WO2017196847A1 - Variable new antigen receptor (vnar) antibodies and antibody conjugates targeting tumor and viral antigens - Google Patents

Variable new antigen receptor (vnar) antibodies and antibody conjugates targeting tumor and viral antigens Download PDF

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WO2017196847A1
WO2017196847A1 PCT/US2017/031758 US2017031758W WO2017196847A1 WO 2017196847 A1 WO2017196847 A1 WO 2017196847A1 US 2017031758 W US2017031758 W US 2017031758W WO 2017196847 A1 WO2017196847 A1 WO 2017196847A1
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seq
antibody
monoclonal antibody
domain
domain monoclonal
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PCT/US2017/031758
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French (fr)
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Mitchell Ho
Mingqian FENG
Martin F. FLAJNIK
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The United States Of America, As Represented By The Secretary, Department Of Health And Human Services
University Of Maryland, Baltimore
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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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1002—Coronaviridae
    • 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
    • C07K16/2896—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against molecules with a "CD"-designation, not provided for elsewhere
    • 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
    • C07K16/32—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products of oncogenes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/569—Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • VNAR VARIABLE NEW ANTIGEN RECEPTOR
  • This disclosure concerns the construction of a phage display variable new antigen receptor (VNAR) antibody library and the identification of antibody clones from the VNAR library that bind tumor and viral antigens.
  • VNAR variable new antigen receptor
  • IgG has become essential to many modern day biotechnologies and therapeutics. For example, flow cytometry and enzyme-linked immunosorbent assay (ELISA) would not be possible without the advancement of antibody production techniques.
  • the use of IgG in new applications can be limited by the size of the immunoglobulin, in particular the size of the binding domain.
  • IgG is best described as a heterodimeric homodimer, which means it consists of two copies of both a heavy chain and a light chain.
  • the antibody has two identical antigen binding regions (Fab) which are determined by the interaction of the heavy chain variable domain (VH) with one light chain variable domain (VL).
  • VNAR and VHH domain antibodies range from 12- 15 kD in size, which is about half the size of the smallest scFv binding unit.
  • IgM immunoglobulin new antigen receptor
  • IgW immunoglobulin new antigen receptor
  • IgNAR antibodies are homodimeric proteins containing only heavy chains with an antigen binding region at the end of the each heavy chain. This class of antibody serves as the major component of the fish' s humoral immune response (Feige et al. , Proc Natl Acad Sci USA
  • VNAR domains share similar, desirable features to the camelid VHH domains, which are well characterized and currently being used in clinical trials. Even though less is known about the VNAR antibodies, they have the potential to be used as biological therapeutics based on several factors, including (i) their small size and potential to penetrate dense tissues inaccessible to IgG (Irving et al. , J Immunol Methods 248:31-45, 2001); (ii) their propensity to bind in protein clefts and hidden enzyme active sites (Stanfield et al. , Science 305: 1770-1773, 2004); (iii) their solubility and robustness in harsh conditions (Simmons et al. , / Immunol Methods 315: 171-184, 2006); and their ability for high-affinity (up to sub-nanomolar) binding.
  • Single-domain monoclonal antibodies selected from a naive shark VNAR antibody library that specifically bind a tumor or viral antigen. Also disclosed is an efficient method of producing a highly diverse VNAR antibody library using overlap extension PCR.
  • single-domain monoclonal antibodies that bind, such as specifically bind, glypican-3 (GPC3), programmed cell death 1 (PD1), HER2, Middle East respiratory syndrome (MERS) virus spike protein or severe respiratory syndrome (SARS) virus spike protein.
  • antibody conjugates that include the single-domain monoclonal antibodies disclosed herein, including antibody-drug conjugates (ADCs), chimeric antigen receptors (CARs), immunoconjugates (such as antibody-toxin conjugates), multi-specific (such as bispecific or trispecific) antibodies, and antibody-nanoparticle conjugates.
  • ADCs antibody-drug conjugates
  • CARs chimeric antigen receptors
  • immunoconjugates such as antibody-toxin conjugates
  • multi-specific antibodies such as bispecific or trispecific
  • antibody-nanoparticle conjugates include the disclosed single-domain monoclonal antibodies and a heterologous protein.
  • compositions that include the antibodies, antibody conjugates and fusion proteins disclosed herein are also provided by the present disclosure. Also provided are nucleic acid molecules and vectors encoding the disclosed single-domain monoclonal antibodies and conjugates thereof.
  • the method includes providing complementary DNA (cDNA) generated from RNA isolated from lymphocytes of one or more cartilaginous fish; providing a vector backbone comprising a vector junction sequence; amplifying VNAR nucleic acid from the cDNA by polymerase chain reaction (PCR) using a VNAR-specific forward primer and at least one reverse primer comprising VNAR- specific sequence and the vector junction sequence to generate VNAR nucleic acid sequences comprising the vector junction sequence; assembling the VNAR nucleic acid sequences comprising the vector junction sequence and the vector backbone comprising the vector junction sequence by overlap extension PCR using the VNAR-specific forward primer and a vector backbone-specific reverse primer, thereby producing linear VNAR vectors; and maintaining the linear VNAR vectors under conditions to permit self-ligation.
  • cDNA complementary DNA
  • FIG. 1 is a schematic outline for generating the shark VNAR library disclosed herein.
  • FIGS. 2A-2C provide a sequence alignment and characterization of randomly picked clones from the VNAR library.
  • FIG. 2A Sequence alignment of HEL-5A7 (SEQ ID NO: 11) and 25 randomly sequenced clones (SEQ ID NOs: 12-36).
  • FIG. 2B Statistical analysis of the types of clones.
  • FIG. 2C CDR3 length distribution of the clones.
  • FIG. 3 is a series of graphs showing identification of the binders by phage ELISA.
  • Monoclonal phage ELISA was carried out to identify the binders to GPC3, Her2, PDl, Middle East respiratory syndrome (MERS) virus spike (S) protein, severe acute respiratory syndrome (SARS) virus S protein, PE38 and human Fc (hFc) (or rabbit Fc - rFc).
