Patent Grant
10668147
This is a US national phase application under 35 USC § 371 of international patent application no. PCT/EP2015/056386, filed Mar. 25, 2015, herein incorporated by reference in its entirety.
The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with file “PCTEP2015056386_SEQ_ID” created on 9 Sep. 2017, filed on 22 Sep. 2017 and having a size of 24 Kilobytes. The sequence listing contained in this ASCII formatted document forms part of the specification and is herein incorporated by reference in its entirety.
The technology provided herein relates to novel complexes suitable for targeting and killing a human target cell comprising a first polypeptide with a binding structure for binding the complex to the cellular surface receptor CD89 presented on the cell surface of the human target cell and a second polypeptide comprising a toxic effector domain; to nucleic acid molecules encoding said complexes, vectors, host cells containing the nucleic acids and methods for preparation and producing such complexes; compositions and methods for using said complexes for the treatment of diseases, in particular of cancer diseases like leukemia.
In the treatment of tumors, autoimmune diseases, allergies and tissue rejection reactions, it is a disadvantage that the currently available medicaments, such as chemotherapeutic agents (Goodin, S., Am J Health Syst Pharm, 2007, 64: p. 15-24) corticosteroids (Stanbury, R. M. & Graham, E. M., Br J Ophthalmol, 1998, 82: p. 704-708) and immunosuppressive agents (Stucker, F. & Ackermann, D., Ther Umsch, 2011, 68: p. 679-686), have a potential of side effects which is sometimes considerable, due to their relative non-specificity. It has been attempted to moderate this by various therapeutical concepts. Especially the use of immunotherapeutic agents is an approach, which resulted in an increase of the specificity of medicaments, especially in tumor treatment.
Immunotoxins (ITs) are proteins originally developed for the treatment of malignant diseases. They comprise a toxic effector domain and a tumor cell-specific binding component, which is usually an antibody or a derivative thereof. Initially the antibody components were derived from mice and the toxins were derived from bacteria or plants, e.g. Pseudomonas aeruginosa exotoxin A (ETA) (Ribbert, T., et al., Br J Dermatol, 2010; 163: p. 279-86), diphtheria toxin (DT) (Potala, S., et al., Drug discovery today, 2008, 13: p. 807-15) or ricin A toxin (RT) (Thepen T., et al., Nature biotechnology, 2000, 18: p. 48-51.). The major advantage of ITs compared to traditional chemotherapy is their exceptional specificity towards targeted cells.
Fusion proteins that consist of a disease-specific binding component (e.g. scFvs, cytokines or peptide ligands) fused to a human toxic effector domain like a pro-apoptotic enzyme are known as ‘human cytolytic fusion proteins’ (hCFPs) and have already proven their potential in several applications (Stahnke, B., et al., Mol Cancer Ther, 2008. 7(9): p. 2924-32; Huhn, M., et al., Cancer Res, 2001. 61(24): p. 8737-42; Krauss, J., et al., Br J Haematol, 2005. 128(5): p. 602-9; Schiffer, S., et al., Antibodies, 2013. 2(1): p. 9-18; Hristodorov, D., et al., Br J Cancer, 2014. 109(6): p. 1570-1578).
The therapeutic activity of most anticancer drugs in clinical use is limited by their general toxicity to proliferating cells, including some normal cells. Although, chemists continue to develop novel cytotoxic agents with unique mechanisms of action, many of these compounds still lack tumor selectivity and have not been therapeutically useful. Antibodies or fragments ablated thereof meaning also ITs and hCFPs bind to specific markers on the surface of cancer cells offer an alternative therapy that is tumor highly specific and thus much less toxic (Chari, R V, Accounts of chemical research, 2008, 41: p. 98-107).
However, in order to obtain the desired cytotoxic effect of ITs and/or hCFPs some processing steps in the targeted cells are crucial. Next to the necessary binding and internalization of the IT- or hCFP-antigen complex, key impact on the activity has the subsequent intracellular routing with and cytosolic delivery Berges, N., et al. Antibodies, 2014, 3(1): p. 92-115).
An example is the treatment of leukaemia using immunotherapy, which requires the targeting of specific antigens on the surface of blasts. The Fc gamma receptor (FcγRI, CD64) has been investigated into details. The CD64-targeting immunotherapy has shown promising efficacy in the targeted ablation of acute myeloid leukaemia (AML) and chronic myeloid leukaemia (CML) cells. Thus far, CD64 is the only Fc receptor deemed suitable as an immunotherapeutic target for both oncogenic and inflammatory diseases. Nevertheless, there are plenty of clinical cases of malignancies lacking the CD64 expression (Schiffer, S., et al., Int J Cancer, 2014, 135: p. 1497-508), which excludes the possibility of efficient CD64-targeting therapy.
Furthermore, the cytotoxic efficacy of the IT- or hCFP is crucially dependent on the used scFv and the subsequent intracellular routing occurring after the IT- or hCFP-antigen complex internalization. Thus, the chosen scFv, in combination with the toxic effector domain, has to fulfill several requirements in order to acquire IT- or CFP cytotoxicity.
As a result thereof, the availability of novel ITs or human cytolytic fusion proteins comprising new binding moiety, which covers all requirements, would be highly advantageous.
In a first aspect, the present disclosure pertains to selected and specific complexes suitable for targeting and killing a human target cell, in particular a human cancer cell, comprising a first polypeptide having a binding structure for binding the complex to the cellular surface receptor CD89 presented on the cell surface of said human target cell and a second polypeptide comprising a toxic effector domain.
Therefore, embodiments of the disclosure provides cytotoxic recombinant ITs and human cytolytic fusion proteins (hCFPs), for example which are suitable to induce apoptosis in human cells, comprising a target cell-specific binding component and a toxic effector domain, wherein the binding component comprises an antibody or an antibody fragment with an antigen-binding site for binding to the cellular surface receptor CD89.
In still another aspect, embodiments of this disclosure provide nucleic acids encoding complexes, in particular recombinant fusion proteins as disclosed herein, as well as vectors and host cells comprising such nucleic acids.
In other aspects, the present disclosure relates to compositions comprising the complexes according to the present disclosure, in particular the recombinant fusion proteins as described herein, wherein the complexes may be useful for, or used in therapeutical, cosmetic and/or diagnostic applications. In an advantageous embodiment, the compositions are used as a therapeutical composition for the treatment of cancer, in particular in the treatment of leukemia.
In still another aspect, embodiments of this disclosure provide medicaments or pharmaceutical composition comprising a complex according to the present disclosure in combinations with a pharmacologically acceptable carrier, diluent, stabilizer or formulation.
In a further aspect, embodiments of the present disclosure relate to methods for producing the complexes, in particular for producing the recombinant fusion proteins in a host cell by transforming the host cell with a DNA construct, advantageously including a promoter having transcriptional activity in the host cell, cultivating the transformed host cell in a suitable culture medium to allow expression of said fusion proteins and producing said fusion proteins. The method may also include isolating/purifying the produced fusion proteins.
A further aspect pertains to methods of treating a malignant disease, an allergy, an autoimmune reaction, a tissue rejection reaction, or a chronic inflammation reaction comprising administering an effective amount of a complex or a pharmaceutical composition according to the present disclosure to a patient in need thereof.
A further aspect relates to polypeptides suitable for the detection of CD89, wherein said polypeptide comprises the amino acid sequence of SEQ ID NO: 1, or a homologous polypeptide, variant or mutation thereof having an amino acid which is at least 85%, preferably 90%, more preferably 95% identical to the amino acid sequence of SEQ ID NO. 1, which are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
Another aspect of the present disclosure pertains to methods for the detection of CD89 contained in a sample, comprising:
(a) contacting a sample with a polypeptide with a fusion tag specific fluorophore that specifically bind the fusion tag coupled to said polypeptide; and
(b) detecting the presence of CD89 in the sample by fluorescence signals associated with the fusion tag specific fluorophore.
Therefore, aspects of the present disclosure pertains also to methods for the diagnosis of CD89+ malignancies, comprising administering to a patient a polypeptide suitable for the detection of CD89 as described herein or contacting a biological sample taken from a patient with a polypeptide suitable for the detection of CD89 as described herein.
