WO2013022782A1

WO2013022782A1 - Humanized universal light chain mice

Info

Publication number: WO2013022782A1
Application number: PCT/US2012/049600
Authority: WO
Inventors: John MCWIRTHER; Lynn Macdonald; Sean Stevens; Samuel Davis; David R. Buckler; Karolina A. Hosiawa; Andrew J. Murphy
Original assignee: Regeneron Pharmaceuticals, Inc.
Priority date: 2011-08-05
Filing date: 2012-08-03
Publication date: 2013-02-14
Also published as: JP6510234B2; NZ727084A; RU2014108208A; JP6724126B2; DK3572517T3; IL273982A; JP7174805B2; JP2023011882A; AU2020277108A1; HRP20192255T1; EP2739740B1; RS61946B1; HRP20210916T1; SI3572517T1; MX2021001074A; IL230766A0; CN107602696A; NZ781020A; AU2012294624B2; ES2872081T3

Abstract

Mice, tissues, cells, and genetic material are provided that comprise a humanized heavy chain immunoglobulin locus, a humanized light chain locus that expresses a universal light chain, and a gene encoding an ADAM6 or ortholog or homolog or functional fragment thereof. Mice are provided that express humanized heavy chains comprising human variable domains, and that express humanized light chains comprising human variable domains wherein the light chains are derived from no more than one, or no more than two, light chain V and J or rearranged V/J sequences. Fertile male mice that express antibodies with universal light chains and humanized heavy chains are provided. Methods and compositions for making bispecific binding proteins are provided.

Description

HUMANIZED UNIVERSAL LIGHT CHAIN MICE

FIELD OF INVENTION

[0001] Genetically modified mice, cells, embryos, tissues, and isolated nucleic acids for making antibodies and sequences encoding human immunoglobulin heavy chain variable domains, including bispecific antibodies, and including bispecific antibodies that comprise universal light chains. Compositions and methods include genetically modified mice with germline replacements at the endogenous mouse heavy chain variable locus, which comprise modified light chain loci that express light chains derived from no more than one or two different light chain V gene segments, wherein the mice are further genetically modified in their germline such that male mice bearing these modifications are fertile.

Genetically modified mice that express universal light chains and humanized heavy chain variable domains are provided, wherein the mice comprise an ADAM6 activity that is functional in a male mouse.

BACKGROUND

[0002] The development of antibodies for use as human therapeutics has a long and complex history. One significant advance has been the ability to make essentially fully human antibody sequences to use in designing effective human therapeutics with reduced potential for immunogenicity. Mice now exist that are modified in their germline to generate human antibody sequences derived from unrearranged gene segments (heavy and light) either as transgenes or as replacements at endogenous mouse immunoglobulin loci.

Replacement of mouse variable sequences with human variable sequences at

endogenous loci in mice, as with VELOCIMMUNE® humanized mice, allow for the mouse immune system to function essentially normally. As a result, exposing these mice to an antigen of choice generates a marvelously diverse, rich population of clonally selected B cells that express high affinity somatically mutated human variable domains that can be used in making fully human antibodies directed against the antigen of choice.

[0003] Human variable domains made in humanized mice can be used to design fully human bispecific antibodies, i.e., binding proteins that are heterodimers of heavy chains, where the identities and binding specificities of the heavy chain variable domains differ. But selecting light chains that can effectively associate and express with the heavy chain heterodimers has no facile solution. Developing human light chain variable domains for use in human therapeutics is certainly possible in humanized mice, but there are no easy solutions to selecting which light chains will effectively associate and express with heavy chains having desired binding characteristics, where the light chains are not detrimental to the expression or binding behavior of both heavy chains. [0004] Thus, there remains a need in the art for compositions and methods for developing human immunoglobulin variable regions for use in human therapeutics, including human immunoglobulin variable regions generated from nucleic acid sequences at endogenous mouse immunoglobulin loci.

SUMMARY

[0005] Mice are described that express human immunoglobulin variable domains that are suitable for use in bispecific binding proteins, including bispecific antibodies, wherein the mice comprise a humanization of an endogenous mouse heavy chain variable locus, wherein male mice comprising the humanization are fertile, and wherein the mice further comprise a humanization of an endogenous immunoglobulin light chain locus that results in the mouse expressing an immunoglobulin light chain repertoire that is derived from no more than one, or no more than two, λ and/or κ V gene segments.

[0006] Genetically engineered mice are provided that select suitable affinity-matured human immunoglobulin heavy chain variable domains derived from a repertoire of unrearranged human heavy chain V, D, and J segments, wherein the affinity-matured human heavy chain variable domains associate and express with a humanized universal light chain. The humanized universal light chain is expressed from a locus that comprises either no more than one or no more than two human light chain V segments and a human J segment operably linked to a light chain constant gene, or no more than one or no more than two rearranged (λ/λ/ϋλ, VK/JK, VX/JK, or VK/J ) human nucleic acid sequences encoding a light chain variable domain operably linked to a light chain constant gene. In various embodiments the universal humanized light chain domain pairs with a plurality of affinity-matured human heavy chain variable domains, wherein the plurality of heavy chain variable domains specifically bind different epitopes or antigens.

[0007] In one aspect, nucleic acid constructs, cells, embryos, mice, and methods are provided for making mice that comprise a humanized heavy chain immunoglobulin variable locus and a humanized light chain immunoglobulin variable locus, wherein the mouse expresses one of no more than two universal light chains, and mice that are males exhibit wild-type fertility.

[0008] In one aspect, a modified mouse is provided that comprises in its germline a humanized heavy chain immunoglobulin variable locus at an endogenous mouse heavy chain locus, and a humanized light chain immunoglobulin variable locus, wherein the mouse expresses a universal light chain, and wherein the mouse comprises a nucleic acid sequence encoding a mouse ADAM6 or ortholog or homolog or functional fragment thereof. In various embodiments the humanized light chain immunoglobulin variable locus is at an endogenous mouse light chain locus.

[0009] In one embodiment, the humanized heavy chain immunoglobulin variable locus comprises a replacement at the endogenous mouse heavy chain variable locus of all or substantially all functional mouse immunoglobulin heavy chain V, D, and J gene segments with one or more human V, human D, and human J gene segments, wherein the one or more human V, D, and J segments are operably linked and capable of rearranging to form a rearranged V/D/J gene that is operably linked to a heavy chain constant sequence.

[0010] In one embodiment, the mouse comprises a light chain locus that this engineered to make a universal light chain, wherein the universal light chain is a light chain that is derived from a light chain locus that comprises no more than one light chain V segment and no more than one light chain J segment, or a light chain locus that comprises a single rearranged light chain V/J sequence. In one embodiment, the mouse comprises an immunoglobulin light chain locus that comprises single human immunoglobulin light chain V segment that is capable of rearranging with a human light chain J gene segment (selected from one or a plurality of J segments) and encoding a human light chain variable domain. In another embodiment, the mouse comprises no more than two human light chain V segments at the light chain locus, each V segment of which is capable of rearranging with a human J gene segment (selected from one or a plurality of light chain J segments) and encoding a rearranged human light chain variable domain.

[0011] In one embodiment, the single human light chain V segment is operably linked to a human light chain J segment selected from JK1 , JK2, JK3, JK4, and JK5, wherein the single human light chain V segment is capable of rearranging to form a sequence encoding a light chain variable region gene with any of the one or more human light chain J segments.

[0012] In one embodiment, the mouse comprises an endogenous light chain locus that comprises a replacement of all or substantially all mouse V and J gene segments with no more than one, or no more than two, rearranged (V/J) nucleic acid sequences. In one embodiment, the no more than one or no more than two rearranged (V/J) nucleic acid sequences are selected from a human VK1 -39JK5, a V 3-20JK1 , and a combination thereof.

[0013] In one embodiment, the mouse lacks a functional endogenous light chain locus that is capable of expressing a mouse light chain variable domain. In one embodiment, the mouse comprises a nucleic acid sequence encoding a variable domain of a universal light chain at a κ locus. In one embodiment, the mouse comprises a nucleic acid sequence encoding a variable domain of a universal light chain at a λ locus. [0014] In one embodiment, the human V segment (or rearranged V/J sequence) is operabiy linked to a human or mouse leader sequence. In one embodiment, the leader sequence is a mouse leader sequence. In a specific embodiment, the mouse leader sequence is a mouse VK3-7 leader sequence.

[0015] In one embodiment, the human V segment (or rearranged V/J sequence) is operabiy linked to an immunoglobulin promoter sequence. In one embodiment, the promoter sequence is a human promoter sequence. In a specific embodiment, the human immunoglobulin promoter is a human VK3-15 promoter.

[0016] In one embodiment, the unrearranged V and J segments or the rearranged (V/J) sequence is operabiy linked to a light chain immunoglobulin constant region gene. In a specific embodiment, the constant region gene is a mouse CK gene.

[0017] In one embodiment, the unrearranged V and J segments or the rearranged (V/J) sequence are present at a κ light chain locus, and the light chain locus comprises a mouse K intronic enhancer, a mouse κ 3' enhancer, or both an intronic enhancer and a 3' enhancer. In a specific embodiment, the κ locus is an endogenous κ locus.

[0018] In one embodiment, the mouse comprises a κ locus comprising a sequence encoding a variable domain of a universal light chain, and the mouse comprises a nonfunctional immunoglobulin lambda (λ) light chain locus. In a specific embodiment, the λ light chain locus comprises a deletion of one or more sequences of the locus, wherein the one or more deletions renders the λ light chain locus incapable of rearranging to form a light chain gene. In another embodiment, all or substantially all of the V segments of the λ light chain locus are deleted. In one another embodiment, the mouse comprises a deletion of all, or substantially all, of the endogenous light chain variable locus.

[0019] In one embodiment, the mouse further comprises in its germline a sequence selected from a mouse κ intronic enhancer 5' with respect to rearranged immunoglobulin light chain sequence or the unrearranged gene segments, a mouse κ 3' enhancer, and a combination thereof.

[0020] In one embodiment, the universal light chain variable domain sequence of the mouse comprises one or more somatic hypermutations; in one embodiment, the variable domain sequence comprises a plurality of somatic hypermutations.

[0021] In one embodiment, the mouse makes a universal light chain that comprises a somatically mutated human variable domain. In one embodiment, the light chain comprises a somatically mutated human variable domain derived from a human V

segment, a human J segment, and a mouse CK gene. In one embodiment, the mouse does not express a λ light chain. [0022] In one embodiment, the human variable sequence is a rearranged human VK1 - 39JK5 sequence, and the mouse expresses a reverse chimeric light chain comprising (i) a variable domain derived from VK1 -39JK5 and (ii) a mouse C_L; wherein the light chain is associated with a reverse chimeric heavy chain comprising (i) a mouse C_H and (ii) a somatically mutated human heavy chain variable domain. In one embodiment, the mouse expresses a light chain that is somatically mutated. In one embodiment the C_L is a mouse

[0023] In one embodiment, the human variable sequence is a rearranged human VK3- 20JK1 sequence, and the mouse expresses a reverse chimeric light chain comprising (i) a variable domain derived from VK3-20JK1 , and (ii) a mouse C_L; wherein the light chain is associated with a reverse chimeric heavy chain comprising (i) a mouse C_H, and (ii) a somatically mutated human heavy chain variable domain.

[0024] In one embodiment, the mouse comprises both a rearranged human VK1 -39JK5 sequence and a rearranged human VK3-20JK1 sequence, and the mouse expresses a reverse chimeric light chain comprising (i) a light chain comprising a variable domain derived from the VK1 -39JK5 sequence or the VK3-20JK1 sequence, and (ii) a mouse C_L; wherein the light chain is associated with a reverse chimeric heavy chain comprising (i) a mouse CH, and (ii) a somatically mutated human heavy chain variable domain. In one embodiment, the mouse expresses a light chain that is somatically mutated. In one embodiment the C_L is a mouse CK.

[0025] In one embodiment, the mouse expresses a reverse chimeric antibody comprising a light chain that comprises a mouse CK and a somatically mutated human variable domain derived from a rearranged human VK1 -39JK5 sequence or a rearranged human VK3-20JK1 sequence, and a heavy chain that comprises a mouse C_H and a somatically mutated human heavy chain variable domain, wherein the mouse does not express a fully mouse antibody and does not express a fully human antibody. In one embodiment the mouse comprises a κ light chain locus that comprises a replacement of endogenous mouse κ light chain gene segments with the rearranged human VK1 -39JK5 sequence or the rearranged human VK3-20JK1 sequence, and comprises a replacement of all or substantially all endogenous mouse heavy chain V, D, and J gene segments with a complete or substantially complete repertoire of human heavy chain V, D, and J gene segments.

[0026] In one aspect, a genetically modified mouse is provided that expresses a single κ light chain derived from no more than one, or no more than two, rearranged κ light chain sequences, wherein the mouse, upon immunization with antigen, exhibits a serum titer that is comparable to a wild type mouse immunized with the same antigen. In a specific embodiment, the mouse expresses a single light chain sequence, wherein the single κ light chain sequence is derived from no more than one rearranged κ light chain sequence. In one embodiment, the serum titer is characterized as total immunoglobulin. In a specific embodiment, the serum titer is characterized as IgM specific titer. In a specific

embodiment, the serum titer is characterized as IgG specific titer. In a more specific embodiment, the rearranged κ light chain sequence is selected from a VK1 -39JK5 and VK3-20JK1 sequence. In one embodiment, the rearranged κ light chain sequence is a VK1 -39JK5 sequence. In one embodiment, the rearranged κ light chain sequence is a VK3-20JK1 sequence.

[0027] In one aspect, a genetically modified mouse is provided that expresses a plurality of immunoglobulin heavy chains associated with a single light chain sequence. In one embodiment, the heavy chain comprises a human sequence. In various

embodiments, the human sequence is selected from a variable sequence, a CH 1 , a hinge, a CH2, a CH3, and a combination thereof. In one embodiment, the single light chain comprises a human sequence. In various embodiments, the human sequence is selected from a variable sequence, a constant sequence, and a combination thereof. In one embodiment, the mouse comprises a disabled endogenous immunoglobulin locus and expresses the heavy chain and/or the light chain from a transgene or extrachromosomal episome. In one embodiment, the mouse comprises a replacement at an endogenous mouse locus of some or all endogenous mouse heavy chain gene segments (i.e. , V, D, J), and/or some or all endogenous mouse heavy chain constant sequences (e.g. , CHi , hinge, CH2, CH3, or a combination thereof), and/or some or all endogenous mouse light chain sequences (e.g. , V, J, constant, or a combination thereof), with one or more human immunoglobulin sequences.

[0028] In one embodiment, the mouse , following rearrangement of the one or more V, D, and J gene segments, or one or more V and J gene segments, the mouse comprises in its genome at least one nucleic acid sequence encoding a mouse ADAM6 gene or homolog or ortholog or functional fragment thereof. In one embodiment, following rearrangement the mouse comprises in its genome at least two nucleic acid sequences encoding a mouse ADAM6 gene or homolog or ortholog or functional fragment thereof. In one embodiment, following rearrangement the mouse comprises in its genome at least one nucleic acid sequence encoding a mouse ADAM6 gene or homolog or ortholog or functional fragment thereof. In one embodiment, the mouse comprises the ADAM6 gene or homolog or ortholog or functional fragment thereof in a B cell. [0029] In one embodiment, the male mice comprise a single unmodified endogenous ADAM6 allele or ortholog of homolog or functional fragment thereof at an endogenous ADAM6 locus.

[0030] In one embodiment, the male mice comprise an ADAM6 sequence or homolog or ortholog or functional fragment thereof at a location in the mouse genome that approximates the location of the endogenous mouse ADAM6 allele, e.g., 3' of a final V gene segment sequence and 5' of an initial D gene segment.

[0031] In one embodiment, the male mice comprise an ADAM6 sequence or homolog or ortholog or functional fragment thereof flanked upstream, downstream, or upstream and downstream (with respect to the direction of transcription of the ADAM6 sequence) of a nucleic acid sequence encoding an immunoglobulin variable region gene segment. In a specific embodiment, the immunoglobulin variable region gene segment is a human gene segment. In one embodiment, the immunoglobulin variable region gene segment is a human gene segment, and the sequence encoding the mouse ADAM6 or ortholog or homolog or fragment thereof functional in a mouse is between human V gene segments; in one embodiment, the mouse comprises two or more human V gene segments, and the sequence is at a position between the final V gene segment and the penultimate V gene segment; in one embodiment, the sequence is at a position following the final V gene segment and the first D gene segment.

[0032] In one embodiment, the humanized heavy chain immunoglobulin variable locus lacks an endogenous mouse ADAM6 gene. In one embodiment, the humanized heavy chain immunoglobulin variable locus comprises an ADAM6 gene that is functional in a male mouse. In a specific embodiment, the ADAM6 gene that is functional in the male mouse is a mouse ADAM6 gene, and the mouse ADAM6 gene is placed within or immediately adjacent to the humanized heavy chain immunoglobulin variable locus.

[0033] In one embodiment, the humanized heavy chain immunoglobulin variable locus lacks an endogenous mouse ADAM6 gene, and the mouse comprises an ectopic ADAM6 sequence that is functional in a male mouse. In one embodiment, the ectopic ADAM6 gene that is functional in the male mouse is a mouse ADAM6 gene. In one embodiment, the mouse ADAM6 gene is on the same chromosome as the humanized heavy chain immunoglobulin variable locus. In one embodiment, the mouse ADAM6 gene is on a different chromosome than the humanized heavy chain immunoglobulin variable locus. In one embodiment, the mouse ADAM6 gene is on an episome.

[0034] In one embodiment, the mouse comprises a first endogenous heavy chain allele and a second endogenous heavy chain allele, and the first endogenous heavy chain allele comprises a deletion of a mouse ADAM6 locus, and the first endogenous heavy chain allele comprises a replacement of all or substantially all functional mouse V, D, and J segments with one or more human V, D, and J segments. In one embodiment, the first and the second endogenous heavy chain alleles each comprise a deletion of an

endogenous mouse ADAM6 locus, and the first and the second endogenous heavy chain alleles comprise a replacement of all or substantially all functional mouse V, D, and J segments with one or more human V, D, and J segments. In one embodiment, the first and/or the second allele comprises an ectopic nucleic acid sequence that encodes a mouse ADAM6 or ortholog or homolog or functional fragment thereof. In one embodiment, the ectopic nucleic acid sequence is located 3' (with respect to the transcriptional directionality of the heavy chain variable locust) of a final mouse V gene segment and located 5' (with respect to the transcriptional directionality of the constant sequence) of a mouse (or chimeric human/mouse) heavy chain constant gene or fragment thereof (e.g., a nucleic acid sequence encoding a human and/or mouse: C_H1 and/or hinge and/or C_H2 and/or C_H3). In one embodiment, the ectopic nucleic acid sequence is located downstream (with respect to direction of transcription of the V segment locus) of a V segment and upstream of a D segment. In one embodiment, the ectopic nucleic acid sequence is located between the penultimate 3'-most V segment and the ultimate 3'-most V segment. In a specific embodiment, the ectopic nucleic acid sequence is located between human V segment V_H1 -2 and human V segment V_H6-1 . In one embodiment, the nucleotide sequence between the two human V gene segments is placed in opposite transcription orientation with respect to the human V gene segments. In a specific embodiment, nucleotide sequence encodes, from 5' to 3' with respect to the direction of transcription of ADAM6 genes, and ADAM6a sequence followed by an ADA 6b sequence. In a specific embodiment, the ADA 6 gene(s) is oriented in opposite transcriptional orientation as compared with the upstream and downstream flanking V segments.

[0035] In one embodiment, the nucleic acid sequence comprises a sequence encoding mouse ADAM6a or functional fragment thereof and/or a sequence encoding mouse ADAM6b or functional fragment thereof, wherein the ADAM6a and/or ADAM6b or functional fragment(s) thereof is operably linked to a promoter. In one embodiment, the promoter is a human promoter. In one embodiment, the promoter is the mouse ADAM6 promoter. In a specific embodiment, the ADAM6 promoter comprises sequence located between the first codon of the first ADAM6 gene closest to the mouse 5'-most D_H gene segment and the recombination signal sequence of the 5'-most DH gene segment, wherein 5' is indicated with respect to direction of transcription of the mouse immunoglobulin genes. In one embodiment, the promoter is a viral promoter. In a specific embodiment, the viral promoter is a cytomegalovirus (CMV) promoter. In one embodiment, the promoter is a ubiquitin promoter. [0036] In one embodiment, the mouse ADAM6a and/or ADAM6b are selected from the ADA 6a of SEQ ID NO: 1 and/or ADAM6b of sequence SEQ ID NO:2. In one

embodiment, the mouse ADAM6 promoter is a promoter of SEQ ID NO:3. In a specific embodiment, the mouse ADAM6 promoter comprises the nucleic acid sequence of SEQ ID NO:3 directly upstream (with respect to the direction of transcription of ADAM6a) of the first codon of ADAM6a and extending to the end of SEQ ID NO:3 upstream of the ADAM6 coding region. In another specific embodiment, the ADAM6 promoter is a fragment extending from within about 5 to about 20 nucleotides upstream of the start codon of ADAM6a to about 0.5kb, 1 kb, 2kb, or 3kb or more upstream of the start codon of ADAM6a.

[0037] In one embodiment, the nucleic acid sequence comprises SEQ ID NO:3 or a fragment thereof that when placed into a mouse that is infertile or that has low fertility due to a lack of ADAM6, improves fertility or restores fertility to about a wild-type fertility. In one embodiment, SEQ ID NO:3 or a fragment thereof confers upon a male mouse the ability to produce a sperm cell that is capable of traversing a female mouse oviduct in order to fertilize a mouse egg.

[0038] In one embodiment, the mice comprise a nucleic acid sequence that encodes an ADAM6 protein, or ortholog or homolog or fragment thereof, that is functional in a male mouse. In a specific embodiment, the nucleic acid sequence is within or adjacent to a human nucleic acid sequence that comprises one or more immunoglobulin variable region gene segment. In one embodiment, the one or more immunoglobulin variable region gene segments is at a modified endogenous mouse immunoglobulin heavy chain variable locus. In one embodiment, the modification comprises a replacement of all or substantially all functional mouse immunoglobulin heavy chain variable gene segments with a plurality of unrearranged human heavy chain gene segments that are operably linked to an

endogenous mouse constant region gene. In a specific embodiment, the nucleic acid sequence is between two human V segments. In a specific embodiment, the nucleic acid sequence is between a human V segment and a human D segment. In a specific embodiment, the nucleic acid sequence is between a human D segment and a human J segment. In a specific embodiment, the nucleic acid sequence is upstream of the 5'-most (with respect to direction of transcription of the V segment) human V segment. In a specific embodiment, the nucleic acid sequence is between a human J segment and an endogenous mouse heavy chain constant region gene sequence.

[0039] In one embodiment, the male mice are capable of generating offspring by mating, with a frequency that is about the same as a wild-type mouse. In one embodiment, the male mice produce sperm that can transit from a mouse uterus through a mouse oviduct to fertilize a mouse egg; in a specific embodiment, sperm of the mice transit through the oviduct about as efficiently as sperm from a wild-type mouse. In one embodiment, about 50% or more of the sperm produced in the mouse exhibit the ability to enter and/or transit an oviduct to fertilize a mouse egg.

[0040] In one embodiment, the mouse lacks a functional endogenous ADAM6 locus, wherein the mouse comprises an ectopic nucleotide sequence that complements the loss of mouse ADAM6 function in a male mouse. In one embodiment, the ectopic nucleotide sequence confers upon the male mouse an ability to produce offspring that is comparable to a corresponding wild-type male mouse that contains a functional endogenous ADAM6 gene. In one embodiment, the sequence confers upon the mouse an ability to form a complex of ADAM2 and/or ADAM3 and/or ADAM6 on the surface of sperm cell of the mouse. In one embodiment, the sequence confers upon the mouse an ability to travel from a mouse uterus through a mouse oviduct to a mouse ovum to fertilize the ovum.

[0041] In one embodiment, the mouse lacks a functional endogenous ADAM6 locus and comprises an ectopic nucleotide sequence encoding an ADAM6 or ortholog or homolog or fragment thereof that is functional in a male mouse and wherein the male mouse produces at least about 50%, 60%, 70%, 80%, or 90% of the number of litters a wild-type mouse of the same age and strain produces in a six-month time period.

[0042] In one embodiment, the mouse lacking the functional endogenous ADAM6 gene and comprising the ectopic nucleotide sequence produces at least about 1.5-fold, about 2-fold, about 2.5-fold, about 3-fold, about 4-fold, about 6-fold, about 7-fold, about 8- fold, or about 10-fold or more progeny when bred over a six-month time period than a mouse of the same age and the same or similar strain that lacks the functional

endogenous ADAM6 gene and that lacks the ectopic nucleotide sequence that is bred over substantially the same time period and under substantially the same conditions.

[0043] In one embodiment, the mouse lacking the functional endogenous ADAM6 gene and comprising the ectopic nucleotide sequence produces an average of at least about 2-fold, 3-fold, or 4-fold higher number of pups per litter in a 4- or 6-month breeding period than a mouse that lacks the functional endogenous ADAM6 gene and that lacks the ectopic nucleotide sequence, and that is bred for the same period of time.

[0044] In one embodiment, the mouse lacking the functional endogenous ADAM6 gene and comprising the ectopic nucleotide sequence is a male mouse, and the male mouse produces sperm that when recovered from oviducts at about 5-6 hours post- copulation reflects an oviduct migration that is at least 10-fold, at least 20-fold, at least 30- fold, at least 40-fold, at least 50-fold, at least 60-fold, at least 70-fold, at least 80-fold, at least 90-fold, 100-fold, 1 10-fold, or 120-fold or higher than sperm of a mouse that lacks the functional endogenous ADAM6 gene and that lacks the ectopic nucleotide sequence.

[0045] In one embodiment, the mouse lacking the functional endogenous ADAM6 gene and comprising the ectopic nucleotide sequence when copulated with a female mouse generates sperm that is capable of traversing the uterus and entering and traversing the oviduct within about 6 hours at an efficiency that is about equal to sperm from a wild-type mouse.

[0046] In one embodiment, the mouse lacking the functional endogenous ADAM6 gene and comprising the ectopic nucleotide sequence produces about 1.5-fold, about 2- fold, about 3-fold, or about 4-fold or more litters in a comparable period of time than a mouse that lacks the functional ADAM6 gene and that lacks the ectopic nucleotide sequence.

[0047] In one aspect, a mouse is provided that comprises a humanized endogenous mouse heavy chain variable immunoglobulin locus and a modification of a mouse light chain immunoglobulin locus, wherein the mouse expresses a B cell that comprises a rearranged human heavy chain immunoglobulin sequence operably linked to a human or mouse heavy chain constant region gene sequence, and the B cell comprises in its genome (e.g., on a B cell chromosome) a gene encoding an ADAM6 or ortholog or homolog or fragment thereof that is functional in a male mouse (e.g., a mouse ADAM6 gene, e.g., mouse ADAM6a and/or mouse ADAM6b), wherein the variable domains of immunoglobulin λ or κ light chains of the mice are derived from no more than one or no more than two light chain V gene segments.

[0048] In one embodiment, the rearranged immunoglobulin sequence operably linked to the heavy chain constant region gene sequence comprises a human heavy chain V, D, and/or J sequence; a mouse heavy chain V, D, and/or J sequence; a human or mouse light chain V and/or J sequence. In one embodiment, the heavy chain constant region gene sequence comprises a human or a mouse heavy chain sequence selected from the group consisting of a CH1 , a hinge, a C_H2, a C_H3, and a combination thereof.

[0049] In one aspect, a mouse suitable for making antibodies that have the same light chain is provided, wherein all or substantially all antibodies made in the mouse are expressed with the same light chain, wherein the light chain comprises a human variable domain, and wherein the antibodies comprise a heavy chain that comprises a human variable domain.

[0050] In one aspect, a mouse is provided that is characterized by an inability of the mouse to make a B cell that expresses an immunoglobulin light chain variable domain that is derived from a rearranged light chain sequence that is not a human VK1 -39JK5 or a human VK3-20JK1 sequence.

[0051] In one embodiment, the mouse exhibits a κ:λ light chain ratio that is about the same as a mouse that comprises a wild type complement of immunoglobulin light chain V and J gene segments. [0052] In one aspect, a mouse as described herein is provided that expresses an immunoglobulin light chain derived from a human VK1 -39JK5 or a human V 3-20JK1 sequence, wherein the mouse comprises a replacement of all or substantially all endogenous mouse heavy chain variable region gene segments with one or more human heavy chain variable region gene segments, and the mouse exhibits a ratio of (a) CD19⁺ B cells that express an immunoglobulin having a λ light chain, to (b) CD19⁺ B cells that express an immunoglobulin having a κ light chain, of about 1 to about 20.

[0053] In one embodiment, the mouse expresses a single κ light chain, wherein the single κ light chain is derived from a human VK1 -39JK5 sequence, and the ratio of CD1 9⁺ B cells that express an immunoglobulin having a λ light chain to CD19⁺ B cells that express an immunoglobulin having a κ light chain is about 1 to about 20; in one embodiment, the ratio is about 1 to at least about 66; in a specific embodiment, the ratio is about 1 to 66.

[0054] In one embodiment, the mouse expresses a single κ light chain, wherein the single κ light chain is derived from a human VK3-20JK5 sequence, and the ratio of CD1 9⁺ B cells that express an immunoglobulin having a λ light chain to CD19⁺ B cells that express an immunoglobulin having a κ light chain is about 1 to about 20; in one embodiment, the ratio is about 1 to about 21. In specific embodiments, the ratio is 1 to 20, or 1 to 21 .

[0055] In one embodiment, the percent of

B cells in the mouse is about the same as in a wild type mouse. In a specific embodiment, the percent of ^κ⁺^λ⁺ B cells in the mouse is about 2 to about 6 percent. In a specific embodiment, the percent of lgK⁺lg ⁺ B cells in a mouse wherein the single rearranged κ light chain is derived from a V 1 -39JK5 sequence is about 2 to about 3; in a specific embodiment, about 2.6. In a specific embodiment, the percent of lgic⁺lg ⁺ B cells in a mouse wherein the single rearranged κ light chain is derived from a VK3-20JK1 sequence is about 4 to about 8; in a specific embodiment, about 6.

[0056] In one embodiment, the mouse is does not comprise a modification that reduces or eliminates an ability of the mouse to somatically mutate any functional light chain locus of the mouse. In one embodiment, the only functional light chain locus in the mouse expresses a light chain that comprises a human variable domain derived from a rearranged sequence selected from a human VK1 -39JK5 sequence, a human VK3-20JK1 sequence, and a combination thereof.

[0057] In one aspect, a genetically modified mouse is provided that expresses a single K light chain derived from no more than one, or no more than two, rearranged κ light chain sequences, wherein the mouse exhibits usage of the κ light chain that is about 100-fold or more, at least about 200-fold or more, at least about 300-fold or more, at least about 400- fold or more, at least about 500-fold or more, at least about 600-fold or more, at least about 700-fold or more, at least about 800-fold or more, at least about 900-fold or more, at least about 1000-fold or more greater than the usage of the same light chain (i.e., derived from the same V segment and the same J segment, or derived from the same rearranged V/J segment) exhibited by a mouse bearing a complete or substantially complete human κ light chain locus. In a specific embodiment, the mouse bearing a complete or substantially complete human κ light chain locus lacks a functional unrearranged mouse κ light chain sequence. In a specific embodiment, the mouse expresses the single κ light chain from no more than one rearranged κ light chain sequence. In one embodiment, the mouse comprises one copy of a rearranged κ light chain sequence (e.g., a heterozygote). In one embodiment, the mouse comprises two copies of a rearranged κ light chain sequence (e.g., a homozygote). In a more specific embodiment, the rearranged κ light chain sequence is selected from a VK1-39JK5 and VK3-20J 1 sequence. In one embodiment, the rearranged κ light chain sequence is a VK1-39JK5 sequence. In one embodiment, the rearranged κ light chain sequence is a VK3-20JK1 sequence.

[0058] In one aspect, a genetically modified mouse is provided that expresses a single light chain derived from no more than one, or no more than two, rearranged κ light chain sequences, wherein the light chain in the genetically modified mouse exhibits a level of expression that is at least 10-fold to about 1 , 000-fold, 100-fold to about 1 ,000-fold, 200-fold to about 1 ,000-fold, 300-fold to about 1 , 000-fold, 400-fold to about 1 ,000-fold, 500-fold to about 1 ,000-fold, 600-fold to about 1 , 000-fold, 700-fold to about ,000-fold, 800-fold to about 1 ,000-fold, or 900-fold to about 1 ,000-fold higher than expression of the same rearranged light chain exhibited by a mouse bearing a complete or substantially complete human κ light chain variable locus. In one embodiment, the light chain comprises a human sequence. In one embodiment, the single light chain is derived from a rearranged κ light chain sequence selected from a human VK1-39JK5, a human VK3-20JK1 , and a

combination thereof.

