Patent Application
20210395397
The present invention relates to polypeptides comprising unpaired antibody variable domains, e.g., unpaired VH domains, for binding antigen. The invention also relates to animals, e.g., mice, that express antibodies comprising one or more heavy chains or heavy chain variable domains, wherein the antibodies are devoid of light chain variable domains that pair with the heavy chain variable domains to form paired antigen binding sites.
The antigen-binding region of a native human immunoglobulin is composed of two variable domains—the heavy chain variable (VH) domain and the light chain variable (VL) domain—which pair together to form an Fv region. The Fv region has an antigen-binding site provided by six loops of variable amino acid sequence—the complementarity determining regions (CDRs). The VH domain comprises HCDR1, HCDR2 and HCDR3 interspersed with framework regions (FRs) and the VL domain comprises LCDR1, LCDR2 and LCDR3 interspersed with FRs. One or more CDRs of the VH domain and/or of the VL domain bind to the antigen. Binding may be mediated by CDRs of both the VH and the VL domain, or by CDRs of one domain alone. HCDR3 of the VH domain often has a major role in antigen-binding, although other CDRs of both domains can and often do contribute. Even where an antigen binds solely or mainly to CDRs of the VH domain, the presence of the VL domain in the Fv may stabilise the VH in a functional binding conformation.
Antibody variable domains are generated in vivo through combinatorial rearrangement of gene segments at the immunoglobulin (Ig) loci within cells of B lymphocyte lineage, which provides a repertoire of encoded amino acid sequences capable of binding to the diverse immunogenic stimuli encountered by the immune system. The Ig heavy chain locus in humans has approximately 41 functional V gene segments, 27 functional D gene segments and 6 functional J gene segments, depending on haplotype. Nucleic acid encoding a VH domain is generated through V-D-J gene segment recombination. The V gene segment encodes the N terminal region of the polypeptide chain comprising FR1, HCDR1, FR2, HCDR2, FR3 and the start of HCDR3, while the D gene segment is encompassed within HCDR3 and the J gene segment provides the end of HCDR3 and the C terminal framework region FR4. The highly variable nature of HCDR3 sequences in an antibody repertoire reflects the combinatorial diversity generated by rearrangement of the many different V, D and J segments. Humans have two Ig light chain loci, kappa (κ) and lambda (λ). The human Ig light chain loci have approximately 40 functional Vκ segments, 5 functional Jκ segments, 29 functional VA segments and 4 functional JA segments, depending on haplotype. Nucleic acid encoding a VL domain is produced by the recombination of two gene segments, V and J, at either the kappa (κ) or lambda (λ) locus. The v gene segment encodes the FR1, LCDR1, FR2, LCDR2, FR3 and the first part of LCDR3, while the J gene segment forms the second part of LCDR3 and the FR4. In addition to the combinatorial diversity arising from V-D-J and V-J recombination and from VH/VL pairing, further antibody sequence diversity is generated by junctional mutations at the point of gene segment joining and by the in vivo process of somatic hypermutation in response to antigen binding.
WO90/05144 (MRC) disclosed that VH domains, when isolated from complete antibodies comprising heavy and light chains, were able to bind to antigen in a 1:1 ratio and with binding constants of equivalent magnitude to those of complete antibody molecules.
Camelids (the animal family including camels and llamas) naturally produce antibodies which bind antigen with unpaired VH domains in the absence of a VL. These antibodies completely lack the immunoglobulin light chain, and are bivalent binders composed of homodimeric heavy chains each comprising an antigen-binding single VH or “VHH” domain, a hinge region and a dimerising constant region comprising CH2 and CH3 domains. While homologous to the heavy chains of classical mammalian antibodies, these “heavy chain antibodies” (“HCAbs”) lack the first domain of the constant region (CH1), which is spliced out during mRNA processing (WO94/04678 Casterman & Hamers; WO96/34103 Hamers & Muyldermans).
An analogous mutation occurs in a pathological setting in humans, known as heavy chain disease. Immunoglobulin heavy chains are expressed comprising the VH, CH2 and CH3 domains, but lacking a CH1 domain. In patients with this disease the heavy chains are found to accumulate instead of pairing with light chains to form normal antibodies.
Cartilaginous fish such as sharks also have antibodies composed of heavy chains and lacking any light chain. These antibodies are termed IgNAR (immunoglobulin new antigen receptor) and have been used as a source of single domain antibodies called VNAR fragments.
Researchers have worked to develop single variable domain antibodies into pharmaceutical products. These molecules, known as domain antibodies (dAbs), are bioactive as monomers and, owing to their small size and inherent stability, are also well suited for incorporation into larger molecules to create drugs with prolonged serum half lives and/or other pharmacological activities. Antigen-binding molecules comprising single variable domains of antibodies include immunoconjugates (e.g., dAb-toxin) and chimaeric antigen receptors (CARs). To this end, antibody single variable domain binders have been cloned and expressed in recombinant systems, and in vitro libraries of such binders have been generated for selection and screening using systems such as phage display.
Laboratory animals such as mice have been genetically engineered to express heavy chain antibodies as a further source of single antigen-binding variable domains. One can begin by knocking out (deleting or inactivating) the endogenous Ig light chain loci of the animal (WO92/03918 Genpharm; WO03/000737 The Babraham Institute). The heavy chain alone is then expressed, and homodimerises (
Mouse strains used for producing heavy chain antibodies have therefore been engineered to have a genetic deletion of the CH1 domain of the immunoglobulin heavy chain and knockout of the light chains. Such mice produce antibodies comprising dimeric heavy chains and lacking light chains, each heavy chain having a variable (VH) domain and constant regions CH2 and CH3. The constant regions dimerise to form an Fc region, while the two VH domains are available for divalent antigen binding (
Erasmus Universiteit Rotterdam have described transgenic mice whose genomes comprise exons from camelid VHH domains or “camelised” VH domains and heavy chain constant region genes which did not express a functional CH1 domain (WO02/085944, WO02/085945, WO2006/008548, WO2010/109165). “Camelised” VH are human (or other non-camelid) VH sequences which have been mutated to resemble camelid VHH. In these transgenic platforms, the heavy chain genes are engineered to exclude functional CH1 domains. As reported in WO02/085944, the absence of the CH1 rendered the heavy chain antibodies unable to associate with light chains to form “conventional” antibodies, since the CH1 was the natural partner for the constant domain of the light chain. WO2006/008548 reported that normal B-cell maturation and antibody production in the mice was dependent on the complete absence of CH1 sequences from each heavy chain constant region present in the transgenic locus. WO2004/049794 (The Babraham Institute) describes production of HCAbs from a YAC transgene in mice, in which the CH1 domain of the heavy chain is spliced out during mRNA processing. The resulting mice could then be crossed with mice in which endogenous heavy and light chain genes had been knocked out, to generate mice which only expressed the desired HCAbs.
Unfortunately, “heavy chain only” mice carrying CH1 deletions in their Ig heavy chains do not have normal B cell populations. Mice in which DNA encoding the CH1 domain was deleted from both the μ and the γ heavy chain constant region genes produced IgM heavy chains lacking CH1 (CH1Δμ) and IgG heavy chains lacking CH1 (CH1Δγ), but the proportion of immature B cells in these mice was increased, with impaired differentiation into follicular zone B cells and marginal zone B cells. Nevertheless, the deletion of CH1 was essential for the expression of both IgM and IgG antibodies in the mice, since the inclusion of the CH1 domain in either the μ or γ heavy chain resulted in non-productive expression[1].
Human VH domains are desirable for administration to humans since they are associated with lower immunogenic side effects in patients compared with administration of polypeptides of non-human origin such as camelid VHH. Transgenic mice expressing human antibody heavy chains are a source of human VH domains that undergo in vivo selection for antigen-binding. However, human antibodies naturally contain both heavy and light chains, and only a subset of heavy chain variable regions are able to generate functional heavy chain antibodies in the absence of the light chain. Human VH domains from heavy chain antibodies produced in heavy chain only mice therefore lack the sequence diversity of VH domains from full immunoglobulins. The limitation of the human VH domain repertoire in such mice is compounded where the human Ig heavy chain genes are introduced at a random insertion point in the mouse genome, since the ectopic transgenic locus produces VH domains with HCDR3 sequences which are shorter than in humans (believed to result from limited N-addition occurring during VDJ recombination) and which undergo limited hypermutation, resulting in an already low diversity of VH domains. This appears to be an intrinsic limitation of known random insertion transgenic platforms for human antibody generation. The latter issue can be addressed by integrating the human immunoglobulin genes at the endogenous immunoglobulin locus of the host animal, rather than at a random position in the genome[2]. Recombination and somatic hypermutation at the native loci in such mice generate a broader diversity of sequences from which to evolve less soluble VH domains into ones with improved biophysical properties (such as solubility) in vivo.
WO2011/072204 (Regeneron Pharmaceuticals) described mice expressing heavy chain antibodies comprising human VH domains and mouse constant regions with deleted CH1 domains. These mice were said to comprise a germline deletion of the sequence encoding CH1 in an endogenous Ig constant region gene, rendering them incapable of expressing an IgG mRNA that comprised a sequence encoding a CH1 domain, but the mice retained the ability to express normal functional IgM antibody as the CH1 domain of the IgM isotype constant domain was not deleted. WO2013/171505 (Kymab Limited) described a mouse engineered to express normal IgM antibodies and CH1-deleted IgG antibodies, where stage-specific class switching from IgM to IgG in lymphocytes was accompanied by inactivation of the endogenous Ig light chain loci and genetic deletion of CH1 from the IgG constant region, so that IgG antibodies were expressed by the cell in the absence of light chain expression. This modification enabled antibody and B-cell compartment development to pass through a favourable 4-chain (H2L2) endogenous IgM stage before proceeding to a subsequent IgG stage which selected solely heavy chain only (H2) antibodies from the good pool of heavy chain VDJ recombinations provided by the earlier 4-chain IgM stage, this subsequent stage essentially eliminating the possibility for 4-chain antibodies.
WO2018/039180 (Teneobio, Inc.) reported that HCAbs with less propensity for aggregation could be prepared by replacement of the native amino acid residue at the first position of FR4 of an HCAb by another amino acid residue to disrupt a surface-exposed hydrophobic patch which, in a normal Fv, would be buried in the VH-VL interface. The exposure of the hydrophobic patch was identified as being a causal factor in the unwanted aggregation of heavy chains in the absence of light chain, as well as in VH-VL domain pairing in the presence of light chain. Rats were genetically engineered to express HCAbs including identified VH residue mutations, and heavy chain homodimerisation was enforced by inactivation of the endogenous light chain loci.
Although less common than heavy chain only antibodies, the art has also described production of antibodies comprising unpaired VL domains. WO2009/143472 (Aliva Biopharmaceuticals) and WO2015/143414 (Regeneron Pharmaceuticals) described a method of generating antibodies with unpaired VL domains in transgenic animals, by linking gene sequences encoding a human VL domain to heavy chain constant regions with a deletion of the CH1 domain.
In the field of antibodies comprising unpaired variable domains and transgenic animals for producing them, the present invention represents a shift away from “heavy chain only” antibodies and “heavy chain only mice” which have to date been the theme of this technical area. The inventors realised that neither CH1 deletion nor light chain absence were necessary to produce antibodies which bind antigen through their VH domain alone. In the present invention, the VL domain of an antibody is deleted, while the CL domain is retained. This produces an antibody comprising a heavy chain and a light chain, wherein the heavy chain comprises an unpaired VH domain for binding antigen and a constant region including a CH1 domain, and wherein the light chain comprises a CL domain and no VL domain (
Through analogous modifications it is also possible to generate antibodies that bind antigen through the VL domain in the absence of a paired VH domain. Further modifications may optionally be included in antibodies comprising unpaired VH and/or VL domains, e.g., changes in antibody format and design.
Transgenic animals such as mice can be engineered to produce antibodies according to the present invention, for in vivo generation and selection of antigen-specific variable domains that are capable of binding antigen outside the context of a VH-VL pair (Fv). By retaining CH1 and permitting its pairing and stabilisation with a shield domain, the antibody repertoire that can be generated in animals expressing antibodies of the present invention may be significantly greater than CH1-deleted antibody platforms in which the in vivo immune response was limited in some respects. On immunisation with a target antigen of interest, an animal according to the present invention generates antibodies against the target, wherein the antibodies comprise unpaired variable domains that bind the target. These antibodies and/or their encoding nucleic acid may be recovered from the animal, and DNA encoding the variable domain can then be recombinantly expressed, optionally incorporating the unpaired variable domain into a binding molecule (e.g., antibody or chimaeric antigen receptor) comprising the variable domain and one or more further protein domains. The unpaired variable domains, antibodies and other binding molecules comprising them, their encoding nucleic acid, cells and transgenic animals containing such nucleic acid, and methods of generating and using the foregoing are all aspects of the present invention.
In a first aspect, the invention provides an antibody comprising an unpaired variable domain (VH domain or VL domain) linked to a constant region, wherein the constant region comprises a CH1 domain and a domain which pairs with the CH1 domain. The domain which pairs with the CH1 domain is herein termed “shield domain”, and its interface with the heavy chain CH1 domain may serve to stabilise the CH1 domain, promoting solubility and/or inhibiting aggregation of the antibodies. The shield domain may be a polypeptide domain, e.g., an immunoglobulin domain, i.e., a polypeptide domain comprising an immunoglobulin fold. It may be a CL domain (Cκ or Cλ) or the Ig domain of a surrogate light chain λ5 protein. An example of a λ5 protein may be a human λ5 domain that is devoid of the 50 amino acid unique region at the N-terminal end of human λ5, or an example of a λ5 protein may be a non-human λ5 domain that is devoid of the region that corresponds to the 50 amino acid unique region at the N-terminal end of human λ5. Preferably, the shield domain is a CL domain, e.g., Cκ, so that the constant region comprises a CH1:CL domain pair. The unpaired variable domain may be linked to either the CH1 domain or the shield domain, e.g., as a fusion protein. This core structure of an unpaired variable domain linked to a constant region comprising a CH1:CL or CH1:λ5 domain pair may be provided in isolation (a protein consisting of that structure) or as part of a larger polypeptide molecule, optionally comprising further antibody constant domains and/or functional moieties. Although such further domains and moieties may be included, the antibody of the present invention characteristically comprises an unpaired variable domain for binding antigen and so is devoid of any polypeptide domain that pairs with said variable domain to provide an antigen-binding site.
The constant region may comprise two polypeptide chains, one comprising the CH1 domain and one comprising the shield domain. Thus, the antibody may comprise
a first polypeptide comprising an unpaired variable domain, and
a second polypeptide,
wherein the first polypeptide comprises a CH1 domain and the second polypeptide comprises a shield domain which pairs with the CH1 domain, or wherein the first polypeptide comprises the shield domain and the second polypeptide comprises the CH1 domain.
For example, the antibody may comprise
a first polypeptide comprising an unpaired variable domain (e.g., VH domain) and a CH1 domain, and
a second polypeptide comprising a shield domain which pairs with the CH1 domain (e.g., CL or λ5). In the first polypeptide, the variable domain is preferably an N-terminal domain, followed by an adjacent CH1 domain. The second polypeptide lacks an N-terminal variable domain, thereby leaving the variable domain of the first polypeptide unpaired. The second polypeptide may comprise the shield domain and be devoid of additional domains, or it may consist of the shield domain and a C terminal extension of one or more further domains (e.g., Ig constant domains) and/or functional moieties. Optionally the second polypeptide consists of the shield domain.
Alternatively, the antibody may comprise
a first polypeptide comprising a variable domain (e.g., VH domain) and a shield domain, and
a second polypeptide comprising a CH1 domain which pairs with said shield domain, wherein the second polypeptide lacks a variable domain, thereby leaving the variable domain of the first polypeptide unpaired. In the first polypeptide, the variable domain is preferably an N-terminal domain, followed by an adjacent shield domain. The second polypeptide lacks an N-terminal variable domain, thereby leaving the variable domain of the first polypeptide unpaired. The second polypeptide may comprise the CH1 domain and be devoid of additional domains, or may consist of the CH1 domain and a C terminal extension of one or more further domains (e.g., Ig constant domains) and/or functional moieties. Optionally the second polypeptide consists of the CH1 domain.
Pairing of the CH1 domain with its shield domain forms a constant region, which may additionally comprise further domains such as CH2, CH3 and/or CH4, typically as C-terminal domains. The first or second polypeptide may comprise CH2-CH3 linked to the C terminus of the CH1 or shield domain respectively. A first polypeptide may comprise (in an N to C direction) the unpaired variable domain linked to CH1-CH2-CH3 (e.g., VH-CH1-CH2-CH3) and a second polypeptide may comprise or consist of the shield domain (e.g., CL or λ5), lacking an N terminal variable domain. As another example, a first polypeptide may comprise (in an N to C direction) the unpaired variable domain linked to CH1 (e.g., VH-CH1) and a second polypeptide may comprise or consist of (in an N to C direction) the shield domain linked to CH2-CH3 (e.g., CL or λ5 linked to CH2-CH3). Domains may be directly linked by a peptide bond, or by a peptide linker. A hinge region is usually present immediately upstream of the CH2 domain, so the polypeptide may comprise the CH1 or shield domain linked via an antibody hinge region to CH2-CH3. The constant region of an antibody according to the present invention may be a human constant region. It may comprise or consist of the amino acid sequence of the constant region of a native human IgG, e.g., human IgG1. Alternatively, the constant region may be from a non-human animal such as a rodent (e.g., a mouse constant region or rat constant region). In a non-human animal as herein described, the constant region may be an endogenous constant region encoded by the endogenous immunoglobulin locus in the non-human animal's genome.
