WO2024069165A1 - Molécules de liaison à cll1 - Google Patents

Molécules de liaison à cll1 Download PDF

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Publication number
WO2024069165A1
WO2024069165A1 PCT/GB2023/052497 GB2023052497W WO2024069165A1 WO 2024069165 A1 WO2024069165 A1 WO 2024069165A1 GB 2023052497 W GB2023052497 W GB 2023052497W WO 2024069165 A1 WO2024069165 A1 WO 2024069165A1
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seq
antibody
antigen binding
cell
binding fragment
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PCT/GB2023/052497
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English (en)
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Simon BORNSCHEIN
Youlia LAMPI
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Coding Bio Limited
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2851—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the lectin superfamily, e.g. CD23, CD72
    • 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
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • 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
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4631—Chimeric Antigen Receptors [CAR]
    • 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
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)

Definitions

  • the present invention relates to C-type lectin-like molecule 1 (CLL1) binding molecules, in particular to anti-CLL1 antibodies and antigen binding fragments.
  • the present invention further relates to recombinant molecules comprising said CLL1 binding molecules, such as, chimeric antigen receptors (CARs), BiTEs and ADCs.
  • Another object of the present invention is an engineered immune cell, suitably, a regulatory T cell comprising said CAR. Uses thereof in therapeutic methods of said antibody, said recombinant molecule and said engineered immune cell are further described.
  • the C-type lectin-like molecule 1 (CLL1) glycoprotein (also known as CLEC12A, DCAL2, MICL, KLRL1) is a type II transmembrane protein comprising a single C-type lectin-like domain, a transmembrane domain, a stalk region, and a cytoplasmic tail containing an immunoreceptor tyrosine-based inhibitory motif (ITIM) (https://www.uniprot.org/uniprotkb/Q5QGZ9/entry; Marshall et al. 2006. Human CLL1 is differentially glycosylated and is down-regulated following cellular activation. Eur. J. Immunol., 36, 2159-2169.).
  • ITIM immunoreceptor tyrosine-based inhibitory motif
  • CLL1 functions as a cell surface receptor and is expressed on myeloid lineage cells.
  • the cytoplasmic ITIM motif is a conserved sequence of amino acids, commonly found in a number of immune-function related receptors, which contains a tyrosine residue that may be phosphorylated and thereby effect a signalling cascade which is thought to be important for regulating cellular maturation and activation.
  • CLL1 is expressed on myeloid lineage cells (pre-activation), it shows limited expression in other cell lineages and tissues, and it is not expressed on haematopoietic stem cells (HSCs). Furthermore, CLL1 has been found to be expressed in more than 80% of acute myeloid leukaemia (AML) patients. Therefore, CLL1 represents a good target for immunotherapy as it appears to be an attractive protein to discriminate between AML and non-AML cells.
  • AML acute myeloid leukaemia
  • AML typically affects middle aged and older adults and represents approximately 1 % of new cancer cases every year in the USA (Cancer Stat Facts: Leukemia-Acute Myeloid Leukemia (AML). Available online: https://seer.cancer.gov/statfacts/html/amyl.html (accessed on 05 September 2022)). Historically, AML has been challenging to treat and is associated with a high mortality rate. For example, in the USA, AML has a 5-year relative survival rate of 30.5% (Cancer Stat Facts: Leukemia — Acute Myeloid Leukemia (AML). Available online: https://seer.cancer.gov/statfacts/html/amyl.html (accessed on 05 September 2022)).
  • HSCs haematopoietic stem cells
  • CLL1 is also implicated with other cancers and diseases including but not limited to: AML, chronic myeloid (myelogenous) leukemia (CML), chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia, atypical chronic myeloid leukemia, acute promyelocytic leukemia (APL), acute monocytic leukemia, acute monoblastic leukemia, acute erythroid leukemia, acute megakaryoblastic leukemia, myelodysplastic syndrome (MDS), myeloproliferative disorder, myeloid neoplasm, myeloid sarcoma), Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN), or combinations thereof.
  • AML chronic myeloid (myelogenous) leukemia
  • CML chronic myelomonocytic leukemia
  • CMML chronic myelomonocytic leukemia
  • APL acute promy
  • CLL1 may additionally play a role in inflammatory or autoimmune diseases such as rheumatoid arthritis, psoriasis, allergies, asthma, Crohn’s disease, IBD, IBS, fibromyalga, mastocytosis, and Celiac disease.
  • inflammatory or autoimmune diseases such as rheumatoid arthritis, psoriasis, allergies, asthma, Crohn’s disease, IBD, IBS, fibromyalga, mastocytosis, and Celiac disease.
  • immunotherapy treatments that make use of the immune system or immune cells are known as immunotherapy treatments.
  • immunotherapy treatment relies on antibodies to an antigen on a target cell triggering or promoting cell death or inhibiting cell-division.
  • Antigens may be targeted using antibody or antigen binding fragments, such as a single chain variable fragment (scFv). Examples of antibodies that target CLL1 have been previously described e.g. U.S. Patent No. 9,163,090 B2.
  • the antibody or antigen binding domain can be linked or conjugated to a synthetic molecule, such as a synthetic molecule that binds to a T-cell antigen, suitably via a flexible linker, such as a flexible peptide linker to form a bi-specific T-cell engager (BiTE), or a dual-affinity retargeting antibody (DART) or other bi-specific, tri-specific or multi-specific T-cell engagers.
  • a synthetic molecule such as a synthetic molecule that binds to a T-cell antigen, suitably via a flexible linker, such as a flexible peptide linker to form a bi-specific T-cell engager (BiTE), or a dual-affinity retargeting antibody (DART) or other bi-specific, tri-specific or multi-specific T-cell engagers.
  • antibodies or antigen binding fragments may be linked or conjugated with a synthetic molecule such as a label, cytotoxic agent (antibody-drug conjugates or ADCs), or therapeutic isotope.
  • a synthetic molecule such as a label, cytotoxic agent (antibody-drug conjugates or ADCs), or therapeutic isotope.
  • CAR T-cell therapy consists of obtaining T-cells from a patient and incorporating an engineered receptor to recognise an antigen found on the cancerous cells. The resulting CAR T-cells are then incorporated back into the patient, where they may then act to mount an immune response against the antigen i.e. against the cancerous cells, and kill the cancerous cells.
  • an antibody or antigen binding fragment can be linked or conjugated with a synthetic molecule comprising other protein domains, such as hinge domains, transmembrane domains, costimulation domains and activation domains to form a CAR that is capable of effecting an immune response towards the antigen-containing cell.
  • This CAR is then expressed in a T-cell.
  • Previous anti-CLL1 CARs have shown varying levels of effectiveness at eliciting an immune response and killing cancer cells. The reasons for this remain unknown, but it may be related to a low binding affinity of the antibody or antibody derivative portion of the CAR, which results in poor binding to CLL1 and weaker activation of the immune response. Alternatively, this may be due to the lack of optimisation or co-optimisation of the remaining functional domains of the CAR, which also affect T-cell activation.
  • an antibody, or antigen binding fragment, which binds to CLL1 selected from the group consisting of:
  • Antibody 5 comprising:
  • Antibody 1 comprising:
  • Antibody 2 comprising:
  • Antibody 3 comprising;
  • Antibody 4 comprising:
  • Antibody 6 comprising:
  • Antibody 7 comprising:
  • Antibody 8 comprising:
  • Antibody 9 comprising:
  • Antibody 10 comprising:
  • the antibody, or antigen binding fragment, which binds to CLL1 selected from the group consisting of: Antibody 4, Antibody 5 and Antibody 7.
  • the antibody, or antigen binding fragment, which binds to CLL1 is Antibody 5.
