Antibodies against ykl-40 and uses thereof
Patent Information
- Authority / Receiving Office
- EP · EP
- Patent Type
- Applications
- Current Assignee / Owner
- Filing Date
- 2024-04-26
- Publication Date
- 2026-03-04
AI Technical Summary
Solid malignant tumours pose a challenge due to elevated interstitial fluid pressure (IFP) that hampers the access of therapeutic agents, limiting their distribution and effectiveness in treating cancer.
Development of YKL-40 antibodies that can bind to human and murine YKL-40, reducing IFP within tumours, thereby enhancing the permeability and accessibility of anti-cancer agents to the tumour interior without promoting tumour proliferation.
The YKL-40 antibodies effectively decrease interstitial fluid pressure, facilitating the uptake of anti-cancer agents into solid neoplasms, potentially leading to increased treatment efficacy while minimizing tumour growth.
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Abstract
Description
[0001] Antibodies against YKL-40 and uses thereof
[0002] Technical field
[0003] The present invention relates to YKL-40 antibodies capable of binding to human and murine YKL-40. These antibodies are useful for multiple purposes, including for detection of YKL-40, for treatment of cancers, or delaying the onset of cancers or for treatment of other diseases associated with aberrant YKL-40 expression, in particular YKL-40 overexpression. Such diseases include e.g. inflammatory diseases. In particular, the antibodies are useful for reducing interstitial fluid pressure in tumours or other tissues, which is useful in treatment of conditions associated with increased interstitial fluid pressure. In addition, the invention relates to the treatment of solid malignant tumours with YKL-40 antibodies, said treatment resulting in increase in malignant tumour permeability thereby allowing or facilitating access of any anti-cancer agent to the malignant tumour.
[0004] Background
[0005] YKL-40 is a 40 kDa heparin- and chitin-binding glycoprotein also known as human cartilage glycoprotein 39 (HC gp-39), 38-kDa heparin-binding glycoprotein or chitinase- 3-like protein 1 (CHI3L1). The abbreviation YKL-40 is based on the one letter code for the first three N-terminal amino acids, tyrosine (Y), lysine (K) and leucine (L) and the apparent molecular weight of YKL-40.
[0006] YKL-40 was first identified as a protein secreted in large amounts by a human osteosarcoma cell line MG63 in vitro. Later studies have found that YKL-40 is secreted in vitro by a variety of cells and seems especially involved in activation of the innate immune system and in cell processes in relation to extracellular matrix remodeling.
[0007] The crystallographic structure of human YKL-40 has been described and the protein contains two globular domains: a big core domain which consists of a (p / a)s domain structure with a triose-phosphatase isomerase (TIM) barrel fold and a small a / p domain, composed of five antiparallel p-strands and one a-helix, inserted in the loop between strand p7 and helix a7. This confers the active site of YKL-40 a groove-like character. The folded protein contains two potential hyaluronan binding sites predicted by in silico methods. Binding of short and long oligosaccharides to human YKL-40 are also possible.
[0008] YKL-40 possesses several biological activities. It has been shown that human YKL-40 can act as a growth factor for cells of connective tissue, such as chondrocytes and synovial cells. YKL-40 also promotes the growths of fibroblasts in a fashion like insulinlike growth factor 1 (IGF-1). It has also been demonstrated that YKL-40 can act as a chemoattractant for endothelial cells and stimulates migration of these cells comparable to stimulation by basic fibroblast growth factor. YKL-40 is also found to modulate vascular endothelial cell morphology by promoting formation of branching tubules. A strong expression of YKL-40 mRNA in human liver has been shown to be associated with the presence of fibrosis. Immunohistochemical studies of liver biopsies have shown YKL-40 protein expression in areas of the liver with fibrosis, whereas no expression was observed in hepatocytes. Patients with non-malignant diseases characterized by inflammation and fibrosis such as active rheumatoid arthritis, severe bacterial infections, active inflammatory bowel disease, and liver fibrosis have elevated serum levels of YKL-40.
[0009] YKL-40 is expressed and secreted by several types of human malignancies. Furthermore, YKL-40 is found to be secreted in vitro by the osteoscarcoma cell line MG63, glioblastoma cells and myeloid leukemia cell lines. Several studies have reported an elevated level of YKL-40 protein in serum of cancer patients.
[0010] Thus, YKL-40 activity is found to be associated with cell growth, survival, differentiation, apoptosis, angiogenesis, extracellular matrix remodeling, development of metastasis, development of liver or tissue fibrosis, development of rheumatoid arthritis and / or development of inflammation.
[0011] The effectiveness of anticancer drug therapy in treating solid malignant tumours depends on the drug reaching all cancer cells in the malignant tumour. The drug distribution in malignant tumour tissue is dependent on the plasma pharmacokinetics and pharmacodynamics, the structure and function of the malignant tumour vasculature and the ability of the drug to move through microvessel walls and its diffusion and convection across the ECM and the layers of the malignant tumour. For chemotherapy of solid malignant tumours for example, the drug must be able to traverse walls of blood vessels and the surrounding ECM to reach malignant tumour cells. Often malignant tumours form several layers of malignant tumour and / or matrix cells which all must be penetrated. Matrix cells may for example be fibrous connective tissue. The structure and flow distribution in the system of microvessels supplying the malignant tumour and the properties of extravascular tissue components such as ECM, normal cells, malignant tumour cells and interstitial spaces play a major role in this regard.
[0012] Treatment of metastatic solid malignant tumours with classical chemotherapeutic antineoplastic drugs, formulations of chemotherapeutic drugs increasing accessibility to the matrix surrounding the malignant tumour as Caleux®, Onyvide® or abraxane®, kinase inhibitors, small molecules and / or therapeutic monoclonal antibodies is increasingly used in clinical medicine. However, a cure of widespread distant metastases has not been achieved; about two-thirds of the cancer patients die from them. The reason for this failure might reside in the increased interstitial fluid pressure (IFP) observed in solid malignant tumours which hampers the access of the antibodies and other drugs including small molecules to cancer cells (Bockemann et al, 2020. Indeed, solid malignant tumours have a raised IFP due to high vessel permeability, low lymphatic drainage, poor perfusion, and high cell density around the blood vessels (Ferretti et al. 2009). The raised interstitial fluid barrier creates a distribution barrier which prevents convection within solid malignant tumours, which limits the access of therapeutic agents towards all malignant cells.
[0013] Solid malignant tumours form organoid like structures, which may be composed of a variety of tissue components. First there are the malignant tumour cells themselves, which in the case of solid malignant tumours, cancers, generally form epithelial structures as the cells are linked to each other by cell to cell junctions including desmosomes, tight junctions, gap junctions. These junctions are responsible for the formation of a “cancer tissue”, which is composed of several cancer cells of the same type. In addition to the cancer cells themselves the malignant tumour typically builds around its vascular supply which is sheathed in a connective tissue ECM, collectively called the malignant tumour stroma. The stromal component of normal organs contains blood and lymphatic vessels, the latter being absent in cancer tissue stroma. This absence of functioning lymphatic vessels has considerable consequences for the flow of fluids within malignant tumours. In order to understand this process, the normal fluid transport within tissues has to be understood. In the arterial part of the capillary, fluid is pressed out (exudate) into the ECM surrounding the capillary. While the fluid and with it small molecules are pressed out into the ECM the large molecules such as proteins remain partially in the capillaries. These remaining osmotically active macromolecules suck the fluid of the ECM back into the venous part of the capillaries. However, about 10% of the exsudated fluid is not sucked back into the venous part of the capillary but remains in the extracellular matrix. There it is transported away by a process called convection, which is a directed fluid flow from the blood capillaries to the lymphatic capillaries. Thereby the fluid exchange in normal organs is balanced resulting in a slightly negative to zero interstitial fluid pressure. In contrast to normal organs, organoid like malignant tumours do not contain functioning lymphatic vessels, thereby this excess fluid is not drained away and accumulates within the malignant tumour thus building up the interstitial fluid pressure.
[0014] This fluid pressure is believed to limit the access of therapeutic antibodies and of classical small molecular weight chemotherapeutic drugs (small molecule drugs) to areas within the malignant tumour which are located 100 pm around the small exchange blood vessels. Thereby most of the malignant tumour cells within solid malignant tumours are not reached by the possible therapeutic drugs and / or antibodies.
[0015] Summary
[0016] There is an unmet need of additional YKL-40 antibodies, and in particularly for YKL-40 antibodies useful in treatment of cancer characterised by the presence of at least one solid neoplasm.
[0017] As outlined above, in general solid neoplasms are difficult to treat due to reduced access of antibodies or any other anti-cancer agents to areas within the solid neoplasms. The present invention provides YKL-40 antibodies, which upon administration to an individual suffering from cancer, are capable of entering into the interior of solid neoplasms. Thus, the YKL-40 antibodies of the invention can act in the interior of solid neoplasms. In addition, the YKL-40 antibodies of the present invention are preferably capable of reducing the interstitial fluid pressure (IFP) within solid neoplasms. Surprisingly, the composition of the YKL-40 antibodies can lower the fluid pressure without increasing proliferation of the tumor. The present invention thereby provides a breakthrough in treatment of diseases characterized by the presence of tissues with high interstitial fluid pressure (IFP). Such diseases may be difficult to treat, because of the difficulty for active compounds entering such tissues due to the high IFP. On the other hand, lowering of IFP may lead to enhanced accessibility to the interior of such tissues, not only for active compounds, but also for unwanted substances. In the case of solid neoplasms lowering IFP may lead increased influx of compounds promoting proliferation, which is not desirable.
[0018] The present invention provides YKL-40 antibodies as well as combinations of YKL-40 antibodies, which can lower IFP in solid neoplasms, can facilitate uptake of active compounds to the interior of solid neoplasms, but which in the same time also do not negatively affect tumour weight and / or volume. In fact, the antibodies may even reduce tumour weight and / or volume by themselves.
[0019] This renders the antibodies of the invention extremely useful in a clinical setting. The YKL-40 antibodies as well as combinations of YKL-40 antibodies of the invention may thus significantly increase efficacy of known anti-cancer agents by facilitating their access to solid neoplasms, and in the same time the antibodies may even aid reducing tumour weight and / or volume by themselves.
[0020] Furthermore, the YKL-40 antibodies of the present invention are preferably capable of facilitating access of other compounds into the inner mass of a malignant tumour, thereby facilitating access of e.g. anti-cancer agents. Thus, YKL-40 antibodies may facilitate the access of anti-cancer agents to solid neoplasms, and thus anti-cancer agents may advantageously be administered to an individual suffering from a solid neoplasm either together with or before or subsequent to administration of the YKL-40 antibodies. Without being bound by theory it is hypothesized that the reduction in IFP results in increased accessibility of other compounds to the interior of tumours.
[0021] In addition, the YKL-40 antibodies of the present invention alone or in combination are preferably capable of reducing IFP and / or facilitating access of other compounds into the inner mass of other tissues associated with high IFP. Furthermore, the invention provides antibodies useful for administration to human beings because said antibodies contains either mainly human sequences (e.g. B3 of SEQ ID NO: 3 or B10 of SEQ ID NO: 4) or chimeric sequences comprising human sequences in the complementary-determining regions (e.g. H7 of SEQ ID NO: 14 and SEQ ID NO: 15).
[0022] The invention is further defined by the claims attached hereto.
[0023] Description of Drawings
[0024] Figure 1: shows three common antibody formats. Different fragments from the immunoglobulin are often used in recombinant formats, especially the variable domains of the heavy chain VH have been used repeatedly. A) a variable domain of the heavy chain (VH) linked to a constant region of the heavy chain (Fc region). B) a variable domain of the heavy chain ( H). Domain antibodies may consists of only a VH C) Example of a chimeric antibody. There are three human / murine chimeric complementary-determining regions (DDRs) (CDR1 , 2 and 3) arranged non- consecutively on the amino acid sequence of a variable domain of an antigen receptor.
[0025] Figure 2 shows, that B3 (SEQ ID NO: 3) binds to both human and mouse YKL-40, but does not bind to calmodulin (Fig. 3). A dot blot was performed by adding 0.4 pg and 0.2 pg of hYKL-40, 0.4 pg and 0.2 pg mYKL-40, 0.4 pg and 0.2 pg of calmodulin (negative control) and PBS (negative control) onto the nitrocellulose membrane. The membrane was incubated with B3 (SEQ ID NO: 3)-hFc.
[0026] Figure 3 shows, that B10 (SEQ ID NO: 4) -hFc binds to both human and mouse YKL- 40. For the western blot 0.5 pg hYKL-40 or mYKL-40 were loaded onto a 4-20% SurePAGE, Bis-TRIS gel. The gel was run at 120V for 70 min and afterwards the samples were transferred to a nitrocellulose membrane using iBIot system. The membrane was incubated with 1 pg / ml primary antibody B10 (SEQ ID NO: 4)-hFc.
[0027] Figure 4 shows, that B3 (SEQ ID NO: 3) fused to a murine Fc region (mFc)(B3 mouse) and B10 (SEQ ID NO: 4) fused to a mFc (B10 mouse) bind to murine YKL-40 (mYKL- 40). A 96-well ELISA plate was coated with 2.5 pg / ml mYKL-40 or 2.5 pg / ml calmodulin as control. 0.25 pg / ml (8), 0.5 pg / ml (7), 1 pg / ml (6), 2.5 pg / ml (5), 6.25 pg / ml (4), 12.5 g / ml (3), 15 pg / ml (2) and 20 pg / ml (1) of the antibodies B3 (SEQ ID NO: 3)-mFc or B10 (SEQ ID NO: 4)-mFc were added.
[0028] Figure 5 shows, that B3 (SEQ ID NO: 3) fused to a murine Fc (mFc)(B3 mouse) and B10 (SEQ ID NO: 4) fused to mFc (B10 mouse) bind to human YKL-40 (hYKL-40). A 96-well ELISA plate were coated with 2.5 pg / ml hYKL-40 or 2.5 pg / ml calmodulin as control. 0.25 pg / ml (8), 0.5 pg / ml (7), 1 pg / ml (6), 2.5 pg / ml (5), 6.25 pg / ml (4), 12.5 pg / ml (3), 15 pg / ml (2) and 20 pg / ml (1) of the antibodies B3 (SEQ ID NO: 3)-mFc or B10 (SEQ ID NO: 4)-mFc were added.
[0029] Figure 6 shows, that YKL-40 antibody 201 F9 binds hYKL-40 at a different epitope than B3 (SEQ ID NO: 3)-hFc or B10 (SEQ ID NO: 4)-hFc. The competitive ELISA was performed by first adding 2.5 pg / ml 201 F9 before the wells were washed three times and B3 (SEQ ID NO: 3)-hFc or B10 (SEQ ID NO: 4)-hFc added in different concentrations.
[0030] Figure 7 shows, that B3 (SEQ ID NO: 3)-mFc and B10 (SEQ ID NO: 4)-mFc decrease the tumour weight and volume when administered separately or simultaneously, in SCID mice injected with human colon cancer cell line SW480. The interstitial fluid pressure increased slightly when the mice were treated with only B3 (SEQ ID NO: 3)- mFc or B10 (SEQ ID NO: 4)-mFc, but significantly decreased when both antibodies were administered simultaneously, An equivalent volume of PBS was used as control. A: shows the weight of the analysed tumour tissue of the mice. B: shows the volume of the analysed tumour tissue of the mice. C: shows the interstitial fluid pressure (IFP) in the mice.
[0031] Figure 8 shows that the administration of B3 (SEQ ID NO: 3)-mFc and B10 (SEQ ID NO: 4)-mFc increase the cisplatin uptake in SCID mice injected with the human colon cancer cell line, SW480. The mice were treated with either the anti YKL-40 antibodies B3 (SEQ ID NO: 3)-mFc, B10 (SEQ ID NO: 4)-mFc, B3 (SEQ ID NO: 3)-mFc and B10 (SEQ ID NO: 4)-mFc or an equivalent volume of PBS as control. Cisplatin was administered to the mice 12 h before mice were sacrificed.
[0032] Figure 9: Monoclonal antibody H7 comprising SEQ ID NO: 14 (light chain variable region) and SEQ ID NO: 15 (heavy chain variable region) decreases the interstitial fluid pressure in SCID mice injected with the human melanoma cell line LOX. The mice were treated with a monoclonal antibody H7 or an equivalent volume of PBS as control. A: shows the volume of the analysed tumour tissue of the mice. B) shows the tumor weight of the analysed tumour tissue of the mice.C) The interstitial fluid pressure is decreased in mice treated with H7 comprising SEQ ID NO: 14 (light chain variable region) and SEQ ID NO: 15 (heavy chain variable region) D) The ratio of the interstitial fluid pressure to tumour weight is decreased in mice treated with H7 comprising SEQ ID NO: 14 (light chain variable region) and SEQ ID NO: 15 (heavy chain variable region).
[0033] Figure 10: H7 (comprising VL of SEQ ID NO: 14 and VH of SEQ ID NO: 15) antibody stains human tissue sections. Positive staining can be observed in tissue from human foetus hands and human foetus gut system. H7 (comprising L of SEQ ID NO: 14 and H of SEQ ID NO: 15) antibody does not stain mouse tissue sections. Scale bar: 200 pm.
[0034] Figure 11: Epitope mapping of H7 antibody
[0035] Epitope mapping of H7 (SEQ ID NO: 14 and SEQ ID NO: 15) antibody was performed using linear peptide arrays as described in Geysen et al. Peptides were synthesized as mimics. Peptides were either 15-mers with 14 amino acid overlap, an additional set of 10-mers, looped 8-mers, helical-stabilized peptides of 19 amino acid length or continuous beta-turn mimics of 20 amino acid length. Epitopes of H7 comprising or positioned within a sequence selected from amino acids 123-130 or 218-224 or 259- 265 or 269-286 or 303-315 of SEQ ID NO: 1. The epitope of H7 is thus believed to comprise or be positioned within the aforementioned sequences (shown in black).
[0036] Figure 12 shows, that H7 (SEQ ID NO: 14 and 15) binds to human YKL-40 and to a lesser extent to murine YKL-40 in a dose dependent manner in a ELISA assay. Different concentrations of H7 antibody was tested as indicated in Example 13.
[0037] Figure 13: Models created by Nanobodybuilder2
[0038] Fig. 13 A shows a model of B3 variable domain created by Nanobodybuilder2. Fig. 13
[0039] B shows a model of B10 variable domain created by Nanobodybuilder2.
[0040] Figure 14: Models created by Haddock2.4 Fig. 14 A shows B3 docked onto YKL40 using the haddock software. Fig. 14 B shows B10 docked onto YKL40 using the software Haddock.
[0041] Figure 15: Epitope of B3
[0042] Fig. 15 A shows the fitting of the association and dissociation steps of Biolayer interferometry experiments performed with YKL-40 mutants and B3 antibody. Fig. 15 B shows a bar plot representation of the KD value (M) calculated for B3 when interacting with each YKL-40 mutant.
[0043] Figure 16: Epitope of B10
[0044] Fig. 16 A shows the fitting of the association and dissociation steps of Biolayer interferometry experiments performed with YKL-40 mutants and B10 antibody. Fig. 16 B shows a bar plot representation of the KD value (M) calculated for B10 when interacting with each YKL-40 mutant.
