Patent Application
20070014796
The present invention relates to the production of substantially non-immunogenic proteins, especially antibodies, and their uses. The invention uses a combination of recombinant DNA and monoclonal antibody technology for the generation of novel therapeutic and in vivo diagnostic agents for particular use in man.
The use of rodent, especially mouse, monoclonal antibodies for therapeutic and in vivo diagnostic applications in man was found to be limited by immune responses made by patients to the rodent antibody. The development of so-called “HAMA” (human anti-mouse antibody) responses in patients was shown to limit the ability of antibodies to reach their antigenic targets resulting in a reduced effectiveness of the antibodies. In order to reduce the HAMA response, chimeric antibodies were developed (see, for example, WO-A-8909622) in which the mouse variable (V) regions were joined to human constant (C) regions. Such antibodies have proved clinically useful although the mouse V region component still provides the basis for generating immunogenicity in patients (see, for example, LoBuglio et al., Proc. Nat'l. Acad. Sci. USA, 86: 4220-4224 (1989)). Therefore, technology for humanized antibodies were developed whereby the complementarity determining regions or “CDRs” from the rodent antibody were transplanted onto human V regions and joined to human C regions to create humanized antibodies whereby the only non-human components were the CDRs which were adjacent to human V region “frameworks”. The transplanted CDRs corresponded either to hypervariable regions as defined by Kabat et al. (“Sequences of Proteins of Immunological Interest”, Kabat E., et al., U.S. Dept. of Health and Human Services, 1983) or to the hypervariable loops in 3-dimensional structures of antibodies (Chothia and Lesk, J Mol. Biol., 196: 901-917 (1987)). One of the first examples of such humanized antibodies by Riechmann et al. (Nature, 332: 323-326 (1988)) illustrated, however, that simple transplantation of CDRs often resulted in reduced affinity of the humanized antibody and consequently that the introduction of certain non-human amino acids (i.e. from the corresponding position in the rodent sequence) in the human V region framework as required in order to restore affinity. A number of methods have been proposed for the substitution of human framework residues in order to restore affinity including those disclosed in EP-A-0239400, EP-A-0438310, WO-A-9109967 and WO-A-9007861. In particular, patent publications by Protein Design Labs., Inc. (e.g. WO-A-9007861 and related EP-B-0451216) purport to provide a general method for producing humanized antibodies in which one or more human framework residues are altered in order to restore binding affinity.
A common aspect of all of the above mentioned methods for production of chimeric or humanized antibodies is that the objective of these methods was to create antibodies which are substantially non-immunogenic in humans (e.g. EP-B-0451216, page 3, line 6). However, the means for achieving this objective has been the introduction into the rodent antibody of as much human sequence as possible and it has been assumed that such a general introduction of human sequence will render the antibodies non-immunogenic. It is known that certain short peptide sequences (“epitopes”) can be immunogenic in humans and none of the methods for chimeric or humanized antibodies have considered how to eliminate or avoid such epitopes in the resultant antibody. Furthermore, most of the methods (e.g. EP-B-0451216) have advocated the introduction of non-human amino acids into human V region frameworks without considering the possible creation of immunogenic epitopes, and none of the methods has provided any means for avoiding or eliminating immunogenic epitopes at framework:CDR junctions and, where practical, within CDRs themselves. Thus, of the methods devised with the objective of creating substantially non-immunogenic antibodies, none can be considered as actually achieving the creation of such substantially non-immunogenic antibodies. The same can be said of proteins (especially therapeutic proteins) other than antibodies.
The present invention provides, for the first time, a general method for creating substantially non-immunogenic proteins such as antibodies and also provides antibodies and other proteins created by this method.
According to a first aspect of the invention, there is provided a method of rendering a protein, or part of a protein, non-immunogenic, or less immunogenic, to a given species, the method comprising:
(a) determining at least part of the amino acid sequence of the protein;
(b) identifying in the amino acid sequence one or more potential epitopes for T-cells (“T-cell epitopes”) of the given species; and
(c) modifying the amino acid sequence to eliminate at least one of the T-cell epitopes identified in step (b) thereby to eliminate or reduce the immunogenicity of the protein or part thereof when exposed to the immune system of the given species.
The term “T-cell epitopes” refers to specific peptide sequences which either bind with reasonable efficiency to MHC class II molecules or which, from previous or other studies, show the ability to stimulate T-cells via presentation on MHC class II. However, it will be understood that not all such peptide sequences will be delivered into the correct MHC class II cellular compartment for MHC class II binding or will be suitably released from a larger cellular protein for subsequent MHC class II binding. It will also be understood that even such peptides which are presented by MHC class II on the surface of antigen-presenting cells will elicit a T-cell response for reasons including a lack of the appropriate T-cell specificity and tolerance by the immune system to the particular peptide sequence.
Potential epitopes for B-cells of the given species may additionally be compromised in a similar manner.
The invention has particular application to rendering regions of immunoglobulins non-immunogenic (which term will be used in this specification to include less immunogenic, unless the context dictates otherwise): constant or, especially, variable regions of immunoglobulins (or of course natural or artificial molecules containing both such regions) constitute proteins, or parts of proteins, to which the invention is well suited to being applied.
However, it will be understood to those skilled in the art that the present invention could also be applied to produce therapeutic proteins other than immunoglobulins or antibodies. As with antibodies, proteins which would otherwise be immunogenic in man could be de-immunized by removal of T-cell epitopes. In addition, if a reference human protein is available with similar secondary structure and identifiable surface amino acids, the B-cell epitopes could additionally be removed from the protein by substituting surface amino from the reference human protein in place of the corresponding amino acids in the non-human or potentially immunogenic protein. For example, clinical use of the thrombolytic agent bacterial streptokinase is limited by human immune responses against the molecule; such molecules could be engineered to remove potential T-cell epitopes in order to remove the immunogenicity.