[0059] In one embodiment, the level of expression of the light chain, for the purpose of comparing the expression of the light chain with expression in a mouse comprising a substantially completely humanized light chain variable locus, is characterized by quantitating mRNA of transcribed light chain sequence (from the one or two rearranged sequences), and comparing it to transcribed light chain sequence of a mouse bearing a complete or substantially complete light chain locus.

[0060] In one aspect, a method for making an antibody is provided, comprising expressing in a cell (a) a first human heavy chain variable domain nucleic acid sequence of an immunized mouse as described herein fused with a human C_H gene sequence; (b) a human light chain variable domain nucleic acid sequence of an immunized mouse as described herein fused with a human C_L gene sequence; and, (c) maintaining the cell under conditions sufficient to express a fully human antibody, and isolating the antibody. In one embodiment, the cell comprises a second human heavy chain variable domain nucleic acid sequence of a second immunized mouse as described herein fused with a human C_H gene sequence, the first heavy chain nucleic acid sequence encodes a first heavy chain variable domain that recognizes a first epitope, and the second heavy chain nucleic acid sequence encodes a second heavy chain variable domain that recognizes a second epitope, wherein the first epitope and the second epitope are not identical.

[0061] In one aspect, a method for making an epitope-binding protein is provided, comprising exposing a mouse as described herein with an antigen that comprises an epitope of interest, maintaining the mouse under conditions sufficient for the mouse to generate an immunoglobulin molecule that specifically binds the epitope of interest, and isolating the immunoglobulin molecule that specifically binds the epitope of interest;

wherein the epitope-binding protein comprises a heavy chain that comprises a somatically mutated human variable domain and a mouse C_H, associated with a light chain comprising a mouse C_L and a human variable domain derived from a rearranged human VK1-39JK5 or a rearranged human VK3-20JK1.

[0062] In one aspect, a method for making a bispecific antigen-binding protein is provided, comprising exposing a first mouse as described herein to a first antigen of interest that comprises a first epitope, exposing a second mouse as described herein to a second antigen of interest that comprises a second epitope, allowing the first and the second mouse to each mount immune responses to the antigens of interest, identifying in the first mouse a first human heavy chain variable region that binds the first epitope of the first antigen of interest, identifying in the second mouse a second human heavy chain variable region that binds the second epitope of the second antigen of interest, making a first fully human heavy chain gene that encodes a first heavy chain that binds the first epitope of the first antigen of interest, making a second fully human heavy chain gene that encodes a second heavy chain that binds the second epitope of the second antigen of interest, expressing the first heavy chain and the second heavy chain in a cell that expresses a single fully human light chain derived from a human VK1-39 or a human VK3- 20 gene segment to form a bispecific antigen-binding protein, and isolating the bispecific antigen-binding protein.

[0063] In one embodiment, the first antigen and the second antigen are not identical.

[0064] In one embodiment, the first antigen and the second antigen are identical, and the first epitope and the second epitope are not identical. In one embodiment, binding of the first heavy chain variable region to the first epitope does not block binding of the second heavy chain variable region to the second epitope.

[0065] In one embodiment, the first antigen is selected from a soluble antigen and a cell surface antigen (e.g., a tumor antigen), and the second antigen comprises a cell surface receptor. In a specific embodiment, the cell surface receptor is an immunoglobulin receptor. In a specific embodiment, the immunoglobulin receptor is an Fc receptor. In one embodiment, the first antigen and the second antigen are the same cell surface receptor, and binding of the first heavy chain to the first epitope does not block binding of the second heavy chain to the second epitope.

[0066] In one embodiment, the light chain variable domain of the light chain comprises 2 to 5 somatic mutations. In one embodiment, the light chain variable domain is a somatically mutated cognate light chain expressed in a B cell of the first or the second immunized mouse with either the first or the second heavy chain variable domain.

[0067] In one aspect, a cell that expresses an epitope-binding protein is provided, wherein the cell comprises: (a) a human nucleotide sequence encoding a human light chain variable domain that is derived from a rearranged human VK1-39JK5 or a rearranged human VK3-20JK1 , wherein the human nucleic acid sequence is fused (directly or through a linker) to a human immunoglobulin light chain constant domain nucleic acid sequence (e.g., a human κ constant domain DNA sequence); and, (b) a first human heavy chain variable domain nucleic acid sequence encoding a human heavy chain variable domain derived from a first human heavy chain variable domain nucleotide sequence, wherein the first human heavy chain variable domain nucleotide sequence is fused (directly or through a linker) to a human immunoglobulin heavy chain constant domain nucleic acid sequence (e.g., a human lgG1 , lgG2, lgG3, lgG4, or IgE sequence); wherein the epitope-binding protein recognizes a first epitope. In one embodiment, the epitope-binding protein binds the first epitope with a dissociation constant of lower than 10^"6 M, lower than 10^"8 M, lower than 10^"9 M, lower than 1 CT¹⁰ M, lower than 10 ¹ M, or lower than 10^"12 M. In one embodiment, the cell comprises a second human nucleotide sequence encoding a second human heavy chain variable domain, wherein the second human sequence is fused (directly or through a linker) to a human immunoglobulin heavy chain constant domain nucleic acid sequence, and wherein the second human heavy chain variable domain does not specifically recognize the first epitope (e.g., displays a dissociation constant of, e.g., 10 ⁶ M, 10^"5 M, 10^"4 M, or higher), and wherein the epitope-binding protein binds both the first epitope and the second epitope, and wherein the first and the second immunoglobulin heavy chains each associate with a light chain according to (a). In one embodiment, the second V_H domain binds the second epitope with a dissociation constant that is lower than 10^"6 M, lower than 10^"7 M, lower than 10^~8 M, lower than 10^"9 M, lower than 10^"10 M, lower than 10^"11 M, or lower than 10^"12 M.

[0068] In one embodiment, the epitope-binding protein comprises a first

immunoglobulin heavy chain and a second immunoglobulin heavy chain, each associated with a universal light chain (e.g. , a light chain derived from a rearranged human light chain variable sequence selected from a human VK1-39JK5 or a human V 3-20JK1), wherein the first immunoglobulin heavy chain binds a first epitope with a dissociation constant in the nanomolar (e.g. , 1 nM to 100 nM) to picomolar range (e.g. , 1 pM to 100 pM), the second immunoglobulin heavy chain binds a second epitope with a dissociation constant in the nanomolar to picomolar range (e.g. , 1 pM to 100 nM), the first epitope and the second epitope are not identical, the first immunoglobulin heavy chain does not bind the second epitope or binds the second epitope with a dissociation constant weaker than the micromolar range (e.g., the millimolar range), the second immunoglobulin heavy chain does not bind the first epitope or binds the first epitope with a dissociation constant weaker than the micromolar range (e.g., the millimolar range), and one or more of the variable domains (i.e., one or more of the light chain variable domain, the heavy chain variable domain of the first immunoglobulin heavy chain, and the heavy chain variable domain) of the second immunoglobulin heavy chain is somatically mutated. In one embodiment, binding of the epitope-binding protein to the first epitope does not block binding of the epitope-binding protein to the second epitope.

[0069] In one embodiment, the first immunoglobulin heavy chain comprises a wild type protein A binding determinant, and the second heavy chain lacks a wild type protein A binding determinant. In one embodiment, the first immunoglobulin heavy chain binds protein A under isolation conditions, and the second immunoglobulin heavy chain does not bind protein A or binds protein A at least 10-fold, a hundred-fold, or a thousand-fold weaker than the first immunoglobulin heavy chain binds protein A under isolation conditions. In a specific embodiment, the first and the second heavy chains are lgG1 isotypes, wherein the second heavy chain comprises a modification selected from 95R (EU 435R), 96F (EU 436F), and a combination thereof, and wherein the first heavy chain lacks such

modification.

[0070] In aspect, a mouse, embryo, or cell as described herein comprises a κ light chain locus that retains endogenous regulatory or control elements, e.g. , a mouse κ intronic enhancer, a mouse κ 3' enhancer, or both an intronic enhancer and a 3' enhancer, wherein the regulatory or control elements facilitate somatic mutation and affinity maturation of an expressed sequence of the κ light chain locus. [0071] In one aspect, a mouse cell is provided that is isolated from a mouse as described herein. In one embodiment, the cell is an ES cell. In one embodiment, the cell is a lymphocyte. In one embodiment, the lymphocyte is a B cell. In one embodiment, the B cell expresses a chimeric heavy chain comprising a variable domain derived from a human V gene segment; and a light chain derived from (a) a rearranged human VK1 -39/J sequence, (b) a rearranged human VK3-20/J sequence, or (c) a combination thereof;

wherein the heavy chain variable domain is fused to a mouse constant region and the light chain variable domain is fused to a mouse or a human constant region. In one

embodiment, the mouse cell comprises at least one gene that encodes a mouse ADAM6 or ortholog or homolog or functional fragment thereof. In one embodiment, the cell is a B cell and the B cell comprises a sequence encoding a rearranged human heavy chain immunoglobulin variable domain and a sequence encoding a universal light chain variable domain, wherein the B cell comprises on a chromosome a nucleic acid sequence encoding an ADAM6 protein or ortholog or homolog or fragment thereof that is functional in a male mouse; in one embodiment, the mouse B cell comprises two alleles of the nucleic acid sequence.

[0072] In one aspect, a mouse cell is provided, comprising a first chromosome that comprises a humanized immunoglobulin heavy chain locus comprising unrearranged human V, D, and J segments; a second chromosome that comprises a humanized immunoglobulin light chain locus that encodes or is capable of rearranging to encode a light chain, wherein the light chain locus comprises no more than one V segment (or no more than two V segments) and no more than one J segment (or no more than two J segments) operably linked to a light chain constant region gene, or no more than one or no more than two rearranged light chain V/J sequences operably linked to a light chain constant gene; and a third chromosome that comprises nucleic acid sequence encoding a mouse ADAM6 or ortholog or homolog or fragment thereof that is functional in a male mouse. In one embodiment, the first and third chromosomes are the same. In one embodiment, the second and third chromosomes are the same. In one embodiment, the first, the second, and the third chromosomes are each different. In one embodiment, the nucleic acid sequence encoding the mouse ADAM6 or ortholog or homolog or functional fragment thereof is present in two copies. In one embodiment, the cell is a somatic cell. In a specific embodiment, the somatic cell is a B cell. In one embodiment, the cell is a germ cell.

[0073] In one aspect, a hybridoma is provided, wherein the hybridoma is made with a B cell of a mouse as described herein. In a specific embodiment, the B cell is from a mouse as described herein that has been immunized with an antigen comprising an epitope of interest, and the B cell expresses a binding protein that binds the epitope of interest, the binding protein has a somatically mutated human heavy chain variable domain and a mouse heavy chain constant region, and has a human light chain variable domain derived from a rearranged human VK1 -39JK5 or a rearranged human VK3-20JK1 and a mouse C_L.

[0074] In one aspect, a cell is provided that comprises a fully human heavy chain gene comprising a nucleic acid sequence encoding a first heavy chain variable domain of a mouse as described herein, and a fully human light chain gene comprising a nucleic acid sequence encoding a universal light chain sequence as described herein. In one embodiment, the cell further comprises a nucleic acid sequence encoding a second heavy chain variable domain of a mouse as described herein, wherein the first and the second heavy chain variable domains are different. In one embodiment, the cell is selected from CHO, COS, 293, HeLa, and a retinal cell expressing a viral nucleic acid sequence (e.g., a PERC.6™ cell).

[0075] In one aspect, a mouse embryo is provided, wherein the embryo comprises a donor ES cell that is derived from a mouse as described herein.

[0076] In one aspect, use of a mouse embryo that comprises a genetic modification as described herein is provided, wherein the use comprises making a genetically modified mouse as described herein.

[0077] In one aspect, a human heavy chain variable domain and a human light chain variable domain amino acid sequence of an antibody made in a mouse as described herein are provided.

[0078] In one aspect, a human heavy chain variable domain nucleotide sequence and a human light chain variable domain nucleotide sequence of an antibody made in a mouse as described herein is provided.

[0079] In one aspect, an antibody or antigen-binding protein or antigen-binding fragment thereof (e.g., Fab, F(ab)₂, scFv) made in a mouse as described herein is provided.

[0080] In one aspect, a mouse made using a targeting vector, nucleotide construct, or cell as described herein is provided.

[0081] In one aspect, a progeny of a mating of a first mouse as described herein with a second mouse that is a wild-type mouse or genetically modified is provided.

[0082] In one aspect, use of a mouse as described herein to make a fully human antibody, or a fully human antigen-binding protein comprising an immunoglobulin variable domain or functional fragment thereof, is provided.

[0083] In one aspect, use of a mouse or tissue or cell as described herein to make a fully human bispecific antibody is provided. [0084] In one aspect, use of a nucleic acid sequence made by a mouse as described herein is provided, wherein the use comprises expressing the nucleic acid sequence in the manufacture of a human therapeutic.

[0085] In one aspect, use of a mouse as described herein to make an immortalized cell line is provided.

[0086] In one aspect, use of a mouse as described herein to make a hybridoma or quadroma is provided.

[0087] In one aspect, use of a mouse as described herein to make a nucleic acid sequence encoding an immunoglobulin variable region or fragment thereof is provided. In one embodiment, the nucleic acid sequence is used to make a human antibody or antigen- binding fragment thereof. In one embodiment, the mouse is used to make an antigen- binding protein selected from an antibody, a multispecific antibody (e.g., a bispecific antibody), an scFv, a bis-scFV, a diabody, a triabody, a tetrabody, a V-NAR, a VHH, a VL, an F(ab), an F(ab)₂, a DVD (i.e. , dual variable domain antigen-binding protein), an SVD (i.e. , single variable domain antigen-binding protein), or a bispecific T-cell engager (BiTE).

[0088] In one aspect, use of the mouse as described herein for the manufacture of a medicament (e.g. , an antigen-binding protein), or for the manufacture of a sequence encoding a variable sequence of a medicament (e.g., an antigen-binding protein), for the treatment of a human disease or disorder is provided.

[0089] Any of the embodiments and aspects described herein can be used in conjunction with one another, unless otherwise indicated or apparent from the context. Other embodiments will become apparent to those skilled in the art from a review of the ensuing description.

BRIEF DESCRIPTION OF THE FIGURES

[0090] FIG. 1A shows a general illustration, not to scale, for direct genomic

replacement of about three megabases (Mb) of the mouse immunoglobulin heavy chain variable gene locus (closed symbols) with about one megabase (Mb) of the human immunoglobulin heavy chain variable gene locus (open symbols).

[0091] FIG. 1 B shows a general illustration, not to scale, for direct genomic

replacement of about three megabases (Mb) of the mouse immunoglobulin κ light chain variable gene locus (closed symbols) with about 0.5 megabases (Mb) of the first, or proximal, of two nearly identical repeats of the human immunoglobulin κ light chain variable gene locus (open symbols).

[0092] FIG. 2A shows a detailed illustration, not to scale, for three initial steps (A-C) for direct genomic replacement of the mouse immunoglobulin heavy chain variable gene locus that results in deletion of all mouse V_H, D_H and J_H gene segments and replacement with three human V_H, all human D_H and J_H gene segments. A targeting vector for the first insertion of human immunoglobulin heavy chain gene segments is shown (3hV_H BACvec) with a 67 kb 5' mouse homology arm, a selection cassette (open rectangle), a site-specific recombination site (open triangle), a 145 kb human genomic fragment and an 8 kb 3' mouse homology arm. Human (open symbols) and mouse (closed symbols)

immunoglobulin gene segments, additional selection cassettes (open rectangles) and site- specific recombination sites (open triangles) inserted from subsequent targeting vectors are shown.

[0093] FIG. 2B shows a detailed illustration, not to scale, for six additional steps (D-l) for direct genomic replacement of the mouse immunoglobulin heavy chain variable gene locus that results in the insertion of 77 additional human V_H gene segments and removal of the final selection cassette. A targeting vector for insertion of additional human V_H gene segments (18hV_H BACvec) to the initial insertion of human heavy chain gene segments (3hV_H-CRE Hybrid Allele) is shown with a 20 kb 5' mouse homology arm, a selection cassette (open rectangle), a 196 kb human genomic fragment and a 62 kb human homology arm that overlaps with the 5' end of the initial insertion of human heavy chain gene segments which is shown with a site-specific recombination site (open triangle) located 5' to the human gene segments. Human (open symbols) and mouse (closed symbols) immunoglobulin gene segments and additional selection cassettes (open rectangles) inserted by subsequent targeting vectors are shown.

[0094] FIG. 2C shows a detailed illustration, not to scale, for three initial steps (A-C) for direct genomic replacement of the mouse immunoglobulin κ light chain variable gene locus that results in deletion of all mouse VK, and JK gene segments (IgK-CRE Hybrid Allele). Selection cassettes (open rectangles) and site-specific recombination sites (open triangles) inserted from the targeting vectors are shown.

[0095] FIG. 2D shows a detailed illustration, not to scale, for 5 additional steps (D-H) for direct genomic replacement of the mouse immunoglobulin κ light chain variable gene locus that results in the insertion of all human VK and JK gene segments in the proximal repeat and deletion of the final selection cassette (40hVKdHyg Hybrid Allele). Human (open symbols) and mouse (closed symbols) immunoglobulin gene segments and additional selection cassettes (open rectangles) inserted by subsequent targeting vectors are shown.

[0096] FIG. 3A shows a general illustration of the locations of quantitative PCR (qPCR) primer/probe sets for screening ES cells for insertion of human heavy chain gene sequences and loss of mouse heavy chain gene sequences. The screening strategy in ES cells and mice for the first human heavy gene insertion is shown with qPCR primer/probe sets for the deleted region ("loss" probes C and D), the region inserted ("hlgH" probes G and H) and flanking regions ("retention" probes A, B, E and F) on an unmodified mouse chromosome (top) and a correctly targeted chromosome (bottom).

[0097] FIG. 3B shows a representative calculation of observed probe copy number in parental and modified ES cells for the first insertion of human immunoglobulin heavy chain gene segments. Observed probe copy number for probes A through F were calculated as 2/2AACt. AACt is calculated as ave[ACt(sampIe) - medACt(controI)] where ACt is the difference in Ct between test and reference probes (between 4 and 6 reference probes depending on the assay). The term medACt(control) is the median ACt of multiple (>60) non-targeted DNA samples from parental ES cells. Each modified ES cell clone was assayed in sextuplicate. To calculate copy numbers of IgH probes G and H in parental ES cells, these probes were assumed to have copy number of 1 in modified ES cells and a maximum Ct of 35 was used even though no amplification was observed.

[0098] FIG. 3C shows a representative calculation of copy numbers for four mice of each genotype were calculated in a similar manner using only probes D and H. Wild-type mice: WT Mice; Mice heterozygous for the first insertion of human immunoglobulin gene segments: HET Mice; Mice homozygous for the first insertion of human immunoglobulin gene segments: Homo Mice.

[0099] FIG. 4A shows an illustration of the three steps employed for the construction of the 3hV_H BACvec by bacterial homologous recombination (BHR). Human (open symbols) and mouse (closed symbols) immunoglobulin gene segments, selection cassettes (open rectangles) and site-specific recombination sites (open triangles) inserted from targeting vectors are shown.

[00100] FIG. 4B shows pulse-field gel electrophoresis (PFGE) of three BAC clones (B1 , B2 and B3) after Notl digestion. Markers M1 , M2 and M3 are low range, mid range and lambda ladder PFG markers, respectively (New England BioLabs, Ipswich, MA).

[00101] FIG. 5A shows a schematic illustration, not to scale, of sequential modifications of the mouse immunoglobulin heavy chain locus with increasing amounts of human immunoglobulin heavy chain gene segments. Homozygous mice were made from each of the three different stages of heavy chain humanization. Open symbols reflect human sequence; closed symbols reflect mouse sequence.

[00102] FIG. 5B shows a schematic illustration, not to scale, of sequential modifications of the mouse immunoglobulin κ light chain locus with increasing amounts of human immunoglobulin κ light chain gene segments. Homozygous mice were made from each of the three different stages of κ light chain humanization. Open symbols reflect human sequence; closed symbols reflect mouse sequence.

[00103] FIG. 6 shows FACS dot plots of B cell populations in wild type and

VELOCIMMUNE® humanized mice. Cells from spleen (top row, third row from top and bottom row) or inguinal lymph node (second row from top) of wild type (wt) or

VELOCIMMUNE® 1 (V1 ), VELOCIMMUNE® 2 (V2) or VELOCIMMUNE® 3 (V3) mice were stained for surface IgM expressing B cells (top row, and second row from top), surface immunoglobulin containing either κ or λ light chains (third row from top) or surface IgM of specific haplotypes (bottom row), and populations separated by FACS.

[001 04] FIG. 7A shows representative heavy chain CDR3 sequences of randomly selected VELOCIMMUNE® antibodies around the V_H-D_H-JH (CDR3) junction,

demonstrating junctional diversity and nucleotide additions. Heavy chain CDR3 sequences are grouped according to D_H gene segment usage, the germline of which is provided above each group in bold. V_H gene segments for each heavy chain CDR3 sequence are noted within parenthesis at the 5' end of each sequence (e.g. 3-72 is human V_H3-72). J_H gene segments for each heavy chain CDR3 are noted within parenthesis at the 3' end of each sequence (e.g. 3 is human J_H3). SEQ ID NOs for each sequence shown are as follows proceeding from top to bottom: SEQ ID NO:21 ; SEQ ID NO:22; SEQ ID NO:23; SEQ ID NO:24; SEQ ID NO:25; SEQ ID NO:26; SEQ ID NO:27; SEQ ID NO:28; SEQ ID NO:29; SEQ ID NO:30; SEQ ID NO:31 ; SEQ ID NO:32; SEQ ID NO:33; SEQ ID NO:34; SEQ ID NO:35; SEQ ID NO:36; SEQ ID NO:37; SEQ ID NO:38; SEQ ID NO:39.

[001 05] FIG. 7B shows representative light chain CDR3 sequences of randomly selected VELOCIMMUNE® antibodies around the VK-JK (CDR3) junction, demonstrating junctional diversity and nucleotide additions. VK gene segments for each light chain CDR3 sequence are noted within parenthesis at the 5' end of each sequence (e.g. 1 -6 is human VK1 -6). JK gene segments for each light chain CDR3 are noted within parenthesis at the 3' end of each sequence (e.g. 1 is human JK1 ). SEQ ID NOs for each sequence shown are as follows proceeding from top to bottom: SEQ ID NO:40; SEQ ID NO:41 ; SEQ ID NO:42; SEQ ID NO:43; SEQ ID NO:44; SEQ ID NO:45; SEQ ID NO:46; SEQ ID NO:47; SEQ ID NO:48; SEQ ID NO:49; SEQ ID NO:50; SEQ ID NO:51 ; SEQ ID NO:52; SEQ ID NO:53; SEQ ID NO:54; SEQ ID NO:55; SEQ ID NO:56; SEQ ID NO:57; SEQ ID NO:58.

[00106] FIG. 8 shows somatic hypermutation frequencies of heavy and light chains of VELOCIMMUNE® antibodies scored (after alignment to matching germline sequences) as percent of sequences changed at each nucleotide (NT; left column) or amino acid (AA; right column) position among sets of 38 (unimmunized IgM), 28 (unimmunized IgG), 32 (unimmunized Igi from IgG), 36 (immunized IgG) or 36 (immunized IgK from IgG) sequences. Shaded bars indicate the locations of CDRs.

[00107] FIG. 9A shows levels of serum immunoglobulin for IgM and IgG isotypes in wild type (open bars) or VELOCIMMUNE® mice (closed bars).

[00108] FIG. 9B shows levels of serum immunoglobulin for IgA isotype in wild type (open bars) or VELOCIMMUNE® mice (closed bars).

[00109] FIG. 9C shows levels of serum immunoglobulin for IgE isotype in wild type (open bars) or VELOCIMMUNE® mice (closed bars).

[00110] FIG. 10A shows antigen specific IgG titers against interleukin-6 receptor of serum from seven VELOCIMMUNE® (VI) and five wild type (WT) mice after two (bleed 1) or three (bleed 2) rounds of immunization with interleukin-6 receptor ectodomain.

[00111] FIG. 10B shows anti-interleukin-6 receptor-specific IgG isotype-specific titers from seven VELOCIMMUNE® (VI) and five wild type (WT) mice.

[00112] FIG. 11 A shows the affinity distribution of anti-interleukin-6 receptor monoclonal antibodies generated in VELOCIMMUNE® mice.

[00113] FIG. 11 B shows the antigen-specific blocking of anti-interleukin-6 receptor monoclonal antibodies generated in VELOCIMMUNE® (VI) and wild type (WT) mice.

[00114] FIG. 12 shows a schematic illustration, not to scale, of mouse ADAM6a and ADAM6b genes in the mouse immunoglobulin heavy chain locus. A targeting vector (mADAM6 Targeting Vector) used for the insertion of mouse ADAM6a and ADAM6b into a humanized endogenous heavy chain locus is shown with a selection cassette (HYG:

hygromycin) flanked by site-specific recombination sites (Frt) including engineered restriction sites on the 5' and 3' ends.

[00115] FIG. 13 shows a schematic illustration, not to scale, of a human ADAM6 pseudogene (hADAM6W) located between human heavy chain variable gene segments 1 - 2 (V_H1 -2) and 6-1 (V_H6-1). A targeting vector for bacterial homologous recombination (ΙιΑϋΑΜβΨ Targeting Vector) to delete a human ADAM6 pseudogene and insert unique restriction sites into a human heavy chain locus is shown with a selection cassette (NEO: neomycin) flanked by site-specific recombination sites (loxP) including engineered restriction sites on the 5' and 3' ends. An illustration, not to scale, of the resulting targeted humanized heavy chain locus containing a genomic fragment that encodes for the mouse ADAM6a and ADAM6b genes including a selection cassette flanked by site-specific recombination sites is shown.

[00116] FIG. 14A shows FACS contour plots of lymphocytes gated on singlets for surface expression of IgM and B220 in the bone marrow for mice homozygous for human heavy and human κ light chain variable gene loci (Η/κ) and mice homozygous for human heavy and human κ light chain variable gene loci having an inserted mouse genomic fragment comprising mouse ADAM6 genes (Η/κ-Α6). Percentage of immature

(B220^intlgM⁺) and mature (B220^highlgM⁺) B cells is noted in each contour plot.

[00117] FIG. 14B shows the total number of immature (B220^intlgM⁺) and mature (B220^hl9hlgM⁺) B cells in the bone marrow isolated from femurs of mice homozygous for human heavy and human κ light chain variable gene loci (Η/κ) and mice homozyogous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment encoding for mouse ADAM6 genes (Η/κ-Α6).

[00118] FIG. 15A shows FACS contour plots of CD19⁺-gated B cells for surface expression of c-kit and CD43 in the bone marrow for mice homozygous for human heavy and human κ light chain variable gene loci (Η/κ) and mice homozyogous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment encoding for mouse ADAM6 genes (Η/κ-Α6). Percentage of pro-B (CD19⁺CD43⁺ckit⁺) and pre-B (CD19⁺CD43 ckif) cells is noted in the upper right and lower left quadrants, respectively, of each contour plot.

[00119] FIG. 15B shows the total number of pro-B cells (CD19⁺CD43⁺ckit⁺) and pre-B cells (CD19⁺CD43^"ckif) in the bone marrow isolated from femurs of mice homozygous for human heavy and human κ light chain variable gene loci (Η/κ) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment comprising mouse ADAM6 genes (Η/κ-Α6).

[00120] FIG. 16A shows FACS contour plots of lymphocytes gated on singlets for surface expression of CD19 and CD43 in the bone marrow for mice homozygous for human heavy and human κ light chain variable gene loci (H/K) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment encoding for mouse ADA 6 genes (Η/κ-Α6). Percentage of immature B (CD19⁺CD43^"), pre-B (CD19⁺CD43^int) and pro-B (CD19⁺CD43⁺) cells is noted in each contour plot.

[00121] FIG. 16B shows histograms of immature B (CD19⁺CD43 ) and pre-B

(CD19⁺CD43'^nt) cells in the bone marrow of mice homozygous for human heavy and human κ light chain variable gene loci (H/K) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment encoding for mouse ADAM6 genes (Η/κ-Α6).

[00122] FIG. 17A shows FACS contour plots of lymphocytes gated on singlets for surface expression of CD19 and CD3 in splenocytes for mice homozygous for human heavy and human κ light chain variable gene loci (Η/κ) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment encoding for mouse ADAM6 genes (Η/ -Α6). Percentage of B (CD19⁺CD3^~) and T (CD19OD3⁺) cells is noted in each contour plot.

[00123] FIG. 17B shows FACs contour plots for CD19⁺-gated B cells for surface expression of \g and Ig light chain in the spleen of mice homozygous for human heavy and human light chain variable gene loci (Η/κ) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment comprising mouse ADAM6 genes (Η/κ-Α6). Percentage of (upper left quadrant) and lgK⁺ (lower right quadrant) B cells is noted in each contour plot.

[00124] FIG. 17C shows the total number of CD19⁺ B cells in the spleen of mice homozygous for human heavy and human κ light chain variable gene loci (Η/κ) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment comprising mouse ADAM6 genes (Η/κ-Α6).

[00125] FIG. 18A shows FACs contour plots of CD19⁺-gated B cells for surface expression of IgD and IgM in the spleen of mice homozygous for human heavy and human K light chain variable gene loci (Η/κ) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment comprising mouse ADAM6 genes (Η/κ-Α6). Percentage of mature B cells (CD19⁺lgD^highlgM^int) is noted for each contour plot. The arrow on the right contour plot illustrates the process of maturation for B cells in relation to IgM and IgD surface expression.

[00126] FIG. 18B shows the total number of B cells in the spleen of mice homozygous for human heavy and human κ light chain variable gene loci (Η/ ) and mice homozygous for human heavy and human κ light chain variable gene loci having an ectopic mouse genomic fragment encoding for mouse ADAM6 genes (Η/κ-Α6) during maturation from CD19⁺lgM^highlgD^int to CD19⁺lgM^intlgD^high.

[00127] FIG. 19 illustrates a targeting strategy for replacing endogenous mouse immunoglobulin light chain variable region gene segments with a human VK1 -39JK5 gene region.

[00128] FIG. 20 illustrates a targeting strategy for replacing endogenous mouse immunoglobulin light chain variable region gene segments with a human V 3-20JK1 gene region.

[00129] FIG. 21 illustrates a targeting strategy for replacing endogenous mouse immunoglobulin light chain variable region gene segments with a human VpreB/J 5 gene region. [00130] FIG. 22 shows the percent of CD19⁺ B cells (y-axis) from peripheral blood for wild type mice (WT), mice homozyogous for an engineered human rearranged VK1-39JK5 light chain region (VK1-39JK5 HO) and mice homozygous for an engineered human rearranged VK3-20JK1 light chain region (VK3-20JK1 HO).

[00131] FIG. 23A shows the relative mRNA expression (y-axis) of a νκΙ-39-derived light chain in a quantitative PCR assay using probes specific for the junction of an engineered human rearranged VK1-39JK5 light chain region (V 1-39JK5 Junction Probe) and the human VK1-39 gene segment (VK1-39 Probe) in a mouse homozygous for a replacement of the endogenous VK and JK gene segments with human VK and JK gene segments (Ηκ), a wild type mouse (WT), and a mouse heterozygous for an engineered human rearranged VK1 -39JK5 light chain region (VK1-39JK5 HET). Signals are normalized to expression of mouse CK. N.D. : not detected.

[00132] FIG. 23B shows the relative mRNA expression (y-axis) of a νκΙ -39-derived light chain in a quantitative PCR assay using probes specific for the junction of an engineered human rearranged VK1-39JK5 light chain region (VK1 -39JK5 Junction Probe) and the human VK1-39 gene segment (VK1-39 Probe) in a mouse homozygous for a replacement of the endogenous VK and JK gene segments with human VK and JK gene segments (Ηκ), a wild type mouse (WT), and a mouse homozygous for an engineered human rearranged VK1-39JK5 light chain region (VK1 -39JK5 HO). Signals are normalized to expression of mouse CK.

[00133] FIG. 23C shows the relative mRNA expression (y-axis) of a VK3-20-derived light chain in a quantitative PCR assay using probes specific for the junction of an engineered human rearranged VK3-20JK1 light chain region (VK3-20JK1 Junction Probe) and the human VK3-20 gene segment (VK3-20 Probe) in a mouse homozygous for a replacement of the endogenous VK and JK gene segments with human VK and JK gene segments (Ηκ), a wild type mouse (WT), and a mouse heterozygous (H ET) and homozygous (HO) for an engineered human rearranged VK3-20JK1 light chain region. Signals are normalized to expression of mouse CK.