Before the disclosure is described in detail, it is to be understood that this disclosure is not limited to the particular complexes, in particular the ITs and hCFPs and production methods described in the present disclosure. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include singular and/or plural referents unless the context clearly dictates otherwise. It is moreover to be understood that, in case parameter ranges are given which are delimited by numeric values, the ranges are deemed to include these limitation values.
The present disclosure provides potent, novel immunotherapeutic agents, in particular complexes suitable for CD89-specific targeting and killing/destroying of human cancer cells.
According to the present disclosure, the therapeutic potential of FcαRI (CD89) as a new target polypeptide immunotoxin target antigen expressed by different cancer cells like myeloid leukemic cell populations for immunotoxins (ITs) or human cytolytic fusion proteins (hCFPs) is shown the first time with the present disclosure. Some embodiment of the present disclosure pertains to isolated a recombinant fusion proteins comprising an anti-human CD89 single chain fragment variable (scFv) and the well-characterized truncated version of the potent Pseudomonas exotoxin A (ETA′).
These novel therapeutic approach achieved in vitro EC50 values in range 0.2-3 nM depending on applied stimuli, i.e. interferon gamma (IFNγ) or tumour necrosis factor α (TNFα).
A dose-dependent apoptosis-mediated cytotoxicity was also observed, which resulted in the eradication of up to 90% of the target cells within 72 h. These findings were also confirmed ex vivo using e.g. leukaemic primary cells from peripheral blood samples.
CD89-specific targeting of leukaemia cell lines can be achieved in vitro and the efficient elimination of leukaemic primary cells supports the potential of CD89-ETA′ as a potent, novel immunotherapeutic agent.
Therefore, in a first aspect the present disclosure pertains to selected and specific complexes suitable for targeting and killing human target cells, in particular of human cancer cells, comprising a first polypeptide with a binding structure for binding said complex to the cellular surface receptor CD89 presented on the cell surface of said human target cell and a second polypeptide comprising a toxic effector domain.
Advantageous embodiments of the present disclosure pertains to Immunotoxins (ITs) and recombinant human cytolytic fusion proteins (hCFPs) suitable for killing a target cell like a human cancer cell, e.g. by inducing apoptosis, comprising a target cell-specific binding component (binding structure) and a toxic effector domain, wherein the binding component comprises an antibody or an antibody fragment with an antigen-binding site for binding to the cellular surface receptor CD89 presented on the surface of the target cell.
In an advantageous embodiment, the complex or at least the toxic effector domain are transferred into the target cell. Therefore, the toxic effector domain is preferably transferable into the target cell after binding to the CD89 protein.
The terms “polypeptide”, “peptide”, or “protein” are used interchangeably herein to designate a linear series of amino acid residues connected one to the other by peptide bonds between the alpha-amino and carboxyl groups of adjacent residues. The amino acid residues are preferably in the natural “L” isomeric form. However, residues in the “D” isomeric form can be substituted for any L-amino acid residue, as long as the desired functional property is retained by the polypeptide. In addition, the amino acids, in addition to the 20 “standard” amino acids, include modified and unusual amino acids.
As mentioned above, the present disclosure relates to isolated/purified complexes, in particular isolated recombinant fusion proteins, comprising at least one component A (binding structure) and at least one component B (toxic effector domain), characterized in that component A has a binding activity for the cellular surface receptor CD89 presented on the surface of a target cell, and component B is a compound having cytotoxic and/or cytolytic activity.
The terms “recombinant fusion protein” and “fusion protein” are used herein interchangeably to refer for example to a protein produced by recombinant technology which comprises segments i.e. amino acid sequences, from heterologous sources, such as different proteins or different organisms. The segments are joined either directly or indirectly to each other via peptide bonds. By indirect joining it is meant that an intervening amino acid sequence, such as a peptide linker is juxtaposed between segments forming the fusion protein. A recombinant fusion protein is encoded by a nucleotide sequence, which is obtained by genetically joining nucleotide sequences derived from different regions of one gene and/or by joining nucleotide sequences derived from two or more separate genes.
Furthermore, the encoding nucleotide sequences may be synthesized in vitro without the need for initial template DNA samples e.g. by oligonucleotide synthesis from digital genetic sequences and subsequent annealing of the resultant fragments. Desired protein sequences can be “reverse translated” e.g. using appropriate software tools. Due to the degeneracy of the universal genetic code, synonymous codons within the open-reading frame (i.e. the recombinant protein coding region) can be exchanged in different ways, e.g. to remove cis-acting instability elements (e.g. AUUUA), to remove, introduce or modify the secondary and tertiary mRNA structures (e.g. pseudoknots, stem-loops, . . . ), to avoid self-complementary regions that might trigger post-transcriptional gene silencing (PGTS), to change the overall AT:GC content, or to adjust the codon-usage to the expression host. Such changes can be designed manually or by using appropriate software tools or through a combination.
A complex comprising a first polypeptide having binding activity for the cellular surface receptor CD89 presented on the surface of a CD89 expressing target cell and a second polypeptide comprising a toxic effector domain can be a recombinant product prepared using recombinant DNA methodology and expression in a suitable host cell, as is known in the art (see for example (Sambrook, J. & Russell, D., Molecular Cloning: a Laboratory Manual, 2001, 3rd ed).
In an advantageous embodiment, the complexes according to the present disclosure, in particular the recombinant fusion proteins are isolated. The term “isolated” when used in relation to a nucleic acid or protein refers to a nucleic acid sequence or protein that is identified and separated from at least one contaminant (nucleic acid or protein, respectively) with which it is ordinarily associated in its natural source. Isolated nucleic acid or protein is present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids or proteins are found in the state they exist in nature.
According to the present disclosure, the first polypeptide comprising a binding structure (component A) and the second polypeptide comprising a toxic effector domain (component B) are preferably linked to each other in a complex. “Linked” refers to non-covalent or covalent bonding between two or more molecules. Linking may be direct or indirect. Two molecules are indirectly linked when the two molecules are linked via a connecting molecule (linker). Two molecules are directly linked when there is no intervening molecule linking them. As mentioned above, the isolated protein domains are linked either directly or indirectly to each other, preferably via peptide bonds or disulfide bonds. An example of indirect covalent linking is that an intervening amino acid sequence, such as a peptide linker is juxtaposed between segments forming the fusion protein.
In some embodiments, the components A and B are directly linked to each other. In other embodiments, the components are indirectly linked to each other via a linker, wherein in some examples the linker is a polypeptide with a size of less or equal twenty amino acids, in particular 2 to 6 amino acids.
The term “binding structure” used herein comprises polypeptides having a binding activity for the cellular surface receptor CD89, in particular to the extracellular part of CD89 (SEQ ID NO. 6). For example, the polypeptide comprises a cell targeting moiety that is a moiety that binds to and/or is internalized by only a selected population of cells such as cells expressing the cellular receptor CD89. Such a cell targeting moiety may, for example, comprise an antibody, a growth factor, a hormone, a cytokine, an aptamer or an avimer that binds to CD89. Examples for binding moieties comprised in the ligand are affinity moieties from affinity substances or affinity substances in their entirety selected from the group consisting of antibodies, antibody fragments, receptor ligands, enzyme substrates, lectins, cytokines, lymphokines, interleukins, angiogenic or virulence factors, allergens, peptidic allergens, recombinant allergens, allergen-idiotypical antibodies, autoimmune-provoking structures, tissue-rejection-inducing structures, immunoglobulin constant regions and their derivatives, mutants or combinations thereof. In particular the target cell-specific binding component specifically binds to CD89.
In an advantageous embodiment, the binding structure is an antibody or an antibody fragment selected from the group consisting of a monoclonal antibody, Fab, scFv; single domain, or a fragment thereof, bis scFv, Fab2, Fab3, minibody, diabody, triplebody, tetrabody and tandab.
An antibody is in particular specific for a particular antigen if it binds that particular antigen in preference to other antigens. In particular, the antibody may not show any significant binding to molecules other than that particular antigen, and specificity may be defined by the difference in affinity between the target antigen and other non-target antigens. An antibody may also be specific for a particular epitope which may be carried by a number of antigens, in which case the antibody will be able to bind to the various antigens carrying that epitope. For example, specific binding may exist when the dissociation constant for a dimeric complex of antibody and antigen is 1 μM, preferably 100 nM and most preferably 1 nM or lower.