  • the antibody or antigen binding fragment is comprised in a single chain variable fragment (scFv).
  • scFv is selected from the group consisting of: SEQ ID NOs 3 to 12.
  • the scFv is selected from the group consisting of: SEQ ID Nos 6, 7 and 9.
  • the scFv is SEQ ID No. 7.
  • the antibody or antigen binding fragment is humanised.
  • the antibody or antigen binding fragment is conjugated to a synthetic molecule.
  • the antibody or antigen binding fragment is a chimeric antigen receptor and the synthetic molecule comprises a transmembrane region and an intracellular T-cell receptor signaling domain.
  • the transmembrane region is from CD8A or CD28 and/or the intracellular signaling domain is from CD247 (CD3-zeta).
  • the chimeric antigen receptor further comprises an intracellular domain of a costimulatory protein receptor.
  • the costimulatory domain is from CD137 or CD28.
  • the antibody or antigen binding fragment is a bi-specific T-cell engager (BiTE) and the synthetic molecule comprises an antigen binding domain which binds to a T-cell antigen.
  • the antigen binding domain comprises an antibody fragment that specifically binds CD3.
  • the antibody fragment that specifically binds CD3 comprises:
  • the antibody is an antigen-drug conjugate and the synthetic molecules is a cytotoxic drug or a therapeutic radioisotope.
  • the invention provides a vector encoding the antibody, or antigen binding fragment, of the first aspect of the invention.
  • the invention provides a pharmaceutical composition comprising the antibody or antigen binding fragment, of the first aspect of the invention and a pharmaceutically acceptable carrier.
  • the invention provides a chimeric antigen receptor comprising: a) The antibody or antigen binding fragment as claimed in any one of the first aspect; b) A transmembrane region; c) An intracellular T-cell receptor signaling domain.
  • the transmembrane region and intracellular T-cell receptor signaling domain of the chimeric antigen receptor of the fourth aspect of the invention are from CD3 zeta.
  • the chimeric antigen receptor further comprises a transmembrane domain or an intracellular signaling domain of a costimulatory protein receptor.
  • the chimeric antigen receptor further comprises a hinge region to create flexibility or increased intercellular spacing.
  • the CAR of the fourth aspect of the invention comprises: a. a human CD247 (CD3-zeta) cytoplasmic domain (SEQ ID NO:113), a human CD137 co-stimulatory domain (SEQ ID NO:114); a human CD8A transmembrane domain (SEQ ID NO:115), a human CD8A hinge domain (SEQ ID NO:116); antibody or antigen binding fragment of the first aspect; and an CD8A extracellular signal peptide (SEQ ID NO:119); or b.
  • a human CD247 (CD3-zeta) cytoplasmic domain SEQ ID NO:113
  • a human CD137 co-stimulatory domain SEQ ID NO:114
  • a human CD8A transmembrane domain SEQ ID NO:115
  • a human CD8A hinge domain SEQ ID NO:116
  • antibody or antigen binding fragment of the first aspect and an CD8A extracellular signal peptide (SEQ ID NO:119); or b.
  • a human CD247 (CD3-zeta) cytoplasmic domain (SEQ ID NO:113), a human CD28 costimulatory domain (SEQ ID NQ:120); a human CD28 transmembrane domain (SEQ ID NO:121), a human CD28 hinge domain (SEQ ID NO:122); antibody or antigen binding fragment of the first aspect; and an CD8A extracellular signal peptide (SEQ ID NO:119).
  • the CAR has a sequence selected from SEQ ID NOS: 93 to 102.
  • the CAR has a sequence selected from SEQ ID Nos. 96; 97 and 99.
  • the CAR has a sequence of SEQ ID No. 97.
  • the invention provides a recombinant T cell comprising the chimeric antigen receptor of the fourth aspect of the invention.
  • a bispecific T-cell engager comprising: a) The antibody or antigen binding fragment of the first aspect; b) An antigen binding domain which binds to a T-cell antigen; c) A linker joining (a) and (b).
  • the antigen binding domain comprises an antigen binding fragment that specifically binds CD3.
  • the antibody fragment that specifically binds CD3 comprises:
  • the linker is a flexible linker.
  • the linker is a peptide or protein linker.
  • the linker is a flexible peptide linker covalently attached to (a) and (b).
  • an antibody-drug conjugate comprising: a) The antibody or antigen binding fragment of the first aspect; b) A synthetic molecule; c) A linker joining (a) and (b).
  • the synthetic molecule is a cytotoxic drug.
  • the linker is cleavable or non-cleavable.
  • the linker is a chemical linker that separately covalently attaches to (a) and (b).
  • an antibody, or antigen binding fragment, of any the first aspect a pharmaceutical composition of the third aspect, a chimeric antigen receptor of the fourth aspect, a recombinant T-cell of the fifth aspect, a bi-specific T-cell engager of sixth aspect or a antibody-drug conjugate of the seventh aspect for use as a medicament.
  • an antibody, or antigen binding fragment, of any the first aspect a pharmaceutical composition of the third aspect, a chimeric antigen receptor of the fourth aspect, a recombinant T-cell of the fifth aspect, a bi-specific T-cell engager of sixth aspect or a antibodydrug conjugate of the seventh aspect for use in killing or inhibiting the growth of cells expressing CLL1 .
  • an antibody, or antigen binding fragment, of any the first aspect a pharmaceutical composition of the third aspect, a chimeric antigen receptor of the fourth aspect, a recombinant T-cell of the fifth aspect, a bi-specific T-cell engager of sixth aspect or a antibodydrug conjugate of the seventh aspect for use in the treatment of a disease or disorder related to an elevated expression of CLL1 .
  • an antibody, or antigen binding fragment, of any the first aspect a pharmaceutical composition of the third aspect, a chimeric antigen receptor of the fourth aspect, a recombinant T-cell of the fifth aspect, a bi-specific T-cell engager of sixth aspect or a antibody-drug conjugate of the seventh aspect for use in medicine.
  • cancers such as AML, chronic myeloid (
  • a method of killing or inhibiting the growth of cells expressing CLL1 in a subject comprising administering an effective amount of the antibody, or antigen binding fragment, of the first aspect, the pharmaceutical composition of the third aspect, the chimeric antigen receptor of the fourth aspect, the recombinant T-cell of the fifth aspect, the bi-specific T-cell engager of sixth aspect or the antibody-drug conjugate of the seventh aspect.
  • a fourteenth aspect of the invention there is provided a method of treating a disease or condition associated with the expression of CLL1 , said method comprising administering to a patient in need thereof an effective amount of an the antibody, or antigen binding fragment, of the first aspect, the pharmaceutical composition of the third aspect, the chimeric antigen receptor of the fourth aspect, the recombinant T-cell of the fifth aspect, the bi-specific T-cell engager of sixth aspect or the antibody-drug conjugate of the seventh aspect.
  • the disease or condition is selected from the group consisting of: cancers, such as AML, chronic myeloid (myelogenous) leukemia (CML), chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia, atypical chronic myeloid leukemia, acute promyelocytic leukemia (APL), acute monocytic leukemia, acute monoblastic leukemia, acute erythroid leukemia, acute megakaryoblastic leukemia, myelodysplastic syndrome (MDS), myeloproliferative disorder, myeloid neoplasm, myeloid sarcoma), Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN); autoimmune diseases such as rheumatoid arthritis, psoriasis, allergies, asthma, Crohn’s disease, IBD, IBS, fibromyalga, mastocytosis, and C
  • cancers such as AML, chronic my
  • Figure 1 shows (A) an embodiment of the general structure of the antibody chain or antigen binding fragment (scFv) of the present invention, with (i) a first VH chain, a linker and a VL chain as defined in the exemplified examples, and an alternative antibody configuration that is also encompassed by the present invention, with (ii) a first VL chain, a linker and a VH chain; (B) an example chimeric antigen receptor scaffold 1 of an embodiment of the present invention comprising a CD8A hinge and CD8A TM region (‘CD8A-CAR’); and (C) exemplified example chimeric antigen receptor scaffold 2 of an embodiment of the present invention comprising a CD28 hinge and CD28 TM region (‘CD28-CAR’).