Generally, the invention will be used to reduce the immunogenicity of a protein or part thereof (exemplified by a V region of an immunoglobulin) of a first species in relation to the immune system of a second species. The first species may be non-human, and the second species may be human. Examples of typical non-human species useful in relation to embodiments of the invention relating to immunoglobulins include mammals, especially rodents such as rats and, in particular, mice, and farm animals such as sheep and cattle. However, as made clear above in relation to bacterial streptokinase, the first species may be taxonomically far removed from the second species; when the first species is non-human, it may be non-mammalian and even non-eukaryotic. In much of the following description of preferred embodiments of the invention, reference will be made to humanizing antibodies, but it is to be understood that the invention also relates to species other than man and to proteins, particularly therapeutic proteins, generally, including specific binding molecules other than whole antibodies.
The method of the invention is based on the consideration of how an immune response against a monoclonal is usually created in humans as the basis for avoiding or eliminating sequences within the antibody which are involved in this immune response. When a therapeutic antibody or other immunoglobulin, or partial immunoglobulin, molecule (“antibody”, for short) is administered to a human patient, the antibody is subjected to surveillance by both the humoral and cellular arms of the immune system which will respond to the antibody if it is recognized as foreign and if the immune system is not already tolerant to the immunogenic sequence within the antibody. For the humoral immune response, immature B-cells displaying surface immunoglobulins (slg) can bind to one or more sequences within the therapeutic antibody (“B-cell epitopes”) if there is an affinity fit between the an individual sIg and the B-cell epitope and if the B-cell epitope is exposed such that sIg can access the B-cell epitope. The process of sIg binding to the therapeutic antibody can, in the presence of suitable cytokines, stimulate the B-cell to differentiate and divide to provide soluble forms of the original sIg which can complex with the therapeutic antibody to limit its effectiveness and facilitate its clearance from the patient. However, for an effective B-cell response, a parallel T-cell response is required in order to provide the cytokines and other signals necessary to give rise to soluble antibodies. An effective T-cell response requires the uptake of the therapeutic antibody by antigen-presenting cells (APCs) which can include B-cells themselves or other professional APCs such as macrophages, dendritic cells and other monocytes. In addition, non-professional APCs such as the cells to which the antibody binds can take up the therapeutic antibody and provide intermediate processing of the antibody such that professional APCs can then absorb the antibody components. Having taken up the therapeutic antibody, APCs can then present suitable peptides from the therapeutic antibody (“T-cell epitopes”) complexed with MHC class II molecules at the cell surface. Such peptide-MHC class II complexes can be recognized by helper T-cells via the T-cell receptor and this results in stimulation of the T-cells and secretion of cytokines which provides “help” for B-cells in their differentiation to full antibody producing cells. In addition, the T-cell response can also result in deleterious effects on the patient for example through inflammation and allergic reactions.
An effective primary immunogenic response to a therapeutic antibody therefore usually requires a combination of B- and T-cell responses to B- and T-cell epitopes. Therefore, avoidance of a primary immunogenic response requires the avoidance or elimination of both B- and T-cell epitopes within the therapeutic antibody. Without either the B- or T-cell response, the primary immunogenic response to a therapeutic antibody is likely to be muted or absent. The present invention therefore provides methods for avoiding or eliminating T-cell epitopes, or a combination of both B- and T-cell epitopes, from therapeutic antibodies in order to create substantially non-immunogenic antibodies with particular emphasis on avoiding such epitopes in the V region of the therapeutic antibody. For B-cell epitopes, the method takes advantage of the fact sIg can only bind to accessible regions of the therapeutic antibody, i.e., sequences of exposed surface amino acids. For a starting mouse antibody for subsequent human use, the method then incorporates into the V region of the therapeutic antibody, human amino acids at positions corresponding to those of the exposed mouse amino acids. For T-cell epitopes, sequences of overlapping peptides within the therapeutic antibody are analyzed, with particular emphasis on the V region, in order to identify putative peptides suitable for presentation by MHC class II molecules. By scanning the V region of a potential therapeutic antibody and, where T-cell epitopes are identified, changing one or more individual amino acids to eliminate the T-cell epitope, then an antibody can be created devoid of T-cell epitopes. For the C regions of the therapeutic antibody or other immunoglobulin molecule, contiguous natural C regions from human antibodies can be used, although the invention also encompasses the identification and elimination of T-cell epitopes in the C regions if desirable or necessary.
It will be understood that the invention is not just applicable to whole antibodies, but rather to any specific binding molecule comprising a V region of an immunoglobulin, including without limitation whole Ig light (κ and λ) and heavy (γ, α, μ, δ, and ∈) chains, light/heavy chain dimers, SCAs (single-chain antibodies), and antibody or immunoglobulin fragments including those designated Fab, F(ab′)2, Fab′, Fd and Fv.
While the usefulness of the invention is not confined to making an antibody or other V region-containing molecule of one particular species therapeutically or diagnostically administrable to any other particular species, the most significant utility of the invention will be in “humanizing” non-human antibodies, particularly rodent antibodies such as murine antibodies (or parts of them). In that case, the “first species” referred to above will be a mouse, and the “second species” will be a human.
Therefore, a particular embodiment of the present invention comprises the following key steps:
(a) determining the amino acid sequence of the V region of a starting antibody, which will usually be non-human, e.g. mouse;
(b) optionally modifying the amino acid sequence, for example by recombinant DNA techniques, to change those non-CDR residues on the exposed surface of the antibody structure to the corresponding human amino acids taken from a reference (e.g. closely matched) human V region sequence (which may be a human germ-line V region sequence);
(c) analyzing the amino acid sequence to identify potential T-cell epitopes and modifying the amino acid sequence, for example by recombinant DNA techniques, to change one or more residues in order to eliminate at least some, and preferably all, of the T-cell epitopes, particularly framework epitopes but including those within CDRs if this does not undesirably reduce or eliminate binding affinity or undesirably alter specificity; and
(d) optionally adding human C regions via recombinant DNA to create a complete antibody which is substantially non-immunogenic.