As used herein, an “antibody” refers to a protein consisting of one or more polypeptides substantially encoded by immunoglobulin genes or fragments of immunoglobulin genes. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.
A typical immunoglobulin (antibody) structural unit is known to comprise a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains, respectively.
Antibodies exist as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′2, a dimer of Fab which itself is a light chain joined to V.sub.H-C.sub.H1 by a disulfide bond. The F(ab)′2 may be reduced under mild conditions to break the disulfide linkage in the hinge region thereby converting the (Fab′)2 dimer into two Fab′ monomers. The Fab′ monomer is essentially a Fab with part of the hinge region (Paul, W E., Fundamental immunology, 1993, 3rd ed). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such Fab′ fragments may be synthesized de novo either chemically or by utilizing recombinant DNA technology. Thus, the term antibody, as used herein also includes antibody fragments either produced by the modification of whole antibodies or synthesized de novo using recombinant DNA technologies. Preferred antibodies include single chain antibodies (antibodies that exist as a single polypeptide chain), more preferably single chain Fv antibodies (scFv) in which a variable heavy and a variable light chain are joined together (directly or through a peptide linker) to form a continuous polypeptide. The single chain Fv antibody is a covalently linked VH-VL heterodimer which may be expressed from a nucleic acid including VH- and VL-encoding sequences either joined directly or joined by a peptide-encoding linker (Huston, J S., et al., Proc Natl Acad Sci USA, 1988, 85: p. 5879-83). While the VH and VL are connected to each as a single polypeptide chain, the VH and VL domains associate non-covalently.
An “antigen-binding site” or “binding moiety” in an antibody or antibody fragment refers to the part of an immunoglobulin molecule that participates in antigen binding. The antigen binding site is formed by amino acid residues of the N-terminal variable (“V”) regions of the heavy (“H”) and light (“L”) chains. Three highly divergent stretches within the V regions of the heavy and light chains are referred to as “hypervariable regions” which are interposed between more conserved flanking stretches known as “framework regions” or “FRs”. Thus, the term “FR” refers to amino acid sequences which are naturally found between and adjacent to hypervariable regions in immunoglobulins. In an antibody molecule, the three hypervariable regions of a light chain and the three hypervariable regions of a heavy chain are disposed relative to each other in three dimensional space to form an antigen binding “surface”. This surface mediates recognition and binding of the target antigen. The three hypervariable regions of each of the heavy and light chains are referred to as “complementarity determining regions” or “CDRs” and are characterized, for example by Kabat et al. Sequences of proteins of immunological interest, 4th ed. U.S. Dept. Health and Human Services, Public Health Services, Bethesda, Md. (1987).
Therefore, the term antibody includes, but is not limited to, polyclonal antibodies, monoclonal antibodies, single chain antibodies, humanized antibodies, minibodies, diabodies, triplebodies as well as antibody fragments, such as Fab′, Fab, F(ab′)2, single domain antibodies. In an advantageous embodiment, the antibody is a human antibodies and the antibody fragment is a human antibody fragment.
Therefore, as mentioned above, the binding structure is preferably an antibody or an antibody fragment selected from the group consisting of a monoclonal antibody, Fab, scFv; single domain, or a fragment thereof, bis scFv, Fab2, Fab3, minibody, diabody, triplebody, tetrabody and tandab that is able to bind to the cellular surface receptor CD89 presented on the cell surface of said human target cell.
The binding activity of the targeting moiety can be verified by flow cytometry assisted measurement using said human target cells in appropriate stage and appropriate detection antibodies suitable for the mentioned analysis.
In an advantageous embodiment, the complex according to the present disclosure comprises a CD89-specific single-chain variable fragment (scFv) as the binding structure for binding the complex to the cellular surface receptor CD89 presented on the cell surface of a human target cell.
As used herein, the term “single chain antibody fragments” (scFv) refers to antibodies prepared by determining the binding domains (both heavy and light chains) of a binding antibody, and supplying a linking moiety, which permits preservation of the binding function. This forms, in essence, a radically abbreviated antibody, having only that part of the variable domain necessary for binding to the antigen. Determination and construction of single chain antibodies are described in U.S. Pat. No. 4,946,778 by Ladner et al.
In an advantageous embodiment, the binding structure is a human or humanized antibody or an antibody fragment. As used herein, the term “human antibody” or “human antibody fragment” means that the framework regions of an immunoglobulin or an immunoglobulin fragment are derived from human immunoglobulin sequences. In an advantageous embodiment, the binding structure is a human or humanized antibody or an antibody fragment.
The phrase “specifically binds to CD89” refers to a binding reaction, which is determinative of the presence of the CD89 protein in the presence of a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies or antibody fragments bind to CD89 and do not bind in a significant amount to other proteins present in the sample. Specific binding to a protein under such conditions may require an antibody or antibody fragment that is selected for its specificity for CD89.
The binding activity of the targeting moiety can be verified by flow cytometry assisted measurement using said human target cells in appropriate stage and appropriate detection antibodies suitable for the mentioned analysis.
As used herein, the term “CD89” refers to a human surface Fc alpha-receptor (FcαR, CD89). Under normal physiological conditions the Fc alpha-receptor is present on monocytes, neutrophils, macrophages and eosinophils. Its biological function is to interact with IgA-opsonised targets, triggering several immunological defence processes, e.g. phagocytosis, antibody-dependent cell-mediated cytotoxicity, and the stimulation of inflammatory mediators (Morton, H C. & Brandtzaeg, P., Arch Immunol Ther Exp 1 2001; 49: 217-29). In many human tissues, most of the CD89+ cells are neutrophils and monocytes/macrophages. Furthermore, although monocytes in the blood express relatively high levels of CD89, most tissue macrophages (particularly those located in the gut lamina propria) tend not to express CD89 on the surface, with a parallel down regulation of CD14 (Hamre, R., et al., Scand J Immunol, 2003, 57: p. 506-16). This suggests that the abundance of CD89 depends on the differentiation stage of myeloid cells. The biological relevance of CD89 down regulation during the maturation of myeloid precursor cells is unknown.
On the other hand, the presence of anomalous numbers of myeloid cells in the blood is indicative of several myelogenous haematological malignancies, with AML and CML the most common (Horner, M J R L., et al., National Cancer Institute, 2009). The different forms of myeloid leukaemia have been categorised using the French-American-British (FAB) system into eight subtypes (M0-M7) and the World Health Organisation (WHO) uses similar criteria (Sander, C A., et al., Clin Lymphoma 2001, 2: p 86-100). A standard panel of markers is used for detailed diagnosis and classification, including FcγRI (CD64) that is present on AML subtypes M0-M5 in varying degrees (Dunphy, C H. and Tang W., Archives of pathology & laboratory medicine, 2007, 131: p. 748-54). Thus far, there was no evidence that other Fc receptors can be used as diagnostic antigens or therapeutic targets in AML or other forms of myeloid leukaemia.
As used herein, the expression “killing a human target cell” is to be understood as implying an inhibition of protein synthesis or induction of apoptosis resulting in elimination or death of these cells; various molecular mechanisms may be employed; for example mechanisms that alter the function of a cell, those that alter the gene expression pattern of a cell or those that directly affect the viability of a cell may be used.
As used “killing a human target cell” herein may also comprise to inhibit the cell growth (e.g., referring to cells) intending to include any measurable decrease in the growth of a cell when contacted with an anti-CD89 complex according to the present disclosure as compared to the growth of the same cell not in contact with an anti-CD89 complex according to the present disclosure, e.g., the inhibition of growth of a cell by at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 99%, or 100%.
As used herein, the expression “CD89 expressing cells” refers to cells with CD89 as surface antigen. Any type of cell expressing CD89 may be envisaged for treatment with the cytotoxic/cytolytic complexes of the present disclosure.
A “target cell” refers to a cell or cell-type characterized by the expression or overexpression of the target molecule CD89 that is for example characteristic for some tumor cells like leukemia cells including myeloid leukaemic cells. CD89 (FcαR) was initially identified on the surface of several human phagocytic cells, including neutrophils, monocytes and macrophages. CD89-expressing immune cells have a protective function in the immune system, but they are also involved in pathogenesis of different diseases. For example, neutrophils contribute to several autoimmune disorders (e.g. systemic lupus erythematosus), inflammatory disorders, NETosis and cystic fibrosis.