[0045] Figure 17: Epitope of H7
[0046] Fig. 17 A shows the fitting of the association and dissociation steps of Biolayer interferometry experiments performed with YKL-40 mutants and H7 antibody. Fig. 17 B shows a bar plot representation of the KD value (M) calculated for H7 when interacting with each YKL-40 mutant.
[0047] Detailed description Definitions
[0048] The term “antibody” as used herein refers to a polypeptide, which is capable of binding a specific antigen via an epitope on the antigen. An antibody comprises at least one antigen binding site, wherein said antigen binding site comprises 3 Complementaritydetermining regions (CDRs), such as a CRD1 , CDR2 and CDR3. The antigen binding site may in particular be a variable region, such as a heavy chain or light chain variable region. Whereas most antibodies comprises a heavy chain comprising an antigen binding site and a light chain comprising another an antigen binding site, some antibodies are single-domain antibodies comprising only one antigen binding site. Single-domain antibodies consisting of heavy chains only are e.g. found in camelids. Typically, the antigen binding site of an antibody is positioned within an antibody variable region. Suitable variable regions include, but are not necessarily limited to Fv fragments, heavy chain variable regions and light chain variable regions. Variable regions may be connected and thus they may form or be part of e.g. single chain Fv (scFv) and disulphide-bonded Fv, Fab-like fragments (e.g. Fab fragments, Fab’ fragments and F (ab) 2 fragments), and domain antibodies (dAbs, including single and dual formats [i.e. dAb-linker-dAb]). Variable regions may be linked to an Fc region. Thus, an antibody heavy chain usually consists of a heavy chain variable region and a heavy chain Fc region. Similarly, an antibody light chain usually consists of a light chain variable region and a light chain Fc region. Single-domain antibodies typically consists of variable region comprising 3 CDRs and a constant region of a heavy chain in one polypeptide. Various antibody chains may be linked to each other, e.g. by disulphide bonds. Thus, a heavy chain and a light chain may be linked to each other.
[0049] Furthermore, a heavy chain and a light chain pair, may be linked to another (frequently identical) heavy chain / light chain pair. The heavy chain of a single domain antibody may also be linked to another (frequently identical) heavy chain, e.g. by disulphide bonds, thereby forming an antibody made up of two constant domains of the heavy chains and two variable domains of the heavy chain, wherein said Fc regions are joined by disulphide bonds (see Fig. 1).
[0050] “Cellular cytotoxicity therapy” involves the transfer of immune cells (e.g. T-cells, NK- cells, dendritic cells, granulocytes and / or macrophages) with anti-malignant tumour activity into cancer patients. It is a treatment approach that usually involves the identification of cells with anti-malignant tumour activity, the expansion of these cells to large numbers and their infusion into the cancer-bearing host.
[0051] The term “decreased permeability” refers to malignant tumours having a barrier preventing or reducing the ability of drugs from reaching the interior of said cancers. For example, anti-cancer drug may be prevented from entry into the cancer, e. g. from reaching further than 100 pm into said cancer.
[0052] An “effective amount” or “therapeutically effective amount” of a compound is that amount of compound which is sufficient to provide a beneficial effect to the subject to which the compound is administered. The phrase “therapeutically effective amount,” as used herein, may refer to an amount of antibody that is sufficient or effective to treat (delay or prevent the onset of, prevent the progression of, inhibit, decrease or reverse) a clinical condition, e.g. an inflammatory condition or cancer. The term “Fc region” is abbreviated form of “fragment crystallisable region”. “Fc region” as used herein refers to the C-terminal constant region of an immune globulin heavy chain. The Fc region may be a “native” or “wild-type” sequence Fc region, or a variant Fc region. The Fc region may be any constant region of IgM, IgD, IgG IgA and IgE. A native Fc region is normally homodimeric and comprises two polypeptide chains. In respect of preparing YKL-40 antibodies a variable domain, such as VH, may be linked to a “single-chain” Fc region (scFc region), which may later form a dimeric antibody comprising two VH domains and two scFc regions.
[0053] The term “Immunotherapeutic agent” refers to an agent capable of inducing, enhancing and / or suppressing an immune response. In particular, an immunotherapeutic agent is an agent useful in the treatment of disease.
[0054] The term “immunotherapy” refers to treatment of disease by activating, augmenting and / or suppressing the natural, humoral and / or adaptive immune system. Immunotherapy may be cell-based therapy such as cellular cytotoxicity therapy or noncell based. Immunotherapy may be antibody therapy with antibodies from either the natural or the adaptive immune system. Immunotherapy may also be therapy with immunomodulators such as cytokines, interleukins and / or chemokines. Immunotherapy may also be treatment aimed at modulating or enhancing interactions with immunomodulators and classical anti-neoplastic agents. Examples of useful types of immunotherapies are described in the figure 3 of the review article by Melero et al. Evolving synergistic combinations of targeted immunotherapies to combat cancer. Nature Reviews 2015, 15:457472. Other useful types of immunotherapies are described below.
[0055] The term ’’naturally occurring antibody " refers to an antibody comprising two identical heavy chains and two identical light chains linked to another, wherein the heavy and light chains of the antibody have been made and paired by the immune system of a multi-cellular organism. Spleen, lymph nodes and bone marrow are examples of tissues that produce natural antibodies. For example, the antibodies produced by the antibody producing cells isolated from a first animal immunized with an antigen are natural antibodies. Naturally occurring antibody are heterotetra meric glycoproteins capable of recognising and binding an antigen and comprising two identical heavy (H) chains and two identical light (L) chains inter-connected by disulfide bonds. Each heavy chain comprises a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region (abbreviated herein as CH). Each light chain comprises a light chain variable region (abbreviated herein as VL) and a light chain constant region (abbreviated herein as CL). The VH and L regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDRs), interspersed with regions that are more conserved, termed framework regions (FRs). Antibodies may comprise several identical heterotetramers.
[0056] The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e. , the individual antibodies making up the population are identical except for possible minor differences. Said minor differences may be the result of post-translational modification and / or degradation or they may be caused by naturally occurring mutations that may be present in minor amounts.
[0057] The terms “solid neoplasm”, “solid malignant tumour”, and “malignant tumour” are herein used interchangeably. The term “cancer” refers to a disease, which may be characterised by the presence of at least one “solid neoplasm”, “solid malignant tumour” or “malignant tumour”.
[0058] The term "variable" in the context of variable domain of antibodies, refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies. The variable domains are for binding and determine the specificity of each particular antibody for its specifically recognized antigen. However, the variability is not evenly distributed through the variable domains of antibodies. It is concentrated in three segments called complementarity determining regions (CDRs) also known as hypervariable regions both in the light chain and the heavy chain variable domains.
[0059] The term “treatment” refers to any kind of treatment, including preventive, ameliorating / palliative or curative treatment. Treatment may thus result in the prevention, decrease and / or amelioration / palliation of causes and / or symptoms of malignant tumours and cancers. Moreover, the treatment can also stop or slow down disease progression, e.g. it may stop or slow down cancer formation, development, or growth. YKL-40 antibody
[0060] A YKL-40 antibody may be any antibody specifically binding YKL-40. For example, the YKL-antibody of the present invention may be any YKL-40 antibody, wherein said YKL- 40 antibody comprises a variable region as defined herein below in the section “Variable region”. Thus, the present invention provides antibodies capable of binding to YKL-40, and preferably capable of binding human and murine YKL-40. In particular, said antibodies are capable of binding to an amino acid sequence of SEQ ID NO:1 and of SEQ ID NO:2.
[0061] In some embodiments, the YKL-40 antibody comprises a variable region comprising a CDR1, CDR2 and CDR3, wherein,
[0062] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;
[0063] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; and
[0064] CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7. In particular, the YKL-40 antibody may be a single domain antibody comprising a variable region comprising aforementioned CDRs. The antibody may also be a bi- or multispecific antibody made up of several single domain antibodies one of which contains a variable region comprising aforementioned CDRs.
[0065] In some embodiments, the YKL-40 antibody comprises a variable region comprising a CDR1, CDR2 and CDR3, wherein,
[0066] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8;
[0067] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; and CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10. In particular, the YKL-40 antibody may be a single domain antibody comprising a variable region comprising aforementioned CDRs. The antibody may also be a bi- or multispecific antibody made up of several single domain antibodies one of which contains a variable region comprising aforementioned CDRs.
[0068] In some embodiments, the at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1, CDR2 and CDR3, wherein,
[0069] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;
[0070] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; and CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7 and wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1, CDR2 and CDR3, wherein, CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8;
[0071] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; and
[0072] CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10.
[0073] In some embodiments, the YKL-40 antibody comprises two variable regions each comprising a CDR1, CDR2 and CDR3, wherein,
[0074] CDR1 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 16;
[0075] CDR2 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 17;
[0076] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 18;
[0077] CDR1 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 19;
[0078] CDR2 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 20; and
[0079] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 21.
[0080] In some embodiments, the YKL-40 antibody comprises at least one variable region comprising or consisting of SEQ ID NO: 3. In particular, the YKL-40 antibody may be a single domain antibody comprising a variable region comprising or consisting of SEQ ID NO: 3. The antibody may also be a bi- or multispecific antibody made up of several single domain antibodies one of which contains a variable region comprising or consisting of SEQ ID NO: 3.
[0081] In some embodiments, the YKL-40 antibody comprises at least one variable region comprising or consisting of SEQ ID NO: 4. In particular, the YKL-40 antibody may be a single domain antibody comprising a variable region comprising or consisting of SEQ ID NO: 4. The antibody may also be a bi- or multispecific antibody made up of several single domain antibodies one of which contains a variable region comprising or consisting of SEQ ID NO: 4. In some embodiments, the YKL-40 antibody comprises at least one variable region of the light chain comprising or consisting of an amino acid sequence of SEQ ID NO: 14 and at least one variable region of the heavy chain comprising or consisting of an amino acid sequence of SEQ ID NO: 15.
[0082] In some embodiments, the YKL-40 antibody comprises a variable region comprising a CDR1 comprising or consisting of an amino acid sequence selected from the group consisting of SEQ ID NO: 5 and SEQ ID NO: 8.
[0083] In some embodiments, the YKL-40 antibody comprises variable regions comprising a CDR1 of the light chain comprising or consisting of an amino acid sequence of SEQ ID NO: 16 and a CDR1 of the heavy chain comprising or consisting of an amino acid sequence of SEQ ID NO: 19.
[0084] In some embodiments, the YKL-40 antibody comprises a light chain variable region comprising a CDR2 comprising or consisting of an amino acid sequence selected from the group consisting of SEQ ID NO: 6 and SEQ ID NO: 9.
[0085] In some embodiments, the YKL-40 antibody comprises variable regions comprising a CDR2 of the light chain comprising or consisting of an amino acid sequence of SEQ ID NO: 17 and a CDR2 of the heavy chain comprising or consisting of an amino acid sequence of SEQ ID NO: 20.
[0086] In some embodiments, the YKL-40 antibody comprises a light chain variable region comprising a CDR3 comprising or consisting of an amino acid sequence selected from the group consisting of SEQ ID NO: 7 or SEQ ID NO 10.
[0087] In some embodiments, the YKL-40 antibody comprises variable regions comprising a CDR3 of the light chain comprising or consisting of an amino acid sequence of SEQ ID NO: 18 and a CDR3 of the heavy chain comprising or consisting of an amino acid sequence of SEQ ID NO: 21.
[0088] In some embodiments, the antibody comprises or consists of a variable region comprising or consisting of an amino acid sequence selected from the group consisting of SEQ ID NO:3 or SEQ ID NO:4. The YKL-40 antibody of the invention comprising any of the aforementioned variable region may further comprise constant regions. In embodiments, of the invention where the antibody is a single domain antibody, the antibody typically comprises only one of the aforementioned variable regions, e.g. a variable region comprising the CDRs of B3 or B10 fused to one constant region, e.g. an Fc region as described below. In embodiments of the invention, where the antibody comprises two variable regions, each variable region may be fused to a constant region, e.g. to Fc regions. Thus, the YKL-40 antibody may comprise a light chain variable region and a heavy chain variable region comprising the CDRs of H7, each variable region being fused to constant regions, such as Fc regions.
[0089] In some embodiments the antibody of the invention is a bi- or multispecific antibody. A bispecific antibody comprises two different antigen binding sites, e.g. different variable regions, specifically binding different epitopes. Preferably, said bi- or multispecific antibody binds to different epitopes on YKL-40. In other words, the bi- or multispecific antibody comprises two different variable regions each binding to YKL-40. Similarly, a multispecific antibody comprises several different antigen binding sites, e.g. different variable regions, specifically binding different epitopes. The antibodies of the invention may thus comprise two or more different variable regions, wherein each variable region may be fused to a constant region, e.g. to Fc regions. Bi- or multispecific antibodies may also be IgA comprising two (or 4) or IgM comprising five (or 10) different variable regions having different epitope specificities. Bi-specific antibodies may be prepared based on any of the YKL-40 antibodies described herein, e.g. using any of the methods described in Wang, Q. et aL, 2019.
[0090] In one embodiment, the YKL-40 antibody may be a bi-specific antibody comprising or consisting of two different single domain antibodies each capable of specifically binding YKL-40. Each of the single domain antibodies may comprise a variable region specifically binding YKL-40 fused to a constant region, e.g. an Fc region. The skilled person is aware of how to prepare a bi-specific antibody based on two single domain antibodies. This may for example be done by fusing the variable region of the single domain antibodies to different Fc regions comprising mutations allowing for binding between the different Fc regions, e.g. using the knobs and holes strategy (Wang, Q. et al., 2019). For example, one single domain antibody may comprise the heavy chain mutations S354C and T366W, whereas the other single domain antibody may comprise the heavy chain mutations Y349C, T366S, and L368A.
[0091] In one embodiment, the YKL-40 antibody may comprise one or more variable regions comprising the CDRS of B3, i.e. CDRs of SEQ ID NOs: 5, 6 and 7 and one or more variable regions comprising the CDRS of B10, i.e. CDRs of SEQ ID NOs: 8, 9 and 10. Each of said variable regions may be attached to a constant region, e.g. an Fc region, and may made into a bi-specific format as described above.
[0092] In one embodiment, the YKL-40 antibody may comprise one or more variable regions comprising or consisting of the variable region of B3, i.e. SEQ ID NO: 3 and one or more variable regions comprising or consisting of the variable region of B10, i.e. SEQ ID NO:4. Each of said variable regions may be attached to a constant region, e.g. an Fc region, and may made into a bi-specific format as described above.
[0093] In one embodiment, the YKL-40 antibody may comprise one or more variable regions comprising the CDRS of B3, i.e. CDRs of SEQ ID NO: 5-7 and one or more variable regions made up of a VL and VH, wherein the VL comprises the CDRs of the light chain variable region of H7, i.e. CDRs of SEQ ID NO: 16-18, and the VH comprises the CDRs of the heavy chain variable region of H7, i.e. CDRs of SEQ ID NO: 19-21.
[0094] In one embodiment, the YKL-40 antibody may comprise one or more variable regions comprising the CDRS of B10, i.e. the CDRs of SEQ ID NO: 8-10 and one or more variable regions made up of a L and VH, wherein the VL comprises the CDRs of the light chain variable region of H7, i.e. CDRs of SEQ ID NO: 16-18, and the VH comprises the CDRs of the heavy chain variable region of H7, i.e. CDRs of SEQ ID NO: 19-21.
[0095] In, one embodiment the YKL-40 antibody may comprise one or more variable regions comprising the CDRS of B3 of SEQ ID NO: 5-7, one or more variable regions comprising the CDRS of B10 of SEQ ID NO: 8-10 and one or more variable regions made up of a VL and VH, wherein the VL comprises the CDRs of the light chain variable region of H7, i.e. CDRs of SEQ ID NO: 16-18, and the VH comprises the CDRs of the heavy chain variable region of H7, i.e. CDRs of SEQ ID NO: 19-21. In some embodiments, the composition comprises antibodies binding to YKL-40, with the proviso that the antibodies do not comprise any of the following combinations of CDRs: specifically binding YKL-40. It is preferred that the YKL-40 antibody of the invention is capable of penetrating into the interior of a solid tumour or solid neoplasm in vivo. It is also preferred that the YKL- 40 antibody of the invention is capable of penetrating into other tissues, such as swelled extracellular matrix. Thus, upon systemic administration of the antibody to an individual affected by a solid neoplasm, it is preferred that the antibody is capable of distributing throughout said solid neoplasm. Distribution of antibodies within a solid neoplasm may e.g. be determined by obtaining a sample (e.g. a biopsy) or a solid neoplasm removed by surgery or after individual is deceased, and detecting the presence of YKL-40 antibodies.
[0096] It is preferable that the antibodies of the invention are capable of reducing the interstitial fluid pressure within a solid neoplasm, either alone or in combination with one or more other anti-YKL-40 antibodies. In some embodiments, the interstitial fluid pressure is decreased by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20% compared to administration of PBS to said individual, and administration of an anti-cancer agent to said individual. It is also preferable that the antibodies of the invention are capable of reducing the interstitial fluid pressure within other tissues characterised by high IFP, e.g. in swelled extracellular matrix, e.g. swelled extracellular matrix of joints.
[0097] The YKL-40 antibody of the invention may be an antibody capable of facilitating penetration of other agents, such as diagnostic substances or therapeutic agents into the interior of a tissue characterised by high IFP. Such tissues may be solid neoplasms or swelled extracellular matrix, e.g. swelled extracellular matrix of joints.
[0098] In particular, the YKL-40 antibody of the invention may be an antibody capable of facilitating penetration of an anti-cancer agent into the interior of a solid neoplasm. Thus, in preferred embodiments of the invention, the YKL-40 antibody of the invention is capable of increasing uptake of an anticancer agent (e.g. cisplatin) into a solid tumour by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20% compared to administration of PBS to said individual. The amount of cisplatin taken up into a solid tumour may in particular be determined by graphite-furnace atomic absorption spectrometry as described in Example 9 below.
[0099] In some embodiments, the interstitial fluid pressure is reduced by a composition of at least one YKL-40 antibody, such as two YKL-antibodies, such as three YKL-40 antibodies, such as five YKL-40 antibodies. In a preferred embodiment, the interstitial fluid pressure is reduced by a composition of two YKL-40 antibodies. The antibodies can bind the same or different epitopes in YKL-40. The interstitial fluid pressure is decreased by the composition by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20% compared to administration of PBS to said individual, and administration of an anti-cancer agent to said individual.
[0100] In some embodiments, the uptake of a drug into a solid neoplasm is increased by a composition of at least one YKL-40 antibody, such as two YKL-antibodies, such as three YKL-40 antibodies, such as five YKL-40 antibodies. In a preferred embodiment, the uptake of a drug into a solid neoplasm is increased by a composition of two YKL-40 antibodies. The antibodies can bind the same or different epitopes in YKL-40. The uptake of a drug into a solid neoplasm is increased by the composition by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20% compared to administration of PBS to said individual, and administration of an anti-cancer agent to said individual.
[0101] In some embodiments, the two YKL-40 antibodies are administered in a ratio of 1:1 , such as 1 :2, such as 1 :3, such as 1 :4, such as 1 :5, such as 1 :10, such as 1:100.