  • MERS Middle East respiratory syndrome
  • SARS severe acute respiratory syndrome
  • PE38 human Fc (hFc) (or rabbit Fc - rFc).
  • FIGS. 4A-4C provide a sequence alignment of the identified binders and analysis of the binders.
  • FIG. 4A Sequence alignment of the identified binders (SEQ ID NOs: 1-10 and 37-47).
  • FIG. 4B VNAR type analysis of the binders.
  • FIG. 4C CDR3 length of the binders.
  • FIGS. 5A-5D are flow cytometry plots and graphs showing characterization of the GPC3 binder.
  • FIG. 5A Phage flow cytometry showing the GPC3-F1 clone binding GPC3-positive Gl cells. PD1-A1, which binds PDl antigen, was used as the phage control.
  • FIG. 5B Purified GPC3-Fl-hFc fusion protein binds GPC3-positive HepG2 and Gl cells.
  • FIG. 5C The cell binding affinity of GPC3-Fl-hFc (K D 124 nM) was measured by flow cytometry on Gl cells.
  • FIG. 5D Epitope mapping of GPC3-F1 showing its epitope is not competitive with YP7 (generated by immunizing mice using the same GPC3 peptide 511-560).
  • FIG. 6A shows the results of a phage ELISA demonstrating binding of the PE clone to PE38, but not mPE24.
  • FIG. 6B shows structural models of PE38 and PE24. Seven B-cell epitopes (indicated by balls) were mutated.
  • FIG. 7 is a graph showing binding specificity of the hFc binders.
  • FIG. 8 shows PCR amplification of VN AR fragments using primer pair IgNAR-F/IgNAR-Rl
  • FIGS. 9A-9J provide sequence alignments of each VN AR antibody with the four most closely related sequences identified by Basic Local Alignment Search Tool (BLAST). (FIG. 9A)
  • GPC3-F1 (SEQ ID NOs: 1 and 48-51).
  • FIG. 9B PD1-A1 (SEQ ID NOs: 2 and 52-55).
  • FIG. 9C PD1-A1 (SEQ ID NOs: 2 and 52-55).
  • HER2-A6 SEQ ID NOs: 3 and 56-59.
  • HER2-B7 SEQ ID NOs: 4 and 60-63.
  • MERS-A3 SEQ ID NOs: 5 and 64-67.
  • FIG. 9F MERS-A7 (SEQ ID NOs: 6 and 68-71).
  • FIG. 9G MERS-A8 (SEQ ID NOs: 7 and 72-75).
  • FIG. 9H MERS-B4 (SEQ ID NOs: 8 and 76-
  • FIG. 91 MERS-B5 (SEQ ID NOs: 9 and 80-83).
  • FIG. 9J SARS-01 (SEQ ID NOs: 10 and
  • nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand.
  • sequence Listing is submitted as an ASCII text file, created on May 8, 2017, 94.4 KB, which is incorporated by reference herein. In the accompanying sequence listing:
  • SEQ ID NO: 1 is the amino acid sequence of VNAR clone GPC3-F1.
  • SEQ ID NO: 2 is the amino acid sequence of VNAR clone PD1-A1.
  • SEQ ID NO: 3 is the amino acid sequence of VNAR clone HER2-A6.
  • SEQ ID NO: 4 is the amino acid sequence of VNAR clone HER2-B7.
  • SEQ ID NO: 5 is the amino acid sequence of VNAR clone MERS-A3.
  • SEQ ID NO: 6 is the amino acid sequence of VN AR clone MERS-A7.
  • SEQ ID NO: 7 is the amino acid sequence of VNAR clone MERS-A8.
  • SEQ ID NO: 8 is the amino acid sequence of VN AR clone MERS-B4.
  • SEQ ID NO: 9 is the amino acid sequence of VNAR clone MERS-B5.
  • SEQ ID NO: 10 is the amino acid sequence of VNAR clone SARS-01.
  • SEQ ID NO: 11 is the amino acid sequence of VNAR antibody HEL-5A7.
  • SEQ ID NOs: 12-36 are the amino acid sequences of randomly sequenced clones from the shark VNAR library (shown in FIG. 2).
  • SEQ ID NOs: 37-47 are the amino acid sequences of VNAR clones that bind hFc or hFc/rFc (shown in FIG. 4).
  • SEQ ID NOs: 48-87 are the amino acid sequences of VNAR antibodies identified during BLAST searches (shown in FIGS. 9A-9J).
  • SEQ ID NOs: 88-92 are primer sequences.
  • SEQ ID NO: 93 is a codon-optimized nucleotide sequence encoding VNAR clone GPC3-F1.
  • SEQ ID NO: 94 is a codon-optimized nucleotide sequence encoding VNAR mutant Fl-
  • SEQ ID NO: 95 is the amino acid sequence of VNAR mutant F1-Y29C.
  • SEQ ID NO: 96 is a codon-optimized nucleotide sequence encoding VNAR mutant Fl-
  • SEQ ID NO: 97 is the amino acid sequence of VNAR mutant F1-C96S.
  • Antibody A polypeptide ligand comprising at least one variable region that recognizes and binds (such as specifically recognizes and specifically binds) an epitope of an antigen.
  • Mammalian immunoglobulin molecules are composed of a heavy (H) chain and a light (L) chain, each of which has a variable region, termed the variable heavy (VH) region and the variable light (VL) region, respectively. Together, the VH region and the VL region are responsible for binding the antigen recognized by the antibody.
  • VH variable heavy
  • VL variable light
  • Antibody isotypes not found in mammals include IgX, IgY, IgW and IgNAR.
  • IgY is the primary antibody produced by birds and reptiles, and has some functionally similar to mammalian IgG and IgE.
  • IgW and IgNAR antibodies are produced by cartilaginous fish, while IgX antibodies are found in amphibians.
  • Antibody variable regions contain "framework" regions and hypervariable regions, known as “complementarity determining regions” or "CDRs.”
  • the CDRs are primarily responsible for binding to an epitope of an antigen.