A preferred method of the present invention therefore combines the removal of both B- and T-cell epitopes from a therapeutic antibody, a process which is termed “de-immunization”. For removal of human B-cell epitopes from the V region of a therapeutic antibody, the method of Padlan (Padlan E. A., Molecular Immunology, 28: 489-498 (1991) and EP-A-0519596) provides a suitable procedure whereby surface amino acids in a particular antibody sequence are identified with reference to 3-dimensional structures or models of antibody V regions and are converted to the corresponding human residues in a process which has been called “veneering”. A derivative of this method (EP-A-0592106) models the V regions of the therapeutic antibody itself in order to identify surface amino acids in a process which has been called “resurfacing”.
The present invention provides for removal of human (or other second species) T-cell epitopes from the V regions of the therapeutic antibody (or other molecule) whereby the sequences of the V region can be analyzed for the presence of MHC class II-binding motifs by any suitable means. For example, a comparison may be made with databases of MHC-binding motifs such as, for example by searching the “motifs” database at the world-wide web site of the Walter and Eliza Hall Institute of Medical Research. Alternatively, MHC class II-binding peptides may be identified using computational threading methods such as those devised by Altuvia et al. (J. Mol. Biol., 249: 244-250 (1995)) whereby consecutive overlapping peptides from the V region sequences are testing for their binding energies to MIC class II proteins. In order to assist the identification of MHC class II-binding peptides, associated sequence features which relate to successfully presented peptides such as amphipathicity and Rothbard motifs, and cleavage sites for cathepsin B and other processing enzymes can be searched for.
Having identified potential second species (e.g. human) T-cell epitopes, these epitopes are then eliminated by alteration of one or more amino acids, as required to eliminate the T-cell epitope. Usually, this will involve alteration of one or more amino acids within the T-cell epitope itself. This could involve altering an amino acid adjacent the epitope in terms of the primary structure of the protein or one which is not adjacent in the primary structure but is adjacent in the secondary structure of the molecule. The usual alteration contemplated will be amino acid substitution, but it is possible that in certain circumstances amino acid addition or deletion will be appropriate. All alterations can for preference be accomplished by recombinant DNA technology, so that the final molecule may be prepared by expression from a recombinant host, for example by well established methods, but the use of protein chemistry or any other means of molecular alteration is not ruled out in the practice of the invention.
In practice, it has been recognized that potential human T-cell epitopes can be identified even in human germ-line V region framework sequences when comparison is made with databases of MHC-binding motifs. As humans do not generally mount an ongoing immune response against their own antibodies, then either humans are tolerant to these epitopes or these potential epitopes cannot be presented by human APCs because they are not processed appropriately. Therefore, such potential T-cell epitopes which are represented in germ-line V region sequences may, in practice, be retained in the de-immunized antibody. In order to minimize the creation of additional T-cell epitopes during the elimination of potential T-cell epitopes from the therapeutic antibody sequence, the elimination of T-cell epitopes is preferably (but not necessarily) achieved by conversion to second species (usually human) germ-line amino acids at positions corresponding to those of the first species (usually mouse) amino acids within T-cell epitopes. Once initially identified T-cell epitopes are removed, the de-immunized sequence may be analyzed again to ensure that new T-cell epitopes have not been created and, if they have, the epitope(s) can be deleted, as described above; or the previous conversion to a corresponding human germ-line amino acid is altered by conversion of the murine (or other first species) amino acid to a similar non-human (or non-second species) amino acid (i.e. having similar size and/or charge, for example) until all T-cell epitopes are eliminated.
For the C region of a therapeutic de-immunized antibody or other molecule subjected to the method of the invention, it is not necessary to systematically eliminate potential B- and T-cell epitopes as the use of contiguous natural human C region domains has so far proved safe and substantially non-immunogenic in patients; thus the combination of de-immunized V regions and human C regions is sufficient for creation of a substantially non-immunogenic antibody or other immunoglobulin V region-containing molecule. However, as human C regions have sites of amino acid allotypic variation which might create potential T-cell epitopes for some allotypes, then the method of Lynxvale Ltd. (Clark) published in WO-A-9216562 and EP-A-0575407 might be useful. Equally, the method of the invention may be applied to a C region in a similar manner as it is applied to a V region.
For the CDRs of a therapeutic antibody, it is common for one or more potential T-cell epitopes to overlap or fall within the CDRs whereby removal of the epitopes requires alteration of residues within the CDRs. In order to eliminate the induction of a T-cell response to such epitopes, it is desirable to eliminate these although this may reduce the binding affinity of the resultant antibody and thus any potential alteration of CDRs may need to be tested for any alteration of resultant antigen binding.
A typical therapeutic de-immunized antibody from the present invention will comprise heavy and light chain V region sequences (VH, VL) with several amino acid substitutions which constitute departures from the prototype rodent sequence. Typically, for a VH or VL region, there will be 10 to 15 substitutions with human residues to eliminate B-cell epitopes and 1 to 10 human or non-human substitutions to eliminate T-cell epitopes. The typical therapeutic de-immunized antibody will also comprise human C regions for the heavy and light chains.
EP-B-045 1216 discloses the use of at least one amino acid substitution outside of complementarity determining regions (CDRs) as defined in the production of a humanized immunoglobulin, wherein said amino acid substitution is from the non-CDR variable region of a non-human donor immunoglobulin, and in which humanized immunoglobulin the variable region amino acid sequence other than the CDRs comprises at least 70 amino acid residues identical to an acceptor human immunoglobulin variable region amino acid sequence, and the CDRs are from the variable region of said non-human donor immunoglobulin.