[0102] In some embodiments, the two YKL-40 antibodies are administered sequentially or simultaneously, preferably simultaneously.
[0103] In some embodiments, the two YKL-40 antibodies are selected from a group consisting of antibodies binding to the same epitope as B3 (SEQ ID NO: 3), binding to the same epitope as B10 (SEQ ID NO: 4) and binding to the same epitope as H7 (SEQ ID NO: 14 and SEQ ID NO: 15).
[0104] In some embodiments, the two YKL-40 antibodies is one antibody binding to the same epitope as B3 (SEQ ID NO: 3) and one antibody binding to the same epitope as B10 (SEQ ID NO: 4). Said antibody binding the same epitope as B3, may in particular be an antibody comprising the same CDRs as B3 (i.e. SEQ ID NO: 5, 6 and 7), for example an antibody comprising the variable region of B3 (i.e. SEQ ID NO:3). Said antibody binding the same epitope as B10, may in particular be an antibody comprising the same CDRs as B10 (i.e. SEQ ID NO: 8, SEQ ID NO:9 and SEQ ID NO:10), for example an antibody comprising the variable region of B10 (i.e. SEQ ID NO:4).
[0105] YKL-40 is an extracellular matrix protein, specifically a secretory glycoprotein, which belongs to the mammalian chitinase like family. YKL-40 has been shown to bind collagen, heparin, hyaluronan and chitin. It is mainly produced by macrophages, neutrophils and cancer cells. YKL-40 plasma levels are increased in cancer patients compared to healthy subjects.
[0106] An antibody that is contemplated for use in the present invention can be in any of a variety of forms, including a whole immunoglobulin, an antibody fragment such as Fv, Fab, Fab’ or F(ab’)2 fragments, a single chain antibody which comprises the variable regions of a heavy and a light chain linked together or single domain antibodies.
[0107] In one embodiment, the antibody of the invention is a single domain antibody. Single domain antibodies usually comprises a variable region optionally linked to an Fc region. Thus, the antibody of the invention may consist of a variable region. Alternatively, the antibody may consist of a variable region linked to an Fc region. The variable region may for example consist of either of a VH domain or a VL domain, or another similar variable region. In particular, the single domain antibody may comprise a variable region and an Fc region derived from a human antibody, e.g. from a human heavy chain.
[0108] In one embodiment, the antibody comprises a variable region comprising a CDR1 , CDR2 and CDR3 as defined herein below. The variable region may be selected from the group consisting of a VH domain, VL domain or scFv. It is preferred that the variable region comprises or consists of a VH domain.
[0109] In another embodiment, the variable region of said antibody is linked to an Fc region, optionally by a linker. Thus, the antibody according to the invention may comprise or consist of a VH domain linked to an Fc region, optionally via a linker. Hereby forming a single chain antibody, which comprises the CDRs of a variable domain of the heavy chain and the constant region of the heavy chain in one polypeptide.
[0110] In yet another embodiment, the antibody may comprise or consist of two single domain antibodies. Thus, the antibody according to the invention may consist or comprise of two VH domains, wherein each VH domain is linked to an Fc region, wherein said Fc regions are linked to each other by bonds, such as by disulphide bonds.
[0111] The antibodies according to the present invention are in general monoclonal antibodies. In one embodiment, the antibody of the invention is a chimeric antibody. Chimeric antibodies retains CDRs from its original species incorporated into the antibody from another species, such as humans. Other chimeric antibodies retain the variable regions from its original species fused to constant regions of another species, such a humans. Advantages of chimeric antibodies are a reduced immunogenicity in humans compared to murine antibodies and a cheaper production compared to what is required for generating a fully humanized antibody. In the United States, several different chimeric antibodies have already been approved for clinical use by the Food and Drug Administration (FDA).
[0112] The antibody can be a multispecific antibody (e.g. bispecific antibody) formed from at least two different antibodies, and / or antibody fragments so long as they exhibit binding to YKL-40.
[0113] In one embodiment, the antibody is a human antibody or an antibody based on human scaffold. For example, the antibody may be a human single domain antibody. Human single domain antibodies may in particular comprise or consists of a human VH domain optionally linked to a human Fc region. The antibody may also be a single domain antibody based on human sequences, wherein diversity has been generated synthetically. Such antibodies are useful in the treatment of human beings. The antibody may also be a humanised antibody comprising CDR regions (and possibly a few other residues) transferred from another species having the desired specificity, affinity, and capacity. Humanised antibodies may also comprise synthetic CDR regions, e.g. from a synthetic antibody library.
[0114] The generation of antibodies may be achieved by any standard methods in the art for producing antibodies.
[0115] For generation and / or selection of YKL-40 antibodies, YKL-40 protein or a fragment thereof is used. Preferably, the method comprises use of a natural YKL-40 protein, such as a secreted and optionally purified YKL-40 protein. Alternatively, a recombinant YKL-40 protein or fragment thereof may also be employed. In particular, YKL-40 secreted from MG63 cells may be employed. Medium in which MG63 cells have been cultivated may be used in crude form or YKL-40 may be partly or fully purified from such medium. Alternatively, YKL-40 secreted from the mouse myeloma cell line NSO may be employed. Medium in which the mouse myeloma cell line NSO have been cultivated may be used in crude form or YKL-40 may be partly or fully purified from such medium. Recombinant antibodies may be isolated from libraries of genes encoding fragments of antibodies, e.g. using aforementioned YKL-40 protein or fragments thereof for selection. The fragments of antibodies can for example be any of the aforementioned antibody fragments, such as Fab, Fv fragments, single chain fragment of heavy and light chain variable domains or single domain antibodies, such as polypeptides comprising or consisting of VH or VL domains. The libraries of genes may be obtained from natural sources, as in the case of naive or immunised libraries, or they may be created by synthetic means. Isolation of specific antibodies from the libraries can be mediated by panning of phage displayed antibody libraries on specific antigens or complex mixtures, such as described in Mandrup et aL, 2013. Libraries may be obtained by panning of phage displayed antibody libraries on a specific antigen from several species in several rounds. The phage displayed antibody libraries may be screened by successive selection on YKL-40 or a fragment thereof from humans followed by panning the phage displayed antibody libraries on YKL-40 from mice or a fragment of murine YKL-40 corresponding to the fragment from human YKL-40. These pannings may be performed in either order. Alternatively, methods such as yeast display, bacterial display, ribosome display, etc. can be applied in the selection of monoclonal recombinant antibodies.
[0116] The antibody may be a human single domain antibody or a single domain antibody based on human sequences, wherein diversity has been artificially generated. Several different libraries of useful human single domain antibodies are available. Thus, the antibody may be selected by screening any library of human single domain antibodies with YKL-40 protein or fragment(s) thereof. Such libraries include, but are not limited to human domain antibody libraries using the HEL4 scaffold, as well as such libraries, which have been counter-selected for aggregation, wherein the CDR regions of the resulting clones have been sub-cloned and used for generating a new library with diversity in all three CDR regions as described in Christ et aL, 2007. Other useful libraries include Pansri et aL, 2009, Rothe et aL, 2008, Fellouse et aL, 2007, Hust et la., 2004, Silacci et aL, 2005 and Brockmann et aL, 2011 . A preferred library to be used is the domain antibody library with constant CDR1 and restricted randomizations at 4 and 7 positions in the CDR2 and CDR3 described in Mandrup et aL, 2013. This library is based on the aggregation resistant human HEL4 domain antibody scaffold with the inclusion of a hydrophilic mutation at position 29. The diversity of this library is designed to reflect the amino acid composition of CDR regions from known functional human antibody clones.
[0117] Once a variable domain capable of binding YKL-40 has been selected, said variable domain may be used as YKL-40 antibody per se, but it may also be fused to other domains, e.g. an Fc domain.
[0118] This may e.g. be achieved by using an expression vector allowing fusion of single chain Fv antibodies or single domains, such as single VH domains to Fc regions of immunoglobulins. This method is useful for the generation of multi-species antibodies and enables fusion of single chain Fv antibodies or single VH domains with human, mouse or rabbit Fc and can be applied to natural monoclonal antibodies cloned as single chain Fv antibodies. The expression vector can be for example a pFuse expression system, such as pFUSE-hFc1 or pFUSE-mFc1 as described by Moutel et aL, 2009. Thus, an antibody comprising or consisting of a VH domain linked to an Fc region can be generated. Such antibodies can then dimerize and form an antibody of two VH domain which are each linked to an Fc region, wherein the two Fc regions are linked by disulphide bonds. Preferably, said Fc region is a human Fc region. Nonlimiting examples of useful Fc regions include the Fc region of SEQ ID NO: 22 or SEQ ID NO: 23. In other embodiments the Fc region is a murine Fc, such as the Fc region of SEQ ID NO:62.
[0119] In one embodiment, the antibody is a chimeric antibody wherein the variable part is fused with an Fc region of a different species.
[0120] This means, that a portion of the heavy and / or light chain of the antibody is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainer of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (Morrison et al. 1984).
[0121] The invention contemplates human and humanized forms of non-human (e.g. murine) antibodies. Such humanized antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other antigen-binding subsequences of antibodies) that contain a minimal sequence derived from non-human immunoglobulin, such as the epitope recognising sequence. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a nonhuman species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. Alternatively, humanized antibodies are human immunoglobulins (recipient antibody) in which the entire variable region has been replaced by a variable region from a nonhuman species. Humanized antibodies containing a minimal sequence of antibodies of the invention, such as a sequence recognising the epitopes described herein, is a preferred embodiment of the invention. In particular, in some embodiments, the invention relates to humanized forms of mouse anti-human YKL-40 monoclonal antibody H7 (SEQ ID NO: 14 and SEQ ID NO: 15). Alternatively, humanized antibodies are human immunoglobulins (recipient antibody) in which the entire variable region has been replaced by a variable region from a nonhuman species.
[0122] In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and optimize antibody performance. In general, humanized antibodies will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., 1986). In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 123-130 or 218-224 or 259-265 or 269-286 or 303-315 of SEQ ID NO: 1.
[0123] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 46-58 or 76-127 or 192-203 or 213-225 or 234-247 or 250-269 or 274-286 or 294-314 or 359-373 of SEQ ID NO: 1.
[0124] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 76-92 or 99-131 or 134-158 or 161-182 or 212-225 or 240-263 or 275-286 or 303-324 or 326-348 of SEQ ID NO: 1.
[0125] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 123-127 or 218-224 or 259-263 or 275-286 or 303-314 of SEQ ID NO: 1.
[0126] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 123-127 or 218-224 or 259-263 or 275-286 or 304-314 of SEQ ID NO: 1.
[0127] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 218-224 of SEQ ID NO: 1.
[0128] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 218-224 or 269-273 of SEQ ID NO: 1.
[0129] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 46-58 or 76-92 or 192-201 or 216-225 or 234-247 or 274-286 or 294-300 or 359-373 of SEQ ID NO: 1. In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 76-92 or 145-158 or 161-182 or 216-225 or 240-250 or 314-324 or 326- 348 of SEQ ID NO: 1.
[0130] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 44, 93, 104, 108, 134 or 145 of SEQ ID NO: 63.
[0131] In some embodiments, the YKL-40 antibody is binding an epitope comprising at least 3, preferably at least 4, more preferably at least 5, even more preferably all of amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
[0132] In some embodiments, the YKL-40 antibody is binding an epitope comprising at least 3, preferably at least 5, more preferably at least 8, yet more preferably at least 11, even more preferably all of amino acids at positions 212, 213, 214, 215, 270, 271, 272, 273, 274, 275, 276, -277, 308 or 321 of SEQ ID NO.1.
[0133] In some embodiments, the YKL-40 antibody is binding an epitope comprising the amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1, wherein said epitope does not comprise at least 1 , such as does not comprise at least 2, preferably does not comprise at least 5, more preferably does not comprise at least 7, even more preferably comprises none of amino acids at positions 115, 116, 117, 126, 127, 128, 167,169 or 169 of SEQ ID NO: 1.
[0134] In some embodiments, the YKL-40 antibody is binding an epitope comprising one or more of amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1, preferably all of amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1.
[0135] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 44, 93-96, 104- 108, 134 or 145-148 of SEQ ID NO: 63. In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 191-194, 249- 256, 287 or 300 of SEQ ID NO.63.
[0136] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 44, 93, 104, 108, 134 or 145 of SEQ ID NO: 63 and said antibody alone or together with other antibodies is capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
[0137] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 44, 93-96, 104- 108, 134 or 145-148 of SEQ ID NO: 63 and said antibody alone or together with other antibodies is capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
[0138] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 191-194, 249- 256, 287 or 300 of SEQ ID NO: 63 and said antibody alone or together with other antibodies is capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
[0139] SEQ ID NO:1 provides the sequence of full length YKL-40, whereas SEQ ID NO:63 provides the sequence of YKL-40 lacking amino acid 1-21.
[0140] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
[0141] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO.1. In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 212-215, 270- 277, 308 or 321 of SEQ ID NO.1.
[0142] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 114-117, 125- 129, 155 or 166-169 of SEQ ID NO: 1 and said antibody alone or together with other antibodies is capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
[0143] In some embodiments, the YKL-40 antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids 212-215, 270- 277, 308 or 321 of SEQ ID NO.1 and said antibody alone or together with other antibodies is capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
[0144] In some embodiments, the antibody is binding an epitope comprising at least 4 amino acids, such as at least 5 amino acids, such as at least 6 amino acids, such as at least 7 amino acids selected from amino acids at positions 65, 114, 125, 129, 155, 166 or 307 of SEQ ID NO: 1.
[0145] In some embodiments, the antibody is binding an epitope comprising at least 4 amino acids, such as at least 5 amino acids, such as at least 6 amino acids, such as at least 7 amino acids selected from amino acids 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
[0146] In some embodiments, the antibody is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
[0147] In some embodiments, the antibody is binding an epitopes comprising amino acids at positions 65, 114, 117, 128 or 169 of SEQ ID NO: 1.
[0148] In some embodiments, the composition comprises one antibody specifically binding YKL-40, wherein the antibody is binding one or more epitopes comprising or positioned within a sequence selected from amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1; and another antibody binding one or more epitopes comprising or positioned within a sequence selected from amino acids at position 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO.1.
[0149] Variable region
[0150] The antibody according to the present invention comprises a variable region. The variable region can be in any form, comprising a CDR1 , CDR2 and CDR3. Thus, the variable region may be a single domain consisting of either VH or VL domains, scFv, Fab, Fab’ or F(ab’)2 fragments. In some embodiments, the variable region is a VH domain, for example a human H domain or a VH domain based on human sequences, such as a VH domain as described by Mandrup et al., 2013. In other embodiments, the variable region is a VH domain, for example, a chimeric VH domain based on human and murine sequences, such as a VH domain as described by Jones et aL, 1986.
[0151] The variable domains are for binding and determine the specificity of each particular antibody for its particular antigen. However, the variable region is not normally evenly distributed thought the variable region of antibodies. It is concentrated in CDRs also known as hyper variable regions. The more highly conserved portions of variable domains are called the framework (FR). The variable domains of native heavy and light chains each comprise four FR regions connected by three CDRs. It is preferred that the FR regions are human FR regions, or at least highly identical to human FR regions.
[0152] In one embodiment, the antibody binds to YKL-40, wherein binding to YKL-40 inhibits or prevents binding of YKL-40 to another molecule. Binding of the antibody to YKL-40 can result in activation, stimulation or inhibition of YKL-40. Thus, binding of the antibody to YKL-40 may results in activation, stimulation or inhibition of YKL-40.
[0153] In one embodiment, the antibody is an inhibitor of YKL-40. Thus, the YKL-40 antibody may result in inhibition of at least one function of YKL-40.
[0154] In one embodiment, the antibody binds to an epitope on human and murine YKL-40. Thereby, the antibody binds partially or completely to an epitope within residues 1-383 of YKL-40, such as residues 1-50 of YKL-40, such as residues 50-100 of YKL-40, such as residues 100-150 of YKL-40, such as residues 150-200 of YKL-40, such as residues 200-250 of YKL-40, such as residues 250-300 of YKL-40, such as residues 300-350 of YKL-40, such as residues 350-383 of YKL-40. In one embodiment, the YKL-40 antibody binds preferably to the same epitope as an YKL-40 antibody comprising the variable region of SEQ ID NO:3.
[0155] In one embodiment, the YKL-40 antibody binds preferably to the same epitope as an YKL-40 antibody comprising the variable region of SEQ ID NO:4.
[0156] In one embodiment, the YKL-40 antibody binds preferably to the same epitope as an YKL-40 antibody comprising a light chain variable region of SEQ ID NO: 14 and a heavy chain variable regions of SEQ ID NO:15.
[0157] Constant region or Fc region
[0158] The antibody according to the present invention comprises a variable region, which may be linked to any constant region, for example any Fc region.
[0159] Traditionally, antibodies have been grouped based on the constant domain of their heavy chains, i.e. Fc region, into five classes IgM, IgD, IgG IgA and IgE. Which can be further divided into subclasses (isotypes), e.g. lgG-1 , lgG-2, lgG-3 and lgG-4; IgA-1 and IgA-2.
[0160] In some embodiments, the heavy chain has the amino acid sequence of a human IgA heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a human IgM heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a human IgE heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a human IgG heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a human IgD heavy chain.
[0161] In some embodiments, the heavy chain has the amino acid sequence of a mouse IgA heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a mouse IgM heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a mouse IgE heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a mouse IgG heavy chain. In some embodiments, the heavy chain has the amino acid sequence of a mouse IgD heavy chain.
[0162] In some embodiments, the antibody according to the present invention comprises a variable region which may be linked to any constant region of another antibody. The constant region may be identical to a “native” or “wild-type” Fc region, or a variant Fc region with at least one alteration of an amino acid.
[0163] In one embodiment, the Fc region has the amino acid sequence of a human IgE Fc region, e.g. the sequence provided herein as SEQ ID NO: 61. A suitable Fc region is described in Moutel et aL, 2009.
[0164] As mentioned herein above, the antibody may be a bispecific antibody, which e.g. may be designed as described in Wang et aL, 2019. In such cases the variable regions may be linked to slightly different Fc regions as described above.
[0165] Method of treatment
[0166] The present invention also concerns a method of treating diseases associated with aberrant YKL-40 expression. Such method comprises administering an YKL-40 antibody as described herein above, to a subject in need thereof.
[0167] Said treatment may be a curative treatment, but it may also be preventive treatment to delay onset of said disease, or it may be treatment to delay disease progression. Further, it may be ameliorating treatment or treatment of symptoms of said disease.
[0168] The disease may for example be cancer, such as any of the cancers described herein below.
[0169] In one embodiment, the invention relates to a method of treating cancer, the method comprising administering an YKL-40 antibody according to the invention to a subject in need thereof. In a preferred embodiment, the invention relates to a method of treating cancer, the method comprising administering a composition of at least one YKL-40 antibody, such as two YKL-40 antibodies, such as three YKL-40 antibodies, such as five YKL-40 antibodies according to the invention to a subject in need thereof.