[00134] FIG. 24A shows IgM (left) and IgG (right) titer in wild type (WT; N=2) and mice homozygous for an engineered human rearranged VK1-39JK5 light chain region (VK1- 39JK5 HO; N=2) immunized with β-galatosidase.

[00135] FIG. 24B shows total immunoglobulin (IgM, IgG, IgA) titer in wild type (WT; N=5) and mice homozygous for an engineered human rearranged VK3-20JK1 light chain region (VK3-20JK1 HO; N=5) immunized with β-galatosidase. DETAILED DESCRIPTION

[00136] The term "antibody", as used herein, includes immunoglobulin molecules comprising four polypeptide chains, two heavy (H) chains and two light (L) chains interconnected by disulfide bonds. Each heavy chain comprises a heavy chain variable (V_H) region and a heavy chain constant region (C_H). The heavy chain constant region comprises three domains, CH1 , C_H2 and C_H3. Each light chain comprises a light chain variable (V_L) region and a light chain constant region (C_L). The V_H and V_L regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each V_H and V_L comprises three CDRs and four FRs, arranged from amino- terminus to carboxy-terminus in the following order: FR1 , CDR1 , FR2, CDR2, FR3, CDR3, FR4 (heavy chain CDRs may be abbreviated as HCDR1 , HCDR2 and HCDR3; light chain CDRs may be abbreviated as LCDR1 , LCDR2 and LCDR3. The term "high affinity" antibody refers to an antibody that has a K_D with respect to its target epitope about of 10^"9 M or lower (e.g., about 1 x 10^"9 M, 1 x 10^~10 M, 1 x 10^"11 M, or about 1 x 10 ¹² M). In one embodiment, K_D is measured by surface plasmon resonance, e.g., BIACORE™; in another embodiment, K_D is measured by ELISA.

[001 37] The phrase "bispecific antibody" includes an antibody capable of selectively binding two or more epitopes. Bispecific antibodies generally comprise two nonidentical heavy chains, with each heavy chain specifically binding a different epitope— either on two different molecules (e.g., different epitopes on two different immunogens) or on the same molecule (e.g., different epitopes on the same immunogen). If a bispecific antibody is capable of selectively binding two different epitopes (a first epitope and a second epitope), the affinity of the first heavy chain for the first epitope will generally be at least one to two or three or four or more orders of magnitude lower than the affinity of the first heavy chain for the second epitope, and vice versa. Epitopes specifically bound by the bispecific antibody can be on the same or a different target (e.g., on the same or a different protein). Bispecific antibodies can be made, for example, by combining heavy chains that recognize different epitopes of the same immunogen. For example, nucleic acid sequences encoding heavy chain variable sequences that recognize different epitopes of the same immunogen can be fused to nucleic acid sequences encoding the same or different heavy chain constant regions, and such sequences can be expressed in a cell that expresses an immunoglobulin light chain. A typical bispecific antibody has two heavy chains each having three heavy chain CDRs, followed by (N-terminal to C-terminal) a C_H1 domain, a hinge, a C_H2 domain, and a C_H3 domain, and an immunoglobulin light chain that either does not confer epitope-binding specificity but that can associate with each heavy chain, or that can associate with each heavy chain and that can bind one or more of the epitopes bound by the heavy chain epitope-binding regions, or that can associate with each heavy chain and enable binding or one or both of the heavy chains to one or both epitopes.

[00138] The term "cell" includes any cell that is suitable for expressing a recombinant nucleic acid sequence. Cells include those of prokaryotes and eukaryotes (single-cell or multiple-cell), bacterial cells (e.g., strains of E. coli, Bacillus spp., Streptomyces spp., etc.), mycobacteria cells, fungal cells, yeast cells (e.g., S. cerevisiae, S. pombe, P. pastoris, P. methanolica, etc.), plant cells, insect cells (e.g., SF-9, SF-21 , baculovirus-infected insect cells, Trichoplusia ni, etc.), non-human animal cells, human cells, or cell fusions such as, for example, hybridomas or quadromas. In some embodiments, the cell is a human, monkey, ape, hamster, rat, or mouse cell. In some embodiments, the cell is eukaryotic and is selected from the following cells: CHO (e.g., CHO K1 , DXB-11 CHO, Veggie-CHO), COS (e.g., COS-7), retinal cell, Vero, CV1 , kidney (e.g., HEK293, 293 EBNA, MSR 293, MDCK, HaK, BHK), HeLa, HepG2, WI38, MRC 5, Colo205, HB 8065, HL-60, (e.g., BHK21 ), Jurkat, Daudi, A431 (epidermal), CV-1 , U937, 3T3, L cell, C127 cell, SP2/0, NS-0, MMT 060562, Sertoli cell, BRL 3A cell, HT1080 cell, myeloma cell, tumor cell, and a cell line derived from an aforementioned cell. In some embodiments, the cell comprises one or more viral genes, e.g., a retinal cell that expresses a viral gene (e.g., a PER.C6™ cell).

[00139] The phrase "complementarity determining region," or the term "CDR," includes an amino acid sequence encoded by a nucleic acid sequence of an organism's

immunoglobulin genes that normally (i.e., in a wild type animal) appears between two framework regions in a variable region of a light or a heavy chain of an immunoglobulin molecule (e.g., an antibody or a T cell receptor). A CDR can be encoded by, for example, a germline sequence or a rearranged or unrearranged sequence, and, for example, by a naive or a mature B cell or a T cell. A CDR can be somatically mutated (e.g., vary from a sequence encoded in an animal's germline), humanized, and/or modified with amino acid substitutions, additions, or deletions. In some circumstances (e.g., for a CDR3), CDRs can be encoded by two or more sequences (e.g., germline sequences) that are not contiguous (e.g., in an unrearranged nucleic acid sequence) but are contiguous in a B cell nucleic acid sequence, e.g., as the result of splicing or connecting the sequences (e.g., V-D-J recombination to form a heavy chain CDR3).

[00140] The term "conservative," when used to describe a conservative amino acid substitution, includes substitution of an amino acid residue by another amino acid residue having a side chain R group with similar chemical properties (e.g., charge or

hydrophobicity). In general, a conservative amino acid substitution will not substantially change the functional properties of interest of a protein, for example, the ability of a variable region to specifically bind a target epitope with a desired affinity. Examples of groups of amino acids that have side chains with similar chemical properties include aliphatic side chains such as glycine, alanine, valine, leucine, and isoleucine; aliphatic- hydroxyl side chains such as serine and threonine; amide-containing side chains such as asparagine and glutamine; aromatic side chains such as phenylalanine, tyrosine, and tryptophan; basic side chains such as lysine, arginine, and histidine; acidic side chains such as aspartic acid and glutamic acid; and, sulfur-containing side chains such as cysteine and methionine. Conservative amino acids substitution groups include, for example, valine/leucine/isoleucine, phenylalanine/tyrosine, Iysine/arginine, alanine/valine, glutamate/aspartate, and asparagine/glutamine. In some embodiments, a conservative amino acid substitution can be substitution of any native residue in a protein with alanine, as used in, for example, alanine scanning mutagenesis. In some embodiments, a conservative substitution is made that has a positive value in the PAM250 log-likelihood matrix disclosed in Gonnet et al. (1992) Exhaustive Matching of the Entire Protein

Sequence Database, Science 256:1443-45, hereby incorporated by reference. In some embodiments, the substitution is a moderately conservative substitution wherein the substitution has a nonnegative value in the PAM250 log-likelihood matrix.

[00141] In some embodiments, residue positions in an immunoglobulin light chain or heavy chain differ by one or more conservative amino acid substitutions. In some embodiments, residue positions in an immunoglobulin light chain or functional fragment thereof (e.g., a fragment that allows expression and secretion from, e.g., a B cell) are not identical to a light chain whose amino acid sequence is listed herein, but differs by one or more conservative amino acid substitutions.

[00142] The phrase "epitope-binding protein" includes a protein having at least one CDR and that is capable of selectively recognizing an epitope, e.g., is capable of binding an epitope with a K_D that is at about one micromolar or lower (e.g., a K_D that is about 1 x 10⁶ M, 1 x 10^"7 M, 1 x 10^"9 M, 1 x 10^~9 M, 1 x 10^"10 M, 1 x 10^"11 M, or about 1 x 1 CT¹² M). Therapeutic epitope-binding proteins (e.g., therapeutic antibodies) frequently require a K_D that is in the nanomolar or the picomolar range.

[00143] The phrase "functional fragment" includes fragments of epitope-binding proteins that can be expressed, secreted, and specifically bind to an epitope with a K_D in the micromolar, nanomolar, or picomolar range. Specific recognition includes having a K_D that is at least in the micromolar range, the nanomolar range, or the picomolar range.

[00144] The term "germline" includes reference to an immunoglobulin nucleic acid sequence in a non-somatically mutated cell, e.g., a non-somatically mutated B cell or pre-B cell or hematopoietic cell.

[00145] The phrase "heavy chain," or "immunoglobulin heavy chain" includes an immunoglobulin heavy chain constant region sequence from any organism. Heavy chain variable domains include three heavy chain CDRs and four FR regions, unless otherwise specified. Fragments of heavy chains include CDRs, CDRs and FRs, and combinations thereof. A typical heavy chain has, following the variable domain (from N-terminal to C- terminal), a C_H1 domain, a hinge, a CH2 domain, and a C_H3 domain. A functional fragment of a heavy chain includes a fragment that is capable of specifically recognizing an epitope (e.g., recognizing the epitope with a K_D in the micromolar, nanomolar, or picomolar range), that is capable of expressing and secreting from a cell, and that comprises at least one CDR.

[00146] The term "identity" when used in connection with sequence, includes identity as determined by a number of different algorithms known in the art that can be used to measure nucleotide and/or amino acid sequence identity. In some embodiments described herein, identities are determined using a ClustalW v. 1.83 (slow) alignment employing an open gap penalty of 10.0, an extend gap penalty of 0.1 , and using a Gonnet similarity matrix (MacVector™ 10.0.2, MacVector Inc., 2008). The length of the sequences compared with respect to identity of sequences will depend upon the particular sequences, but in the case of a light chain constant domain, the length should contain sequence of sufficient length to fold into a light chain constant domain that is capable of self-association to form a canonical light chain constant domain, e.g., capable of forming two beta sheets comprising beta strands and capable of interacting with at least one C_H1 domain of a human or a mouse. In the case of a C_H1 domain, the length of sequence should contain sequence of sufficient length to fold into a C_H1 domain that is capable of forming two beta sheets comprising beta strands and capable of interacting with at least one light chain constant domain of a mouse or a human.

[00147] The phrase "immunoglobulin molecule" includes two immunoglobulin heavy chains and two immunoglobulin light chains. The heavy chains may be identical or different, and the light chains may be identical or different.

[00148] The phrase "light chain" includes an immunoglobulin light chain sequence from any organism, and unless otherwise specified includes human κ and λ light chains and a VpreB, as well as surrogate light chains. Light chain variable (V_L) domains typically include three light chain CDRs and four framework (FR) regions, unless otherwise specified.

Generally, a full-length light chain includes, from amino terminus to carboxyl terminus, a V_L domain that includes FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4, and a light chain constant domain. Light chains include those, e.g., that do not selectively bind either a first or a second epitope selectively bound by the epitope-binding protein in which they appear. Light chains also include those that bind and recognize, or assist the heavy chain with binding and recognizing, one or more epitopes selectively bound by the epitope-binding protein in which they appear. [00149] Universal light chains, or common light chains, refer to light chains made in mice as described herein, wherein the mice are highly restricted in the selection of gene segments available for making a light chain variable domain. As a result, such mice make a light chain derived from, in one embodiment, no more than one or two unrearranged light chain V segments and no more than one or two unrearranged light chain J segments (e.g., one V and one J, two V's and one J, one V and two J's, two V's and two J's). In one embodiment, no more than one or two rearranged light chain V/J sequences, e.g., a rearranged human VK1-39JK5 sequence or a rearranged human VK3-20JK1 sequence. In various embodiments universal light chains include somatically mutated (e.g., affinity matured) versions.

[00150] The phrase "somatically mutated" includes reference to a nucleic acid sequence from a B cell that has undergone class-switching, wherein the nucleic acid sequence of an immunoglobulin variable region (e.g., a heavy chain variable domain or including a heavy chain CDR or FR sequence) in the class-switched B cell is not identical to the nucleic acid sequence in the B cell prior to class-switching, such as, for example, a difference in a CDR or framework nucleic acid sequence between a B cell that has not undergone class- switching and a B cell that has undergone class-switching. "Somatically mutated" includes reference to nucleic acid sequences from affinity-matured B cells that are not identical to corresponding immunoglobulin variable region sequences in B cells that are not affinity- matured (i.e., sequences in the genome of germline cells). The phrase "somatically mutated" also includes reference to an immunoglobulin variable region nucleic acid sequence from a B cell after exposure of the B cell to an epitope of interest, wherein the nucleic acid sequence differs from the corresponding nucleic acid sequence prior to exposure of the B cell to the epitope of interest. The phrase "somatically mutated" refers to sequences from antibodies that have been generated in an animal, e.g., a mouse having human immunoglobulin variable region nucleic acid sequences, in response to an immunogen challenge, and that result from the selection processes inherently operative in such an animal.

[00151] The term "unrearranged," with reference to a nucleic acid sequence, includes nucleic acid sequences that exist in the germline of an animal cell.

[00152] The phrase "variable domain" includes an amino acid sequence of an immunoglobulin light or heavy chain (modified as desired) that comprises the following amino acid regions, in sequence from N-terminal to C-terminal (unless otherwise indicated): FR1 , CDR1 , FR2, CDR2, FR3, CDR3, FR4.

Mice with Humanized Immunoglobulin Loci [00153] The mouse as a genetic model has been greatly enhanced by transgenic and knockout technologies, which have allowed for the study of the effects of the directed over- expression or deletion of specific genes. Despite all of its advantages, the mouse still presents genetic obstacles that render it an imperfect model for human diseases and an imperfect platform to test human therapeutics or make them. First, although about 99% of human genes have a mouse homolog (Waterston, R.H., et. al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.), potential therapeutics often fail to cross-react, or cross-react inadequately, with mouse orthologs of the intended human targets. To obviate this problem, selected target genes can be "humanized," that is, the mouse gene can be eliminated and replaced by the corresponding human orthologous gene sequence (e.g., US 6,586,251 , US 6,596,541 and US 7,105,348, incorporated herein by reference). Initially, efforts to humanize mouse genes by a

"knockout-plus-transgenic humanization" strategy entailed crossing a mouse carrying a deletion (i.e., knockout) of the endogenous gene with a mouse carrying a randomly integrated human transgene (see, e.g., Bril, W.S., et al. (2006). Tolerance to factor VIII in a transgenic mouse expressing human factor VIII cDNA carrying an Arg(593) to Cys substitution. Thromb Haemost 95, 341-347; Homanics, G.E., et al. (2006). Production and characterization of murine models of classic and intermediate maple syrup urine disease. BMC Med Genet 7, 33; Jamsai, D., et al. (2006). A humanized BAC transgenic/knockout mouse model for HbE/beta-thalassemia. Genomics 88(3):309-15; Pan, Q., et al. (2006). Different role for mouse and human CD3delta/epsilon heterodimer in preT cell receptor (preTCR) function: human CD3delta/epsilon heterodimer restores the defective preTCR function in CD3gamma- and CD3gammadelta-deficient mice. Mol Immunol 43, 1741 -1750). But those efforts were hampered by size limitations; conventional knockout technologies were not sufficient to directly replace large mouse genes with their large human genomic counterparts. A straightforward approach of direct homologous replacement, in which an endogenous mouse gene is directly replaced by the human counterpart gene at the same precise genetic location of the mouse gene (i.e., at the endogenous mouse locus), is rarely attempted because of technical difficulties. Until now, efforts at direct replacement involved elaborate and burdensome procedures, thus limiting the length of genetic material that could be handled and the precision with which it could be manipulated.

[00154] Exogenously introduced human immunoglobulin transgenes rearrange in precursor B-cells in mice (Alt, F.W., Blackwell, T.K., and Yancopoulos, G.D. (1985).

Immunoglobulin genes in transgenic mice. Trends Genet 1 , 231-236). This finding was exploited by engineering mice using the knockout-plus-transgenic approach to express human antibodies (Green, L.L. et al. (1994). Antigen-specific human monoclonal antibodies from mice engineered with human Ig heavy and light chain YACs. Nat Genet 7, 13-21 ; Lonberg, N. (2005). Human antibodies from transgenic animals. Nat Biotechnol 23, 1117- 1125; Lonberg, N., et al. (1994). Antigen-specific human antibodies from mice comprising four distinct genetic modifications. Nature 368, 856-859; Jakobovits, A., et al. (2007). From XenoMouse technology to panitumumab, the first fully human antibody product from transgenic mice. Nat Biotechnol 25, 1 134-1 143). The endogenous mouse immunoglobulin heavy chain and κ light chain loci were inactivated in these mice by targeted deletion of small but critical portions of each endogenous locus, followed by introducing human immunoglobulin gene loci as randomly integrated large transgenes, as described above, or minichromosomes (Tomizuka, K., et al. (2000). Double trans-chromosomic mice:

maintenance of two individual human chromosome fragments containing Ig heavy and kappa loci and expression of fully human antibodies. Proc Natl Acad Sci U S A 97, 722- 727). Such mice represented an important advance in genetic engineering; fully human monoclonal antibodies isolated from them yielded promising therapeutic potential for treating a variety of human diseases (Gibson, T.B., et al. (2006). Randomized phase III trial results of panitumumab, a fully human anti-epidermal growth factor receptor monoclonal antibody, in metastatic colorectal cancer. Clin Colorectal Cancer 6, 29-31 ; Jakobovits et al., 2007; Kim, Y.H., et al. (2007). Clinical efficacy of zanolimumab (HuMax-CD4): two Phase II studies in refractory cutaneous T-cell lymphoma. Blood 109(1 1 ):4655-62; Lonberg, 2005; Maker, A.V., et al. (2005). Tumor regression and autoimmunity in patients treated with cytotoxic T lymphocyte-associated antigen 4 blockade and interleukin 2: a phase l/ll study. Ann Surg Oncol 12, 1005-1016; cClung, M.R., et al. (2006). Denosumab in

postmenopausal women with low bone mineral density. N Engl J Med 354, 821-831 ). But, as discussed above, these mice exhibit compromised B cell development and immune deficiencies when compared to wild type mice. Such problems potentially limit the ability of the mice to support a vigorous humoral response and, consequently, generate fully human antibodies against some antigens. The deficiencies may be due to: (1 ) inefficient functionality due to the random introduction of the human immunoglobulin transgenes and resulting incorrect expression due to a lack of upstream and downstream control elements (Garrett, F.E., et al. (2005). Chromatin architecture near a potential 3' end of the igh locus involves modular regulation of histone modifications during B-Cell development and in vivo occupancy at CTCF sites. Mol Cell Biol 25, 151 1-1525; Manis, J. P., et al. (2003).

Elucidation of a downstream boundary of the 3' IgH regulatory region. Mol Immunol 39, 753-760; Pawlitzky, I., et al. (2006). Identification of a candidate regulatory element within the 5' flanking region of the mouse Igh locus defined by pro-B cell-specific hypersensitivity associated with binding of PU.1 , Pax5, and E2A. J Immunol 176, 6839-6851); (2) inefficient interspecies interactions between human constant domains and mouse components of the B-cell receptor signaling complex on the cell surface, which may impair signaling processes required for normal maturation, proliferation, and survival of B cells (Hombach, J., er a/. (1990). Molecular components of the B-cell antigen receptor complex of the IgM class. Nature 343, 760-762); and (3) inefficient interspecies interactions between soluble human immunoglobulins and mouse Fc receptors that might reduce affinity selection (Rao, S.P., et al, (2002). Differential expression of the inhibitory IgG Fc receptor FcgammaRIIB on germinal center cells: implications for selection of high-affinity B cells. J Immunol 169, 1859-1868) and immunoglobulin serum concentrations (Brambell, F.W., et al. (1964). A Theoretical Model of Gamma-Globulin Catabolism. Nature 203, 1352-1354; Junghans, R.P., and Anderson, C.L. (1996). The protection receptor for IgG catabolism is the beta2- microglobulin-containing neonatal intestinal transport receptor. Proc Natl Acad Sci U S A 93, 5512-5516; Rao et al. , 2002; Hjelm, F., et al. (2006). Antibody-mediated regulation of the immune response. Scand J Immunol 64, 177-184; Nimmerjahn, F., and Ravetch, J.V. (2007). Fc-receptors as regulators of immunity. Adv Immunol 96, 179-204). These deficiencies can be corrected by in situ humanization of only the variable regions of the mouse immunoglobulin loci within their natural locations at the endogenous heavy and light chain loci. This would effectively result in mice that make reverse chimeric (i.e., human V: mouse C) antibodies that would be capable of normal interactions and selection with the mouse environment based on retaining mouse constant regions. Further, such reverse chimeric antibodies are readily reformatted into fully human antibodies for therapeutic purposes.

[00155] A method for a large in situ genetic replacement of the mouse germline immunoglobulin variable genes with human germline immunoglobulin variable genes while maintaining the ability of the mice to generate offspring is described. Specifically, the precise replacement of six megabases of both the mouse heavy chain and κ light chain immunoglobulin variable gene loci with their human counterparts while leaving the mouse constant regions intact is described. As a result, mice have been created that have a precise replacement of their entire germline immunoglobulin variable repertoire with equivalent human germline immunoglobulin variable sequences, while maintaining mouse constant regions. The human variable regions are linked to mouse constant regions to form chimeric human-mouse immunoglobulin loci that rearrange and express at physiologically appropriate levels. The antibodies expressed are "reverse chimeras," i.e., they comprise human variable region sequences and mouse constant region sequences. These mice having humanized immunoglobulin variable regions that express antibodies having human variable regions and mouse constant regions are called VELCOIMMUNE® humanized mice.

[00156] VELOCIMMUNE® humanized mice exhibit a fully functional humoral immune system that is essentially indistinguishable from that of wild-type mice. They display normal cell populations at all stages of B cell development. They exhibit normal lymphoid organ morphology. Antibody sequences of VELOCIMMUNE® humanized mice exhibit normal variable segment rearrangement and normal somatic hypermutation. Antibody populations in these mice reflect isotype distributions that result from normal class switching (e.g., normal isotype c/s-switching). Immunizing VELOCIMMUNE® humanized mice results in robust humoral responses that generate a large diversity of antibodies having human immunoglobulin variable domains suitable as therapeutic candidates. This platform provides a plentiful source of affinity-matured human immunoglobulin variable region sequences for making pharmaceutically acceptable antibodies and other antigen- binding proteins.

[00157] It is the precise replacement of mouse immunoglobulin variable sequences with human immunoglobulin variable sequences that allows for making VELOCIMMUNE® humanized mice. Yet even a precise replacement of endogenous mouse immunoglobulin sequences at heavy and light chain loci with equivalent human immunoglobulin sequences, by sequential recombineering of very large spans of human immunoglobulin sequences, may present certain challenges due to divergent evolution of the immunoglobulin loci between mouse and man. For example, intergenic sequences interspersed within the immunoglobulin loci are not identical between mice and humans and, in some

circumstances, may not be functionally equivalent. Differences between mice and humans in their immunoglobulin loci can still result in abnormalities in humanized mice, particularly when humanizing or manipulating certain portions of endogenous mouse immunoglobulin heavy chain loci. Some modifications at mouse immunoglobulin heavy chain loci are deleterious. Deleterious modifications can include, for example, loss of the ability of the modified mice to mate and produce offspring.

[00158] A precise, large-scale, in situ replacement of six megabases of the variable regions of the mouse heavy and light chain immunoglobulin loci (V_H-D_H-JH and VK-JK) with the corresponding 1 .4 megabases human genomic sequences was performed, while leaving the flanking mouse sequences intact and functional within the hybrid loci, including all mouse constant chain genes and locus transcriptional control regions (Figure 1 ).

Specifically, the human V_H, D_H, JH_> V and JK gene sequences were introduced through stepwise insertion of 13 chimeric BAC targeting vectors bearing overlapping fragments of the human germline variable loci into mouse ES cells using VELOCIGENE® genetic engineering technology (see, e.g., US Pat. No. 6,586,251 and Valenzuela, D.M., et al. (2003). High-throughput engineering of the mouse genome coupled with high-resolution expression analysis. Nat Biotechnol 21 , 652-659). [00159] Humanization of the mouse immunoglobulin genes represents the largest genetic modification to the mouse genome to date. While previous efforts with randomly integrated human immunoglobulin transgenes have met with some success (discussed above), direct replacement of the mouse immunoglobulin genes with their human counterparts dramatically increases the efficiency with which fully-human antibodies can be efficiently generated in otherwise normal mice. Further, such mice exhibit a dramatically increased diversity of fully-human antibodies that can be obtained after immunization with virtually any antigen, as compared with mice bearing disabled endogenous loci and fully human antibody transgenes. Multiple versions of replaced, humanized loci exhibit completely normal levels of mature and immature B cells, in contrast to mice with randomly integrated human transgenes, which exhibit significantly reduced B cell populations at various stages of differentiation. While efforts to increase the number of human gene segments in human transgenic mice have reduced such defects, the expanded

immunoglobulin repertoires have not altogether corrected reductions in B cell populations as compared to wild-type mice.

[00160] Notwithstanding the near wild-type humoral immune function observed in mice with replaced immunoglobulin loci, there are other challenges encountered when employing a direct replacement of the immunoglobulin that is not encountered in some approaches that employ randomly integrated transgenes. Differences in the genetic composition of the immunoglobulin loci between mice and humans has lead to the discovery of sequences beneficial for the propagation of mice with replaced

immunoglobulin gene segments. Specifically, mouse ADAM genes located within the endogenous immunoglobulin locus are optimally present in mice with replaced

immunoglobulin loci, due to their role in fertility.

Genomic Location and Function of Mouse ADAM6

[00161] Male mice that lack the ability to express any functional ADAM6 protein exhibit a severe defect in the ability of the mice to mate and to generate offspring. The mice lack the ability to express a functional ADAM6 protein by virtue of a replacement of all or substantially all mouse immunoglobulin variable region gene segments with human variable region gene segments. The loss of ADAM6 function results because the ADAM6 locus is located within a region of the endogenous mouse immunoglobulin heavy chain variable region gene locus, proximal to the 3' end of the V_H gene segment locus that is upstream of the D_H gene segments. In order to breed mice that are homozygous for a replacement of all or substantially all endogenous mouse heavy chain variable gene segments with human heavy chain variable gene segments, it is generally a cumbersome approach to set up males and females that are each homozygous for the replacement and await a productive mating. Successful litters are relatively rare, and average litter size is very low. Instead, males heterozygous for the replacement have been employed to mate with females homozygous for the replacement to generate progeny that are heterozygous for the replacement, then breed a homozygous mouse therefrom. The inventors have determined that the likely cause of the loss in fertility in the male mice is the absence in homozygous male mice of a functional ADAM6 protein.

[00162] The ADAM6 protein is a member of the ADAM family of proteins, where ADAM is an acronym for A Disintegrin And Metalloprotease. The ADAM family of proteins is large and diverse, with diverse functions. Some members of the ADAM family are implicated in spermatogenesis and fertilization. For example, ADAM2 encodes a subunit of the protein fertilin, which is implicated in sperm-egg interactions. ADAM3, or cyritestin, appears necessary for sperm binding to the zona pellucida. The absence of either ADAM2 or ADAM 3 results in infertility. It has been postulated that ADAM2, ADAM3, and ADAM6 form a complex on the surface of mouse sperm cells.

[00163] The human ADAM6 gene, normally found between human V_H gene segments V_H1-2 and V_H6-1 , appears to be a pseudogene (Figure 12). In mice, there are two ADAM6 genes— ADAM6a and ADAM6b— that are found in an intergenic region between mouse V_H and D_H gene segments, and in the mouse the a and b genes are oriented in a

transcriptional orientation opposite to that of the transcription orientation of the surrounding immunoglobulin gene segments (Figure 11 ). In mice, a functional ADAM6 locus is apparently required for normal fertilization. A functional ADAM6 locus or sequence, then, refers to an ADAM6 locus or sequence that can complement, or rescue, the drastically reduced fertilization exhibited in male mice with missing or damaged endogenous ADAM6 loci. [00164] The position of the intergenic sequence in mice that encodes ADAM6a and ADAM6b renders the intergenic sequence susceptible to modification when modifying an endogenous mouse heavy chain. When V_H gene segments are deleted or replaced, or when D_H gene segments are deleted or replaced, there is a high probability that a resulting mouse will exhibit a severe deficit in fertility. In order to compensate for the deficit, the mouse is modified to include a nucleotide sequence that encodes a protein that will complement the loss in ADAM6 activity due to a modification of the endogenous mouse ADAM6 locus. In various embodiments, the complementing nucleotide sequence is one that encodes a mouse ADAM6a, a mouse ADAM6b, or a homolog or ortholog or functional fragment thereof that rescues the fertility deficit.

[00165] The nucleotide sequence that rescues fertility can be placed at any suitable position. It can be placed in the intergenic region, or in any suitable position in the genome (i.e., ectopically). In one embodiment, the nucleotide sequence can be introduced into a transgene that randomly integrates into the mouse genome. In one embodiment, the sequence can be maintained episomally, that is, on a separate nucleic acid rather than on a mouse chromosome. Suitable positions include positions that are transcriptionally permissive or active, e.g., a ROSA26 locus.

[00166] The term "ectopic" is intended to include a displacement, or a placement at a position that is not normally encountered in nature (e.g., placement of a nucleic acid sequence at a position that is not the same position as the nucleic acid sequence is found in a wild-type mouse). The term in various embodiments is used in the sense of its object being out of its normal, or proper, position. For example, the phrase "an ectopic nucleotide sequence encoding ... " refers to a nucleotide sequence that appears at a position at which it is not normally encountered in the mouse. For example, in the case of an ectopic nucleotide sequence encoding a mouse ADAM6 protein (or an ortholog or homolog or fragment thereof that provides the same or similar fertility benefit on male mice), the sequence can be placed at a different position in the mouse's genome than is normally found in a wild-type mouse. A functional homolog or ortholog of mouse ADA 6 is a sequence that confers a rescue of fertility loss (e.g., loss of the ability of a male mouse to generate offspring by mating) that is observed in an ADA 6^"'^" mouse. Functional homologs or orthologs include proteins that have at least about 89% identity or more, e.g., up to 99% identity, to the amino acid sequence of ADAM6a and/or to the amino acid sequence of ADAM6b, and that can complement, or rescue ability to successfully mate, of a mouse that has a genotype that includes a deletion or knockout of ADAM6a and/or ADAM6b.

[00167] The ectopic position can be anywhere (e.g., as with random insertion of a transgene containing a mouse ADAM6 sequence), or can be, e.g., at a position that approximates (but is not precisely the same as) its location in a wild-type mouse (e.g., in a modified endogenous mouse immunoglobulin locus, but either upstream or downstream of its natural position, e.g., within a modified immunoglobulin locus but between different gene segments, or at a different position in a mouse V-D intergenic sequence). One example of an ectopic placement is placement within a humanized immunoglobulin heavy chain locus. For example, a mouse comprising a replacement of one or more endogenous V_H gene segments with human V_H gene segments, wherein the replacement removes an endogenous ADAM6 sequence, can be engineered to have a mouse ADAM6 sequence located within sequence that contains the human V_H gene segments. The resulting modification would generate an (ectopic) mouse ADAM6 sequence within a human gene sequence, and the (ectopic) placement of the mouse ADAM6 sequence within the human gene sequence can approximate the position of the human ADAM6 pseudogene (i.e., between two V segments) or can approximate the position of the mouse ADAM6 sequence (i.e., within the V-D intergenic region).

[00168] In various aspects, mice that comprise deletions or replacements of the endogenous heavy chain variable region locus or portions thereof can be made that contain an ectopic nucleotide sequence that encodes a protein that confers similar fertility benefits to mouse ADAM6 (e.g., an ortholog or a homolog or a fragment thereof that is functional in a male mouse). The ectopic nucleotide sequence can include a nucleotide sequence that encodes a protein that is an ADAM6 homolog or ortholog (or fragment thereof) of a different mouse strain or a different species, e.g., a different rodent species, and that confers a benefit in fertility, e.g., increased number of litters over a specified time period, and/or increased number of pups per litter, and/or the ability of a sperm cell of a male mouse to traverse through a mouse oviduct to fertilize a mouse egg.