  • scFv antibody chain or antigen binding fragment
  • FIG. 2 shows median fluorescence intensity (MFI) from primary human T cells transduced with the different CLL1-CAR constructs.
  • the median fluorescence intensity indicates the affi n ity/a vid ity with which the T cells with different CARs bind to CLL1 .
  • the cells were expanded for eight days and stained with CLL1-Fc fusion protein.
  • cells were stained with PE- conjugated anti-Fc and an APC-conjugated anti-CD34 antibodies.
  • Median fluorescence intensity of CLL1-Fc staining is shown for CD34+ CAR-T cells.
  • Figure 2A shows a first T cell donor and
  • Figure 2B shows a second experiment, with a different T cell donor.
  • Figure 3 shows the expansion of human primary T cells transduced with different CLL1 CAR constructs and their average fold expansion between day 4 and day 8 of the CAR-T manufacturing process.
  • Cells were counted using a LUNA FL cell counter (Logos Biosystems) and fluorescence live/dead dye.
  • Figure 4 shows %CD69 upregulation by human primary T cells transduced with the different CLL1- CAR constructs or mock transduced T cells, expanded for eight days and co-cultured for 24h with CLL1- expressing cancer cell line (HL60 cell line). Flow cytometry was performed to separate CLL1 -CAR-T cells from the cancer cells. CD69 up-regulation on CD3+ and CD34+ CAR-T was assessed by flow cytometry
  • Figure 5 shows killing capacity of CLL1 -CAR-T cells against CLL1 -expressing HL60 cancer cell line.
  • HL60 cells were cultured in the absence of T cells. After 24h HL60 cells were quantified by flow cytometry and percentage of killed HL60 cells was calculated, relative to HL60 cells cultured alone.
  • Figure 6 shows potency of CLL1 -CAR-T cells after stimulation with CLL1 -expressing HL60 cancer cell line or non-stimulated controls.
  • the bar on the left indicates CLL1 -CAR-T cells that are stimulated with HL60, and the bar on the right indicates non-stimulated controls.
  • CAR-T cells, transduced with anti-CLL1 CAR constructs or mock transduced T cells, were co-cultured with HL60 cancer cells at a 1 :1 ratio for 24h. After 24h supernatant was assessed for IFNg production via cytokine ELISA.
  • the articles ‘a’, ‘an’ and ‘the’ are used to refer to one or to more than one (i.e. to at least one) of the grammatical object of the article.
  • the term ‘comprising’ means any of the recited elements are necessarily included and other elements may optionally be included as well.
  • Consisting essentially of means any recited elements are necessarily included, elements which would materially affect the basic and novel characteristics of the listed elements are excluded, and other elements may optionally be included.
  • Consisting of means that all elements other than those listed are excluded. Embodiments defined by each of these terms are within the scope of this invention.
  • antibody refers to all isotypes of immunoglobulins (IgG, IgA, IgE, IgM, IgD, and IgY) including various monomeric, polymeric and chimeric forms, unless otherwise specified. Specifically encompassed by the term ‘antibody’ are polyclonal antibodies, monoclonal antibodies (mAbs), single domain antibodies, human (FHVH) or heavy-chain antibodies found in camelids (VHH) and antibodylike polypeptides, such as chimeric antibodies and humanized antibodies.
  • mAbs monoclonal antibodies
  • FHVH single domain antibodies
  • VHH heavy-chain antibodies found in camelids
  • antibodylike polypeptides such as chimeric antibodies and humanized antibodies.
  • the term ‘monoclonal antibody’ refers to an antibody produced by a single clone of cells or cell line and consisting of identical antibodies.
  • antigen-binding fragments refers to any protein structure that may exhibit binding affinity for a particular antigen.
  • Antigen-binding fragments include those provided by any known technique, such as enzymatic cleavage, peptide synthesis, and recombinant techniques. Some antigenbinding fragments are composed of portions of intact antibodies that retain antigen-binding specificity of the parent antibody molecule.
  • antigen-binding fragments may comprise at least one variable region (either a heavy chain or light chain variable region) or one or more CDRs of an antibody known to bind a particular antigen.
  • antigen-binding fragments include, without limitation diabodies and single-chain molecules as well as Fab, F(ab')2, Fc, Fabc, and Fv molecules, single chain (sc) antibodies, individual antibody light chains, individual antibody heavy chains, chimeric fusions between antibody chains or CDRs and other proteins, protein scaffolds, heavy chain monomers or dimers, light chain monomers or dimers, dimers consisting of one heavy and one light chain, a monovalent fragment consisting of the VL, VH, CL and CH1 domains, or a monovalent antibody as described in W02007059782, bivalent fragments comprising two Fab fragments linked by a disulfide bridge at the hinge region, a Fd fragment consisting essentially of the VH and CH1 domains; a Fv fragment consisting essentially of the VL and VH domains of a single arm of an antibody, a dAb fragment (Ward et al., Nature 341 , 544-546 (1989)), which consists essentially of
  • antigen-binding fragments may include non-antibody proteinaceous frameworks that may successfully incorporate polypeptide segments in an orientation that confers affinity for a given antigen of interest, such as protein scaffolds.
  • Antigen-binding fragments may be recombinantly produced or produced by enzymatic or chemical cleavage of intact antibodies.
  • the phrase ‘an antibody or antigenbinding fragment’ may be used to denote that a given antigen binding fragment incorporates one or more amino acid segments of the antibody referred to in the phrase.
  • antigen binding domain refers to a peptide sequence that is intended or able to bind a target of interest.
  • the antigen binding domain is an antigen-binding fragment as defined above. All types of antigen binding domains are encompassed by the present invention. Examples of some antigen binding domains are scFvs, VHH single domain antibodies or nanobodies, and antigen binding fragments.
  • an scFv is a fusion of the variable regions of the heavy (VH) and light chains (VL) of an antibody for a given target connected by a short linker.
  • the VH and VL regions may be in any order around the linker, for example, the scFv may have (i) a first VH chain, a linker and a VL chain or (ii) a first VL chain, a linker and a VH chain.
  • Antigen binding domains may comprise ‘CDRs’ or ‘complementarity determining regions’ which are predominantly responsible for target binding. On a typical antibody, multiple CDRs exist and may be selected or varied independently to achieve multiple points of diversity.
  • a ‘recognition sequence’ refers to the nucleic acid sequence encoding one or more antigen binding domains.
  • ‘Specific binding’ or ‘immunospecific binding’ or derivatives thereof when used in the context of antibodies, or antibody fragments, represents binding via domains encoded by immunoglobulin genes or fragments of immunoglobulin genes to one or more epitopes of a protein of interest, without preferentially binding other molecules in a sample containing a mixed population of molecules.
  • an antibody binds to a cognate antigen with a Kd of less than about 1x10 -8 M, as measured by a surface plasmon resonance assay or a cell binding assay.
  • Phrases such as ‘[antigen] -specific’ antibody e.g. CLL1 -specific antibody
  • isolated means a biological component (such as a nucleic acid, peptide or protein) has been substantially separated, produced apart from, or purified away from other biological components of the organism in which the component naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA, and proteins.