[0170] In some embodiments, the invention relates to a method of treating cancer, the method comprising administering two different YKL-40 antibodies. Preferably, said two antibodies are selected from a group consisting of antibodies binding to the same epitope as B3 (SEQ ID NO: 3), binding to the same epitope as B10 (SEQ ID NO: 4) and binding to the same epitope as H7 (SEQ ID NO: 14 and SEQ ID NO: 15). In some embodiments, the invention relates to a method of treating cancer, the method comprising administering two different YKL-40 antibodies. Preferably, one YKL-40 antibody binds to the same epitope as B3 (SEQ ID NO: 3) and the other YKL-40 antibody binds to the same epitope as B10 (SEQ ID NO: 4). In preferred embodiments, one YKL-40 antibody comprises the same CDRs as B3 (i.e. SEQ ID NO: 5, 6 and 7) and the other YKL-40 antibody comprises the same CDRs as B10 (i.e. SEQ ID NO: 8, SEQ ID NO:9 and SEQ ID NQ:10). Even more preferably, one antibody comprises the variable region of B3 (i.e. SEQ ID NO:3) and the other antibody comprises the variable region of B10 (i.e. SEQ ID NO:4).
[0171] In another embodiment, the invention relates to a method for delaying onset of cancer, the method comprising administering a therapeutically effective amount of an YKL-40 antibody according to the invention, to a subject in need thereof
[0172] The disease to be treated with the YKL-40 antibody according to the invention may also be an inflammatory disease. For example the disease may be an inflammatory disease on the lungs, such as asthma and / or rheumatic diseases. In some embodiments, the rheumatic disease to be treated with the YKL-40 antibody according to the invention is arthritis, such as osteoarthritis. Interesting, the YKL-40 antibodies of the invention may be capable of reducing the interstitial fluid pressure in hyaline cartilage.
[0173] The subject to be treated with the antibody of the invention may in particular be a human being, because the antibodies of the invention preferably are based on human antibody sequences.
[0174] The invention also comprises diagnostic and theranostic methods useful to determine whether a subject is susceptible to a method of treatment. The term "theranostics" generally refers to therapy-specific diagnostics, which is the use of diagnostic testing to determine the efficacy of a given treatment regime for that disease, and / or monitor the patient response to therapy. Theranostic tests can be used to predict and assess response in individual patients, and can be used to improve efficacy by selecting treatments effective for a given patient. As explained herein elsewhere, the antibodies of the invention (alone or in combination) may reduce the IFP of e.g. a tumour, thereby facilitating access other compounds to said tumour. Thus, the antibodies of the invention may be used to facilitate the update of diagnostic substances into the interior of tissues characterised by high IFP, e.g. into tumours.
[0175] It is thus an aspect of the invention to provide a kit-of-parts comprising a. one or more YKL-40 antibodies of the invention; and b. a diagnostic substance.
[0176] It is also an aspect of the invention to provide a method of determining efficacy of treatment of a disease, said method comprising administering to an individual receiving said treatment a. one or more YKL-40 antibodies of the invention; and b. a diagnostic substance, and determining the efficacy of the treatment on the basis of the diagnostic substance.
[0177] Said method may preferably be a theranostic method.
[0178] The kit-of-parts may be administered to any individual suffering from the disease, either sequentially or simultaneously. The disease may in particular be a cancer characterised by the presence of at least one solid neoplasm,
[0179] The treatment to be monitored may be any treatment, for example a radiotherapy.
[0180] The diagnostic substance may be any substance used in in vivo diagnosis. In particular such diagnostic substances, where it is advantageous that they can enter the interior of a solid neoplasm. Non-limiting examples of useful diagnostic substances are described in Benfante et aL, 2023 and Chakraborty et al., 2023, and the diagnostic substance may thus for example be any of the radiopharmaceutical or radionuclides or radiolablled peptides described therein. The diagnostic substance may for example be a radioactively labelled substance, for example a substance labelled with 64Cu-, 68Ga- , 125I-, or 99mTc. The diagnostic substance may for example be a PSMA labelled radionuclide, such as 177Lu-prostate-specific membrane antigen (PSMA) labelled radionuclides. This may in particular be the case if the disease to be monitored is prostate cancer.
[0181] Anti-cancer agent
[0182] The present invention YKL-40 antibodies alone or in combination may facilitate the penetration of an anti-cancer agent into the interior of a solid malignant tumour. Without being bound by theory it is believed that the YKL-40 antibodies of the invention facilitate said penetration by lowering the IFP. Thus, anti-cancer agents may advantageously be administered together with or subsequent or prior to a YKL-40 antibody or a combination of YKL-40 antibodies. In particular, anti-cancer agents, which otherwise cannot penetrate a solid malignant tumour or which only penetrates solid malignant tumours to a low extend (e.g. only within 100 pm of blood vessels) may advantageously be administered together with or subsequent to a YKL-40 antibody or a combination of YKL-40 antibodies of the invention.
[0183] Thus, the anti-cancer agent may be any anti-cancer agent. The invention is not limited to a particular type of anti-cancer agent, because increasing permeability facilitates penetration of all compounds into solid malignant tumour. Thus, the anti-cancer agent may be small molecules, biological macro-molecules, cells, hormones or mixtures thereof.
[0184] In one embodiment, the anti-cancer agent is selected from the group consisting of a chemotherapeutic agent, an immunotherapeutic agent, a biologic agent, checkpoint inhibitors, anti-cancer antibodies, a cytostatic small molecule and statins.
[0185] In one embodiment the anti-cancer agent is a small molecule. Small molecules according to the invention are preferably an organic compound with a molecular weight of <900 daltons. In particular, said small molecule may be a chemotherapeutic agent.
[0186] The chemotherapeutic agent may be any chemotherapeutic agent. For example, the chemotherapeutic agent may be selected from the group consisting of antimetabolites, anti-malignant tumour antibiotics, topoisomerase inhibitors, mitotic inhibitors, kinase inhibitors, vinca alkaloids, anthracyclines, aromatase inhibitors, mTor inhibitors and retinoids.
[0187] In one embodiment, the anti-malignant tumour antibiotic is daunorumycin or doxorubicin. In another embodiment, the chemotherapeutic agent is cisplatin.
[0188] In one embodiment, the anti-cancer agent is a small molecule inhibitor for example a small molecule kinase inhibitor, a small molecule proteasome inhibitor and a small molecule inhibitor targeting the apoptosis.
[0189] In one embodiment, the chemotherapeutic agent is selected form the group Fluorouracil (5-FU), Irinotecan, Oxaliplatin, Capecitabin, Gemcitabin, Nab-paclitaxel and cisplatin.
[0190] In one embodiment, the immunotherapeutic agent is a cell-based immunotherapy. In a preferred embodiment, the immunotherapeutic agent is T-cell therapy. The T cell therapy can involve adoptive cell transfer where T cells are extracted, cultivated and transfused in the subject. Genetically engineered T cells and genetically and non- genetically modified NK-cell can also be used as T or NK-cell cell therapy. Harvested T cells are infected with a retrovirus that contains a copy of a T cell receptor (TCR) gene that is specialised to recognise malignant tumour antigens. T cells are expanded and transfused in the subject. T-cells for adoptive Immunotherapy of cancer may for example be any of the ones described in Karahan et aL, 2022. The immunotherapeutic agent can also be an autologous enhancement therapy where the subjects own or allogenic immune cells such as natural killer cells, cytotoxic T cells, mesenchymal stem cells or other immune cells are expanded in vitro and then transfused into the said subject.
[0191] Immune checkpoints are inhibitory regulators that act as inhibitors on the immune response. Targeting these checkpoints prevents cancers / malignant tumours from evading the immune system. In one embodiment, the checkpoint inhibitors are selected from the group consisting of inhibitors of PDL-1 , PD1 , CTLA4, and / or LAG3. In one embodiment, it is preferred that the anti-cancer agent is not an immune checkpoint inhibitor. In one embodiment, it is preferred that the anti-cancer agent is not an immunotherapeutic agent.
[0192] In one embodiment, the anti-cancer agent is an anti-cancer antibody. Multiple antibodies are known to be useful in the treatment of cancer. The anti-cancer agent may be any such antibody. For example, the anti-cancer agent may be selected from the group consisting of Trastuzumab, Bevacizumab, Cetuximab, Panitumumab, Ipilimumab, Rituximab, Alemtuzumab and Ofatumumab.
[0193] In one embodiment, the anti-cancer agent is a cytostatic small molecule. The cytostatic small molecule may for example be a tyrosine-kinase inhibitor. It can also be a small molecule kinase inhibitor, a small molecule proteasome inhibitor and a small molecule inhibitor targeting apoptosis. It can also be a serine / threonine-kinase inhibitor such as Temsirolimus, Everolimus, Vemurafenib, Trametinib and Dabrafenib. In another embodiment, the cytostatic small molecule is selected from the group consisting of Imatinib, Gefitinib, Erlotinib, Sorafenib, Sunitinib, Dasatinib, Lapatinib, Nilotinib, Bortezomib, tamoxifen, janus kinas inhibitors, ALK inhibitors, Bcl-2 inhibitors, PARP inhibitors, e. g. olaparib, APatinib, Braf inhibitors, MEK inhibitors, CDK inhibitors, Hsp90 inhibitors, and salinomycin.
[0194] In one embodiment, the statins are selected from the group consisting of avastatin, lovastatin, rosuvastatin, simvastatin, fluvastatin, pitavastatin, and pravastatin.
[0195] In one embodiment, the anti-cancer agent is an antibody-drug conjugate (ADC). For example the ADC may bind a malignant tumour-associated target antigen and deliver a cytotoxic agent to the malignant tumour. The ADC is composed of a monoclonal antibody, a linker and a cytotoxin. For example, the ADC is Trastuzumab emtansine which is an antibody-drug conjugate consisting of the monoclonal antibody trastuzumab linked to the cytotoxic agent emtansine (DM1).
[0196] In another embodiment, the anti-cancer agent is coupled to ADCC thereby utilizing the response of innate immune cells to provide anti-malignant tumour cytotoxicity triggered by the interaction of the Fc portion of an antibody with the Fc receptor on the immune cell. In another embodiment the anti-cancer agent is associated with a nano-particle or a liposome. Thus the anticancer agent may e.g. be protein-bound paclitaxel, also known as nanoparticle albumin-bound paclitaxel or nab-paclitaxel. In this formulation, paclitaxel is bonded to albumin as a delivery vehicle. In another embodiment, the anticancer agent may be for example Abraxane ® or a pegylated (polyethylene glycol coated) liposome-encapsulated form of doxorubicin, as e.g. Caelyx®. In yet another embodiment, the anti-cancer agent may be for example liposomal irinotecan. These are liposomal constructs that have been engineered to encapsulate chemotherapy thereby preventing premature metabolism, improving distribution and minimizing toxicity (i.e. Onyvide®).
[0197] In one embodiment, the anti-cancer agent is selected from the therapeutic groups listed in table 1. In another embodiment, the anti-cancer agent is selected from the drug examples listed in table 1.
[0198] In one embodiment, the anti-cancer agent is immunotherapy, such as any of the immunotherapies described in Melero et al. 2015 (see above), such as any of the therapies shown in Fig. 3 of Melero et al. 2015 (see above). In one embodiment, the anti-cancer agent is immunotherapy. For example, immunotherapy can be immunostimulatory monoclonal antibodies, neutralizing immune inhibitors, cytokines, adoptive T cell therapy, cancer vaccines and microbial adjuvants.
[0199] In one embodiment, the immunostimulatory monoclonal antibodies are selected from the group consisting of antibodies to CTLA4, PD1 , PDL1, LAG3, TIM3, CD137, 0X40, GITR and CD40. In another embodiment, the neutralizing immune inhibitors are selected from the group consisting of TGFbeta, IL-10 and IDOl .ln yet another embodiment, the cytokines are selected from the group consisting of IFN alpha, IL-2 and IL-12. In one embodiment, the microbial adjuvants are selected from the group consisting of TLR agonists, alpha-GalCer and STING activators. However, as noted above in some embodiments it is preferred that the anti-cancer agent is not an immune checkpoint inhibitor.
[0200] The immunotherapy may also be a cell based immunotherapy, for example the immunotherapy may be based on T-cells, NK-cells, dendritic cells, mesenchymal stem cells or modified cells such as CAR-T Cells, CAR-NK cells or T-cells used in conjunction with the BiTE (Bi-specific T cell engager).
[0201] In one embodiment, the anti-cancer agent is selected from the group consisting of radiotherapy, chemotherapy and signal transduction inhibitors. In another embodiment, the chemotherapy is selected from the group consisting of alkylating agents, platinum, antimetabolites, tubulin-inhibitors, antibiotics with anti-cancer effect and cytostatic molecules. In another embodiment, the signal transduction inhibitors are selected from the group consisting of protein kinase inhibitors, signal inhibitors not affecting the protein kinases, the monoclonal antibodies in cancer therapy, hormones and hormone antagonists, cytokines, antibodies towards immunological checkpoints, oncolytic virus, immunological adjuvants, T-cell or dendritic cell therapy and cancer vaccines.
[0202] The anti-cancer agent may be a radioactive substance, e.g. substannces used in iodine therapy of thyroid cancer. Other radioactive anti-cancer agents may be any of the
[0203] Radiopharmaceuticals us described in Benfante et al., 2023 and Chakraborty et aL, 2023.
[0204] Table 1: Synergistic therapeutic groups, chemical groups and drug examples
[0205] Solid neoplasm and cancer
[0206] The invention provides antibodies to YKL-40 and compositions of at least one YKL-40 antibody, such as two YKL-40 antibodies, such as three YKL-40 antibodies, such as five YKL-40 antibodies, which may be useful in methods of treating cancer. Furthermore, the invention relates to kits-of-parts and compositions for treatment of cancer characterised by the presence of at least one solid neoplasm. Said solid neoplasm may have an increase in interstitial fluid pressure and / or a decreased permeability.
[0207] Anti-cancer agents can typically reach single malignant tumour cells or small malignant tumour cell aggregates. This situation changes once tumours grow to an organoid like structure. Without being bound by theory, it is believed that the IFP rises with the growth of the malignant tumour until it reaches a plateau resulting in poor permeability of such tumours.
[0208] Cancers having a decreased permeability refers to cancers having a barrier preventing drugs from reaching the interior of said cancers. For example, anti-cancer treatment may be prevented from entry into the interior of the cancer, e.g. prevented from penetrating more than approx. 100 pm from blood vessels. The decreased permeability may prevent antibodies from penetrating the cancer and thus the antibodies remain in the contour of the malignant tumour.
[0209] Solid neoplasms frequently consist of malignant cells generally of epithelial origin, in which the cells are linked together by cell adhesions molecules and structurally recognisable cell junctions, namely desmosomes, tight junctions and gap junctions. These hold the cells together in clusters. Between these clusters, connective tissue stroma can frequently be found, in which the tumour blood vessels may be found. Stroma and cell junctions both contribute to the distribution barrier in solid tumours. From about 200 pm onwards, growing tumours start to build up an increased fluid pressure which can reach a plateau. Thus, in one embodiment the cancer to be treated may comprise at least one solid neoplasm at least 200 pm in diameter.
[0210] In addition to classical cancers, non-cancer malignancies such as sarcomas and melanomas also build up an increased fluid pressure. Thus such diseases can also be treated according to the methods of the invention. The solid neoplasm may be a primary malignant tumour or a metastasis thereof. Thus, the methods of the invention are useful both in the treatment of primary malignant tumours as well as metastatic cancers.
[0211] The cancer may for example be selected from the group consisting of solid neoplasm, metastases and fiber rich Hodgkin type of malignant tumour (lymphomas). For example, the solid neoplasm may be selected from the group consisting of breast-, colorectal-, pancreas-, bile duct-, stomach-, hepatocellular-, other gastrointestinal-, lung-, small cell lung-, ovarian-, uterine-, cervix-, testis-, prostate, bladder-, renal-, thyroid- and head / neck carcinoma, malignant melanoma, other skin cancers, neuroblastoma, glioblastoma, astrocytoma, malignant meningioma and other forms of brain cancer, osteosarcoma, chondrosarcoma, myosarcoma, fibrosarcoma and germ cell malignant tumours.
[0212] In a particular embodiment, the cancer is malignant melanoma. In another particular embodiment, the cancer is colon cancer.
[0213] Method of treatment of cancer
[0214] The present invention provides a method for treatment of cancer in an individual in need thereof.
[0215] In one embodiment, the invention provides a method for treating a cancer characterized by the presence of at least one solid neoplasm. Said method may comprise the steps of
[0216] • administering a therapeutically effective of one or more YKL-40 antibodies to an individual in need thereof thereby increasing the permeability of said solid neoplasm; and
[0217] • administering a therapeutically effective amount of an anti-cancer agent to said individual, thereby treating the cancer.
[0218] The YKL-40 antibodies of the invention may also be used for treatment in combination with radiotherapy. The YKL-40 antibody may in particular be any of the antibodies described herein above in the section “YKL-40 antibody”.
[0219] The YKL-40 antibody may be formulated together with or separately from the anticancer agent. Thus, in one embodiment method may comprise administering a therapeutically effective amount of a composition comprising an YKL-40 antibody and an anti-cancer agent.
[0220] In some embodiments, the invention provides a method for treating a cancer characterized by the presence of at least one solid neoplasm. Said method may comprise the steps of
[0221] • administering a therapeutically effective amount of two different YKL-40 antibodies to an individual in need thereof thereby increasing the permeability of said solid neoplasm; and
[0222] • administering a therapeutically effective amount of an anti-cancer agent to said individual, thereby treating the cancer.
[0223] It is also comprised within the present invention that YKL-40 antibody and the anticancer agent may be linked covalently to each other.
[0224] In embodiments of the invention where the YKL-40 antibody and the anti-cancer agent are formulated separately they may be administered simultaneously or sequentially. Typically, it is preferred that said anti-cancer agent is administered simultaneously with or subsequent to the YKL-40 antibody.
[0225] In one embodiment, the YKL-40 antibody can be administered in combination with an anti-cancer agent. In another embodiment, the YKL-40 antibody is administered first to a patient in need thereof followed by administration of a cancer agent at a later time point. The YKL-40 antibody and anti-cancer agents can be administered multiple times in said individual either simultaneously or independently of each other. Thus, when the YKL-40 antibody and anti-cancer agents are administered separately, they may also be administered a different number of times. The individual may be any individual suffering from or at risk of acquiring a cancer characterized by the presence of at least one solid neoplasm. In general the individual will be a mammal, and more preferably the individual will be a human being.
[0226] The YKL-40 antibody and anti-cancer agents can be administered by any suitable route known in the art. In general, the YKL-40 antibody is administered parenterally, for example by intravenous infusion. Other examples of routes of administration include intraperitoneal, intrathecal and intralymphatic. In some embodiments, administration may be by injection, e.g. subcutaneously.
[0227] The anti-cancer agent may be administered in any manner useful for the particular anticancer agent. Suitable modes of administration are known to the skilled person. Many anti-cancer agents are administered parenterally, for example by intravenous infusion. Other examples of routes of administration of anti-cancer agents include intraperitoneal, intrathecal and intralymphatic. In some embodiments, administration may be injection directly to the solid malignant tumour or subcutaneously.
[0228] The dosage of antibody is dependent on several factors, for example the dosage could be in the range of 1 to 50 mg / kg, such as 4 to 10 mg / kg of anti YKL-40 antibody per kg body weight. In one embodiment, the antibody is administered to the subject in need thereof once or more than once. For example, the antibody may be administered more than once with an interval of in the range of a couple of days to several weeks.