[00169] In one embodiment, the ADAM6 is a homolog or ortholog that is at least 89% to 99% identical to a mouse ADAM6 protein (e.g., at least 89% to 99% identical to mouse ADAM6a or mouse ADAM6b). In one embodiment, the ectopic nucleotide sequence encodes one or more proteins independently selected from a protein at least 89% identical to mouse ADAM6a, a protein at least 89% identical to mouse ADAM6b, and a combination thereof. In one embodiment, the homolog or ortholog is a rat, hamster, mouse, or guine pig protein that is or is modified to be about 89% or more identical to mouse ADAM6a and/or mouse ADAM6b. In one embodiment, the homolog or ortholog is 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a mouse ADAM6a and/or mouse ADAM6b.

Ectopic ADA 6 in Humanized Heavy Chain Mice [00170] Mice that make human antibodies have been available for some time now. Although they represent an important advance in the development of human therapeutic antibodies, these mice display a number of significant abnormalities that limit their usefulness. For example, they display compromised B cell development. The

compromised development may be due to a variety of differences between the transgenic mice and wild-type mice.

[00171] Human antibodies might not optimally interact with mouse pre B cell or B cell receptors on the surface of mouse cells that signal for maturation, proliferation, or survival during clonal selection. Fully human antibodies might not optimally interact with a mouse Fc receptor system; mice express Fc receptors that do not display a one-to-one correspondence with human Fc receptors. Finally, various mice that make fully human antibodies do not include all genuine mouse sequences, e.g., downstream enhancer elements and other locus control elements, which may be required for wild-type B cell development.

[00172] Mice that make fully human antibodies generally comprise endogenous immunoglobulin loci that are disabled in some way, and human transgenes that comprise variable and constant immunoglobulin gene segments are introduced into a random Iocation in the mouse genome. As long as the endogenous locus is sufficiently disabled so as not to rearrange gene segments to form a functional immunoglobulin gene, the goal of making fully human antibodies in such a mouse can be achieved— albeit with compromised B cell development.

[00173] Although compelled to make fully human antibodies from the human transgene locus, generating human antibodies in a mouse is apparently an unfavored process. In some mice, the process is so unfavored as to result in formation of chimeric human variable/mouse constant heavy chains (but not light chains) through the mechanism of frans-switching. By this mechanism, transcripts that encode fully human antibodies undergo isotype switching in trans from the human isotype to a mouse isotype. The process is in trans, because the fully human transgene is located apart from the endogenous locus that retains an undamaged copy of a mouse heavy chain constant region gene. Although in such mice frans-switching is readily apparent the phenomenon is still insufficient to rescue B cell development, which remains frankly impaired. In any event, frans-switched antibodies made in such mice retain fully human light chains, since the phenomenon of frans-switching apparently does not occur with respect to light chains; frans-switching presumably relies on switch sequences in endogenous loci used (albeit differently) in normal isotype switching in c/s. Thus, even when mice engineered to make fully human antibodies select a frans-switching mechanism to make antibodies with mouse constant regions, the strategy is still insufficient to rescue normal B cell development. [00174] A primary concern in making antibody-based human therapeutics is making a sufficiently large diversity of human immunoglobulin variable region sequences to identify useful variable domains that specifically recognize particular epitopes and bind them with a desirable affinity, usually— but not always— with high affinity. Prior to the development of VELOCIMMUNE® humanized mice, there was no indication that mice expressing human variable regions with mouse constant regions would exhibit any significant differences from mice that made human antibodies from a transgene. That supposition, however, was incorrect.

[00175] VELOCIMMUNE® humanized mice, which contain a precise replacement of mouse immunoglobulin variable regions with human immunoglobulin variable regions at the endogenous mouse loci, display a surprising and remarkable similarity to wild-type mice with respect to B cell development. In a surprising and stunning development, VELOCIMMUNE® humanized mice displayed an essentially normal, wild-type response to immunization that differed only in one significant respect from wild-type mice— the variable regions generated in response to immunization are fully human.

[00176] VELOCIMMUNE® humanized mice contain a precise, large-scale replacement of germline variable regions of mouse immunoglobulin heavy chain (IgH) and

immunoglobulin light chain (e.g., κ light chain, IgK) with corresponding human

immunoglobulin variable regions, at the endogenous loci. In total, about six megabases of mouse loci are replaced with about 1.4 megabases of human genomic sequence. This precise replacement results in a mouse with hybrid immunoglobulin loci that make heavy and light chains that have a human variable regions and a mouse constant region. The precise replacement of mouse V_H-D_H-JH and VK-JK segments leave flanking mouse sequences intact and functional at the hybrid immunoglobulin loci. The humoral immune system of the mouse functions like that of a wild-type mouse. B cell development is unhindered in any significant respect and a rich diversity of human variable regions is generated in the mouse upon antigen challenge.

[00177] VELOCIMMUNE® humanized mice are possible because immunoglobulin gene segments for heavy and κ light chains rearrange similarly in humans and mice, which is not to say that their loci are the same or even nearly so— clearly they are not. However, the loci are similar enough that humanization of the heavy chain variable gene locus can be accomplished by replacing about 3 million base pairs of contiguous mouse sequence that contains all the V_H, D_H, and JH gene segments with about 1 million bases of contiguous human genomic sequence covering basically the equivalent sequence from a human immunoglobulin locus. [00178] In some embodiments, further replacement of certain mouse constant region gene sequences with human gene sequences (e.g., replacement of mouse C_H1 sequence with human C_H1 sequence, and replacement of mouse C_L sequence with human C_L sequence) results in mice with hybrid immunoglobulin loci that make antibodies that have human variable regions and partly human constant regions, suitable for, e.g., making fully human antibody fragments, e.g., fully human Fab's. Mice with hybrid immunoglobulin loci exhibit normal variable gene segment rearrangement, normal somatic hy permutation, and normal class switching. These mice exhibit a humoral immune system that is

indistinguishable from wild type mice, and display normal cell populations at all stages of B cell development and normal lymphoid organ structures— even where the mice lack a full repertoire of human variable region gene segments. Immunizing these mice results in robust humoral responses that display a wide diversity of variable gene segment usage.

[00179] The precise replacement of mouse germline variable region gene segments allows for making mice that have partly human immunoglobulin loci. Because the partly human immunoglobulin loci rearrange, hypermutate, and class switch normally, the partly human immunoglobulin loci generate antibodies in a mouse that comprise human variable regions. Nucleotide sequences that encode the variable regions can be identified and cloned, then fused (e.g., in an in vitro system) with any sequences of choice, e.g., any immunoglobulin isotype suitable for a particular use, resulting in an antibody or antigen- binding protein derived wholly from human sequences.

[00180] Large-scale humanization by recombineering methods were used to modify mouse embryonic stem (ES) cells to precisely replace up to 3 megabases of the mouse heavy chain immunoglobulin locus that included essentially all of the mouse V_H, D_H, and J_H gene segments with equivalent human gene segments with up to a 1 megabase human genomic sequence containing some or essentially all human V_H, D_H, and J_H gene segments. Up to a 0.5 megabase segment of the human genome comprising one of two repeats encoding essentially all human VK and JK gene segments was used to replace a 3 megabase segment of the mouse immunoglobulin κ light chain locus containing essentially all of the mouse VK and JK gene segments.

[00181] Mice with such replaced immunoglobulin loci can comprise a disruption or deletion of the endogenous mouse ADAM6 locus, which is normally found between the 3'- most V_H gene segment and the 5'-most D_H gene segment at the mouse immunoglobulin heavy chain locus. Disruption in this region can lead to reduction or elimination of functionality of the endogenous mouse ADAM6 locus. If the 3'-most V_H gene segments of the human heavy chain repertoire are used in a replacement, an intergenic region containing a pseudogene that appears to be a human ADAM6 pseudogene is present between these V_H gene segments, i.e., between human VH1-2 and V_H1 -6. However, male mice that comprise this human intergenic sequence exhibit little or no fertility.

[00182] Mice are described that comprise the replaced loci as described above, and that also comprise an ectopic nucleic acid sequence encoding a mouse ADAM6, where the mice exhibit essentially normal fertility. In one embodiment, the ectopic nucleic acid sequence is SEQ ID NO:3, placed between human V_H1 -2 and V_H1-6 at the modified endogenous mouse heavy chain locus. The direction of transcription of the ADAM6 genes of SEQ ID NO:3 are opposite with respect to the direction of transcription of the

surrounding human V_H gene segments. Although examples herein show rescue of fertility by placing the ectopic sequence between the indicated human V_H gene segments, skilled persons will recognize that placement of the ectopic sequence at any suitable

transcriptionally-permissive locus in the mouse genome (or even extrachromosomally) will be expected to similarly rescue fertility in a male mouse.

[00183] The phenomenon of complementing a mouse that lacks a functional ADAM6 locus with an ectopic sequence that comprises a mouse ADAM6 gene or ortholog or homolog or functional fragment thereof is a general method that is applicable to rescuing any mice with nonfunctional or minimally functional endogenous ADAM6 loci. Thus, a great many mice that comprise an ADAM6-disrupting modification of the immunoglobulin heavy chain locus can be rescued with the compositions and methods of the invention. Accordingly, the invention comprises mice with a wide variety of modifications of immunoglobulin heavy chain loci that compromise endogenous ADAM6 function. Some (non-limiting) examples are provided in this description. In addition to the

VELOCIMMUNE® humanized mice described, the compositions and methods related to ADAM6 can be used in a great many applications, e.g., when modifying a heavy chain locus in a wide variety of ways.

[00184] In one aspect, a mouse is provided that comprises an ectopic ADAM6 sequence that encodes a functional ADAM6 protein (or ortholog or homolog or functional fragment thereof), a replacement of all or substantially all mouse V_H gene segments with one or more human V_H gene segments, a replacement of all or substantially all mouse D_H gene segments and JH gene segments with human D_H and human J_H gene segments; wherein the mouse lacks a C_H1 and/or hinge region. In one embodiment, the mouse makes a single variable domain binding protein that is a dimer of immunoglobulin chains selected from: (a) human V_H - mouse C_H1 - mouse CH2 - mouse C_H3; (b) human V_H - mouse hinge - mouse C_H2 - mouse C_H3; and, (c) human V_H - mouse C_H2 - mouse C_H3.

[00185] In one aspect, the nucleotide sequence that rescues fertility is placed within a human immunoglobulin heavy chain variable region sequence (e.g., between human V_H1-2 and V_H1 -6 gene segments) in a mouse that has a replacement of all or substantially all mouse immunoglobulin heavy chain variable gene segments (mV_H's, mD_H's, and mJ_H's) with one or more human immunoglobulin heavy chain variable gene segments (hV_H's, hDH's, and hJ_H's), and the mouse further comprises a replacement of all or substantially all mouse immunoglobulin κ light chain variable gene segments (m s, ITIJK'S) with one or more human immunoglobulin κ light chain variable gene segments (hWs and IIJK'S). In one embodiment, the nucleotide sequence is placed between a human V_H1-2 gene segment and a human V_H1-6 gene segment in a VELOCIMMUNE® humanized mouse (US 6,596,541 and US 7,105,348, incorporated herein by reference). In one embodiment, the VELOCIMMUNE® humanized mouse so modified comprises a replacement with all or substantially all human immunoglobulin heavy chain variable gene segments (all hV_H's, hD_H's, and hJ_H's) and all or substantially all human immunoglobulin κ light chain variable gene segments (hWs and hJK's).

[00186] In one aspect, a functional mouse ADAM6 locus (or ortholog or homolog or functional fragment thereof) can be placed in the midst of human V_H gene segments that replace endogenous mouse V_H gene segments. In one embodiment, all or substantially all mouse V_H gene segments are removed and replaced with one or more human V_H gene segments, and the mouse ADAM6 locus is placed immediately adjacent to the 3' end of the human V_H gene segments, or between two human V_H gene segments. In a specific embodiment, the mouse ADAM6 locus is placed between two V_H gene segments near the 3' terminus of the inserted human V_H gene segments. In a specific embodiment, the replacement includes human V_H gene segments V_H1-2 and V_H6-1 , and the mouse ADAM6 locus is placed downstream of the V_H1-2 gene segment and upstream of the V_H6-1 gene segment. In a specific embodiment, the arrangement of human V_H gene segments is then the following (from upstream to downstream with respect to direction of transcription of the human V_H gene segments): human V_H1-2 - mouse ADAM6 locus - human V_H6-1. In a specific embodiment, the ADAM6 pseudogene between human V_H1-2 and human V_H6-1 is replaced with the mouse ADAM6 locus. In one embodiment, the orientation of one or more of mouse ADAM6a and mouse ADAM6b of the mouse ADAM6 locus is opposite with respect to direction of transcription as compared with the orientation of the human V_H gene segments. Alternatively, the mouse ADAM6 locus can be placed in the intergenic region between the 3'-most human V_H gene segment and the 5'-most D_H gene segment. This can be the case whether the 5'-most D_H segment is mouse or human.

[00187] Similarly, a mouse modified with one or more human V_L gene segments (e.g., VK or νλ segments) replacing all or substantially all endogenous mouse V_H gene segments can be modified so as to either maintain the endogenous mouse ADAM6 locus, as described above, e.g., by employing a targeting vector having a downstream homology arm that includes a mouse ADAM6 locus or functional fragment thereof, or to replace a damaged mouse ADAM6 locus with an ectopic sequence positioned between two human V_L gene segments or between the human V_L gene segments and a D_H gene segment (whether human or mouse, e.g., \/λ + m/hD_H), or a J gene segment (whether human or mouse, e.g., VK + J_H). In one embodiment, the replacement includes two or more human V_L gene segments, and the mouse ADAM6 locus or functional fragment thereof is placed between the two 3'-most V_L gene segments. In a specific embodiment, the arrangement of human V_L gene segments is then the following (from upstream to downstream with respect to direction of transcription of the human gene segments): human V_L3'-1 - mouse ADAM6 locus - human V_L3'. In one embodiment, the orientation of one or more of mouse

ADAM6a and mouse ADAM6b of the mouse ADAM6 locus is opposite with respect to direction of transcription as compared with the orientation of the human V_L gene segments. Alternatively, the mouse ADAM6 locus can be placed in the intergenic region between the 3'-most human V_L gene segment and the 5'-most DH gene segment. This can be the case whether the 5'-most D_H segment is mouse or human.

[00188] In one aspect, a mouse is provided with a replacement of one or more endogenous mouse V_H gene segments, and that comprises at least one endogenous mouse D_H gene segment. In such a mouse, the modification of the endogenous mouse V_H gene segments can comprise a modification of one or more of the 3'-most V_H gene segments, but not the 5'-most D_H gene segment, where care is taken so that the modification of the one or more 3'-most V_H gene segments does not disrupt or render the endogenous mouse ADAM6 locus nonfunctional. For example, in one embodiment the mouse comprises a replacement of all or substantially all endogenous mouse V_H gene segments with one or more human V_H gene segments, and the mouse comprises one or more endogenous D_H gene segments and a functional endogenous mouse ADAM6 locus.

[00189] In another embodiment, the mouse comprises the modification of endogenous mouse 3'-most V_H gene segments, and a modification of one or more endogenous mouse D_H gene segments, and the modification is carried out so as to maintain the integrity of the endogenous mouse ADAM6 locus to the extent that the endogenous ADAM6 locus remains functional. In one example, such a modification is done in two steps: (1 ) replacing the 3'-most endogenous mouse V_H gene segments with one or more human V_H gene segments employing a targeting vector with an upstream homology arm and a downstream homology arm wherein the downstream homology arm includes all or a portion of a functional mouse ADAM6 locus; (2) then replacing and endogenous mouse D_H gene segment with a targeting vector having an upstream homology arm that includes a all or a functional portion of a mouse ADAM6 locus. [00190] In various aspects, employing mice that contain an ectopic sequence that encodes a mouse ADAM6 protein or an ortholog or homolog or functional homolog thereof are useful where modifications disrupt the function of endogenous mouse ADAM6. The probability of disrupting endogenous mouse ADAM6 function is high when making modifications to mouse immunoglobulin loci, in particular when modifying mouse immunoglobulin heavy chain variable regions and surrounding sequences. Therefore, such mice provide particular benefit when making mice with immunoglobulin heavy chain loci that are deleted in whole or in part, are humanized in whole or in part, or are replaced (e.g., with VK or \ λ sequences) in whole or in part. Methods for making the genetic modifications described for the mice described below are known to those skilled in the art.

[00191] Mice containing an ectopic sequence encoding a mouse ADAM6 protein, or a substantially identical or similar protein that confers the fertility benefits of a mouse ADAM6 protein, are particularly useful in conjunction with modifications to a mouse immunoglobulin heavy chain variable region gene locus that disrupt or delete the endogenous mouse ADAM6 sequence. Although primarily described in connection with mice that express antibodies with human variable regions and mouse constant regions, such mice are useful in connection with any genetic modifications that disrupt the endogenous mouse ADAM6 gene. Persons of skill will recognize that this encompasses a wide variety of genetically modified mice that contain modifications of the mouse immunoglobulin heavy chain variable region gene locus. These include, for example, mice with a deletion or a replacement of all or a portion of the mouse immunoglobulin heavy chain gene segments, regardless of other modifications. Non-limiting examples are described below.

[00192] In some aspects, genetically modified mice are provided that comprise an ectopic mouse, rodent, or other ADAM6 gene (or ortholog or homolog or fragment) functional in a mouse, and one or more human immunoglobulin variable and/or constant region gene segments.

[00193] In one aspect, a mouse is provided that comprises an ectopic ADAM6 sequence that encodes a functional ADAM6 protein, a replacement of all or substantially all mouse V_H gene segments with one or more human V_H gene segments; a replacement of all or substantially all mouse D_H gene segments with one or more human D_H gene segments; and a replacement of all or substantially all mouse J_H gene segments with one or more human J_H gene segments.

[00194] In one embodiment, the mouse further comprises a replacement of a mouse C_H1 nucleotide sequence with a human C_H1 nucleotide sequence. In one embodiment, the mouse further comprises a replacement of a mouse hinge nucleotide sequence with a human hinge nucleotide sequence. In one embodiment, the mouse further comprises a replacement of an immunoglobulin light chain variable locus (V_L and J_L) with a human immunoglobulin light chain variable locus. In one embodiment, the mouse further comprises a replacement of a mouse immunoglobulin light chain constant region nucleotide sequence with a human immunoglobulin light chain constant region nucleotide sequence. In a specific embodiment, the V_L, JL, and C_L are immunoglobulin κ light chain sequences. In a specific embodiment, the mouse comprises a mouse C_H2 and a mouse C_H3 immunoglobulin constant region sequence fused with a human hinge and a human C_H1 sequence, such that the mouse immunoglobulin loci rearrange to form a gene that encodes a binding protein comprising (a) a heavy chain that has a human variable region, a human C_H1 region, a human hinge region, and a mouse C_H2 and a mouse C_H3 region; and (b) a gene that encodes an immunoglobulin light chain that comprises a human variable domain and a human constant region.

[001 95] In one aspect, a mouse is provided that comprises an ectopic ADAM6 sequence that encodes a functional ADAM6 protein, a replacement of all or substantially all mouse V_H gene segments with one or more human V_L gene segments, and optionally a replacement of all or substantially all D_H gene segments and/or J_H gene segments with one or more human DH gene segments and/or human J_H gene segments, or optionally a replacement of all or substantially all D_H gene segments and J_H gene segments with one or more human J_L gene segments.

[00196] In one embodiment, the mouse comprises a replacement of all or substantially all mouse V_H, D_H, and J_H gene segments with one or more V_L, one or more D_H, and one or more J gene segments (e.g., JK or ϋλ), wherein the gene segments are operably linked to an endogenous mouse hinge region, wherein the mouse forms a rearranged

immunoglobulin chain gene that contains, from 5' to 3' in the direction of transcription, human V_L - human or mouse D_H - human or mouse J - mouse hinge - mouse CH2 - mouse C_H3. In one embodiment, the J region is a human JK region. In one embodiment, the J region is a human J_H region. In one embodiment, the J region is a human J region. In one embodiment, the human V_L region is selected from a human νλ region and a human VK region.

[001 97] In specific embodiments, the mouse expresses a single variable domain antibody having a mouse or human constant region and a variable region derived from a human VK, a human D_H and a human JK; a human VK, a human D_H, and a human J_H; a human VX, a human D_H, and a human J ; a human νλ, a human D_H, and a human J_H; a human VK, a human D_H, and a human λ; a human V , a human D_H, and a human JK. In specific embodiment, recombination recognition sequences are modified so as to allow for productive rearrangements to occur between recited V, D, and J gene segments or between recited V and J gene segments. [00198] In one aspect, a mouse is provided that comprises an ectopic ADAM6 sequence that encodes a functional ADAM6 protein (or ortholog or homolog or functional fragment thereof), a replacement of all or substantially all mouse V_H gene segments with one or more human V_L gene segments, a replacement of all or substantially all mouse D_H gene segment and J_H gene segments with human J_L gene segments; wherein the mouse lacks a C_H1 and/or hinge region.

[00199] In one embodiment, the mouse lacks a sequence encoding a C_H1 domain. In one embodiment, the mouse lacks a sequence encoding a hinge region. In one

embodiment, the mouse lacks a sequence encoding a C_H1 domain and a hinge region.

[00200] In a specific embodiment, the mouse expresses a binding protein that comprises a human immunoglobulin light chain variable domain (λ or κ) fused to a mouse C_H2 domain that is attached to a mouse CH3 domain.

[00201] In one aspect, a mouse is provided that comprises an ectopic ADAM6 sequence that encodes a functional ADAM6 protein (or ortholog or homolog or functional fragment thereof), a replacement of all or substantially all mouse V_H gene segments with one or more human V_L gene segments, a replacement of all or substantially all mouse D_H and J_H gene segments with human J_L gene segments.

[00202] In one embodiment, the mouse comprises a deletion of an immunoglobulin heavy chain constant region gene sequence encoding a C_H1 region, a hinge region, a CH1 and a hinge region, or a C_H1 region and a hinge region and a C_H2 region.

[00203] In one embodiment, the mouse makes a single variable domain binding protein comprising a homodimer selected from the following: (a) human V_L - mouse C_H1 - mouse CH2 - mouse C_H3; (b) human V_L - mouse hinge - mouse CH2 - mouse C_H3; (c) human V_L - mouse C_H2 - mouse C_H3.

[00204] In one aspect, a mouse is provided with a disabled endogenous heavy chain immunoglobulin locus, comprising a disabled or deleted endogenous mouse ADAM6 locus, wherein the mouse comprises a nucleic acid sequence that expresses a human or mouse or human/mouse or other chimeric antibody. In one embodiment, the nucleic acid sequence is present on a transgene integrated that is randomly integrated into the mouse genome. In one embodiment, the nucleic acid sequence is on an episome (e.g., a chromosome) not found in a wild-type mouse.

Common, or Universal, Light Chain

[00205] Prior efforts to make useful multispecific epitope-binding proteins, e.g., bispecific antibodies, have been hindered by variety of problems that frequently share a common paradigm: in vitro selection or manipulation of sequences to rationally engineer, or to engineer through trial-and-error, a suitable format for pairing a heterodimeric bispecific human immunoglobulin. Unfortunately, most if not all of the in vitro engineering approaches provide largely ad hoc fixes that are suitable, if at all, for individual molecules. On the other hand, in vivo methods for employing complex organisms to select appropriate pairings that are capable of leading to human therapeutics have not been realized.

[00206] Generally, native mouse sequences are frequently not a good source for human therapeutic sequences. For at least that reason, generating mouse heavy chain immunoglobulin variable regions that pair with a common human light chain is of limited practical utility. More in vitro engineering efforts would be expended in a trial-and-error process to try to humanize the mouse heavy chain variable sequences while hoping to retain epitope specificity and affinity while maintaining the ability to couple with the common human light chain, with uncertain outcome. At the end of such a process, the final product may maintain some of the specificity and affinity, and associate with the common light chain, but ultimately immunogenicity in a human would likely remain a profound risk.

[00207] Therefore, a suitable mouse for making human therapeutics would include a suitably large repertoire of human heavy chain variable region gene segments in place of endogenous mouse heavy chain variable region gene segments. The human heavy chain variable region gene segments should be able to rearrange and recombine with an endogenous mouse heavy chain constant domain to form a reverse chimeric heavy chain (i.e., a heavy chain comprising a human variable domain and a mouse constant region). The heavy chain should be capable of class switching and somatic hypermutation so that a suitably large repertoire of heavy chain variable domains are available for the mouse to select one that can associate with the limited repertoire of human light chain variable regions.

[00208] A mouse that selects a common light chain for a plurality of heavy chains has a practical utility. In various embodiments, antibodies that express in a mouse that can only express a common light chain will have heavy chains that can associate and express with an identical or substantially identical light chain. This is particularly useful in making bispecific antibodies. For example, such a mouse can be immunized with a first immunogen to generate a B cell that expresses an antibody that specifically binds a first epitope. The mouse (or a mouse genetically the same) can be immunized with a second immunogen to generate a B cell that expresses an antibody that specifically binds the second epitope. Variable heavy regions can be cloned from the B cells and expresses with the same heavy chain constant region, and the same light chain, and expressed in a cell to make a bispecific antibody, wherein the light chain component of the bispecific antibody has been selected by a mouse to associate and express with the light chain component. [00209] The inventors have engineered a mouse for generating immunoglobulin light chains that will suitably pair with a rather diverse family of heavy chains, including heavy chains whose variable regions depart from germline sequences, e.g., affinity matured or somatically mutated variable regions. In various embodiments, the mouse is devised to pair human light chain variable domains with human heavy chain variable domains that comprise somatic mutations, thus enabling a route to high affinity binding proteins suitable for use as human therapeutics.

[00210] The genetically engineered mouse, through the long and complex process of antibody selection within an organism, makes biologically appropriate choices in pairing a diverse collection of human heavy chain variable domains with a limited number of human light chain options. In order to achieve this, the mouse is engineered to present a limited number of human light chain variable domain options in conjunction with a wide diversity of human heavy chain variable domain options. Upon challenge with an antigen, the mouse maximizes the number of solutions in its repertoire to develop an antibody to the antigen, limited largely or solely by the number or light chain options in its repertoire. In various embodiments, this includes allowing the mouse to achieve suitable and compatible somatic mutations of the light chain variable domain that will nonetheless be compatible with a relatively large variety of human heavy chain variable domains, including in particular somatically mutated human heavy chain variable domains.

[00211] To achieve a limited repertoire of light chain options, the mouse is engineered to render nonfunctional or substantially nonfunctional its ability to make, or rearrange, a native mouse light chain variable domain. This can be achieved, e.g., by deleting the mouse's light chain variable region gene segments. The endogenous mouse locus can then be modified by an exogenous suitable human light chain variable region gene segment of choice, operably linked to the endogenous mouse light chain constant domain, in a manner such that the exogenous human variable region gene segments can combine with the endogenous mouse light chain constant region gene and form a rearranged reverse chimeric light chain gene (human variable, mouse constant). In various embodiments, the light chain variable region is capable of being somatically mutated. In various embodiments, to maximize ability of the light chain variable region to acquire somatic mutations, the appropriate enhancer(s) is retained in the mouse. For example, in modifying a mouse κ light chain locus to replace endogenous mouse κ light chain gene segments with human κ light chain gene segments, the mouse κ intronic enhancer and mouse K 3' enhancer are functionally maintained, or undisrupted.

[00212] A genetically engineered mouse is provided that expresses a limited repertoire of reverse chimeric (human variable, mouse constant) light chains associated with a diversity of reverse chimeric (human variable, mouse constant) heavy chains. In various embodiments, the endogenous mouse κ light chain gene segments are deleted and replaced with a single (or two) rearranged human light chain region, operably linked to the endogenous mouse CK gene. In embodiments for maximizing somatic hypermutation of the rearranged human light chain region, the mouse κ intronic enhancer and the mouse κ 3' enhancer are maintained. In various embodiments, the mouse also comprises a nonfunctional λ light chain locus, or a deletion thereof or a deletion that renders the locus unable to make a λ light chain.

[00213] A genetically engineered mouse is provided that, in various embodiments, comprises a light chain variable region locus lacking endogenous mouse light chain V_L and J_L gene segments and comprising a rearranged human light chain variable region, in one embodiment a rearranged human V_L/JL sequence, operably linked to a mouse constant region, wherein the locus is capable of undergoing somatic hypermutation, and wherein the locus expresses a light chain comprising the human V_L/JL sequence linked to a mouse constant region. Thus, in various embodiments, the locus comprises a mouse κ 3' enhancer, which is correlated with a normal, or wild type, level of somatic hypermutation.

[00214] The genetically engineered mouse in various embodiments when immunized with an antigen of interest generates B cells that exhibit a diversity of rearrangements of human immunoglobulin heavy chain variable regions that express and function with one or with two rearranged light chains, including embodiments where the one or two light chains comprise human light chain variable regions that comprise, e.g., 1 to 5 somatic mutations. In various embodiments, the human light chains so expressed are capable of associating and expressing with any human immunoglobulin heavy chain variable region expressed in the mouse.

Epitope-binding Proteins That Bind More Than One Epitope

[00215] The compositions and methods of described herein can be used to make binding proteins that bind more than one epitope with high affinity, e.g., bispecific antibodies. Advantages of the invention include the ability to select suitably high binding (e.g., affinity matured) heavy chain immunoglobulin chains each of which will associate with a single light chain.

[00216] Synthesis and expression of bispecific binding proteins has been problematic, in part due to issues associated with identifying a suitable light chain that can associate and express with two different heavy chains, and in part due to isolation issues. The methods and compositions described herein allow for a genetically modified mouse to select, through otherwise natural processes, a suitable light chain that can associate and express with more than one heavy chain, including heavy chains that are somatically mutated (e.g., affinity matured). Human V_L and V_H sequences from suitable B cells of immunized mice as described herein that express affinity matured antibodies having reverse chimeric heavy chains (i.e., human variable and mouse constant) can be identified and cloned in frame in an expression vector with a suitable human constant region gene sequence (e.g., a human lgG1 ). Two such constructs can be prepared, wherein each construct encodes a human heavy chain variable domain that binds a different epitope. One of the human V_Ls (e.g., human VK1 -39JK5 or human VK3-20JK1 ), in germline sequence or from a B cell wherein the sequence has been somatically mutated, can be fused in frame to a suitable human constant region gene (e.g., a human κ constant gene). These three fully-human heavy and light constructs can be placed in a suitable cell for expression. The cell will express two major species: a homodimeric heavy chain with the identical light chain, and a heterodimeric heavy chain with the identical light chain. To allow for a facile separation of these major species, one of the heavy chains is modified to omit a Protein A-binding determinant, resulting in a differential affinity of a homodimeric binding protein from a heterodimeric binding protein. Compositions and methods that address this issue are described in USSN 12/832,838, filed 25 June 2010, entitled "Readily Isolated Bispecific Antibodies with Native Immunoglobulin Format," published as US 2010/0331527A1 , hereby incorporated by reference.

[00217] In one aspect, an epitope-binding protein as described herein is provided, wherein human V_L and V_H sequences are derived from mice described herein that have been immunized with an antigen comprising an epitope of interest.

[00218] In one embodiment, an epitope-binding protein is provided that comprises a first and a second polypeptide, the first polypeptide comprising, from N-terminal to C-terminal, a first epitope-binding region that selectively binds a first epitope, followed by a constant region that comprises a first C_H3 region of a human IgG selected from lgG1 , lgG2, lgG4, and a combination thereof; and, a second polypeptide comprising, from N-terminal to C- terminal, a second epitope-binding region that selectively binds a second epitope, followed by a constant region that comprises a second C_H3 region of a human IgG selected from lgG1 , lgG2, lgG4, and a combination thereof, wherein the second C_H3 region comprises a modification that reduces or eliminates binding of the second C_H3 domain to protein A.

[00219] In one embodiment, the second C_H3 region comprises an H95R modification (by IMGT exon numbering; H435R by EU numbering). In another embodiment, the second C_H3 region further comprises a Y96F modification (IMGT; Y436F by EU). [00220] In one embodiment, the second C_H3 region is from a modified human lgG1 , and further comprises a modification selected from the group consisting of D16E, L18M, N44S, K52N, V57M, and V82I (IMGT; D356E, L358M, N384S, K392N, V397M, and V422I by EU).

[00221 ] In one embodiment, the second C_H3 region is from a modified human lgG2, and further comprises a modification selected from the group consisting of N44S, 52N, and V82I (IMGT; N384S, K392N, and V422I by EU).

[00222] In one embodiment, the second C_H3 region is from a modified human lgG4, and further comprises a modification selected from the group consisting of Q15R, N44S, K52N, V57M, R69K, E79Q, and V82I (IMGT; Q355R, N384S, K392N, V397M, R409K, E419Q, and V422I by EU).