  • Nucleic acids, peptides and proteins that have been isolated thus include nucleic acids and proteins purified by standard purification methods. Isolated nucleic acids, peptides and proteins can be part of a composition and still be isolated if such composition is not part of the native environment of the nucleic acid, peptide, or protein.
  • the term also embraces nucleic acids, peptides and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
  • An ‘isolated’ antibody or antigen-binding fragment as used herein, is intended to refer to an antibody or antigen- binding fragment which is substantially free of other antibodies or antigen-binding fragments having different antigenic specificities (for instance, an isolated antibody that specifically binds to CLL1 is substantially free of antibodies that specifically bind antigens other than CLL1).
  • An isolated antibody that specifically binds to an epitope, isoform or variant of CLL1 may, however, have cross-reactivity to other related antigens, for instance from other species (such as CLL1 species homologs).
  • chimeric antigen receptor refers to transmembrane receptor that has been engineered to target or bind to a non-native substrate or antigen. In this way the intracellular signalling of the receptor may triggered by binding of a non-native substrate or antigen.
  • CAR refers to a chimeric receptor (i.e. a receptor composed of two or more parts from different sources) that has at least a binding moiety or recognition sequence with a specificity for a target such as an antigen or protein and an intracellular signaling domain that can invoke a signal in the cell in which the CAR is expressed (e.g. a CD247 (CD3 zeta) chain).
  • a ‘chimeric antigen receptor’ or ‘CAR’ is formed of at least three domains: an extracellular antigen binding domain (as defined elsewhere herein), a transmembrane domain and an intracellular domain.
  • a hinge domain between the antigen binding domain and the transmembrane domain is often used to improve recognition of the target.
  • a costimulatory domain may optionally be present in the intracellular domain to modulate the response.
  • the domains of the CAR must be ordered correctly.
  • CARs are often used on T-cells (to produce ‘CAR T-cells’) to effect recognition and elicit an appropriate intracellular response which both binds the T-cell to a target cell and triggers the innate immune response of the T-cell, typically causing lysis of the target cell.
  • Such cells have found use in therapy.
  • a ‘transmembrane domain’ or ‘TM domain’ as used herein is any membrane-spanning protein domain.
  • the TM domain in a CAR is derived from a known transmembrane protein sequence. However, it can also be artificially designed.
  • a ‘transmembrane sequence’ refers to the nucleic acid sequence encoding a transmembrane domain.
  • hinge domain refers to a peptide sequence that connects the antigen binding domain and transmembrane region of a CAR.
  • the hinge domain is located between the antigen binding fragment and the T cell plasma membrane (Moritz D, et al. Gene Ther. 1995;2(8):539-46)
  • the signaling domain typically comprises a domain derived from a receptor that signals by itself in immune cells, such as the T Cell Receptor (TCR) complex or the Fc receptor or DAP10/DAP12 receptors. Additionally, it may contain a costimulatory domain (i.e. a domain derived from a receptor that is required in addition to the TCR to obtain full activation of T cells).
  • the costimulatory domain can be from an activating costimulatory receptor or from an inhibitory costimulatory receptor.
  • An ‘intracellular domain sequence’ refers to the nucleic acid sequence encoding an intracellular signaling domain.
  • bi-specific refers to an antibody molecule (i.e. an antibody or antigen binding fragment conjugated to a synthetic molecule) that comprises one or more further antigen binding domains such that the antibody molecule can have specificity for more than one antigen.
  • bispecific T-cell engager or ‘BiTE’ is used synonymously to refer to a single polypeptide chain molecule having two antigen binding domains, one of which binds to a T-cell antigen (e.g., CD3) and the second of which binds to an antigen present on the surface of a target cell (e.g. CLL1), these two antigen binding domains separated by a linker, specifically a flexible linker, more specifically a flexible protein linker (WO 05/061547; Baeuerle, et al. (2008) Drugs of the Future 33:137-147; Bargou, et al. (2008) Science 321 :974-977).
  • a linker specifically a flexible linker, more specifically a flexible protein linker
  • BiTE antibodies have been constructed to various target antigens including CD19, EpCAM, Her2/neu, EGFR, CD66e (or CEA, CEACAM5), CD33, EphA2, and MCSP (or H MW- MAA) (Baeuerle, et al. (2009) Curr. Opin. Mol. Ther. 11 :22-30).
  • Key hallmarks of BiTE antibodies that, in their combination, distinguish them from other bispecific antibody constructs, include a high potency of redirected lysis with EC50 values ranging from 0.1 to 50 pmol/L (2-1 ,000 pg/mL) (Baeuerle, et al. (2009) supra); strict target cell-dependent activation of T cells (Brischwein, et al.
  • BiTE antibodies are typically produced as recombinant, glycosylated proteins secreted by higher eukaryotic cell lines.
  • the terms ‘bi-specific T- Cell engager’ and/or ‘BiTE’ as herein defined encompass, but are not limited to, the specific bi-specific T-Cell engager structure encompassed by the trademark ‘BITE®’ in the name of Amgen Research (Munich) GmbH.
  • DARTTM Dual Affinity Re-Targeting reagent diabody refers to an immunoglobulin molecule that comprises at least two polypeptide chains that associate (for example, through a covalent interaction) to form at least two antigen binding domains, which may recognize the same or different antigens.
  • Each of the polypeptide chains of a DARTTM diabody comprise an immunoglobulin light chain variable region and an immunoglobulin heavy chain variable region, but these regions do not interact to form an antigen binding domain. Rather, the immunoglobulin heavy chain variable region of one (e.g., the first) of the DARTTM diabody polypeptide chains interacts with the immunoglobulin light chain variable region of a different (e.g.
  • DARTTM diabodies may be monospecific, bispecific, trispecific, etc., thus being able to simultaneously bind one, two, three or more different antigens (which may be of the same or of different antigens).
  • DARTTM diabodies may additionally be monovalent, bivalent, trivalent, tetravalent, pentavalent, hexavelent, etc., thus being able to simultaneously bind one, two, three, four, five, six or more molecules.
  • DARTTM diabodies ⁇ i.e., degree of specificity and valency may be combined, for example to produce bispecific antibodies ⁇ i.e., capable of binding two antigens) that are tetravalent ⁇ i.e., capable of binding four sets of epitopes), etc.
  • DARTTM diabody molecules are disclosed in PCT applications published as WO 2006/1 13665, WO 2008/157379, and WO 2010/080538.
  • antibody-drug conjugate means a biopharmaceutical drug that comprises an antibody or antigen binding fragment, and a drug substance, typically a cytotoxic drug substance, connected via a linker, suitably a covalent, chemical linker.
  • high-throughput screening refers to any assay or screening methodology that allows for a higher rate of screening than would be achieved by traditional or previous state of the art techniques.
  • high-throughput screening enables automation to prepare, screen and/or evaluate libraries of test samples in parallel, reproducibly and rapidly.
  • High-throughput screening can also make use of combinatorial or pooled or mixed sample screening strategies, with associated deconvolution of hits.
  • the number of samples for test may be of any size larger than that typically used in prior art non-high-throughput methods.
  • the number of samples may be more than 10.
  • the number of samples may be more than 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 100, 200 or more.
  • the term ‘recognition sequence library’ refers to a set of one or more antigen binding domain sequences or recognition sequences that may be used for cloning into a CAR construct (wherein a CAR construct comprises all components required for a functioning CAR including one or more antigen binding domains, a hinge domain, a transmembrane domain and an intracellular domain) to prepare a CAR library.
  • An ‘scFv library’ is a recognition sequence library formed of scFv recognition sequences from antibodies.
  • the number of recognition sequences present in the recognition sequence library may be more than 1 or more than 2.
  • the number of hinge region sequences present in the hinge region sequence library may be more than 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 100, 200 or more.