“Target cell” shall mean further any undesirable cell in a subject (e.g., a human or animal) that can be targeted by a complex or polypeptide of the present disclosure. In one embodiment, the target cell is a cell expressing or overexpressing CD89. In another embodiment, target cells include tumor cells. Tumor cells that can be targeted are tumor cells of any type of cancer, including cancer of breast, ovarian, prostate, testicular, lung, colon, rectum, pancreas, liver, central nervous system, kidney, head, neck, bone, blood, and lymphatic system. In addition to tumor cells, the effector cell can be targeted against auto-antibody producing lymphocytes for treatment of autoimmune disease or an IgE-producing lymphocyte for treatment of allergy. The target can also be microorganism (bacterium or virus) or a soluble antigen (such as rheumatoid factor, or other auto-antibodies and toxins). A microorganism is intended to include pathogens, e.g., viruses, bacteria, fungi, protozoa.
Therefore, the complexes according to the present disclosure may be used in different indications like the treatment of malignant diseases, such as acute myeloid leukemia, allergies, chronic inflammatory diseases, autoimmune diseases, including graft versus host, macrophage activation syndrome, arthritis, rheumatoid arthritis, juvenile arthritis and the elimination of myeloid-derived suppressor cells. In particular, the complexes according to the present disclosure may be used in the treatment of leukemia, neutrophilia, acute and chronic neutrophilic leukaemia (CNL), chronicmyeloid leukemia (CML).
Therefore, the complexes of the present disclosure are suitable for targeting and killing a human CD89 expressing cell (human target cell) comprising a first polypeptide comprising a binding structure for binding the complex to the cellular surface receptor CD89 presented on the cell surface of said human target cell and a second polypeptide comprising a toxic effector domain.
A compound or a substance can be tested for its toxic effect in one or both of the following assays: XTT-based colorimetric cell viability assay (Roehm, N W., et al., J Immunol Methods, 1991, 142: p. 257-) and AnnexinV/PI apoptosis assay (Vermes, I., et al., J Immunol Methods 1995; 184: 39-51).
The “toxic effector domain”, here also called “target cell killing domain” comprised in the complex is a peptide or polypeptide that has toxic activity in the targeted cell and may be selected from the group consisting of a human protease, a human serine protease such as granzyme B, a bacteria-originated toxic protein such as the Pseudomonas aeruginosa exotoxin A, a human hydrolase such as angiogenin, a human cytoskeleton-associated protein such as the microtubule-associated protein tau, a photosensitizer or a plant-originated toxin such as Ricin A, or variants or functional fragments thereof.
Further examples include ADP ribosylating enzymes like pseudomonas exotoxin A, diphteria, cholera-, pertussis- and botulinotoxin and ribosome inactivating proteins like diathin, saporin, bryodin, gelonin, ricin, abrin or restrictocin. Further, ribonucleases (Phosphodiesterases) RNAse H, angiogenin, eosinophil-derived neurotoxin (EDN), eosinophilic cationic protein, onconase and bullfrog lektin. Further examples are prodrug activating enzymes as caliceamicin, glucoseoxidase, carboxypeptidase, alkaline phosphatase, cytosindeaminase, beta-glycosidase, beta-glucoronidase, beta-lactamase, nitroreductase, thymidinkinase or purin-nucleosid phosphorylase. Furthermore, cathepsines, granzymes and combinations and possible variations of the before mentioned protein families. Preferred embodiments are validated toxins as ricin A, alpha sarcin (family of lectins), diphteriatoxin and pseudomonas exotoxin A since these toxins are subjects of several clinical studies and their efficacy is well documented. In an advantageous embodiment, the complex according to the present disclosure comprises a second polypeptide selected from the group consisting of Pseudomonas aeruginosa exotoxin A (ETA), granzyme B or a variant thereof comprising the substitution R201K (GbR201K, disclosed in EP2758527), angiogenin or a variant thereof comprising the substitution GGRR (Ang GGRR) and microtubule associated protein Tau (MAPtau) as the toxic effector domain.
In some advantageous embodiments, the complexes according to the present disclosure are immunotoxins (ITs) or human cytolytic fusion proteins (hCFP) as described above.
As used herein, the term “immunotoxin” refers to chimeric molecules in which a cell-binding monoclonal antibody or fragments thereof are chemically coupled or genetically fused to a bacterial (e.g. ETA) or plant protein-based toxin (e.g. RT). Immunotoxins per se as well as their constructions are well known to the person skilled in the art.
As used herein, the term “human cytolytic fusion protein” or “hCFP” refers to a completely human immunotoxins in which a cell-binding human ligand or fragments thereof are chemically coupled or genetically fused to a human enzyme (e.g. GranzymeB etc), inhibitory proteins (e.g. MAP) or at least a partial sequence, thereof, the partial sequence having maintained the binding function to a microtubule.
In some further advantageous embodiments, the complexes according to the present disclosure is an Immunotoxin comprising a CD89-specific single-chain variable fragment (scFv) and as the toxic effector domain the Pseudomonas aeruginosa exotoxin A (ETA), in particular in particular as a recombinant fusion protein.
The isolated complexes and polypeptides according to the present disclosure are characterized by specific amino acids and is encoded by specific nucleic acid sequences. It will be understood that such sequences include analogues and variants produced by recombinant or synthetic methods wherein such polypeptide sequences have been modified by substitution, insertion, addition or deletion of one or more amino acid residues in the recombinant polypeptides and the complexes according to the present disclosure still are suitable to bind and kill a human cancer cell. Substitutions are preferably “conservative”. Substitutions are preferably silent substitutions in the codon usage, which will not lead to any change in the amino acid sequence, but may be introduced to enhance the expression of the protein.
In some advantageous embodiments, the complexes according to the present disclosure comprises as the binding structure for binding the complex to the cellular surface receptor CD89 the amino acid sequence of SEQ ID NO: 1, or homologous polypeptides thereof having an amino acid which is at least 85%, preferably 90%, more preferably 95% identical to the amino acid sequence of SEQ ID NO. 1, which are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
In some advantageous embodiments, the complexes according to the present disclosure comprises an amino acid sequence of SEQ ID NO: 2, or homologous polypeptides thereof, which are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
In some advantageous embodiments, the complexes according to the present disclosure comprises an amino acid sequence of SEQ ID NO: 3, or homologous polypeptides thereof, which are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
In some advantageous embodiments, the complexes according to the present disclosure comprises an amino acid sequence of SEQ ID NO: 4, or homologous polypeptides thereof, which are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
In some advantageous embodiments, the complexes according to the present disclosure comprises an amino acid sequence of SEQ ID NO: 5, or homologous polypeptides thereof, which are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
Furthermore, the complex according to the present disclosure comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4 and SEQ ID NO: 5, or homologous polypeptides, variants or mutations thereof having an amino acid which is at least 85%, preferably 90%, more preferably 95% identical to the amino acid sequence of SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4 or SEQ ID NO. 5, and that are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
“Percent sequence identity”, with respect to two amino acid or polynucleotide sequences, refers to the percentage of residues that are identical in the two sequences when the sequences are optimally aligned. Thus, 80% amino acid sequence identity means that 80% of the amino acids in two optimally aligned polypeptide sequences are identical. Percent identity can be determined, for example, by a direct comparison of the sequence information between two molecules by aligning the sequences, counting the exact number of matches between the two aligned sequences, dividing by the length of the shorter sequence, and multiplying the result by 100. Readily available computer programs can be used to aid in the analysis, such as ALIGN14, National Biomedical Research Foundation, Washington, D.C., which adapts the local homology algorithm of Smith and Waterman for peptide analysis.15. Programs for determining nucleotide sequence identity are available in the Wisconsin Sequence Analysis Package, Version 8 (available from Genetics Computer Group, Madison, Wis.) for example, the BESTFIT, FASTA and GAP programs, which also rely on the Smith and Waterman algorithm. These programs are readily utilized with the default parameters 5 recommended by the manufacturer and described in the Wisconsin Sequence Analysis Package referred to above. An example of an algorithm that is suitable for determining sequence similarity is the BLAST algorithm, which was described before. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). Likewise, computer programs for determining percent homology are also readily available.