[00223] One method for making an epitope-binding protein that binds more than one epitope is to immunize a first mouse in accordance with the invention with an antigen that comprises a first epitope of interest, wherein the mouse comprises an endogenous immunoglobulin light chain variable region locus that does not contain an endogenous mouse V_L that is capable of rearranging and forming a light chain, wherein at the endogenous mouse immunglobulin light chain variable region locus is a single rearranged human V_L region operably linked to the mouse endogenous light chain constant region gene, and the rearranged human V_L region is selected from a human VK1 -39JK5 and a human VK3-20JK1 , and the endogenous mouse V_H gene segments have been replaced in whole or in part with human V_H gene segments, such that immunoglobulin heavy chains made by the mouse are solely or substantially heavy chains that comprise human variable domains and mouse constant domains. When immunized, such a mouse will make a reverse chimeric antibody, comprising only one of two human light chain variable domains (e.g., one of human V 1-39JK5 or human V 3-20J 1 ). Once a B cell is identified that encodes a V_H that binds the epitope of interest, the nucleotide sequence of the VH (and, optionally, the V_L) can be retrieved (e.g., by PCR) and cloned into an expression construct in frame with a suitable human immunoglobulin constant domain. This process can be repeated to identify a second V_H domain that binds a second epitope, and a second V_H gene sequence can be retrieved and cloned into an expression vector in frame to a second suitable immunoglobulin constant domain. The first and the second immunoglobulin constant domains can the same or different isotype, and one of the immunoglobulin constant domains (but not the other) can be modified as described herein or in US

2010/0331527A1 , and epitope-binding protein can be expressed in a suitable cell and isolated based on its differential affinity for Protein A as compared to a homodimeric epitope-binding protein, e.g., as described in US 2010/0331527A1. [00224] In one embodiment, a method for making a bispecific epitope-binding protein is provided, comprising identifying a first affinity-matured (e.g., comprising one or more somatic hypermutations) human V_H nucleotide sequence (V_H1 ) from a mouse as described herein, identifying a second affinity-matured (e.g., comprising one or more somatic hypermutations) human VH nucleotide sequence (V_H2) from a mouse as described herein, cloning V_H1 in frame with a human heavy chain lacking a Protein A-determinant modification as described in US 2010/0331527A1 for form heavy chain 1 (HC1 ), cloning V_H2 in frame with a human heavy chain comprising a Protein A-determinant as described in US 2010/0331527A1 to form heavy chain 2 (HC2), introducing an expression vector comprising HC1 and the same or a different expression vector comprising HC2 into a cell, wherein the cell also expresses a human immunoglobulin light chain that comprises a human νκΙ -39/human JK5 or a human VK3-20/human JK1 fused to a human light chain constant domain, allowing the cell to express a bispecific epitope-binding protein comprising a V_H domain encoded by V_H1 and a V_H domain encoded by V_H2, and isolating the bispecific epitope-binding protein based on its differential ability to bind Protein A as compared with a monospecific homodimeric epitope-binding protein. In a specific embodiment, HC1 is an lgG1 , and HC2 is an lgG1 that comprises the modification H95R (IMGT; H435R by EU) and further comprises the modification Y96F (IMGT; Y436F by EU). In one embodiment, the VH domain encoded by V_H , the V_H domain encoded by V_H2, or both, are somatically mutated.

Human V_H Genes That Express with a Common Human V_L

[00225] A variety of human variable regions from affinity-matured antibodies raised against four different antigens were expressed with either their cognate light chain, or at least one of a human light chain selected from human VK1 -39JK5, human VK3-20JK1 , or human VpreBJ S (see Example 10). For antibodies to each of the antigens, somatically mutated high affinity heavy chains from different gene families paired successfully with rearranged human germline VK1 -39JK5 and VK3-20JK1 regions and were secreted from cells expressing the heavy and light chains. For VK1 -39J 5 and VK3-20JK1 , V_h domains derived from the following human V_H gene families expressed favorably: 1 -2, 1 -8, 1 -24, 2- 5, 3-7, 3-9, 3-1 1 , 3-13, 3-15, 3-20, 3-23, 3-30, 3-33, 3-48, 4-31 , 4-39, 4-59, 5-51 , and 6-1 . Thus, a mouse that is engineered to express a limited repertoire of human V_L domains from one or both of VK1 -39JK5 and VK3-20JK1 will generate a diverse population of somatically mutated human V_H domains from a V_H locus modified to replace mouse V_H gene segments with human V_H gene segments. [00226] Mice genetically engineered to express reverse chimeric (human variable, mouse constant) immunoglobulin heavy chains associated with a single rearranged light chain (e.g., a VK1 -39/J or a VK3-20/J), when immunized with an antigen of interest, generated B cells that comprised a diversity of human V_H rearrangements and expressed a diversity of high-affinity antigen-specific antibodies with diverse properties with respect to their ability to block binding of the antigen to its ligand, and with respect to their ability to bind variants of the antigen (see Examples 14 through 15).

[00227] Thus, the mice and methods described herein are useful in making and selecting human immunoglobulin heavy chain variable domains, including somatically mutated human heavy chain variable domains, that result from a diversity of

rearrangements, that exhibit a wide variety of affinities (including exhibiting a K_D of about a nanomolar or less), a wide variety of specificities (including binding to different epitopes of the same antigen), and that associate and express with the same or substantially the same human immunoglobulin light chain variable region.

[00228] In one aspect, a first mouse comprising a humanized heavy chain variable region locus is bred with a second mouse comprising a nucleic acid sequence encoding a common, or universal, light chain locus as described herein. In one embodiment, the first or the second mouse comprises an ectopic nucleic acid sequence encoding a mouse ADAM6 or ortholog or homolog or functional fragment thereof. Progeny are bred to obtain mice homozygous for a humanized heavy chain locus, and homozygous for the universal light chain locus. In one embodiment, the first mouse or the second mouse comprises a modification of an endogenous mouse light chain locus to render the endogenous mouse light chain locus nonfunctional (e.g. , a deletion or a knockout of, e.g., a λ and/or κ endogenous locus). In one embodiment, the first mouse comprises a replacement of all or substantially all functinoal endogenous mouse V, D, and J gene segments with one or more unrearranged human V, D, and J gene segments {e.g., all or substantially all functional human V, D, and J gene segments); and the mouse comprises a replacement of all or substantially all functional light chain V and J gene segments with no more than one or no more than two rearranged light chain V/J sequences. In one embodiment the first mouse further comprises an ectopic nucleic acid sequence that encodes a mouse ADAM6 or ortholog or homolog or functional fragment thereof. In one embodiment, the ectopic nucleic acid sequence is at a humanized immunoglobulin heavy chain locus.

[00229] In one embodiment, mice that comprise the ectopic sequence and that are homozygous for the universal light chain locus and for the humanized heavy chain locus are immunized with an antigen of interest to generate antibodies that comprise a plurality of somtatically mutated human variable domains that associate and express with a universal light chain. In one embodiment, human heavy chain variable domain nucleic acid sequences identified in the mouse are employed in an expression system to make a fully human antibody comprising the human heavy chain variable domain and a light chain comprising a universal light chain sequence of the mouse.

[00230] The following examples are provided so as to describe to those of ordinary skill in the art how to make and use methods and compositions of the invention, and are not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, efc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is average molecular weight, temperature is indicated in Celsius, and pressure is at or near atmospheric.

EXAMPLES

Example I

Humanization of Mouse Immunoglobulin Genes

[00231] Human and mouse bacterial artificial chromsomes (BACs) were used to engineer 13 different BAC targeting vectors (BACvecs) for humanization of the mouse immunoglobulin heavy chain and κ light chain loci. Tables 1 and 2 set forth detailed descriptions of the steps performed for the construction of all BACvecs employed for the humanization of the mouse immunoglobulin heavy chain and κ light chain loci,

respectively.

[00232] Identification of human and mouse BACs.

[00233] Mouse BACs that span the 5' and 3' ends of the immunoglobulin heavy chain and K light chain loci were identified by hybridization of filters spotted with BAC library or by PCR screening mouse BAC library DNA pools. Filters were hybridized under standard conditions using probes that corresponded to the regions of interest. Library pools were screened by PCR using unique primer pairs that flank the targeted region of interest.

Additional PCR using the same primers was performed to deconvolute a given well and isolate the corresponding BAC of interest. Both BAC filters and library pools were generated from 129 SvJ mouse ES cells (Incyte Genomics/lnvitrogen). Human BACs that cover the entire immunoglobulin heavy chain and κ light chain loci were identified either by hybridization of filters spotted with BAC library (Caltech B, C, or D libraries & RPCI-1 1 library, Research Genetics/I nvitrogen) through screening human BAC library pools (Caltech library, Invitrogen) by a PCR-based method or by using a BAC end sequence database (Caltech D library, TIGR). [00234] Construction of BACvecs (Tables 1 and 2).

[00235] Bacterial homologous recombination (BHR) was performed as described (Valenzuela et al., 2003; Zhang, Y., er a/. (1998). A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet 20, 123-128). In most cases, linear fragments were generated by ligating PCR-derived homology boxes to cloned cassettes followed by gel isolation of ligation products and electroporation into BHR-competent bacteria harboring the target BAC. After selection on appropriate antibiotic petri dishes, correctly recombined BACs were identified by PCR across both novel junctions followed by restriction analysis on pulsed-field gels (Schwartz, D.C., and Cantor, C.R. (1984)

Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67-75) and spot-checking by PCR using primers distributed across the human sequences.

[00236] A 3hV_H BACvec was constructed using three sequential BHR steps for the initial step of humanization of the immunoglobulin heavy chain locus (FIG. 4A and Table 1 ). In the first step (Step 1 ), a cassette was introduced into a human parental BAC upstream from the human V_H1 -3 gene segment that contains a region of homology to the mouse immunoglobulin heavy chain locus (HB1), a gene that confers kanamycin resistance in bacteria and G418 resistance in animals cells (kanR) and a site-specific recombination site (e.g., loxP). In the second step (Step 2), a second cassette was introduced just downstream from the last J_H segment that contains a second region of homology to the mouse immunoglobulin heavy chain locus (HB2) and a gene that confers resistance in bacteria to spectinomycin (specR). This second step included deleting human

immunoglobulin heavy chain locus sequences downstream from J_H6 and the BAC vector chloramphenicol resistance gene (cmR). In the third step (Step 3), the doubly modified human BAC (B1 ) was then linearized using l-Ceul sites that had been added during the first two steps and integrated into a mouse BAC (B2) by BHR through the two regions of homology (HB1 and HB2). The drug selections for first (cm/kan), second (spec/kan) and third (cm/kan) steps were designed to be specific for the desired products. Modified BAC clones were analyzed by pulse-filed gel electrophoresis (PFGE) after digestion with restriction enzymes to determine appropriate construction (FIG. 4B).

[00237] In a similar fashion, 12 additional BACvecs were engineered for humanization of the heavy chain and κ light chain loci. In some instances, BAC ligation was performed in lieu of BHR to conjoin two large BACs through introduction of rare restriction sites into both parental BACvecs by BHR along with careful placement of selectable markers. This allowed for the survival of the desired ligation product upon selection with specific drug marker combinations. Recombinant BACs obtained by ligation after digestion with rare restriction enzymes were identified and screened in a similar fashion to those obtained by BHR (as described above).

Table 1

BACvec Step Description Process

5

Swap selection cassette from neo to hyg using UbCp and pA

9 BHR as homolgy boxes to create 39hV_H BACvec

1 Insert specR at proximal end of human CTD-3074b5 BAC BHR

2 Insert AscI site at distal end of human CTD-3074b5 BAC BHR

Insert hygR and AscI site at proximal end of mouse distalhV_H 3 BHR homology arm using CT7-253i20 BAC

4 Ligate mouse distal homology arm onto construct from step 2 Ligation

Swap selection cassette from hyg to neo using UbCp and pA

5 BHR as homolgy boxes to create 53hV_H BACvec

Insert Pl-Scel and l-Ceul sites flanking spec at distal end of

1 BHR human CTD-2195p5 BAC

Insert l-Ceul site at proximal end of RP11-926p12 BAC for

2 BHR ligation to CTD-2195p5 BAC

Insert Pl-Scel and AscI sites at distal end of RP1 1 -926p12hV_H 3 BHR

BAC for ligation of mouse arm

4 Ligate mouse distal homology arm onto construct from step 3 Ligation

Ligate mouse distal homology arm and hlgH fragment from

5 RP11 -926p12 BAC onto CTD-2195p5 BAC to create 70 hV_H Ligation BACvec

Insert l-Ceul and AscI sites flanking hygR at distal end of CTD-

1 BHR 2313e3 BAC

hV_H

Ligate mouse dista homology arm onto human CTD-2313e3

2 Ligation BAC from step 1 to create 80hV_H BACvec

Table 2

[00238] Modification of embryonic stem (ES) cells and generation of mice.

[00239] ES cell (F1 H4) targeting was performed using the VELOCIGENE® genetic engineering method as described (Valenzuela et al., 2003). Derivation of mice from modified ES cells by either blastocyst (Valenzuela et al., 2003) or 8-cell injection

(Poueymirou et al., 2007) was as described. Targeted ES cells and mice were confirmed by screening DNA from ES cells or mice with unique sets of probes and primers in a PCR based assay (e.g., FIG. 3A, 3B and 3C). All mouse studies were overseen and approved by Regeneron's Institutional Animal Care and Use Committee (IACUC).

[00240] Karyotype Analysis and Fluorescent in situ Hybridization (FISH).

[00241] Karyotype Analysis was performed by Coriell Cell Repositories (Coriell Institute for Medical Research, Camden, NJ). FISH was performed on targeted ES cells as described (Valenzuela et al., 2003). Probes corresponding to either mouse BAC DNA or human BAC DNA were labeled by nick translation (Invitrogen) with the fluorescently labeled dUTP nucleotides spectrum orange or spectrum green (Vysis).

[00242] Immunoglobulin Heavy Chain Variable Gene Locus.

[00243] Humanization of the variable region of the heavy chain locus was achieved in nine sequential steps by the direct replacement of about three million base pairs (Mb) of contiguous mouse genomic sequence containing all V_H, D_H and J_H gene segments with about one Mb of contiguous human genomic sequence containing the equivalent human gene segments (FIG. 1A and Table 1 ) using VELOCIGENE® genetic engineering technology (see, e.g., US Pat. No. 6,586,251 and Valenzuela et al., 2003).

[00244] The intron between J_H gene segments and constant region genes (the J-C intron) contains a transcriptional enhancer (Neuberger, M.S. (1983) Expression and regulation of immunoglobulin heavy chain gene transfected into lymphoid cells. EMBO J 2, 1373-1378) followed by a region of simple repeats required for recombination during isotype switching (Kataoka, T. et al. (1980) Rearrangement of immunoglobulin gamma 1- chain gene and mechanism for heavy-chain class switch. Proc Natl Acad Sci U S A 77, 919-923). The junction between human V_H-D_H-JH region and the mouse C_H region (the proximal junction) was chosen to maintain the mouse heavy chain intronic enhancer and switch domain in order preserve both efficient expression and class switching of the humanized heavy chain locus within the mouse. The exact nucleotide position of this and subsequent junctions in all the replacements was possible by use of the VELOCIGENE® genetic engineering method (supra), which employed bacterial homologous recombination driven by synthesized oligonucleotides. Thus, the proximal junction was placed about 200 bp downstream from the last JH gene segment and the distal junction was placed several hundred upstream of the most 5' V_H gene segment of the human locus and about 9 kb downstream from the mouse V_H1-86 gene segment, also known as J558.55. The mouse V_H1 -86 (J558.55) gene segment is the most distal heavy chain variable gene segment, reported to be a pseudogene in C57BL/6 mice, but potentially active, albeit with a poor RSS sequence, in the targeted 129 allele. The distal end of the mouse heavy chain locus reportedly may contain control elements that regulate locus expression and/or

rearrangement (Pawlitzky et al., 2006).

[00245] A first insertion of human immunoglobulin DNA sequence into the mouse was achieved using 144 kb of the proximal end of the human heavy chain locus containing 3 V_H, all 27 D_H and 9 J_H human gene segments inserted into the proximal end of the mouse IgH locus, with a concomitant 16.6 kb deletion of mouse genomic sequence, using about 75 kb of mouse homology arms (Step A, FIG. 2A; Tables 1 and 3, 3hV_H). This large 144kb insertion and accompanying 16.6 kb deletion was performed in a single step (Step A) that occurred with a frequency of 0.2% (Table 3). Correctly targeted ES cells were scored by a loss-of-native-allele (LONA) assay (Valenzuela et al., 2003) using probes within and flanking the deleted mouse sequence and within the inserted human sequence, and the integrity of the large human insert was verified using multiple probes spanning the entire insertion (FIG. 3A, 3B and 3C). Because many rounds of sequential ES cell targeting were anticipated, targeted ES cell clones at this, and all subsequent, steps were subjected to karyotypic analysis {supra) and only those clones showing normal karyotypes in at least 17 of 20 spreads were utilized for subsequent steps.

[00246] Targeted ES cells from Step A were re-targeted with a BACvec that produced a 19 kb deletion at the distal end of the heavy chain locus (Step B, FIG. 2A). The Step B BACvec contained a hygromycin resistance gene (hyg) in contrast to the neomycin resistance gene (neo) contained on the BACvec of Step A. The resistance genes from the two BACvecs were designed such that, upon successful targeting to the same

chromosome, approximately three Mb of the mouse heavy chain variable gene locus containing all of the mouse V_H gene segments other than V_H1 -86 and all of the D_H gene segments other than DQ52, as well as the two resistance genes, were flanked by loxP sites; DQ52 and all of the mouse J_H chain gene segments were deleted in Step A. ES cell clones doubly targeted on the same chromosome were identified by driving the 3hV_H proximal cassette to homozygosity in high G418 (Mortensen, R.M. ef al. (1992) Production of homozygous mutant ES cells with a single targeting construct. Mol Cell Biol 12:2391- 2395) and following the fate of the distal hyg cassette. Mouse segments up to four Mb in size, having been modified in a manner to be flanked by loxP sites, have been successfully deleted in ES cells by transient expression of CRE recombinase with high efficiencies (up to =1 1 %) even in the absence of drug selection (Zheng, B., ef al. (2000). Engineering mouse chromosomes with Cre-loxP: range, efficiency, and somatic applications. Mol Cell Biol 20:648-655). In a similar manner, the inventors achieved a three Mb deletion in 8% of ES cell clones following transient Cre expression (Step C, FIG. 2A; Table 3). The deletion was scored by the LONA assay using probes at either end of the deleted mouse sequence, as well as the loss of neo and hyg and the appearance of a PCR product across the deletion point containing the sole remaining loxP site. Further, the deletion was confirmed by fluorescence in situ hybridization (data not shown).

[00247] The remainder of the human heavy chain variable region was added to the 3hV_H allele in a series of 5 steps using the VELOCIGENE® genetic engineering method (Steps E-H, FIG. 2B), with each step involving precise insertion of up to 210 kb of human gene sequences. For each step, the proximal end of each new BACvec was designed to overlap the most distal human sequences of the previous step and the distal end of each new BACvec contained the same distal region of mouse homology as used in Step A. The BACvecs of steps D, F and H contained neo selection cassettes, whereas those of steps E and G contained hyg selection cassettes, thus selections were alternated between G418 and hygromycin. Targeting in Step D was assayed by the loss of the unique PCR product across the distal loxP site of 3hV_H Hybrid Allele. Targeting for Steps E through I was assayed by loss of the previous selection cassette. In the final step (Step I, FIG. 2B), the neo selection cassette, flanked by Frt sites (McLeod, M. et al. (1986) Identification of the crossover site during FLP-mediated recombination in the Saccharomyces cerevisiae plasmid 2 microns circle. Mol Cell Biol 6, 3357-3367), was removed by transient FLPe expression (Buchhoiz, F. et al. (1998) Improved properties of FLP recombinase evolved by cycling mutagenesis. Nat Biotechnol 16, 657-662). The human sequences of the BACvecs for Steps D, E and G were derived from two parental human BACs each, whereas those from Steps F and H were from single BACs. Retention of human sequences was confirmed at every step using multiple probes spanning the inserted human sequences (as described above, e.g. FIG. 3A, 3B and 3C). Only those clones with normal karyotype and germline potential were carried forward in each step. ES cells from the final step were still able to contribute to the germline after nine sequential manipulations (Table 3). Mice homozygous for each of the heavy chain alleles were viable, appeared healthy and demonstrated an essentially wild-type humoral immune system (see Example 3). Table 3

[00248] Immunoglobulin κ Light Chain Variable Gene Locus.

[00249] The light chain variable region was humanized in eight sequential steps by the direct replacement of about three Mb of mouse sequence containing all VK and JK gene segments with about 0.5 Mb of human sequence containing the proximal human VK and JK gene segments in a manner similar to that of the heavy chain (FIG. 1 B; Tables 2 and 4).

[00250] The variable region of the human κ light chain locus contains two nearly identical 400 kb repeats separated by a 800 kb spacer (Weichhold, G.M. et al. (1993) The human immunoglobulin kappa locus consists of two copies that are organized in opposite polarity, Genomics 16:503-51 1 ). Because the repeats are so similar, nearly all of the locus diversity can be reproduced in mice by using the proximal repeat. Further, a natural human allele of the κ light chain locus missing the distal repeat has been reported

(Schaible, G. et al. (1993) The immunoglobulin kappa locus: polymorphism and haplotypes of Caucasoid and non-Caucasoid individuals, Hum Genet 91 :261 -267). About three Mb of mouse K light chain variable gene sequence were replaced with about 0.5 Mb of human κ light chain variable gene sequence to effectively replace all of the mouse VK and JK gene segments with the proximal human VK and all of the human JK gene segments (FIG. 2C and 2D; Tables 2 and 4). In contrast to the method described in Example 1 for the heavy chain locus, the entire mouse VK gene region, containing all VK and JK gene segments, was deleted in a three-step process before any human sequence was added. First, a neo cassette was introduced at the proximal end of the variable region (Step A, FIG. 2C). Next, a hyg cassette was inserted at the distal end of the κ locus (Step B, FIG. 2C). LoxP sites were again situated within each selection cassette such that Cre treatment induced deletion of the remaining 3 Mb of the mouse VK region along with both resistance genes (Step C, FIG. 2C).

[00251] A human genomic fragment of about 480 kb in size containing the entire immunoglobulin κ light chain variable region was inserted in four sequential steps (FIG. 2D; Tables 2 and 4), with up to 150 kb of human immunoglobulin κ light chain sequence inserted in a single step, using methods similar to those employed for the heavy chain (see Example 1). The final hygromycin resistance gene was removed by transient FLPe expression. As with the heavy chain, targeted ES cell clones were evaluated for integrity of the entire human insert, normal karyotype and germ-line potential after every step. Mice homozygous for each of the κ light chain chain alleles were generated and found to be healthy and of normal appearance.

Table 4

Example II

Generation of Fully Humanized Mice by

Combination of Multiple Humanized Immunoglobulin Alleles

[00252] At several points, ES cells bearing a portion of the human immunoglobulin heavy chain or κ light chain variable repertoires as described in Example 1 were microinjected and the resulting mice bred to create multiple versions of VELOCIMMUNE® humanized mice with progressively larger fractions of the human germline immunoglobulin repertoires (Table 5; FIG. 5A and 5B). VELOCIMMUNE® 1 (V1 ) humanized mice possess 18 human V_H gene segments and all of the human D_H and J_H gene segments combined with 16 human VK gene segments and all the human JK gene segments.

VELOCIMMUNE® 2 (V2) humanized mice and VELOCIMMUNE® (V3) humanized mice have increased variable repertoires bearing a total of 39 V_H and 30 VK, and 80 V_H and 40 VK, respectively. Since the genomic regions encoding the mouse V_H, D_H and J_H gene segments, and VK and JK gene segments, have been completely replaced, antibodies produced by any version of VELOCIMMUNE® humanized mice contain human variable regions linked to mouse constant regions. The mouse λ light chain loci remain intact in all versions of the VELOCIMMUNE® humanized mice and serve as a comparator for efficiency of expression of the various VELOCIMMUNE® humanized κ light chain loci.

[00253] Mice doubly homozygous for both immunoglobulin heavy chain and κ light chain humanizations were generated from a subset of the alleles described in Example 1 . All genotypes observed during the course of breeding to generate the doubly homozygous mice occurred in roughly Mendelian proportions. Male progeny homozygous for each of the human heavy chain alleles showed reduced fertility. Reduced fertility resulted from loss of mouse ADAM6 activity. The mouse heavy chain variable gene locus contains two embedded functional ADAM6 genes (ADAM6a and ADAM6b). During humanization of the mouse heavy chain variable gene locus, the inserted human genomic sequence contained an ADAM6 pseudogene. Mouse ADAM6 may be required for fertility, and thus lack of mouse ADAM6 genes in humanized heavy chain variable gene loci might lead to reduced fertility in these mice notwithstanding the presence of the human pseudogene. Examples 7-9 describe the precise replacement of deleted mouse ADAM6 genes back into a humanized heavy chain variable gene locus, and restoration of a wild-type level of fertility in mice with a humanized heavy chain immunoglobulin locus.

Table 5

Version of Heavy Chain K Light Chain

VELOCIMMUNE® Human 5' V_H

Mouse Allele

V_H gene

Example III

Lymphocyte Populations in Mice with Humanized Immunoglobulin Genes

[00254] Mature B cell populations in the three different versions of VELOCIMMUNE® mice were evaluated by flow cytometry.

[00255] Briefly, cell suspensions from bone marrow, spleen and thymus were made using standard methods. Cells were resuspended at 5x10⁵ cells/mL in BD Pharmingen FACS staining buffer, blocked with anti-mouse CD16/32 (BD Pharmingen), stained with the appropriate cocktail of antibodies and fixed with BD CYTOFIX™ all according to the manufacturer's instructions. Final cell pellets were resuspended in 0.5 mL staining buffer and analyzed using BD FACSCALIBUR™ and BD CELLQUEST PRO™ software. All antibodies (BD Pharmingen) were prepared in a mass dilution/cocktail and added to a final concentration of 0.5 mg/10⁵ cells. Antibody cocktails for bone marrow (A-D) staining were as follows: A: anti-mouse lgM^b-FITC, anti-mouse lgM^a-PE, anti-mouse CD45R(B220)-APC; B: anti-mouse CD43(S7)-PE, anti-mouse CD45R(B220)-APC; C: anti-mouse CD24(HSA)- PE; anti-mouse CD45R(B220)-APC; D: anti-mouse BP-1-PE, anti-mouse CD45R(B220)- APC. Antibody cocktails for spleen and inguinal lymph node (E-H) staining were as follows: E: anti-mouse lgM^b-FITC, anti-mouse lgM^a-PE, anti-mouse CD45R(B220)-APC; F: anti-mouse Ig, λ1 , λ2, λ3 Light Chain-FITC, anti mouse \g Light Chain-PE, anti-mouse CD45R(B220)-APC; G: anti-mouse Ly6G/C-FITC, anti-mouse CD49b(DX5)-PE, anti- mouse CD1 1 b-APC; H: anti-mouse CD4(L3T4)-FITC, anti-mouse CD45R(B220)-PE, anti- mouse CD8a-APC. Results are shown in FIG. 6.

[00256] Lymphocytes isolated from spleen or lymph node of homozygous

VELOCIMMUNE® humanized mice were stained for surface expression of the markers B220 and IgM and analyzed using flow cytometry (FIG. 6). The sizes of the B220⁺ lgM⁺ mature B cell populations in all versions of VELOCIMMUNE® humanized mice tested were virtually identical to those of wild type mice, regardless of the number of VH gene segments they contained. In addition, mice containing homozygous hybrid humanized

immunoglobulin heavy chain loci, even those with only 3 V_H gene segments but normal mouse immunoglobulin κ light chain loci or mice containing homozygous hybrid humanized K light chain loci with normal mouse immunoglobulin heavy chain loci, also had normal numbers of B220⁺ lgM⁺ cells in their peripheral compartments (not shown). These results indicate that chimeric loci with human variable gene segments and mouse constant regions can fully populate the mature B cell compartment. Further, the number of variable gene segments at either the heavy chain or κ light chain loci, and thus the theoretical diversity of the antibody repertoire, does not correlate with the ability to generate wild type populations of mature B cells. In contrast, mice with randomly integrated fully-human immunoglobulin transgenes and inactivated mouse immunoglobulin loci have reduced numbers of B cells in these compartments, with the severity of the deficit depending on the number of variable gene segments included in the transgene (Green, L.L., and Jakobovits, A. (1998)

Regulation of B cell development by variable gene complexity in mice reconstituted with human immunoglobulin yeast artificial chromosomes, J Exp Med 188:483-495). This demonstrates that the "in situ genetic humanization" strategy results in a fundamentally different functional outcome than the randomly integrated transgenes achieved in the "knockout-plus-transgenic" approach.

[00257] Allelic Exclusion and Locus Choice.

[00258] The ability to maintain allelic exlusion was examined in mice heterozygous for different versions of the humanized immunoglobulin heavy chain locus.

[00259] The humanization of the immunoglobulin loci was carried out in an F1 ES line (F1 H4 (Valenzuela et al., 2003)), derived from 129S6/SvEvTac and C57BL/6NTac heterozygous embryos. The human heavy chain germline variable gene sequences are targeted to the 129S6 allele, which carries the lgM^a haplotype, whereas the unmodified mouse C576BL/6N allele bears the lgM^b haplotype. These allelic forms of IgM can be distinguished by flow cytometry using antibodies specific to the polymorphisms found in the lgM^a or lgM^b alleles. As shown in FIG. 6 (bottom row), the B cells identified in mice heterozygous for each version of the humanized heavy chain locus only express a single allele, either lgM^a (the humanized allele) or lgM^b (the wild type allele). This demonstrates that the mechanisms involved in allelic exclusion are intact in VELOC!MMUNE® humanized mice. In addition, the relative number of B cells positive for the humanized allele (lgM^a) is roughly proportional to the number of V_H gene segments present. The humanized immunoglobulin locus is expressed in approximately 30% of the B cells in VELOCIMMUNE® 1 humanized heterozygote mice, which have 18 human V_H gene segments, and in 50% of the B cells in VELOCIMMUNE® 2 and 3 (not shown) humanized heterozygote mice, with 39 and 80 human V_H gene segments, respectively. Notably, the ratio of cells expressing the humanized versus wild type mouse allele (0.5 for

VELOCIMMUNE® 1 humanized mice and 0.9 for VELOCIMMUNE® 2 humanized mice) is greater than the ratio of the number of variable gene segments contained in the humanized versus wild type loci (0.2 for VELOCIMMUNE® 1 humanized mice and 0.4 for

VELOCIMMUNE® 2 humanized mice). This may indicate that the probability of allele choice is intermediate between a random choice of one or the other chromosome and a random choice of any particular V segment RSS. Further, there may be a fraction of B- cells, but not all, in which one allele becomes accessible for recombination, completes the process and shuts down recombination before the other allele becomes accessible. In addition, the even distribution of cells that have surface IgM (slgM) derived from either the hybrid humanized heavy chain locus or the wild type mouse heavy chain locus is evidence that the hybrid locus is operating at a normal level. In contrast, randomly integrated human immunoglobulin transgenes compete poorly with wild type mouse immunoglobulin loci (Bruggemann, M., et al. (1989) A repertoire of monoclonal antibodies with human heavy chains from transgenic mice. PNAS 86, 6709-6713; Green et al. (1994); Tuaillon, N. er a/. (1993) Human immunoglobulin heavy-chain minilocus recombination in transgenic mice: gene-segment use in mu and gamma transcripts, Proc Natl Acad Sci USA 90:3720-3724). This further demonstrates the immunoglobulins produced by VELOCIMMUNE® humanized mice are functionally different than those produced by randomly integrated transgenes in mice made by "knockout-plus-transgenic" approaches.

[00260] Polymorphisms of the CK regions are not available in 129S6 or C57BL/6N to examine allelic exclusion of humanized versus non-humanized κ light chain loci. However, VELOCIMMUNE® humanized mice all possess wild type mouse λ light chain loci, therefore, it is possible to observe whether rearrangement and expression of humanized κ light chain loci can prevent mouse λ light chain expression. The ratio of the number of cells expressing the humanized κ light chain relative to the number of cells expressing mouse λ light chain was relatively unchanged in VELOCIMMUNE® humanized mice compared with wild type mice, regardless of the number of human VK gene segments inserted at the κ light chain locus (FIG. 6, third row from top). In addition there was no increase in the number of double positive (κ plus λ) cells, indicating that productive recombination at the hybrid κ light chain loci results in appropriate suppression of recombination of the mouse λ light chain loci. In contrast, mice containing randomly integrated κ light chain transgenes with inactivated mouse κ light chain loci— but wild type mouse λ light chain loci— exhibit dramatically increased λ/κ ratios (Jakobovits, 1998), implying that the introduced κ light chain transgenes do not function well in such mice. This further demonstrates the different functional outcome observed in immunoglobulins made by VELOCIMMUNE® humanized mice as compared to those made by "knockout- plus-transgenic" mice. [00261] B cell Development.