In certain preferred de-immunized antibodies of the present invention, the variable region amino acid sequence other than the CDRs comprises fewer than 70 amino acid residues identical to an acceptor human immunoglobulin variable region amino acid sequence (i.e., a reference human variable region sequence such as a germ-line variable region sequence).
EP-B-0451216 also discloses a method of producing a humanized immunoglobulin chain having a framework region from a human acceptor immunoglobulin and complementarity determining regions (CDR's) from a donor immunoglobulin capable of binding to an antigen, said method comprising substituting at least one non-CDR framework amino acid of the acceptor immunoglobulin with a corresponding amino acid from the donor immunoglobulin at a position in the immunoglobulins where:
(a) the amino acid in the human framework region of the acceptor immunoglobulin is rare for said position and the corresponding amino acid of the donor immunoglobulin is common for said position in human immunoglobulin sequences; or
(b) the amino acid is immediately adjacent to one of the CDR's; or
(c) the amino acid is predicted to have a side chain capable of interacting with the antigen or with the CDR's of the humanized immunoglobulin.
In the present invention, preferred de-immunized antibody variable region amino acid sequence other than CDRs would exclude amino acids from the starting antibody which are rare at the corresponding position in human immunoglobulins or which are adjacent to CDRs or which have a side-chain capable of interacting with the antigen or with the CDRs of the de-immunized antibody.
It will be understood by those skilled in the art that there can be several variations of the method of the present invention which will fall within the scope of the present invention. Whilst the present invention relates principally to therapeutic antibodies from which human B- and T-cell epitopes have been deleted, it will be recognized that the removal of T-cell epitopes alone might, in some cases, also be effective in avoiding an immunogenic response in patients. As an alternative to the de-immunized antibodies of the present invention, part of the method of the first aspect of the present invention may be used to analyze pre-existing antibodies in therapeutic use in order to predict the basis for immunogenic responses to these antibodies and to eliminate them by induction of B- or T-cell tolerance to the appropriate B- and T-cell epitopes or by other methods for ablating the immune response. In addition, it should be considered within the scope of the present invention to redesign a pre-existing therapeutic antibody to which a human immune response has been detected and characterized to delete the epitopes relating to the observed immune response in humans. Additionally, as discussed above, therapeutic and other proteins apart from antibodies may benefit from the application of the invention.
It should be understood that the method of the present invention could be used to render a V region of an immunoglobulin either wholly non-immunogenic or partially immunogenic, whereby certain B- or T-cell epitopes may be left within the final molecule in order to elicit an immune reaction in patients, for example with an anti-idiotype antibody where only usually part of the V region is involved in mimicking the original antigen. It should also be understood that the present invention can apply to the production of antibodies for uses other than in human medicine and that de-immunized antibodies could be produced for specific therapeutic or diagnostic use in animals whereby de-immunization eliminates the specific animal's B- and T-cell epitopes.
As indicated above, the method of the present invention may also be used to render constant regions of immunoglobulins non-immunogenic. For example, in a typical humanization of a non-human antibody, instead of incorporating a human constant region into the final molecule, the non-human constant region could be screened for the presence of T-cell epitopes which would then be eliminated preferably without altering any of the biochemical properties of the constant region such as the ability to fix complement. Alternatively, the equivalent human biological properties could be deliberately incorporated into the de-immunized constant regions by incorporating corresponding human residues, for example for binding to efficient binding to human Fc receptors. If required, certain properties of non-human constant regions could be retained in the de-immunized constant regions, for example to retain the co-operative binding effect of mouse IgG3 antibodies.
According to a second aspect of the invention, there is provided a molecule of a first species (such as a non-human species), wherein the variable region is modified to eliminate epitopes for T-cells, and optionally also epitopes for B-cells, of a second species (such as human). The molecule will generally be proteinaceous and may comprising at least a variable region of an immunoglobulin, in which case the first species may be mouse. The variable region may be modified to the minimum extent necessary to eliminate the T-cell epitopes. Alternatively or additionally, it may be modified to eliminate only T-cell epitopes which are non-germ-line.
The invention extends also to a molecule which has been prepared by a method in accordance with the first aspect of the invention.
The invention has particular and widespread application in the field of therapeutic molecules including monoclonal antibodies whereby rodent or other non-human antibodies can be de-immunized for applications in humans and whereby previously humanized or chimeric antibodies with B- or T-cell epitopes could be converted into a less immunogenic form for use in humans. It will also be understood that even antibodies derived from human immunoglobulin genes such as antibodies derived from bacteriophage-display libraries (Marks et al., J Mol. Biol., 222: 581-597 (1991)), transgenic mice with human immunoglobulin genes (Bruggermann et al., Proc. Nat'l. Acad. Sci. USA, 86: 6709-6713 (1989)) and natural human monoclonal antibodies can carry B- and T-cell epitopes especially as somatic mutations are introduced into framework sequences in immunoglobulin genes during the maturation of antibodies. Therefore, de-immunization may be required in order to prepare such antibodies for use in humans. Finally, it will be understood that CDRs from any naturally derived antibodies have been subjected to selection by somatic mutation of V region genes and thus might have T-cell epitopes capable of triggering immune responses in humans. The de-immunization method might be applicable without severe loss of antibody binding affinity (depending on the contribution of particular CDRs to antigen binding).
According to a third aspect of the invention, there is provided a molecule which has been prepared by a method in accordance with the first aspect of the invention, or a molecule in accordance with the second aspect, for use in medicine or diagnosis.