The term “mutation” refers to the substitution or replacement of single or multiple nucleotide triplets, insertions or deletions of one or more codons, homologous or heterologous recombination between different genes, fusion of additional coding sequences at either end of the encoding sequence, or insertion of additional encoding sequences or any combination of these methods, which result in a polynucleic acid sequence encoding the desired protein.
Thus, the term “mutations” also refers to all of the changes in the polypeptide sequence encoded by the polynucleic acid sequence modified by one or more of the above-described changes.
The term “variant” means that the amino acid sequence has been modified but retains the same functional characteristics, in particular the binding and destroying effect on human cancer cells. A variant has a sequence identity of at least 70% or preferably at least 80%, 85%, 90%, 95%, 97% or 99% to the parent amino acid sequence.
The term “variant” refers further to a polypeptide having one or more residues chemically derivatized by reaction of a functional side group. Such derivatized molecules include for example, those molecules in which free amino groups have been derivatized to form amine hydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups, t-butyloxycarbonyl groups, chloroacetyl groups or formyl groups. Free carboxyl groups may be derivatized to form salts, methyl and ethyl esters or other types of esters or hydrazides. Free hydroxyl groups may be derivatized to form O-acyl or Oalkyl derivatives. The imidazole nitrogen of histidine may be derivatized to form N-im-benzylhistidine. Also included as derivatives are those peptides which contain one or more naturally occurring amino acid derivatives of the twenty standard amino acids. For example: 4-hydroxyproline may be substituted for proline; 5-hydroxylysine may be substituted for lysine; 3methylhistidine may be substituted for histidine; homoserine may be substituted for serine; and ornithine may be substituted for lysine.
The above mentioned fusion proteins may also include on the N-Terminus prior to the single chain sequence: a pelB leader sequence for periplasmic transport, a His10-Tag for affinity purification and enterokinase cleavage site allowing removal of tags after use in purification.
To express a fusion protein according to the present disclosure in a recombinant expression system, a DNA encoding the fusion protein or parts thereof, may be inserted into an expression vector such that the gene is operably linked to transcriptional and translational control sequences. In this context, the term “operably linked” means that a protein gene is ligated into a vector such that transcriptional and translational control sequences within the vector serve their intended function of regulating the transcription and translation of the protein gene. The expression vector and expression control sequences are chosen to be compatible with the expression host cell used. The isolated protein domain sequences are typically inserted into the same expression vector. The protein genes are inserted into the expression vector by standard methods. Additionally, the recombinant expression vector can encode a signal peptide that facilitates co-translational translocation of the nascent polypeptide chain into the endoplasmic reticulum (ER). The folded polypeptide (recombinant fusion protein according to this disclosure) may be secreted from a host cell or may be retained within the host cell. Intracellular retention or targeting can be achieved by the use of an appropriate targeting peptide such as C-terminal KDEL-tag for ER retrieval.
In general, those skilled in the art are well able to construct vectors and design protocols for recombinant gene expression. For further details see, for example, Molecular Cloning: a Laboratory Manual: 2nd edition, Sambrook et al., 1989, Cold Spring Harbor Laboratory Press (or later editions of this work) and Current Protocols in Molecular Biology, Second Edition, Ausubel et al. eds., John Wiley & Sons, 1992, which are incorporated herein by reference.
Furthermore, the present disclosure relates to nucleic acid molecules or nucleic acids encoding such a fusion protein as well as to vectors comprising the nucleic acid molecule and host cells comprising a nucleic acid molecule encoding said fusion protein or a vector comprising said vector. The disclosure pertains also to methods of manufacturing said recombinant fusion proteins in a recombinant expression system.
The term “vector” includes a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a “plasmid”, which refers to a circular double stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g. non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as “recombinant expression system” or “recombinant expression vectors” (or simply, “expression vectors”). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” may be used interchangeably as the plasmid is the most commonly used form of vector. However, the disclosure is intended to include such other forms of expression vectors, such as viral vectors (e.g. replication-defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
The present disclosure is also directed to a host cell with a vector comprising the recombinant fusion proteins according to the present disclosure. The phrase “recombinant host cell” (or simply “host cell”) includes a cell into which a recombinant expression vector has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell but to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein.
Host cells include progeny of a single host cell, and the progeny may not necessarily be completely identical (in morphology or in total DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation and/or change. A host cell includes a cell transfected or infected in vivo or in vitro with a recombinant vector or a polynucleotide of the present disclosure. A host cell, which comprises a recombinant vector of the disclosure, may also be referred to as a “recombinant host cell”.
The term “host cell(s)” refers to cell(s), which may be used in a process for purifying a recombinant protein in accordance with the present disclosure. Such host cells carry the protein of interest (POI). A host cell may also be referred to as a protein-expressing cell. A host cell, according to the present invention, may be, but is not limited to, prokaryotic cells, eukaryotic cells, archaebacteria, bacterial cells, insect cells, yeast, mammal cells, and/or plant cells. Bacteria envisioned as host cells can be either gram-negative or gram-positive, e.g. Escherichia coli, Erwinia sp., Klebsellia sp., Lactobacillus sp. or Bacillus subtilis. Typical yeast host cells are selected from the group consisting of Saccharomyces cerevisiae, Hansenula polymorpha and Pichia pastoris. In some advantageous embodiments, the host cell is a HEK293T cell.
The complex of the present disclosure can be used with a “pharmaceutically acceptable carrier” which includes any and all solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g. antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, such like materials and combinations thereof, as would be known to one of ordinary skill in the art.
Therefore, as used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. Preferably, the carrier is suitable for intravenous, intramuscular, subcutaneous, parenteral, spinal or epidermal administration (e.g., by injection or infusion). Depending on the route of administration, the active compound, i.e., antibody, bispecific and multispecific molecule, may be coated in a material to protect the compound from the action of acids and other natural conditions that may inactivate the compound.
The complex of the present disclosure can be used with a “pharmaceutically acceptable alst” which includes any salt that retains the desired biological activity of the parent compound and does not impart any undesired toxicological effects (see e.g., Berge, S. M., et al. (1977) J. Pharm. Sci. 66:1-19). Examples of such salts include acid addition salts and base addition salts. Acid addition salts include those derived from nontoxic inorganic acids, such as hydrochloric, nitric, phosphoric, sulfuric, hydrobromic, hydroiodic, phosphorous and the like, as well as from nontoxic organic acids such as aliphatic mono- and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids, aromatic acids, aliphatic and aromatic sulfonic acids and the like. Base addition salts include those derived from alkaline earth metals, such as sodium, potassium, magnesium, calcium and the like, as well as from nontoxic organic amines, such as N,N′-dibenzylethylenediamine, N-methylglucamine, chloroprocaine, choline, diethanolamine, ethylenediamine, procaine and the like.
The actual dosage amount of a complex or composition of the present disclosure administered to a subject can be determined by physical and physiological factors such as body weight, severity of condition, the type of disease being treated, previous or concurrent therapeutic interventions, idiopathy of the patient and on the route of administration. The practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject.
A complex composition of the present disclosure can be administered by a variety of methods known in the art. As will be appreciated by the skilled artisan, the route and/or mode of administration will vary depending upon the desired results. The active compounds can be prepared with carriers that will protect the compound against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known to those skilled in the art. See, e.g., Sustained and Controlled Release Drug Delivery Systems, J. R. Robinson, ed., Marcel Dekker, Inc., New York, 1978.
To administer a complex or composition of the present disclosure by certain routes of administration, it may be necessary to coat the complex compound with, or co-administer the compound with, a material to prevent its inactivation. For example, the compound may be administered to a subject in an appropriate carrier, for example, liposomes, or a diluent. Pharmaceutically acceptable diluents include saline and aqueous buffer solutions. Liposomes include water-in-oil-in-water CGF emulsions as well as conventional liposomes (Strejan et al. (1984) J Neuroimmunol. 7:27).
Pharmaceutically acceptable carriers include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. The use of such media and agents for pharmaceutically active substances is known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the pharmaceutical compositions of the invention is contemplated. Supplementary active compounds can also be incorporated into the compositions.