Exemplary pairings of first and second polypeptides (showing domains in an N to C direction) in antibodies of the present invention are shown in Table 1 below.
A polypeptide comprising CH2-CH3 may comprise further domains, e.g., some antibody isotypes include CH4.
In a given CH1:shield domain pair, any further constant domains (e.g., CH2-CH3) are normally linked to only one of either the CH1 domain and the shield domain. However, CH2-CH3 constant regions naturally dimerise to form an antibody Fc region. A polypeptide comprising CH2-CH3 may associate with a second polypeptide comprising CH2-CH3 via inter-chain pairing between the CH2 and/or CH3 regions, to form an Fc region comprising dimerised CH2-CH3. Inter-chain disulphide bonds may form, and these are normally present in naturally occurring antibodies. Such dimerisation may produce an antibody comprising multiple antigen binding sites. For example, an antibody may comprise two unpaired variable domains, each linked to a constant region comprising CH2 and/or CH3.
An antibody may comprise two first polypeptides and two second polypeptides. Pairs of first and second polypeptides may be independently selected from those shown in Table 1 above. The antibody may comprise two first polypeptides and two second polypeptides, wherein
each first polypeptide comprises an unpaired variable domain and a CH1 domain, and each second polypeptide comprises a shield domain which pairs with the CH1 domain, wherein
one or both of said second polypeptides lacks a variable domain.
Preferably, the antibody comprises two unpaired variable domains. For example, a four chain antibody may comprise two unpaired variable domains (e.g., two VH domains), each linked to a CH1:shield domain pair, and an Fc region. Optionally, a four-chain antibody comprises two first polypeptides and two second polypeptides, wherein the first and second polypeptides both consist of the same domain structure, e.g., two first polypeptides VH-CH1-CH2-CH3 and two second polypeptides CL. The four-chain antibody may thus comprise two first polypeptides, wherein the first polypeptide is any of the first polypeptides shown in Table 1, and two second polypeptides, wherein the second polypeptide is the corresponding second polypeptide shown in Table 1. The two first polypeptides may have identical amino acid sequences, i.e., the antibody may comprise two copies of the same first polypeptide. The two second polypeptides may have identical amino acid sequences, i.e., the antibody may comprise two copies of the same second polypeptide. Alternatively, the sequences of the two first polypeptides may differ from each other and/or the sequences of the two second polypeptides may differ from each other. Differences in sequence are optionally in (e.g., only in) variable domains, e.g., an antibody may comprise two different unpaired variable domains.
With reference to the structure of a full four chain immunoglobulin comprising two heavy-light chain pairs, each heavy chain comprising VH-CH1-CH2-CH3 and each light chain comprising VL-CL, antibodies with unpaired VH domains can be produced by removing one or both VL domains, leaving the CL domains in place. An antibody according to the present invention may comprise two heavy chains and two light chains, each heavy chain comprising a VH domain and a constant region comprising a CH1 domain, and each light chain comprising a CL domain, wherein one or both light chains lack a VL domain, thereby leaving one or both VH domains unpaired. Conversely, antibodies with unpaired VL domains can be produced by removing one or both VH domains, leaving the CH1 domains in place. Variations may be described with reference to other antibody formats, a number of which are discussed herein. Expression in transgenic animals and selection for antigen-binding is facilitated when the four-chain antibody is composed of two identical first polypeptides (e.g., two identical heavy chains) and two identical second polypeptides (e.g., two identical light chains), since this affects the natural mode of expression, assembly and display of antibodies on the surface of antibody-producing cells in animals such as mice and humans.
In a preferred embodiment, both VL domains of an antibody are deleted, thereby producing a four-chain immunoglobulin having the natural structure of an immunoglobulin (e.g., IgG or IgM) except for the absence of the VL domains (
An antibody according to the present invention may comprise two heavy chains and two light chains, wherein
each heavy chain comprises an unpaired VH domain for binding a target antigen, and a heavy chain constant region comprising a CH1 domain, and wherein
each light chain comprises a shield domain (e.g., CL domain), wherein the light chain lacks a VL domain.
The light chain may comprise the shield domain and be devoid of additional domains, or may consist of the shield domain and a C-terminal extension of one or more further domains (e.g., Ig constant domains) and/or functional moieties. Optionally, the light chain consists of the shield domain. The antibody is devoid of VL domains or other domains that pair with the VH domain to form an antigen-binding site, so that the unpaired VH domain provides a binding site for a target antigen.
Optionally, the positions of the CH1 and shield domain (e.g., CL) may be interchanged relative to their positions in a natural human antibody. In a four-chain antibody comprising two binding arms, the positions of the CH1 and shield domain may be interchanged in one arm only, or in both arms. Thus, the overall format of the molecule may be symmetrical or asymmetrical.
Similarly, the natural positions of the VH and VL domains are interchangeable, so that optionally a VH domain is linked to a shield domain or a VL domain is linked to a CH1 domain.
Different antibody chain formats may be combined to form heterodimers (e.g., each half of the heterodimer comprising an unpaired variable domain and two-chain constant region), optionally wherein the heterodimer is bispecific for antigen-binding. An antibody may comprise one unpaired variable domain specific for one antigen or epitope and a second unpaired variable domain specific for a different antigen or epitope. Bispecific antibodies comprising unpaired variable domains capable of binding first and second antigens or epitopes respectively may also be assembled by dimerisation of polypeptides of identical format (each half of the dimer comprising an unpaired variable domain and two-chain constant region). Thus, optionally only the unpaired variable domains differ in amino acid sequence and the antibody molecule is otherwise symmetrical. Additional antigen-binding regions may optionally be incorporated to provide trispecificity or further-order multispecific binding.
Polypeptide domains and antibodies according to the present invention are preferably human. Unpaired variable domains may be human. Antibodies may be fully human.
Non-human animal genomes may be engineered to produce the antibodies according the present invention. For generation of antibodies comprising unpaired human variable domains, these will be transgenic animals comprising genomes into which human immunoglobulin genes have been incorporated. A non-human animal may have a genome comprising immunoglobulin loci engineered to express antibodies comprising unpaired variable domains according to the present invention. B-lymphocytes of such animals are capable of expressing antibodies according to the invention in response to antigenic stimulation, and antibodies comprising unpaired variable domains can be generated by administering a target antigen to the animal. Non-human animals and cells thereof for the production of antibodies with unpaired variable domains, methods of producing them by genetic engineering, and use of the animals or cells for generating the antibodies all represent further aspects of the invention. Suitable non-human animals include laboratory animals such as rodents, e.g., mice and rats.
In one embodiment, an animal according to the present invention, e.g., a mouse, expresses an antibody comprising one or more heavy chains or VH domains, wherein the antibody is devoid of VL domains that pair with the VH domains to form Fv regions, characterised in that the heavy chain comprises a CH1 domain (or the VH domain is linked to a CH1 domain) and the antibody comprises a shield domain that pairs with the CH1 domain.
The genome of a non-human animal or a non-human animal cell may be engineered for expression of an antibody according to the present invention, e.g., it may be engineered to comprise
a plurality of variable region gene segments capable of rearrangement to encode a variable domain, upstream of DNA encoding an immunoglobulin constant region comprising a CH1 domain, and
a gene encoding a shield domain, e.g., CL domain, which lacks functional expression of variable region gene segments.
In another embodiment, an animal according to the present invention, e.g., a mouse, expresses an antibody comprising one or more heavy chains or VH domains, wherein the antibody is devoid of VL domains that pair with the VH domains to form Fv regions, characterised in that the heavy chain comprises a shield domain (or the VH domain is linked to a shield domain), and the antibody comprises a CH1 domain that pairs with the shield domain.
The genome of a non-human animal or a non-human animal cell may be engineered to comprise
a plurality of variable region gene segments capable of rearrangement to encode a variable domain, upstream of DNA encoding a shield domain (e.g., CL domain), which lacks functional expression of variable region gene segments, and
a gene encoding an immunoglobulin constant region comprising a CH1 domain, which lacks functional expression of variable region gene segments.
For expression of antibodies comprising unpaired VH domains for binding antigen, functional expression of endogenous light chain variable domains may be inactivated in the animal, e.g., by knocking out endogenous expression of variable region gene segments from the lambda and/or kappa loci. Preferably, VJ rearrangement of light chain gene segments does not occur, or is non-productive, in B-lymphocytes of animals according to the present invention. Functional expression of VpreB may be inactivated in the animal if desired, e.g., by deleting or mutating the endogenous VpreB gene to render it non-functional, so that the animal does not functionally express a VpreB polypeptide. Animals, cells (e.g., B-lymphocytes) and antibodies according to the present invention may be devoid of VL domains and VpreB. Alternatively, the expression of VL domains and/or VpreB in a cell or animal (e.g., in B-lymphocytes of the animal) may be minimal, e.g., less than 10%, optionally less than 5%, compared with their expression of antibodies comprising unpaired VH domains.
Animals according to the present invention represent a change of direction from prior art platforms for producing antibodies with unpaired variable domains. Until now, binding molecules comprising or consisting of single binding domains were made in the context of heavy chain only (or light chain only) antibodies, expressing the heavy (or light) chain in isolation and engineering the molecule to counter the loss of stability, solubility and/or other properties compared with antibodies in which the binding site is provided by a VH-VL pair. The problem of aggregation caused by the heavy chain CH1 domain was previously resolved by deleting that domain, and a variety of different antibody discovery platforms were produced based on a CH1-deletion approach. The present invention uniquely provides an antibody discovery platform in which the CH1 domain is retained and stabilised through pairing with a shield domain, reflecting the CL:CH1 pairing of a natural four-chain antibody and enabling single binding domains to be selected in vivo from a repertoire of immunoglobulins which present unpaired antibody variable domains in the context of an otherwise native antibody structure. Antibodies of interest can be selected directly from repertoires of antibodies generated in transgenic animals according to the present invention. The unpaired variable domains of such antibodies can also be selected and used as binders, in the form of single domain binding molecules, or they can be incorporated into larger binding molecules such as chimaeric antigen receptors (CARs) in which the unpaired variable domain provides the antigen binding site.
The genome of a non-human animal or a non-human animal cell may be engineered to comprise
a first immunoglobulin locus capable of expressing a heavy chain or first polypeptide according to the present invention, the heavy chain or first polypeptide comprising a variable domain (e.g., VH domain) and a CH1 domain, and
a second immunoglobulin locus capable of expressing a light chain or second polypeptide according to the present invention, the light chain or second polypeptide comprising a shield domain (e.g., Cκ domain) which pairs with said CH1 domain, wherein the light chain or second polypeptide lacks a variable domain,
wherein the heavy chain or first polypeptide and the light chain or second polypeptide expressed from said respective loci are capable of pairing through association of the CH1 domain with the shield domain, wherein the absence of a variable domain in the light chain or second polypeptide leaves the variable domain of the heavy chain or first polypeptide unpaired.
For example, the genome of a non-human animal or non-human animal cell may be engineered to comprise
an immunoglobulin heavy chain locus encoding or capable of rearrangement to encode an immunoglobulin heavy chain comprising a human VH domain and a CH1 domain, and
an immunoglobulin locus which is engineered to express a polypeptide comprising a shield domain (e.g., lambda or kappa CL domain, or λ5) that pairs with CH1, wherein the polypeptide does not comprise a variable domain. Nucleic acid encoding the VL domain of the light chain may be absent and/or V-J rearrangement at the locus may be inactivated. Preferably the animal entirely lacks functional expression of light chains comprising a VL domain—thus the endogenous light chain loci may be modified to prevent functional expression of VL domains.
Preferably, the immunoglobulin heavy and/or light chain locus is the endogenous immunoglobulin locus in the animal. Thus, the endogenous immunoglobulin heavy chain locus (or loci) on chromosome 12 of a mouse may be engineered to contain DNA of the human heavy chain locus, expressing a heavy chain comprising the human VH. The immunoglobulin light chain locus (or loci) may be the endogenous immunoglobulin kappa light chain locus on mouse chromosome 6 and/or the endogenous immunoglobulin lambda light chain locus (or loci) on mouse chromosome 16. The immunoglobulin domain for pairing with CH1 (shield domain) may be expressed under control of human or endogenous transcriptional control elements (promoter/enhancers) at an endogenous immunoglobulin locus of the animal, e.g., a polypeptide comprising a CL domain may be expressed at an endogenous light chain locus. The light chain locus may be lambda or kappa. Optionally, both the lambda and kappa loci are engineered to express a light chain comprising a CL domain and lacking a VL domain.
A non-human animal according to the present invention may comprise B-lymphocytes expressing an antibody comprising an unpaired VH domain for binding antigen, wherein the genome of the animal comprises
a plurality of variable region gene segments capable of rearrangement to encode a variable domain, upstream of DNA encoding an immunoglobulin constant region comprising a CH1 domain, and
a gene encoding a CL domain which lacks functional expression of variable region gene segments.
Within B-lymphocytes of the animal, the genome is functional to express antibody comprising
an antigen-binding variable domain linked to the CH1 domain and
a light chain comprising a CL domain, wherein the light chain lacks a VL domain, thereby leaving the antigen-binding variable domain unpaired.
For the generation of a non-human animal comprising B-lymphocytes expressing an antibody comprising an unpaired VH domain for binding antigen, a suitable method comprises:
engineering the genome of a non-human animal cell (e.g., an embryonic stem cell or a zygote) to comprise
a plurality of variable region gene segments capable of rearrangement to encode a variable domain, upstream of DNA encoding an immunoglobulin constant region comprising a CH1 domain, and
a gene encoding a CL domain which lacks functional expression of variable region gene segments, and
generating an animal from said cell or from a group of cells comprising said cell.
Variable region gene segments are capable of rearrangement to encode a VH or VL domain for binding a target antigen. A VH domain is generated through rearrangement of one V gene segment, one D gene segment and one J gene segment, and the genome may be engineered to comprise one or more V gene segments, one or more D gene segments and one or more J gene segments for rearrangement to encode a VH domain. A minimum would be one V, one D and one J, but the inclusion of a larger number of V, D and/or J gene segments provides a greater diversity of encodable VH domains. Alternatively, where the unpaired variable domain of the antibody is to be a VL domain, the genome may be engineered to comprise one or more V gene segments and one or more J gene segments for rearrangement to encode the VL domain. A minimum would be one V and one J, but the inclusion of a larger number of V and J gene segments provides a greater diversity of encodable VL domains.
Preferably the gene segments are human. For example, a full set of human heavy chain V, D and J gene segments may be included, or a full set of human light chain V and J gene segments may be included. The genome may comprise 41 human heavy chain V gene segments. It may comprise human heavy chain D gene segments. It may comprise 6 human heavy chain J gene segments. The genome may comprise 38 light chain κ V gene segments. It may comprise 5 human light chain κ J gene segments. Preferably the CL domain is a human CL domain, e.g., human Cκ or human Cλ.
The gene encoding the CL domain may comprise inserted DNA of a human Ig light chain locus, comprising an exon encoding a light chain variable region leader sequence (e.g., human vκ leader sequence) and an exon encoding the CL domain (e.g., human Cκ domain), separated by an intron comprising a J-C intron enhancer element. Transcription of the DNA results in splicing out of the intron thereby joining the two exons, resulting in nucleic acid (e.g., comprising nucleotide sequence SEQ ID NO: 5) encoding the CL domain linked to an upstream (5′) leader sequence encoding a signal peptide. Human light chain variable region gene segments are not functionally expressed, and may be absent (deleted from or not included in the animal genome) or inactivated. The encoded CL domain may be a human Cκ domain comprising SEQ ID NO: 4. The encoded sequence may comprise or consist of SEQ ID NO: 6 which includes the N-terminal signal peptide SEQ ID NO: 2, which may be post-translationally cleaved to leave the Cκ domain sequence SEQ ID NO: 4.
Human variable region gene segments may be inserted at the endogenous immunoglobulin heavy chain locus of the genome. The gene encoding the human CL domain may be inserted at the endogenous light chain locus (e.g., Igκ locus) of the genome. In an embodiment, human transcriptional control elements are included together with the coding sequence. However, optionally the inserted human DNA may be placed under control of endogenous transcriptional control elements in the animal genome. In an embodiment, the inserted human DNA is under the control of one or more control elements (e.g., a promoter and/or enhancer (such as an intronic enhancer and/or 3′ locus enhancer) selected from:
In another example, the control element(s) may be mammalian.
Expression of the endogenous Ig heavy and/or light chains may be inactivated, e.g., by deletion or inactivation of variable region gene segments. In an example, the endogenous lambda loci comprise a deletion of at least 100, 150 or 200 kb of DNA to inactivate endogenous lambda variable domain expression (optionally, this is in combination with endogenous kappa loci that have been modified to encode a shield domain as described herein). In an example, the endogenous kappa loci comprise a deletion of at least 100, 150 or 200 kb of DNA to inactivate endogenous kappa variable domain expression (optionally, this is in combination with endogenous lambda loci that have been modified to encode a shield domain as described herein).