  • the framework regions of an antibody serve to position and align the CDRs in three-dimensional space.
  • the amino acid sequence boundaries of a given CDR can be readily determined using any of a number of well-known numbering schemes, including those described by Kabat et al. ⁇ Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991; the "Kabat” numbering scheme), Chothia et al. (see
  • ImMunoGeneTics database (see, Lefranc, Nucleic Acids Res 29:207-9, 2001; the "IMGT” numbering scheme).
  • the Kabat and IMGT databases are maintained online.
  • single-domain antibody refers to an antibody having a single domain (a variable domain) that is capable of specifically binding an antigen, or an epitope of an antigen, in the absence of an additional antibody domain.
  • Single-domain antibodies include, for example, VNAR antibodies, camelid VHH antibodies, VH domain antibodies and VL domain antibodies.
  • VNAR antibodies are produced by cartilaginous fish, such as nurse sharks, wobbegong sharks, spiny dogfish and bamboo sharks.
  • Camelid VHH antibodies are produced by several species including camel, llama, alpaca, dromedary, and guanaco, which produce heavy chain antibodies that are naturally devoid of light chains.
  • a “monoclonal antibody” is an antibody produced by a single clone of lymphocytes or by a cell into which the coding sequence of a single antibody has been transfected. Monoclonal antibodies are produced by methods known to those of skill in the art. Monoclonal antibodies include humanized monoclonal antibodies.
  • a “chimeric antibody” has framework residues from one species, such as human, and CDRs (which generally confer antigen binding) from another species, such as a VNAR that specifically binds a tumor or viral antigen.
  • a “humanized” antibody is an immunoglobulin including a human framework region and one or more CDRs from a non-human (for example a shark, mouse, rabbit, rat, or synthetic) immunoglobulin.
  • the non-human immunoglobulin providing the CDRs is termed a "donor,” and the human immunoglobulin providing the framework is termed an "acceptor.”
  • all CDRs are from the donor immunoglobulin in a humanized immunoglobulin. Constant regions need not be present, but if they are, they must be substantially identical to human immunoglobulin constant regions, i.e. , at least about 85-90%, such as about 95% or more identical.
  • a humanized immunoglobulin all parts of a humanized immunoglobulin, except possibly the CDRs, are substantially identical to corresponding parts of natural human immunoglobulin sequences.
  • a humanized antibody binds to the same antigen as the donor antibody that provides the CDRs.
  • Humanized or other monoclonal antibodies can have additional conservative amino acid substitutions which have substantially no effect on antigen binding or other immunoglobulin functions.
  • Methods of humanizing shark VNAR antibodies has been previously described (Kovalenko et al. , / Biol Chem 288(24): 17408-17419, 2013).
  • ADC Antibody-drug conjugate
  • ADC A molecule that includes an antibody (or antigen- binding fragment of an antibody) conjugated to a drug, such as a cytotoxic agent.
  • ADCs can be used to specifically target a drug to cancer cells through specific binding of the antibody to a tumor antigen expressed on the cell surface.
  • exemplary drugs for use with ADCs include anti- microtubule agents (such as maytansinoids, auristatin E and auristatin F) and interstrand crosslinking agents (e.g. , pyrrolobenzodiazepines; PDBs).
  • Anti-microtubule agent A type of drug that blocks cell growth by stopping mitosis.
  • Anti-microtubule agents also referred to as “anti-mitotic agents,” are used to treat cancer.
  • Binding affinity Affinity of an antibody for an antigen.
  • affinity is calculated by a modification of the Scatchard method described by Frankel et al. (Mol. Immunol. , 16: 101-106, 1979).
  • binding affinity is measured by an antigen/antibody dissociation rate.
  • binding affinity is measured by a competition radioimmunoassay.
  • binding affinity is measured by ELISA.
  • An antibody that "specifically binds" an antigen is an antibody that binds the antigen with high affinity and does not significantly bind other unrelated antigens.
  • Bispecific antibody A recombinant protein that includes antigen-binding fragments of two different monoclonal antibodies, and is thereby capable of binding two different antigens.
  • bispecific antibodies are used for cancer immunotherapy by simultaneously targeting, for example, both CTLs (such as a CTL receptor component such as CD3) or effector natural killer (NK) cells, and a tumor antigen.
  • CTLs such as a CTL receptor component such as CD3
  • NK effector natural killer
  • a multi-specific antibody is a recombinant protein that includes antigen-binding fragments of at least two different monoclonal antibodies, such as two, three or four different monoclonal antibodies.
  • Breast cancer A type of cancer that forms in the tissues of the breast, typically in the ducts and lobules.
  • a patient with breast cancer is node -positive, meaning the breast cancer has spread to the lymph nodes.
  • Cartilaginous fish A class of fish that have a skeleton made of cartilage, instead of bone. These fish also have paired fins, paired nostrils, scales and a two-chambered heart. Cartilaginous fish are in the class Chondrichthyes, and include sharks, skates, rays and chimaeras (also known as ghost sharks).
  • the cartilaginous fish is a shark, such as a shark of the species Ginglymostoma cirratum, Orectolobus maculatus, Squalus acanthias, Triakis scyUium or Chiloscyllium plagiosum.
  • Chemotherapeutic agent Any chemical agent with therapeutic usefulness in the treatment of diseases characterized by abnormal cell growth. Such diseases include tumors, neoplasms, and cancer as well as diseases characterized by hyperplastic growth, such as psoriasis.
  • a chemotherapeutic agent is a radioactive compound.
  • chemotherapeutic agent of use see for example, Slapak and Kufe, Principles of Cancer Therapy, Chapter 86 in Harrison's Principles of Internal Medicine, 14th edition; Perry et al, Chemotherapy, Ch. 17 in Abeloff, Clinical Oncology 2 nd ed., ⁇ 2000 Churchill Livingstone, Inc; Baltzer, L., Berkery, R.
  • chemotherapy is the administration of more than one agent to treat cancer.
  • One example is the administration of an antibody (or immunoconjugate or ADC) that binds a tumor antigen used in combination with a radioactive or chemical compound.