Therapeutic compositions typically must be sterile and stable under the conditions of manufacture and storage. The composition can be formulated as a solution, microemulsion, liposome, or other ordered structure suitable to high drag concentration. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, monostearate salts and gelatin.
Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by sterilization microfiltration. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying (lyophilization) that yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Dosage regimens are adjusted to provide the optimum desired response (e.g., a therapeutic response). For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subjects to be treated; each unit contains a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on (a) the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and (b) the limitations inherent in the art of compounding such an active compound for the treatment of sensitivity in individuals. Examples of pharmaceutically-acceptable antioxidants include: (1) water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and (3) metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
Actual dosage levels of the active ingredients in the pharmaceutical compositions of the present disclosure may be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient. The selected dosage level will depend upon a variety of pharmacokinetic factors including the activity of the particular compositions of the present disclosure employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion of the particular compound being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compositions employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts.
A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could start doses of the compounds of the invention employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved. In general, a suitable daily dose of compositions of the invention will be that amount of the compound which is the lowest dose effective to produce a therapeutic effect. Such an effective dose will generally depend upon the factors described above. It is preferred that administration be intravenous, intramuscular, intraperitoneal, or subcutaneous, preferably administered proximal to the site of the target. If desired, the effective daily dose of therapeutic compositions may be administered as two, three, four, five, six or more sub-doses administered separately at appropriate intervals throughout the day, optionally, in unit dosage forms. While it is possible for a compound of the present * invention to be administered alone, it is preferable to administer the compound as a pharmaceutical formulation (composition).
In advantageous embodiments, recombinant human cytolytic fusion proteins according to the disclosure are used for treating a malignant disease, an allergy, autoimmune disease, tissue rejection reaction, or chronic inflammation reaction.
Further embodiments of the present disclosure pertain to polypeptides suitable for the detection of CD89, wherein said polypeptide comprises the amino acid sequence of SEQ ID NO: 1, or a homologous polypeptide, variant or mutation thereof having an amino acid which is at least 85%, preferably 90%, more preferably 95% identical to the amino acid sequence of SEQ ID NO. 1, which are produced by recombinant or synthetic methods by substitution, insertion, addition or deletion of one or more amino acid residues, or fragments thereof.
In further embodiments, homologous polypeptides, variants or mutations of said polypeptides suitable for the detection of CD89 shows a sequence identity of at least 70% or preferably at least 80%, 85%, 90%, 95%, 97% or 99% to the parent amino acid sequence.
In some examples, the polypeptides are coupled to a detectable label like an affinity label. As used herein, the term “affinity label” refers to a substance, molecule or biomolecule, which is coupled to the polypeptides suitable for the detection of CD89 to form a “fusion tag” or a “affinity tag”, by a means, e.g., expression, and which is further capable of specifically binding to a fluorescent label. In particular, the fusion tag is a fusion tag protein. Examples of the fusion tag proteins are SNAP-tags, CLIP-tags, Lumio tags, or HaloTags.
In some embodiments, the detectable CD89-protein is presented on a human target cell or a fragment thereof like parts of the cell membrane of a disrupted target cell.
In further embodiments, the present disclosure pertains to a method for the detection of CD89 contained in a sample, comprising:
(a) contacting a sample with a polypeptide suitable for the detection of CD89 as described in the present disclosure and with fusion tag specific fluorophores that specifically bind the fusion tags coupled to said polypeptide; and
(b) detecting the presence of CD89 in the sample by fluorescence signals associated with the fusion tag specific fluorophores.
As used herein, the terms “fluorescent label”, “fluorophore”, “dyes”, and “fluorescent molecule” may have the same or similar meaning in the invention and are interchangeable throughout the invention. For example, the term “fluorophore”, “fluorochrome”, or “chromophore”, as used herein, refers to a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores may typically contain several combined aromatic groups, or plane or cyclic molecules with several ii bonds.
Fluorophores may sometimes be used alone, as a tracer in fluids, as a dye for staining of certain structures, as a substrate of enzymes, or as a probe or indicator (when its fluorescence is affected by environment such as polarity, ions, et. al.). But more generally fluorophore may be covalently bonded to a macromolecule, serving as a marker (or dye, or tag, or reporter) for affine or bioactive reagents (antibodies, peptides, nucleic acids, et. al.). Fluorophores may notably be used to stain tissues, cells, or materials in a variety of analytical methods, i.e. fluorescent imaging and spectroscopy.
The affinity tag may be any molecules or biomolecules which are capable of specifically linking to one fluorescent molecule as the fluorophore (fluorescent label). Specifically, the affinity tag may be proteins having suicidal enzymatic activity, also called suicide enzymes. Suicide enzymes are proteins whose enzymatic activity is modified by specific mutations allowing them to bind a substrate rapidly, covalently, and irreversibly, as these enzymes can each bind only one fluorescent molecule, and the further binding activity of the enzyme is blocked by the binding of the substrate.
The fluorophore or fluorescent label may be any fluorescent molecules or dyes. Specifically, the fluorophore or fluorescent label may be a dye compatible with the fluorescent detection equipment being used. Some examples of these dyes may be seen below. All of these dyes may be commercially available as fluorescent substrates for fusion tags, and each binds covalently to a different tag. Most developed fusion tags may have many fluorescent variations of the ligand to cover a broad portion of the UV spectrum. Any suitable fluorescent molecules or dyes may be used for the present invention. In a preferred embodiment of the present invention, a microfluidic system such as LabChip systems (available from Caliper) may be equipped with a 635 nm excitation light source, and a 700 nm emission filter, making dyes with excitation and emission maxima near these wavelengths ideal choices when selecting a fluorophore for use on a LabChip system. Any fluorescent molecules or dyes having suitable excitation and emission maxima near the required wavelength may be used for the present invention.
In advantageous embodiments of the present disclosure, the polypeptides suitable for the detection of CD89 as described in the present disclosure can be used for the diagnosis of CD89+ malignancies. The diagnosis may be in vivo or ex vivo. Therefore, the present disclosure pertains also to methods for the diagnosis of CD89+ malignancies, comprising administering to a patient a polypeptide suitable for the detection of CD89 as described in the present disclosure or contacting a biological sample taken from a patient with a polypeptide suitable for the detection of CD89 as described in the present disclosure.
Advantageous embodiments refers to methods of detecting the presence of CD89 or a cell expressing CD89 in a sample, comprising: contacting the sample with the polypeptides suitable for the detection of CD89 as described in the present disclosure under conditions that allow for formation of a complex between the polypeptide and CD89; and detecting the formation of the complex.
Further embodiments of the present disclosure relate to methods for detecting in vitro or in vivo the presence of CD89 in a sample, e.g., for diagnosing a CD89-related disease. In one embodiment, this is achieved by contacting a sample to be tested, optionally along with a control sample, with a polypeptide suitable for the detection of CD89 as described in the present disclosure under conditions that allow for formation of a complex between the polypeptide and CD89. Complex formation is then detected (e.g. using an ELISA). When using a control sample along with the test sample, complex is detected in both samples and any statistically significant difference in the formation of complexes between the samples is indicative the presence of CD 89 in the test sample.
The following methods and examples are offered for illustrative purposes only, and are not intended to limit the scope of the present disclosure in any way.
It should be understood that the following examples are for illustrative purpose only and are not to be construed as limiting this disclosure in any manner. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.
For specific targeting and killing, a complex (recombinant fusion protein) was constructed comprising an anti-human CD89 single chain fragment variable (scFv) and the Pseudomonas exotoxin A (ETA′).
Furthermore, human cytolytic fusion proteins (hCPs) were generated by fusing the CD89-specific scFv to human derived effect domains like a granzyme B variant comprising the substitution R201K (GbR201K, disclosed in EP2758527), a angiogenin variant GGRR (Ang GGRR) (Cremer, C., et al., Journal of Immunotherapy, 2014) or microtubule associated protein Tau (MAPtau).
In the following examples it was shown that FcαR (CD89) is expressed by a subset of leukaemic cells and can be used not only as a diagnostic marker but also as a novel immunotherapeutic target. It was demonstrated that a CD89-specific fusion proteins can eliminate myeloid cell lines derived from different AML subtypes in vitro, as well as AML and CMML cells ex vivo.