[00262] Because the mature B cell populations in VELOCIMMUNE® humanized mice resemble those of wild type mice (described above), it is possible that defects in early B cell differentiation are compensated for by the expansion of mature B cell populations. The various stages of B cell differentiation were examined by analysis of B cell populations using flow cytometry. Table 6 sets forth the ratio of the fraction of cells in each B cell lineage defined by FACs, using specific cell surface markers, in VELOCIMMUNE® humanized mice compared to wild type littermates.

[00263] Early B cell development occurs in the bone marrow, and different stages of B cell differentiation are characterized by changes in the types and amounts of cell surface marker expression. These differences in surface expression correlate with the molecular changes occurring at the immunoglobulin loci inside the cell. The pro-B to pre-B cell transition requires the successful rearrangement and expression of functional heavy chain protein, while transition from the pre-B to mature B stage is governed by the correct rearrangement and expression of a κ or λ light chain. Thus, inefficient transition between stages of B cell differentiation can be detected by changes in the relative populations of B cells at a given stage.

Table 6

Bone Marrow Spleen

Version of pro-B pre-B Immature Mature Emerging Mature

B220^hi

B220hi lgM⁺

lgM+ igD*

1 .1 1 .0

1.0 1 .0

1.0 1 .1

[00264] No major defects were observed in B cell differentiation in any of the

VELOCIMMUNE® humanized mice. The introduction of human heavy chain gene segments does not appear to affect the pro-B to pre-B transition, and introduction of human κ light chain gene segments does not affect the pre-B to B transition in

VELOCIMMUNE® humanized mice. This demonstrates that "reverse chimeric" immunoglobulin molecules possessing human variable regions and mouse constants function normally in the context of B cell signaling and co-receptor molecules leading to appropriate B cell differentiation in a mouse environment. In contrast, the balance between the different populations during B cell differentiation are perturbed to varying extents in mice that contain randomly integrated immunoglobulin transgenes and inactivated endogenous heavy chain ΟΓ Κ light chain loci (Green and Jakobovits (1998)).

Example IV

Variable Gene Repertoire in Humanized Immunoglobulin Mice

[00265] Usage of human variable gene segments in the humanized antibody repertoire of VE LOCI MM UN E® humanized mice was analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) of human variable regions from multiple sources including splenocytes and hybridoma cells. Variable region sequence, gene segment usage, somatic hypermutation, and junctional diversity of rearranged variable region gene segments were determined.

[00266] Briefly, total RNA was extracted from 1 x 10⁷-2 x 10⁷ splenocytes or about 10⁴- 10⁵ hybridoma cells using TRIZOL™ (Invitrogen) or Qiagen RNEASY™ Mini Kit (Qiagen) and primed with mouse constant region specific primers using the SUPERSCRIPT™ III One-Step RT-PCR system (Invitrogen). Reactions were carried out with 2-5 μΙ_ of RNA from each sample using the aforementioned 3' constant specific primers paired with pooled leader primers for each family of human variable regions for both the heavy chain and κ light chain, separately. Volumes of reagents and primers, and RT-PCR/PCR conditions were performed according to the manufacturer's instructions. Primers sequences were based upon multiple sources (Wang, X. and Stollar, B.D. (2000) Human immunoglobulin variable region gene analysis by single cell RT-PCR, J Immunol Methods 244:217-225; Ig- primer sets, Novagen). Where appropriate, nested secondary PCR reactions were carried out with pooled family-specific framework primers and the same mouse 3' immunoglobulin constant-specific primer used in the primary reaction. Aliquots (5 μΙ_) from each reaction were analyzed by agarose electrophoresis and reaction products were purified from agarose using a MONTAGE™ Gel Extraction Kit (Millipore). Purified products were cloned using the TOPO™ TA Cloning System (Invitrogen) and transformed into DH10β E.coli cells by electroporation. Individual clones were selected from each transformation reaction and grown in 2 ml_ LB broth cultures with antibiotic selection overnight at 37°C. Plasmid DNA was purified from bacterial cultures by a kit-based approach (Qiagen). [00267] Immunoglobulin Variable Gene Usage.

[00268] Plasmid DNA of both heavy chain and κ light chain clones were sequenced with either 17 or 13 reverse primers on the ABI 3100 Genetic Analyzer (Applied Biosystems). Raw sequence data were imported into SEQUENCHER™ (v4.5, Gene Codes). Each sequence was assembled into contigs and aligned to human immunoglobulin sequences using IMGT V-Quest (Brochet, X. ef al. (2008) IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis. Nucleic Acids Res 36:W503-508) search function to identify human V_H, D_H, JH and VK, JK segment usage. Sequences were compared to germline sequences for somatic hypermutation and recombination junction analysis.

[00269] Mice were generated from ES cells containing the initial heavy chain

modification (3hV_H-CRE Hybrid Allele, bottom of FIG. 2A) by RAG complementation (Chen, J. et al. (1993) RAG-2-deficient blastocyst complementation: an assay of gene function in lymphocyte development, Proc Natl Acad Sci USA 90:4528-4532), and cDNA was prepared from splenocyte RNA. The cDNA was amplified using primer sets (described above) specific for the predicted chimeric heavy chain mRNA that would arise by V(D)J recombination within the inserted human gene segments and subsequent splicing to either mouse IgM or IgG constant domains. Sequences derived from these cDNA clones (not shown) demonstrated that proper V(D)J recombination had occurred within the human variable gene sequences, that the rearranged human V(D)J gene segments were properly spliced in-frame to mouse constant domains and that class-switch recombination had occurred. Further sequence analysis of mRNA products of subsequent hybrid

immunoglobulin loci was performed.

[00270] In a similar experiment, B cells from non-immunized wild type and

VELOCIMMUNE® humanized mice were separated by flow cytometry based upon surface expression of B220 and IgM or IgG. The B220⁺ lgM⁺ or surface lgG⁺ (slgG⁺) cells were pooled and V_H and VK sequences were obtained following RT-PCR amplification and cloning (described above). Representative gene usage in a set of RT-PCR amplified cDNAs from unimmunized VELOCIMMUNE® 1 humanized mice (Table 7) and

VELOCIMMUNE® 3 humanized mice (Table 8) was recorded ("defective RSS; fmissing or pseudogene). Table 7

DN Observed

Table 8

V Observed

3-9 31

1-8 7

3-7 1 1

2-5 1

1 -3 0

1 -2 6

6-1 9

[00271] As shown in Tables 7 and 8, nearly all of the functional human V_H, D_H, JH, VK and JK gene segments are utilized. Of the functional variable gene segments described but not detected in the VELOCIMMUNE® humanized mice of this experiment, several have been reported to possess defective recombination signal sequences (RSS) and, thus, would not be expected to be expressed (Feeney, A.J. (2000) Factors that influence formation of B cell repertoire. Immunol Res 21 :195-202). Analysis of several other sets of immunoglobulin sequences from various VELOCIMMUNE® humanized mice, isolated from both naive and immunized repertoires, has shown usage of these gene segments, albeit at lower frequencies (data not shown). Aggregate gene usage data has shown that all functional human V_H, D_H, JH, VK, and JK gene segments contained in VELOCIMMUNE® humanized mice have been observed in various naive and immunized repertoires (data not shown). Although the human V_H7-81 gene segment has been identified in the analysis of human heavy chain locus sequences (Matsuda, F. et al. (1998) The complete nucleotide sequence of the human immunoglobulin heavy chain variable region locus, J Exp Med 188:2151-2162), it is not present in the VELOCIMMUNE® humanized mice as confirmed by re-sequencing of the entire VELOCIMMUNE® 3 humanized mouse genome.

[00272] Sequences of heavy and light chains of antibodies are known to show exceptional variability, especially in short polypeptide segments within the rearranged variable domain. These regions, known as hypervariable regions or complementary determining regions (CDRs) create the binding site for antigen in the structure of the antibody molecule. The intervening polypeptide sequences are called framework regions (FRs). There are three CDRs (CDR1 , CDR2, CDR3) and 4 FRs (FR1 , FR2, FR3, FR4) in both heavy and light chains. One CDR, CDR3, is unique in that this CDR is created by recombination of both the V_H, D_H and JH and VK and JK gene segments and generates a significant amount of repertoire diversity before antigen is encountered. This joining is imprecise due to both nucleotide deletions via exonuclease activity and non-template encoded additions via terminal deoxynucleotidyl transferase (TdT) and, thus, allows for novel sequences to result from the recombination process. Although FRs can show substantial somatic mutation due to the high mutability of the variable region as a whole, variability is not, however, distributed evenly across the variable region. CDRs are concentrated and localized regions of high variability in the surface of the antibody molecule that allow for antigen binding. Heavy chain and light chain sequences of selected antibodies from VELOCIMMUNE® humanized mice around the CDR3 junction

demonstrating junctional diversity are shown in FIG. 7A and 7B, respectively.

[00273] As shown in FIG. 7A, non-template encoded nucleotide additions (N-additions) are observed at both the V_H-D_H and D_H-JH joint in antibodies from VELOCIMMUNE® humanized mice, indicating proper function of TdT with the human segments. The endpoints of the V_H, D_H and J_H segments relative to their germline counterparts indicate that exonuclease activity has also occurred. Unlike the heavy chain locus, the human κ light chain rearrangements exhibit little or no TdT additions at CDR3, which is formed by the recombination of the VK and JK segments (FIG. 7B). This is expected due to the lack of TdT expression in mice during light chain rearrangements at the pre-B to B cell transition. The diversity observed in the CDR3 of rearranged human VK regions is introduced predominantly through exonuclease activity during the recombination event.

[00274] Somatic hypermutation.

[00275] Additional diversity is added to the variable regions of rearranged

immunoglobulin genes during the germinal center reaction by a process termed somatic hypermutation. B cells expressing somatically mutated variable regions compete with other B cells for access to antigen presented by the follicular dendritic cells. Those B cells with higher affinity for the antigen will further expand and undergo class switching before exiting to the periphery. Thus, B cells expressing switched isotypes typically have encountered antigen and undergone germinal center reactions and will have increased numbers of mutations relative to naive B cells. Further, variable region sequences from predominantly naive slgM⁺ B cells would be expected to have relatively fewer mutations than variable sequences from slgG⁺ B cells which have undergone antigen selection.

[00276] Sequences from random V_H or VK clones from slgM⁺ or slgG⁺ B cells from non- immunized VELOCIMMUNE® humanized mice or slgG⁺ B cells from immunized mice were compared with their germline variable gene segments and changes relative to the germline sequence annotated. The resulting nucleotide sequences were translated in silico and mutations leading to amino acid changes also annotated. The data were collated from all the variable regions and the percent change at a given position was calculated (FIG. 8).

[00277] As shown in FIG. 8, human heavy chain variable regions derived from slgG⁺ B cells from non-immunized VELOCIMMUNE® humanized mice exhibit many more nucleotides relative to slgM⁺ B cells from the same splenocyte pools, and heavy chain variable regions derived from immunized mice exhibit even more changes. The number of changes is increased in the complementarity-determining regions (CDRs) relative to the framework regions, indicating antigen selection. The corresponding amino acid sequences from the human heavy chain variable regions also exhibit significantly higher numbers of mutations in IgG vs IgM and even more in immunized IgG. These mutations again appear to be more frequent in the CDRs compared with the framework sequences, suggesting that the antibodies were antigen-selected in vivo. A similar increase in the number the nucleotide and amino acid mutations are seen in the VK sequences derived from lgG⁺ B cells from immunized mice.

[00278] The gene usage and somatic hypermutation observed in VELOC IMMUNE® humanized mice demonstrate that essentially all gene segments present are capable of rearrangement to form fully functionally reverse chimeric antibodies in these mice. Further, VELOCIMMUNE® humanized mouse derived antibodies fully participate within the mouse immune system to undergo affinity selection and maturation to create fully mature human antibodies that can effectively neutralize their target antigen. VELOCIMMUNE®

humanized mice are able to mount robust immune responses to multiple classes of antigens that result in usage of a wide range of human antibodies that are both high affinity and suitable for therapeutic use (data not shown).

Example V

Analysis of Lymphoid Structure and Serum Isotypes

[00279] The gross structures of spleen, inguinal lymph nodes, Peyer's patches and thymus of tissue samples from wild type or VELOCIMMUNE® humanized mice stained with H&E were examined by light microscopy. The levels of immunoglobulin isotypes in serum collected from wild-type and VELOCIMMUNE® humanized mice were analyzed using LUMINEX™ technology.

[00280] Lymphoid Organ Structure.

[00281] The structure and function of the lymphoid tissues are in part dependent upon the proper development of hematopoietic cells. A defect in B cell development or function may be exhibited as an alteration in the structure of the lymphoid tissues. Upon analysis of stained tissue sections, no significant difference in appearance of secondary lymphoid organs between wild type and VELOCIMMUNE® humanized mice was identified (data not shown).

[00282] Serum Immunoglobulin Levels.

[00283] The level of expression of each isotype is similar in wild type and

VELOCIMMUNE® humanized mice (FIG. 9A, 9B and 9C). This demonstrates that humanization of the variable gene segments had no apparent adverse effect upon class switching or immunoglobulin expression and secretion and therefore apparently maintain all the endogenous mouse sequences necessary for these functions.

Example VI

Immunization and Antibody Production in Humanized Immunoglobulin Mice

[00284] Different versions of VELOCIMMUNE® humanized mice were immunized with antigen to examine the humoral response to foreign antigen challenge.

[00285] Immunization and Hybridoma Development.

[00286] VELOCIMMUNE® humanized and wild-type mice can be immunized with an antigen in the form of protein, DNA, a combination of DNA and protein, or cells expressing the antigen. Animals are typically boosted every three weeks for a total of two to three times. Following each antigen boost, serum samples from each animal are collected and analyzed for antigen-specific antibody responses by serum titer determination. Prior to fusion, mice received a final pre-fusion boost of 5 pg protein or DNA, as desired, via intraperitoneal and/or intravenous injections. Splenocytes are harvested and fused to Ag8.653 myeloma cells in an electrofusion chamber according to the manufacture's suggested protocol (Cyto Pulse Sciences Inc., Glen Burnie, MD). Ten days after culture, hybridomas are screened for antigen specificity using an ELISA assay (Harlow, E. and Lane, D. (1988) Antibodies: A Laboratory Manual. Cold Spring Harbor Press, New York). Alternatively, antigen specific B cells are isolated directly from immunized VELOCIMMUNE® humanized mice and screened using standard techniques, including those described here, to obtain human antibodies specific for an antigen of interest.

[00287] Serum Titer Determination.

[00288] To monitor animal anti-antigen serum response, serum samples are collected about 10 days after each boost and the titers are determined using antigen specific ELISA. Briefly, Nunc MAXISORP™ 96 well plates are coated with 2 pg/mL antigen overnight at 4° C and blocked with bovine serum albumin (Sigma, St. Louis, MO). Serum samples in a serial 3 fold dilutions are allowed to bind to the plates for one hour at room temperature. The plates are then washed with PBS containing 0.05% Tween-20 and the bound IgG are detected using HRP-conjugated goat anti-mouse Fc (Jackson Immuno Research

Laboratories, Inc., West Grove, PA) for total IgG titer, or biotin-labeled isotype specific or light chain specific polyclonal antibodies (SouthernBiotech Inc.) for isotype specific titers, respectively. For biotin-labeled antibodies, following plate wash, HRP-conjugated streptavidin (Pierce, Rockford, IL) is added. All plates are developed using colorimetric substrates such as BD OPTEIA™ (BD Biosciences Pharmingen, San Diego, CA). After the reaction is stopped with 1 M phosphoric acid, optical absorptions at 450 nm are recorded and the data are analyzed using PRISM™ software from Graph Pad. Dilutions required to obtain two-fold of background signal are defined as titer.

[00289] In one experiment, VELOCIMMUNE® humanized mice were immunized with human interleukin-6 receptor (hlL-6R). A representative set of serum titers for

VELOCIMMUNE® and wild type mice immunized with hlL-6R is shown in FIG. 10A and

10B.

[00290] VELOCIMMUNE® humanized and wild-type mice mounted strong responses towards the IL-6R with similar titer ranges (FIG. 10A). Several mice from the

VELOCIMMUNE® humanized and wild-type cohorts reached a maximal response after a single antigen boost. These results indicate that the immune response strength and kinetics to this antigen were similar in the VELOCIMMUNE® humanized and wild type mice. These antigen-specific antibody responses were further analyzed to examine the particular isotypes of the antigen-specific antibodies found in the sera. Both

VELOCIMMUNE® humanized and wild type groups predominantly elicited an lgG1 response (FIG. 10B), suggesting that class switching during the humoral response is similar in mice of each type.

[00291] Affinity Determination of Antibody Binding to Antigen in Solution.

[00292] An ELISA-based solution competition assay is typically designed to determine antibody-binding affinity to the antigen.

[00293] Briefly, antibodies in conditioned medium are premixed with serial dilutions of antigen protein ranging from 0 to 10 mg/mL. The solutions of the antibody and antigen mixture are then incubated for two to four hours at room temperature to reach binding equilibria. The amounts of free antibody in the mixtures are then measured using a quantitative sandwich ELISA. Ninety-six well MAXISORB™ plates (VWR, West Chester, PA) are coated with 1 pg/mL antigen protein in PBS solution overnight at 4°C followed by BSA nonspecific blocking. The antibody-antigen mixture solutions are then transferred to these plates followed by one-hour incubation. The plates are then washed with washing buffer and the plate-bound antibodies were detected with an HRP-conjugated goat anti- mouse IgG polyclonal antibody reagent (Jackson Immuno Research Lab) and developed using colorimetric substrates such as BD OPTEIA™ (BD Biosciences Pharmingen, San Diego, CA). After the reaction is stopped with 1 M phosphoric acid, optical absorptions at 450 nm are recorded and the data are analyzed using PRISM™ software from Graph Pad. The dependency of the signals on the concentrations of antigen in solution are analyzed with a 4 parameter fit analysis and reported as IC₅o, the antigen concentration required to achieve 50% reduction of the signal from the antibody samples without the presence of antigen in solution. [00294] In one experiment, VELOC IMMUNE® humanized mice were immunized with hlL-6R (as described above). FIG. 11 A and 1 1 B show a representative set of affinity measurements for anti-hlL6R antibodies from VELOCIMMUNE® humanized and wild-type mice.

[00295] After immunized mice receive a third antigen boost, serum titers are determined by ELISA. Splenocytes are isolated from selected wild type and VELOCIMMUNE® humanized mouse cohorts and fused with Ag8.653 myeloma cells to form hybridomas and grown under selection (as described above). Out of a total of 671 anti-IL-6R hybridomas produced, 236 were found to express antigen-specific antibodies. Media harvested from antigen positive wells was used to determine the antibody affinity of binding to antigen using a solution competition ELISA. Antibodies derived from VELOCIMMUNE®

humanized mice exhibit a wide range of affinity in binding to antigen in solution (FIG. 1 1 A). Furthermore, 49 out of 236 anti-IL-6R hybridomas were found to block IL-6 from binding to the receptor in an in vitro bioassay (data not shown). Further, these 49 anti-IL-6R blocking antibodies exhibited a range of high solution affinities similar to that of blocking antibodies derived from the parallel immunization of wild type mice (FIG. 11 B).

Example VII

Construction of a Mouse ADAM6 Targeting Vector

[00296] A targeting vector for insertion of mouse ADAM6a and ADAM6b genes into a humanized heavy chain locus was constructed using VELOCIGENE® genetic engineering technology (supra) to modify a Bacterial Artificial Chromosome (BAC) 929d24 obtained from Dr. Fred Alt (Havard University). 929d24 BAC DNA was engineered to contain genomic fragments containing the mouse ADAM6a and ADAM6b genes and a hygromycin cassette for targeted deletion of a human ADAM6 pseudogene (ΙιΑϋΑΜδΨ) located between human V_H1-2 and V_H6-1 gene segments of a humanized heavy chain locus (FIG. 12).

[00297] First, a genomic fragment containing the mouse ADAM6b gene, ~800 bp of upstream (5') sequence and ~4800 bp of downstream (3') sequence was subcloned from the 929d24 BAC clone. A second genomic fragment containing the mouse ADAM6a gene, ~300 bp of upstream (5') sequence and -3400 bp of downstream (3') sequence, was separately subcloned from the 929d24 BAC clone. The two genomic fragments containing the mouse ADAM6b and ADAM6a genes were ligated to a hygromycin cassette flanked by Frt recombination sites to create the targeting vector (Mouse ADAM6 Targeting Vector, Figure 20; SEQ ID NO:3). Different restriction enzyme sites were engineered onto the 5' end of the targeting vector following the mouse ADAM6b gene and onto the 3' end following the mouse ADAM6a gene (bottom of FIG. 12) for ligation into the humanized heavy chain locus.

[00298] A separate modification was made to a BAC clone containing a replacement of the mouse heavy chain locus with the human heavy chain locus, including the human ADAM6 pseudogene located between the human V_H1-2 and V_H6-1 gene segments of the humanized locus for the subsequent ligation of the mouse ADAM6 targeting vector (FIG. 13).

[00299] Briefly, a neomycin cassette flanked by loxP recombination sites was engineered to contain homology arms containing human genomic sequence at positions 3' of the human V_H1 -2 gene segment (5' with respect to ΙιΑΟΑΜδΨ) and 5' of human V_H6-1 gene segment (3' with respect to ΙιΑΟΑΜΘΨ; see middle of FIG. 13). The location of the insertion site of this targeting construct was about 1 .3 kb 5' and ~350 bp 3' of the human ADAM6 pseudogene. The targeting construct also included the same restriction sites as the mouse ADAM6 targeting vector to allow for subsequent BAC ligation between the modified BAC clone containing the deletion of the human ADAM6 pseudogene and the mouse ADAM6 targeting vector.

[00300] Following digestion of BAC DNA derived from both constructs, the genomic fragments were ligated together to construct an engineered BAC clone containing a humanized heavy chain locus containing an ectopically placed genomic sequence comprising mouse ADAM6a and ADAM6b nucleotide sequences. The final targeting construct for the deletion of a human ADAM6 gene within a humanized heavy chain locus and insertion of mouse ADAM6a and ADAM6b sequences in ES cells contained, from 5' to 3', a 5' genomic fragment containing ~13 kb of human genomic sequence 3' of the human V_H1-2 gene segment, ~800 bp of mouse genomic sequence downstream of the mouse ADAM6b gene, the mouse ADAM6b gene, ~4800 bp of genomic sequence upstream of the mouse ADAM6b gene, a 5' Frt site, a hygromycin cassette, a 3' Frt site, -300 bp of mouse genomic sequence downstream of the mouse ADAM6a gene, the mouse ADAM6a gene, ~3400 bp of mouse genomic sequence upstream of the mouse ADAM6a gene, and a 3' genomic fragment containing ~30 kb of human genomic sequence 5' of the human V_H6-1 gene segment (bottom of FIG. 13).

[00301] The engineered BAC clone (described above) was used to electroporate mouse ES cells that contained a humanized heavy chain locus to created modified ES cells comprising a mouse genomic sequence ectopically placed that comprises mouse ADAM6a and ADAM6b sequences within a humanized heavy chain locus. Positive ES cells containing the ectopic mouse genomic fragment within the humanized heavy chain locus were identified by a quantitative PCR assay using TAQMAN™ probes (Lie, Y.S. and Petropoulos, C.J. (1998) Advances in quantitative PCR technology: 5'nuclease assays. Curr Opin Biotechnol 9(1):43-48). The upstream and downstream regions outside of the modified portion of the humanized heavy chain locus were confirmed by PCR using primers and probes located within the modified region to confirm the presence of the ectopic mouse genomic sequence within the humanized heavy chain locus as well as the hygromycin cassette. The nucleotide sequence across the upstream insertion point included the following, which indicates human heavy chain genomic sequence upstream of the insertion point and an l-Ceu I restriction site (contained within the parentheses below) linked contiguously to mouse genomic sequence present at the insertion point:

(CCAGCTTCAT TAGTAATCGT TCATCTGTGG TAAAAAGGCA GGATTTGAAG

CGATGGAAGA TGGGAGTACG GGGCGTTGGA AGACAAAGTG CCACACAGCG CAGCCTTCGT CTAGACCCCC GGGCTAACTA TAACGGTCCT AAGGTAGCGA G) GGGATGACAG ATTCTCTGTT CAGTGCACTC AGGGTCTGCC TCCACGAGAA TCACCATGCC CTTTCTCAAG ACTGTGTTCT GTGCAGTGCC CTGTCAGTGG (SEQ ID NO:4). The nucleotide sequence across the downstream insertion point at the 3' end of the targeted region included the following, which indicates mouse genomic sequence and a Pl-Sce I restriction site (contained within the parentheses below) linked contiguously with human heavy chain genomic sequence downstream of the insertion point:

(AGGGGTCGAG GGGGAATTTT ACAAAGAACA AAGAAGCGGG CATCTGCTGA CATGAGGGCC GAAGTCAGGC TCCAGGCAGC GGGAGCTCCA CCGCGGTGGC GCCATTTCAT TACCTCTTTC TCCGCACCCG AC ATAG ATAAAG CTT) ATCCCCCACC AAGCAAATCC CCCTACCTGG GGCCGAGCTT CCCGTATGTG GGAAAATGAA TCCCTGAGGT CGATTGCTGC ATGCAATGAA ATTCAACTAG (SEQ ID NO:5).

[00302] Targeted ES cells described above were used as donor ES cells and introduced into an 8-cell stage mouse embryo by the VELOCIMOUSE® mouse engineering method (see, e.g., US Pat. Nos. 7,6598,442, 7,576,259, 7,294,754). Mice bearing a humanized heavy chain locus containing an ectopic mouse genomic sequence comprising mouse ADAM6a and ADAM6b sequences were identified by genotyping using a modification of allele assay (Valenzuela et al., 2003) that detected the presence of the mouse ADAM6a and ADAM6b genes within the humanized heavy chain locus.

[00303] Mice bearing a humanized heavy chain locus that contains mouse ADAM6a and ADAM6b genes are bred to a FLPe deletor mouse strain (see, e.g., Rodriguez, C.I. et al. (2000) High-efficiency deleter mice show that FLPe is an alternative to Cre-/oxP.

Nature Genetics 25:139-140) in order to remove any FRTed hygromycin cassette introduced by the targeting vector that is not removed, e.g., at the ES cell stage or in the embryo. Optionally, the hygromycin cassette is retained in the mice.

[00304] Pups are genotyped and a pup heterozygous for a humanized heavy chain locus containing an ectopic mouse genomic fragment that comprises mouse ADAM6a and ADAM6b sequences is selected for characterizing mouse ADAM6 gene expression and fertility.

Example VIII

Characterization of ADAM6 Rescue Mice

[00305] Flow Cytometry.

[00306] Three mice at age 25 weeks homozygous for human heavy and human κ light chain variable gene loci (Η/κ) and three mice at age 18-20 weeks homozygous for human heavy and human κ light chain having the ectopic mouse genomic fragment encoding the mouse ADAM6a and ADAM6b genes within both alleles of the human heavy chain locus (H/K-A6) were sacrificed for identification and analysis of lymphocyte cell populations by FACs on the BD LSR II System (BD Bioscience). Lymphocytes were gated for specific cell lineages and analyzed for progression through various stages of B cell development.

Tissues collected from the animals included blood, spleen and bone marrow. Blood was collected into BD microtainer tubes with EDTA (BD Biosciences). Bone marrow was collected from femurs by flushing with complete RPMI medium supplemented with fetal calf serum, sodium pyruvate, HEPES, 2-mercaptoethanol, non-essential amino acids, and gentamycin. Red blood cells from blood, spleen and bone marrow preparations were lysed with an ammonium chloride-based lysis buffer (e.g., ACK lysis buffer), followed by washing with complete RPMI medium.

[00307] For staining of cell populations, 1 x 10⁶ cells from the various tissue sources were incubated with anti-mouse CD16/CD32 (2.4G2, BD Biosciences) on ice for 10 minutes, followed by labeling with one or a combination of the following antibody cocktails for 30 min on ice.

[00308] Bone marrow: anti-mouse FITC-CD43 (1 B1 1 , BioLegend), PE-ckit (2B8, BioLegend), PeCy7-lgM (11/41 , eBioscience), PerCP-Cy5.5-lgD (1 1-26c.2a, BioLegend), APC-eFluor780-B220 (RA3-6B2, eBioscience), A700-CD19 (1 D3, BD Biosciences).

[00309] Peripheral blood and spleen: anti-mouse FITC-K (187.1 , BD Biosciences), ΡΕ-λ (RML-42, BioLegend), PeCy7-lgM (11/41 , eBioscience), PerCP-Cy5.5-lgD (11-26c.2a, BioLegend), APC-CD3 (145-2C1 1 , BD), A700-CD19 ( D3, BD), APC-eFluor780-B220 (RA3-6B2, eBioscience). Following incubation with the labeled antibodies, cells were washed and fixed in 2% formaldehyde. Data acquisition was performed on an LSRII flow cytometer and analyzed with FlowJo. Results from a representative Η/κ and Η/κ-Α6 mouse are shown in FIGs. 14-18.

[00310] The results demonstrate that B cells of Η/κ-Α6 mice progress through the stages of B cell development in a similar fashion to Η/κ mice in the bone marrow and peripheral compartments, and show normal patterns of maturation once they enter the periphery. Η/κ-Α6 mice demonstrated an increased CD43^,ntCD19⁺ cell population as compared to Η/κ mice (FIG. 16B). This may indicate an accelerated IgM expression from the humanized heavy chain locus containing an ectopic mouse genomic fragment comprising the mouse ADAM6a and ADAM6b sequences in Η/κ-Α6 mice. In the periphery, B and T cell populations of Η/κ-Α6 mice appear normal and similar to Η/κ mice.

[00311] Testis Morphology and Sperm Characterization.

[00312] To determine if infertility in mice having humanized immunoglobulin heavy chain variable loci is due to testis and/or sperm production defects, testis morphology and sperm content of the epididymis was examined.

[00313] Briefly, testes from two groups of five mice per group (Group 1 : mice

homozygous for human heavy and κ light chain variable gene loci, mADAM6^'A; Group 2: mice heterozygous for human heavy chain variable gene loci and homozygous for ic light chain variable gene loci, mADAM6^+/") were dissected with the epididymis intact and weighed. The specimens were then fixed, embedded in paraffin, sectioned and stained with hematoxylin and eosin (HE) stain. Testis sections (2 testes per mouse, for a total of 20) were examined for defects in morphology and evidence of sperm production, while epididymis sections were examined for presence of sperm.

[00314] In this experiment, no differences in testis weight or morphology was observed between mADAM6^~'^~ mice and mADAM6^{+ "} mice. Sperm was observed in all genotypes, both in the testes and the epididymis. These results establish that the absence of mouse ADAM6a and ADAM6b genes does not lead to detectable changes in testis morphology, and that sperm is produced in mice in the presence and absence of these two genes.

Defects in fertility of male ADA 6^"'^" mice are therefore not likely to be due to low sperm production.

[00315] Sperm Motility and Migration.

[00316] Mice that lack other ADAM gene family members are infertile due to defects in sperm motility or migration. Sperm migration is defined as the ability of sperm to pass from the uterus into the oviduct, and is normally necessary for fertilization in mice. To determine if the deletion of mouse ADAM6a and ADAM6b affects this process, sperm migration was evaluated in mADAMS^mice. Sperm motility was also examined.

[00317] Briefly, sperm was obtained from testes of (1 ) mice heterozygous for human heavy chain variable gene loci and homozygous for human κ light chain variable gene locui (ADAM6^{+ "}); (2) mice homozyogous for human heavy chain variable gene loci and homozygous for human κ light chain variable gene loci (ADAM6^"'^"); (3) mice homozygous for human heavy chain variable gene loci and homozygous for wild-type κ light chain (ADAM6 Ίηκ); and, (4) wild-type C57 BL/6 mice (WT). No significant abnormalities were observed in sperm count or overall sperm motility by inspection. For all mice, cumulus dispersal was observed, indicating that each sperm sample was able to penetrate the cumulus cells and bind the zona pellucida in vitro. These results establish that ADAM6^"'^" mice have sperm that are capable of penetrating the cumulus and binding the zona pellucida.