[0229] Whilst it is possible for the YKL-40 antibody and the anti-cancer agents to be administered as raw compounds, it is preferred to present them in the form of a pharmaceutical formulation. The pharmaceutical formulation comprises the YKL-40 antibody and / or the anti-cancer agents and one or more pharmaceutically acceptable carriers. The pharmaceutical formulations may be prepared by conventional techniques, e.g. as described in Remington: The Science and Practice of Pharmacy 2013, Pharmaceutical Press.
[0230] In some embodiments, the method comprises administration of at least one YKL-40 antibody to said individual, and administration of an anti-cancer agent to said individual, whereby the anti cancer agent uptake is increased by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20%. In some embodiments, the method comprises administration of at least one YKL-40 antibody to said individual, and administration of an anti-cancer agent to said individual, whereby the interstitial fluid pressure is decreased by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20%.
[0231] The compounds of the present invention may be formulated in a wide variety of formulations for parenteral administration. For injections and infusions the formulations may take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles. Alternatively, the active ingredient may be in powder form for constitution before use with a suitable vehicle, e.g., sterile, pyrogen-free water. The formulations can be presented in unit-dose or multi-dose sealed containers, such as ampoules, vials, pre-filled syringes, infusion bags, or can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid excipient, for example, water, for injections, immediately prior to use.
[0232] The formulations of the present embodiment may also include agents useful for pH maintenance, solution stabilization, or for the regulation of salt content and / or osmotic pressure.
[0233] The methods of the invention may be performed as the sole therapy, but frequently they are combined with other cancer therapies. The cancer may be treated by surgery and subsequently with the methods of the invention. The cancer may also be treated by irradiation as well as by the methods of the invention.
[0234] Items
[0235] The invention may further be defined by any of the following items:
[0236] 1. A composition comprising one or more antibodies specifically binding YKL-40, wherein, when said one or more antibodies alone or together are capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
[0237] 2. A composition comprising one or more antibodies specifically binding YKL-40, wherein said one or more antibodies alone or together are capable of increasing uptake of a drug into the interior of a solid neoplasm expressing
[0238] YKL-40 in mammal when administered to said mammal. A composition comprising one or more antibodies specifically binding YKL-40, wherein at least one of the antibodies is binding an epitope comprising at least 3 of amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 or at least one of the antibodies is binding an epitope comprising at least 3 of amino acids at positions 212, 213, 214, 215, 270, 271 , 272, 273, 274, 275, 276, -277, 308 or 321 of SEQ ID NO.1 ; wherein said one or more antibodies alone or together are capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal. A composition comprising one or more antibodies specifically binding YKL-40, wherein at least one of the antibodies is binding an epitope comprising at least 3, preferably at least 5, more preferably at least 7, even more preferably all of amino acids at positions 65, 114, 125, 129, 155, 166, 307 or 321 of SEQ ID NO: 1 or at least one of the antibodies is binding an epitope comprising at least 3, preferably at least 6, more preferably at least 9, even more preferably all of amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168, 169, 213, 304 or 308 or at least one of the antibodies is binding an epitope comprising at least 3, preferably at least 5, more preferably at least 7, even more preferably all of amino acids at positions amino acids at positions 63, 212, 213, 214, 215, 270, 271 , 272, 273, 274, 275, 276, -277, 305,308 or 321 of SEQ ID NO.1 ; wherein, when said one or more antibodies alone or together are capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal. A composition comprising one or more antibodies specifically binding YKL-40 wherein at least one of the antibodies is binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 99-131 and / or 134-158 and / or 161-182; or binding one or more epitopes comprising, partly positioned within or positioned within a sequence selected from amino acids 212-225 or 240-263 and / or 275- 286 and / or 303-324 of SEQ ID NO: 1 , wherein, when said one or more antibodies alone or together are capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
[0239] 6. The composition according to any one of the preceding items, wherein at least one of the antibodies is binding an epitope comprising at least 4 amino acids, preferably at least 5 amino acids, more preferably all 6 amino acids selected from amino acids 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
[0240] 7. The composition according to any one of the preceding items, at least one of the antibodies is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 , wherein said epitope does not comprise at least one of amino acids at positions 115, 116, 117, 126, 127, 128, 167,169 or 169 of SEQ ID NO: 1.
[0241] 8. The composition according to any one of the preceding items, at least one of the antibodies is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 , wherein said epitope does not comprise at least 2, preferably at least 5, more preferably at least 7, even more preferably none of amino acids at positions 115, 116, 117, 126, 127, 128, 167, 168 or 169 of SEQ ID NO: 1.
[0242] 9. The composition according to any one of the preceding items, wherein at least one of the antibodies is binding an epitope comprising one or more of amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1 , preferably all of amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1.
[0243] 10. The composition according to any one of the preceding claims, wherein the one or more antibodies specifically binding YKL-40 wherein at least two of the antibodies is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
[0244] 11. The composition according to any one of the preceding items, wherein the composition comprises only two antibodies, wherein at least one of the antibodies is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 , wherein said epitope does not comprise at least one of amino acids at positions 115, 116, 117, 126, 127, 128, 167,169 or 169 of SEQ ID NO: 1 , and the other antibody is binding an epitope comprising amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1. The composition according to any one of the preceding items, wherein at least one of the antibodies is binding an epitope comprising at least 5 amino acids, preferably at least 8 amino acids, more preferably 11 amino acids, even more preferably all of the amino acids selected from amino acids at positions 212- 215, 270-277, 308 or 321 of SEQ ID NO.1. The composition according to any one of the preceding items, wherein the composition comprises only one antibody and said antibody is binding an epitope comprising amino acids at positions 212-215, 270-277, 308 and 321 of SEQ ID NO.1. The composition according to any one of the preceding items, wherein at least one of the antibodies is binding an epitope partly positioned within or positioned within a sequence selected from amino acids 99-131 and 134-158 and 161-182. The composition according to any one of the preceding items, wherein at least one of the antibodies is binding an epitope partly positioned within or positioned within a sequence selected from amino acids 212-225 and 275-286 and / 303- 324. A composition comprising one or more antibodies specifically binding YKL-40, wherein at least one of the antibodies comprises at least one variable region comprising a CDR1, CDR2 and CDR3, wherein, a)
[0245] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;
[0246] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; and
[0247] CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7 ; or b)
[0248] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8;
[0249] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; and CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10; or c)
[0250] CDR1 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 16;
[0251] CDR2 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 17;
[0252] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 18;
[0253] CDR1 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 19;
[0254] CDR2 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 20; and
[0255] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 21.
[0256] 17. The composition according to any one of the preceding items, wherein the composition comprises two different antibodies specifically binding YKL-40.
[0257] 18. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1 comprising or consisting of an amino acid sequence of SEQ ID NO: 5.
[0258] 19. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1 comprising or consisting of an amino acid sequence of SEQ ID NO: 8.
[0259] 20. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises variable regions comprising a CDR1 of the light chain comprising or consisting of an amino acid sequence of SEQ ID NO: 16 and a CDR1 of the heavy chain comprising or consisting of an amino acid sequence of SEQ ID NO: 19. 21. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprising a variable region comprising a CDR2 comprising or consisting of an amino acid sequence of the general formula: ISAXXGSTYYADSVKG (SEQ ID NO: 12), wherein X may be any amino acid.
[0260] 22. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR2 comprising or consisting of an amino acid sequence of SEQ ID NO: 6.
[0261] 23. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR2 comprising or consisting of an amino acid sequence of SEQ ID NO: 9.
[0262] 24. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 antibody comprises variable regions comprising a CDR2 of the light chain comprising or consisting of an amino acid sequence of SEQ ID NO: 17 and a CDR2 of the heavy chain comprising or consisting of an amino acid sequence of SEQ ID NO: 20.
[0263] 25. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR3 comprising or consisting of an amino acid sequence of the general formula: XYNYXXWFDY (SEQ ID NO:13), wherein X may be any amino acid.
[0264] 26. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR3 comprising or consisting of an amino acid sequence of SEQ ID NO: 7.
[0265] 27. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR3 comprising or consisting of an amino acid sequence of SEQ ID NO: 10.
[0266] 28. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 antibody comprises variable regions comprising a CDR3 of the light chain comprising or consisting of an amino acid sequence of SEQ ID NO: 18 and a CDR3 of the heavy chain comprising or consisting of an amino acid sequence of SEQ ID NO: 21.
[0267] 29. The composition according to any one of the preceding items, wherein the antibody comprises two or more different variable regions, wherein each variable region may be fused to a constant region, e.g. to Fc regions.
[0268] 30. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1, CDR2 and CDR3, wherein,
[0269] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;
[0270] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; and
[0271] CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7.
[0272] 31. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1, CDR2 and CDR3, wherein,
[0273] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8; CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; and CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10.
[0274] 32. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YLK-40 antibody comprises or consists of a variable region comprising or consisting of an amino acid sequence of SEQ ID NO:3.
[0275] 33. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YLK-40 antibody comprises or consists of a variable region comprising or consisting of an amino acid sequence of SEQ ID NO:4. 34. The composition according to any one of the preceding items, wherein the variable region(s) are linked to an Fc region, optionally via a linker.
[0276] 35. The composition according to any one of the preceding items, wherein said antibody specifically binding YKL-40 comprises two variable regions, wherein each variable region is linked to an Fc region, optionally by a linker.
[0277] 36. The composition according to item 31, wherein said Fc regions are linked to each other.
[0278] 37. The composition according to item 31, wherein said Fc regions are linked together by disulphide bonds.
[0279] 38. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YLK-40 consists of a variable region consisting of the amino acid sequence SEQ ID NO:3 linked to an Fc region, wherein said antibody optionally forms dimers.
[0280] 39. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YLK-40 consists of a variable region consisting of the amino acid sequence SEQ ID NO:4 linked to an Fc region, wherein said antibody optionally forms dimers.
[0281] 40. The composition according to any one of the preceding items, wherein the Fc region is a constant region of IgE, for example an Fc region of SEQ ID NO:61.
[0282] 41. The composition according to any one of the preceding items, wherein the Fc region is a human Fc region.
[0283] 42. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 comprises an Fc region comprising or consisting of amino acid sequence SEQ ID NO: 22 or SEQ ID NO: 23 or SEQ ID NO:62. 43. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 antibody comprises or consists of variable regions comprising a CDR1, CDR2 and CDR3, wherein,
[0284] CDR1 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 16;
[0285] CDR2 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 17;
[0286] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 18;
[0287] CDR1 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 19;
[0288] CDR2 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 20; and
[0289] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 21.
[0290] 44. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 is capable of binding an epitope present in both human and murine YKL-40.
[0291] 45. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 is capable of binding the same YKL-40 epitope bound by any of the antibodies defined in any one of the preceding items.
[0292] 46. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 binds the same YKL-40 epitope bound by the antibodies of item 19.
[0293] 47. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 binds the same YKL-40 epitope bound by the antibodies of item 20.
[0294] 48. The composition according to any one of the preceding items, wherein at least one antibody specifically binding YKL-40 binds the same YKL-40 epitope bound by the antibodies of item 30. The composition according to any one of the preceding items, wherein the composition comprises at least two different antibodies specifically binding YLK- 40, wherein said antibodies are as defined in any one of the preceding items. The composition according to any one of the preceding items, wherein the composition comprises one antibody with a variable region comprising a CDR1 , CDR2 and CDR3, wherein,
[0295] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;
[0296] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; and
[0297] CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7 ; and another antibody with a variable region comprising a CDR1 , CDR2 and
[0298] CDR3, wherein,
[0299] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8;
[0300] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; and
[0301] CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10. A composition according to any one of the preceding items, wherein the composition comprises one antibody specifically binding YKL-40, wherein the antibodies is binding one or more epitopes comprising or positioned within a sequence selected from amino acids at positions 65, 114, 125, 129, 155 and 166 of SEQ ID NO: 1; and another antibody binding one or more epitopes comprising or positioned within a sequence selected from amino acids at position 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168, 169 of SEQ ID NO.1. The composition according to any one of the preceding items, wherein the composition comprises one antibody comprising a variable region comprising a CDR1, CDR2 and CDR3, wherein,
[0302] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;
[0303] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; and
[0304] CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7 ; and another antibody with variable region(s) comprising a CDR1 , CDR2 and
[0305] CDR3, wherein, CDR1 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 16; CDR2 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 17;
[0306] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 18;
[0307] CDR1 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 19;
[0308] CDR2 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 20; and
[0309] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 21 , The composition according to any one of the preceding items, wherein the composition comprises one antibody comprising a variable region comprising a CDR1, CDR2 and CDR3, wherein,
[0310] CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8;
[0311] CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; and CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10; and another antibody comprising variable regions comprising a CDR1 , CDR2 and CDR3, wherein, CDR1 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 16;
[0312] CDR2 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 17;
[0313] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 18;
[0314] CDR1 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 19;
[0315] CDR2 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 20; and
[0316] CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 21. The composition according to any one of the preceding items, wherein the composition comprises a bi- or multispecific antibody comprising at least two different variable regions each specifically binding YKL-40, for example a bi- or multispecific antibody comprising one or more variable regions comprising a CDR1 of SEQ ID NO: 5, a CDR2 of SEQ ID NO: 6 and a CDR3 of SEQ ID NO:7 and one or more variable regions comprising a CDR1 of SEQ ID NO: 8, a CDR2 of SEQ ID NO: 9 and a CDR3 of SEQ ID NQ:10.
[0317] 55. The composition according to any one of the preceding items, wherein the composition comprises a bi- or multispecific antibody comprising one or more variable regions comprising a CDR1 of SEQ ID NO: 5, a CDR2 of SEQ ID NO: 6 and a CDR3 of SEQ ID NO:7 and one or more variable regions made up of a VL and VH, wherein the VL comprises a CDR1 of SEQ ID NO: 16, a CDR2 of SEQ ID NO: 17 and a CDR3 of SEQ ID NO:18, and the VH comprises a CDR1 of SEQ ID NO: 19, a CDR2 of SEQ ID NO: 20 and a CDR3 of SEQ ID NO:21.
[0318] 56. The composition according to any one of the preceding items, wherein the composition comprises a bi- or multispecific antibody comprising one or more variable regions comprising CDR1 of SEQ ID NO: 8, a CDR2 of SEQ ID NO: 9 and a CDR3 of SEQ ID NO: 10 and one or more variable regions made up of a L and VH, wherein the VL comprises a CDR1 of SEQ ID NO: 16, a CDR2 of SEQ ID NO: 17 and a CDR3 of SEQ ID NO:18, and the VH comprises a CDR1 of SEQ ID NO: 19, a CDR2 of SEQ ID NO: 20 and a CDR3 of SEQ ID NO:21.
[0319] 57. The composition according to any one of the preceding items, wherein the composition comprises a bi- or multispecific antibody comprising one or more variable regions comprising or consisting of SEQ ID NO: 3 and one or more variable regions comprising or consisting of SEQ ID NO:4.
[0320] 58. The composition according to any one of the preceding items, wherein the composition comprises at least two different antibodies specifically binding YLK- 40, wherein the first antibody is an antibody as defined in any one of items 5, 8, 9, 12, 17, 19, 25 or 33 and the second antibody is an antibody as defined in any one of items 6, 8, 10, 14, 18, 20, 26 or 34.
[0321] 59. A kit-of-parts and / or a composition comprising a. a composition comprising one or more YKL-40 antibodies according to any one of items 1 to 58; and b. an anti-cancer agent; for use in the treatment of cancer in an individual in need thereof, wherein said cancer is characterised by the presence of at least one solid neoplasm.
[0322] 60. A method of treating disease associated with expression of YKL-40, the method comprising administering a therapeutically effective amount of the composition or the kit-of-parts according to any one of the preceding items to a subject in need thereof.
[0323] 61. A method for treating cancer in an individual suffering from cancer characterised by the presence of at least one solid neoplasm, said method comprising increasing permeability of said solid neoplasm by administration of a composition or a kit-of-parts according to any one of items 1 to 59 to said individual, and administration of an anti-cancer agent to said individual.
[0324] 62. A composition or kit-of-parts according to any one of items 1 to 59 for use in a method of treating a disease associated with YKL-40 expression.
[0325] 63. Use of a composition or a kit-of-parts according to any one of items 1 to 59 in the preparation of a medicament for use in a method of treating a disease associated with YKL-40 expression.
[0326] 64. Use of a kit-of-parts and / or a composition comprising a. At least one YKL-40 antibody according to any one of items 1 to 59; and b. an anti-cancer agent; for the preparation of a medicament for use in the treatment of a cancer characterised by the presence of at least one solid neoplasm.
[0327] 65. The method, composition for use or the use according to any one of items 60 to 64, wherein the disease is cancer.
[0328] 66. The method, composition for use or the use according to any one of items 60 to 64, wherein the disease is an inflammatory disease.
[0329] 67. The method, composition for use or the use according to any one of items 60 to 66, wherein the disease is arthritis, such as osteoarthritis. The method, composition for use or the use according any one of items 60 to
[0330] 67, wherein the method comprises administering a therapeutically effective amount of two different YKL-40 antibodies to a subject in need thereof, wherein said antibodies are as defined in any one of the preceding items. The method, composition for use or the use according any one of items 60 to
[0331] 68, wherein the method comprises administering a therapeutically effective amount of two different YKL-40 antibodies to a subject in need thereof, wherein said antibodies are as defined in any one of the preceding items, wherein said antibodies are administered simultaneously or sequentially. The method, composition for use or the use according any one of items 60 to
[0332] 69, wherein the composition or kit-of-parts comprises two different YKL-40 antibodies, wherein said antibodies are as defined in any one of the preceding items. The method, composition for use or the use according any one of items 60 to
[0333] 70, whereby the two antibodies comprises or consists of amino acid sequences SEQ ID NO:3 or SEQ ID NO: 4. The method, composition for use or the use according to any one of 60 to 71 , said method comprising administration of at least one YKL-40 antibody to said individual, and administration of an anti-cancer agent to said individual, whereby the anticancer agent uptake is increased by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20% compared to administration of PBS and said anti-cancer agent to said individual. The method, composition for use or the use according to any one of 60 to 72, wherein the method comprises administration of at least one YKL-40 antibody to said individual, and administration of an anti-cancer agent to said individual, whereby the interstitial fluid pressure is decreased by at least 1%, such as 2%, preferably 5%, more preferably, 7%, more preferably 10%, most preferably 20% compared to administration of PBS and an anti-cancer agent to said individual. 74. The method, the kit-of-parts, the composition or the use according to any one of items 60 to 73, wherein the method is a method for inhibiting the progression of cancer.
[0334] 75. The method, the kit-of-parts, the composition or the use according to any one of items 60 to 74, wherein the anti-cancer agent is selected from the group consisting of a chemotherapeutic agent, an immunotherapeutic agent, checkpoint inhibitors, anti-cancer antibodies, and cytostatic small molecule.
[0335] 76. The method, the kit-of-parts, the composition or the use according to any one of items 60 to 75, wherein the anti-cancer agent is a chemotherapeutic agent.
[0336] 77. The method, the kit-of-parts, the composition or the use according to any one of items 60 to 76, wherein the anti-cancer agent is platinum containing cytotoxic compound, such as a square planar coordination complex of platinum.