According to a fourth aspect of the invention, there is provided the use of a molecule prepared by a method in accordance with the first aspect of the invention, or a molecule in accordance with the second aspect, in the manufacture of an therapeutic or diagnostic antibody or other specific binding molecule. The invention therefore extends to a method of treating or preventing a disease or condition, the method comprising administering to a subject an effective amount of a molecule prepared by a method in accordance with the first aspect of the invention, or a molecule in accordance with the second aspect. The invention also extends to the use of such molecules in in vivo and in vitro diagnosis.
Preferred features of each aspect of the invention are as for each other aspect, mutatis mutandis.
The invention will now be illustrated, but not limited, by the following examples. The examples refer to the drawings, in which:
mRNA was isolated from 5×106 hybridoma 340 cells (Durrant et al., Prenatal Diagnostics, 14: 131 (1994) using TRIzol.TM. reagent (Life Technologies, Paisley, UK) according to the manufacturer's instructions. The mRNA was converted to cDNA/mRNA hybrid using Ready-To-Go.TM. T-primed First-Strand kit (Pharmacia Biotech, St. Albans, UK). Variable region heavy (VH) and light (VL) chain cDNAs were amplified using primer sets using the method of Jones and Bendig (Bio/Technology, 9: 188 (1991). PCR products were cloned into pCRII (Invitrogen, Netherlands) and six individual clones each of VH and VL were sequenced in both directions using the Applied Biosystems automated sequencer model 373A (Applied Biosystems, Warrington, UK). Resultant VH and VL DNA sequences are shown in
A humanized antibody was generated by substituting the mouse V region frameworks 1 to 3 for corresponding frameworks from the human germ-line V region sequences HSIGDP54 (SEQ ID NO: 1; Tomlinson et al., J. Mol. Biol., 227: 776 (1992) for VH. and HSIGKV38 (SEQ ID NO: 2; Victor et al., J. Clin. Invest., 87: 1603 (1991)) for VL. For the 4th framework, the human JH6 was substituted in the VH and the human JK4 in the VL. In addition, some key amino acids from the murine sequences which were expected to be important to restore binding in the humanized antibody were substituted for the corresponding human framework residues. The amino acid sequences of the humanized VH and VL are shown in
The humanized VH and VL regions were constructed by the method of overlapping PCR recombination using long synthetic oligos described by Daugherty et al., (Nucleic Acids Research, 19: 2471 (1991)). The required sequence was synthesized as four long oligonucleotides of 96 to 105 bp with complementary overlapping ends of 18 base pairs (
The humanized VH gene complete with 5′ and 3′ flanking sequences was cloned into the expression vector, pSVgpt (Riechmann et al., Nature, 332: 323 (1988)) which includes the human IgG1 constant region domain (Takahashi et al., Cell, 29: 671 (1982)) and the gpt gene for selection in mammalian cells. The humanized VL gene complete with 5′ and 3′ flanking sequences was cloned into the expression vector, pSVhyg (Riechmann et al., ibid.), in which the gpt gene is replaced by the gene for hygromycin resistance (hyg) and a human κ constant region is included (Hieter et al., Cell, 22: 197 (1980)).
The heavy and light chain expression vectors were co-transfected into NSO, a non-immunoglobulin producing mouse myeloma, obtained from the European Collection of Animal Cell Cultures, Porton Down, UK, ECACC No 85110505, by electroporation. Colonies expressing the gpt gene were selected in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% (v/v) FCS and antibiotics (Life Technologies Ltd, Paisley, UK) and with 0.8 μg/ml mycophenolic acid and 250 μg/ml xanthine (Sigina, Poole, UK).
Production of human antibody by transfected cell clones was measured by ELISA for human IgG (Tempest et al., Bio/Technology, 9: 266 (1991)). Cell lines secreting antibody were expanded and antibody purified by protein A affinity chromatography (Harlow E, Lane D; in “Antibodies, a Laboratory Manual”, Cold Spring Harbor Laboratory (1988) page 309).
A de-immunized antibody was generated by analysis of the sequence of
A chimeric antibody comprising murine 340 VH and VL regions and human IgG1/kappa C regions was generated as detailed in Orlandi et al., ibid.
Comparative antibody binding to an epidermal growth factor receptor (EGFR) preparation from placenta. 30-40 g of human placenta was washed in PBS containing phenyl methyl sulfonyl, chopped finely, homogenized, lysed in 1% NP-40 and centrifuged at 10,000 g for 10 minutes. The supernatant was then loaded onto a CNBr-activated antibody 340 column (2 mg antibody per ml of gel) and eluted fractions were monitored by SDS-PAGE and protein analysis. ELISA plates were coated with fractions of EGFR preparation to give OD450 of 1.0 with murine 340 antibody using anti-mouse IgG peroxidase conjugate (Sigma). 1005 μl serial dilutions of the test recombinant antibodies and an irrelevant humanized antibody were incubated overnight in the ELISA plates and detected using peroxidase-labeled gamma chain-specific anti-human IgG antibody (Sigma). Results are shown in
In this example, a range of antibodies were tested in mice to compare immune responses. As a source of antibody to elicit an immune response in mice, the humanized VH fragment from Example 1 was deliberately altered to insert two murine MHC class II epitopes as shown in
The murine de-immunized VH fragment from above and the humanized and murine VH fragments from Example 1 were joined either to human or murine C region fragments of isotope IgG2. For human, a 7.2 kb HindIII-BamHI genomic fragment from IgG2 C region (Bruggemann et al., J. Exp. Med., 166: 1351 (1987)) was used and, for murine, a 4.2 kb EcoRI-Bg/II fragment from mouse IgG2bb (Ollo and Rougeon, Nature, 296: 761 (1982)) was used. Fragments were blunt-ended using the Klenow fragment of DNA polymerase and Bg/II linkers were added (according to the manufacturer's instructions (New England Biolabs, Beverly, Mass., USA) for cloning into the BamHI site of pSVgpt (Riechmann, ibid.). Recombinant plasmids were transfected by electroporation into J558L cells which secrete lambda light chains. Antibodies were purified from culture supernatants by protein A affinity chromatography as above.