The genome of a mouse or a mouse cell may be modified by insertion of a plurality of human variable region gene segments capable of rearrangement to encode a human variable domain, upstream of human DNA encoding an immunoglobulin constant region comprising a human CH1 domain, at the endogenous immunoglobulin heavy chain locus on mouse chromosome 12. Similarly, DNA encoding a human CL domain (e.g., Cκ) may be inserted at the endogenous Igκ light chain locus on mouse chromosome 6. DNA encoding a human CL domain (e.g., Cλ) may alternatively or additionally be inserted at the endogenous IgA locus on mouse chromosome 16. Expression of mouse heavy and light chains (κ and/or λ) may be inactivated, e.g., by deletion of encoding DNA or by rendering its expression non-functional.
Antibodies according to the present invention may be generated in the animals. The antibodies will generally be expressed in B-lymphocytes of the animal. A naïve repertoire of unpaired variable domains is obtainable from the animal before immunisation with an antigen. An antigen-specific repertoire is obtainable after immunisation with an antigen. At least 50% of antibody-expressing B-lymphocytes in the animal (e.g., 75% or more, or all antibody-expressing B-lymphocytes) may express antibodies comprising unpaired variable domains in accordance with the invention. Following immunogenic exposure of the animal to a target antigen, B-lymphocytes expressing antibodies comprising unpaired variable domains that bind the target antigen will be positively selected by the immune system and will undergo expansion and somatic hypermutation, generating a repertoire of variable domains that recognise the target antigen. One or more such antibodies, or the antigen-binding variable domains thereof, or their encoded nucleic acid, can then be recovered from the animal and used in downstream steps such as recombinant expression, incorporation into larger antigen-binding polypeptides, and/or therapeutic use, examples of which are described herein.
A method of generating an antibody comprising an unpaired variable domain for binding antigen may comprise exposing a non-human animal of the present invention to immunogenic stimulation with target antigen. The antibody and/or its encoding nucleic acid can then be isolated from the animal (e.g., by isolating B-lymphocytes from blood, bone marrow and/or spleen), enabling identification of the variable domain sequence (nucleotide and/or amino acid sequence). Optionally, mutations may be introduced into the sequence, such as reversion of non-germline framework residues to germline, insertion, substitution or deletion of residues within the variable domain, e.g., in one or more CDRs, or in one or more FRs, to refine properties of the variable domain such as binding affinity or physical properties such as stability and solubility. DNA encoding the variable domain comprising one or more mutations may then be provided, e.g., in a vector such as a plasmid, expression vector, transfection vector or cloning vector. The sequence encoding the variable domain may be provided as part of larger sequence encoding a polypeptide comprising the variable domain and one or more additional domains. Examples of such polypeptides include antibodies and CARs, which are detailed elsewhere herein. Preferably, the variable domain is the N-terminal domain of such a polypeptide, as this is its natural position in an immunoglobulin and exposes the CDRs of the variable domain binding site, although other formats are possible and the variable domain may be connected to an N-terminal domain, optionally via a peptide linker, and still retain its antigen-binding ability. The encoding nucleic acid may be introduced into the genome of a host cell, and the cells comprising the recombinant DNA can then be cultured for expression of the antibody, isolated variable domain or the polypeptide comprising the unpaired variable domain. The antibody, isolated variable domain or polypeptide is then purified from the cells or from the cell culture medium, and may be formulated into a composition comprising a pharmaceutically acceptable excipient and may be used therapeutically in treatment (optionally preventative treatment) of diseases and conditions amenable to treatment by binding the target antigen recognised by the unpaired variable domain. The encoding nucleic acid, and/or cells comprising it, also represent potential therapeutic products themselves. For example, a T-lymphocyte may be engineered to express a CAR comprising the unpaired variable domain, and the T-lymphocyte may be used for immunotherapy through targeting the antigen recognised by the unpaired variable domain.
Antibodies according to the present invention may also be used in vitro, e.g., in diagnostic methods, for binding antigen. An antibody which binds a target antigen may be used in a method of detecting whether a target antigen is present in a sample, optionally for quantifying the target antigen, or for selecting a target antigen from a mixture (optionally in solution) comprising that antigen among other molecules. The antibody may optionally be immobilised on a surface, e.g., a bead, or a matrix, optionally within a column) to facilitate isolation of antibody:antigen complex. Conversely, a target antigen (optionally immobilised on a surface, e.g., a bead, or a matrix, optionally within a column) may be used to select an antibody of the present invention that is capable of binding that target antigen, by contacting a mixture (e.g., a solution) comprising that antibody among other molecules (e.g., other antibodies with different unpaired variable domains). Binding of the unpaired variable domain of the antibody to the target antigen forms an antibody:antigen complex, which may then be isolated (e.g., separated from the solution). One or more washing steps may be performed to remove unbound antibody or unbound antigen. In general, a method of preparing an antibody:antigen complex may comprise
exposing a target antigen to an antibody according to the present invention in vitro,
allowing binding of the unpaired variable domain to the target antigen, thereby forming an antibody:antigen complex, and
isolating the antibody:antigen complex.
The method may further comprise determining the sequence or identity of the antibody or antigen in the antibody:antigen complex, and/or quantifying the number of antibody:antigen complexes formed.
The invention will now be described in more detail, with reference to the accompanying drawings. Headings within this document are included solely to assist navigation and should not be construed as limiting. Embodiments of the invention that are separately described may be combined, except where the context indicates otherwise. Those skilled in the art will additionally recognise, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be within the scope of protection of the appended claims.
Pairing between polypeptide domains refers to a molecular association at an interface between spatially adjacent domains. Pairing generally involves non-covalent bonding (e.g., hydrophobic and/or electrostatic interactions) although the domains may additionally be covalently linked e.g., via one or more disulphide bonds or other molecular linkers. Paired domains may optionally be part of the same polypeptide, and therefore covalently linked as well as non-covalently paired, and may be adjacent in the primary polypeptide sequence or separated by one or more other domains. Examples of paired domains are a VH:VL pair of an antibody Fv region (whether formed by separate polypeptides comprising the VH and VL domain respectively, or by a single chain Fv (scFv)), a CH1:CL pair between heavy and light chains of an antibody, and a (CH2-CH3):(CH2-CH3) pair between constant regions in an antibody Fc region. Paired domains may be heterodimeric or homodimeric. By extension, the concept of paired polypeptides involves molecular association between two polypeptides, e.g., via pairing of domains of the respective polypeptides. For example, an antibody can be referred to as comprising paired heavy and light chains (or “a heavy:light chain pair”), wherein for example the CH1 domain of the heavy chain pairs with the CL domain of the light chain.
An unpaired domain is a domain which is not paired with another domain. An unpaired variable domain corresponds to an antibody Fv region from which either the VH or VL domain has been removed. The unpaired variable domain may be a VH or a VL. The unpaired variable domain may be capable of binding antigen outside the context of an Fv. Thus, a VH domain may not require the presence of a paired VL domain for antigen-binding. Conversely, a VL domain may not require the presence of a paired VH domain for antigen-binding. Indeed, in many cases, especially where variable domains are selected for antigen-binding in their unpaired state (as described in methods herein, such as methods of generating antigen-specific antibodies in vivo by immunisation of transgenic mice), an unpaired variable domain may specifically bind its target antigen with affinity that is comparable to the affinity of Fv regions from “normal” antibodies raised against that target. Moreover, for at least certain categories of antigen, including those with clefts or deep binding pockets in their three dimensional structure, antibodies comprising unpaired variable domains according to the present invention are preferred over whole Fv regions since the narrower structure of an unpaired variable domain presents a smaller binding site which may reach epitopes buried within antigens whereas such epitopes may be inaccessible or less accessible to binding by a full Fv region. Example target antigens and the raising of antibodies against them are discussed in more detail elsewhere herein.
While pairing indicates non-covalent interaction (optionally supplemented by inter-domain covalent bonding), reference to linking herein generally indicates a covalent attachment. Domains of a polypeptide may be linked via a peptide bond or peptide linker. Moieties may be linked by other suitable covalent attachment, a range of which will be apparent to the protein chemist.
A domain of a polypeptide comprises a sequence which adopts a folded structure, e.g., an immunoglobulin fold or other stable conformation. Where a polypeptide comprises a domain as part of a longer polypeptide sequence, the domain will generally have a tertiary structure independent of or distinguishable from the rest of the polypeptide. Generally, domains are responsible for discrete functional properties of proteins and in many cases may be added, removed or transferred to other proteins without loss of function of the remainder of the protein and/or of the domain.
Antibodies comprise immunoglobulin domains, which have an “immunoglobulin fold” of two β-sheets of antiparallel β-strands linked by a disulphide bond and hydrophobic interactions. A constant domain referred to herein may be an immunoglobulin constant domain, e.g., a CH1, CH2, CH3 or CL domain. A constant region may comprise one or more constant domains, linked and/or paired with each other. Antibody constant regions are described in more detail elsewhere herein.
Where multiple domains of a polypeptide are recited herein, they will usually be ordered in the standard N- to C-terminal direction, unless the context indicates otherwise. E.g., unless indicated to the contrary, a polypeptide comprising a VH domain and a CH1 domain comprises the VH domain “upstream of” the CH1 domain. A polypeptide may be represented by its domain structure such as VH-CH1, where the domains are shown in an N- to C-terminal direction from left to right.
Optionally, antibodies or polypeptide chains according to the present invention may be fused or conjugated to additional polypeptide sequences and/or to labels, tags, toxins or other molecules, e.g., to form immunocytokines. For example, an antibody constant region or shield domain may be linked to a cytokine such as IL-2. Linkage between polypeptide or peptide sequences can conveniently be made by generating a fusion protein comprising their two (or more) sequences in series.
The term “antibody” herein includes monoclonal antibodies (including full length antibodies which have an immunoglobulin Fc region), antibody compositions with polyepitopic specificity, multispecific antibodies (e.g., bispecific antibodies), and single-chain molecules, as well as antibody fragments. Antibodies comprising unpaired variable domains according to the present invention may comprise a natural or known antibody structure, subject to the modification that one or more Fv region of the antibody is replaced with an unpaired variable domain. This may be envisaged as the removal of either a VL (or VH) domain from the Fv, leaving the remaining VH (or VL) domain unpaired.
Antibodies and polypeptide domains herein may be human. Human variable domains are preferred for their lower immunogenicity in compositions intended for administration to humans. Constant regions of antibodies may be human (especially in the context of antibodies for administration to humans, as noted), although they may be generated in transgenic non-human animals as chimaeric antibodies comprising human variable regions and non-human animal constant regions, followed by exchange of the non-human animal constant regions for human constant regions to provide fully human antibodies. Alternatively, fully human antibodies may be generated directly from transgenic animals whose genomes have been engineered to contain human variable region gene segments and human constant region genes. Accordingly, an antibody of the invention may be a human antibody or a chimaeric antibody comprising one or more human variable regions and one or more non-human (e.g., mouse) constant regions. It may comprise at least one unpaired human variable region linked to a human constant region.
An antibody variable domain (e.g., unpaired variable domain as described herein) provides a binding site for antigen. Recognition between an antibody and its cognate antigen may be referred to as specific binding, contrasting with non-specific binding whereby an antibody or other polypeptide binds non-target molecules through relatively low affinity interactions. Antigen-binding of a variable domain is via contact between the antigen and one or (usually) multiple residues in the CDRs (HCDRs or LCDRs). One or more FR residues of the variable domain may also make contact with the antigen. The region of the antigen bound by the antibody is referred to as its epitope. The region of the antibody which binds the antigen is referred to as its paratope.
A variable domain or binding site that “specifically binds to” or is “specific for” a particular antigen or epitope may be one that binds to that particular antigen or epitope without substantially binding to other antigens or epitopes. For example, binding to the antigen or epitope is specific when the antibody binds with a Ko of 1 mM or less, e.g., 100 μM or less, 10 μM or less, 1 μM or less, 100 nM or less, e.g., 10 nM or less, 1 nM or less, 500 μM or less, 100 μM or less, or 10 μM or less. The binding affinity (KD) can be determined using standard procedures as will be known by the skilled person, e.g., binding in ELISA and/or affinity determination using surface plasmon resonance (SPR) (e.g., Biacore™, Proteon™ or KinExA™ solution phase affinity measurement which can detect down to fM affinities (Sapidyne Instruments, Idaho)). In one embodiment, SPR is carried out at 25° C. In another embodiment, the SPR is carried out at 37° C. In one embodiment, the SPR is carried out at physiological pH, such as about pH 7 or at pH 7.6 (e.g., using Hepes buffered saline at pH 7.6 (also referred to as HBS-EP)). In one embodiment, the SPR is carried out at a physiological salt level, e.g., 150 mM NaCl. In one embodiment, the SPR is carried out at a detergent level of no greater than 0.05% by volume, e.g., in the presence of P20 (polysorbate 20; eg, Tween-20TM) at 0.05% and EDTA at 3 mM. The SPR may be carried out at 25° C. or 37° C. in a buffer at pH 7.6, 150 mM NaCl, 0.05% detergent (eg, P20) and 3 mM EDTA. The buffer can contain 10 mM Hepes. In one example, the SPR is carried out at 25° C. or 37° C. in HBS-EP. HBS-EP is available from Teknova Inc (California; catalogue number H8022).
In an example, the affinity is determined using SPR by
1. Coupling anti-human or anti-mouse (or other relevant non-human vertebrate, to match the C region of an antibody for example) IgG (eg, Biacore BR-1008-38) to a biosensor chip (e.g., GLM chip) such as by primary amine coupling;
2. Exposing the IgG to a test antibody (or heavy chain thereof) comprising a constant region to capture the test antibody (or heavy chain thereof) on the chip;
3. Passing the test antigen over the chip's capture surface at 1024 nM, 256 nM, 64 nM, 16 nM, 4 nM with a 0 nM (i.e., buffer alone) control; and
4. Determining the affinity of binding of test antibody/chain to test antigen using surface plasmon resonance, eg, under an SPR condition discussed above (e.g., at 25° C. in physiological buffer). SPR can be carried out using any standard SPR apparatus, such as by Biacore™ or using the ProteOn XPR36™ (Bio-Rad®).
Regeneration of the capture surface can be carried out with 10 mM glycine at pH 1.7. This removes the captured antibody and allows the surface to be used for another interaction. The binding data can be fitted to 1:1 model inherent using standard techniques, eg, using a model inherent to the ProteOn XPR36™ analysis software.
A constant region of an antibody may comprise one or more human constant domains, and may be a human constant region. For example, an unpaired variable domain (e.g., VL domain) may be attached at its C-terminal end to an antibody light chain κ or λ constant domain. An unpaired variable domain (e.g., VH domain) may be attached at its C-terminal end to all or part (e.g. a CH1 domain or Fc region) of an immunoglobulin heavy chain constant region derived from any antibody isotype, e.g. IgG, IgA, IgE and IgM and any of the isotype sub-classes, such as IgG1 or IgG4.
An antibody constant region may comprise a human IgG, IgM, IgA, IgD or IgE constant region. An antibody heavy chain constant region may comprise a human heavy chain IgG, IgM, IgA, IgD or IgE constant region.
Sequences of exemplary human constant regions are provided in the appended Table A.
Constant regions of antibodies of the invention may alternatively be non-human constant regions. For example, when antibodies are generated in transgenic animals (examples of which are described elsewhere herein), chimaeric antibodies may be produced comprising human variable regions and non-human (host animal) constant regions. Some transgenic animals generate fully human antibodies. Others have been engineered to generate antibodies comprising chimaeric heavy chains and fully human light chains. Where antibodies comprise one or more non-human constant regions, these may be replaced with human constant regions to provide antibodies more suitable for administration to humans as therapeutic compositions, as their immunogenicity is thereby reduced.
Digestion of whole immunoglobulins with the enzyme papain results in two identical antigen-binding fragments, known also as “Fab” fragments, and a “Fc” fragment, having no antigen-binding activity but having the ability to crystallize. “Fab” when used herein refers to a fragment of an antibody that includes one constant and one variable domain of each of the heavy and light chains. The term “Fc region” herein is used to define a C-terminal region of an immunoglobulin heavy chain, including native-sequence Fc regions and variant Fc regions. The “Fc fragment” refers to the carboxy-terminal portions of both H chains held together by disulphides. The effector functions of antibodies are determined by sequences in the Fc region, the region which is also recognised by Fc receptors (FcR) found on certain types of cells.
A non-human animal genome may be engineered to contain one or more human heavy chain V gene segments, one or more human heavy chain D gene segments and one or more human heavy chain J gene segments, for expression of a human VH domain. It may contain a full set of all human heavy chain V, D and J gene segments. The human VDJ gene segments may be inserted upstream of a constant region, for production of VH domains linked to a constant region.
Similarly, the non-human animal genome may be engineered to contain one or more human light chain V gene segments and one or more human light chain J gene segments, for expression of a human VL domain. Gene segments may be κ or λ. The non-human animal genome may contain a full set of all human K or A gene segments. The human VJ gene segments may be inserted upstream of a constant region, for production of VL domains linked to a constant region.