  • CAR scaffold refers to the part of the CAR sequence that comprises the components, parts, modules, domains of the CAR excluding the antigen binding domain, that form the sequence of a CAR in a CAR library.
  • the CAR scaffold is formed of the sequences of the individual components, or groups thereof, and combined with the recognition sequence to form a sequence encoding a CAR in any suitable manner, for example, sequentially, convergently, with the recognition sequence being incorporated at any suitable point, i.e. the recognition sequence may be joined to a single unitary sequence of the CAR scaffold, or may be joined to a component part of the CAR scaffold initially and the full CAR sequence of the recognition sequence and scaffold completed subsequently.
  • the component parts of the CAR scaffold may derive from single sequences leading to one or a small number of CAR scaffolds for addition to a recognition sequence, or the component parts of the CAR scaffold may derive from libraries of one or more of the individual components leading to a CAR scaffold library comprising a plurality of sequences.
  • a CAR scaffold library may be formed by combination, suitably in a combinatorial, or directed, manner of the individual components or component libraries.
  • CAR library refers to a set of sequences encoding a functional CAR structure, including a recognition domain, such as an scFv, a hinge domain, a transmembrane domain and intracellular domain(s).
  • the number of CARs present in the CAR library may be more than 10.
  • the number of CARs present in the CAR library may be more than 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 100, 200 or more.
  • the term ‘CAR library’ may also be used interchangeably to refer to the plasmid or vector, or otherwise modified sequence of the sequence(s) encoding for a functional CAR structure.
  • CAR-cell library refers to a collection or set of cells expressing CARs on their surface.
  • Each cell in the CAR-cell library may express a single CAR (i.e. express only one CAR encoded by a single sequence), or a single cell in the CAR-cell library may express two or more CARs, each encoded by a different sequence.
  • each cell in the CAR-cell library expresses a single CAR or all CARs present in the library.
  • the number of CARs present in the CAR-cell library may be more than 10.
  • the number of CARs present in the CAR-cell library may be more than 11 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 100, 200 or more.
  • NGS next generation sequencing
  • nucleic acid molecule synonymously referred to as ‘nucleotides’ or ‘nucleic acids’ or ‘polynucleotide’ refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
  • Nucleic acid molecules include, without limitation single- and double-stranded DNA, DNA that is a mixture of single- and double- stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single- stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions.
  • polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • the term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons.
  • Modified’ bases include, for example, tritylated bases and unusual bases such as inosine.
  • a variety of modifications may be made to DNA and RNA; thus, ‘polynucleotide’ embraces chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells.
  • Polynucleotide’ also embraces relatively short nucleic acid chains, often referred to as oligonucleotides.
  • nucleic acid sequence may be inserted into a genome, including but not limited to plasmid or vector transfection, transposition and genome editing. All are contemplated for use in the present invention.
  • a ‘vector’ is a replicon, such as plasmid, phage, cosmid, or virus in which another nucleic acid segment may be operably inserted so as to bring about the replication or expression of the segment.
  • a ‘transposon’ or ‘transposable elements’ are DNA sequences that can change their position within a genome.
  • Gene editing refers to the ability to edit the genome to insert the required sequence, for example using CRISPR-Cas9 genome editing technology.
  • a ‘clone’ is a population of cells derived from a single cell or common ancestor by mitosis.
  • a ‘cell line’ is a clone of a primary cell that is capable of stable growth in vitro for many generations.
  • cells are transformed by transfecting the cells with DNA.
  • express and ‘produce’ are used synonymously herein and refer to the biosynthesis of a gene product. These terms encompass the transcription of a gene into RNA. These terms also encompass translation of RNA into one or more polypeptides, and further encompass all naturally occurring post-transcriptional and post-translational modifications.
  • subject refers to human and non-human animals, including all vertebrates, e.g., mammals and non-mammals, such as non-human primates, mice, rabbits, sheep, goats, dogs, cats, horses, cows, chickens, amphibians, and reptiles. In most particular embodiments of the described methods, the subject is a human.
  • treating refers to any success or indicia of success in the attenuation or amelioration of an injury, pathology or condition, including any objective or subjective parameter such as abatement, remission, diminishing of symptoms or making the condition more tolerable to the patient, slowing in the rate of degeneration or decline, making the final point of degeneration less debilitating, improving a subject's physical or mental well-being, or prolonging the length of survival.
  • the treatment may be assessed by objective or subjective parameters; including the results of a physical examination, neurological examination, or psychiatric evaluations.
  • CLL1 when referring to CLL1 , it will be appreciated that reference thereto encompasses fragments thereof, as well as related polypeptides, which include, but are not limited to, allelic variants, splice variants, derivative variants, substitution variants, deletion variants, and/or insertion variants including the addition of an N-terminal methionine, fusion polypeptides, and interspecies homologs.
  • a CLL1 polypeptide includes terminal residues, such as, but not limited to, leader sequence residues, targeting residues, amino terminal methionine residues, lysine residues, tag residues and/or fusion protein residues.
  • Amino acid sequence of an example isoform of CLL1 to which the antibodies of the present invention bind is provided as SEQ ID NO: 1 .
  • CLL1 SEQ ID NO: 1.
  • Splice variants and other isoforms of CLL1 are known and are encompassed by the present disclosure,
  • the amino acid sequence of CLL1 encompasses a polypeptide that has at least 50%, 60%, 70%, 80%, 90%, 95% or 99% complete sequence identity to CLL1 (for example SEQ ID NO: 1).
  • the CLL1 polynucleotide sequence can comprise a polynucleotide that has at least 50%, 60%, 70%, 80%, 90%, 95% or 99% complete sequence identity to CLL1 (for example, SEQ ID NO: 2).
  • Sequence identity can also be to a fragment or portion of the full length polynucleotide or polypeptide.
  • a sequence may have only 50% overall sequence identity with a sequence of the invention but in a particular region, domain or subunit could share 80%, 90%, or as much as 99% sequence identity with sequence of the invention.
  • homology to the nucleic acid sequence of SEQ ID NOs: 3 to 92 is not limited simply to sequence identity. Many nucleic acid sequences can demonstrate biologically significant homology to each other despite having apparently low sequence identity. In the present invention homologous nucleic acid sequences are considered to be those that will hybridise to each other under conditions of low stringency (Sambrook J. et al, Molecular Cloning: a Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, NY).
  • the present application is the first to show a systematic high-throughout screen output of a CAR-T cell library.
  • This allowed identification of multiple novel antibody or antigen binding fragments (e.g. scFvs) and their associated light chain and heavy chain CDRs, that bind to CLL1 , and outperform other known antibody or antigen binding fragments in several experimental models.
  • the invention provides an antibody or antigen binding fragments having specificity for CLL1 (Antibody Nos. 1 to 10), wherein the antibody or antigen binding fragments have an antigen binding domain comprising the amino acid sequences (SEQ ID NOS: 3 to 92) as shown in Table 1 below:
  • the antibodies, or antigen binding fragments, of the present invention were identified from a functional high-throughput screen of CAR-T cells, wherein the CAR-T cells express a unique chimeric antigen receptor (CARs), each CAR comprising an antibody or antigen binding fragment and/or scFv derived from a diverse scFv library.
  • CARs unique chimeric antigen receptor
  • the antibodies or antigen binding fragments as identified in Table 1 are those exhibiting surprisingly good functional response (i.e. were positive hits) in various assays against cells expressing CLL1 and are therefore deemed to be superior CAR-T cells over that known in the art and provide novel and effective antibodies or antigen binding fragments of CLL1.
  • the antibody or antigen binding fragment can be an isolated antibody having specificity for CLL1 (suitably human CLL1) and can be a full-length antibody or an antibody fragment.