To study immune responses, groups of five 6-8 week-old female BALB/c or C57BL/6 mice were injected intraperitoneally with 40 μg of recombinant antibody or murine 340 antibody in CFA. Serum was taken for analysis after 30 days and mice were boosted with the same antibodies in IFA; serum was again taken 10 days later. Antibody responses were measured in ELISA assays with the immobilized antibody used for immunization. Dilutions of sera were added and incubated for 2 hours at 37° C. Binding was then detected using biotinylated anti-mouse kappa chain antibody (Harlan-Seralab, Crawley, UK) and HRP-streptavidin (Pierce and Warriner, Chester, UK) according to the supplier's instructions. Color was developed with OPD (o-phenylenediamine) substrate (Sigma, Poole, UK). The results were expressed as serial dilutions from an average of 5 mice per group, (SD<20%) which gave half maximum binding to immobilized antibody on the ELISA plate.
The results are shown in
mRNA was isolated from 5×106 hybridoma 708 cells (Durrant et al., Int. J. Cancer, 50: 811 (1992) using TRIZOL™ reagent (Life Technologies, Paisley, UK) according to the manufacturers' instructions. The MRNA was converted to cDNA/mRNA hybrid using READY-TO-GO™ T-primed First Strand Kit (Pharmacia Biotech, St. Albans, UK). Variable region heavy (VH) and light (VL) chain cDNAs were amplified using the primer sets using the method of Jones and Bendig (Bio/Technology, 9: 188 (1991)). PCR products were cloned into pBLUESCRIPT II SK (Stratagene, Cambridge, UK) or pCRTM3 (Invitrogen, The Netherlands) and six individual clones each of VH and VL were sequenced ion both directions using the Applied Biosystems automated sequencer model 373A (Applied Biosystems, Warrington, UK). Resultant VH and VL sequences are shown in
A de-immunized antibody was generated by analysis of the sequence of
A set of vaccine molecules were constructed based on the 708 antibody. As before, the various VH and VL molecules were assembled from long synthetic oligonucleotides using the method of PCR recombination (Daugherty et al, ibid.). Cloning, sequencing, addition of human IgG1 and κ constant regions and expression in NS0 cells was as for the 340 antibody (Example 1).
The first antibody vaccine (“Vaccine 1”) comprised the 708 heavy and light chains from which all potential human T-cell epitopes have been removed from both antibody chains, using the method described in Example 1, including epitopes found in the CDRs, apart from the region encompassing CDRs 2 and 3 and framework 3 of the heavy chain which contains the desired human epitopes. The antibody chains were not “veneered” to remove B-cell epitopes. The resultant protein sequences are shown in
The second antibody vaccine (“Vaccine 2”) comprised 708 heavy and light chains with epitopes from carcinoembryonic antigen (CEA) inserted into CDRH2 and CDRH3 and CDRL1 and CDRL3. The resultant sequence was checked using the method described in Example 1 for generation of new human T-cell epitopes apart from those deliberately inserted. Single amino acid substitutions were made in the framework regions in order to remove any additional epitopes detected. The final protein sequences are shown in
The third antibody vaccine (“Vaccine 3”) comprised 708 antibody with CEA and CD55 epitopes inserted. The heavy chain was as Vaccine 2, with an epitope from CD55 inserted from position 14 to 33 (Framework 1 into CDR1). The resultant sequence was checked using the method described in Example 1 for generation of new human T-cell epitopes apart from those deliberately inserted. Single amino acid substitutions were made in the framework regions in order to remove any additional epitopes detected. The final protein sequence is shown in
A chimeric 708 antibody was prepared to provide a control for comparison with the above antibody vaccine constructs. This consisted of 708 murine variable regions combined with human IgG1 and κ constant regions. The oligonucleotides for assembly of 708 chimeric VH and VK are shown in
The present invention provides a method for the redesign of a pre-existing therapeutic antibody to which a human immune response has been detected. The invention provides the method by which the therapeutic antibody may be characterized to identify epitopes relating to the observed immune response in humans. An example of this is provided in a humanized version of monoclonal antibody A33. The monoclonal antibody (mAb) A33 antigen is a transmembrane glycoprotein expressed in normal colonic and bowel epithelium and >95% of human colon cancers. The A33 antigen has been considered a useful target for colon cancer radioimmunotherapy and encouraging pre-clinical data documented (Heath J. K. et al., Proc. Nat'l. Acad. Sci. USA, 94: 469-474 (1997)). A humanized version of mAb A33 has been produced using the CDR grafting strategy described elsewhere (WO-A-9109967, Adair J. R. et al.). Clinical trials of the humanized antibody were conducted during which a HAMA response to humanized mAb A33 was reported in a number of patients. In the present example, the variable region protein sequences for the humanized A33 antibody (
Potential MHC class II binding motifs in the variable region protein sequences of humanized antibody A33 were identified by the following method of peptide threading. The procedure involves computing a score for all possible candidate binding motifs (peptides) by considering the predicted three-dimensional conformations and interactions between an MHC class II molecule and the peptide complex. The computed score indicates the predicted binding affinity for the particular peptide and MHC allele, and is used to predict peptides likely to bind, or not to bind, with the particular MHC allele.
