglobulin heavy and light chain loci that are capable of undergoing rearrangement and expression in B-cells to produce a human immunoglobulin in response to exposure to one or more antigens, wherein said immunoglobulin loci comprise:
(a) a gene encoding one or more human antibody heavy chains comprising at least a human IgG heavy chain, a human IgA heavy chain or both human IgG and IgA heavy chains, wherein each gene encoding an antibody heavy chain is operatively linked to its own class switch regulatory element upstream of the human antibody heavy chain;
(b) a gene encoding one or more human antibody light chains; and
(c) a gene encoding a human-ungulate chimeric IgM heavy chain constant region encoding constant heavy (CH) domains CH1, CH2, CH3 and CH4, and transmembrane domains (TM) TM1 and TM2, wherein the encoded CH1, CH2, and CH3 domains are human, and the encoded CH4, TM1 and TM2 domains are ungulate;
wherein at least one class switch regulatory element of the genes encoding the one or more human antibody heavy chains is replaced with an ungulate class switch regulatory element selected from the group consisting of Imu-Smu (Iμ-Sμ), Igamma-Sgamma (Iγ-Sγ), Ialpha-Salpha (Iα-Sα), and Iepsilon-Sepsilon (Iε-Sε) ungulate class switch regulatory elements.

2. The HAC of claim 1, wherein the gene encoding the one or more human antibody heavy chains is a human IgG antibody heavy chain.

3. The HAC vector of claim 2, wherein the IgG heavy chain is an IgG1 antibody heavy chain.

4. The HAC vector of claim 1, wherein the gene encoding the one or more human antibody heavy chains is a human IgA antibody heavy chain.

5. The HAC vector of claim 1, wherein the gene encoding the one or more human antibody heavy chains further comprises a human IgM antibody heavy chain.

6. The HAC vector of claim 1, wherein the one or more human antibody heavy chains is selected from the group consisting of IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2.

7. The HAC vector of claim 1, wherein the gene encoding the human-ungulate chimeric IgM heavy chain constant region is further modified so that:
(a) the encoded CH1 domain is a human-ungulate chimeric CH1 domain, and the encoded CH2, CH3, CH4, and TM1 and TM2 domains are ungulate; or
(b) the encoded CH1 domain is human, the encoded CH2 domain is a human-ungulate chimeric CH2 domain, and the encoded CH3, CH4, and TM1 and TM2 domains are ungulate.

8. The HAC vector of claim 7, wherein the encoded CH2, CH3, CH4, and TM1 and TM2 ungulate domains are bovine, the human-ungulate chimeric CH1 domain is a human-bovine chimeric CH1 domain and the human-ungulate chimeric CH2 domain is a human-bovine chimeric CH2 domain.

9. The HAC of claim 1, wherein the one or more human antibody heavy chains comprises a human IgG antibody heavy chain, wherein a transmembrane domain and an intracellular domain of a constant region of the human IgG heavy antibody chain are replaced with a transmembrane domain and an intracellular domain of an ungulate IgG antibody heavy chain constant region.

10. The HAC vector of claim 9, wherein the human IgG antibody heavy chain is a human IgG1 antibody heavy chain.

11. The HAC vector of claim 9, wherein the ungulate IgG antibody heavy chain constant region is a bovine IgG antibody heavy chain constant region.

12. The HAC vector of claim 1, wherein the ungulate class switch regulatory element is an Igamma-Sgamma (Iγ-Sγ) class switch regulatory element.

13. The HAC vector of claim 12, wherein the Iγ-Sγ class switch regulatory element is an Igamma1-Sgamma1 (Iγ1-Sγ1).

14. The HAC vector of claim 1, wherein each class switch regulatory element of the genes encoding the one or more human antibody heavy chains is replaced with an ungulate class switch regulatory element.

15. The HAC vector of claim 1, wherein the ungulate class switch regulatory element(s) are bovine class switch regulatory elements.

16. The HAC vector of claim 1, wherein the HAC vector comprises one or more genes encoding a human antibody surrogate light chain selected from the group consisting of pre-B lymphocyte 1 (VpreB1), pre-B lymphocyte 3(VpreB3) and lambda 5 (λ5) human antibody surrogate light chains.

17. The HAC vector of claim 1, further comprising an ungulate enhancer operatively linked to one or more genes encoding the one or more human antibody heavy chains.

18. The HAC vector of claim 17, wherein the enhancer is a 3′enhancer alpha (3′Ea enhancer).

19. A transgenic ungulate comprising the HAC vector of claim 1.

20. The transgenic ungulate of claim 19, wherein the transgenic ungulate is a transgenic bovine.

21. The HAC vector of claim 1, wherein the gene encoding the one or more human antibody light chains encodes at least a human kappa (κ) light chain, a human lambda (λ) light chain or both human kappa and lambda light chains.

22. The HAC vector of claim 6, further comprising one or more human antibody IgE and IgD human antibody heavy chains.