  • Chimeric antigen receptor A chimeric molecule that includes an antigen-binding portion (such as a single domain antibody) and a signaling domain, such as a signaling domain from a T cell receptor (e.g. CD3 ⁇ ).
  • CARs are comprised of an antigen-binding moiety, a transmembrane domain and an endodomain.
  • the endodomain typically includes a signaling chain having an immunoreceptor tyrosine-based activation motif (IT AM), such as CD3 ⁇ or FceRIy.
  • IT AM immunoreceptor tyrosine-based activation motif
  • the endodomain further includes the intracellular portion of at least one additional co-stimulatory domain, such as CD28 and/or CD137.
  • Codon-optimized nucleic acid refers to a nucleic acid sequence that has been altered such that the codons are optimal for expression in a particular system (such as a particular species or group of species).
  • a nucleic acid sequence can be optimized for expression in mammalian cells or in a particular mammalian species (such as human cells).
  • a nucleic acid sequence is optimized for expression in bacterial cells, such as for production of protein (such as an antibody or immunotoxin). Codon optimization does not alter the amino acid sequence of the encoded protein.
  • CDR Complementarity determining region
  • Conservative variant “Conservative” amino acid substitutions are those substitutions that do not substantially affect or decrease the affinity of a protein.
  • a monoclonal antibody that specifically binds a target antigen can include at most about 1, at most about 2, at most about 5, at most about 10, or at most about 15 conservative substitutions and specifically bind the target antigen.
  • the term "conservative variant” also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid, provided that the antibody specifically binds the target antigen. Non-conservative substitutions are those that reduce an activity or binding to the target antigen.
  • a "conjugate” is an antibody or antibody fragment (such as an antigen-binding fragment) covalently linked to an effector molecule or a second protein (such as a second antibody).
  • the effector molecule can be, for example, a drug, toxin, therapeutic agent, detectable label, protein, nucleic acid, lipid, nanoparticle, carbohydrate or recombinant virus.
  • An antibody conjugate is often referred to as an "immunoconjugate.”
  • the conjugate comprises an antibody linked to a drug (e.g.
  • antibody-drug conjugate a cytotoxic agent
  • ADC antibody-drug conjugate
  • Other antibody conjugates include, for example, multi-specific (such as bispecific or trispecific) antibodies and chimeric antigen receptors (CARs).
  • Placement in direct physical association includes both in solid and liquid form.
  • Cytotoxic agent Any drug or compound that kills cells.
  • Cytotoxicity The toxicity of a molecule, such as an immunotoxin, to the cells intended to be targeted, as opposed to the cells of the rest of an organism.
  • toxicity refers to toxicity of an immunotoxin to cells other than those that are the cells intended to be targeted by the targeting moiety of the immunotoxin
  • animal toxicity refers to toxicity of the immunotoxin to an animal by toxicity of the immunotoxin to cells other than those intended to be targeted by the immunotoxin.
  • Degenerate variant refers to a polynucleotide encoding a polypeptide or an antibody that includes a sequence that is degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon. Therefore, all degenerate nucleotide sequences are included as long as the amino acid sequence of the polypeptide or antibody encoded by the nucleotide sequence is unchanged.
  • Diagnostic Identifying the presence or nature of a pathologic condition, such as, but not limited to, cancer. Diagnostic methods differ in their sensitivity and specificity.
  • the "sensitivity” of a diagnostic assay is the percentage of diseased individuals who test positive (percent of true positives).
  • the "specificity” of a diagnostic assay is one minus the false positive rate, where the false positive rate is defined as the proportion of those without the disease who test positive. While a particular diagnostic method may not provide a definitive diagnosis of a condition, it suffices if the method provides a positive indication that aids in diagnosis.
  • “Prognostic” is the probability of development (e.g., severity) of a pathologic condition, such as cancer or metastasis.
  • Drug Any compound used to treat, ameliorate or prevent a disease or condition in a subject.
  • the drug is an anti-cancer agent, for example a cytotoxic agent, such as an anti-mitotic or anti-microtubule agent.
  • Effector molecule The portion of an antibody conjugate (or immunoconjugate) that is intended to have a desired effect on a cell to which the conjugate is targeted. Effector molecules are also known as effector moieties (EMs), therapeutic agents, diagnostic agents, or similar terms.
  • Therapeutic agents include such compounds as small molecules, nucleic acids, proteins, peptides, amino acids or derivatives, glycoproteins, radioisotopes, lipids, nanoparticles, carbohydrates, or recombinant viruses.
  • Nucleic acid therapeutic and diagnostic moieties include antisense nucleic acids, derivatized oligonucleotides for covalent cross-linking with single or duplex DNA, and triplex forming oligonucleotides.
  • the effector molecule can be contained within an encapsulation system, such as a nanoparticle, liposome or micelle, which is conjugated to the antibody. Encapsulation shields the effector molecule from direct exposure to the circulatory system.
  • Means of preparing liposomes attached to antibodies are well known to those of skill in the art (see, for example, U.S. Patent No. 4,957,735; and Connor et al , Pharm Ther 28:341-365, 1985).
  • Diagnostic agents or moieties include radioisotopes and other detectable labels (e.g. , fluorophores, chemiluminescent agents, and enzymes). Radioactive isotopes include 35 S, n C, 13 N, 15 0, 18 F, 19 F, 99m Tc, 131 1, 3 H, 14 C, 15 N, 90 Y, 99 Tc, i n In and 125 I.
  • Epitope An antigenic determinant. These are particular chemical groups or peptide sequences on a molecule that are antigenic, i.e. that elicit a specific immune response. An antibody specifically binds a particular antigenic epitope on a polypeptide.
  • Framework region Amino acid sequences interposed between CDRs.
  • the framework regions serve to hold the CDRs in an appropriate orientation for antigen binding.
  • Fusion protein A protein comprising at least a portion of two different (heterologous) proteins.