The abundance of CD89 on AML-derived cell lines and primary cells from AML and CMML patients was described. CD89 is a suitable immunotherapeutic target for haematological malignancies because it is not found on pluripotent stem cells or CD34+ hematopoietic progenitor cells, so the homeostasis of normal FcαR+ immune effector cells and the recovery of the haematopoietic system after therapeutic intervention remains unaffected. Earlier immunotherapeutic approaches for the treatment of myeloid malignancies include Gemtuzumab-ozogamicin (GO), a humanised CD33-specific monoclonal antibody (mAb) chemically coupled to the cytostatic drug calicheamicin (Albo, C., et al. Haematologica, 2004, 89(7): p. 845-851). GO was withdrawn from the market in 2010 because only limited efficacy was demonstrated in clinical trials. Nevertheless, GO showed promising results in recent clinical phase II-III studies, underlining its importance as an alternative in AML therapy. In addition to this antibody-drug conjugate (ADC), a variety of recombinant immunotherapeutic agents, such as bispecific/trispecific scFv, T-cells with chimeric antigen receptors (CARs), and ITs, are currently under investigation. Here we focused on the generation and characterisation of a recombinant, scFv-based IT and hCFPs specific for CD89. One advantage of scFvs over full size mAbs is the lack of the Fc region. Hence, scFvs show a reduced immunogenicity and no binding to Fc-receptor expressing cells, which thereby avoids the rapid clearance of the ITs. Several recombinant ETA′-based ITs have been developed over the last decade, targeting and eliminating a variety of myeloid malignancies including CD7+, CD33+, CD64+ and CD123+ cells (Gasiorowski, R E. et al., Br J Haematol, 2014, 164: p. 481-95, Monnier, P., et al., Antibodies, 2013, 2: p. 193-208, Schwemmlein, M., et al., Br J Haematol, 2006, 133: p. 141-151, Stein, C., et al., Br J Haematol, 2010, 148: p. 879-889, Thorpe, S. J., et al., Scand J Immunol 2003, 57: p. 85-92, Tur, M K., et al., Cancer Res, 2003; 63: p. 8414-9). In addition different hCFPs specific for the elimination CD64+ target cells and myeloid malignancies were already described in literature (Schiffer, S., et al., Int J Cancer, 2014, 135: p. 1497-508, Hristodorov, D., et al., Br J Cancer, 2013, 109: p. 1570-8, Cremer, C., et al., Journal of Immunotherapy, 2014).
In the present disclosure the construction of a CD89(scFv)-ETA′ IT and the successful in vitro and ex vivo elimination of cells derived from different AML subtypes and myeloid malignancies, respectively, is shown for the first time.
1. Cloning and Expression of CD89(scFv)-fusion Proteins
The open reading frame (ORF) for the anti-human CD89(scFv) (Guettinger, Y., et al., J Immunol, 2010, 184: p. 1210-1217) was capped with 5′ SfiI and 3′ NotI restriction sites using adapted PCR primers and the product was ligated into the pMT vector, already containing the ETA′ sequence using the SfiI and NotI sites. (Berges, et al 2014) The plasmid was cloned in Escherichia coli strain DH5α(New England Biolabs, UK) and successful cloning was confirmed by test digestion and sequencing. The CD89(scFv)-ETA′ fusion protein was expressed in E. coli strain BL21 (DE3), purified and characterised as previously described for H22(scFv)-ETA′ (Ribbert, T., et al., Br J Dermatol, 2010; 163: p. 279-86, Tur, M K., et al., Cancer Res, 2003; 63: p. 8414-9).
For the human cytolytic fusion proteins (hCFPs) the CD89(scFv) was transferred from the pMT vector system, described above, into the pMS vector system using the cloning SfiI and NotI as restriction sites. The pMS vector template was containing the sequence of the effector protein: a microtubule-associated protein tau (MAPtau), a mutant of angiogenin (Ang GGRR) or a mutant form of granzyme B (EGbR201K). Analogously to CD89(scFv)-ETA′, the successfully cloned constructs were transformed into E. coli DH5α and the sequences of the constructs were verified by sequencing. The expression of the pMS based constructs (CD89(scFv)-Ang GGRR, CD89(scFv)-MAPtau and EGbR201K-CD89(scFv) was carried out transiently in HEK293T cells as previously described by Stocker, et al. The purification and characterization procedures were conducted as described for CD89(scFv)-ETA′.
Construction, Expression and Binding Characteristics of the Fusion Protein CD89(scFv)-ETA′
We generated a fusion of a CD89-specific scFv derived from the humanised full-size anti-human CD89 mAb A77, to the truncated toxin ETA′ (
2. Patient Samples and Cell Lines
AML cell lines HL-60 (FAB, AML M2; DSMZ no. ACC 3), Mono-Mac-1 (FAB, AML M5; DSMZ no. ACC 252), THP-1 (FAB, AML M5 (Martino, et al 2006), DSMZ no. ACC 16), the histiocytic lymphoma cell line U937 (DSMZ no. ACC 5), and the Burkitt lymphoma cell line Ramos (DSMZ no. ACC 603) were grown in standard RPMI 1640 medium (Invitrogen) supplemented with 10% (v/v) foetal calf serum (BioChrom), 50 μg/ml penicillin and 100 μg/ml streptomycin (Gibco) at 37° C., 5% CO2 and 100% humidity. The cells were stimulated with either IFNγ or TNFα for 24 h prior to flow-cytometry and cytotoxicity assays. Primary mononuclear cells were isolated by density gradient centrifugation using Biocoll separating solution (Biochrom AG). The cells were isolated from the peripheral blood of pre-treatment leukaemia patients (diagnosis based on the WHO classification is shown in Table 1), after receiving informed consent and with the approval of the Clinical Research Ethics Board of the University of Aachen. Cells from AML CMML patients were cultivated under the conditions described above.
3. Analysis of CD64 and CD89 Expression and Receptor Density
The expression of CD64 and CD89 in the different cell lines was analysed by flow cytometry. Cells were incubated with a 150 ng fluorophore-labelled mAb in PBS (pH 7.4) containing 2 mM EDTA and 1% (w/v) human blocking serum (BioChrom) for 30 min on ice followed by two washing steps with PBS. CD64 was blocked with 50 nM of the H22(scFv) antibody fragment (Hristodorov, D., et al., MAbs, 2014, 6: p. 1283-1289). The fluorescence was then analysed on a FACSCalibur™ flow cytometer (Becton Dickinson). The following antibodies were used for detection: mouse anti-human CD64 [10.1]:APC (eBioscience) and mouse anti-human CD89 [MIP8]:FITC (AbD Serotec). The number of CD89 and CD64 molecules expressed on the cell surface was determined using the Qifikit® (Dako). Flow cytometry was carried out according to the manufacturer's protocol using mouse anti-human CD64 [10.1]:PE, mouse anti-human CD89[A59]:PE, goat anti-mouse IgG [Poly4053]:PE and a mouse IgG1:PE isotype control mAb, all purchased at Biolegend. All experiments were carried out in triplicates.
Confirmation of CD64 and CD89 Expression and Receptor Density in AML Cell Lines
The expression levels of CD64 and CD89 in different AML cell lines were estimated using double staining to determine the number of cells expressing CD64 and CD89 under normal conditions and after stimulation with IFNγ or TNFα. The expression of CD64 and CD89 was detectable on all AML cell lines (HL-60>90%; Mono-Mac-1>30% and THP-1>25%) under normal conditions and in the presence of IFNγ and TNFα(
The expression levels of CD89 and CD64 were determined using the Qifikit® showing that receptor expression was clearly stimulus-dependent. Neither the growth medium nor the presence of IFNγ influenced the abundance of CD89, which ranged from less than 1000 receptors on the surface of Mono-Mac-1 and THP-1 cells up to ˜1500 receptors on the surface of HL-60 cells (
4. Cell-Binding Analysis by Flow Cytometry
We incubated 5×105 cells with 100 ng CD89(scFv)-ETA′ and 500 ng CD89(scFv)-fusion proteins in PBS (pH 7.4) containing 2 mM EDTA and 0.5% (w/v) bovine serum albumin for 30 min on ice, followed by two washes with PBS. The cells were then incubated with 0.125 ng of an anti-His5-Alexa Fluor 488 mAb (Qiagen) for 30 min on ice in the dark before two further washes with PBS.