[0337] 78. The method, the kit-of-parts, the composition or the use according to any one of items 60 to 77, wherein the anti-cancer agent is cisplatin.
[0338] 79. The method, the kit-of-parts, the composition or the use according to any one of items 60 to 78, wherein the anti-cancer agent is a radioactive substance, such as radioactive iodine.
[0339] 80. A method of determining efficacy of treatment of a disease, said method comprising administering to an individual receiving said treatment a. a composition according to any one of items 1 to 59; and b. a diagnostic substance, and determining the efficacy of the treatment on the basis of the diagnostic substance.
[0340] 81. A kit-of-part comprising a. a composition according to any one of items 1 to 59; and b. a diagnostic substance.
[0341] 82. A kit-of-part according to item 81 for use in a method of determining the efficacy of treatment of a disease in an individual receiving said treatment. 83. The method or the kit-of-part according to any one of items 80 to 82, wherein said individual is suffering from a cancer characterised by the presence of at least one solid neoplasm.
[0342] 84. The method or the kit-of-part according to any one of items 80 to 83, wherein the treatment is radiotherapy.
[0343] 85. The method or the kit-of-part according to any one of items 80 to 84, wherein the diagnostic substance is a radioactively labelled substance.
[0344] 86. The method or the kit-of-part according to any one of items 80 to 85, wherein the diagnostic substance is a substance labelled with 64Cu-, 68Ga-, 125I-, or 99mTc.
[0345] 87. The method or the kit-of-part according to any one of items 80 to 86, wherein the diagnostic substance is a PSMA labelled radionuclide, such as 177Lu- prostate-specific membrane antigen (PSMA) labelled radionuclides.
[0346] 88. The method according to item 87, wherein the disease is prostate cancer.
[0347] Examples
[0348] Example 1: Selection of phage antibodies B3 and B10 recognizing YKL-40
[0349] Aim:
[0350] To select antibodies, which recognize human and murine YKL-40.
[0351] Materials and methods:
[0352] YKL-40 protein hYKL-40 protein was obtained from the supernatant of MG63 cells or was purchased from Biotech (Catalogue #2599-CH). MG63 production flasks were seeded at 1.8 x 104cells / cm2in RPMI-40 (Irvine Scientific) plus newborn calf serum, 100 mL / L (Irvine Scientific), 0.1 mol / L HEPES, and 50 mg / L vitamin C (complete medium). Flasks were incubated at 37 °C with humidity and CO2-enriched (100 mL / L) atmosphere for 6-8 days, replacing spent medium with fresh every 2-3 days. The cultures were then switched to serum-free medium (complete medium minus the newborn calf serum). The supernatants were harvested and the media replaced every 1-3 days for 30 days. hYKL-40 protein was purified from the supernatants by concentrating glass-fiber- filtered material 20-fold with a 30-kDa screen channel cassette with tangential flow (Filtron) and then affinity-purifying over a heparin- Sepharose CL-6B column (Pharmacia Biotech) equilibrated with a solution of 10 mmol / L sodium phosphate and 50 mmol / L sodium chloride, pH 7.5. Bound material was eluted with a sodium chloride gradient (from 50 mmol / L to 2 mol / L) in 10 mmol / L sodium phosphate, pH 7.5, and 4- mL fractions were collected and pooled according to: absorbance at 280 nm, hYKL-40 protein concentration by immunoassay and purity by sodium dodecyl sulfatepolyacrylamide gel electrophoresis. mYKL-40 were purchased from Biotech (Catalogue #: 2649-CH). Alternatively, mYKL-40 can be obtained from supernatant of the mouse myeloma cell line NS0.
[0353] Phage rescue
[0354] Selection of phage antibodies recognizing YKL-40 were performed using a predator antibody library, which is a single scaffold domain library with variation in CDR2 and CDR3 (Mandrup, Friis et al. 2013) against the purified YKL-40 protein. Thus, the antibodies of this library are single domain antibodies.
[0355] First a plastic immunotube was coated overnight with YKL-40 at 4°C, so the antigen could be partially absorbed by the plastic and anchored to the inner surface of the tube. The day after the tube was washed 5 times with PBS and incubated with 2% BSA in PBS for 2 hours at room temperature (RT). After another round of washing, 100 pl of the phage antibody library pREDATOR was added in 4 ml of 2% BSA in PBS. The phage antibody library was incubated for 60 min at RT rotating using an under- and over turntable and then further 60 min at RT standing on the bench. Unbound phages were washed away with 10 washes in PBS containing 0,1% Tween 20 and 10 washes with PBS.
[0356] Bound phages were eluted by adding 500 pl of trypsin- PBS (50 pl of 10 mg / ml trypsin stock solution added to 450 pl PBS) and incubating on rotating for 10 min at RT. The eluent was then incubated with 10 ml of TG1 (E.coli) in exponential growth (at an OD 600 of 0.4) for 30 min at 37°C. The bacteria were then plated on TYE plates containing 100 pg / ml ampicillin and 1% glucose and grown overnight at 30°C. The following day individual colonies from the plates were picked up with a toothpick for monoclonal phage antibody rescue and the remaining bacteria were scraped into 2xTY media containing 100 pg / ml ampicillin and 1% glucose for polyclonal rescue. The monoclonal picked colonies were put in a well of a 96 cell-well plate containing 2xTY medium with 100 pg / ml ampicillin and 1% glucose and grown on a shaker overnight at 37°C. The day after a transfer device was used to transfer a small inoculum from this plate (the master plate) to a second 96 cell- well plate containing the same medium. Bacteria were grown shaking at 37°C for 2 hours, new medium containing Helper phage, KM13 was added. The plate were incubated for 1 hour at 37°C to let the Helper infect the cell, after this media was changed to 2xTY medium containing 100pg / ml Ampicillin and 50pg / ml of Kanamycin, finally the bacteria were incubate at 30°C, on shaking, overnight. The supernatant was used for ELISA.
[0357] The polyclonal scraped bacteria were grown shaking at 37°C for 2 hours, new medium containing Helper phage, KM13 was added. The plates were incubated for 1 hour at 37°C to let the Helper infect the cell, after this media was changed to 2xTY medium containing 100pg / ml Ampicillin and 50pg / ml of Kanamycin, finally the bacteria were incubate at 30°C, on shaking, overnight. The phage antibodies produced in the media were precipitated by adding % volume of a solution containing 20 % PEG 6000 and 2.5 M NaCL The precipitated phage were used for successive rounds of selection. In successive rounds of selection human and murine YKL40 were used for selection to allow phage antibodies binding both to be enriched.
[0358] Screening rounds
[0359] Preliminary screening
[0360] After selection the eluted phages were infected in the E. coli TG-1 and spread on Amp selective agar plates. Around 500 colonies were obtained. These were inoculated in 100 pl 2xTY in 96 well plates. Phage antibodies were produced from the plates using the helper phage KM 13 according to standard procedures.
[0361] Example of Preliminary screening
[0362] After coating with used (MG63 conditioned) or fresh media, the ELISA plates were blocked with 2% skimmed milk powder in PBS. After blocking 50 pl of the phage supernatant was added to each well and incubated. The plates were washed and incubated with 1 :5000 diluted anti-M13 antibody (HRP conjugated). After washing the ELISA plate were developed using TMB and the plate read in an ELISA reader. Dilution series of the PEG precipitated phages
[0363] Selected clones which were judged potential positive in the preliminary screening were grown in 50 ml culture and rescued using the KM 13 helper phage. After overnight growth the supernatant were PEG precipitated according to standard procedures, and the pellet resuspended in 1 ml PBS. As phage antibody concentration is highly enriched by growing in 50 ml baffled flasks, the phage antibody concentration after PEG precipitation is 100-1000 more concentrated compared to the initial screen.
[0364] The PEG precipitated phage were used in validating ELISA, were a dilution series of the PEG precipitated phage were applied to ELISA plates coated with MG63 conditioned media or Fresh media. ELISA was performed as above.
[0365] Secondary screening - validation of binding to YKL-40
[0366] After phage rescue supernatants containing selected single-domain antibodies were applied in ELISA to test for binding to YKL-40. Serum free media (RPMI 1640 with 1 % Non-essential amino acids) were conditioned by growing MG63 cell line for 4 days. The supernatant was coated in ELISA plates. Fresh media without conditioning with MG63 were used as controls.
[0367] An ELISA was performed with the PEG precipitated phage from above (obtained under the section “Dilution series of the PEG precipitated phages")-.
[0368] In the first round the plate was coated using conditioned MG63 media containing hYKL-40
[0369] In the second round the plate was coated with 0,5 pg purified mYKL-40 The ELISA was performed as above. The results are shown in Table 1 below. The numbers (1-12) on the top and the letter (A-H) on the left indicate the tested phages and their corresponding well.
[0370] Sequencing of antibodies
[0371] All the clones validated to bind to YKL-40 were next sequenced.
[0372] Cloning The two clones B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) can be cloned into a vector pFuse- hlgE as described in Moutel et al., 2009, or a vector containing another immunoglobulin constant part. The vectors can be transfected into a suitable cell, such as ExpiCHO cells and expressed in this cell. This transfection leads to antibodies of VH domains fused to human IgE or other Fc regions expressed by the vector.
[0373] After transient transfection of suitable cells with the expression plasmid, secreted antibodies can be purified from the supernatant.
[0374] Results:
[0375] Monoclonal ELISA from individual colonies from titration plates after selection using predator library (first round selection against hYKL-40 and second round selection against mYKL-40) are provided in Table. The OD obtained after the second round of screening is shown in the table, where a higher number indicates increased binding.
[0376] Table 1:
[0377] Conclusion:
[0378] Several antibodies had a value over 1. B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) bind to purified human and murine YKL-40 and were selected as the best candidates.
[0379] Example 2: B3-hFc does not bind a linear Epitope of YKL-40
[0380] Aim:
[0381] SUBSTITUTE SHEET (RULE 26) To investigate if B3 (SEQ ID NO: 3) fused to a human Fc (hFc) (referred to as B3- hFc)bind human and murine YKL-40. The sequence of the human Fc is provided herein as SEQ ID NO: 23.
[0382] Western Blot:
[0383] First, samples for the western blot were prepared. Therefore, 1.04 pl (0.5 pg) hYKL-40 were mixed with 2.5 pl 4x sample buffer, 1 pl 1M DTT and 5.46 pl water. 5 pl (0.5 pg) mYKL-40 were mixed with 2.5 pl 4x sample buffer, 1 pl 1M DTT and 1.5 pl water. As a negative control, 5 pl PBS were mixed with 2.5 pl 4x sample buffer, 1 pl 1 M DTT and 1.5 pl water. As a positive control, 3 pl mouse anti-vimentin antibody (Sigma Aldrich, V6389) was mixed with 2.5 pl 4x sample buffer, 1 pl 1M DTT and 3.5 pl water. Afterwards, the samples were heated at 95 °C for 10 min and the samples were loaded on a 4-20% SurePAGE, Bis-TRIS gel. The gel was run at 120V for 70 min and afterwards the samples were transferred to a nitrocellulose membrane using iBIot system. The membrane was blocked over night at 4 °C in PBS with 0.1% Tween and washed at the next day three times with PBST. The membrane was incubated with 1 pg / ml primary antibody B3-hFc in PBS with 0.1% Tween for 2h at RT. Afterwards, the membrane was washed again three times with PBS with 0.1% Tween and incubated with a HRP conjugated anti-mouse or anti-human secondary antibody for 2h at RT.
[0384] After washing the blot another 3 times with PBS and 0.1% Tween, the western blot was developed with detection reagent.
[0385] Dot blot:
[0386] A dot blot was performed by adding 0.4 pg and 0.2 pg of hYKL-40, 0.4 pg and 0.2 pg mYKL-40, 0.4 pg and 0.2 pg of calmodulin (negative control) and PBS (negative control) onto the nitrocellulose membrane. The area that the solution penetrates was minimized. The membrane was dried for 1h at room temperature (RT). Afterwards the membrane was blocked in PBS with 0.1% Tween overnight at 4°C followed by three washing steps with PBS with 0.1% Tween. The membrane was incubated with B3-hFc (1 pg / mL) in blocking buffer for 2h at RT in a shaker followed by three washing steps with PBS with 0.1% Tween. The membrane was incubated with HRP anti-human secondary antibody for 2 hours at RT in shaker followed by three washing steps with PBS with 0.1% Tween. The western blot was developed with western blotting detection reagent. Results:
[0387] The dot blot results indicate that B3 (SEQ ID NO: 3) fused to human Fc (hFc) binds to both human and mouse YKL-40, but does not bind to calmodulin (Fig. 2). The antibody did not appear to bind to a linear epitope, and it is thus believed that B3 (SEQ ID NO: 3)-hFc likely binds to a conformational epitope of both human and mouse YKL-40.
[0388] Example 3: B10 binds human and murine YKL-40
[0389] Aim:
[0390] To investigate if B10 (SEQ ID NO: 4) fused to a human Fc (referred to as B10-hFc) bind to human and murine YKL-40. The sequence of the human Fc is provided herein as SEQ ID NO: 23.
[0391] Material and Methods:
[0392] The western blot was performed according to the description in Example 2 except, that the western blot was incubated with B10-hFc.
[0393] Results:
[0394] B10-hFc binds to both human and mouse YKL-40 (Fig. 3). It appears that B10-hFc binds to a linear epitope of both human and mouse YKL-40.
[0395] Example 4: B3 and B10 bind to mYKL-40
[0396] Aim:
[0397] To investigate if B3 (SEQ ID NO: 3) fused to murine Fc (mFc)(herein referred to as B3- mFc) and B10 (SEQ ID NO: 4) fused to mFC (herein referred to as B10-mFc) bind to murine YKL-40. The sequence of the murine Fc is provided herein as SEQ ID NO: 62.
[0398] Material and Methods:
[0399] A 96-well ELISA plate was coated overnight at RT with 100 pl per well of 2.5 pg / ml mYKL-40 or 2.5 pg / ml calmodulin as control. Afterwards, the wells were washed three times with PBS and blocked with 200 pl Casein per well for 2h at RT. After another three times washing with PBS, 100 pl of primary antibody B3-mFc or B10-mFc at different concentrations were added for 1h at RT. The concentrations were 0.25 pg / ml, 0.5 pg / ml, 1 pg / ml, 2.5 pg / ml, 6.25 pg / ml, 12.5 pg / ml, 15 pg / ml and 20 pg / ml. Subsequently, the wells were washed 3 times with PBS with 0.1% Tween before 100 l of HRP conjugated anti-mouse secondary antibody were added for 1h at RT. After another three times washing with PBS with 0.1 % Tween, 100 pl of substrate solution TMB were added to each well till a blue colour is developed. The reaction was stopped by adding 450 pl 1M sulphuric acid. The OD was read at 650 nm and 450 nm. Subsequently the OD 650 were subtracted from OD 450.
[0400] Results:
[0401] B3-mFc and B10-mFc bind to mYKL-40 (Fig. 4).
[0402] Example 5: B3 and B10 bind to hYKL-40
[0403] Aim:
[0404] To investigate if B3 (SEQ ID NO: 3) fused to mFc (herein referred to as B3-mFc) and B10 (SEQ ID NO: 4) fused to mFc (herein referred to as B10-mFc) bind to human YKL- 40.
[0405] Material and Methods:
[0406] The ELISA was performed according to example 5. hYKL-40 was used to coat the ELISA plate.
[0407] Results:
[0408] B3 (SEQ ID NO: 3)-mFc and B10 (SEQ ID NO: 4)-mFc bind to hYKL-40 (Fig. 5).
[0409] Conclusion:
[0410] The inventors of the present disclosure have realized that B3 (SEQ ID NO:3)-mFc and B10 (SEQ ID NO:4) -mFc are able to bind hYKL-40.
[0411] Example 6: 201 F9 binds to hYKL-40 but not the same epitope as B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4)
[0412] Aim:
[0413] It was investigated if the YKL-40 antibody named 201 F9 binds hYKL-40 and if it binds to the same epitopes as B3-hFc and B10-hFc.
[0414] Material and Methods: The competitive ELISA was performed essentially as described in example 5 with the exception, that first 2.5 pg / ml 201 F9 were added into the wells for 1h at RT before the wells were washed three times with PBS with 0.1% Tween and B3-hFc or B10-hFc were added in different concentrations.
[0415] Results:
[0416] The results are shown in figure 6. Please note that the left hand panel of figure 6 shows decreasing concentrations of B3-hFc, whereas the right hand panel shows increasing concentrations of B10-hFc. The signal of B3-hFc were decreasing with decreasing concentration. The signal of B10-hFc were increasing with increasing concentration (Fig- 6).
[0417] Conclusion:
[0418] 201F9 binds hYKL-40 at a different epitope than B3 (SEQ ID NO: 3)-hFc or B10 (SEQ ID NO: 4)-hFc.
[0419] Example 7: Solid tumours
[0420] Aim:
[0421] To investigate if B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) decrease the tumour weight, volume and interstitial fluid pressure in SCID mice injected with the human colon cell line SW480. For this experiment B3 (SEQ ID NO: 3) fused to mFc and B10 (SEQ ID NO: 4) fused to mFc were used. The antibodies were linked to the Fc region by cloning into a pFUSE expression system as described in Moutel et aL, 2009. B3 and B10 have the advantage that they recognise and bind both murine and human YKL-40. It can be advantageous to use antibodies fused to a murine Fc for mouse studies. For use in humans, it is advantageous to use B3 or B10 antibodies fused to human Fc.
[0422] Material and Methods:
[0423] To investigate penetration of YKL-40 antibodies in vivo, pathogen free BALB / c SCID (scid / scid) mice were used. The mice were 8-16 weeks old and weigh 20-30 g at the beginning of the experiments. They were housed in filter top cages and provided with sterile water and food ad libitum. For injection, human colon cancer cells SW480 were harvested by trypsinisation and viable cells (5x106) were suspended in 1 ml of cell culture medium. An aliquot of 200 ml of this suspension was injected subcutaneously between the scapulae of each SCID mouse. Human SW480 cells have been shown to express YKL-40 by immunohistochernistry in xenograft tumours.
[0424] Treatment with antibody started on day 3 and continued for 3 times per week for a total of 12 injections. 12 hours before sacrifice mice were injected 7,5 mg Cisplatin I kg body weight intraperitoneally. Mice received either YKL-40 antibody, comprising the variable region of antibody B3 (SEQ ID NO: 3) fused to mFc or B10 (SEQ ID NO: 4) fused to mFc, or both B3 (SEQ ID NO: 3)-mFc and B10 (SEQ ID NO: 4)-mFc simultaneously. As a control unspecific IgG antibody was injected.
[0425] Once mice carried tumours of approximately 1 cm3, the experiment was terminated.
[0426] Mice were sacrificed, intracardially perfused with NaCI and tumours were removed. Tumor size during experiments was measured with calipers, and the tumour weight at the end of treatment was determined. Where applicable, interstitial fluid pressure (IFP) in tumors was measured using a commercially available Raumedic Neurovent P - Temp ICP - Catheter, originally developed for intraparenchymal intracranial pressure and temperature monitoring.