  • Glypican-3 A member of the glypican family of heparan sulfate (HS) proteoglycans that are attached to the cell surface by a glycosylphosphatidylinositol anchor (Filmus and Selleck, / Clin Invest 108:497-501, 2001).
  • the GPC3 gene codes for a core protein of approximately 70 kD, which can be cleaved by furin to produce an N-terminal 40 kD fragment and a C-terminal 30 kD fragment.
  • Two HS chains are attached on the C-terminal portion of GPC3.
  • GPC3 and other glypican family proteins play a role in cell division and cell growth regulation.
  • GPC3 is highly expressed in HCC and some other human cancers including melanoma, squamous cell carcinomas of the lung, and clear cell carcinomas of the ovary (Ho and Kim, Eur J Cancer
  • GPC3 is also known as SGB, DGSX, MXR7, SDYS, SGBS, OCI-5, SGBS1 and GTR2-2.
  • isoforms 1-4 There are four known isoforms of human GPC3 (isoforms 1-4). Nucleic acid and amino acid sequences of the four isoforms of GPC3 are known, including GenBank Accession numbers:
  • NM_001164618 and NP_001158090 (isoform 3); and NM_001164619 and NP_001158091 (isoform 4).
  • the antibodies disclosed herein bind one or more of the four human GPC3 isoforms, or a conservative variant thereof.
  • GPC3-positive cancer A cancer that overexpresses GPC3.
  • GPC3-positive cancers include, but are not limited to, HCC, melanoma, squamous cell carcinoma of the lung and ovarian clear cell carcinoma.
  • Hepatocellular carcinoma A primary malignancy of the liver typically occurring in patients with inflammatory livers resulting from viral hepatitis, liver toxins or hepatic cirrhosis
  • HCC is also called malignant hepatoma.
  • HER2 A member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. This protein has no ligand binding domain of its own and therefore cannot bind growth factors. However, it does bind tightly to other ligand-bound EGF receptor family members to form a heterodimer, stabilizing ligand binding and enhancing kinase-mediated activation of downstream signaling pathways, such as those involving mitogen-activated protein kinase and phosphatidylinositol-3 kinase. Amplification and/or overexpression of the HER2 gene has been reported in numerous cancers, including breast and ovarian tumors.
  • EGF epidermal growth factor
  • HER2 is also known as v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene, epidermal growth factor receptor 2 (EGFR2), ERBB2 and Her-2/neu.
  • EGFR2 epidermal growth factor receptor 2
  • Her-2/neu Her-2/neu.
  • HER2-positive cancer A cancer that overexpresses HER2.
  • HER2-positive cancers include, but are not limited to, breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma and head and neck carcinoma.
  • Immune response A response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus.
  • the response is specific for a particular antigen (an "antigen-specific response").
  • an immune response is a T cell response, such as a CD4 + response or a CD8 + response.
  • the response is a B cell response, and results in the production of antigen-specific antibodies.
  • Immunoconjugate A covalent linkage of an effector molecule to an antibody or functional fragment thereof.
  • the effector molecule can be a detectable label or an immunotoxin.
  • toxins include, but are not limited to, abrin, ricin, Pseudomonas exotoxin (PE, such as PE35, PE37, PE38, and PE40), diphtheria toxin (DT), botulinum toxin, or modified toxins thereof, or other toxic agents that directly or indirectly inhibit cell growth or kill cells.
  • PE and DT are highly toxic compounds that typically bring about death through liver toxicity. PE and DT, however, can be modified into a form for use as an immunotoxin.
  • PE Pseudomonas exotoxin
  • DT diphtheria toxin
  • botulinum toxin or modified toxins thereof, or other toxic agents that directly or indirectly inhibit cell growth or kill cells.
  • PE and DT are highly toxic compounds that typically bring about death through liver toxicity
  • a "chimeric molecule” is a targeting moiety, such as a ligand or an antibody, conjugated (coupled) to an effector molecule.
  • conjugated or “linked” refers to making two polypeptides into one contiguous polypeptide molecule.
  • an antibody is joined to an effector molecule.
  • an antibody joined to an effector molecule is further joined to a lipid or other molecule to a protein or peptide to increase its half-life in the body.
  • the linkage can be either by chemical or recombinant means.
  • the linkage is chemical, wherein a reaction between the antibody moiety and the effector molecule has produced a covalent bond formed between the two molecules to form one molecule.
  • a peptide linker (short peptide sequence) can optionally be included between the antibody and the effector molecule.
  • immunoconjugates were originally prepared from two molecules with separate functionalities, such as an antibody and an effector molecule, they are also sometimes referred to as "chimeric molecules.”
  • Immunoglobulin new antigen receptor (IgNAR) antibody One of the three isotypes of immunoglobulin molecules produced by cartilaginous fish. IgNAR antibodies are homodimers of one variable new antigen receptor (VNAR) domain and five constant new antigen receptor (CNAR) domains (Roux ⁇ ?i al , Proc Natl Acad Sci USA 95: 11804- 11809, 1998). IgNAR antibodies are a major component of the immune system of cartilaginous fish.
  • Immunoliposome A liposome with antibodies or antibody fragments conjugated to its surface. Immunoliposomes can carry cytotoxic agents or other drugs to antibody-targeted cells, such as tumor cells.
  • Interstrand crosslinking agent A type of cytotoxic drug capable of binding covalently between two strands of DNA, thereby preventing DNA replication and/or transcription.
  • Isolated An "isolated" biological component, such as a nucleic acid, protein (including antibodies) or organelle, has been substantially separated or purified away from other biological components in the environment (such as a cell) in which the component naturally occurs, i.e. , other chromosomal and extra-chromosomal DNA and RNA, proteins and organelles.
  • Nucleic acids and proteins that have been "isolated” include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
  • Label A detectable compound or composition that is conjugated directly or indirectly to another molecule, such as an antibody or a protein, to facilitate detection of that molecule.
  • labels include fluorescent tags, enzymatic linkages, and radioactive isotopes.
  • a "labeled antibody” refers to incorporation of another molecule in the antibody.