  • the antibody can be polyclonal, monoclonal, recombinant, chimeric, or humanised.
  • the antibody can be of any isotype including without limitation IgA, IgD, IgE, IgG, or IgM.
  • the antibody can be any IgA such as lgA1 or lgA2, or any IgG such as IgG 1 , lgG2, lgG3, lgG4, or synthetic IgG.
  • the antibody can also be any antibody fragment having specificity for CLL1 , such as F(ab)2, Fv, scFv, F(ab' )2, F(ab), VL, VH, dsFv, Fv, scFv-Fc, (scFv)2, a diabody, and a bivalent antibody.
  • the antibody can be any modified or synthetic antibody, including, but not limited to, non-depleting IgG antibodies, T-bodies, or other Fe or Fab variants of antibodies.
  • the invention provides an antibody or antigen binding fragment with avidity for CLL1 of about 10 pM or less, 5 pM or less, 2 pM or less, 1 pM or less, 500 nM or less, 400 nM or less, 300 nM or less, or 200 nM or less, or 100 nM or less, or 75 nM or less, or 50 nM or less, or 25 nM or less, or 10 nM or less, or 5 nM or less.
  • Avidity can be measured using art-known techniques, such as ELISA or BIACORE.
  • the antibody or antigen binding fragment of the invention can be produced by any suitable technique, for example, using any suitable eukaryotic or non-eukaryotic expression system.
  • the antibody is produced using a mammalian expression system.
  • the antibody or antigen binding fragment of the invention can be produced using a suitable non-eukaryotic expression system such as a bacterial expression system.
  • Bacterial expression systems can be used to produce fragments such as a F(ab)2, Fv, scFv, F(ab' )2, F(ab), VL, VH, dsFv, Fv, scFv-Fc, (scFv)2, and diabodies.
  • the antibody or antigen binding fragment of the invention can be conjugated to a synthetic molecule. Conjugation of the antibody or antigen binding fragment of the invention to the synthetic molecule may be by any suitable method, for example recombinant engineering.
  • the synthetic molecule can be any molecule such as a drug targeting a tumour or tumour cells.
  • the synthetic molecule can also be a peptide/protein or an antibody or an antigen binding fragment such that the resultant molecule has specificity for more than one antigen, wherein the resulting fusion protein can be produced by conventional recombinant protein expression systems and methods.
  • CARs are engineered receptors, which confer specificity for a desired antigen onto an immune effector cell, such as a T-cell.
  • CARs may be expressed on the extracellular surface of a cell. Expression may be by any suitable means via retroviral vector expression.
  • the most common form of these molecules are fusions of an antibody or antigen binding fragment, such as an scFv, to the transmembrane and intracellular domains of a native T-cell activation receptor, such as CD3, typically CD3-zeta.
  • Such molecules result in the transmission of a signal, suitable an activation signal, in response to recognition by the scFv of its target.
  • ‘First-generation’ CARs typically have the intracellular domain from the CD3- zeta chain, which is the primary transmitter of signals from endogenous TCRs. ‘Second-generation’ CARs add intracellular signaling domains from various costimulatory protein receptors (e.g., CD28, CD137, 41 BB, ICOS) to the intracellular portion of the CAR to provide additional signals to the T cell (see Figure 1). Preclinical studies have indicated that the second generation of CAR designs improves the antitumor activity of T cells (Maher, et al. (2002) Nat. Biotechnol. 20:70-75; Kowolik, et al. (2006) Cancer Res. 66: 10995-11004).
  • costimulatory protein receptors e.g., CD28, CD137, 41 BB, ICOS
  • a CAR comprises an anti-CLL1 antibody or antigen binding fragment, such as an scFv fragment, as defined in SEQ ID NOS 3 to 12.
  • CARs of this invention can be prepared using standard recombinant protein techniques using sequences of CD3, e.g. CD247 (CD3-zeta) and optionally other costimulatory molecules known in the art.
  • CD247 (CD3-zeta) sequence is available under GENBANK accession number NP_932170
  • the human CD28 sequence is available under GENBANK accession number NP 006130
  • the human CD8A sequence is available under GENBANK accession number AAH25715
  • the human CD137 sequence is available under GENBANK accession number NP_001552.
  • the CAR of the present invention are represented by the SEQ ID NOS: 93 to 112. These CARs include, but not necessarily limited to, either:
  • the CARs of the present invention have sequences defined in SEQ ID NOs: 93 to 102.
  • the antibody or antigen binding fragment can be conjugated to a synthetic molecule that can confer specificity for one or more antigens in addition to CLL1 .
  • the antibody of the invention can be engineered (e.g. as a bivalent diabody or a conjugated Fab dimer or trimer) to have specificity for CLL1 and another tumour antigen, e.g., an antigen associated with a disease or disorder as disclosed herein.
  • the antibody can be engineered to have specificity for CLL1 and an antigen that promotes activation or targeting of other cells, such as cytotoxic effector cells or T cells.
  • the invention also includes bispecific, tri-specific and multi-specific molecules such as BiTEs (bi-specific T-cell engagers) and DARTTMs (dual affinity retargeting reagents).
  • a bi-specific T-cell engager refers to a single polypeptide chain molecule having two antigen binding domains, one of which binds to a T-cell antigen (e.g., CD3) and the second of which binds to an antigen present on the surface of a target cell (WO 05/061547; Baeuerle, et al. (2008) Drugs of the Future 33:137-147; Bargou, et al. (2008) Science 321 :974-977).
  • a T-cell antigen e.g., CD3
  • BiTE antibodies have been constructed to various target antigens including CD19, EpCAM, Her2/neu, EGFR, CD66e (or CEA, CEACAM5), CD33, EphA2, and MCSP (or H MW- MAA) (Baeuerle, et al. (2009) Curr. Opin. Mol. Ther. 11 :22-30).
  • an anti-CLL1 antibody or antigen binding fragment e.g. a scFv
  • BiTE bi-specific T-cell engager
  • the bi-specific T-cell engager (BiTE) of this invention is composed of an anti-CLL1 antibody or antigen binding fragment and an anti-CD3 antibody fragment fused together by a linker, e.g., a flexible protein linker. See, for example, US 5,929,212.
  • a linker e.g., a flexible protein linker.
  • the term ‘BiTE’ as used herein may encompass but is not limited to the bispecific T-cell engager named BiTE® available from Amgen®.
  • the antibody fragment that specifically binds CD3 comprises:
  • the invention provides the antibody or antigen binding fragment of the invention coupled to a synthetic molecule as defined herein to provide a DARTTM.
  • DARTTM refers to an immunoglobulin molecule that includes at least two polypeptide chains that associate (especially through a covalent interaction) to form at least two antigen binding sites, which may recognize the same or different antigens.
  • Each of the polypeptide chains of a DARTTM include an immunoglobulin light chain variable region and an immunoglobulin heavy chain variable region, but these regions do not interact to form an epitope binding site.
  • the immunoglobulin heavy chain variable region of one (e.g., the first) of the DARTTM polypeptide chains interacts with the immunoglobulin light chain variable region of a different (e.g. the second) DARTTM polypeptide chain to form an epitope binding site.
  • the immunoglobulin light chain variable region of one (e.g. the first) of the DARTTM polypeptide chains interacts with the immunoglobulin heavy chain variable region of a different (e.g., the second) DARTTM polypeptide chain to form an epitope binding site.
  • DARTTMs may be monospecific, bi-specific, tri- specific, etc., thus being able to simultaneously bind one, two, three or more different antigens (which may be of the same or of different antigens).