[0427] Results:
[0428] The tumour weight was decreased by treatment with B3 (SEQ ID NO: 3) or B10 (SEQ ID NO: 4), whereas the tumour weight was not significantly affected in mice that received both antibodies simultaneously. The treatment displayed a decreased tumour volume in mice treated with B3 (SEQ ID NO: 3) or B10 (SEQ ID NO: 4), and in mice that received both antibodies simultaneously. The interstitial fluid pressure (IFP) in the tumours was appeared to have increased in mice treated with B3 (SEQ ID NO: 3) or B10 (SEQ ID NO: 4) alone, but significantly reduced in mice treated with both antibodies simultaneously (Fig. 7).
[0429] Conclusion:
[0430] The inventors of the present disclosure have shown that treatment with YKL-40 antibodies B3 (SEQ ID NO: 3) or B10 (SEQ ID NO: 4) decrease tumour weight and tumour volume. The simultaneous treatment with YKL-40 antibodies B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) simultaneously decreases interstitial fluid pressure. Example 8: B3 and B10 increase cisplatin uptake into interior of solid tumours
[0431] Aim:
[0432] To investigate if B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) increase cisplatin (Pt) uptake into interior of solid tumours. The antibodies used in this study were as described in Example 7.
[0433] Material and Methods:
[0434] The experiment was performed according to the description in Example 7. Afterwards, parts of tumours were then embedded in paraffin. The paraffin sections were stained for the distribution of cisplatin / DNA adducts as described below.
[0435] Cisplatin immunohistochemistry
[0436] Formalin-fixed and paraffin-embedded sections were deparaffinized in two changes of xylene (5 min each) and rehydrated in a series of graded ethanol (100, 96, 70 and 50% for 5 min each). Sections were then washed in aqua dest for 2 min. The following incubation steps were carried out in a moist chamber. For epitope retrieval, samples were treated for 5 min with Fast Enzyme (Zytomed Systems, Bargteheide, Germany) at room temperature, following two 5 min washes in Tris-buffered saline / 0.1% Tween20 (TBS-T) and one 5 min wash in TBS (pH 7.6). Blocking with 4% BSA in TBS was performed for 30 min to prevent nonspecific antibody binding. Afterwards, sections were incubated with primary rat anti-Pt-[GpG] monoclonal antibody diluted 1:1000 in antibody diluent (medac, Wedel, Germany) or rat lgG2a kappa at a dilution of 1:500 (eBioscience, San Diego, USA) for 80 min at room temperature and then rinsed twice with TBS-T as well as with TBS for 5 min each. Subsequently, the secondary biotin- conjugated rabbit anti-rat antibody (Dako, Glostrup, Denmark) was incubated at a dilution of 1:100 in antibody diluent for 30 min at room temperature, followed by rinsing twice with TBS-T and once with TBS for 5 min each. Sections were treated with Vectastain® ABC-AP Kit (Vector Laboratories, Burlingame, CA, US) according to the manufacturer’s recommendations for 30 min at RT and again washed in TBS-T and TBS as described above. Finally, alkaline phosphatase enzyme activity was visualized by incubating the sections with Permanent Red solution (Dako, Glostrup Denmark) for 20 min and counterstained with hematoxylin for 4 s, with intermediate washes under running tap water (3 min) and in aqua dest (2 min). Slides were dehydrated in a series of graded ethanol (70% for 15 s, 96 and 100% for 5 min each) and three changes of xylene (5 min each) and finally covered with Eukitt® Mounting Medium (Sigma-Aldrich, Steinheim, Germany) and coverslips.
[0437] HC-processed sections were first evaluated using a ZEISS Axiophot 2 microscope (Carl Zeiss, Jena, Germany). Digital images were obtained with a ZEISS Axio Scan Z1 slide scanner equipped with a ZEISS EC Plan-Neofluar 20x / 0.50 Pol M27 objective (Carl Zeiss, Jena, Germany) and a Hitachi HV-F20SCL camera with 1600 x 1200 pixels (Hitachi Kokusai Electric America Ltd., New York, USA). For image acquisition, ZEISS ZEN 2.3 software was used (Carl Zeiss, Jena, Germany). Images were further processed with netScope Viewer software (Net-Base Software, Freiburg, Germany).
[0438] Microscopy of immunohistochemical stainings
[0439] Furthermore, the cisplatin concentration in the tumours was determined by graphitefurnace atomic absorption spectrometry as described in Bernhard Welz, Michael Sperling: Atomabsorptionsspektrometrie, WILEY-VCH-Verlag Weinheim, 1997, pages 572 - 573. To perform the analysis a GF-AAS-(Graphite Furnace - Atomic Absorption Spectrometry) machine from Perkin-Elmer, Model AAnalyst 600 was used.
[0440] Results:
[0441] Furnace atomic absorption spectrometry revealed that tumours from mice injected with YKL-40 antibodies B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) simultaneously showed an increased uptake of cisplatin compared to the control group (Figure 8).
[0442] Conclusion:
[0443] The inventors of the present disclosure have realized that the treatment with YKL-40 antibodies B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) simultaneously facilitated the permeability of cisplatin in the tumour (Fig. 8).
[0444] Example 9: Monoclonal antibody comprising the sequence of H7 decreases interstitial fluid pressure in solid tumors
[0445] Aim:
[0446] To investigate if a monoclonal antibody , H7 (SEQ ID NO: 14 and SEQ ID NO: 15) decreases the interstitial fluid pressure in solid tumours.
[0447] Material and Methods: The antibody H7 was prepared by fusing variable regions from a mouse monoclonal antibody specifically binding YKL-40 with constant regions of a human IgG antibody. This was done by using the pCAGGS vector system. A DNA sequence encoding the murine light chain variable region of H7 (SEQ ID NO: 14) fused to a human constant domain of the light chain was inserted into one pCAGGS vector. In another pCAGG vector, a DNA sequence encoding the murine variable heavy chain of H7 (SEQ ID NO: 15) fused to human Ch1, Ch2 and Ch3 from a human lgG1 was inserted. The sequences of the variable regions of the light and heavy chains of H7 are provided herein as SEQ ID NO: 14 and SEQ ID NO: 15, respectively.
[0448] To investigate penetration of YKL-40 antibodies in vivo, pathogen free BALB / c SCID (scid / scid) mice were used. The mice were 8-16 weeks old and weigh 20-30 g at the beginning of the experiments. They were housed in filter top cages and provided with sterile water and food ad libitum. For injection, human LOX melanoma cells were harvested by trypsinisation and viable cells (5x106) were suspended in 1 ml of cell culture medium. An aliquot of 200 ml of this suspension was injected subcutaneously between the scapulae of each SCID mouse. Human LOX cells have been shown to express YKL-40 by flow cytometry.
[0449] Once mice carried tumours, 10 pg antibody dissolved in PBS was injected intraperitoneally into LOX melanoma bearing mice. Five mice received anti-YKL-40 monoclonal antibody, comprising of the variable region of H7 (SEQ ID NO: 14 and SEQ ID NO: 15) antibody linked to an Fc region by cloning into a pFUSE expression system as described in Moutel et aL, 2009. Another five mice received the antibodies with an equivalent volume of PBS as control.
[0450] Treatment with antibody started on day 3 and continued for 3 times per week for a total of 7 injections. Interstitial fluid pressure (IFP) in tumors was measured using a commercially available Raumedic Neurovent P - Temp ICP - Catheter, originally developed for intraparenchymal intracranial pressure and temperature monitoring (Figure 9C).
[0451] Mice were sacrificed, intracardially perfused with NaCI and tumours were removed.
[0452] Tumor size during experiments was measured with calipers, and the tumour volume and weight at the end of treatment was determined (Figure 9A and B). The relationship between IFP and tumor weight was calculated (Figure 9D).
[0453] Results:
[0454] Themonoclonal antibody , H7 (SEQ ID NO: 14 and SEQ ID NO: 15) decreases the interstitial fluid pressure in solid tumours (Figure 9)
[0455] Conclusion:
[0456] The inventors of the present disclosure have realized that the treatment with a monoclonal YKL-40 antibody H7 reduced interstitial fluid pressure.
[0457] Example 10: Epitope mapping of B3 antibody
[0458] Aim:
[0459] To identify the epitopes of the B3 (SEQ ID NO: 3) antibody.
[0460] Material and Methods:
[0461] Epitope mapping of B3 (SEQ ID NO: 3) antibody was performed using linear peptide arrays as described in Geysen et al. Peptides were synthesized as mimics. Peptides were either 15-mers with 14 amino acid overlap, an additional set of 10-mers, looped 8- mers, helical-stabilized peptides of 19 amino acid length or continuous beta-turn mimics of 20 amino acid length.
[0462] Relative binding response of 0.1 ug / mL B3-mFc compared to 0.5 ug / ml Mouse IgG 1 S1A1 of each peptide was analyzed. The cut-off criteria were at least 10-fold signal over control and at least two peptides in a peak.
[0463] Results and Conclusion:
[0464] The following sequences were identified using the criteria indicated above: amino acids 46-58 or 76-127 or 192-203 or 213-225 or 234-247 or 250-269 or 274-286 or 294-314 or 359-373 of SEQ ID NO: 1. The epitope of B3 is thus believed to comprise or be positioned within the aforementioned sequences.
[0465] Example 11: Epitope mapping of B10 antibody
[0466] Aim:
[0467] To identify the epitopes of the B10 (SEQ ID NO: 4) antibody. Material and Methods:
[0468] Epitope mapping of B10 (SEQ ID NO: 4) antibody was performed using linear peptide arrays as described in Geysen et al. Peptides were synthesized as mimics. Peptides were either 15-mers with 14 amino acid overlap, an additional set of 10-mers, looped 8- mers, helical-stabilized peptides of 19 amino acid length or continuous beta-turn mimics of 20 amino acid length.
[0469] Relative binding response of 0.1 ug / mL B10-mFc compared to 0.5 ug / ml Mouse IgG 1 S1 A1 of each peptide was analyzed. The cut-off criteria were at least 10-fold signal over control and at least two peptides in a peak.
[0470] Results and Conclusion:
[0471] The following sequences were identified using the criteria indicated above: amino acids 76-92 or 99-131 or 134-158 or 161-182 or 212-225 or 240-263 or 275-286 or 303-324 or 326-348 of SEQ ID NO: 1. The epitope of B10 is thus believed to comprise or be positioned within the aforementioned sequences.
[0472] Example 12: Epitope mapping of H7 antibody
[0473] Aim:
[0474] To identify the epitopes of the H7 (SEQ ID NO: 14 and SEQ ID NO: 15) antibody.
[0475] Material and Methods:
[0476] Epitope mapping of H7 (SEQ ID NO: 14 and SEQ ID NO: 15) antibody was performed using linear peptide arrays as described in Geysen et al. Peptides were synthesized as mimics. Peptides were either 15-mers with 14 amino acid overlap, an additional set of 10-mers, looped 8-mers, helical-stabilized peptides of 19 amino acid length or continuous beta-turn mimics of 20 amino acid length.
[0477] Relative binding response of 0.1 ug / mL H7-hFc compared to 0.18 pg / ml Hu lgG1 MA16 MY1804 of each peptide was analyzed. The cut-off criteria were at least 2-fold signal over control and at least two peptides in a peak.
[0478] Results and Conclusion:
[0479] The following sequences were identified using the criteria indicated above: Epitopes of H7 are comprising or positioned within a sequence selected from amino acids 123-130 or 218-224 or 259-265 or 269-286 or 303-315 of SEQ ID NO: 1. The epitope of H7 is thus believed to comprise or be positioned within the aforementioned sequences (Figure 11).
[0480] Example 13: H7 binds human YKL-40
[0481] Human tissue sections obtained from human foetus hands and human foetus gut system were stained with H7 antibody according to standard immunohistochemical methods. The H7 antibody comprises a VL of SEQ ID NO: 14 and a VH of SEQ ID NO: 15 fused to human Fc regions. Positive staining was observed in tissue from human foetus hands and human foetus gut system (see figure 10). the staining pattern corresponds to the pattern observed with other antibodies binding human YKL-40 indicating that H7 indeed binds human YKL-40. However, the H7 antibody did not stain mouse tissue sections to any significant extent.
[0482] In addition an ELISA experiment was done essentially as described in Example 1. The ELISA plates were coated with either 2.5 pg / mL human YKL-40 or 2.5 pg / mL murine YKL-40.
[0483] H7 antibody comprising a VL of SEQ ID NO: 14 and a H of SEQ ID NO: 15 fused to human Fc regions was used as primary antibody. This antibody is also referred to as H7-hFc herein. A dilution series of the antibody was prepared with the following concentrations:
[0484] 1: 20 ug / ml
[0485] 2: 15 ug / ml
[0486] 3: 12,5 ug / ml
[0487] 4: 6,25 ug / ml
[0488] 5: 2,5 ug / ml
[0489] 6: 1 ug / ml 7: 0,5 ug / ml 8: 0,25 ug / ml
[0490] As secondary antibody an anti-human HRP conjugate was used. The result is shown in figure 12. H7 binds human YKL-40 in a dose dependent manner, and to a lesser extent to murine YKL-40 in an ELISA assay. Example 14: Epitope mapping of B3 and B10 on human YKL40 using in silico modelling
[0491] Aim:
[0492] To identify the epitopes recognized by the antibodies B3 and B10 using in silico modelling.
[0493] Material and Methods:
[0494] The structure of human YKL40 was retrieved from the PDB database, accession number 1NWR. The structure of the variable parts of the antibodies B3 (SEQ ID NO:3) and B10 (SEQ ID NO: 4) were modelled using the software NanoBodybuilder2 (https: / / opig.stats.ox.ac.uk / webapps / sabdab-sabpred / sabpred / nanobodybuilder2 / ) with the input sequences for the variable domains of B3 (SEQ ID NO: 3) and B10 (SEQ ID NO 4). The output from the NanoBodybuilder2 is shown in Figure 13. The NanoBodybuilder2 received structures were used to perform docking of B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) onto human YKL40 (SEQ ID NO: 1) using the software Haddock2.4 (https: / / wenmr.science.uu.ni / haddock2.4 / ) . Figure 14 shows one of the possible solutions to the docking of the antibody fragments with YKL40.
[0495] Results and Conclusion:
[0496] The B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) antibodies have potential overlapping epitopes, distinct from the epitope suggested for the 201 F9 antibody.
[0497] Example 15: Epitope mapping of B3, B10 and H7 on mutants of human YKL40
[0498] Aim:
[0499] To identify the epitopes recognized by the antibodies B3 (SEQ ID NO: 3), B10 (SEQ ID NO: 4) and H7 (SEQ ID NO: 14 and SEQ ID NO: 15) by performing a physical interaction study with mutants of human YKL40 (SEQ ID NO: 63) expressed in CHO cells.
[0500] Material and Methods:
[0501] Based on the epitope mapping studies of example 10 to 12 and the In Silico docking of B3 (SEQ ID NO: 3), B10 (SEQ ID NO: 4) and H7 (SEQ ID NO: 14 and SEQ ID NO: 15) on human YKL40 (SEQ ID NO: 1). SEQ ID NO:1 provides the sequence of full length YKL-40, whereas SEQ ID NO:63 provides the sequence of YKL-40 lacking amino acid 1-21. Mutants of YKL-40 of SEQ ID NO:63 were designed as follows:
[0502] The following amino acid positions corresponding to positions 42, 44, 92, 96, 100, 104, 107, 108, 134, 135, 141 , 142, 145, 148, 149, 172, 175, 191 , 192, 194, 249, 250, 256, 283, 286, 287, 288, 289, 300, 302 in SEQ ID NO: 63 were mutated to Ala. These amino acid positions correspond to positions 63, 65, 113, 121 , 125, 128, 129, 155, 156, 162, 163, 166, 169, 170, 193, 196, 212, 213, 215, 270, 271 , 277, 304, 307, 308, 309, 321 , 323 in SEQ ID NO: 1 respectively. The following amino acid positions corresponding to positions 284 and 301 in SEQ ID NO: 63 were mutated to Arg. These amino acid positions correspond to positions 305 and 322 in SEQ ID NO: 1 respectively.
[0503] The criteria used were: 1 ) positions indicated to be part of the epitope by the epitope mapping studies of example 10 to 12, 2) positions indicated to be part of the epitope by In Silico docking, 3) Surface exposed side chain.
[0504] All the constructs were ordered from Geneuniversal and delivered in the mammalian expression vector pcDNA3.1 with a Myc tag and a 6x HIS tag inserted at the C-terminal end of the gene encoding YKL40. The leader sequence for YKL40 was inserted in front of the gene encoding YKL40.
[0505] ExpiCHO cells were maintained in expression ExpiCHO media from Thermo Fisher Scientific and at a viability of 96 % cells were transfected in 12 well plates and grown shaking at 120 rpm. 0.15x106 cells / mL and 1.5 mL per well were used for transfection. After 9 days the cultures were terminated.
[0506] Mutant YKL40 were purified from the culture supernatants using His-SPIN trap from Cytiva using the manufactures instructions. Following expression of the mutant YKL40, interactions studies were performed using Biolayerinterferometry on the Octet platform provided by Sartorius.
[0507] Results regarding B3:
[0508] The different YKL-40 mutants showed variations in their association pattern to the B3 (SEQ ID NO: 3) antibody with respect to the wild-type YKL-40 (Figure 15 A). The curves indicate the 2:1 binding model that was used to perform the data analysis. The variations in the relative affinity of B3 (SEQ ID NO: 3) antibody to the different YKL-40 mutants was calculated in the form of dissociation constant (KD) (Table 3). A relative quantification of the recombinant YKL40 were performed based on a Coomassie stained gel and plotted for visual representation (Figure 15 B). Results regarding B10:
[0509] The different YKL-40 mutants showed variations in their association pattern to the B10 (SEQ ID NO: 4) antibody with respect to the wild-type YKL-40 (Figure 16 A). The curves indicate the 2:1 binding model that was used to perform the data analysis. The variations in the affinity of B10 (SEQ ID NO: 4) antibody to the different YKL-40 mutants was calculated in the form of dissociation constant (KD) (Table 4) A relative quantification of the recombinant YKL40 were performed based on a Coomassie stained gel and plotted for visual representation (Figure 16 B). Table 4.
[0510] Results regarding H7:
[0511] The different YKL-40 mutants showed variations in their association pattern to the H7 (SEQ ID NO: 14 and SEQ ID NO: 15) antibody with respect to the wild-type YKL-40 (Figure 17 A). The curves indicate the 2:1 binding model that was used to perform the data analysis.
[0512] The variations in the affinity of H7 antibody to the different YKL-40 mutants was calculated in the form of dissociation constant (KD) (Table 5). A relative quantification of the recombinant YKL40 were performed based on a Coomassie stained gel and plotted for visual representation (Figure 17 B). Table 5.
[0513] Results and Conclusion:
[0514] The epitopes recognised by B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) are partial overlapping.
[0515] The epitope on YKL40 bound by the antibody B3 cover the area involving the following residues 44, 93, 104, 108, 134 and 145 of SEQ ID NO:63.
[0516] The epitope on YKL40 bound by the antibody B10 cover the area involving the following residues 44, 93-96, 104-108, 134 and 145-148 of SEQ ID NO:63.