Since antibodies of the present invention comprise the VH or VL domain in unpaired form, the genome may comprise heavy chain gene segments in the absence of light chain gene segments (or wherein expression of light chain gene segments is inactivated), or it may comprise light chain gene segments in the absence heavy chain gene segments (or wherein expression of heavy chain gene segments is inactivated).
Recombination of V(D)J gene segments generates combinatorial diversity in each variable domain. With the inclusion of a full set of human heavy (or light) chain gene segments, the full combinatorial diversity of human variable domains can be incorporated into a transgenic animal platform. Affinity maturation of these variable domains then proceeds through the natural in vivo processes of somatic hypermutation and selection, providing an extensive and diverse sequence repertoire from which antigen-specific variable domains with desirable properties may be identified and their sequences recovered. The antibody production platforms described herein take advantage of the natural ability of CH1 to pair with a shield domain, enabling a complete human heavy chain repertoire to be maintained and avoiding the need to re-engineer the human heavy chain. Preferably the heavy chain immunoglobulin locus is or comprises an unmodified human heavy chain locus and/or expresses human immunoglobulin heavy chains that are comparable in all respects to those generated in humans. Such a platform can deliver a full repertoire of antibodies comprising unpaired human VH domains for binding antigen, enabling selection of desired molecules of interest, suitable for development into pharmaceutical products.
Methods of generating transgenic animals having genomes comprising all or part of human immunoglobulin loci are well known in this technical field. Such animals have been used to discover and produce several antibodies comprising human variable domains which are currently on the market as pharmaceutical products, with a great many more in the development pipeline. Methods of engineering the non-human animal genome to contain human immunoglobulin gene segments are described for example in WO2011/004192 (Genome Research Limited), which is incorporated herein by reference. Examples of transgenic non-human animals include Kymouse™ (e.g., as described in WO2011/004192), VelociMouse®, OmniMouse®, Omnirat®, XenoMouse®, HuMab Mouse® and MeMo Mouse®.
In addition to the variable region, the genome of the non-human animal encodes the constant region of an antibody described herein. The locus comprising the variable region gene segments further comprises a constant region gene or genes, e.g., a heavy chain constant region comprising CH1 (e.g., comprising domains CH1, CH2 and CH3), or a constant region comprising CL (e.g., comprising domains CL, CH2 and CH3). The constant region at a locus may be a human constant region, i.e., wherein the domains are of human origin. The non-human animal genome may be engineered to contain one or more human constant region genes. It may contain the full repertoire of human constant region genes: M, D, G3, G1, A1, G2, G4, E and A2 respectively, optionally by insertion of a fragment of human genomic DNA containing these genes.
A constant region may comprise a fragment of a human IgH locus including the Cμ to (and optionally including) the 5′-most yl exon; optionally including all γ1 CH1-3 or CH1-M2 exons. In an alternative, the fragment is from and including Sp or Ep. In an alternative, the fragment is from a point within the first 400, 500, 600, 700 800 or 900 nucleotides of the IgH J-C intron, wherein the fragment comprises intronic DNA 5′ of and contiguous with Eμ and Cμ.
The constant region may comprise at least one IgH C gene segment, e.g., a Cmu gene segment, and optionally also one or more of an alpha, delta, epsilon and gamma (eg, gamma-1) C gene segment. In an embodiment, the constant region comprises a Cmu and a Cgamma (e.g., gamma-1, human gamma-1, mouse gamma-1 or rat gamma-1 C segment). One or both of the Cmu and Cgamma can be endogenous to the non-human animal; e.g., the Cmu is endogenous and Cgamma is endogenous or human. In an example, the gene segments of the C region are in germline order of C segments found in an IgH or IgL locus of a human, rodent, rat or mouse genome. In an example, the gene segments of the C region are in germline order of C segments found in an IgH or IgL locus of a mouse genome. This order is known to the skilled addressee.
In an example, the antibody C gene segment(s) are endogenous segments of the non-human animal, optionally wherein the constant region is an endogenous heavy chain constant region at an endogenous heavy chain locus, or an endogenous light chain (kappa or lambda) constant region at an endogenous light chain locus. Thus, when the animal is a mouse, the C segment(s) are those on chromosome 12 (for IgH C segment(s)), 6 (for Igκ C segment(s)) or 16 (for Igλ C segment(s)).
A non-human animal genome may be engineered to comprise first and second loci, wherein the first locus is engineered to express a first polypeptide or a heavy chain according to the present invention and wherein the second locus is engineered to express a second polypeptide or a light chain according to the present invention. The first and second loci may be on the same or different chromosomes.
The first locus may be engineered to comprise a fragment of the human immunoglobulin heavy chain locus, comprising VDJ segments and constant region genes together with intergenic regions and regulatory elements. Alternatively, the first locus may be engineered to comprise a fragment of the human immunoglobulin K or A light chain locus, comprising VJ segments and constant region genes together with intergenic regions and regulatory elements.
The V(D)J gene segments may be linked to a constant region which is the endogenous non-human animal constant region. This can be achieved by inserting the human variable region gene segments into the non-human animal genome upstream of the endogenous constant region at the endogenous immunoglobulin locus. Alternatively, the constant region is human, and human DNA comprising V(D)J gene segments and human constant region may be inserted at the endogenous locus, thereby fully humanising that locus. Intergenic and regulatory elements of the human immunoglobulin locus are preferably also included.
Human heavy chain genes may be inserted at the mouse heavy chain locus on chromosome 12 to provide a first locus encoding a first polypeptide or heavy chain locus as described herein.
The second locus may be engineered for expression of a shield domain. It may comprise DNA of a human κ light chain locus comprising the human κ constant region gene and optionally the associated human intergenic and regulatory elements. Thus, the non-human animal genome may be engineered to comprise a fragment of the human κ locus comprising the constant region genes and regulatory elements. Productive rearrangement of the variable region gene segments is inactivated, e.g., by deletion of all Jκ gene segments. The human Cκ gene may be inserted at the mouse κ locus on chromosome 6.
Expression of endogenous variable region gene segments from an endogenous Ig locus or loci in the non-human animal may be inactivated, e.g., by deletion or inversion of a stretch of DNA comprising endogenous V(D)J regions. Optionally the endogenous A locus is unmodified. However, it too may be inactivated if desired (
In an example, the human heavy chain variable region and/or constant region DNA is integrated at an endogenous antibody locus of the non-human animal (e.g., mouse). Optionally the donor and recipient loci are matched, thus human heavy chain locus DNA may be integrated at the endogenous heavy chain locus, and human κ light chain locus DNA may be integrated at an endogenous κ light chain locus and human λ light chain locus DNA may be integrated at an endogenous λ light chain locus, although such matching is not essential.
A constant region may comprise an endogenous (e.g., mouse) antibody constant gene segment. It may additionally comprise one or more human constant gene segments. The antibody locus may be an IgH locus and the constant region comprise an endogenous Cμ constant gene segment and human Cy constant gene segments. The antibody locus may be an IgH locus and comprise an endogenous Sp operably linked upstream of a Cμ (e.g., an endogenous Cμ). For example, the locus comprises an endogenous intronic enhancer (e.g., Ep when the antibody locus is an IgH; or iEκ when the antibody locus is an Igκ). The locus may comprise an endogenous 3′ enhancer of the antibody locus.
Alternatives to targeted integration of human DNA at an endogenous immunoglobulin locus of the non-human animal include random integration of the human DNA into the animal genome, or targeted integration of the human DNA at a locus separate from (optionally on a different chromosome from) the endogenous immunoglobulin loci. The Rosa26 locus may be a convenient target. Optionally therefore the first and/or second locus is not an endogenous antibody locus, e.g., the DNA may have been randomly inserted into the germline genome of the animal. In an embodiment, the constant region comprises an exogenous antibody constant gene segment (so the antibody does not comprise an endogenous antibody constant gene segment). The exogenous constant gene segment may be of the same or a different species to the animal, e.g., a human or rodent (such as mouse or rat) constant gene segment.
Transgenic non-human animals and non-human animal cell genomes preferably comprise a fully humanised heavy chain locus containing the full repertoire of human V, D and J gene segments and all human constant region genes plus human enhancers. In situ targeting of the human immunoglobulin locus DNA to the endogenous immunoglobulin loci of the non-human animal, in contrast with random insertion, facilitates the correct and precise regulation of the immune response. Transgenic animals of the present invention can thus display a robust immune response, including somatic hypermutation and affinity maturation of antibody variable domains, following exposure to an immunogenic composition comprising target antigen. Expression of mouse heavy chains from the endogenous mouse heavy chain locus may be inactivated by inversion of the variable region and replacement of the mouse constant region with the human heavy chain constant region genomic fragment. Deletion of mouse variable region gene segments is an alternative to displacement and/or inversion of the endogenous DNA. For example, the mouse heavy chain V and/or J gene segments may be deleted.
Well validated methods are now available for genomic engineering of animals and the available techniques continue to improve. Engineering of ES cells may be performed by homologous recombination or recombinase cassette exchange [2; WO2011/004192] and chromosomal engineering may also be performed in zygotes [3].
In one embodiment, the first locus is produced by insertion of variable region gene segments at an endogenous IgH locus of an embryonic stem cell (ES cell) or iPS cell of the species of said animal (e.g., mouse cell). Subsequently, the second locus can be introduced as a transgene into the genome of the cell (or a progeny cell or zygote thereof), wherein the transgene is inserted into the genome of the cell or zygote. The non-human animal is then developed from the cell, zygote or a progeny thereof. Alternatively, as is known in the art, loci can be engineered in separate non-human animal cells (e.g., ES cells, iPS cells or zygotes), which are developed into animals comprising the engineered loci in their germline DNA, and the separate animals are bred together to combine the loci in the germline genome of a progeny animal. Thus, a first animal whose germline genome comprises the first locus and a second animal whose germline genome comprises the second locus are mated to produce a progeny animal whose germline genome comprises both loci. The progeny animal can be observed to produce lymphocytes expressing antibodies as described herein.
An animal according to the present invention may be homozygous for the first locus or heavy chain locus and/or homozygous for the second locus or light chain locus as described herein. In an alternative, the vertebrate is heterozygous for the or each such locus. Preferably the animals are homozygous at humanised heavy and light chain loci. They may be homozygous at all three immunoglobulin loci, i.e., heavy locus, A locus and K locus. As noted, heterozygous animals can be generated initially for each locus and bred to generate double or triple homozygous animals (depending on the number of modified loci) and a stable breeding population is thus produced. A breeding colony of transgenic animals may be housed in an animal house, optionally under sterile or specific pathogen free (SPF) conditions. Male and female mice may be grouped separately or together.
In one example, mice comprising a humanised heavy chain locus described herein, animals comprising a humanised K locus as described herein, and optionally animals comprising an inactivated A locus as described herein, are generated separately and then bred together to produce a strain in which fully human heavy chains are expressed at the endogenous Ig heavy locus, the VJ rearrangement at the endogenous κ locus is inactivated by deletion of the J region, and the locus expresses a Cκ fragment (e.g., SEQ ID NO: 4).
The endogenous λ locus of a mouse may be inactivated (e.g., deleted in whole or in part) so that it does not express a light chain comprising a VL domain. There may be no functional polypeptide expression from the λ locus. However, in other embodiments the λ locus of the mouse may be unmodified. Expression from the λ locus naturally occurs at only a low level in the mouse. Moreover, where the κ locus is active, for example where the K locus encodes and expresses a shield domain (e.g., a CL or λ5 domain), the λ locus may be silenced through the natural process of allelic exclusion in B-lymphocytes. Thus, expression from the λ locus may be silenced in B-lymphocytes of animals (e.g., mice) according to the present invention, whether naturally by allelic exclusion, by engineering of the genome or in any other way. Inactivation of the locus by deletion is illustrated in Example 3.
Aspects herein may be expressed in terms of the non-human animal being a mouse, but it is to be understood that other laboratory or livestock animal or any other non-human vertebrate may be suitable for performing the present invention. The vertebrate may be a rodent, e.g., a mouse or rat. In other examples, the vertebrate is a bird (e.g., chicken), fish (e.g., shark or zebrafish), mammal (e.g., rabbit), livestock animal (e.g., cow, sheep, pig or goat), or camelid (e.g., llama, alpaca or camel). In an embodiment, the mouse strain is 129 (or a 129 hybrid), C57BL6 (or C57BL6 hybrid), or derived from an AB2.1, AB2.2, JM8, BALB/c, or F1H4 ES cell line.
Knockouts can be used to provide access to human/non-human (e.g., human/mouse) cross-reactive antibodies. Thus, in addition to the modifications above, expression of an endogenous target may be inactivated in the genome of the non-human animal. The resulting knockout animals can be used for immunisation with the target antigen and may generate a stronger immune response (e.g., higher antibody titre and/or greater antibody diversity) to the target compared with animals that express the endogenous target. This is because, where a target antigen (e.g., human protein X) shares homology with the endogenous target in the non-human animal (e.g., mouse protein X), the non-human animal's immune repertoire will have undergone negative selection against the self-antigen, so that immunisation with the human protein predominantly generates antibodies that are selective for the human protein and are not cross-reactive with the endogenous protein from the non-human animal. Use of a knockout animal thus increases the diversity of antibodies obtained from immunisation, including those that recognise epitopes conserved between species, and can generate potentially useful cross-reactive antibodies.
Development of B-lymphocytes (B cells) is characterised by the ordered rearrangement of immunoglobulin variable region genes. After the VDJ rearrangement of heavy chain gene segments, a precursor B cell (pre-B cell) is generated. After the VJ rearrangement of light chain gene segments, pre-B cells develop into mature B cells bearing IgM on the cell surface where it can be presented to antigen. Assembled antibodies comprising heavy and light chains are transported to the B cell surface, while free heavy chains are retained in the endoplasmic reticulum (ER) in association with the 70 kDa heat shock protein chaperone BiP.
A critical step in B cell differentiation is the selective expansion of cells with a functional μ heavy chain resulting from productive rearrangement of heavy chain gene segments. This is achieved by the association of the μ heavy chain with surrogate light chain proteins λ5 and VpreB and a signal transducing heterodimer Igαβ to form a pre-B-cell receptor (pre-BCR). The surrogate light chain has the overall structure of a light chain but is a non-covalent heterodimer of VpreB (homologous to VL) and λ5 (homologous to CL). The N-terminal region of λ5 represents an extra 3 strand which is not part of the typical Ig domain, while the Ig domain in VpreB lacks one of the canonical p strands. Complementation of the incomplete Ig domain in VpreB by the extra p strand in λ5 is necessary and sufficient for the folding and assembly of these proteins to make the surrogate light chain[4]. λ5 can be disulphide bonded to μ heavy chains in pre-B cells. A high-resolution structure of a pre-BCR Fab-like fragment was published in 2007, showing that the unique regions of VpreB and λ5 interact with each other and with the heavy chain CDR3, potentially influencing selection of the antibody repertoire[5].
The surrogate light chain acts as a chaperone, displacing the ER-resident BiP from the CH1 domain and escorting the heavy chain μ to the cell surface together with Igαβ[6]. The expression and formation of the pre-BCR dramatically improves the efficiency of pre-B and B cell production, by signalling proliferative expansion of pre-B cells. The surface display of membrane-bound p chains is essential for the clonal expansion of these cells and their initiation of light chain gene rearrangement.
The surrogate light chain is then repressed while the light chain gene segments undergo rearrangement. The product of a successfully rearranged light chain gene will pair with the heavy chain to form a BCR with antigen-binding capability on the surface of immature B-cells. These cells migrate to the peripheral blood and secondary lymphoid organs, and develop into mature B cells ready for subsequent encounter with antigen[7]. Since expression of VpreB and λ5 is silenced after the pro- and pre-B cell stages, these proteins are not naturally present in B-lymphocytes.
In 1996, Papavasiliou, Jankovic and Nussenzweig[8] described evidence for the two pathways for induction of B cell development; one activated through surrogate light chain (λ5) and IgM and one through conventional light chain (κ or λ) and IgM. In the absence of κ and λ light chain expression in the mice under study, λ5 expression rescued surface display of IgM which delivered the signal for B cell development. Guloglu et al[9] also later reported that although heavy chains were not expressed in B cells of RAG/λ5 double knockout mice transfected with heavy chain DNA, they could be expressed on the mouse surface of B cells if co-transfected with either λ5 or a truncated λ5 excluding the N-terminal unique region preceding the λ5 immunoglobulin fold.
Using VpreB knockout mice, it has been shown that VpreB is required for efficient B cell development, particularly for the transition to pre-BCR bearing cells (pre-BII stage)[7, 10]. In HEK cells expressing a heavy chain mutant that did not require Igαβ for signalling, expression of a complete λ5 polypeptide without VpreB did not result in surface presentation of IgM. However, expression of truncated λ5 without VpreB did enable surface presentation of IgM. Indeed, surface presentation of IgM in cells expressing only the truncated λ5 surpassed surface presentation of IgM in cells expressing a full surrogate light chain (both VpreB and λ5). Surface presentation of IgM was even higher if Igκ light chain was expressed[11].