The HLA-DRB1*0101 molecule is currently the only example of a class II MHC molecule for which the structure is available (Stem et al., Nature, 368: 215-221 (1994)). This structure was used to predict peptide binding with HLA-DRB1. To predict peptide binding to other class II MHC alleles, models for particular alleles were constructed based on the known HLA-DRB1 structure. Models were constructed assuming the backbone structure of all class II MHC alleles are identical to HLA-DRB1. This assumption is supported by experimental data (Ghosh P. et al., Nature, 378: 457-462 (1995)) and the high degree of homology between different MHC class II molecules. Models were built by identification of the sequence differences between the known HLA-DRB1 structure and the target allele. Side-chains in the known structure were replaced to match the target allele. The side-chain conformation near the binding groove were adjusted to give favorable steric and electrostatic arrangement whilst maintaining the largest possible binding pocket. The latter feature of the approach is significant in ensuring that modeled peptide side-chains are most readily accommodated within the binding groove, so reducing the number of candidate fragments rejected due to steric overlap with the MHC.
The structural data of HLA-DRB1*0101 was obtained from the Protein Data Bank (Bernstein F. C. et al., J. Mol. Biol., 112: 535-542 (1977)). The ten most frequent HLA-DRB1 alleles in the human Caucasian population were modeled on the HLA-DRB1*0101 structure. Homology modeling of HLA-DRB1*03011, HLA-DRB1*0302, HLA-DRB1*0401, HLA-DRB1*0801, HLA-DRB1*09011, HLA-DRB1*11011, HLA-DRB1*1201, HLA-DRB1*1301, HLA-DRB1*1401 and HLA-DRB1*15011 was conducted using molecular the modeling package “Quanta” (Molecular Simulations Inc, University of York, England). Side-chain conformations in amino acids differing between a particular target allele and the HLA-DRB1*0101 solved structure were adjusted interactively. In most cases, torsion angles were chosen to result in minimal or nil steric overlap between mutated residues and surrounding atoms. Where non-conserved residues which were either charged, or carry side-chains able to form hydrogen bonds, were required to be inserted into the model, the potential to form favorable interactions was also considered.
All possible overlapping 13 amino-acid peptides from the humanized A33 antibody variable region protein sequences were examined. Each peptide sequence was used to form a three-dimensional model of the candidate peptide in complex with the given MHC allele. Peptide model structures were built assuming a backbone conformation and location relative to the MHC backbone structure identical to that of the previously solved structure for HLA-DRB1 in complex with an influenza hemagglutinin protein (Stem L. J. et al., ibid.). This assumption is supported by available evidence (Jardetzky T. S. et al., Nature, 368: 711-718 (1994); Ghosh P. et al., ibid.). Side-chains in the peptide were modeled automatically to match the sequence of the peptide under investigation, and the conformational space of each side chain was explored automatically to minimize or eliminate steric overlap and unfavorable atomic contacts, whilst also maximizing favorable atomic contacts.
A score for each peptide was computed based upon the predicted inter-atomic contacts between peptide and MHC residues. Pair-wise residue-residue interaction scores were used to reward and penalize specific inter-residue contacts. The geometric constraints imposed on the peptide by the shape of the MHC binding groove play an important part of the scoring function. To reflect this, the scoring function awards favorable packing arrangements, whilst interactions involving steric overlap are penalized. Published data (Ghosh P. et al., ibid.; Stem L. J. et al., ibid.; Marshall K. W. et al., J. Immunol., 152: 4946-4957 (1994); Hammer J. et al., Cell, 74:197-203 (199); Sinigaglia F. & Hammer J. Current Opin. Immunol., 6: 52-56 (1994)] indicate that larger pockets within the MHC class II binding groove are more important in determining which peptides can bind compared with smaller pockets. The scores contributed by each pocket are also weighted based on pocket size. Peptides with the highest scores are predicted to be the best binders to the particular MHC allele.
Results from this approach are given by way of examples in Tables 1-4. These tables show output from the peptide threading process for heavy and light chains against HLA-DRB1*0101 and HLA-DRB1*03011 alleles only, although threading was performed using structural models compiled for a total of 11 HLA-DRB1 alleles. Following subtraction of sequence strings in the variable regions which are present in a database of human germ-line immunoglobulin variable region genes, four regions containing potential MHC class II binding motifs in the heavy and light chain humanized A33 variable regions are identified. This result is concordant with comparative searching of an MHC-binding motif database as resident on the world wide web site of the Walter and Eliza Hall Institute of Medical Research.
The potential MHC class II binding motifs identified by the use of peptide threading and corroborated with MHC-binding motif database searching were eliminated from the humanized A33 variable region protein sequences by amino-acid substitutions at specific residues (
In this example the method of the present invention is used to identify and eliminate potential epitopes from the murine sequence of antibody A33 (King D. J. et al., Brit. J. Cancer, 72: 1364-1372 (1995)). The humanized version of A33 was described in example 5, in the present example the starting point is the murine A33 antibody. The sequences of the VH and VL of the murine A33 antibody are shown in
The present invention details a process whereby potentially immunogenic epitopes within a non-autologous protein may be identified and offers methodology whereby such epitopes may be eliminated. There are a number of proven therapeutic proteins for which their therapeutic use is curtailed on account of their immunogenicity in man. In the present example the therapeutic protein streptokinase is analyzed for the presence of potential MHC binding motifs and a method disclosed for the removal of a number of these from the molecule.
Streptokinase (SK) is a single chain protein of approximate molecular weight 47 kDa that is produced by certain strains of β-hemolytic streptococci (Huang T. T. et al., Mol. Biol., 2: 197-205 (1989)). The protein has no inherent enzymatic activity but has considerable clinical importance owing to its ability to efficiently bind human plasminogen, potentiating its activation to plasmin and thereby promoting the dissolution of fibrin filaments in blood clots. Several studies have shown that SK is an effective thrombolytic agent in the treatment of 5 coronary thrombosis, improving survival (ISIS-2 Collaborative Group, Lancet, 2: 349-360 (1988)) and preserving left ventricular function following myocardial infarction (ISAM Study Group, N. Engl. J. Med., 314: 1465-1471 (1986); Kennedy J. W. et al., Circulation, 77; 345-352 (1988)). Despite the undoubted therapeutic value of SK, the non-autologous origin of the protein is disadvantageous due to its immunogenicity in humans. The production of neutralizing antibodies in the patient in generally limits the protein to a single use.
