Classifications

• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
  • A61K39/39533—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals
  • A61K39/39558—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals against tumor tissues, cells, antigens
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2803—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/566—Immunoassay; Biospecific binding assay; Materials therefor using specific carrier or receptor proteins as ligand binding reagents where possible specific carrier or receptor proteins are classified with their target compounds
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
  • G01N33/56966—Animal cells
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/5758—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
  • G01N33/6854—Immunoglobulins
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
  • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
  • G01N2333/70596—Molecules with a "CD"-designation not provided for elsewhere in G01N2333/705

Definitions

• the antibody is further characterized by not binding to NKp46-negative cells (cells that do not express NKp46) in a paraffin-embedded cell pellet.
• the antibody is further characterized by binding to NK cells in paraffin-embedded tissue sections.
• the disclosure provides an antibody binds an epitope present on NKp46 expressed by purified NK cells in culture and/or in frozen tissue section and/or recombinant NKp46 polypeptide, wherein the epitope is also present on (i.e. is a common antigenic determinant shared with) formalin fixed NK cells.
• the present invention provides a method of detecting (e.g., characterizing, quantifying) NK cells in a formalin-treated and/or paraffin- embedded tissue sample from an individual, the method comprising the steps of a) contacting the tissue sample with an anti-NKp46 antibody and with an antibody that binds a non-NKp46 polypeptide (e.g. a non-lineage specific polypeptide discussed herein), optionally a non-NKp46 polypeptide capable of being expressed by NK cells; and b) detecting the presence of the bound antibodies in the tissue sample.
• the tissue sample is contacted with 1 , 2, 3, 4, 5, or 10 more different monoclonal antibodies that bind different non-NKp46 polypeptides.
• the present invention provides a therapeutic and/or prognostic method for a therapeutic agent, the method comprising the steps of: a) contacting a formalin-treated and/or paraffin- embedded disease tissue sample from an individual having a disease (e.g. a cancer, an infectious or an inflammatory disorder) with an anti-NKp46 antibody and with an antibody that binds a polypeptide targeted by an immunotherapeutic agent (e.g. a therapeutic antibody); and b) detecting the presence of the bound antibodies in the tissue sample.
• a disease e.g. a cancer, an infectious or an inflammatory disorder
• an immunotherapeutic agent e.g. a therapeutic antibody
• the present invention provides a method of treating an individual having a lymphoma, e.g., a CTCL or a PTCL, the method comprising a) providing a formalin-treated and/or paraffin-embedded cancer sample from the individual; b) detecting NKp46 in the cancer samples; optionally a detection of NKp46 indicates the individual is suitable for treatment with an anti-NKp46 agent (e.g. an agent that depletes NKp46- expressing cells).
• an anti-NKp46 agent e.g. an agent that depletes NKp46- expressing cells.
• the paraffin-embedded cancer sample is a paraffin- embedded cell pellet.
• the present invention provides a method of treating an individual with a cancer, the method comprising a) providing a formalin-treated and/or paraffin-embedded cancer sample from the individual; b) detecting NKp46 in the cancer samples, wherein a detection of NKp46 indicates the individual is suitable for treatment with an anti-NKp46 agent; and optionally: c) if NKp46 expression is detected in the cancer sample, administering a therapeutic agent that leads to the elimination of NKp46-expressing cells (e.g., an anti-NKp46 antibody) to the patient.
• a therapeutic agent that leads to the elimination of NKp46-expressing cells (e.g., an anti-NKp46 antibody) to the patient.
• paraffin-embedded sample refers to cells or tissues taken from an organism or from in vitro cell culture that have been fixed, embedded in paraffin, sectioned, deparaffinized, and transferred to a slide.
• fixation and paraffin embedding is a common practice that can vary in many aspects, e.g., with respect to the fixation and embedding methods used, with respect to the protocol followed, etc., and that for the purposes of the present invention any such variant method is encompassed, so long as it involves fixation of the tissue (such as by formalin treatment), embedding in paraffin or equivalent material, sectioning and transfer to a slide.
• variable region as used herein is meant the region of an antibody that comprises one or more Ig domains substantially encoded by any of the VL (including Vkappa (VK) and Vlambda) and/or VH genes that make up the light chain (including kappa and lambda) and heavy chain immunoglobulin genetic loci respectively.
• VL or VH consists of a "framework” or “FR” region interrupted by three hypervariable regions referred to as “complementarity determining regions” or "CDRs". The extent of the framework region and CDRs have been precisely defined, for example as in Kabat (see “Sequences of Proteins of Immunological Interest," E.
• epitope refers to an antigenic determinant, and is the area or region on an antigen to which an antibody or polypeptide binds.
• a protein epitope may comprise amino acid residues directly involved in the binding as well as amino acid residues which are effectively blocked by the specific antigen binding antibody or peptide, i.e. , amino acid residues within the "footprint” of the antibody. It is the simplest form or smallest structural area on a complex antigen molecule that can combine with e.g., an antibody or a receptor.
• Epitopes can be linear or conformational/structural.