Co-expression of a shield domain with a polypeptide comprising a CH1 domain provides significant immunological advantages and greatly facilitates discovery of antibodies comprising unpaired variable domains. However, there are situations in which it is nevertheless still desirable to generate antibodies that comprise unpaired variable domains linked to constant regions bearing CH1 deletions. Where this is desired, it is best achieved after the antibodies have undergone affinity maturation (rather than having a CH1 deletion present in the pre-BCR). Accordingly, heavy chain constant regions present in class-switched antibodies may be selectively engineered to carry CH1 deletions.
The CH1 domain is optionally deleted from heavy chain constant region genes other than IgM, and retained in the μ constant region gene. IgM heavy chains may be expressed and combined with a shield domain of the present invention (e.g., λ5, or Cκ, from an engineered K locus as detailed elsewhere herein). A CH1-deleted non-mu heavy chain (e.g., IgG or IgA heavy chain) may then subsequently be expressed following class switching in the lymphocytes. In B-lymphocytes comprising this combination of genome modifications, the shield domain pairs with CH1 of the μ heavy chain to form IgM antibodies, and class-switching in the B-lymphocytes then generates heavy chain only antibodies having a heavy chain comprising an unpaired VH domain and a constant region lacking a CH1 domain, e.g., CH1-deleted IgG and CH1-deleted IgA. WO2013/171505 (Kymab Limited) described non-human animals expressing normal IgM antibodies and CH1-deleted IgG antibodies, where stage-specific class switching from IgM to IgG in lymphocytes was accompanied genetic deletion of CH1 from the IgG constant region, so that IgG heavy chain only antibodies were expressed. The methods and embodiments of WO2013/171505, incorporated herein by reference, may be employed in the present invention.
In one embodiment, the CH1-encoding region is deleted from the IgA constant region gene in the heavy chain locus of the non-human animal (e.g., humanised heavy chain locus in a transgenic animal). The CH1 domain is optionally deleted in the context of the complete human heavy chain locus inserted at the endogenous heavy chain locus of the non-human animal. IgA is highly abundant, and switching from IgG to IgA is frequently observed. Thus, selective CH1 deletion in the IgA isotype while retaining the full heavy chain in the IgM isotype will allow initial B cell development with complete heavy chains, which will undergo affinity maturation in the normal way, followed by isotype switching to IgA antibodies comprising heavy chains with a CH1 deletion. The antibodies may comprise the unpaired variable domain (e.g., VH domain) throughout this in vivo evolution, ensuring selection for repertoires of variable domains that are effective as single isolated antigen-binding domains.
An antibody according to the present invention may exhibit bispecific or multispecific antigen-binding. Thus, it may comprise first and second unpaired variable domains, wherein the first unpaired variable domain specifically binds a first antigen or epitope and the second unpaired variable domain specifically binds a second antigen or epitope. The first and second variable domains may have amino acid sequences that differ from one another, for binding to different first and second antigens/epitopes respectively. The different epitopes may be epitopes of one antigen or of different antigens. Thus, for example the first unpaired variable domain may specifically bind antigen A (and not antigen B) and the second unpaired variable domain may specifically bind antigen B (and not antigen A).
Just as the “heavy chain only” antibodies of the prior art were a format that was often chosen for bispecific and multispecific antibodies, so too the antibodies of the present invention also lend themselves to this purpose.
There are advantages to providing an antigen-binding site within an unpaired variable domain which is expressible as part of a single polypeptide chain, since a bispecific antibody can be generated through the association (e.g., following coexpression) of two such polypeptides comprising different variable domains (and thus different antigen-binding sites). This contrasts with the more complex generation of a typical four-chain bispecific antibody which comprises two different heavy:light chain pairs and thus 4 different polypeptide chains, which if expressed together could assemble into 10 different potential antibody molecules including homodimers (homodimeric anti-A binding arms and homodimeric anti-B binding arms), molecules in which one or both light chains are swapped between the H-L pairs, as well as the “correct” bispecific heterodimeric structure.
The antibody format of the present invention allows the antibody to be expressed as a relatively simple two-chain or three-chain molecule. This may be combined with design of the constant region to strongly favour assembly into the desired bispecific format.
“Knobs into holes” technology for making bispecific antibodies was described in [12] and in U.S. Pat. No. 5,731,168, both incorporated herein by reference. The principle is to engineer paired CH3 domains of heterodimeric heavy chains so that one CH3 domain contains a “knob” and the other CH3 domains contains a “hole” at a sterically opposite position. Knobs are created by replacing small amino acid side chain at the interface between the CH3 domains, while holes are created by replacing large side chains with smaller ones. The knob is designed to insert into the hole, to favour heterodimerisation of the different CH3 domains while destabilising homodimer formation. In in a mixture of antibody heavy and light chains that assemble to form a bispecific antibody, the proportion of IgG molecules having paired heterodimeric heavy chains is thus increased, raising yield and recovery of the active molecule
Mutations Y349C and/or T366W may be included to form “knobs” in an IgG CH3 domain. Mutations E356C, T366S, L368A and/or Y407V may be included to form “holes” in an IgG CH3 domain. Knobs and holes may be introduced into any human IgG CH3 domain, e.g., an IgG1, IgG2, IgG3 or IgG4 CH3 domain. A preferred example is IgG4. The IgG4 may include further modifications such as the “P” and/or “E” mutations. A “P” substitution at position 228 in the hinge (S228P) stabilises the hinge region of the heavy chain. An “E” substitution in the CH2 region at position 235 (L235S) abolishes binding to FcγR. A bispecific antibody of the present invention may contain an IgG4 PE human heavy chain constant region, optionally comprising two such paired constant regions, optionally wherein one has “knobs” mutations and one has “holes” mutations.
While knobs-into-holes technology involves engineering amino acid side chains to create complementary molecular shapes at the interface of the paired CH3 domains in the bispecific heterodimer, another way to promote heterodimer formation and hinder homodimer formation is to engineer the amino acid side chains to have opposite charges. Association of CH3 domains in the heavy chain heterodimers is favoured by the pairing of oppositely charged residues, while paired positive charges or paired negative charges would make homodimer formation less energetically favourable. WO2006/106905 described a method for producing a heteromultimer composed of more than one type of polypeptide (such a heterodimer of two different antibody heavy chains) comprising a substitution in an amino acid residue forming an interface between said polypeptides such that heteromultimer association will be regulated, the method comprising:
(a) modifying a nucleic acid encoding an amino acid residue forming the interface between polypeptides from the original nucleic acid, such that the association between polypeptides forming one or more multimers will be inhibited in a heteromultimer that may form two or more types of multimers;
(b) culturing host cells such that a nucleic acid sequence modified by step (a) is expressed; and
(c) recovering said heteromultimer from the host cell culture,
wherein the modification of step (a) is modifying the original nucleic acid so that one or more amino acid residues are substituted at the interface such that two or more amino acid residues, including the mutated residue(s), forming the interface will carry the same type of positive or negative charge.
An example of this is to suppress association between heavy chains by introducing electrostatic repulsion at the interface of the heavy chain homodimers, for example by modifying amino acid residues that contact each other at the interface of the CH3 domains, including:
positions 356 and 439
positions 357 and 370
positions 399 and 409,
the residue numbering being according to the EU numbering system.
By modifying one or more of these pairs of residues to have like charges (both positive or both negative) in the CH3 domain of a first heavy chain, the pairing of heavy chain homodimers is inhibited by electrostatic repulsion. By engineering the same pair or pairs of residues in the CH3 domain of a second (different) heavy chain to have an opposite charge compared with the corresponding residues in the first heavy chain, the heterodimeric pairing of the first and second heavy chains is promoted by electrostatic attraction.
In one example, amino acids at the heavy chain constant region CH3 interface are modified to introduce charge pairs, the mutations being listed in Table 1 of WO2006/106905. It was reported that modifying the amino acids at heavy chain positions 356, 357, 370, 399, 409 and 439 to introduce charge-induced molecular repulsion at the CH3 interface had the effect of increasing efficiency of formation of the intended bispecific antibody. WO2006/106905 also exemplified bispecific IgG antibodies in which the CH3 domains of IgG4 were engineered with knobs-into-holes mutations.
Further examples of charge pairs are disclosed in WO2013/157954, which described a method for producing a heterodimeric CH3 domain-comprising molecule from a single cell, the molecule comprising two CH3 domains capable of forming an interface. The method comprised providing in the cell
(a) a first nucleic acid molecule encoding a first CH3 domain-comprising polypeptide chain, this chain comprising a K residue at position 366 according to the EU numbering system and
(b) a second nucleic acid molecule encoding a second CH3 domain-comprising polypeptide chain, this chain comprising a D residue at position 351 according to the EU numbering system, the method further comprising the step of culturing the host cell, allowing expression of the two nucleic acid molecules and harvesting the heterodimeric CH3 domain-comprising molecule from the culture.
Further methods of engineering electrostatic interactions in polypeptide chains to promote heterodimer formation over homodimer formation were described in WO2011/143545.
Another example of engineering at the CH3-CH3 interface is strand-exchange engineered domain (SEED) CH3 heterodimers. The CH3 domains are composed of alternating segments of human IgA and IgG CH3 sequences, which form pairs of complementary SEED heterodimers referred to as “SEED-bodies” [13; WO2007/110205].
Bispecifics have also been produced with heterodimerised heavy chains that are differentially modified in the CH3 domain to alter their affinity for binding to a purification reagent such as Protein A. WO2010/151792 described a heterodimeric bispecific antigen-binding protein comprising
a first polypeptide comprising, from N-terminal to C-terminal, a first epitope-binding region that selectively binds a first epitope, an immunoglobulin constant region that comprises a first CH3 region of a human IgG selected from IgG1, IgG2, and IgG4; and
a second polypeptide comprising, from N-terminal to C-terminal, a second epitope-binding region that selectively binds a second epitope, an immunoglobulin constant region that comprises a second CH3 region of a human IgG selected from IgG1, IgG2, and IgG4, wherein the second CH3 region comprises a modification that reduces or eliminates binding of the second CH3 domain to Protein A.
Antibodies of the present invention may employ any of these techniques and molecular formats as desired.
Further aspects of the invention are the use of non-human animals described herein for producing antibodies comprising unpaired variable domains that specifically bind target antigens. An antibody comprising an unpaired variable domain may be produced by exposing a non-human animal as described herein to immunogenic stimulation with the target antigen.
A method of producing an antibody that binds a target antigen may comprise providing a non-human animal having a genome as described herein and
(a) immunising the animal with the target antigen (e.g., with cells expressing the antigen or with purified recombinant antigen);
(b) isolating antibodies generated by the animal;
(c) testing the antibodies for ability to bind the antigen; and
(d) selecting one or more antibodies that binds the antigen.
The non-human animal may be a knockout animal wherein endogenous expression of the target (e.g., of an orthologue of a human target antigen) has been inactivated.
A non-human animal as described herein can be challenged with the target antigen, and lymphatic cells (such as B cells) can then recovered from animals that express antibodies. The lymphatic cells may be 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 specific to the antigen of interest. Nucleic acid encoding the variable regions may be isolated and linked to desirable isotypic constant regions. Such an antibody may be produced in a cell, such as a CHO cell. Alternatively, nucleic acid encoding the variable domains may be isolated directly from lymphocytes.
Nucleic acid encoding an antibody heavy chain variable domain and/or an antibody light chain variable domain of a selected antibody may be isolated. Such nucleic acid may encode the full antibody heavy chain and/or light chain, or the variable domain without associated constant region. As noted, encoding nucleotide sequences may be obtained from lymphocytes.
Antibody discovery is made significantly easier by working with antibodies comprising unpaired variable domains (provided by either a heavy chain or a light chain) rather than paired antigen-binding domains (provided by heavy:light chain pairs) because the identification of correctly paired sequences is not required. Leading techniques of antibody discovery in vivo involve bulk sequencing of variable domains from B cells, which in a “classical” system generates vast numbers of VH and VL domain sequences for which it is strongly desirable to keep track of which VH domain sequence was paired with which VL domain sequence. Pairwise tracking can add an extra layer of complexity, e.g., requiring sorting of single cells into individual wells of a plate for analysis, so that VH and VL sequence information are co-identified from each cell. By contrast, where the variable domain sequence information is contained in a single VH or VL domain sequence per B cell, antibody sequences may conveniently be processed in bulk rather than as individual cells. Bulk sequencing of B cells of immunised animals may be performed with or without a step of antigen-specific cell sorting.
Optionally, once nucleic acid encoding the variable domain has been obtained it is conjugated to a nucleotide sequence encoding a desired constant region or other polypeptide domain(s) to provide nucleic acid encoding a polypeptide comprising an unpaired variable domain.
Where the immunised mammal produces chimaeric antibodies with non-human constant regions, these may be replaced with human constant regions to generate an antibody that will be less immunogenic when administered to humans as a medicament. Provision of particular human isotype constant regions is also significant for determining the effector function of the antibody, and a number of suitable heavy chain constant regions are discussed herein. Nucleic acid encoding the variable domain may alternatively be linked to non-antibody polypeptide domains e.g., to encode a CAR.
Other alterations to nucleic acid encoding the antibody heavy and/or light chain variable domain may be performed, such as mutation of residues and generation of variants. There are many reasons why it may be desirable to create variants, which include optimising the sequence for large-scale manufacturing, facilitating purification, enhancing stability or improving suitability for inclusion in a desired pharmaceutical formulation. Protein engineering work can be performed at one or more chosen residues in the sequence, e.g., to substituting one amino acid with an alternative amino acid (optionally, generating variants containing all naturally occurring amino acids at this position, with the possible exception of Cys and Met), and monitoring the impact on function and expression to determine the best substitution. It is in some instances undesirable to substitute a residue with Cys or Met, or to introduce these residues into a sequence, as to do so may generate difficulties in manufacturing—for instance through the formation of new intramolecular or intermolecular cysteine-cysteine bonds. Where a lead candidate has been selected and is being optimised for manufacturing and clinical development, it will generally be desirable to change its antigen-binding properties as little as possible, or at least to retain the affinity and potency of the parent molecule. However, variants may also be generated in order to modulate key antibody characteristics such as affinity, cross-reactivity or neutralising potency.
The isolated (optionally mutated) nucleic acid may be introduced into host cells, e.g., CHO cells. Host cells are then cultured under conditions for expression of a polypeptide comprising the variable domain.
The antibody may bind a cell-surface receptor, e.g., the extracellular domain of such a receptor. Cells expressing the antigen or a desired fragment thereof on their cell surface (e.g., cells transfected with nucleic acid encoding the antigen or fragment, and expressing that antigen or fragment at high level), may be used for immunisation.
Example categories of antigens include transmembrane receptors such as 7-pass transmembrane receptors, e.g., G-protein coupled receptors (GPCRs). A receptor may comprise an extracellular (EC) domain, a transmembrane domain and a cytosolic domain. It is common to target an EC domain of a receptor using an antibody, since the EC domain is more accessible to antibody that has been injected into a patient. Receptors of interest may bind ligands such as hormones, neurotransmitters, cytokines, growth factors, cell adhesion molecules, or nutrients. The target antigen may be an antigen of a pathogen, for generation of antibodies (and isolated unpaired variable domains) binding to the pathogen or to infected cells.
In many envisaged situations the target antigen is a human antigen.
Antibodies produced according to the present invention may bind a human antigen and a non-human orthologue of the antigen, e.g., may bind both human and rodent (e.g., mouse or rat) antigen. Antibodies generated by methods described herein may be tested to confirm specific binding to human and non-human animal target antigen. Cross-reactive antibodies can thus be selected, which may be screened for other desirable properties as described herein.
Methods of generating antibodies to an antigen (e.g., a human antigen), through immunisation of animals with the antigen where expression of the endogenous antigen (e.g., endogenous mouse antigen) has been knocked-out in the animal, may be performed in animals capable of generating antibodies comprising human variable domains. The genomes of such animals can be engineered to comprise a human or humanised immunoglobulin locus encoding human variable region gene segments, and optionally an endogenous constant region or a human constant region. Recombination of the human variable region gene segments generates human antibodies, which may have either a non-human or human constant region. Non-human constant regions may subsequently be replaced by human constant regions where the antibody is intended for in vivo use in humans. Such methods and knockout transgenic animals are described elsewhere herein and in WO2013/061078.
Isolated nucleic acid may be provided, encoding antibodies according to the present invention. Nucleic acid may be DNA and/or RNA. Genomic DNA, cDNA, mRNA or other RNA, of synthetic origin, or any combination thereof can encode an antibody.
The present invention provides constructs in the form of plasmids, vectors, transcription or expression cassettes which comprise at least one polynucleotide as above. Exemplary nucleotide sequences are included in the sequence listing. Reference to a nucleotide sequence as set out herein encompasses a DNA molecule with the specified sequence, and encompasses an RNA molecule with the specified sequence in which U is substituted for T, unless context requires otherwise.
The present invention also provides a recombinant host cell that comprises one or more nucleic acids encoding the antibody. Methods of producing the encoded antibody may comprise expression from the nucleic acid, e.g., by culturing recombinant host cells containing the nucleic acid. The antibody may thus be obtained, and may be isolated and/or purified using any suitable technique, then used as appropriate. A method of production may comprise formulating the product into a composition including at least one additional component, such as a pharmaceutically acceptable excipient.