[00318] Fertilization of mouse ova in vitro (IVF) was done using sperm from mice as described above. A slightly lower number of cleaved embryos were present for ADAM6⁺ the day following IVF, as well as a reduced number of sperm bound to the eggs. These results establish that sperm from ADAM6^"'^" mice, once exposed to an ovum, are capable of penetrating the cumulus and binding the zona pellucida.

[00319] In another experiment, the ability of sperm from ADAM6^''^" mice to migrate from the uterus and through the oviduct was determined in a sperm migration assay.

[00320] Briefly, a first group of five superovulated female mice were set up with five ADAM6^"'^" males. A second group of five superovulated female mice were set up with five ADAM6^{+ "} males. The mating pairs were observed for copulation, and five to six hours post-copulation the uterus and attached oviduct from all females were removed and flushed for analysis. Flush solutions were checked for eggs to verify ovulation and obtain a sperm count. Sperm migration was evaluated in two different ways. First, both oviducts were removed from the uterus, flushed with saline, and any sperm identified were counted. The presence of eggs was also noted as evidence of ovulation. Second, oviducts were left attached to the uterus and both tissues were fixed, embedded in paraffin, sectioned and stained (as described above). Sections were examined for presence of sperm, in both the uterus and in both oviducts.

[00321] For the five females mated with the five ADAM6^"'^' males, very little sperm was found in the flush solution from the oviduct. Flush solutions from oviducts of the five females mated with the five ADAM6^+/" males exhibited a sperm level about 25- to 30-fold higher (avg, n = 10 oviducts) than present in flush solutions from the oviducts of the five females mated with the five ADAM6^"'^" males.

[00322] Histological sections of uterus and oviduct were prepared. The sections were examined for sperm presence in the uterus and the oviduct (the colliculus tubarius).

Inspection of histological sections of oviduct and uterus revealed that for female mice mated with ADAM6^"'^" mice, sperm was found in the uterus but not in the oviduct. Further, sections from females mated with ADAM6^"'^" mice revealed that sperm was not found at the uterotubal junction (UTJ). In sections from females mated with ADAM6^{+ "} mice, sperm was identified in the UTJ and in the oviduct. [00323] These results establish that mice lacking ADAM6a and ADAM6b genes make sperm that exhibit an in vivo migration defect. In all cases, sperm was observed within the uterus, indicating that copulation and sperm release apparently occur as normal, but little to no sperm was observed within the oviducts after copulation as measured either by sperm count or histological observation. These results establish that mice lacking

ADAM6a and ADAM6b genes produce sperm that exhibit an inability to migrate from the uterus to the oviduct. This defect apparently leads to infertility because sperm are unable to cross the uterine-tubule junction into the oviduct, where eggs are fertilized. Taken together, all of these results converge to the support the hypothesis that mouse ADAM6 genes help direct sperm with normal motility to migrate out of the uterus, through the uterotubal junction and the oviduct, and thus approach an egg to achieve the fertilization event. The mechanism by which ADAM6 achieves this may be directly by action of the ADAM6 proteins, or through coordinate expression with other proteins, e.g., other ADAM proteins, in the sperm cell, as described below.

[00324] ADAM Gene Family Expression.

[00325] A complex of ADAM proteins are known to be present as a complex on the surface of maturing sperm. Mice lacking other ADAM gene family members lose this complex as sperm mature, and exhibit a reduction of multiple ADAM proteins in mature sperm. To determine if a lack of ADAM6a and ADAM6b genes affects other ADAM proteins in a similar manner, Western blots of protein extracts from testis (immature sperm) and epididymis (maturing sperm) were analyzed to determine the expression levels of other ADAM gene family members.

[00326] In this experiment, protein extracts were analyzed from four ADAM6^"'^" and four ADAM6^+/" mice. The results showed that expression of ADAM2 and ADAM3 were not affected in testis extracts. However, both ADAM2 and ADAM3 were dramatically reduced in epididymis extracts. This demonstrates that the absence of ADAM6a and ADAM6b in sperm of ADAM6^"'^" mice may have a direct affect on the expression and perhaps function of other ADAM proteins as sperm matures (e.g., ADAM2 and ADAM3). This suggests that ADAM6a and ADAM6b are part of an ADAM protein complex on the surface of sperm, which might be critical for proper sperm migration.

Example IX

Human Heavy Chain Variable Gene Usage in ADAM6 Rescue Mice

[00327] Selected human heavy chain variable gene usage was determined for mice homozygous for human heavy and κ light chain variable gene loci either lacking mouse ADAM6a and ADAM6b genes (mADAMe^"'^") or containing an ectopic genomic fragment encoding for mouse ADAM6a and ADAM6b genes (ADAM6 ; see Example 1) by a quantitative PCR assay using TAQMAN™ probes (as described above).

[00328] Briefly, CD19⁺ B cells were purified from the spleens of mADAMe^"'^" and ADAM6^{+ +} mice using mouse CD19 Microbeads (Miltenyi Biotec) and total RNA was purified using the RNEASY™ Mini kit (Qiagen). Genomic RNA was removed using a RNase-free DNase on-column treatment (Qiagen). About 200 ng mRNA was reverse- transcribed into cDNA using the First Stand cDNA Synthesis kit (Invitrogen) and then amplified with the TAQMAN™ Universal PCR Master Mix (Applied Biosystems) using the ABI 7900 Sequence Detection System (Applied Biosystems). Relative expression of each gene was normalized to the mouse κ Constant (ITICK). Table 9 sets forth the

sense/antisense/TAQMAN™ MGB probe combinations used in this experiment.

Table 9

Human V_H Sequence (5'-3') SEQ ID NOs

[00329] In this experiment, expression of all four human V_H genes was observed in the samples analyzed. Further, the expression levels were comparable between ιηΑϋΑΜδ '^" and ADAM6^+/+ mice. These results demonstrate that human V_H genes that were both distal to the modification site (V_H3-23 and V_H1 -69) and proximal to the modification site (V_H1-2 and V_H6-1) were all able to recombine to form a functionally expressed human heavy chain. These results demonstrate that the ectopic genomic fragment comprising mouse ADAM6a and ADAM6b sequences inserted into a human heavy chain genomic sequence did not affect V(D)J recombination of human heavy chain gene segments within the locus, and these mice are able to recombine human heavy chain gene segments in normal fashion to produce functional heavy chain immunoglobulin proteins.

Example X

Identification of Human Heavy Chain Variable Regions That Associate with Selected Human Light Chain Variable Regions

[00330] An in vitro expression system was constructed to determine if a single rearranged human germline light chain could be co-expressed with human heavy chains from antigen-specific human antibodies.

[00331] Methods for generating human antibodies in genetically modified mice are known (see e.g., US 6,596,541 , Regeneron Pharmaceuticals, VELOCIMMUNE®

humanized mouse). The VELOCIMMUNE® humanized mouse technology involves generation of a genetically modified mouse having a genome comprising human heavy and light chain variable regions operably linked to endogenous mouse constant region loci such that the mouse produces an antibody comprising a human variable region and a mouse constant region in response to antigenic stimulation. The DNA encoding the variable regions of the heavy and light chains of the antibodies produced from a VELOCIMMUNE® humanized mouse are fully human. Initially, high affinity chimeric antibodies are isolated having a human variable region and a mouse constant region. As described below, the antibodies are characterized and selected for desirable characteristics, including affinity, selectivity, epitope, etc. The mouse constant regions are replaced with a desired human constant region to generate a fully human antibody containing a non-lgM isotype, for example, wild type or modified lgG1 , lgG2, lgG3 or lgG4. While the constant region selected may vary according to specific use, high affinity antigen-binding and target specificity characteristics reside in the variable region.

[00332] A VELOCIMMUNE® humanized mouse was immunized with a growth factor that promotes angiogenesis (Antigen C) and antigen-specific human antibodies were isolated and sequenced for V gene usage using standard techniques recognized in the art. Selected antibodies were cloned onto human heavy and light chain constant regions and 69 heavy chains were selected for pairing with one of three human light chains: (1 ) the cognate κ light chain linked to a human κ constant region, (2) a rearranged human germline VK1-39JK5 linked to a human κ constant region, or (3) a rearranged human germline VK3-20JK1 linked to a human κ constant region. Each heavy chain and light chain pair were co-transfected in CHO-K1 cells using standard techniques. Presence of antibody in the supernatant was detected by anti-human IgG in an ELISA assay. Antibody titer (ng/ml) was determined for each heavy chain/light chain pair and titers with the different rearranged germline light chains were compared to the titers obtained with the parental antibody molecule (i.e., heavy chain paired with cognate light chain) and percent of native titer was calculated (Table 10). V_H: Heavy chain variable gene. ND: no expression detected under current experimental conditions.

Table 10

Antibody Titer (ng/mL) Percent of Native Titer

V_H

Cognate LC VK1-39JK5 VK3-20JK1 VK1-39JK5 VK3-20JK1

3-33 1 34 16 5600.0 2683.3

3-9 58 112 57 192.9 97.6

3-33 67 20 105 30.1 157.0

3-33 34 21 24 62.7 70.4

3-20 10 49 91 478.4 888.2

3-33 66 32 25 48.6 38.2

3-23 17 59 56 342.7 329.8

- 58 108 19 184.4 32.9

- 68 54 20 79.4 29.9

3-33 42 35 32 83.3 75.4

- 29 19 13 67.1 43.9

3-9 24 34 29 137.3 118.4

3-30/33 17 33 7 195.2 43.1

3-7 25 70 74 284.6 301.6

3-33 87 127 ND 145.1 -

6-1 28 56 ND 201.8 -

3-33 56 39 20 69.9 36.1

3-33 10 53 1 520.6 6.9

3-33 20 67 10 337.2 52.3

3-33 11 36 18 316.8 158.4

3-23 12 42 32 356.8 272.9

3-33 66 95 15 143.6 22.5

3-15 55 68 ND 123.1 -

- 32 68 3 210.9 10.6

1-8 28 48 ND 170.9 -

3-33 124 192 21 154.3 17.0

3-33 0 113 ND 56550.0 -

3-33 10 157 1 1505.8 12.5

3-33 6 86 15 1385.5 243.5

3-23 70 115 22 163.5 31.0

3-7 71 117 21 164.6 29.6

3-33 82 100 47 122.7 57.1

3-7 124 161 41 130.0 33.5

[00333] In a similar experiment, VELOC IMMUNE® humanized mice were immunized with several different antigens and selected heavy chains of antigen specific human antibodies were tested for their ability to pair with different rearranged human germline light chains (as described above). The antigens used in this experiment included an enzyme involved in cholesterol homeostasis (Antigen A), a serum hormone involved in regulating glucose homeostasis (Antigen B), a growth factor that promotes angiogenesis (Antigen C) and a cell-surface receptor (Antigen D). Antigen specific antibodies were isolated from mice of each immunization group and the heavy chain and light chain variable regions were cloned and sequenced. From the sequence of the heavy and light chains, V gene usage was determined and selected heavy chains were paired with either their cognate light chain or a rearranged human germline VK1-39JK5 region. Each heavy/light chain pair was co-transfected in CHO-K1 cells and the presence of antibody in the supernatant was detected by anti-human IgG in an ELISA assay. Antibody titer (pg/rnl) was determined for each heavy chain/light chain pairing and titers with the different rearranged human germline light chains were compared to the titers obtained with the parental antibody molecule (i.e., heavy chain paired with cognate light chain) and percent of native titer was calculated (Table 11). V_H: Heavy chain variable gene. VK: K light chain variable gene. ND: no expression detected under current experimental conditions.

Table 11

Titer (Mg/ml)

Percent of

Antigen Antibody V_H +

V_H Alone V_H + VK Native Titer

VK1-39JK5

724 3-33 1 -17 0.3 2.3 3.4 151

706 3-33 1 -16 0.3 3.6 3.0 84

744 1 -18 1 -12 0.4 5.1 3.0 59

696 3-1 1 1 -16 0.4 3.0 2.9 97

685 3-13 3-20 0.3 0.5 3.4 734

732 3-15 1 -17 0.3 4.5 3.2 72

694 3-15 1 -5 0.4 5.2 2.9 55

743 3-23 1 -12 0.3 3.2 0.3 10

742 3-23 2-28 0.4 4.2 3.1 74

693 3-23 1 -12 0.5 4.2 4.0 94

136 3-23 2-28 0.4 5.0 2.7 55

155 3-30 1 -16 0.4 1 .0 2.2 221

163 3-30 1 -16 0.3 0.6 3.0 506

171 3-30 1 -16 0.3 1 .0 2.8 295

145 3-43 1 -5 0.4 4.4 2.9 65

49 3-48 3-1 1 0.3 1.7 2.6 155

D

51 3-48 1 -39 0.1 1 .9 0.1 4

159 3-7 6-21 0.4 3.9 3.6 92

169 3-7 6-21 0.3 1 .3 3.1 235

1 34 3-9 1 -5 0.4 5.0 2.9 58

141 4-31 1 -33 2.4 4.2 2.6 63

142 4-31 1 -33 0.4 4.2 2.8 67

[00334] The results obtained from these experiments demonstrate that somatically mutated, high affinity heavy chains from different gene families are able to pair with rearranged human germline V 1 -39JK5 and VK3-20JK1 regions and be secreted from the cell as a normal antibody molecule. As shown in Table 10, antibody titer was increased for about 61 % (42 of 69) heavy chains when paired with the rearranged human VK1 -39JK5 light chain and about 29% (20 of 69) heavy chains when paired with the rearranged human VK3-20JK1 light chain as compared to the cognate light chain of the parental antibody. For about 20% (14 of 69) of the heavy chains, both rearranged human germline light chains conferred an increase in expression as compared to the cognate light chain of the parental antibody. As shown in Table 1 1 , the rearranged human germline VK1 -39JK5 region conferred an increase in expression of several heavy chains specific for a range of different classes of antigens as compared to the cognate light chain for the parental antibodies. Antibody titer was increased by more than two-fold for about 35% (15/43) of the heavy chains as compared to the cognate light chain of the parental antibodies. For two heavy chains (31 5 and 316), the increase was greater than ten-fold as compared to the parental antibody. Within all the heavy chains that showed increase expression relative to the cognate light chain of the parental antibody, family three (V_H3) heavy chains are over represented in comparison to other heavy chain variable region gene families. This demonstrates a favorable relationship of human V_H3 heavy chains to pair with rearranged human germline VK1-39JK5 and VK3-20JK1 light chains.

Example XI

Generation of a Rearranged Human Germline Light Chain Locus

[00335] Various rearranged human germline light chain targeting vectors were made using VELOCIGENE® genetic engineering technology (see, e.g., US Pat. No. 6,586,251 and Valenzuela et al. (2003) High-throughput engineering of the mouse genome coupled with high-resolution expression analysis, Nature Biotech. 21 (6):652-659) to modify mouse genomic Bacterial Artificial Chromosome (BAC) clones 302g12 and 254m04 (Invitrogen). Using these two BAC clones, genomic constructs were engineered to contain a single rearranged human germline light chain region and inserted into an endogenous light chain locus that was previously modified to delete the endogenous κ variable and joining gene segments.

[00336] Construction of Rearranged Human Germline Light Chain Targeting Vectors.

[00337] Three different rearranged human germline light chain regions were made using standard molecular biology techniques recognized in the art. The human variable gene segments used for constructing these three regions included rearranged human VK1- 39JK5 sequence, a rearranged human VK3-20JK1 sequence and a rearranged human VpreBJI5 sequence.

[00338] A DNA segment containing exon 1 (encoding the leader peptide) and intron 1 of the mouse VK3-7 gene was made by de novo DNA synthesis (Integrated DNA

Technologies). Part of the 5' untranslated region up to a naturally occurring Blpl restriction enzyme site was included. Exons of human VK1-39 and VK3-20 genes were PCR amplified from human genomic BAC libraries. The forward primers had a 5' extension containing the splice acceptor site of intron 1 of the mouse VK3-7 gene. The reverse primer used for PCR of the human VK1-39 sequence included an extension encoding human JK5, whereas the reverse primer used for PCR of the human VK3-20 sequence included an extension encoding human JK1. The human VpreBJX5 sequence was made by de novo DNA synthesis (Integrated DNA Technologies). A portion of the human JK-CK intron including the splice donor site was PCR amplified from plasmid pBS-296-HA18- PlScel. The forward PCR primer included an extension encoding part of either a human JK5, JK1 , or ϋλ5 sequence. The reverse primer included a Pl-Scel site, which was previously engineered into the intron.

[00339] The mouse VK3-7 exonl/intron 1 , human variable light chain exons, and human JK-CK intron fragments were sewn together by overlap extension PCR, digested with Blpl and Pl-Scel, and ligated into plasmid pBS-296-HA18-PIScel, which contained the promoter from the human VK3-15 variable gene segment. A loxed hygromycin cassette within plasmid pBS-296-HA18-PIScel was replaced with a FRTed hygromycin cassette flanked by NotI and AscI sites. The Notl/PI-Scel fragment of this plasmid was ligated into modified mouse BAC 254m04, which contained part of the mouse JK-CK intron, the mouse CK exon, and about 75 kb of genomic sequence downstream of the mouse κ locus which provided a 3' homology arm for homologous recombination in mouse ES cells. The Notl/Ascl fragment of this BAC was then ligated into modified mouse BAC 302g12, which contained a FRTed neomycin cassette and about 23 kb of genomic sequence upstream of the endogenous κ locus for homologous recombination in mouse ES cells.

[00340] Rearranged Human Germline V 1 -39JK5 Targeting Vector (FIG. 19).

[00341] Restriction enzyme sites were introduced at the 5' and 3' ends of an engineered light chain insert for cloning into a targeting vector: an AscI site at the 5' end and a Pl-Scel site at the 3' end. Within the 5' AscI site and the 3' Pl-Scel site the targeting construct from 5' to 3' included a 5' homology arm containing sequence 5' to the endogenous mouse κ light chain locus obtained from mouse BAC clone 302g12, a FRTed neomycin resistance gene, a genomic sequence including the human VK3-15 promoter, a leader sequence of the mouse VK3-7 variable gene segment, a intron sequence of the mouse VK3-7 variable gene segment, an open reading frame of a rearranged human germline VK1 -39JK5 region, a genomic sequence containing a portion of the human JK-CK intron, and a 3' homology arm containing sequence 3' of the endogenous mouse JK5 gene segment obtained from mouse BAC clone 254m04 (Figure 19, middle). Genes and/or sequences upstream of the endogenous mouse κ light chain locus and downstream of the most 3' JK gene segment (e.g., the endogenous 3' enhancer) were unmodified by the targeting construct (see Figure 19). The sequence of the engineered human VK1-39JK5 locus is shown in SEQ ID NO:59.

[00342] Targeted insertion of the rearranged human germline VK1-39JK5 region into BAC DNA was confirmed by polymerase chain reaction (PCR) using primers located at sequences within the rearranged human germline light chain region. Briefly, the intron sequence 3' to the mouse VK3-7 leader sequence was confirmed with primers ULC-m1 F (AGGTGAGGGT ACAGATAAGT GTTATGAG; SEQ ID NO:60) and ULC-m1 R

(TGACAAATGC CCTAATTATA GTGATCA; SEQ ID NO:61). The open reading frame of the rearranged human germline VK1-39JK5 region was confirmed with primers 1633-h2F (GGGCAAGTCA GAGCATTAGC A; SEQ ID NO:62) and 1633-h2R (TGCAAACTGG ATGCAGCATA G; SEQ ID NO:63). The neomycin cassette was confirmed with primers neoF (ggtggagagg ctattcggc; SEQ ID NO:64) and neoR (gaacacggcg gcatcag; SEQ ID NO:65). Targeted BAC DNA was then used to electroporate mouse ES cells to created modified ES cells for generating chimeric mice that express a rearranged human germline VK1-39JK5 region.

[00343] Positive ES cell clones were confirmed by Taqman™ screening and karyotyping using probes specific for the engineered VK1 -39JK5 light chain region inserted into the endogenous locus. Briefly, probe neoP (TGGGCACAAC AGACAATCGG CTG; SEQ ID NO:66) which binds within the neomycin marker gene, probe ULC-m1 P (CCATTATGAT GCTCCATGCC TCTCTGTTC; SEQ ID NO:67) which binds within the intron sequence 3' to the mouse VK3-7 leader sequence, and probe 1633h2P (ATCAGCAGAA

ACCAGGGAAA GCCCCT; SEQ ID NO:68) which binds within the rearranged human germline VK1-39JK5 open reading frame. Positive ES cell clones were then used to implant female mice to give rise to a litter of pups expressing the germline VK1-39JK5 light chain region.

[00344] Alternatively, ES cells bearing the rearranged human germline VK1-39JK5 light chain region are transfected with a constuct that expresses FLP in order to remove the FRTed neomycin cassette introduced by the targeting construct. Optionally, the neomycin cassette is removed by breeding to mice that express FLP recombinase (e.g., US

6,774,279). Optionally, the neomycin cassette is retained in the mice.

[00345] Rearranged Human Germline VK3-20JK 1 Targeting Vector (FIG. 20).

[00346] In a similar fashion, an engineered light chain locus expressing a rearranged human germline VK3-20JK1 region was made using a targeting construct including, from 5' to 3', a 5' homology arm containing sequence 5' to the endogenous mouse κ light chain locus obtained from mouse BAC clone 302g12, a FRTed neomycin resistance gene, a genomic sequence including the human 3-15 promoter, a leader sequence of the mouse VK3-7 variable gene segment, an intron sequence of the mouse VK3-7 variable gene segment, an open reading frame of a rearranged human germline VK3-20JK1 region, a genomic sequence containing a portion of the human JK-CK intron, and a 3' homology arm containing sequence 3' of the endogenous mouse JK5 gene segment obtained from mouse BAC clone 254m04 (Figure 20, middle). The sequence of the engineered human VK3- 20JK1 locus is shown in SEQ ID NO:69. [00347] Targeted insertion of the rearranged human germline VK3-20JK1 region into BAC DNA was confirmed by polymerase chain reaction (PCR) using primers located at sequences within the rearranged human germline VK3-20JK1 light chain region. Briefly, the intron sequence 3' to the mouse VK3-7 leader sequence was confirmed with primers ULC-m1 F (SEQ ID NO:60) and ULC-m1 R (SEQ ID NO:61 ). The open reading frame of the rearranged human germline VK3-20JK1 region was confirmed with primers 1635-h2F (TCCAGGCACC CTGTCTTTG; SEQ ID NO:70) and 1635-h2R (AAGTAGCTGC

TGCTAACACT CTGACT; SEQ ID NO:71 ). The neomycin cassette was confirmed with primers neoF (SEQ ID NO:64) and neoR (SEQ ID NO:65). Targeted BAC DNA was then used to electroporate mouse ES cells to created modified ES cells for generating chimeric mice that express the rearranged human germline VK3-20JK1 light chain.

[00348] Positive ES cell clones were confirmed by Taqman™ screening and karyotyping using probes specific for the engineered VK3-20JK1 light chain region inserted into the endogenous κ light chain locus. Briefly, probe neoP (SEQ ID NO:66) which binds within the neomycin marker gene, probe ULC-m1 P (SEQ ID NO:67) which binds within the mouse VK3-7 leader sequence, and probe 1635h2P (AAAGAGCCAC CCTCTCCTGC AGGG; SEQ ID NO:72) which binds within the human VK3-20JK1 open reading frame. Positive ES cell clones were then used to implant female mice. A litter of pups expressing the human germline VK3-20JK1 light chain region.

[00349] Alternatively, ES cells bearing human germline V 3-20JK1 light chain region can be transfected with a constuct that expresses FLP in oder to remove the FRTed neomycin cassette introduced by the targeting consruct. Optionally, the neomycin cassette may be removed by breeding to mice that express FLP recombinase (e.g., US 6,774,279). Optionally, the neomycin cassette is retained in the mice.

[00350] Rearranged Human Germline VpreBJI5 Targeting Vector (FIG. 21 ).

[00351] In a similar fashion, an engineered light chain locus expressing a rearranged human germline VpreBJI5 region was made using a targeting construct including, from 5' to 3', a 5' homology arm containing sequence 5' to the endogenous mouse κ light chain locus obtained from mouse BAC clone 302g12, a FRTed neomycin resistance gene, an genomic sequence including the human VK3-15 promoter, a leader sequence of the mouse VK3-7 variable gene segment, an intron sequence of the mouse VK3-7 variable gene segment, an open reading frame of a rearranged human germline VpreB^5 region, a genomic sequence containing a portion of the human JK-CK intron, and a 3' homology arm containing sequence 3' of the endogenous mouse JK5 gene segment obtained from mouse BAC clone 254m04 (Figure 21 , middle). The sequence of the engineered human VpreBJI5 locus is shown in SEQ ID NO:73.

[00352] Targeted insertion of the rearranged human germline VpreBJ 5 region into BAC DNA was confirmed by polymerase chain reaction (PCR) using primers located at sequences within the rearranged human germline VpreBJ 5 region light chain region. Briefly, the intron sequence 3' to the mouse VK3-7 leader sequence was confirmed with primers ULC-m1 F (SEQ ID NO:60 and ULC-m1 R (SEQ ID NO:61 ). The open reading frame of the rearranged human germline VpreBJ 5 region was confirmed with primers 1616-M F (TGTCCTCGGC CCTTGGA; SEQ ID NO:74) and 1616-M R (CCGATGTCAT GGTCGTTCCT; SEQ ID NO:75). The neomycin cassette was confirmed with primers neoF (SEQ ID NO:64) and neoR (SEQ ID NO:65). Targeted BAC DNA was then used to electroporate mouse ES cells to created modified ES cells for generating chimeric mice that express the rearranged human germline VpreBJ 5 light chain.

[00353] Positive ES cell clones are confirmed by Taqman™ screening and karyotyping using probes specific for the engineered VpreBJ 5 light chain region inserted into the endogenous κ light chain locus. Briefly, probe neoP (SEQ ID NO:66) which binds within the neomycin marker gene, probe ULC-m1 P (SEQ ID NO:67) which binds within the mouse lgVK3-7 leader sequence, and probe 1616H1 P (ACAATCCGCC TCACCTGCAC CCT; SEQ ID NO:76) which binds within the human Χ ρΓβΒϋλδ open reading frame.

Positive ES cell clones are then used to implant female mice to give rise to a litter of pups expressing a germline light chain region.

[00354] Alternatively, ES cells bearing the rearranged human germline VpreBJI5 light chain region are transfected with a construct that expresses FLP in order to remove the FRTed neomycin cassette introduced by the targeting consruct. Optionally, the neomycin cassette is removed by breeding to mice that express FLP recombinase (e.g., US

6,774,279). Optionally, the neomycin cassette is retained in the mice.

Example XII

Generation of Mice expressing a single rearranged human light chain

[00355] Targeted ES cells described above were used as donor ES cells and introduced into an 8-cell stage mouse embryo by the VELOCIMOUSE® method (see, e.g., US Pat. No. 7,294,754 and Poueymirou et al. (2007) F0 generation mice that are essentially fully derived from the donor gene-targeted ES cells allowing immediate phenotypic analyses, Nature Biotech. 25(1 ):91-99. VELOCIMICE® independently bearing an engineered human germline VK1-39JK5 light chain region, a VK3-20JK1 light chain region or a Ν ρΓβΒϋλ5 light chain region are identified by genotyping using a modification of allele assay (Valenzuela et al., supra) that detects the presence of the unique rearranged human germline light chain region.

[00356] Pups are genotyped and a pup heterozygous or homozygous for the unique rearranged human germline light chain region are selected for characterizing expression of the rearranged human germline light chain region.

[00357] Flow Cytometry.

[00358] Expression of the rearranged human light chain region in the normal antibody repertoire of common light chain mice was validated by analysis of immunoglobulin κ and λ expression in splenocytes and peripheral blood of common light chain mice. Cell suspensions from harvested spleens and peripheral blood of wild type (n=5), VK1-39JK5 common light chain heterozygote (n=3), VK1-39JK5 common light chain homozygote (n=3), VK3-20JK1 common light chain heterozygote (n=2), and VK3-20JK1 common light chain homozygote (n=2) mice were made using standard methods and stained with CD19⁺, lgl⁺ and lgk⁺ using fluorescently labeled antibodies (BD Pharmigen).

[00359] Briefly, 1 x10⁶ cells were incubated with anti-mouse CD16/CD32 (clone 2.4G2, BD Pharmigen) on ice for 10 minutes, followed by labeling with the following antibody cocktail for 30 minutes on ice: APC conjugated anti-mouse CD19 (clone 1 D3, BD

Pharmigen), PerCP-Cy5.5 conjugated anti-mouse CD3 (clone 17A2, BioLegend), FITC conjugated anti-mouse IgK (clone 187.1 , BD Pharmigen), PE conjugated anti-mouse \g (clone RML-42, BioLegend). Following staining, cells were washed and fixed in 2% formaldehyde. Data acquisition was performed on an LSRII flow cytometer and analyzed with FlowJo™. Gating: total B cells (CD19⁺CD3^"), lgk⁺ B cells (lgk⁺lgrCD19⁺CD3^"), lgl⁺ B cells (lgi ^"lg CD19⁺CD3^"). Data gathered from blood and splenocyte samples

demonstrated similar results. Table 12 sets forth the percent positive CD19⁺ B cells from peripheral blood of one representative mouse from each group that are lgl⁺, lgk⁺, or lgl⁺lgk⁺. Percent of CD19⁺ B cells in peripheral blood from wild type (WT) and mice homozygous for either the VK1-39JK5 or VK3-20JK1 common light chain are shown in FIG. 22.

Table 12

CD19⁺ B cells

Mouse Genotype — - lgl⁺ lgk⁺ lgl⁺lgk⁺

[00360] Common Light Chain Expression.

[00361] Expression of each common light chain (VK1-39JK5 and 3-20 JK1 ) was analyzed in heterozygous and homozygous mice using a quantitative PCR assay (e.g. Taqman™).

[00362] Briefly, CD19⁺ B cells were purified from the spleens of wild type, mice homozygous for a replacement of the mouse heavy chain and κ light chain variable region loci with corresponding human heavy chain and κ light chain variable region loci (Η ), as well as mice homozygous and heterozygous for each rearranged human light chain region (VK1-39JK5 or VK3-20JK1 ) using mouse CD19 Microbeads (Miltenyi Biotec) according to manufacturer's specifications. Total RNA was purified from CD19⁺ B cells using RNeasy™ Mini kit (Qiagen) according to the manufacturer's specifications and genomic RNA was removed using a RNase-free DNase on-column treatment (Qiagen). 200 ng mRNA was reverse-transcribed into cDNA using the First Stand cDNA Synthesis kit (Invitrogen) and the resulting cDNA was amplified with the Taqman™ Universal PCR Master Mix (Applied Biosystems). All reactions were performed using the ABI 7900 Sequence Detection System (Applied Biosystems) using primers and Taqman™ MGB probes spanning (1 ) the VK-JK junction for both common light chains, (2) the VK gene alone (i.e. 1-39 and VK3- 20), and (3) the mouse CK region. Table 13 sets forth the sequences of the primers and probes employed for this assay. Relative expression was normalized to expression of the mouse CK region. Results are shown in FIG. 23A, 23B and 23C.

Table 13

Region Primer/Probe Description (5'-3') SEQ ID NOs:

[00363] Antigen Specific Common Light Chain Antibodies.

[00364] Common light chain mice bearing either a VK1 -39JK5 or VK3-20JK1 common light chain at the endogenous mouse κ light chain locus were immunized with β- galactosidase and antibody titer was measured.

[00365] Briefly, β-galactosidase (Sigma) was emulsified in TITERMAX™ adjuvant (Sigma), as per the manufacturer's instructions. Wild type (n=7), V 1 -39JK5 common light chain homozgyotes (n=2) and VK3-20JK1 common light chain homozygotes (n=5) were immunized by subcutaneous injection with 100 g β-galactosidase/TITERMAX™. Mice were boosted by subcutaneous injection two times, 3 weeks apart, with 50 pg β- galactosidase/TITERMAX™. After the second boost, blood was collected from

anaesthetized mice using a retro-orbital bleed into serum separator tubes (BD

Biosciences) as per the manufacturer's instructions. To measure antr-^-galactosidase IgM or IgG antibodies, ELISA plates (Nunc) were coated with 1 μg mL β-galactosidase overnight at 4°C. Excess antigen was washed off before blocking with PBS with 1 % BSA for one hour at room temperature. Serial dilutions of serum were added to the plates and incubated for one hour at room temperature before washing. Plates were then incubated with HRP conjugated anti-lgM (Southern Biotech) or anti-lgG (Southern Biotech) for one hour at room temperature. Following another wash, plates were developed with TMB substrate (BD Biosciences). Reactions were stopped with 1 N sulfuric acid and OD₄₅₀ was read using a Victor X5 Plate Reader (Perkin Elmer). Data was analyzed with

GRAPHPAD™ Prism and signal was calculated as the dilution of serum that is two times above background. Results are shown in FIG. 24A and 24B.