  • the label is a detectable marker, such as the incorporation of a radiolabeled amino acid or attachment to a polypeptide of biotinyl moieties that can be detected by marked avidin (for example, streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods).
  • marked avidin for example, streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods.
  • Various methods of labeling polypeptides and glycoproteins are known in the art and may be used.
  • labels for polypeptides include, but are not limited to, the following: radioisotopes or radionucleotides (such as 35 S, n C, 13 N, 15 0, 18 F, 19 F, 99m Tc, 131 1, 3 H, 14 C, 15 N, 90 Y, 99 Tc, i n In and 125 I), fluorescent labels (such as fluorescein isothiocyanate (FITC), rhodamine, lanthanide phosphors), enzymatic labels (such as horseradish peroxidase, beta-galactosidase, luciferase, alkaline phosphatase),
  • radioisotopes or radionucleotides such as 35 S, n C, 13 N, 15 0, 18 F, 19 F, 99m Tc, 131 1, 3 H, 14 C, 15 N, 90 Y, 99 Tc, i n In and 125 I
  • fluorescent labels such as fluorescein isothiocyanate (FITC
  • chemiluminescent markers biotinyl groups, predetermined polypeptide epitopes recognized by a secondary reporter (such as a leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags), or magnetic agents, such as gadolinium chelates.
  • labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
  • Linker In some cases, a linker is a peptide within an antibody binding fragment (such as an Fv fragment) which serves to indirectly bond the variable heavy chain to the variable light chain. “Linker” can also refer to a peptide serving to link a targeting moiety, such as an antibody, to an effector molecule, such as a cytotoxin or a detectable label. The terms “conjugating,” “joining,” “bonding” or “linking” refer to making two
  • polypeptides into one contiguous polypeptide molecule, or to covalently attaching a radionuclide, drug or other molecule to a polypeptide, such as an antibody or antibody fragment.
  • the terms include reference to joining a ligand, such as an antibody moiety, to an effector molecule.
  • the linkage can be either by chemical or recombinant means.
  • “Chemical means” refers to a reaction between the antibody moiety and the effector molecule such that there is a covalent bond formed between the two molecules to form one molecule.
  • Liver cancer A type of cancer than forms in the tissues of the liver.
  • Types of liver cancers include, for example, hepatocellular carcinoma (HCC), cholangiocarcinoma (also known as bile duct cancer), angiosarcoma and hepatoblastoma.
  • HCC hepatocellular carcinoma
  • cholangiocarcinoma also known as bile duct cancer
  • angiosarcoma hepatoblastoma.
  • Lung cancer Cancer that forms in tissues of the lung, usually in the cells lining air passages.
  • the two main types are small cell lung cancer and non-small cell lung cancer. These types are diagnosed based on how the cells look under a microscope.
  • Mammal This term includes both human and non-human mammals. Similarly, the term “subject” includes both human and veterinary subjects.
  • Melanoma A form of cancer that originates in melanocytes (cells that make the pigment melanin). Melanocytes are found primary in the skin, but are also present in the bowel and eye. Melanoma in the skin includes superficial spreading melanoma, nodular melanoma, acral lentiginous melanoma, and lentigo maligna (melanoma). Any of the above types may produce melanin or can be amelanotic. Similarly, any subtype may show desmoplasia (dense fibrous reaction with neurotropism) which is a marker of aggressive behavior and a tendency to local recurrence. Other melanomas include clear cell sarcoma, mucosal melanoma and uveal melanoma.
  • MERS virus A coronavirus that was first reported in Saudi Arabia in 2012. This virus causes a severe, acute respiratory illness characterized by fever, cough and shortness of breath. MERS virus, which is also known as MERS-CoV, causes death in about 30-40% of infected patients.
  • the spike (S) protein of MERS virus is a type I membrane glycoprotein that assembles into trimers that constitute the spikes on the surface of the enveloped coronavirus particle. The S protein mediates virus entry into cells by binding cellular receptor dipeptidyl peptidase 4 (DPP4) and is responsible for membrane fusion.
  • DPP4 cellular receptor dipeptidyl peptidase 4
  • Neoplasia malignancy, cancer or tumor: A neoplasm is an abnormal growth of tissue or cells that results from excessive cell division. Neoplastic growth can produce a tumor. The amount of a tumor in an individual is the "tumor burden" which can be measured as the number, volume, or weight of the tumor. A tumor that does not metastasize is referred to as "benign.” A tumor that invades the surrounding tissue and/or can metastasize is referred to as "malignant.” Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence.
  • a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence.
  • operably linked DNA sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.
  • Ovarian cancer Cancer that forms in tissues of the ovary. Most ovarian cancers are either ovarian epithelial carcinomas (cancer that begins in the cells on the surface of the ovary) or malignant germ cell tumors (cancer that begins in egg cells).
  • Ovarian clear cell carcinoma A distinct histopathologic subtype of epithelial ovarian cancer with an incidence of less than 5% of all ovarian malignancies. When viewed under a microscope, the insides of the cells of this type of tumor appear clear.
  • Overlap extension PCR A type of PCR that can be used to insert specific mutations into a nucleic acid or to recombine two DNA sequences. By modifying the sequences incorporated into the 5' ends of primers used to PCR amplify a nucleic acid sequence, any pair of PCR products can be made to share a common sequence at one end. The common sequence allows strands from two different fragments to hybridize to one another, forming an overlap. Extension of this overlap by DNA polymerase yields a recombinant molecule (Horton et al, BioTechniques 54(3):129-133, 2013). Overlap extension PCR is also known as "splicing by overlap extension" or "SOEing.”
  • Pharmaceutical agent A chemical compound or composition capable of inducing a desired therapeutic or prophylactic effect when properly administered to a subject or a cell.
  • compositions and formulations suitable for use are conventional. Remington' s Pharmaceutical Sciences, by E.W. Martin, Mack Publishing Co., Easton, PA, 15th Edition, 1975, describes compositions and formulations suitable for use.
  • parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle.
  • pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle.
  • physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like
  • solid compositions such as powder, pill, tablet, or capsule forms
  • conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate.
  • compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
  • Preventing, treating or ameliorating a disease refers to inhibiting the full development of a disease.
  • Treating refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition after it has begun to develop, such as a reduction in tumor burden or a decrease in the number of size of metastases.
  • “Ameliorating” refers to the reduction in the number or severity of signs or symptoms of a disease, such as cancer.
  • PD1 Programmed cell death protein 1
  • PD1 A cell surface receptor that belongs to the immunoglobulin superfamily.
  • PD1 is expressed on T cells and pro-B cells and binds two ligands - PD-L1 and PD-L2.
  • PD1 functions as an immune checkpoint and plays an important role in down- regulating the immune system by preventing the activation of T cells.
  • PD-L1 is highly expressed in several cancers. Antibodies targeting PD1 can block the interaction between PD1 and PD-L1, thereby enhancing T cell responses important for antitumor immune activity.
  • a purified peptide preparation is one in which the peptide or protein is more enriched than the peptide or protein is in its natural environment within a cell.
  • a preparation is purified such that the protein or peptide represents at least 50% of the total peptide or protein content of the preparation.
  • Substantial purification denotes purification from other proteins or cellular components.
  • a substantially purified protein is at least 60%, 70%, 80%, 90%, 95% or 98% pure.
  • a substantially purified protein is 90% free of other proteins or cellular components.
  • PBD Pyrrolobenzodiazepine
  • Recombinant A recombinant nucleic acid or protein is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or by the artificial manipulation of isolated segments of nucleic acids, for example, by genetic engineering techniques.
  • Sample (or biological sample) A biological specimen containing genomic DNA, RNA (including mRNA), protein, or combinations thereof, obtained from a subject. Examples include, but are not limited to, peripheral blood, tissue, cells, urine, saliva, tissue biopsy, fine needle aspirate, surgical specimen, and autopsy material. In one example, a sample includes a tumor biopsy.
  • Sequence identity The similarity between amino acid or nucleic acid sequences is expressed in terms of the similarity between the sequences, otherwise referred to as sequence identity. Sequence identity is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are. Homologs or variants of a polypeptide or nucleic acid molecule will possess a relatively high degree of sequence identity when aligned using standard methods.
  • BLAST Basic Local Alignment Search Tool
  • NCBI National Center for Biotechnology Information
  • blastp blastn
  • blastx blastx
  • tblastn tblastx
  • Homologs and variants of an antibody that specifically binds a target antigen or a fragment thereof are typically characterized by possession of at least about 75%, for example at least about 80%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity counted over the full length alignment with the amino acid sequence of the antibody using the NCBI Blast 2.0, gapped blastp set to default parameters.
  • the Blast 2 sequences function is employed using the default BLOSUM62 matrix set to default parameters, (gap existence cost of 11, and a per residue gap cost of 1).
  • the alignment should be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties). Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity. When less than the entire sequence is being compared for sequence identity, homologs and variants will typically possess at least 80% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence.
  • Severe acute respiratory syndrome (SARS) virus A coronavirus that causes a severe and acute respiratory illness characterized by muscle pain, headache, fever, cough, dyspnea and pneumonia.
  • SARS virus which is also known as SARS-CoV, was first described in 2003 following an outbreak in Asia.
  • the spike (S) protein of SARS virus is composed of two subunits, SI and S2.
  • the S 1 subunit contains a receptor-binding domain that engages with the host cell receptor angiotensin-converting enzyme 2 (ACE2), while the S2 subunit mediates fusion between the viral and host cell membranes.
  • ACE2 angiotensin-converting enzyme 2
  • Small molecule A molecule, typically with a molecular weight less than about 1000 Daltons, or in some embodiments, less than about 500 Daltons, wherein the molecule is capable of modulating, to some measurable extent, an activity of a target molecule.
  • Subject Living multi-cellular vertebrate organisms, a category that includes both human and veterinary subjects, including human and non-human mammals.
  • Squamous cell carcinoma A type of cancer that originates in squamous cells, thin, flat cells that form the surface of the skin, eyes, various internal organs, and the lining of hollow organs and ducts of some glands. Squamous cell carcinoma is also referred to as epidermoid carcinoma. One type of squamous cell carcinoma is squamous cell carcinoma of the lung.
  • Synthetic Produced by artificial means in a laboratory, for example a synthetic nucleic acid or protein (for example, an antibody) can be chemically synthesized in a laboratory.
  • a synthetic nucleic acid or protein for example, an antibody
  • Therapeutically effective amount A quantity of a specific substance sufficient to achieve a desired effect in a subject being treated. For instance, this can be the amount necessary to inhibit or suppress growth of a tumor, or inhibit a viral infection. In one embodiment, a therapeutically effective amount is the amount necessary to eliminate, reduce the size, or prevent metastasis of a tumor. When administered to a subject, a dosage will generally be used that will achieve target tissue concentrations (for example, in tumors) that has been shown to achieve a desired in vitro effect. Toxin: An agent that directly or indirectly inhibits the growth of and/or kills cells.
  • Toxins include, for example, Pseudomonas exotoxin (PE, such as PE35, PE37, PE38 and PE40), diphtheria toxin (DT), botulinum toxin, abrin, ricin, saporin, restrictocin or gelonin, or modified toxins thereof.
  • PE Pseudomonas exotoxin
  • DT diphtheria toxin
  • botulinum toxin abrin, ricin, saporin, restrictocin or gelonin
  • PE and DT are highly toxic compounds that typically bring about death through liver toxicity.
  • PE and DT can be modified into a form for use as an
  • immunotoxin by removing the native targeting component of the toxin (such as domain la of PE or the B chain of DT) and replacing it with a different targeting moiety, such as an antibody.
  • native targeting component of the toxin such as domain la of PE or the B chain of DT
  • VNAR Variable new antigen receptor
  • VNAR antibodies are comprised of only two CDRs (CDRl and CDR3), but also contain two other hypervariable (HV) regions, referred to as the HV2 and HV4 regions.