Systems for cloning and expression of a polypeptide in a variety of different host cells are well known. Suitable host cells include bacteria, mammalian cells, plant cells, filamentous fungi, yeast and baculovirus systems and transgenic plants and animals.
The expression of antibodies and antibody fragments in prokaryotic cells is well established in the art. A common bacterial host is E co/i. Expression in eukaryotic cells in culture is also available to those skilled in the art as an option for production. Mammalian cell lines available in the art for expression of a heterologous polypeptide include Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney cells, NSO mouse melanoma cells, YB2/0 rat myeloma cells, human embryonic kidney cells, human embryonic retina cells and many others.
Vectors may contain appropriate regulatory sequences, including promoter sequences, terminator sequences, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. Nucleic acid encoding an antibody can be introduced into a host cell. Nucleic acid can be introduced to eukaryotic cells by various methods, including calcium phosphate transfection, DEAE-Dextran, electroporation, liposome-mediated transfection and transduction using retrovirus or other virus, e.g. vaccinia or, for insect cells, baculovirus. Introducing nucleic acid in the host cell, in particular a eukaryotic cell may use a viral or a plasmid-based system. The plasmid system may be maintained episomally or may be incorporated into the host cell or into an artificial chromosome. Incorporation may be either by random or targeted integration of one or more copies at single or multiple loci. For bacterial cells, suitable techniques include calcium chloride transformation, electroporation and transfection using bacteriophage. The introduction may be followed by expressing the nucleic acid, e.g., by culturing host cells under conditions for expression of the gene, then optionally isolating or purifying the antibody.
Nucleic acids of the invention may be integrated into the genome (e.g. chromosome) of the host cell. Integration may be promoted by inclusion of sequences that promote recombination with the genome, in accordance with standard techniques.
The present invention also provides a method that comprises using nucleic acid described herein in an expression system in order to express an antibody.
Antibodies and their encoding nucleic acid according to the present invention may be provided in isolated form and/or in solution, e.g., aqueous solution.
The invention further provides a composition (eg, a pharmaceutical composition or a composition for medical use) comprising an antibody, bispecific antibody, polypeptide, antibody heavy or light chain, VH domain, VL domain or nucleotide sequence thereof obtained or obtainable by a method of the invention as disclosed herein.
Antibodies may be monoclonal or polyclonal, but are preferably provided as monoclonal antibodies for therapeutic use. They may be provided as part of a mixture of other antibodies, optionally including antibodies of different binding specificity.
Antibodies according to the invention, and encoding nucleic acids, will usually be provided in isolated form. Thus, the antibodies, VH and/or VL domains, and nucleic acids may be provided purified from their natural environment or their production environment. Isolated antibodies and isolated nucleic acid will be free or substantially free of material with which they are naturally associated, such as other polypeptides or nucleic acids with which they are found in vivo, or the environment in which they are prepared (e.g., cell culture) when such preparation is by recombinant DNA technology in vitro. Optionally, an isolated antibody or nucleic acid (1) is free of at least some other proteins with which it would normally be found, (2) is essentially free of other proteins from the same source, e.g., from the same species, (3) is expressed by a cell from a different species, (4) has been separated from at least about 50 percent of polynucleotides, lipids, carbohydrates, or other materials with which it is associated in nature, (5) is operably associated (by covalent or noncovalent interaction) with a polypeptide with which it is not associated in nature, or (6) does not occur in nature.
Antibodies or nucleic acids may be formulated with diluents or adjuvants and still for practical purposes be isolated—for example they may be mixed with carriers if used to coat microtitre plates for use in immunoassays, and may be mixed with pharmaceutically acceptable carriers or diluents when used in therapy. As described elsewhere herein, other active ingredients may also be included in therapeutic preparations. Antibodies may be glycosylated, either naturally in vivo or by systems of heterologous eukaryotic cells such as CHO cells, or they may be (for example if produced by expression in a prokaryotic cell) unglycosylated. The invention encompasses antibodies having a modified glycosylation pattern. In some applications, modification to remove undesirable glycosylation sites may be useful, or e.g., removal of a fucose moiety to increase ADCC function [14]. In other applications, modification of galactosylation can be made in order to modify CDC.
Typically, an isolated product constitutes at least about 5%, at least about 10%, at least about 25%, or at least about 50% of a given sample. An antibody may be substantially free from proteins or polypeptides or other contaminants that are found in its natural or production environment that would interfere with its therapeutic, diagnostic, prophylactic, research or other use.
An antibody may have been identified, separated and/or recovered from a component of its production environment (e.g., naturally or recombinantly). The isolated antibody may be free of association with all other components from its production environment, eg, so that the antibody has been isolated to an FDA-approvable or approved standard. Contaminant components of its production environment, such as that resulting from recombinant transfected cells, are materials that would typically interfere with research, diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In some embodiments, the antibody will be purified: (1) to greater than 95% by weight of antibody as determined by, for example, the Lowry method, and in some embodiments, to greater than 99% by weight; (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or silver stain. Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, an isolated antibody or its encoding nucleic acid will be prepared by at least one purification step.
The polypeptides comprising unpaired variable domains (e.g., antibodies), or their encoding nucleic acids, may be formulated for the desired route of administration to a patient, e.g., in liquid (optionally aqueous solution) for injection. Compositions may comprise a polypeptide or nucleic acid in combination with medical injection buffer and/or with adjuvant. Various delivery systems are known and can be used to administer the pharmaceutical composition of the invention. Methods of introduction include, but are not limited to, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral routes.
The composition may comprise a diluent, excipient or carrier. When the composition is a pharmaceutical composition or a composition for medical use, the diluent, excipient or carrier is pharmaceutically acceptable. “Pharmaceutically acceptable” refers to approved or approvable by a regulatory agency of the USA Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, including humans. A “pharmaceutically acceptable carrier, excipient, or adjuvant” refers to a carrier, excipient, or adjuvant that can be administered to a subject, together with an agent, e.g., any antibody, VL or antibody chain described herein, and which does not destroy the pharmacological activity thereof and is nontoxic when administered in doses sufficient to deliver a therapeutic amount of the agent.
Compositions comprising polypeptides or nucleic acids described herein may be contained in a sterile container in vitro. A composition may be in a bag or other medical container connected to an IV syringe. It may be within a phial, syringe or an injection device. In an example, a kit is provided comprising the antibody, polypeptide or nucleic acid, plus packaging and instructions for use in a therapeutic method as described herein.
The invention provides therapeutic compositions comprising polypeptides comprising unpaired variable domains as described herein. Therapeutic compositions comprising nucleic acid encoding such polypeptides are also provided. Encoding nucleic acids are described in more detail elsewhere herein and include DNA and RNA, e.g., mRNA. In therapeutic methods described herein, use of nucleic acid encoding the antibody, and/or of cells containing such nucleic acid, may be used as alternatives (or in addition) to compositions comprising the antibody itself. Cells (e.g., human cells, e.g., human lymphocytes) containing nucleic acid encoding the antibody, optionally wherein the nucleic acid is stably integrated into the genome, thus represent medicaments for therapeutic use in a patient. Cells expressing CARs, e.g., CAR-T cells, are an example. Alternatively, nucleic acid encoding an antibody of the present invention may be introduced into human B lymphocytes, optionally B lymphocytes derived from the intended patient and modified ex vivo. Optionally, memory B cells are used. Administration of cells containing the encoding nucleic acid to the patient provides a reservoir of cells capable of expressing the antibody, which may provide therapeutic benefit over a longer term compared with administration of isolated nucleic acid or isolated antibody.
Antibodies and non-human animals according to the present invention represent a source of unpaired antigen-binding variable domains which may be incorporated into a variety of modular molecular designs, one of which is the chimaeric antigen receptor (CAR). A CAR comprises an antigen-binding moiety fused to a T-cell activating moiety, typically in a transmembrane receptor which also includes a cytosolic T-cell activating domain. CAR-T structures comprising VH domains for binding target antigen have been described [15, 16].
Thus, an unpaired variable domain may be linked to a T-cell activating moiety to provide a CAR. Optionally a T-lymphocyte is engineered to express the CAR on its surface. CARs and cells are preferably human.
It may be desirable to engineer CAR-T cells to express IL-7 and CCL19 as these factors have been reported to be important for the maintenance of T cell zones in lymphoid organs [17].
Following construction of nucleic acid encoding a human CAR using an unpaired variable domain produced as described herein, it may be transfected into human T cells and/or integrated into a T cell genome. Activity of a CAR may be assessed e.g., by introducing CAR-T cells into animals bearing syngenic tumours and/or human cell lines and observing effects on the target cells.
Unless otherwise specified herein or the context does not allow, any unpaired variable domain herein may be a VH (heavy chain variable domain, eg, a human, dog, cat, horse, fish or bird VH domain), VHH (e.g., Camelid variable domain with or without humanisation) or VL (light chain variable domain, such as a kappa or lambda VL, e.g., a human, dog, cat, horse, fish or bird VL domain),
Unless otherwise specified herein or the context does not allow, any unpaired variable domain may be a human, humanised, chimaeric (e.g., mouse-human or rat-human chimaeric), rodent (e.g., mouse or rat), dog, cat, horse, fish or bird variable domain.
Unless otherwise specified herein or the context does not allow, any inserted DNA (e.g., human variable region DNA in a heavy chain locus) and/or shield domain-encoding DNA may be human, humanised, chimaeric (e.g., mouse-human or rat-human chimaeric), rodent (e.g., mouse or rat), dog, cat, horse, fish or bird DNA, preferably human DNA. For example, any heavy chain locus herein may comprise one or more variable region gene segments disclosed in Table C(a), or may comprise at least 50%, 60% or 90% of such gene segments, or may comprise all of such gene segments.
An example shield domain is a CK encoded by the gene segment shown in Table C(b).
An example of a suitable antigen (eg, an antigen with which an animal of the invention is immunised or to which an antibody or variable domain of the invention binds) is selected from the group consisting of ABCF1; ACVR1; ACVR1B; ACVR2; ACVR2B; ACVRL1; ADORA2A; Aggrecan; AGR2; AICDA; AWI; AIG1; AKAP1; AKAP2; AIYIH; AMHR2; ANGPT1; ANGPT2; ANGPTL3; ANGPTL4; ANPEP; APC; APOC1; AR; AZGP1 (zinc-a-glycoprotein); B7.1; B7.2; BAD; BAFF; BAG1; BA11; BCL2; BCL6; BDNF; BLNK; BLR1 (MDR15); B1yS; BMP1; BMP2; BMP3B (GDF10); BMP4; BMP6; BMP8; BMPR1A; BMPR1B; BMPR2; BPAG1 (plectin); BRCA1; Cl9orflO (IL27w); C3; C4A; C5; C5R1; CANT1; CASP1; CASP4; CAV1; CCBP2 (D6/JAB61); CCL1 (1-309); CCL11 (eotaxin); CCL13 (MCP-4); CCL15 (MIP-id); CCL16 (HCC-4); CCL17 (TARC); CCL18 (PARC); CCL19 (MIP-3b); CCL2 (MCP-1); MCAF; CCL20 (MIP-3a); CCL21 (MIP-2); SLC; exodus-2; CCL22 (MDC/STC-1); CCL23 (MPIF-1); CCL24 (MPIF-2 I eotaxin-2); CCL25 (TECK); CCL26 (eotaxin-3); CCL27 (CTACK/ILC); CCL28; CCL3 (MIP-1a); CCL4 (MIP-1b); CCL5 (RANTES); CCL7 (MCP-3); CCL8 (mcp-2); CCNA1; CCNA2; CCND1; CCNE1; CCNE2; CCR1 (CKR1/HM145); CCR2 (mcp-1 RB/RA); CCR3 (CKR3/CMKBR3); CCR4; CCR5 (CMKBR5/ChemR13); CCR6 (CMKBR6/CKR-L3/STRL22/DRY6); CCR7 (CKR7/EBI1); CCR8 (CMKBR8/TER1/CKR-L1); CCR9 (GPR-9-6); CCRL1 (VSHK1); CCRL2 (L-CCR); CD164; CD19; CD1C; CD20; CD200; CD-22; CD24; CD28; CD3; CD37; CD38; CD3E; CD3G; CD3Z; CD4; CD40; CD40L; CD44; CD45RB; CD52; CD69; CD72; CD74; CD79A; CD79B; CD8; CD80; CD81; CD83; CD86; CDH1 (E-cadherin); CDH10; CDH12; CDH13; CDH18; CDH19; CDH20; CDH5; CDH7; CDH8; CDH9; CDK2; CDK3; CDK4; CDK5; CDK6; CDK7; CDK9; CDKN1A (p21Wap1/Cip1); CDKN1B (p27Kip1); CDKNIC; CDKN2A (p161NK4a); CDKN2B; CDKN2C; CDKN3; CEBPB; CER1; CHGA; CHGB; Chitinase; CHST10; CKLFSF2; CKLFSF3; CKLFSF4; CKLFSF5; CKLFSF6; CKLFSF7; CKLFSF8; CLDN3; CLDN7 (claudin-7); CLN3; CLU (clusterin); CMKLR1; CMKOR1 (RDC1); CNR1; COL18A1; COL1A1; COL4A3; COL6A1; CR2; CRP; CSF1 (M-CSF); CSF2 (GM-CSF); CSF3 (GCSF); CTLA4; CTNNB1 (b-catenin); CTSB (cathepsin B); CX3CL1 (SCYDi); CX3CR1 (V28); CXCL1 (GRO1); CXCL10 (IP-10); CXCL11 (I-TAC/IP-9); CXCL12 (SDF1); CXCL13; CXCL14; CXCL16; CXCL2 (GRO2); CXCL3 (GRO3); CXCL5 (ENA-78 I LIX); CXCL6 (GCP-2); CXCL9 (MIG); CXCR3 (GPR9/CKR-L2); CXCR4; CXCR6 (TYMSTR ISTRL33 I Bonzo); CYB5; CYC1; CYSLTR1; DAB21P; DES; DKFZp451J0118; DNCL1; DPP4; E2F1; ECGF1; EDG1; EFNAI; EFNA3; EFNB2; EGF; EGFR; ELAC2; ENG; ENO1; ENO2; ENO3; EPHB4; EPO; ERBB2 (Her-2); EREG; ERK8; ESR1; ESR2; F3 (TF); FADD; FasL; FASN; FCER1A; FCER2; FCGR3A; FGF; FGF1 (aFGF); FGF10; FGF11; FGF12; FGF12B; FGF13; FGF14; FGF16; FGF17; FGF18; FGF19; FGF2 (bFGF); FGF2O; FGF21; FGF22; FGF23; FGF3 (int-2); FGF4 (HST); FGF5; FGF6 (HST-2); FGF7 (KGF); FGF8; FGF9; FGFR3; FIGF (VEGFD); FILL (EPSILON); FILL (ZETA); FLJ12584; FLJ25530; FLRT1 (fibronectin); FLT1; FOS; FOSL1 (FRA-1); FY (DARC); GABRP (GABAa); GAGEBI; GAGEC1; GALNAC4S-65T; GATA3; GDF5; GFI1; GGT1; GM-CSF; GNAS1; GNRH1; GPR2 (CCR1O); GPR31; GPR44; GPR81 (FKSG80); GRCC10 (C10); GRP; GSN (Gelsolin); GSTP1; HAVCR2; HDAC4; EDAC5; HDAC7A; HDAC9; HGF; HIF1A; HIP1; histamine and histamine receptors; HLA-A; HLA-DRA; HM74; HMOX1; HUMCYT2A; ICEBERG; ICOSL; 1D2; IFN-a; IFNA1; IFNA2; IFNA4; IFNA5; IFNA6; IFNA7; IFNB1; I FNgamma; TFNW1; IGBP1; IGF1; IGF1R; IGF2; IGFBP2; I GFBP3; IGFBP6; IL-1; IL10; IL10RA; IL10RB; IL11; IL11RA; IL-12; IL12A; IL12B; IL12RB1; IL12RB2; 1L13; IL13RA1; IL13RA2; 1L14; 1115; IL15RA; IL16; 1L17; IL17B; IL17C; IL17R; 1L18; IL18BP; IL18R1; IL18RAP; 1L19; IL1A; IL1B; IL1F1O; IL1F5; IL1F6; IL1F7; IL1F8; IL1F9; IL1HY1; IL1R1; IL1R2; ILiRAP; IL1RAPL1; IL1RAPL2; IL1RL1; IL1RL2 IL1RN; 1L2; 1L20; IL20RA; IL21R; 1L22; 1L22R; 1L22RA2; IL23; 1L24; 1L25; 1L26; 1L27; 1L28A; 1L28B; 1L29; IL2RA; IL2RB; IL2RG; 1L3; 1L30; IL3RA; 1L4; IL4R; 1L5; IL5RA; 1L6; IL6R; IL6ST (glycoprotein 130); 1L7; TL7R; 1L8; IL8RA; IL8RB; IL8RB; 1L9; IL9R; ILK; INHA; INHBA; INSL3; INSL4; IRAK1; IRAK2; ITGA1; ITGA2; ITGA3; ITGA6 (a6 integrin); ITGAV; ITGB3; ITGB4 (b 4 integrin); JAG1; JAK1; JAK3; JUN; K6HF; KAI1; KDR; MTLG; KLF5 (GC Box BP); KLF6; KLK10; KLK12; KLK13; KLK14; KLK15; KLK3; KLK4; KLK5; KLK6; KLK9; KRT1; KRT19 (Keratin 19); KRT2A; KRTHB6 (hair-specific type II keratin); LAMA5; LEP (leptin); Lingo-p75; Lingo-Troy; LPS; LTA (TNF-b); LTB; LTB4R (GPR16); LTB4R2; LTBR; MACMARCKS; MAG or Omgp; MAP2K7 (c-Jun); MDK; MIB1; midkine; MIF; MIP-2; MK167 (Ki-67); MMP2; MMP9; MS4A1; MSMB; MT3 (metallothionectin-ifi); MTSS 1; MUC 1 (mucin); MYC; MYD88; NCK2; neurocan; NFKB 1; NFKB2; NGFB (NGF); NGFR; NgR-Lingo; NgR-Nogo66 (Nogo); NgR-p75; NgR-Troy; NME1 (NM23A); NOX5; NPPB; NROB1; NROB2; NR1D1; NR1D2; NR1H2; NR1H3; NR1H4; NR112; NR113; NR2C1; NR2C2; NR2E1; NR2E3; NR2F1; NR2F2; NR2F6; NR3C1; NR3C2; NR4A1; NR4A2; NR4A3; NR5A1; NR5A2; NR6A1; NRP1; NRP2; NT5E; NTN4; ODZ1; OPRD1; P2RX7; PAP; PART1; PATE; PAWR; PCA3; PCNA; PDGFA; PDGFB; PECAMi; PF4 (CXCL4); PGF; PGR; phosphacan; PIAS2; PIK3CG; PLAU (uPA); PLG; PLXDC1; PPBP (CXCL7); PPI D; PR1; PRKCQ; PRKD1; PRL; PROC; PROK2; PSAP; PSCA; PTAFR; PTEN; PTGS2 (COX-2); PTN; RAC2 (p21Rac2); RARB; RGS1; RGS13; RGS3; RNF110 (ZNF144); ROBO2; S100A2; SCGB1D2 (lipophilin B); SCGB2A1 (mammaglobin 2); SCGB2A2 (mammaglobin 1); SCYE1 (endothelial Monocyte-activating cytokine); SDF2; SERPINA1; SERPINIA3; SERPINB5 (maspin); SERPINE1 (PAT-i); SERPINF1; SHBG; SLA2; SLC2A2; SLC33A1; SLC43A1; SLIT2; SPP1; SPRR1B (Spri); ST6GAL1; STAB1; STAT6; STEAP; STEAP2; TB4R2; TBX21; TCP10; TDGF1; TEK; TGFA; TGFB1; TGFB1 11; TGFB2; TGFB3; TGFBI; TGFBR1; TGFBR2; TGFBR3; TH1 L; THBS1 (thrombospondin-1); THBS2; THBS4; THPO; TIE (Tie-i); T]MP3; tissue factor; TLR10; TLR2; TLR3; TLR4; TLR5; TLR6; TLR7; TLR8; TLR9; TNF; TNF-α; TNFAIP2 (B94); TNFAIP3; TNFRSF1 1A; TNFRSF1A; TNFRSF1B; TNFRSF21; TNFRSF5; TNFRSF6 (Fas); TNFRSF7; TNFRSF8; TNFRSF9; TNFSF1O (TRAIL); TNFSF1 1 (TRANCE); TNFSF12 (APO3L); TNFSF13 (April); TNFSF13B; TNFSF14 (HVEM-L); TNFSF1 5 (VEGI); TNFSF1 8; TNFSF4 (OX40 ligand); TNFSF5 (CD40 ligand); TNFSF6 (FasL); TNFSF7 (CD27 ligand); TNFSF8 (CD30 ligand); TNFSF9 (4-1BB ligand); TOLLIP; Toll-like receptors; TOP2A (topoisomerase lia); TP53; TPM1; TPM2; TRADD; TRAF1; TRAF2; TRAF3; TRAF4; TRAF5; TRAF6; TREM1; TREM2; TRPC6; TSLP; TWEAK; VEGF; VEGFB; VEGFC; versican; VHL C5; VLA-4; XCL1 (lymphotactin); XCL2 (SCM-Ib); XCR1 (GPR5/CCXCR1); YY1; and ZFPM2.