[00366] As shown in this Example, the ratio of κ/λ B cells in both the splenic and peripheral compartments of VK1 -39JK5 and VK3-20JK1 common light chain mice demonstrated a near wild type pattern (Table 12 and FIG. 22). νρΓβΒϋλδ common light chain mice, however, demonstrated fewer peripheral B cells, of which about 1 -2% express the engineered human light chain region (data not shown). The expression levels of the VK1 -39JK5 and VK3-20JK1 rearranged human light chain regions from the endogenous κ light chain locus were elevated in comparison to an endogenous κ light chain locus containing a complete replacement of mouse VK and JK gene segments with human VK and JK gene segments (FIG. 23A, 23B and 23C). The expression levels of the VpreBJ 5 rearranged human light chain region demonstrated similar high expression from the endogenous κ light chain locus in both heterozygous and homozygous mice (data not shown). This demonstrates that in direct competition with the mouse λ, κ, or both endogenous light chain loci, a single rearranged human V_L/J|_ sequence can yield better than wild type level expression from the endogenous k light chain locus and give rise to normal splenic and blood B cell frequency. Further, the presence of an engineered κ light chain locus having either a human VK1 -39JK5 or human VK3-20JK1 sequence was well tolerated by the mice and appear to function in wild type fashion by representing a substantial portion of the light chain repertoire in the humoral component of the immune response (FIG 24A and 24B).

Example Xill

Breeding of Mice Expressing a Single Rearranged Human Germline Light Chain

[00367] This Example describes several other genetically modified mouse strains that can be bred to any one of the common light chain mice described herein to create multiple genetically modified mouse strains harboring multiple genetically modified immunoglobulin loci.

[00368] Endogenous Ig Knockout (KO).

[00369] To optimize the usage of the engineered light chain locus, mice bearing one of the rearranged human germline light chain regions are bred to another mouse containing a deletion in the endogenous λ light chain locus. In this manner, the progeny obtained will express, as their only light chain, the rearranged human germline light chain region as described in Example 1 1 . Breeding is performed by standard techniques recognized in the art and, alternatively, by a commercial breeder (e.g., The Jackson Laboratory). Mouse strains bearing an engineered light chain locus and a deletion of the endogenous λ light chain locus are screened for presence of the unique light chain region and absence of endogenous mouse λ light chains.

[00370] Humanized Endogenous Heavy Chain Locus.

[00371] Mice bearing an engineered human germline light chain locus are bred with mice that contain a replacement of the endogenous mouse heavy chain variable gene locus with the human heavy chain variable gene locus (see US 6,596,541 ; the

VELOCIMMUNE® humanized mouse, Regeneron Pharmaceuticals, Inc.). The

VELOCIMMUNE® humanized mouse comprises a genome comprising human heavy chain variable regions operably linked to endogenous mouse constant region loci such that the mouse produces antibodies comprising a human heavy chain variable region and a mouse heavy chain constant region in response to antigenic stimulation. The DNA encoding the variable regions of the heavy chains of the antibodies is isolated and operably linked to DNA encoding the human heavy chain constant regions. The DNA is then expressed in a cell capable of expressing the fully human heavy chain of the antibody. [00372] Mice bearing a replacement of the endogenous mouse V_H locus with the human V_H locus and a single rearranged human germline V_L region at the endogenous κ light chain locus are obtained. Reverse chimeric antibodies containing somatically mutated heavy chains (human V_H and mouse C_H) with a single human light chain (human V_L and mouse C_L) are obtained upon immunization with an antigen of interest. V_H and V_L nucleotide sequences of B cells expressing the antibodies are identified and fully human antibodies are made by fusion the V_H and V_L nucleotide sequences to human C_H and C_L nucleotide sequences in a suitable expression system.

Example XIV

Generation of Antibodies from Mice Expressing Human Heavy Chains and a Rearranged Human Germline Light Chain Region

[00373] After breeding mice that contain the engineered human light chain region to various desired strains containing modifications and deletions of other endogenous Ig loci (as described in Example 12), selected mice can be immunized with an antigen of interest.

[00374] Generally, a VELOCIMMUNE® humanized mouse containing one of the single rearranged human germline light chain regions is challenged with an antigen, and lymphatic cells (such as B-cells) are recovered from serum of the animals. The lymphatic cells are fused with a myeloma cell line to prepare immortal hybridoma cell lines, and such hybridoma cell lines are screened and selected to identify hybridoma cell lines that produce antibodies containing human heavy chain variables and a rearranged human germline light chains which are specific to the antigen used for immunization. DNA encoding the variable regions of the heavy chains and the light chain are isolated and linked to desirable isotypic constant regions of the heavy chain and light chain. Due to the presence of the

endogenous mouse sequences and any additional c/s-acting elements present in the endogenous locus, the single light chain of each antibody may be somatically mutated. This adds additional diversity to the antigen-specific repertoire comprising a single light chain and diverse heavy chain sequences. The resulting cloned antibody sequences are subsequently expressed in a cell, such as a CHO cell. Alternatively, DNA encoding the antigen-specific chimeric antibodies or the variable domains of the light and heavy chains are identified directly from antigen-specific lymphocytes.

[00375] Initially, high affinity chimeric antibodies are isolated having a human variable region and a mouse constant region. As described above, the antibodies are

characterized and selected for desirable characteristics, including affinity, selectivity, epitope, etc. The mouse constant regions are replaced with a desired human constant region to generate the fully human antibody containing a somatically mutated human heavy chain and a single light chain derived from a rearranged human germline light chain region of the invention. Suitable human constant regions include, for example wild type or modified lgG1 or lgG4.

[00376] Separate cohorts of VELOCIMMUNE® humanized mice containing a replacement of the endogenous mouse heavy chain locus with human V_H, D_H, and J_H gene segments and a replacement of the endogenous mouse κ light chain locus with either the engineered germline VK1-39JK5 human light chain region or the engineered germline VK3- 20JK1 human light chain region (described above) were immunized with a human cell surface receptor protein (Antigen E). Antigen E is administered directly onto the hind footpad of mice with six consecutive injections every 3-4 days. Two to three micrograms of Antigen E are mixed with 10

of CpG oligonucleotide (Cat # tlrl-modn - ODN1826 oligonucleotide; InVivogen, San Diego, CA) and 25 g of Adju-Phos (Aluminum phosphate gel adjuvant, Cat# H-71639-250; Brenntag Biosector, Frederikssund, Denmark) prior to injection. A total of six injections are given prior to the final antigen recall, which is given 3- 5 days prior to sacrifice. Bleeds after the 4th and 6th injection are collected and the antibody immune response is monitored by a standard antigen-specific immunoassay.

[00377] When a desired immune response is achieved splenocytes are harvested and fused with mouse myeloma cells to preserve their viability and form hybridoma cell lines. The hybridoma cell lines are screened and selected to identify cell lines that produce Antigen E-specific common light chain antibodies. Using this technique several anti- Antigen E-specific common light chain antibodies (i.e. , antibodies possessing human heavy chain variable domains, the same human light chain variable domain, and mouse constant domains) are obtained.

[00378] Alternatively, anti-Antigen E common light chain antibodies are isolated directly from antigen-positive B cells without fusion to myeloma cells, as described in U.S.

2007/0280945A1 , herein specifically incorporated by reference in its entirety. Using this method, several fully human anti-Antigen E common light chain antibodies (i.e., antibodies possessing human heavy chain variable domains, either an engineered human VK1-39JK5 light chain or an engineered human VK3-20JK1 light chain region, and human constant domains) were obtained.

[00379] The biological properties of the exemplary anti-Antigen E common light chain antibodies generated in accordance with the methods of this Example are described in detail below.

Example XV

Heavy Chain Gene Segment Usage in

Antigen-Specific Common Light Chain Antibodies

[00380] To analyze the structure of the human anti-Antigen E common light chain antibodies produced, nucleic acids encoding heavy chain antibody variable regions were cloned and sequenced. From the nucleic acid sequences and predicted amino acid sequences of the antibodies, gene usage was identified for the heavy chain variable region (HCVR) of selected common light chain antibodies obtained from immunized

VELOCIMMUNE® humanized mice containing either the engineered human VK1-39JK5 light chain or engineered human VK3-20JK1 light chain region. Results are shown in Tables 14 and 15, which demonstrate that mice according to the invention generate antigen-specific common light chain antibodies from a variety of human heavy chain gene segments, due to a variety of rearrangements, when employing either a mouse that expresses a light chain from only a human VK1 -39- or a human VK3-20-derived light chain. Human V_H gene segments of the 2, 3, 4, and 5 families rearranged with a variety of human D_H segments and human J_H segments to yield antigen-specific antibodies.

Table 14

VK1 ■39JK5

Common Light Chain Antibodies

HCVR HCVR

Antibody

V_H D_H JH

2949 3-30 6-6 5 6033 3-30 7-27 4

2950 3-30 6-6 5 3004 3-30 7-27 5

2954 3-30 6-6 5 6028 3-30 7-27 6

2978 3-30 6-6 5 3010 4-59 3-16 3

3016 3-30 6-6 5 3019 4-59 3-16 3

3017 3-30 6-6 5 6018 4-59 3-16 3

3033 3-30 6-6 5 6026 4-59 3-16 3

3041 3-30 6-6 5 6029 4-59 3-16 3

5979 3-30 6-6 5 6036 4-59 3-16 3

5998 3-30 6-6 5 6037 4-59 3-16 3

6004 3-30 6-6 5 2964 4-59 3-22 3

6010 3-30 6-6 5 3027 4-59 3-16 4

6019 3-30 6-6 5 3046 5-51 5-5 3

6021 3-30 6-6 5 6000 1 -69 6-13 4

6022 3-30 6-6 5 6006 1-69 6-6 5

6023 3-30 6-6 5 6008 1-69 6-13 4

Table 15

VK3-20JK1

Common Light Chain Antibodies

HCVR HCVR

Antibody

V_H JH

Example XVI

Determination of Blocking Ability of

Antigen-Specific Common Light Chain Antibodies by LUMINEX™ Assay

[00381] Ninety-eight human common light chain antibodies raised against Antigen E were tested for their ability to block binding of Antigen E's natural ligand (Ligand Y) to Antigen E in a bead-based assay. [00382] The extracellular domain (ECD) of Antigen E was conjugated to two myc epitope tags and a 6X histidine tag (Antigen E-mmH) and amine-coupled to carboxylated microspheres at a concentration of 20 pg/mL in MES buffer. The mixture was incubated for two hours at room temperature followed by bead deactivation with 1 M Tris pH 8.0 followed by washing in PBS with 0.05% (v/v) Tween-20. The beads were then blocked with PBS (Irvine Scientific, Santa Ana, CA) containing 2% (w/v) BSA (Sigma-Aldrich Corp., St. Louis, MO). In a 96-well filter plate, supernatants containing Antigen E-specific common light chain antibodies, were diluted 1 :15 in buffer. A negative control containing a mock supernatant with the same media components as for the antibody supernatant was prepared. Antigen E-labeled beads were added to the supernatants and incubated overnight at 4°C. Biotinylated-Ligand Y protein was added to a final concentration of 0.06 nM and incubated for two hours at room temperature. Detection of biotinylated-Ligand Y bound to Antigen E-myc-myc-6His labeled beads was determined with R-Phycoerythrin conjugated to Streptavidin (Moss Inc, Pasadena, MD) followed by measurement in a LUMINEX™ flow cytometry-based analyzer. Background Mean Fluorescence Intensity (MFI) of a sample without Ligand Y was subtracted from all samples. Percent blocking was calculated by division of the background-subtracted MFI of each sample by the adjusted negative control value, multiplying by 100 and subtracting the resulting value from 100.

[00383] In a similar experiment, the same 98 human common light chain antibodies raised against Antigen E were tested for their ability to block binding of Antigen E to Ligand Y-labeled beads.

[00384] Briefly, Ligand Y was amine-coupled to carboxylated microspheres at a concentration of 20 pg/rnL diluted in MES buffer. The mixture and incubated two hours at room temperature followed by deactivation of beads with 1 M Tris pH 8 then washing in PBS with 0.05% (v/v) Tween-20. The beads were then blocked with PBS (Irvine Scientific, Santa Ana, CA) containing 2% (w/v) BSA (Sigma-Aldrich Corp., St. Louis, MO). In a 96- well filter plate, supernatants containing Antigen E-specific common light chain antibodies were diluted 1 :15 in buffer. A negative control containing a mock supernatant with the same media components as for the antibody supernatant was prepared. A biotinylated- Antigen E-mmH was added to a final concentration of 0.42 nM and incubated overnight at 4°C. Ligand Y-labeled beads were then added to the antibody/Antigen E mixture and incubated for two hours at room temperature. Detection of biotinylated-Antigen E-mmH bound to Ligand Y-beads was determined with R-Phycoerythrin conjugated to Streptavidin (Moss Inc, Pasadena, MD) followed by measurement in a LUMINEX™ flow cytometry- based analyzer. Background Mean Fluorescence Intensity (MFI) of a sample without Antigen E was subtracted from all samples. Percent blocking was calculated by division of the background-subtracted MFI of each sample by the adjusted negative control value, multiplying by 100 and subtracting the resulting value from 100.

[00385] Tables 16 and 17 show the percent blocking for all 98 anti-Antigen E common light chain antibodies tested in both LUMINEX™ assays. ND: not determined under current experimental conditions.

Table 16

VK1 -39JK5

Common Light Chain Antibodies

% Blocking of % Blocking of

Antigen E-Labeled Beads Antigen E In Solution

3005 97.4 93.5

3005G 77.5 75.6

3010 98.0 82.6

3010G 97.9 81.0

301 1 87.4 42.8

3011 G 83.5 41 .7

3012 91 .0 60.8

3012G 52.4 16.8

3013 80.3 65.8

3013G 17.5 15.4

3014 63.4 20.7

3014G 74.4 28.5

3015 89.1 55.7

3015G 58.8 17.3

3016 97.1 81.6

3016G 93.1 66.4

3017 94.8 70.2

3017G 87.9 40.8

3018 85.4 54.0

3018G 26.1 12.7

3019 99.3 92.4

3019G 99.3 88.1

3020 96.7 90.3

3020G 85.2 41.5

3021 74.5 26.1

3021 G 81.1 27.4

3022 65.2 17.6

3022G 67.2 9.1

3023 71.4 28.5

3023G 73.8 29.7

3024 73.9 32.6

3024G 89.0 10.0

3025 70.7 15.6

3025G 76.7 24.3

3027 96.2 61 .6

3027G 98.6 75.3

3028 92.4 29.0

3028G 87.3 28.8

3030 6.0 10.6

3030G 41 .3 14.2 3032 76.5 31 .4

3032G 17.7 1 1.0

3033 98.2 86.1

3033G 93.6 64.0

3036 74.7 32.7

3036G 90.1 51.2

3041 95.3 75.9

3041 G 92.4 51.6

3042 88.1 73.3

3042G 60.9 25.2

3043 90.8 65.8

3043G 92.8 60.3

Table 17

VK3-20J 1

Common Light Chain Antibodies

% Blocking of % Blocking of

Antigen E-Labeled Beads Antigen E In Solution

[00386] In the first LUMINEX™ experiment described above, 80 common light chain antibodies containing the VK1 -39JK5 engineered light chain were tested for their ability to block Ligand Y binding to Antigen E-labeled beads. Of these 80 common light chain antibodies, 68 demonstrated >50% blocking, while 12 demonstrated <50% blocking (6 at 25-50% blocking and 6 at <25% blocking). For the 18 common light chain antibodies containing the VK3-20JK1 engineered light chain, 12 demonstrated >50% blocking, while 6 demonstrated <50% blocking (3 at 25-50% blocking and 3 at <25% blocking) of Ligand Y binding to Antigen E-labeled beads.

[00387] In the second LUMINEX™ experiment described above, the same 80 common light chain antibodies containing the VK1 -39JK5 engineered light chain were tested for their ability to block binding of Antigen E to Ligand Y-labeled beads. Of these 80 common light chain antibodies, 36 demonstrated >50% blocking, while 44 demonstrated <50% blocking (27 at 25-50% blocking and 17 at <25% blocking). For the 1 8 common light chain antibodies containing the V 3-20JK1 engineered light chain, 1 demonstrated >50% blocking, while 17 demonstrated <50% blocking (5 at 25-50% blocking and 12 at <25% blocking) of Antigen E binding to Ligand Y-labeled beads.

[00388] The data of Tables 16 and 17 establish that the rearrangements described in Tables 14 and 15 generated anti-Antigen E-specific common light chain antibodies that blocked binding of Ligand Y to its cognate receptor Antigen E with varying degrees of efficacy, which is consistent with the anti-Antigen E common light chain antibodies of Tables 14 and 15 comprising antibodies with overlapping and non-overlapping epitope specificity with respect to Antigen E.

Example XVII

Determination of Blocking Ability of

Antigen-Specific Common Light Chain Antibodies by ELISA

[00389] Human common light chain antibodies raised against Antigen E were tested for their ability to block Antigen E binding to a Ligand Y-coated surface in an ELISA assay.

[00390] Ligand Y was coated onto 96-well plates at a concentration of 2 pg/mL diluted in PBS and incubated overnight followed by washing four times in PBS with 0.05% Tween- 20. The plate was then blocked with PBS (Irvine Scientific, Santa Ana, CA) containing 0.5% (w/v) BSA (Sigma-Aldrich Corp., St. Louis, MO) for one hour at room temperature. In a separate plate, supernatants containing anti-Antigen E common light chain antibodies were diluted 1 :10 in buffer. A mock supernatant with the same components of the antibodies was used as a negative control. Antigen E-mmH (described above) was added to a final concentration of 0.150 nM and incubated for one hour at room temperature. The antibody/Antigen E-mmH mixture was then added to the plate containing Ligand Y and incubated for one hour at room temperature. Detection of Antigen E-mmH bound to Ligand Y was determined with Horse-Radish Peroxidase (HRP) conjugated to anti-Penta-His antibody (Qiagen, Valencia, CA) and developed by standard colorimetric response using tetramethylbenzidine (TMB) substrate (BD Biosciences, San Jose, CA) neutralized by sulfuric acid. Absorbance was read at OD450 for 0.1 sec. Background absorbance of a sample without Antigen E was subtracted from all samples. Percent blocking was calculated by division of the background-subtracted MFI of each sample by the adjusted negative control value, multiplying by 100 and subtracting the resulting value from 100.

[00391] Tables 18 and 19 show the percent blocking for all 98 anti-Antigen E common light chain antibodies tested in the ELISA assay. ND: not determined under current experimental conditions.

Table 18 VK1 -39JK5

Common Light Chain Antibodies

% Blocking of % Blocking of

Antibody Antibody

Antigen E In Solution Antigen E In Solution

3012G 12.6 3041 G 30.7

3013 39.0 3042 39.9

301 3G 9.6 3042G 16.1

3014 5.2 3043 57.4

3014G 1 7.1 3043G 46.1

Table 19

VK3-20JK1

Common Light Chain Antibodies

% Blocking of % Blocking of

Antibody Antibody

Antigen E in Solution Antigen E In Solution

[00392] As described in this Example, of the 80 common light chain antibodies containing the VK1 -39JK5 engineered light chain tested for their ability to block Antigen E binding to a Ligand Y-coated surface, 22 demonstrated >50% blocking, while 58 demonstrated <50% blocking (20 at 25-50% blocking and 38 at <25% blocking). For the 18 common light chain antibodies containing the VK3-20JK1 engineered light chain, one demonstrated >50% blocking, while 17 demonstrated <50% blocking (5 at 25-50% blocking and 12 at <25% blocking) of Antigen E binding to a Ligand Y-coated surface.

[00393] These results are also consistent with the Antigen E-specific common light chain antibody pool comprising antibodies with overlapping and non-overlapping epitope specificity with respect to Antigen E.

Example XVIII

BIACORE™ Affinity Determination for

Antigen-Specific Common Light Chain Antibodies

[00394] Equilibrium dissociation constants (K_D) for selected antibody supernatants were determined by SPR (Surface Plasmon Resonance) using a BIAcore™ T1 00 instrument (GE Healthcare). All data was obtained using HBS-EP (10mM HEPES, 150mM NaCI, 0.3mM EDTA, 0.05% Surfactant P20, pH 7.4) as both the running and sample buffers, at 25°C. Antibodies were captured from crude supernatant samples on a CM5 sensor chip surface previously derivatized with a high density of anti-human Fc antibodies using standard amine coupling chemistry. During the capture step, supernatants were injected across the anti-human Fc surface at a flow rate of 3 pL/min, for a total of 3 minutes. The capture step was followed by an injection of either running buffer or analyte at a concentration of 100 nM for 2 minutes at a flow rate of 35 pL/min. Dissociation of antigen from the captured antibody was monitored for 6 minutes. The captured antibody was removed by a brief injection of 10 mM glycine, pH 1.5. All sensorgrams were double referenced by subtracting sensorgrams from buffer injections from the analyte sensorgrams, thereby removing artifacts caused by dissociation of the antibody from the capture surface. Binding data for each antibody was fit to a 1 :1 binding model with mass transport using BIACORE™ T100 Evaluation software v2.1. Results are shown in Tables 20 and 21 .

Table 20

VK1 •39JK5

Common Light Chain Antibodies

100 nM Antigen E 100 nM Antigen E

Antibody Antibody

K_D (nM) T-i2 (min) K_D (nM) Ti2 (min)

301 1 G 41 .7 5 3036G 18.2 10

3012 9.71 20 3041 6.90 12

3012G 89.9 2 3041 G 22.9 2

3013 20.2 20 3042 9.46 34

3013G 13.2 4 3042G 85.5 3

3014 213 4 3043 9.26 29

3014G 36.8 3 3043G 13.1 22

Table 21

VK3-20JK1

Common Light Chain Antibodies

1 00 nM Antigen E 1 00 nM Antigen E

Antibody

K_D (nM) Ti/2 (min)

[00395] The binding affinities of common light chain antibodies comprising the rearrangements shown in Tables 14 and 15 vary, with nearly all exhibiting a K_D in the nanomolar range. The affinity data is consistent with the common light chain antibodies resulting from the combinatorial association of rearranged variable domains described in Tables 14 and 15 being high-affinity, clonally selected, and somatically mutated. Coupled with data previously shown, the common light chain antibodies described in Tables 14 and 15 comprise a collection of diverse, high-affinity antibodies that exhibit specificity for one or more epitopes on Antigen E.

Example XIX

Determination of Binding Specificities of

Antigen-Specific Common Light Chain Antibodies by LUMINEX™ Assay

[00396] Selected anti-Antigen E common light chain antibodies were tested for their ability to bind to the ECD of Antigen E and Antigen E ECD variants, including the cynomolgous monkey ortholog (Mf Antigen E), which differs from the human protein in approximately 10% of its amino acid residues; a deletion mutant of Antigen E lacking the last 10 amino acids from the C-terminal end of the ECD (Antigen E-ACT); and two mutants containing an alanine substitution at suspected locations of interaction with Ligand Y (Antigen E-Ala1 and AntigenE-Ala2). The Antigen E proteins were produced in CHO cells and each contained a myc-myc-His C-terminal tag.

[00397] For the binding studies, Antigen E ECD protein or variant protein (described above) from 1 mL of culture medium was captured by incubation for 2 hr at room temperature with 1 x 10⁶ microsphere (Luminex™) beads covalently coated with an anti- myc monoclonal antibody (MAb 9E10, hybridoma cell line CRL-1729™; ATCC, Manassas, VA). The beads were then washed with PBS before use. Supernatants containing anti- Antigen E common light chain antibodies were diluted 1 :4 in buffer and added to 96-well filter plates. A mock supernatant with no antibody was used as negative control. The beads containing the captured Antigen E proteins were then added to the antibody samples (3000 beads per well) and incubated overnight at 4°C. The following day, the sample beads were washed and the bound common light chain antibody was detected with a R-phycoerythrin-conjugated anti-human IgG antibody. The fluorescence intensity of the beads (approximately 100 beads counted for each antibody sample binding to each Antigen E protein) was measured with a Luminex™ flow cytometry-based analyzer, and the median fluorescence intensity (MFI) for at least 100 counted beads per bead/antibody interaction was recorded. Results are shown in Tables 22 and 23.

Table 22

VK1-39JK5 Common Light Chain Antibodies

Mean Fluorescence Intensity (MFI)

Antibody Anti en E- Antigen E- Anti en E- Anti en

3012 3233 2221 8543 5637 3307

3012G 968 378 3115 2261 1198

3013 2343 1791 6715 4810 2528

3013G 327 144 1333 1225 370

3014 1225 1089 5436 3621 1718

3014G 1585 851 5178 3705 241 1

3015 3202 2068 8262 5554 3796

3015G 1243 531 4246 2643 161 1

3016 4220 2543 8920 5999 5666

3016G 2519 1277 6344 4288 4091

3017 3545 2553 8700 5547 5098

3017G 1972 1081 5763 3825 3038

3018 2339 1971 6140 4515 2293

3018G 254 118 978 1020 345

3019 5235 1882 7108 4249 54

3019G 4090 1270 4769 3474 214

3020 3883 3107 8591 6602 4420

3020G 2165 1209 6489 4295 2912

3021 1961 1472 6872 4641 2742

3021 G 2091 1005 6430 3988 2935

3022 2418 793 7523 2679 36

3022G 2189 831 6182 3051 132

3023 1692 1411 5788 3898 2054

3023G 1770 825 5702 3677 2648

3024 1819 1467 6179 4557 2450

3024G 100 87 268 433 131

3025 1853 1233 6413 4337 2581

3025G 1782 791 5773 3871 2717

3027 4131 1018 582 2510 22

3027G 3492 814 1933 2596 42

3028 4361 2545 9884 5639 975

3028G 2835 1398 7124 3885 597

3030 463 277 1266 1 130 391

3030G 943 302 3420 2570 1186

3032 2083 1496 6594 4402 2405

3032G 295 106 814 902 292

3033 4409 2774 8971 6331 5825

3033G 2499 1234 6745 4174 4210

3036 1755 1362 6137 4041 1987

3036G 2313 1073 6387 4243 3173 3041 3674 2655 8629 5837 4082

3041 G 2519 1265 6468 4274 3320

3042 2653 2137 7277 5124 3325

3042G 1 1 17 463 4205 2762 1519

3043 3036 2128 7607 5532 3366

3043G 2293 1319 6573 4403 3228

Table 23

VK3-20JK1 Common Light Chain Antibodies

Mean Fluorescence Intensity (MFI)

Antibody Anti en E- Antigen E- Anti en E- Anti en E-

[00400] The anti-Antigen E common light chain antibody supernatants exhibited high specific binding to the beads linked to Antigen E-ECD. For these beads, the negative control mock supernatant resulted in negligible signal (<10 MFI) when combined with the Antigen E-ECD bead sample, whereas the supernatants containing anti-Antigen E common light chain antibodies exhibited strong binding signal (average MFI of 2627 for 98 antibody supernatants; MFI > 500 for 91/98 antibody samples).

[00401] As a measure of the ability of the selected anti-Antigen E common light chain antibodies to identify different epitopes on the ECD of Antigen E, the relative binding of the antibodies to the variants were determined. All four Antigen E variants were captured to the anti-myc LUMINEX™ beads as described above for the native Antigen E-ECD binding studies, and the relative binding ratios (MFI_Variant FI_Antigen E-ECD) were determined. For 98 tested common light chain antibody supernatants shown in Tables 21 and 22, the average ratios ( FI_Variant FI_Antigen E-ECD) differed for each variant, likely reflecting different capture amounts of proteins on the beads (average ratios of 0.61 , 2.9, 2.0, and 1.0 for Antigen E- ACT, Antigen E-Ala1 , Antigen E-Ala2, and Mf Antigen E, respectively). For each protein variant, the binding for a subset of the 98 tested common light chain antibodies showed greatly reduced binding, indicating sensitivity to the mutation that characterized a given variant. For example, 19 of the common light chain antibody samples bound to the Mf Antigen E with MFI_Variant/MFI_Antigen E-ECD of <8%. Since many in this group include high or moderately high affinity antibodies (5 with K_D < 5nM, 15 with K_D < 50 nM), it is likely that the lower signal for this group results from sensitivity to the sequence (epitope) differences between native Antigen E-ECD and a given variant rather than from lower affinities.

[00402] These data establish that the common light chain antibodies described in Tables 14 and 15 represent a diverse group of Antigen-E-specific common light chain antibodies that specifically recognize more than one epitope on Antigen E.

Claims

We claim:

1. A mouse comprising in its germline:

(a) a humanized immunoglobulin heavy chain variable locus comprising at least one unrearranged human V, at least one unrearranged human D, and at least one unrearranged human J segment operably linked to a heavy chain constant region gene;

(b) a humanized immunoglobulin light chain variable locus comprising no more than one, or no more than two, rearranged human light chain V/J sequences operably linked to a light chain constant region gene; and,

(c) an ectopic nucleic acid sequence encoding a mouse ADA 6 protein or ortholog or homolog or functional fragment thereof.

2. The mouse according to claim 1 , wherein the nucleic acid sequence encoding the mouse ADAM6 protein or ortholog or homolog or functional fragment thereof is at a locus other than the immunoglobulin heavy chain variable locus.

3. The mouse according to claim 1 , wherein the heavy chain constant region gene is a mouse gene.

4. The mouse according to claim 1 , wherein the light chain constant region gene is a mouse gene.

5. A mouse comprising a humanized heavy chain immunoglobulin variable locus and a humanized light chain immunoglobulin variable locus, wherein the mouse expresses a single light chain, and wherein the mouse comprises an ectopic nucleic acid sequence encoding an ADAM6 gene functional in a male mouse.

6. The mouse of claim 5, wherein the humanized heavy chain immunoglobulin locus is operably linked to an endogenous mouse heavy chain constant region gene.

7. The mouse of claim 5, wherein the single light chain is encoded from an immunoglobulin light chain variable gene locus that encodes no more than one light chain V gene segment and a light chain J gene segment, operably linked to a light chain constant gene.

8. The mouse of claim 5, wherein the single light chain is derived from an immunoglobulin light chain variable gene locus in the germline of the mouse that encodes no more than one rearranged light chain V/J gene segment in the germline, operably linked to a light chain constant gene.

9. The mouse of claim 5, wherein the ectopic nucleic acid sequence encodes a mouse ADAM6 protein, or encodes a fragment of a mouse ADAM6 protein that is functional in a male mouse.

10. The mouse of claim 5, wherein the ectopic nucleic acid sequence is at a position that is not within an endogenous immunoglobulin heavy chain locus.

11. A genetically modified mouse that expresses a plurality of different IgG heavy chains each comprising a human variable domain, wherein each of the plurality of different IgG heavy chains are associated with a light chain sequence encoding a human immunoglobulin light chain variable domain that is derived from a single human immunoglobulin V gene segment, wherein the mouse comprises an ectopic nucleic acid sequence encoding an ADAM6 protein that is functional in a male mouse.

12. The mouse of claim 11 , wherein the mouse expresses an ADAM6 protein or fragment thereof that is functional in a male mouse, and wherein the ADAM6 protein or fragment thereof is expressed from the ectopic nucleic acid sequence.

13. A mouse cell comprising:

a humanized heavy chain immunoglobulin variable gene locus operably linked to a heavy chain constant gene;

a humanized light chain immunoglobulin locus that comprises no more than one, or no more than two, light chain V gene segments operably linked to a light chain constant gene; and,

an ectopic nucleic acid sequence encoding an ADAM6 protein or fragment thereof, wherein the ADAM6 protein or fragment thereof is functional in a male mouse.

14. The mouse cell of claim 13, wherein the ectopic nucleic acid sequence encodes a mouse ADAM6 protein.

15. The mouse of claim 13, wherein the heavy chain constant gene is a non-human heavy chain constant gene.

16. The mouse of claim 13, wherein the light chain constant gene is a non-human light chain constant gene.

17. The mouse of claim 13, wherein the no more than one, or no more that two, light chain V gene segments are present in a rearranged V/J gene segment.

18. A mouse B cell that expresses a chimeric immunoglobulin heavy chain comprising an immunoglobulin heavy chain variable domain derived from a human heavy chain V gene segment; and a light chain derived from

(a) a rearranged human VK1 -39/J sequence,

(b) a rearranged human V 3-20/J sequence, or

(c) a combination thereof;

wherein the heavy chain variable domain is fused to a constant region and the light chain variable domain is fused to constant region, and wherein the B cell comprises an ectopic ADAM6 nucleic acid sequence.

19. The mouse B cell of claim 18, wherein the constant domain fused to the heavy chain variable domain comprises a mouse constant region.

20. The mouse B cell of claim 18, wherein the constant region fused to the light chain variable domain is selected from a mouse constant region and a human constant region.