The following method was used to identify potential MHC class II binding motifs in streptokinase. The sequence of streptokinase was identified from the GenBank database. The sequence with accession number S46536 was used throughout (
Results of the “searching” process indicate the presence of 395 potential MHC class II binding motifs. Of these, 283 matched sequences identified in a database of human germ-line immunoglobulin variable region protein sequences. These epitopes were not considered further on the basis that immune responses in general are not mounted to autologous circulating proteins such as immunoglobulins. This implies immunological tolerance to the potential T-cell epitopes present in the structure of the immunoglobulins (and indeed the majority of human proteins). Epitopes presented by non-autologous proteins such as SK which are identical or similar to motifs present in immunoglobulin proteins are likely also to be tolerated and in practice may be retained through the de-immunization process.
Following subtraction of the human immunoglobulin protein germ-line motifs, the remaining 112 potential epitopes were analyzed individually for similarity to non-immunoglobulin protein sequences. In practice, predicted anchor residues for each potential epitope was used in a consensus sequence search of human expressed proteins. The SwissProt and GenBank translated sequence databases were interrogated using commercially available software (DNAstar Madison, Wis., USA). Epitopes identified in known circulating human proteins were not considered further and were therefore allowed to remain unchanged within the SK molecule. An example of one such rejected potential epitope is given by the sequence LLKAIQEQL (SEQ ID NO: 83) at positions 79-87 in the SK protein. This sequence represents a predicted consensus binding motif for HLA-DR1*0101 with anchor residues underlined. Database searching using the consensus sequence LxxxAxxxxL identifies >4000 entries in a human protein sub-set of the SwissProt database, including serum albumin protein (SwissProt accession number P02768). An example of an epitope where no match to a human protein considered to be in the general circulation was found is provided by sequence YVDVNTN (SEQ ID NO: 84) at position 299-305 in the SK protein. This sequence represents a potential epitope for presentation by HLA-DR4*0401. Consensus sequence searching identifies <50 human proteins containing this motif, of which many are intracellular proteins of differentiated tissues such as brain. These may be considered as not generally available to the immune system to gain tolerance and therefore identify this as a potential epitope for elimination according to the method of the present invention. Similarly, a further potential HLA-DR1*0101 binding motif was identified in the SK peptide sequence KADLLKAI (SEQ ID NO: 85) at positions 76-83 of the SK protein. This motif identifies <150 human proteins in the same data set and was also identified for modification by the method of the present invention.
The net result of these processes was to identify those residues within the SK molecule which should be altered to eliminate potential MHC class II binding motifs. Individual amino acids within the predicted binding motifs were selected for alteration. With the object of maximizing the likelihood of maintaining protein functional activity, in all cases conservative amino acid substitutions were chosen at any given site. A new (de-immunized) SK sequence was compiled (
The following method was used for the construction of de-immunized SK molecules. PCR primers SK1 (5′-ggaattcatgattgctggacctgagtggctg; SEQ ID NO: 86) and SK2 (5′-tggatccttatttgtcgttagggtatc; SEQ ID NO: 87) were used to amplify the wild-type SK gene from a strain of Streptococcus equisimililis group C (ATCC accession number 9542). The resulting 1233 bp fragment was cloned into pUC19 as a BamHI-EcoRI restriction fragment using standard techniques (Sambrook J., Fritisch E. F. & Maniatis T. (eds) in: “Molecular Cloning: A Laboratory Manual”, Cold Spring Harbor Laboratory Press, New York, USA (1989). The gene sequence was confirmed to be identical to database entries using commercially available reagent systems and instructions provided by the supplier (Amersham, Little Chalfont, UK). Site directed mutagenesis was conducted using synthetic oligonucleotides and the “quick-change” procedure and reagents from Stratagene UK Ltd. Mutated (de-immunized) versions of the gene were confirmed by sequencing. Mutated SK genes were sub-cloned as EcoRI-BamHI fragments into the bacterial expression vector pEKG-3 (Estrada M. P. et al., Bio/Technology, 10: 1138-1142 (1992)) for expression of de-immunized SK. Recombinant protein was purified using a plasminogen affinity column according to the method of Rodriguez et al., [Rodriguez P. et al., Biotechniques, 7: 638-641 (1992)). Fibrinolytic activity was assessed using the casein/plasminogen plate technique and the in vitro clot lysis assay as described by Estrada et al. (ibid.).
| Number | Date | Country | Kind |
|---|---|---|---|
| 9710480.6 | May 1997 | GB | national |
| 9716197.0 | Jul 1997 | GB | national |
| 9725270.4 | Nov 1997 | GB | national |
| 9807751.4 | Apr 1998 | GB | national |
This application is a division of U.S. application Ser. No. 10/300,215, filed on Nov. 20, 2002, which is a continuation of U.S. application Ser. No. 09/438,136 filed on Nov. 10, 1999, now abandoned, which is a continuation of International Application Ser. No. PCT/GB98/01473, filed on May 21, 1998, which designates the United States and claims the benefit of U.S. Provisional Application Ser. No. 60/067,235, the disclosures of which are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 60067235 | Dec 1997 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 10300215 | Nov 2002 | US |
| Child | 11516295 | Sep 2006 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 09438136 | Nov 1999 | US |
| Child | 10300215 | Nov 2002 | US |
| Parent | PCT/GB98/01473 | May 1998 | US |
| Child | 09438136 | Nov 1999 | US |