For example the antigen is selected from the following list (e.g., wherein the antibody or variable domain is for administration to a human or animal subject for treating a cancer or autoimmune condition): immune checkpoint inhibitors (such as PD-L1, PD-1, CTLA-4, TIGIT, TIM-3, LAG-3 and VISTA, e.g. TIGIT, TIM-3 and LAG-3), immune modulators (such as BTLA, hHVEM, CSF1R, CCR4, CD39, CD40, CD73, CD96, CXCR2, CXCR4, CD200, GARP, SIRPα, CXCL9, CXCL10, CXCL11 and CD155, e.g. GARP, SIRPα, CXCR4, BTLA, hVEM and CSF1R), immune activators (such as CD137, GITR, OX40, CD40, CXCR3 (e.g. agonistic anti-CXCR3 antibodies), CD27, CD3, ICOS (e.g. agonistic anti-ICOS antibodies), for example. ICOS, CD137, GITR and OX40).
In an example, a λ5 shield domain herein comprises or consists of an amino acid sequence encoded by SEQ ID NO: 77.
In an example herein, an animal of the invention comprises a light chain locus (a kappa or lambda locus) that comprises SEQ ID NO: 77, 78, 81, 83, 85, 87, 89, 91, 93 or 100.
In an example herein, an animal of the invention expresses SEQ ID NO: 82, 84, 86, 88 90 or 101.
In an example, the animal of the invention comprises a kappa light chain locus (in heterozygous or homozygous state) as herein described. Optionally, the locus comprises a deletion between an endogenous Vκ gene and an endogenous Jκ gene, but retaining the Vκ exon 1 plus endogenous splice junctions at the 5′ end of the Vκ exon 2 and the 3′ end of the J. In another example, the animal of the invention comprises a replacement of endogenous Jκ genes with a targeting vector encoding a variable region promoter, leader (exon 1, intron, partial exon 2) of a mouse or human Vκ plus a fragment of a Jκ retaining endogenous splice junctions at the 5′ end of the Vκ exon 2 and the 3′ end of the J. The result of either of these strategies is a locus that expresses a transcript, under endogenous or human Vκ promoter control, that is spliced to generate a Cκ with a Vκ leader sequence and partial J sequence. This strategy can utilise any Vκ and J of the mouse Kappa repertoire. For strategy one, we will use Vκ3-2 or Vκ3-4 with Jκ5. The reason for this is that Vκ3-2 or Vκ3-4 are close to the 3′ end of the locus, reducing the size of deletion required, plus have been shown in literature to have a fairly high frequency of usage in the mice. See
In an example, all non-coding and regulatory elements in the modified locus are endogenous. For a modified kappa locus, this includes the specific promoter for the Vκ/Jκ/Cκ fragment, the endogenous κ intronic enhancer (located between Jκ5 and Cκ) and the endogenous κ 3′ enhancer. Interaction of these endogenous promoters/enhancers with the endogenous (eg, mouse) effectors involved in expression from the κ locus is likely to be more effective than that of endogenous effectors with the human regulatory sequences, thus potentially resulting a more active locus.
The following numbered clauses, setting out embodiments of the present invention, are part of the description.
1. A composition comprising an isolated antibody in solution, the antibody comprising an unpaired variable domain for binding a target antigen, wherein the unpaired variable domain is linked to a constant region, wherein the constant region comprises a CH1 domain and a shield domain which binds the CH1 domain.
2. A composition according to clause 1, wherein the unpaired variable domain is linked to the CH1 domain of the constant region.
3. A composition comprising
a first polypeptide comprising a human variable domain and a CH1 domain, and
a second polypeptide comprising a shield domain which pairs with said CH1 domain, wherein the second polypeptide lacks a variable domain, thereby leaving the variable domain of the first polypeptide unpaired.
4. A composition according to clause 3, wherein the first polypeptide is an immunoglobulin heavy chain comprising VH-CH1-CH2-CH3.
5. A composition according to clause 3 or clause 4, wherein the second polypeptide consists of the shield domain.
6. A composition according to any of clauses 1 to 5, wherein the shield domain is a CL domain.
7. A composition according to clause 6, wherein the CL is Cκ.
8. A composition according to clause 6, wherein the CL is Cλ.
9. A composition according to any of clauses 1 to 5, wherein the shield domain is a λ5 immunoglobulin domain.
10. A composition according to any preceding clause, comprising an Fc region.
11. A composition according to any preceding clause wherein the unpaired variable domain is a VH domain.
12. A composition according to any preceding clause, which is a four-chain antibody comprising two of said unpaired variable domains.
13. A composition comprising an isolated antibody in solution, the antibody comprising two first polypeptides and two second polypeptides, wherein
each first polypeptide comprises a human variable domain and a CH1 domain, and
each second polypeptide comprises a shield domain which pairs with the CH1 domain of the first polypeptide, wherein
one or both of said second polypeptides lacks a variable domain, thereby leaving one or both variable domains of the first polypeptide unpaired.
14. A composition according to clause 13, wherein the variable domains of both first polypeptides are unpaired variable domains.
15. A composition according to clause 13 or clause 14, each said first polypeptide comprises a VH domain.
16. A composition according to any of clauses 13 to 15, wherein each said first polypeptide comprises VH-CH1-CH2-CH3.
17. A composition according to any of clauses 13 to 16, wherein the two first polypeptides are identical.
18. A composition according to any of clauses 13 to 17, wherein the two second polypeptides are identical.
19. A composition according to any of clauses 13 to 18, wherein each said second polypeptide consists of the shield domain.
20. A composition according to any of clauses 13 to 19, wherein the shield domain is a CL domain.
21. A composition according to clause 20, wherein the CL is Cκ.
22. A composition according to clause 20, wherein the CL is Cλ.
23. A composition according to any of clauses 13 to 19, wherein the shield domain is a λ5 immunoglobulin domain.
24. An antibody comprising a heavy chain and a light chain, wherein
the heavy chain comprises an unpaired human VH domain for binding a target antigen and a heavy chain constant region comprising a CH1 domain, and wherein
the light chain comprises a CL domain, wherein the light chain lacks a VL domain, thereby leaving the VH domain unpaired.
25. An antibody according to clause 24, comprising two heavy chains and two light chains,
each heavy chain comprising a human VH domain and a heavy chain constant region comprising a CH1 domain, and
each light chain comprising a CL domain, wherein
one or both light chains lack a VL domain, thereby leaving one or both VH domains unpaired.
26. An antibody according to clause 25, comprising two heavy chains and two light chains, wherein
each heavy chain comprises an unpaired human VH domain for binding a target antigen, and a heavy chain constant region comprising a CH1 domain, and wherein
each light chain comprises a CL domain, wherein the light chain lacks a VL domain.
27. An antibody according to clause 26, wherein the two unpaired VH domains bind the same antigen or epitope.
28. An antibody according to clause 26 or clause 27, wherein the two unpaired VH domains are identical in amino acid sequence.
29. An antibody according to any of clauses 25 to 28, wherein the two first polypeptides are identical in sequence and/or wherein the two second polypeptides are identical in sequence.
30. An antibody according to any of clauses 24 to 29, wherein the heavy chain constant region comprises the CH1 domain and one or more further CH domains.
31. An antibody according to clause 30, wherein the heavy chain constant region comprises a CH2 domain and a CH3 domain.
32. An antibody according to any of clauses 24 to 31, wherein the CL is Cκ.
33. An antibody according to any of clauses 24 to 28, wherein the CL is Cλ.
34. An antibody according to any of clauses 24 to 33, wherein the light chain consists of the CL domain.
35. An antibody according to any of clauses 24 to 34, wherein the heavy chain constant region is a human heavy chain constant region.
36. An antibody according to any of clauses 24 to 35, wherein the CL is human Cκ or human Cλ.
37. An antibody according to clause 36, wherein the CL comprises human Cκ sequence SEQ ID NO: 4.
38. An antibody according to clause 37, wherein the CL consists of human Cκ sequence SEQ ID NO: 4.
39. A composition according to any of clauses 1 to 23 or an antibody according to any of clauses 24 to 38, wherein the antibody is an IgG.
40. An antibody according to any of clauses 24 to 38, wherein the antibody is an IgM.
41. A composition or an antibody according to any preceding clause, wherein the antibody is a fully human antibody.
43. A composition or an antibody according to any preceding clause, wherein the unpaired variable domain binds a human antigen.
43. A composition or an antibody according to any preceding clause, wherein the unpaired variable domain binds an extracellular domain of a receptor.
44. Nucleic acid encoding an antibody as defined in any preceding clause or a polypeptide or unpaired variable domain thereof.
45. Nucleic acid according to clause 44, comprising nucleotide sequences encoding
a heavy chain comprising a human VH domain for binding a target antigen and a heavy chain constant region comprising a CH1 domain, and
a light chain comprising a CL domain, wherein the light chain lacks a variable domain.
46. Nucleic acid according to clause 45, wherein the light chain comprises a signal peptide fused to a Cκ constant domain.
47. Nucleic acid according to clause 46, wherein the light chain comprises SEQ ID NO: 6.
48. Nucleic acid according to clause 47, comprising a nucleotide sequence SEQ ID NO: 5 encoding the light chain.
49. A non-human animal, or cell thereof, whose genome comprises nucleic acid according to any of clauses 44 to 48.
50. A non-human animal comprising B-lymphocytes expressing an antibody as defined in any of clauses 1 to 43.
51. An animal according to clause 50 wherein, upon immunogenic stimulation, at least 50% of antibody-expressing B-lymphocytes in the animal express an antibody according to any of clauses 1 to 43.
52. An animal according to clause 50 or clause 51, wherein the B-lymphocytes lack functional expression of light chains comprising a VL domain.
53. A non-human animal cell having a genome comprising
a plurality of human variable region gene segments capable of rearrangement to encode a variable domain, upstream of DNA encoding an immunoglobulin constant region comprising a CH1 domain, and
a gene encoding a CL domain which lacks functional expression of variable region gene segments, or a gene encoding the immunoglobulin domain of λ5.
54. A non-human animal comprising B-lymphocytes expressing an antibody comprising an unpaired human VH domain for binding antigen, wherein the genome of the animal comprises
a plurality of human variable region gene segments capable of rearrangement to encode a variable domain, upstream of DNA encoding an immunoglobulin constant region comprising a CH1 domain, and
a gene encoding a CL domain which lacks functional expression of variable region gene segments, or a gene encoding the immunoglobulin domain of λ5.
A λ5 immunoglobulin domain may be a human, rodent, mouse, rat, rabbit or mammalian, vertebrate domain. It may be a domain that has a truncation as described herein.
55. A method of generating a non-human animal comprising B-lymphocytes expressing an antibody comprising an unpaired human VH domain for binding antigen, comprising
engineering the genome of a non-human animal cell to comprise
a plurality of human variable region gene segments capable of rearrangement to encode a variable domain, upstream of DNA encoding an immunoglobulin constant region comprising a CH1 domain, and
a gene encoding a CL domain which lacks functional expression of variable region gene segments, or a gene encoding the immunoglobulin domain of λ5, and
generating an animal from said cell or from a group of cells comprising said cell.
56. A cell according to clause 53 or a method according to clause 55, wherein the cell is an embryonic stem cell or a zygote.
57. An animal, cell or method according to any of clauses 53 to 56, wherein the plurality of variable region gene segments comprises one or more V gene segments, one or more D gene segments and one or more J gene segments capable of rearrangement to encode a VH domain.
58. An animal, cell or method according to clause 57, wherein the one or more V gene segments, one or more D gene segments and one or more J gene segments comprise multiple human V gene segments, multiple human D gene segments and multiple human J gene segments.
59. An animal, cell or method according to any of clauses 53 to 58, wherein the plurality of variable region gene segments are at the endogenous immunoglobulin heavy chain locus of the animal.
60. An animal, cell or method according to any of clauses 53 to 59, wherein the CL domain is a human CL domain.
61. An animal, cell or method according to clause 60, wherein the human CL domain is human Cκ.
62. An animal, cell or method according to any of clauses 53 to 61, wherein the gene encoding the CL domain comprises an exon encoding a light chain variable region leader sequence and an exon encoding the CL domain, separated by an intron comprising a J-C intron enhancer element, wherein the encoded CL domain comprises an N-terminal signal peptide.
63. An animal, cell or method according to clause 62, wherein the gene encoding the CL domain comprises an exon encoding a human Vκ leader sequence and an exon encoding a human Cκ domain, separated by an intron comprising a human J-Cκ intron enhancer element, wherein the encoded CL domain is a human Cκ domain comprising an N-terminal signal peptide.
64. An animal, cell or method according to clause 63, wherein the human Cκ domain comprises SEQ ID NO: 4 or SEQ ID NO: 6.
65. An animal, cell or method according to clause 64, wherein transcription of the gene encoding the CL domain produces nucleic acid comprising SEQ ID NO: 5.