Binding Confirmation of CD89-targeting Fusion Proteins
The cell-binding activity of purified CD89(scFv)-fusion proteins was examined by flow cytometry and could be successfully proven as indicated in
5. In Vitro Functionality of CD89(scFv)-Ang GGRR and GbR201K-CD89(scFv)
The RNase assay was performed to examine the in vitro functionality of the CD89(scFv)-Ang GGRR fusion protein. Therefore different concentrations of the protein were incubated with 600 ng yeast tRNA in assay buffer (30 mM Tris-HCl buffer (pH 7.5) containing 30 mM NaCl) for 1.5 h at 37° C. As positive control 100 ng of RNase A were used and as negative control the tRNA was incubated with RNase free Tris-HCl sample buffer (pH 7.5). The reaction was stopped by adding the 6× loading dye (48% (v/v) formaldehyde, 48% (v/v) glycerin, 0.25% (v/v) bromophenol blue, 20 mM sodium phosphate (pH 7.5)) in a dilution of 1:6. Afterwards the degradation of tRNA was analyzed using a RNase free 1% agarose gel at 100V for 7 min and the bands were visualized by UV illumination.
The activity of GbR201K-CD89(scFv) after enterokinase digestion was detected by cleavage of 200 μM of the colorimetric, synthetic substrate Ac-IETD-pNA (Calbiochem/Merck, Darmstadt) which mimics the cleavage site of pro-caspase 3. A granzyme B standard was used as positive control and was applied in a concentration of 90 ng. For the negative control assay buffer (100 mM NaCl, 50 mM HEPES, 10 mM DTT, 1 mM EDTA, 10% (v/v) glycerin, 0.1% (w/v) CHAPS, pH 7.4) was incubated with the substrate. The reaction was monitored in 96-well plates in a microplate reader at 405 nm and 37° C. at 2 min intervals for 1 h. Afterwards, time was plotted against the absorbance so differences in activity could be evaluated.
Confirmation of Functionality of CD89(scFv)-Ang GGRR and GbR201K-CD89(scFv)
We could confirm the RNase activity of the fusion protein. A concentration dependent degradation of the tRNA was detected, whereas 1 μg, 500 ng and 250 ng of applied CD89(scFv)-Ang GGRR reduced the UV-signal of the used tRNA to 15%, 25% and 50%, respectively (
The activity of the granzyme B part of GbR201K-CD89(scFv) was confirmed by the increasing absorbance over time course using the described above colorimetric kinetic measurement (
6. Apoptosis Assay
An Annexin V/propidium iodide (PI) assay was used to measure the pro-apoptotic activity of CD89(scFv)-ETA′. We incubated 5×105 cells per ml with different concentrations of CD89(scFv)-ETA′ in a 24-well plate (Greiner, Germany) for 72 h at 37° C., 5% CO2 and 100% humidity. Ramos cells (CD89−) were used as a control. After incubation, the cells were washed twice with PBS (pH 7.4) and stained with Annexin V-FITC (eBioscience) in Annexin V binding buffer (10 mM HEPES/NaOH, pH 7.4, 140 mM NaCl, 2.5 mM CaCl2) for 30 min at room temperature in the dark. Finally, the cells were washed as described above, resuspended in Annexin V buffer containing 10 μg/ml PI and analysed by flow cytometry.
Antigen-specific Dose-dependent In Vitro Cytotoxicity of CD89-fusion Proteins
The cytotoxic effector proteins included in ITs should preferably induce apoptosis rather than necrosis or pyroptosis because the former does not cause undesirable inflammatory responses. The ability of CD89(scFv)-ETA′ to induce apoptosis in the different AML cell lines was therefore tested by double staining with Annexin V and PI after treatment for 72 h. Accordingly, CD89(scFv)-ETA′ triggered apoptosis in HL-60 cells regardless of the presence or nature of stimulation but did not affect CD89− Ramos cells. Quantitative experiments confirmed a dose-dependent relationship, i.e. greater concentrations of CD89(scFv)-ETA′ increased the efficiency of apoptosis in HL-60 cells regardless of the presence or nature of stimulation (
Antigen-specific Pro-apoptotic Activity of CD89(scFv)-ETA′
We also investigated the rate of IT-mediated cell death in other AML cell lines and in U937 histiocytic lymphoma cells (
Ex Vivo Cytotoxicity Towards CD89+ Leukaemia Cells
Primary cells obtained from three patients diagnosed with three different forms of myeloid leukaemia were tested: (#1) AML and (#2, #3) CMML. The isolated primary cells were tested for the presence of CD89 and we found the percentage of positive cells was 75% for the AML patient and 69% and 73% for both CMML patients (Table 1). We monitored apoptosis induced by CD89(scFv)-ETA′, CD89(scFv)-Ang GGRR, GbR201K-CD89(scFv) and or CD89(scFv)-MAPtau using the Annexin V/PI staining assay (
7. Colorimetric Cell Proliferation Assay
The cytotoxic effect of the different ITs and hCFPs was determined by measuring the conversion of XTT to a water-soluble orange formazan dye. (Roehm, et al 1991) We seeded 5×105 cells/well into a 96-well microtitre plate and incubated them with different dilutions of the recombinant protein for 72 h at 37° C., 5% CO2 and 100% humidity. We added 50 μl 100:1 XTT/phenanzinemethosulfate (Serva and Sigma-Aldrich) to each well and incubated the plates for 2-4 h. The absorbance at 450-630 nm was measured using an Epoch Microplate Spectrophotometer (Biotek). Data were normalised by setting the 100% and 0% values to cells treated with 10 μg/ml zeocin and untreated cells, respectively. All experiments were carried out in triplicates.
In Vitro Inhibition of Cell Proliferation by CD89(scFv)-fusion Cytotoxic Proteins
The EC50 value of CD89(scFv)-ETA′ towards HL-60 cells was stimulus-dependent, i.e. it was >1 μM in the absence of stimuli, ˜0.2 nM in the presence of IFNγ and ˜3 nM in the presence of TNFα (
8. Analysis of Internalisation
The CD89(scFv)-SNAP protein was produced by secretory expression in HEK293T cells, and coupled to BG-Vista® Green according to the manufacturer's instructions (NEB). Internalisation was verified by incubating 1×106 HL-60 (1000 U/mL TNFα) and Ramos cells with 50 nM (˜2 μg) CD89(scFv)-SNAP-BG-Vista®Green in PBS at 4° C. or 37° C. for 30 min. After washing the cells twice, antigen-dependent internalisation was detected using a Leica TCS SP8 Confocal Microscope (Leica Microsystems).
CD89-dependent Internalisation
Efficient CD89-specific internalisation into HL60 cells was demonstrated using CD89(scFv)-SNAP-BG-Vista® Green, revealing the intracellular accumulation of the labelled protein after incubation for 30 min at 37° C. No internalisation was detected at 4° C. Neither binding nor internalisation was observed when we tested CD89 Ramos cells as a negative control (
9. Statistical Analysis
Statistical analysis and EC50 value calculations were carried our using GraphPad Prism v5 (GraphPad Software, USA). The EC50 was defined as the concentration required to achieve 50% reduction of metabolic activity normalised to untreated control cells and zeocin-treated cells. Data were expressed as the mean±standard deviation (SD). Statistical comparisons were made using a two-tailed unpaired Student's t-test: *p 0.05, **p 0.01, ***p 0.001.
Patient information (e.g. gender and age), diagnosis based on the WHO classification, state of previous treatment and general laboratory parameters (e.g. amount of the white blood cells (WBC) and monocyte percentage thereof, the hemoglobin amount, and platelet count) are filed in the table above according to the standard clinical protocols. Data is kindly provided by the corresponding member(s) in university clinic of Aachen according to the ethical policy.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2015/056386 | 3/25/2015 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2016/150496 | 9/29/2016 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 4946778 | Ladner et al. | Aug 1990 | A |
| 20030082643 | Hudson | May 2003 | A1 |
| Number | Date | Country |
|---|---|---|
| 2 465 536 | Jun 2012 | EP |
| 2007104743 | Sep 2007 | WO |
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| Number | Date | Country | |
|---|---|---|---|
| 20180050102 A1 | Feb 2018 | US |