[0517] H7 (SEQ ID NO: 14 and SEQ ID NO: 15) covers an epitope distinct from B3 (SEQ ID NO: 3) and B10 (SEQ ID NO: 4) and cover a surface constituted in part by amino acid 191-194, 249-256, 287, 300 of SEQ ID NO: 63. Sequence overview
[0518] SEQ ID NO: 1. Human YKL-40 also known as Chitinase-3-like protein 1 (CHI3L1)
[0519] MGVKASQTGFWLVLLQCCSAYKLVCYYTSWSQYREGDGSCFPDALDRFLCTHIIYS
[0520] FANISNDHIDTWEWNDVTLYGMLNTLKNRNPNLKTLLSVGGWNFGSQRFSKIASNTQ
[0521] SRRTFIKSVPPFLRTHGFDGLDLAWLYPGRRDKQHFTTLIKEMKAEFIKEAQPGKKQL
[0522] LLSAALSAGKVTIDSSYDIAKISQHLDFISIMTYDFHGAWRGTTGHHSPLFRGQEDASP
[0523] DRFSNTDYAVGYMLRLGAPASKLVMGIPTFGRSFTLASSETGVGAPISGPGIPGRFTK EAGTLAYYEICDFLRGATVHRILGQQVPYATKGNQWVGYDDQESVKSKVQYLKDRQL AGAMVWALDLDDFQGSFCGQDLRFPLTNAIKDALAAT
[0524] SEQ ID NO: 2. Murine YKL-40
[0525] MHTSTEARMGMRAALTGFAVLMLLQSCSAYKLVCYFTSWSQYREGVGSFLPDAIQPF
[0526] LCTHIIYSFANISSDNMLSTWEWNDESNYDKLNKLKTRNTNLKTLLSVGGWKFGEKRF
[0527] SEIASNTERRTAFVRSVAPFLRSYGFDGLDLAWLYPRLRDKQYFSTLIKELNAEFTKEV
[0528] QPGREKLLLSAALSAGKVAIDTGYDIAQIAQHLDFINLMTYDFHGVWRQITGHHSPLFQ GQKDTRFDRYSNVNYAVQYMIRLGAQASKLLMGIPTFGKSFTLASSENQLGAPISGEG LPGRFTKEAGTLAYYEICDFLKGAEVHRLSNEKVPFATKGNQWVGYEDKESVKNKVG FLKEKKLAGAMVWALDLDDFQGTCQPKEFFPLTNAIKDALA
[0529] SEQ ID NO: 3. B3 predator
[0530] MAEVQLLESGGGLVQPGGSLRLSCAASGFRDSDEDMGWVRQAPGKGLEWVSSISA PGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCASHYNYGHWFDYW GQGTLVTVSSAA
[0531] SEQ ID NO: 4. B10 predator
[0532] MAEVQLLESGGGLVQPGGSLRLSCAASGFRDSDEDMGWVRQAPGKGLEWVSSISA DSGSTYYADSVKGRFTISRDNSKNTL YLQMNSLRAEDTA VYYCASDYNYWYWFDYW GQGTLVTVSSAA
[0533] SEQ ID NO: 5. B3 CDR1
[0534] GFRDSDEDMG
[0535] SEQ ID NO: 6. B3 CDR2
[0536] ISAPGGSTYYADSVKG S Q ID NO: 7. B3 CDR3
[0537] HYNYGHWFDY
[0538] SEQ ID NO: 8. B10 CDR1
[0539] GFRDSDEDMG
[0540] SEQ ID NO: 9. B10 CDR2
[0541] ISADSGSTYYADSVKG
[0542] SEQ ID NO: 10. B10 CDR3
[0543] DYNYWYWFDY
[0544] SEQ ID NO: 11. CDR1 general formula
[0545] GFRDSDEDMG
[0546] SEQ ID NO: 12. CDR2 general formula
[0547] ISAXXGSTYYADSVKG
[0548] SEQ ID NO: 13. CDR3 general formula
[0549] XYNYXXWFDY
[0550] SEQ ID NO: 14. H7 light
[0551] DIQMTQSPASLSASVGETVTITCGASENIYGALNWYQRKQGKSPQLLIYGATTLADGM
[0552] SSRFSGSGSGRQYSLKISSLHPDDVATYYCQNVLTTPWTFGGGTKLEIKTVAAPSVFI
[0553] FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTY
[0554] SLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
[0555] SEQ ID NO: 15. H7 heavy
[0556] EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANG
[0557] NTIYASKFQGKATITRDTSSNTAYMQLSSLTSGDTAVYYCTRGVYYYGGSFYAMDYW
[0558] GQGTSVTVSSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGAL
[0559] TSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD
[0560] KTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYV
[0561] DGVEVHNAKTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTIS KAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTT
[0562] PPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
[0563] SEQ ID NO: 16. H7 CDR1 light
[0564] GASENIYGALN
[0565] SEQ ID NO: 17. H7 CDR2 light
[0566] GATTLAD
[0567] SEQ ID NO: 18. H7 CDR3 light
[0568] QNVLTTPWT
[0569] SEQ ID NO: 19. H7 CDR1 heavy
[0570] GFNIKDT
[0571] SEQ ID NO: 20. H7 CDR2 heavy
[0572] DPANGN
[0573] SEQ ID NO: 21. H7 CDR3 heavy
[0574] GVYYYGGSFYAMDY
[0575] SEQ ID NO: 22. Amino acid sequence of hFc1
[0576] DKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVWDVSHEDPEVKFNW
[0577] YVDGVEVHNAKTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALPAPIEK
[0578] TISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNY
[0579] KTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
[0580] SEQ ID NO: 23. Amino acid sequence of hFc2
[0581] VECPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCWVDVSHEDPEVQFNWYVDG
[0582] MEVHNAKTKPREEQFNSTFRWSVLTWHQDWLNGKEYKCKVSNKGLPAPIEKTISKT
[0583] KGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPP
[0584] MLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
[0585] SEQ ID NO: 24. CDR1 of disclosed YKL-40 antibody FRDSDEDMG SEQ ID NO: 25. CDR2.1
[0586] SIGDESGSTYYADSV
[0587] SEQ ID NO: 26. CDR2.2 SINAPDGSTYYADSV
[0588] SEQ ID NO: 27. CDR2.3
[0589] SISGSDGSTYYADSV
[0590] SEQ ID NO: 28. CDR2.4
[0591] SINNSGGSTYYADSV
[0592] SEQ ID NO: 29. CDR2.5
[0593] SISAESGSTYYADSV
[0594] SEQ ID NO: 30. CDR2.6
[0595] SINYNSGSTYYADSV
[0596] SEQ ID NO: 31. CDR2.7
[0597] SISDEDGSTYYADSV
[0598] SEQ ID NO: 32. CDR2.8
[0599] SISGESGSTYYADSV
[0600] SEQ ID NO: 33. CDR2.9
[0601] SIQSSDGSTYYADSV
[0602] SEQ ID NO: 34. CDR2. 10
[0603] SINNESGSTYYADSV
[0604] SEQ ID NO: 35. CDR2.11
[0605] SIYAPNGSTYYADSV
[0606] SEQ ID NO: 36. CDR2. 12 SIASDSGSTYYADSV
[0607] SEQ ID NO: 37. CDR2. 13
[0608] SIGAGSGSTYYADSV
[0609] SEQ ID NO: 38. CDR2. 14
[0610] SINANDGSTYYADSV
[0611] SEQ ID NO: 39. CDR2. 15
[0612] SIGNYNGSTYYADSV
[0613] SEQ ID NO: 40. CDR2. 16
[0614] SIYGPSGSTYYADSV
[0615] SEQ ID NO: 41. CDR2.17
[0616] SIDAEDGSTYYADSV
[0617] SEQ ID NO: 42. CDR3.1 TSDSYWSFDY
[0618] SEQ ID NO: 43. CDR3.2 QWDDGYAFDY
[0619] SEQ ID NO: 44. CDR3.3 TDYLRSSFDY
[0620] SEQ ID NO: 45. CDR3.4
[0621] TYDWNYSFDY
[0622] SEQ ID NO: 46. CDR3.5 QYGAYHDFDY
[0623] SEQ ID NO: 47. CDR3.6
[0624] TPNLNSSFDY SEQ ID NO: 48. CDR3.7 SGDWWYGFDY
[0625] SEQ ID NO: 49. CDR3.8 VDPLDTYFDY
[0626] SEQ ID NO: 50. CDR3.9 SSQNGYVFDY
[0627] SEQ ID NO: 51. CDR3. 10 TSYYGFDFDY
[0628] SEQ ID NO: 52. CDR3.11 NTYDAFDY
[0629] SEQ ID NO: 53. CDR3.12 SGYAGTVFDY
[0630] SEQ ID NO: 54. CDR3.13 STDARWQFDY
[0631] SEQ ID NO: 55. CDR3. 14 QYDDEFAFDY
[0632] SEQ ID NO: 56. CDR3.15 VSDSGFSFDY
[0633] SEQ ID NO: 57. CDR3. 16 SDWDGYSFDY
[0634] SEQ ID NO: 58. CDR3.17 QDGAYYTFDY
[0635] SEQ ID NO: 59. CDR2.18
[0636] SISTSDGSTYY SEQ ID NO: 60. CDR3.18
[0637] QYDTGYSFDY
[0638] SEQ ID NO: 61. IgE
[0639] STQSPSVFPLTRCCKNIPSNATSVTLGCLATGYFPEPVMVTWDTGSLNGTTMTLPATT
[0640] LTLSGHYATISLLTVSGAWAKQMFTCRVAHTPSSTDWVDNKTFSVCSRDFTPPTVKIL
[0641] QSSCDGGGHFPPTIQLLCLVSGYTPGTINITWLEDGQVMDVDLSTASTTQEGELASTQ
[0642] SELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIR
[0643] KSPTITCLWDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRD
[0644] WIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLI
[0645] QNFMPEDISVQWLHNEVQL
[0646] SEQ ID NO: 62. Amino acid sequence of mFc
[0647] RSPPLKECPPCAAPDLLGGPSVFIFPPKIKDVLMISLSPMVTCVWDVSEDDPDVQISW
[0648] FVNNVEVHTAQTQTHREDYNSTLRWSALPIQHQDWMSGKEFKCKVNNRALPSPIEK
[0649] TISKPRGPVRAPQVYVLPPPAEEMTKKEFSLTCMITGFLPAEIAVDWTSNGRTEQNYK
[0650] NTATVLDSDGSYFMYSKLRVQKSTWERGSLFACSWHEGLHNHLTTKTISRSLGK
[0651] SEQ ID NO: 63. Human YKL-40 PDB ref. 1NWR
[0652] YKLVCYYTSWSQYREGDGSCFPDALDRFLCTHIIYSFANISNDHIDTWEWNDVTLYGM
[0653] LNTLKNRNPNLKTLLSVGGWNFGSQRFSKIASNTQSRRTFIKSVPPFLRTHGFDGLDL
[0654] AWLYPGRRDKQHFTTLIKEMKAEFIKEAQPGKKQLLLSAALSAGKVTIDSSYDIAKISQ
[0655] HLDFISIMTYDFHGAWRGTTGHHSPLFRGQEDASPDRFSNTDYAVGYMLRLGAPASK
[0656] LVMGIPTFGRSFTLASSETGVGAPISGPGIPGRFTKEAGTLAYYEICDFLRGATVHRILG
[0657] QQVPYATKGNQWVGYDDQESVKSKVQYLKDRQLAGAMVWALDLDDFQGSFCGQD
[0658] LRFPLTNAIKDALA AT
[0659] References
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[0661] Brockmann EC, Akter S, Savukoski T, Huovinen T, Lehmusvuori A et al. (2011) Synthetic single-framework antibody library integrated with rapid affinity maturation by VL shuffling. Protein Eng Des Sei 24:691-700. doi:10.1093 / protein / gzr023. PubMed: 21680620.
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[0663] Fellouse FA, Esaki K, Birtalan S, Raptis D, Cancasci VJ et al. (2007) High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol 373: 924-940. doi:10.1016 / j.jmb.2007.08.005. PubMed: 17825836.
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Claims
Claims1. A composition comprising one or more antibodies specifically binding YKL-40, wherein at least one of the antibodies is binding an epitope comprising at least 3 of amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 or at least one of the antibodies is binding an epitope comprising at least 3 of amino acids at positions 212, 213, 214, 215, 270, 271 , 272, 273, 274, 275, 276, -277, 308 or 321 of SEQ ID NO.1 ; wherein said one or more antibodies alone or together are capable of reducing the interstitial fluid pressure in a solid neoplasm expressing YKL-40 in mammal when administered to said mammal.
2. The composition according to any one of the preceding claims, wherein at least one of the antibodies is binding an epitope comprising at least 4 amino acids, preferably at least 5 amino acids, more preferably all 6 amino acids selected from amino acids 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
3. The composition according to any one of the preceding claims, at least one of the antibodies is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 , wherein said epitope does not comprise at least one of amino acids at positions 115, 116, 117, 126, 127, 128, 167,169 or 169 of SEQ ID NO: 1.
4. The composition according to any one of the preceding claims, at least one of the antibodies is binding an epitope comprising the amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 , wherein said epitope does not comprise at least 2, preferably does not comprise at least 5, more preferably does not comprise at least 7, even more preferably comprises none of amino acids at positions 115, 116, 117, 126, 127, 128, 167, 168 or 169 of SEQ ID NO: 1.
5. The composition according to any one of the preceding claims, wherein at least one of the antibodies is binding an epitope comprising one or more of amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1, preferably all of amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1.
6. The composition according to any one of the preceding claims, wherein the one or more antibodies specifically binding YKL-40 wherein at least two of the antibodies is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1.
7. The composition according to any one of the preceding claims, wherein the composition comprises only two antibodies, wherein at least one of the antibodies is binding an epitope comprising amino acids at positions 65, 114, 125, 129, 155 or 166 of SEQ ID NO: 1 , wherein said epitope does not comprise at least one of amino acids at positions 115, 116, 117, 126, 127, 128, 167,169 or 169 of SEQ ID NO: 1 , and the other antibody is binding an epitope comprising amino acids at positions 65, 114, 115, 116, 117, 125, 126, 127, 128, 129, 155, 166, 167, 168 or 169 of SEQ ID NO: 1.
8. The composition according to any one of the preceding claims, wherein at least one of the antibodies is binding an epitope comprising at least 5 amino acids, preferably at least 8 amino acids, more preferably 11 amino acids, even more preferably all of the amino acids selected from amino acids at positions 212- 215, 270-277, 308 or 321 of SEQ ID NO.1.
9. The composition according to any one of the preceding claims, wherein the composition comprises only one antibody and said antibody is binding an epitope comprising amino acids at positions 212-215, 270-277, 308 and 321 of SEQ ID NO.1.
10. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1 comprising or consisting of an amino acid sequence of SEQ ID NO: 5 or SEQ ID NO: 8; and a CDR2 comprising or consisting of an amino acid sequence of the general formula: ISAXXGSTYYADSVKG (SEQ ID NO:12), wherein X may be any amino acid and a CDR3 comprising or consisting of an amino acid sequence of the general formula: XYNYXXWFDY (SEQ ID NO: 13), wherein X may be any amino acid.
11. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1, CDR2 and CDR3, wherein, a) CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; andCDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7 ; or b) CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8;CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; andCDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10; or c) CDR1 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 16;CDR2 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 17;CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 18;CDR1 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 19;CDR2 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 20; andCDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 21.
12. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1 , CDR2 and CDR3, wherein,CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5;CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; andCDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7.
13. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YKL-40 comprises a variable region comprising a CDR1 , CDR2 and CDR3, wherein,CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8;CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; andCDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10.
14. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YLK-40 antibody comprises or consists of a variable region comprising or consisting of an amino acid sequence of SEQ ID NO:3 or SEQ ID NO:4.
15. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YKL-40 antibody comprises variable regions comprising a CDR1 , CDR2 and CDR3, wherein,CDR1 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 16;CDR2 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 17;CDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 18;CDR1 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 19;CDR2 of the heavy chain comprises or consists of an amino acid sequence of SEQ ID NO: 20; andCDR3 of the light chain comprises or consists of an amino acid sequence of SEQ ID NO: 21.
16. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YLK-40 antibody comprises a light chain variable region comprising or consisting of an amino acid sequence of SEQ ID NO: 14 and a heavy chain variable region comprising or consisting of amino acid sequence of SEQ ID NO: 15.
17. The composition according to any one of the preceding claims, wherein at least one antibody specifically binding YKL-40 is capable of binding an epitope present in both human and murine YKL-40 and / or wherein at least one antibodyspecifically binding YKL-40 is capable of binding the same YKL-40 epitope bound by any of the antibodies defined in any one of the preceding claims.
18. The composition according to any one of the preceding claims, wherein the composition comprises a bi- or multispecific antibody comprising at least two different variable regions each specifically binding YKL-40, for example a bi- or multispecific antibody comprising one or more variable regions comprising a CDR1 of SEQ ID NO: 5, a CDR2 of SEQ ID NO: 6 and a CDR3 of SEQ ID NO:7 and one or more variable regions comprising a CDR1 of SEQ ID NO: 8, a CDR2 of SEQ ID NO: 9 and a CDR3 of SEQ ID NQ:10, for example a bi- or multispecific antibody comprising one or more variable regions comprising or consisting of SEQ ID NO: 3 and one or more variable regions comprising or consisting of SEQ ID NO:4.
19. The composition according to any one of the preceding claims, wherein the composition comprises at least two different antibodies specifically binding YLK- 40, wherein said antibodies are as defined in any one of the preceding claims.
20. The composition according to any one of the preceding claims, wherein the composition comprises one antibody with a variable region comprising a CDR1, CDR2 and CDR3, wherein,CDR1 comprises or consists of an amino acid sequence of SEQ ID NO:5; CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 6; and CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 7 ; and another antibody with a variable region comprising a CDR1 , CDR2 and CDR3, wherein,CDR1 comprises or consists of an amino acid sequence of SEQ ID NO: 8; CDR2 comprises or consists of an amino acid sequence of SEQ ID NO: 9; and CDR3 comprises or consists of an amino acid sequence of SEQ ID NO: 10.
21. A kit-of-parts and / or a composition comprising a. a composition comprising at least one YKL-40 antibody according to any one of claims 1 to 20; and b. an anti-cancer agent;for use in the treatment of cancer in an individual in need thereof, wherein said cancer is characterised by the presence of at least one solid neoplasm.
22. A composition or a kit-of-parts according to any one of claims 1 to 21 for use in a method of treating a disease associated with YKL-40 expression, for example cancer or an inflammatory disease, for example arthritis, such as osteoarthritis.
23. The kit-of-parts or composition for use according any one of claims 21 to 22, wherein the method comprises administering a therapeutically effective amount of two different YKL-40 antibodies to a subject in need thereof, wherein said antibodies are as defined in any one of the preceding claims.
24. The kit-of-parts or composition for use according to any one of claims 21 to 23, wherein the anti-cancer agent is selected from the group consisting of a chemotherapeutic agent, an immunotherapeutic agent, checkpoint inhibitors, anti-cancer antibodies, a radioactive substance and cytostatic small molecule.
25. A kit-of-part comprising c. a composition according to any one of claims 1 to 20; and d. a diagnostic substance wherein said kit-of-parts may be for use in a method of determining the efficacy of treatment of a disease in an individual receiving said treatment.