66. An animal, cell or method according to any of clauses 53 to 66, wherein the gene encoding the CL domain is at an endogenous immunoglobulin light chain locus of the animal.
67. An animal, cell or method according to clause 66, wherein the endogenous immunoglobulin light chain locus is the endogenous Igκ locus.
68. An animal, cell or method according to any of clauses 53 to 67, wherein expression of endogenous immunoglobulin light chain variable region gene segments is inactivated.
69. An animal, cell or method according to clause 69, wherein expression of endogenous immunoglobulin light chains is inactivated.
70. An animal, cell or method according to any of clauses 53 to 66, wherein expression of endogenous immunoglobulin heavy chain variable region gene segments is inactivated.
71. An animal, cell or method according to clause 70, wherein expression of endogenous immunoglobulin heavy chains is inactivated.
72. An animal, cell or method according to any of clauses 53 to 71, wherein the animal is a rodent.
73. An animal, cell or method according to clause 72, wherein the animal is a mouse or rat.
74. An animal, cell or method according to clause 73, wherein a plurality of human variable region gene segments capable of rearrangement to encode a human variable domain, upstream of human DNA encoding an immunoglobulin constant region comprising a human CH1 domain, are inserted at the endogenous immunoglobulin heavy chain locus on mouse chromosome 12, and expression of mouse heavy chains is inactivated.
75. An animal, cell or method according to clause 73 or clause 74, wherein a gene encoding a human Cκ domain is inserted at the endogenous Igκ light chain locus on mouse chromosome 6, and expression of mouse Igκ light chains is inactivated.
76. An animal produced by the method of any of clauses 55 to 75.
77. An animal or method according to any of clauses 54 to 76, wherein B-lymphocytes of the animal express antibodies as defined in any of clauses 1 to 43.
78. An animal or method according to clause 77 wherein, upon immunogenic stimulation, at least 50% of antibody-expressing B-lymphocytes in the animal express antibodies as defined in any of clauses 1 to 43.
79. A method of generating an antibody comprising an unpaired VH domain for binding antigen, comprising exposing an animal according to any of clauses 49 to 52, 54 or 57 to 78 to immunogenic stimulation with target antigen.
80. A method according to clause 79, comprising isolating the antibody or its encoding nucleic acid from the animal.
81. A method according to clause 79 or clause 80, comprising identifying the sequence of the unpaired variable domain of the antibody or its encoding nucleic acid.
82. A method according to clause 80 or clause 81 comprising introducing one or more mutations into the nucleotide sequence of nucleic acid encoding the variable domain.
83. A method according to clause 81 or clause 82, comprising providing a DNA vector comprising the encoding nucleic acid.
84. A method according to clause 83, wherein the nucleic acid encodes a polypeptide comprising the variable domain and one or more further domains.
85. A method according to any of clauses 80 to 84, further comprising cloning the encoding nucleic acid into a recombinant host cell.
86. A method according to clause 85, further comprising culturing the cell for expression of a polypeptide comprising the variable domain.
87. A method according to clause 86, comprising recovering and purifying the polypeptide from the cell or culture medium.
88. A method according to any of clauses 84 to 87, wherein the polypeptide is an isolated variable domain, an antibody or a chimaeric antigen receptor.
89. A method according to clause 87 or clause 88, comprising formulating the polypeptide into a composition comprising a pharmaceutically acceptable excipient.
90. An antibody according to any of clauses 1 to 43 for use in treatment of the human body by therapy.
91. A method of preparing an antibody:antigen complex, comprising
exposing a target antigen to an antibody as defined in any of clauses 1 to 43 in vitro,
allowing binding of the unpaired variable domain to the target antigen, thereby forming an antibody:antigen complex, and
isolating the antibody:antigen complex.
Mice are engineered to express antibodies in which a truncated K light chain comprising a Cκ domain fragment pairs with the CH1 of fully human heavy chains comprising unpaired VH domains.
The mouse contains a humanised heavy chain locus on mouse chromosome 12 (
In this mouse the humanised K locus is modified to inactivate normal vj rearrangement and instead express a Cκ domain fragment.
A large deletion (˜90 kb) of the human κ locus removes a 90 kb fragment encompassing exon 2 of Vκ1-5 to Jκ5. This removes all of Vκ2-4, Vκ7-3, Vκ5-2, Vκ4-1, Jκ1, Jκ2, Jκ3, Jκ4 and Jκ5 but leaves exon 1 of Vκ1-5 which encodes the majority of the Vκ1-5 signal peptide, the κ enhancers and the Cκ gene. The latter elements are therefore left intact. Upstream V gene segments cannot rearrange in the absence of the complete set of J gene segments. The normal κ VJ recombination is thus inactivated. The remaining Vκ1-5 exon 1 (i.e., the leader sequence) will therefore be spliced onto the Cκ, creating a novel transcript encoding a Cκ polypeptide comprising a signal peptide (
The nucleotide and protein sequence of the modified K locus of the present invention (
The sequence of the Cκ fragment transcript and resulting protein includes a predicted cleavage site of the signal peptide (
The modified K locus can be generated by creating double strand breaks at defined locations in the κ genomic locus and providing a repair template to promote the desired deletion. The genetic deletion can be performed in mouse cells comprising a humanised K locus, for example in mouse embryonic stem cells containing a humanised K locus, or reagents may be injected into zygotes from mice whose genomes comprise a humanised K locus.
Animals with the desired Cκ locus are then mated with animals containing a fully human heavy chain locus to produce mice that are able to generate fully human antibodies comprising unpaired VH domains.
The λ locus can be either unmodified or inactivated in this platform.
Data are presented in Example 4.
It is known that Ig heavy chain is not expressed on the B cell surface in the absence of light chain. However, λ5 can rescue the surface expression of Ig heavy chains if expressed at stages beyond early B cell development in the bone marrow. A truncated λ5 protein, which is able to rescue surface IgM display in the absence of VpreB[11], appears especially suitable. The 50 amino acid unique region at the N-terminal end of human λ5 is believed to limit the rate of λ5 folding in the absence of VpreB[4]. The immunoglobulin domain of λ5, lacking this N-terminal unique region, binds the heavy chain constant domain CH1 and thus represents a shield domain in the present invention. The λ5 comprises its native signal peptide or a non-native signal peptide such as that encoded by the Vκ1-5 leader or the λ1 leader sequence. Signal peptides may be post-translationally cleaved.
Replacement of the Jκ region of the light chain κ immunoglobulin locus with a gene encoding the λ5 immunoglobulin domain places λ5 expression under control of the Igκ locus. A 5 kb replacement would suffice. The β strand (J) preceding the λ5 Ig fold can be retained. Alternatively, this is omitted, including only the Ig domain itself. In the context of the surrogate light chain this J strand supplies the missing B strand of the VpreB Ig domain[4, 5]. VpreB is not expressed during Igκ (or Igλ) light chain expression, therefore the λ5 will be expressed in the absence of VpreB.
A human Igκ locus comprising the above modification is inserted into the genome of a non-human animal, e.g., mouse, to generate a transgenic animal expressing the human λ5 gene under control of human Igκ transcriptional control elements. The human DNA is inserted at the endogenous Igκ locus of the animal or at an independent (ectopic) locus in the animal genome. Inactivation of κ and/or λ light chain loci in an animal genome can be combined with insertion of a transgene encoding all or part of the human λ5 gene or a mutant thereof. Here the λ5 transgene is inserted in the inactivated κ and/or λ light chain locus and is placed under control of the human κ or A gene control elements including promoter/enhancer elements.
A large deletion (200 kb) of the λ locus removes v2 to v1 (the segment comprising V2, V3, J2C2 and V1) but leaves J3C3, J1C1 and downstream enhancers intact. This inactivates expression of the A light chain.
The locus is generated by creating double strand breaks at defined locations in the A genomic locus and providing a repair template to promote the desired deletion.
The inactivated λ locus is combined by breeding an animal comprising this genomic modification with an animal comprising the fully humanised heavy chain locus and a modified kappa locus as described herein. This ensures that, even in the absence of allelic exclusion, no light chains are expressed from the endogenous λ locus.
In the absence of λ light chain, the Cκ domain pairs with heavy chain CH1 in expressed antibodies.
Mosaic F0 animals generated by cytoplasmic injection, containing the desired fully human Kappa locus with a deletion to enable expression of a truncated Kappa Cκ fragment, which we call a KCF locus (see Example 1), plus a mixture of WT alleles and uncharacterised indel mutations, were mated individually to segregate this mosaicism, generating F1 animals each with a single F0-derived allele. In order to generate F1 animals suitable for early analysis, each mosaic F0 was bred with an animal containing an inactivated Kappa locus (inactivation by insertion of a Neomycin cassette within the Kappa locus, between Jκ5 and Cκ, preventing normal Kappa recombination). The resulting heterozygous animals, containing the desired modified Kappa locus plus inactivated mouse Kappa locus, were analysed at the transcript and protein level.
RNA was extracted from splenocytes, from these heterozygotes and from control animals with an unmodified fully human Kappa locus, using TRlzol® Reagent (Invitrogen™) and a standard protocol. First strand DNA synthesis was performed using a SuperScript III First-Strand Synthesis SuperMix kit (Invitrogen™) and either an oligo specific for the human Cκ coding region or an Oligo(dT) primer. The first strand DNA was then used as a template for PCR with primers specific for the human Kappa constant coding region or 3′ UTR in combination with oligos specific for the human Vκ1-5 leader sequence or 5′ UTR. A single PCR product, with the expected size for the predicted truncated Kappa fragment, was identified from the modified Kappa locus with oligos in the human Vκ1-5 5′UTR and human Cκ 3′UTR. Sequencing of this PCR product confirmed that this transcript contained the predicted splice junction between the human Vκ1-5 exon 1 and the human Cκ gene. This is evidence that the large deletion created in the humanised Kappa locus does indeed result in expression of the predicted truncated Kappa fragment transcript—see
The presence of the correctly spliced transcript for the truncated human Kappa shield domain was confirmed for samples from multiple animals containing the KCF locus.
Embodiments of the invention provide a mouse containing an inactivated Kappa and/or Lambda light chain locus, either endogenous or humanised, combined with insertion of a transgene encoding all or part of the human, rodent, non-human primate or other mammalian Lambda 5 (λ5) gene, or mutant thereof. The λ5 transgene is inserted in the inactivated Kappa and/or Lambda light chain locus and is under the control of endogenous and/or exogenous light chain promoter and enhancers. For example, human promoters and enhancers are used; or mouse promoters and enhancers; or human variable region promoter(s) and mouse enhancers (such as the mouse intronic and 3′ light chain locus enhancers).
Inactivation of the Kappa locus can be achieved by:
Inactivation of the Lambda locus can be achieved by:
A targeting vector encoding a truncated human λ5 coding region (SEQ ID NO:77) and human Kappa intronic region, including human Kappa intronic enhancer, preceded by a human Kappa promoter and leader (human Vκ1-5 derived) (SEQ ID NO: 78), flanked by 800-1 kb arms homologous to the mouse genomic sequence upstream of Kappa J1 and downstream of Kappa Cκ (full transgene including homology arms, SEQ ID NO:79). This sequence was synthesised as a single fragment and cloned into a pUC vector (by Genscript™). See
This vector can be used in one of two ways:
This vector was designed to target the WT mouse Kappa locus and was used in 129 strain mouse embryonic stems cells (mESCs) (AB2.1 cell line). A similar approach, with a modified vector, could be used to target the humanised Kappa locus in mESCs containing such a locus. A similar vector could be used to perform direct modification in mouse 2 cell stage embryos by cytoplasmic injection, modifying either the WT mouse Lambda locus or a humanised Lambda locus.
An alternative strategy would involve modification of the WT mouse Kappa or Lambda locus, or a humanised Kappa/Lambda locus, with a vector containing a truncated λ5 sequence from mouse (see SEQ ID NO: 100 and SEQ ID NO: 101), another rodent, non-human primate or other mammalian source.
mESCs containing the inactivated Kappa locus/human λ5 transgene were microinjected into blastocysts derived from RAG-1 −/− (B6.129S7-Rag1<tm1Mom>/J) mice. Mice homozygous for this RAG-1 mutation have no mature B or T cells due to failure of V(D)J recombination. This allows for early analysis of the functionality of the introduced locus in chimeras generated in this background, as any mature lymphocytes present in the lymphoid organs of these animals will be derived from the transgene-containing mESC line injected. The same mESC lines were also injected into WT CB7bl/6 blastocysts, for generation of stable mouse lines with germline transmission of the transgene.
An additional step was performed in some λ5 mESC lines in order to inactivate the endogenous mouse λ light chain locus. This was achieved by transfecting mESCs with the required reagents to create double strand breaks at defined locations in the A genomic locus and providing a small single stranded DNA donor fragment as a repair template to promote the desired deletion. The region deleted is the same as described in Example 3 (removes V2 to V1 (the segment comprising V2, V3, J2C2 and V1) but leaves J3C3, J1C1 and downstream enhancers intact).
Analysis of initial chimeras generated in RAG-1 −/− background will be performed as follows:
Lymphoid organs from chimaeric mice generated by injection of λ5 transgene into RAG-1 −/− mESCs, either without or with the mouse λ light chain knockout locus are disassociated and the resulting cells are incubated with a staining panel containing markers for mouse lymphocytes along with an anti-human λ5 antibody, followed by flow cytometry analysis. A positive result would suggest successful expression of the human λ5 transgene and assembly with the endogenous mouse Heavy chain to allow cell-surface expression of a ‘VH-only’ antibody in vivo.
Mouse lines positive for λ5 expression on surface of lymphocytes will be cross-bred with other mouse strains to introduce both the fully human Heavy locus and the mouse Lambda knockout. This will result in animals generating fully human VH-only antibodies.
This embodiment is a mouse containing a Kappa locus that has been modified to inactivate normal Kappa light chain rearrangement and to instead express a truncated Kappa chain composed of the Kappa constant region (Ck) plus Vκ leader and partial J fragment. This is achieved by either:
1) Creating a deletion between a mouse endogenous Vκ gene and a mouse Jκ gene, removing most of the coding sequence for the Vκ and Jκ but retaining the Vκ exon 1 plus endogenous splice junctions at the 5′ end of the Vκ exon 2 and the 3′ end of the J.
2) Replacing the mouse Jκ genes with a targeting vector encoding the promoter, leader (exon 1, intron, partial exon 2) of a mouse Vκ plus a small fragment of a Jκ gene, again retaining endogenous splice junctions at the 5′ end of the Vκ exon 2 and the 3′ end of the J.
The result of either of these strategies is a locus that expresses a transcript, under endogenous Vκ promoter control, that is spliced to generate a Cκ with a Vκ leader sequence and partial J sequence. This strategy can utilise any Vκ and J of the mouse Kappa repertoire. For strategy one, we will use Vκ3-2 or Vκ3-4 with Jκ5. The reason for this is that Vκ3-2 or Vκ3-4 are close to the 3′ end of the locus, reducing the size of deletion required, plus have been shown in literature to have a fairly high frequency of usage in the mice. See
This mouse differs from versions with human control elements, in that in the current example all non-coding and regulatory elements in the modified locus are endogenous. This includes the specific promoter for the Vκ/Jκ/Cκ fragment, the mouse κ intronic enhancer (located between Jκ5 and Cκ) and the mouse κ 3′ enhancer. Interaction of these endogenous promoters/enhancers with the mouse effectors involved in expression from the κ locus is likely to be more effective than that of mouse effectors with the human regulatory sequences present in Examples 2 and 4, thus potentially resulting a more active locus.
Generation of the modified locus by strategy 1 involves a large, precise deletion of either 25 kb (for Vκ3-2 version) or 54 kb (Vκ3-4 version). This mouse locus could be generated in multiple ways:
1) Direct modification of the mouse Kappa Locus by cytoplasmic injection: this will be achieved by injecting mouse 1 cell zygotes or 2 cell embryos with the required reagents to create double strand breaks at defined locations in the κ genomic locus and providing a repair template to promote the desired deletion.
2) Modification of the mouse Kappa Locus in mESCs: this will be achieved by transfecting mESCs with the required reagents to create double strand breaks at defined locations in the κ genomic locus and providing a repair template to promote the desired deletion
Generation of the modified locus by strategy 2 involves replacement of a 1.5 kb region of the mouse Kappa locus (Jκ1-5) with a 1.3 kb sequence encoding the partial Vκ/Jκ fragment. This could be achieved by:
Targeting vector inserts will be synthesised as single fragments and cloned into a pUC vector (by Genscript™).
Initial analysis of mESC lines generated by this method will be performed in the same way as in Example 5 i.e. injection into RAG-1 −/− blastocysts followed by analysis of chimera-derived lymphocytes for expression of the truncated Kappa fragment. Mouse lines expressing the truncated mouse Kappa fragment, paired with a Heavy chain, on surface of lymphocytes, will be cross-bred with other lines to introduce both the fully human Heavy locus and the mouse Lambda knockout (as detailed in Example 3). This will result in animals generating VH-only antibodies with a fully human Heavy chain and mouse Kappa Cκ fragment.
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
Homo sapiens
| Number | Date | Country | Kind |
|---|---|---|---|
| 1814529.2 | Sep 2018 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2019/073767 | 9/5/2019 | WO | 00 |