  • DARTTMs may additionally be monovalent, bivalent, trivalent, tetravalent, pentavalent, hexavelent, etc., thus being able to simultaneously bind one, two, three, four, five, six or more molecules.
  • These two attributes of DARTTMs i.e., degree of specificity and valency may be combined, for example to produce bispecific antibodies (i.e., capable of binding two epitopes) that are tetravalent (i.e. capable of binding four sets of antigens/epitopes), etc.
  • DARTTM molecules The construction of DARTTM molecules is disclosed in WO 2006/113665, WO 2008/157379, and WO 2010/080538. Accordingly, in another embodiment of this invention, an anti-CLL1 antibody or antigen binding fragment is included in a DARTTM.
  • the antibody or antigen binding fragment of the present invention is conjugated, linked or joined to other synthetic molecules including therapeutic agents (or ‘payloads’) such as cytotoxic, cytostatic, or anti-angiogenic agents and radioisotopes, labels or nanoparticles.
  • therapeutic agents or ‘payloads’
  • Such molecules are terms antibody-drug conjugates or ADCs.
  • ADCs include: Gemtuzumab ozogamicin, Brentuximab vedotin, Trastuzumab emtansine, Trastuzumab emtansine and Trastuzumab emtansine.
  • the invention provides a method of inhibiting cells that express CLL1 (CLL1 cells) by contacting the cells with an antibody, antigen binding fragment or antibody conjugated to a synthetic molecule (e.g. a bispecific T-cell engager such as a BiTE, DARTTM, or ADC) of the invention.
  • a synthetic molecule e.g. a bispecific T-cell engager such as a BiTE, DARTTM, or ADC
  • the method can be used to inhibit CLL1 cells in vitro or in a subject (i.e., in vivo).
  • the contacted CLL1 cells can be in, for example, a cell culture or animal model of a disorder associated with aberrant expression or levels of CLL1 .
  • the method is useful, for example, to measure and/or rank (relative to another antibody) the antibody's inhibitory activity for a CLL1 cell type.
  • Inhibiting CLL1 cells can include blocking or reducing the activity or growth of CLL1 cells. Inhibiting can also include the killing of CLL1 cells. Cytotoxicity of an antibody, antibody fragment or antibody conjugated to a synthetic molecule such as a BiTE, DARTTM, or ADC of the invention can be assessed using any conventional assay including, e.g. a lactate dehydrogenase cytotoxicity assay such as the CYTOTOX 96 non-radioactive cytotoxicity assay commercially available from PROMEGA. Similarly, the invention provides an antibody, antigen binding fragment or antibody conjugated to a synthetic molecule (e.g. a bispecific T-cell engager such as a BiTE, DARTTM, or ADC) of the invention for use in inhibiting and killing cells expressing CLL1.
  • a synthetic molecule e.g. a bispecific T-cell engager such as a BiTE, DARTTM, or ADC
  • the invention also provides a method of treating a subject that has, is suspected to have, or is at risk for a disorder associated with aberrant levels of CLL1 or CLL1 cells.
  • the term ‘aberrant’ is intended to include increased or decreased CLL1 expression on a cell as compared to expression of CLL1 in normal or healthy cells, or an increase in cells expressing CLL1 .
  • the method of treatment includes administering a therapeutically effective amount of an isolated antibody, antibody fragment or fusion protein of the invention to the subject.
  • the antibody can be any anti-CLL1 antibody, antigen binding fragment (e.g.
  • a synthetic molecule e.g., a bispecific T-cell engager such as a BiTE, DARTTM, or ADC
  • the invention provides an antibody, antigen binding fragment or antibody conjugated to a synthetic molecule (e.g., a bispecific T-cell engager such as a BiTE, DARTTM, or ADC) of the invention for use in medicine, and for the treatment of disease and disorders associated with aberrant or elevated CLL1 expression.
  • disorders that can be treated include, for example, cancers, such as AML, chronic myeloid (myelogenous) leukemia (CML), chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia, atypical chronic myeloid leukemia, acute promyelocytic leukemia (APL), acute monocytic leukemia, acute monoblastic leukemia, acute erythroid leukemia, acute megakaryoblastic leukemia, myelodysplastic syndrome (MDS), myeloproliferative disorder, myeloid neoplasm, myeloid sarcoma), Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN); autoimmune diseases such as rheumatoid arthritis, psoriasis, allergies, asthma, Crohn’s disease, IBD, IBS, fibromyalga, mastocytosis, and Celiac disease, melanomas, and sarcom
  • the invention also provides a method of treating a subject that has, is suspected to have, or is at risk for a disorder associated with elevated levels of CLL1 on a cell, or by elevated levels of CLL1 -cells by adoptive transfer of the recombinant host cells, e.g. T-cells described herein, which express an antibody or antigen binding fragment conjugated to a synthetic molecule of the invention as a CAR that selectively binds CLL1 .
  • the invention provides recombinant cells expressing an antibody or antigen binding fragment conjugated to a synthetic molecule (e.g. CAR) of the invention for use in medicine.
  • Recombinant technology can be used to introduce CAR-encoding genetic material into any suitable T- cells, e.g. effector memory T-cells from the subject to be treated.
  • the recombinant T-cells are transferred, typically by infusion, to the patient.
  • the transferred T-cells of the invention can then mount an immune response against CLL1 expressing cells (CLL1 -cells) in the patient.
  • the adoptive transfer method can be used, for example, to treat subjects that have or are suspected to have cancers, such as AML, chronic myeloid (myelogenous) leukemia (CML), chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia, atypical chronic myeloid leukemia, acute promyelocytic leukemia (APL), acute monocytic leukemia, acute monoblastic leukemia, acute erythroid leukemia, acute megakaryoblastic leukemia, myelodysplastic syndrome (MDS), myeloproliferative disorder, myeloid neoplasm, myeloid sarcoma), Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN); autoimmune diseases such as rheumatoid arthritis, psoriasis, allergies, asthma, Crohn’s disease, IBD, IBS, fibromyalga, mastocytosis, and Celiac
  • the invention also provides a pharmaceutical composition containing an antibody or antigen binding fragment or antibody conjugated to a synthetic molecule (e.g., a CAR, a bispecific T-cell engager such as a BiTE, DARTTM, or ADC) as described herein and a pharmaceutically acceptable carrier.
  • a synthetic molecule e.g., a CAR, a bispecific T-cell engager such as a BiTE, DARTTM, or ADC
  • Pharmaceutical compositions can be prepared from any of the antibody, antigen binding fragment (e.g.
  • a synthetic molecule e.g., a CAR, a bispecific T-cell engager such as a BiTE, DARTTM, or ADC
  • composition of the invention can include a carrier for the antibody or antigen binding fragment, or antibody conjugated to a synthetic molecule, desirably a pharmaceutically acceptable carrier.
  • the pharmaceutically acceptable carrier can be any suitable pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier means one or more compatible solid or liquid fillers, diluents, other excipients, or encapsulating substances, which are suitable for administration into a human or veterinary patient (e.g. a physiologically acceptable carrier or a pharmacologically acceptable carrier).
  • carrier denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application.
  • the pharmaceutically acceptable carrier can be co-mingled with one or more of the active components, e.g., a hybrid molecule, and with each other, when more than one pharmaceutically acceptable carrier is present in the composition in a manner so as not to substantially impair the desired pharmaceutical efficacy.
  • ‘Pharmaceutically acceptable’ materials typically are capable of administration to a patient without the production of significant undesirable physiological effects such as nausea, dizziness, rash, or gastric upset.
  • the pharmaceutical composition can contain suitable buffering agents, including, for example, acetic acid in a salt, citric acid in a salt, boric acid in a salt, and phosphoric acid in a salt.