• linear epitope is defined as an epitope composed of amino acid residues that are contiguous on the linear sequence of amino acids (primary structure).
• NKp46 refers to a protein or polypeptide encoded by the Ncr1 gene or by a cDNA prepared from such a gene. Any naturally occurring isoform, allele or variant is encompassed by the term NKp46 polypeptide (e.g., an NKp46 polypeptide 90%, 95%, 98% or 99% identical to SEQ ID NO 1 , or a contiguous sequence of at least 20, 30, 50, 100 or 200 amino acid residues thereof).
• the 304 amino acid residue sequence of human NKp46 (isoform a) is shown as follows:
• Antibodies have been raised to target specific tumour related antigens including: Receptor Tyrosine Kinase- like Orphan Receptor 1 (ROR1 ), Cripto, CD4, CD20, CD30, CD19, CD38, CD47, Glycoprotein NMB, CanAg, Her2 (ErbB2/Neu), CD22 (Siglec2), CD33 (Siglec3), CD79, CD138, CD171 , PSCA, L1 -CAM, PSMA (prostate specific membrane antigen), BCMA, CD52, CD56, CD80, CD70, E-selectin, EphB2, Melanotransferin, Mud 6 and TMEFF2.
• ROR1 Receptor Tyrosine Kinase- like Orphan Receptor 1
• Cripto CD4, CD20, CD30, CD19, CD38, CD47, Glycoprotein NMB, CanAg, Her2 (ErbB2/Neu), CD22 (Siglec2), CD33 (Siglec3), CD79, CD138
• an antibody is said to compete with 8E5B if the binding obtained with a labeled 8E5B antibody (by a fluorochrome or biotin) on cells preincubated with a saturating amount of test antibody is about 80%, preferably about 50%, about 40%, or less (e. g., about 30%) of the binding obtained without preincubation with the antibody.
• glycine asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan
• nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine
• beta- branched side chains e.g. threonine, valine, isoleucine
• aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine.
• the antibodies described herein can be used for the detection, preferably in vitro, of the presence of NK cells cells, optionally of a pathology where NK cells are involved (e.g. having a beneficial role to ameliorate disease of having a role in exacerbating disease, e.g. in cancer, infection, inflammatory or autoimmune disorders).
• a biological sample e.g. a FFPE sample, deparaffinized
• detecting the formation of immunological complexes resulting from the immunological reaction between the antibody and the biological sample e.g. a FFPE sample, deparaffinized
• the present invention provides a method of treating a patient with cancer, the method comprising a) providing a formalin-treated and/or paraffin-embedded tissue sample from the patient; b) detecting NKp46 in the tissue sample (e.g. tumor tissue) using an anti-NKp46 antibody (and optionally further detecting one or more other markers, e.g. a non-lineage specific marker); and c) if NKp46 expression (optionally together with one or more other markers) is detected in the sample, administering a therapeutic agent (e.g., an immunotherapeutic agent) to the patient.
• the tissue sample comprises a cancer tissue or a cancer adjacent tissue (also referred to as adjacent non-tumorous tissue or normal adjacent tissue).
• the second polypeptide is a polypeptide expressed by a population or sub-population of cells selected from the group consisting of: monocytes, macrophages, neutrophils, basophils, eosinophils, erythrocytes, dendritic cells, T-cells, T h 1 or T h 2 helper T cells, cytotoxic T cells, suppressor or regulatory T cells, M1 and M2 macrophages, tumor associated macrophages, and any other tumor infiltrating and/or tumor associated populations of any of the foregoing.
• the therapeutic agent is an immunotherapeutic agent.
• the immunotherapeutic agent is an agent that modulates the activity of tumor infiltrating and/or cancer adjacent tissue NK cells, optionally further tumor infiltrating and/or cancer adjacent tissue T cells.
• the level of NK cell infiltration can be determined by any suitable method.
• the level of NK cell infiltration can be determined as the number of NK cells present in a given tissue, e.g. a tumor.
• the level of NK cell infiltration is reflected by the number of NK cells per mm 2 of a FFPE tissue section (e.g. a section prepared from a tumor biopsy).
• the level of NK cell infiltration in the tumor is determined in vitro in a tumor and/or tumor-adjacent tissue sample taken from the patient prior to treatment.
• the reference level is a value representative of the level of NK cell infiltration in tumors and/or tumor-adjacent tissues of a population of patients deriving no clinical benefit from the treatment.
• the reference level is determined in vitro in tumor and/or tumor-adjacent tissue samples taken prior to treatment from patients deriving no clinical benefit from the treatment.
• the an immunotherapeutic agent is administered to a patient having a level of NK cell infiltration that is at least 1.5-fold, at least 2-fold or at least 3-fold the reference level.
• kits e.g., for cancer, comprising an antibody according to the invention.
• the kit comprises an antibody of the invention and an antibody (e.g. 1 , 2, 3, 4, 5, 10 or more antibodies) that binds a non-NKp46 polypeptide, for use as a diagnostic or prognostic.
• the kit comprises an antibody of the invention for use as a diagnostic or prognostic, and an immunotherapeutic agent.
• Said kit can additionally comprise means by which to detect the immunological complex resulting from the immunological reaction between the biological sample and an antibody of the invention, in particular reagents enabling the detection of said antibody.
• Human NKp46-His recombinant protein (100 ng, 50 ng and 10 ng) was loaded onto an SDS-PAGE 12% gel under reducing conditions. The gel was then transferred onto an Immobilon-P membrane (Millipore, IPVH00010). The membrane was saturated for 1 H with a 5% BSA, TBS-Tween 0,05% buffer. The 8E5B antibody was used at 1 g/rnl and the staining was performed for 1 H. The membrane was then washed three times with the TBS- Tween buffer.

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