  • suitable buffering agents including, for example, acetic acid in a salt, citric acid in a salt, boric acid in a salt, and phosphoric acid in a salt.
  • suitable preservatives such as benzalkonium chloride, chlorobutanol, parabens, and thimerosal.
  • the pharmaceutical composition can be presented in unit dosage form and can be prepared by any suitable method, many of which are well-known in the pharmaceutical arts. Such methods include the step of bringing the antibody of the invention into association with a carrier that constitutes one or more accessory ingredients. In general, the composition is prepared by uniformly and intimately bringing the active agent into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product.
  • the high-throughout screening method allows resources to be focussed primarily on the diversity of the CAR library and identification of the CARs that are able to demonstrate promising activity in a functional assay relevant to a clinical context.
  • a synthetic human scFv phage library was panned against recombinant human CLL1 protein (R&D BiosystemsTM). To this end, the library was grown to log phase, and then rescued with M13KO7 helper phage (Antibody Design LabTM, PH010L) before being amplified overnight at 32°C in a shaker. The phage library was subsequently precipitated with PEG/NaCI, re-suspended in PBS and stored at -80°C. Protein G coated magnetic beads were coated with hCLL1-Fc or Fc recombinant protein in PBS and subsequently blocked in PBS+ BSA. Phage particles were incubated for 30 minutes with negative magnetic particles.
  • scFv sequences were PCR amplified from the eluted phages or the isolated plasmids using Q5 DNA polymerase (NEB) and scFv-specific forward and reverse primers. Resulting amplicon was cleaned by PCR clean-up and 1 pg PCR product were digested with restriction enzymes for 2h at 37°C.
  • a CAR scaffold library consisting of pooled plasmids containing different CAR scaffolds with variation in hinge domain, transmembrane domain and intracellular signalling domains, was digested using Esp3l .
  • the CAR scaffold library and the scFv amplicons were cleaned by PCR clean-up columns and ligated using T4 DNA ligase (Thermo FisherTM) for 12h over-night.
  • the resulting CAR-library was electroporated into electrocompetent bacteria and grown overnight at 30°C, followed by plasmid maxi-prep isolation.
  • the CAR sequences from the resulting plasmid library were briefly PCR amplified and sequenced on an Oxford Nanopore TechnologyTM MinlONTM, using the amplicon sequencing kit.
  • CAR- T cell library was expanded for six more days after transduction and assessed for CLLI binding.
  • CLL1- CAR-T cell library cells were stained with CLL1-Fc fusion protein or a negative control protein (recombinant Fc, R&D systems).
  • cells were stained with PE-conjugated anti-Fc and APC-conjugated anti-CD34 antibody to detect transduced cells. The expression of CARs on the cell surface was assessed.
  • a CAR-T cell library was produced by activation of Peripheral Blood Mononuclear Cells (PBMCs) with TransActTM (MiltenyiTM) in the presence of human IL-2 (100 lll/ml) and transduced at day two with the lentiviral CLL1 CAR library. The next day, cells were washed and further expanded until day 8 of the process. Transduction was assessed by flow cytometry and transduced cells were enriched through CD34 microbeads (MiltenyiTM). Purity was assessed by flow cytometry. The CAR-T-cell library was cocultured with CLL1-positive cells (HL60) or no cells. After 6h activation, CAR-T cells were prepared for single cell sequencing analysis.
  • PBMCs Peripheral Blood Mononuclear Cells
  • TransActTM TransActTM
  • human IL-2 100 lll/ml
  • CAR-T cell libraries from different donors were prepared for 10x genomics single cell gene expression analysis (1 Ox genomics 3’ sequencing kit V3 or Single Cell 5’ Kit v2) and sequenced on a NovaSeqTM 6000 (IlluminaTM).
  • Cell rangerTM software (10x GenomicsTM) was used for downstream processing and alignment of reads.
  • CAR sequences were amplified using long PCR with a forward read 1 primer and CAR-specific reverse primer. After 10 cycles of PCR, the product was cleaned using SPRI bead clean-up and a second, nested PCR was performed. PCR products were barcoded and an Oxford Nanopore library was prepared using the Oxford Nanopore ligation sequencing kit. Libraries were then sequenced on a MinlON® flow cell and CAR sequences and 10x cell barcodes were determined.
  • Example 5 Example 5:
  • CAR constructs were selected based on best activation propensity from the single cell gene expression analysis, and CAR sequences were synthetized by Integrated DNA technologies (IDT).
  • CAR sequences were cloned into a lentiviral expression construct, encoding a 2A peptide and a truncated CD34 reporter.
  • Lentiviral vectors were produced with the individual CAR constructs and titrated on Jurkat cell line.
  • PBCMs were activated on day 0 with TransActTM (MiltenyiTM) and transduced with equal MOI (Multiplicity of Infection) of lentiviral vectortwo days after activation, in the presence of recombinant human IL2 (MiltenyiTM).
  • TransActTM TransActTM
  • MOI Multiplicity of Infection
  • the labels on the x axis indicate different CAR constructs, as indicated below.
  • CAR 11 and CAR 12 comprise respective antibody/antigen-binding fragments sequences defined as Antibody No. 11 and Antibody No. 12 (Table 2).
  • Table 2 Comparative example antibodies from US2020/0115457A1 and US2013/0295118A1 respectively
  • each of the CARs corresponding to CAR SEQ ID NOs 93 to 102, comprising the scFv SEQ ID NOs 3 to 12 (and the associated CDRs as detailed in Table 1) showed enhanced activity against CLL1 + cells than the prior art CARs.
  • This demonstrates the surprisingly beneficial effect of the antibody/antigen binding fragments of the present invention, and the utility of such antibody/antigen binding fragments in CARs, other bi-specific, tri-specific and multi-specific molecules (such as BiTEs and DARTTMs), and ADCs.
  • Example 6 Example 6:
  • CLL1-CAR T-cells were evaluated for cellular toxicity and activity against cancer cells expressing CLL1 , or controls lacking expression of CLL1.
  • CAR-T cell activation was assessed via CD69 upregulation on CD3+, CD34+ CAR-T cells as an indicator for T-cell activation ( Figure 4).
  • CAR-T potency was assessed by collecting supernatant of CAR-T cells stimulated with HL60 cells or non-stimulated controls. After 24h of co-culture supernatant was collected and assessed for cytokine production via IFNg ELISA (Figure 6). Left bar on each CAR-T number indicate IFNg values of CAR-T cells stimulated with HL60 cells. Right bar indicate non-stimulated controls.
  • each of the CARs corresponding to CAR SEQ ID NOs 93 to 102, comprising the scFvs SEQ ID NOs 3 to 12 (and the associated CDRs as detailed in Table 1) showed enhanced activity via CD69 upregulation against CLL1 + cells than the prior art CARs.
  • This demonstrates the surprisingly beneficial effect of the antibody/antigen binding fragments of the present invention, and the utility of such antibody/antigen binding fragments in CARs, other bi-specific, tri-specific and multispecific molecules (such as BiTEs and DARTTMs), and ADCs.

Abstract

La présente invention concerne une nouvelle classe de molécules de liaison à la molécule 1 analogue à la lectine de type C (CLL1), en particulier des anticorps anti-CLL1 et des fragments de liaison à l'antigène. La présente invention concerne également les molécules synthétiques comprenant les anticorps anti-CLL1 et des fragments de liaison à l'antigène, tels que des récepteurs antigéniques chimériques (CAR), des anticorps BiTE ("bispecific T-Cell engagers") et des conjugués anticorps-médicament (ADC), et l'utilisation des anticorps anti-CLL1 et des fragments de liaison à l'antigène, ou des molécules synthétiques les comprenant, dans le traitement d'une maladie.
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