  • the CDRs and HV regions are surrounded by framework (FW) regions in the following N-terminal to C-terminal order: FW1- CDR1 -FW2-HV2-FW3 a-HV4-FW3b-CDR3 -FW4.
  • the VNAR domain like other variable domains has an immunoglobulin fold that contains ⁇ sheets held together by two canonical cysteine residues.
  • the CDR3 can have one or two additional cysteines that form disulfide bonds with CDRl or other framework regions.
  • IgNAR are classified into four types based on the number and positioning of non-canonical cysteines in the VNAR domain. Type I VNAR domains contain two cysteine residues in CDR3 that form two extra disulfide bonds with FR2 and FR4.
  • Type II VNAR domains have one non-canonical cysteine in CDR3 that forms a disulfide bond with a non-canonical cysteine in CDR1.
  • Type III VNAR domains form a disulfide bond in CDR3 and FR2, and type IV domains have no additional disulfide bonds.
  • type I VNAR usually have flatter antigen binding regions and CDR3 regions that average 21 amino acids long
  • type II are usually shorter with an average of 15 amino acids and have a protruding CDR3 that enables binding to pockets and grooves (Barelle et ⁇ . , ⁇ Exp Med Biol 655:49-62, 2009).
  • HV2 hypervariable region 2
  • HV4 hypervariable region
  • Shark VNAR domains have many unique and advantageous properties that are absent from conventional IgG.
  • sharks are evolutionarily distant from mammals on the tree of life, so sharks have the ability to generate high affinity binders to structurally conservative mammalian drug targets. These may include heparan sulfate proteoglycans, G-protein coupled receptors, ion channels, cytokines and tumor antigens that exhibit poor immunogenicity in mice and rabbits.
  • conventional IgG antibodies have intrinsic drawbacks that can be overcome by shark VNAR domains.
  • the antigen binding region of conventional antibodies can be restricted in its ability to access certain epitopes, for example functional clefts of enzymes (Wesolowski et al , Med Microbiol immunol 198: 157-174, 2009; Barelle et al. , Adv Exp Med Biol 655:49-62, 2009; Nuttall and Walsh, Curr Opin Pharmacol 8:609-615, 2008).
  • IgNAR CDR3 is, on average, much longer (ranging from 9 to 26 amino acids) than the mouse or human counterpart.
  • VNAR domains can be as small as 12-15 kD for their total weight.
  • shark VNAR domain antibodies have structural advantages including high solubility, thermal and chemical stability, refolding capacity, and are easily expressed in E.coli systems (Wesolowski et al , Med Microbiol immunol 198: 157-174, 2009). Sharks enrich their blood with urea to prevent osmotic loss of water in the marine environment, so their antibody structure has evolved over millennia to become particularly stable (Feige et al , Proc Natl Acad Sci USA 111 :8155-8160, 2014). Phage display technology has been used in several shark VNAR engineering studies.
  • VNAR libraries derived from naive sharks (Liu et al , Mol Immunol 44: 1775-1783, 2007) or immunized sharks (Stanfield et al , J Mol Biol 367:358-372, 2007; Dooley et al , Mol Immunol 40:25-33, 2003; Dooley and Flajnik, Eur J Immunol 35:936-945, 2005; Dooley et al , Proc Natl Acad Sci USA 103: 1846-1851, 2006), and synthetic/semisynthetic libraries created in the lab (Shao et al , Mol Immunol 44:656-665, 2007; Liu et al , BMC Biotechnol 7:78, 2007; Nuttall et al , Mol Immunol 38:313-326, 2001 ; Nuttall et al , Eur J Biochem 270:3543-3554, 2003; Nuttall e
  • the present disclosure describes the construction of a large phage-displayed naive shark VNAR library from six sharks. To demonstrate the usefulness of the library, several rounds of panning were used to identify strong binders to important tumor and viral antigens. These included antigens associated with liver and breast cancers, as well as antigens from SARS virus and MERS virus. IV. Shark VNAR Antibodies Specific for Tumor and Viral Antigens
  • single-chain monoclonal antibodies that are specific for a tumor antigen (GPC3, PD1 or HER2), or a viral antigen (MERS virus spike protein or SARS virus spike protein).
  • the disclosed antibodies were isolated from a naive shark VNAR phage display library.
  • the disclosed antibodies can be used in a variety of compositions and conjugates, including chimeric antigen receptors, antibody-drug conjugates, immunoconjugates (e.g. conjugates comprising a toxin, such as PE), multi-specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and pharmaceutical compositions.
  • the antibodies, conjugates and compositions disclosed herein can be used, for example, for the diagnosis and treatment of various types of cancer (such as GPC- or HER2-expressing cancers) or the diagnosis and treatment of MERS virus or SARS virus.
  • VNAR antibodies include a complementarity determining region (CDR) 1 and a CDR3 that contribute to antigen-specific binding.
  • VNAR antibodies also include two hypervariable region (HV) regions, referred to as HV2 and HV4.
  • HV2 and HV4 Provided in the table below are the amino acid sequences of 10 VNAR antibody clones identified from the shark VNAR phage display library disclosed herein.
  • two mutants of clone GPC-Fl which each have a single amino acid substitution relative to the wild-type clone; the amino acid substitution is shown in bold.
  • Residues that comprise the CDR1, HV2, HV4 and CDR3 regions are listed in the table and are indicated by underline.
  • FW regions of a VNAR antibody are surrounded by framework (FW) regions in the following N-terminal to C-terminal order: FWl-CDRl-FW2-HV2-FW3a-HV4-FW3b- CDR3-FW4.
  • the table below provides the amino acid residues of the FW regions for each VNAR disclosed herein.
  • the single-domain antibody comprises at least a portion of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97, such as one or both of the CDRl and CDR3 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the single-domain antibody comprises residues 26-33 and 84- 101 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the single-domain antibody comprises residues 26-33, 45-52, 60- 64 and 84-101 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the single-domain antibody further comprises one or more of the FWl, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the single-domain antibody comprises at least a portion of SEQ ID NO: 2, such as one or both of the CDR1 and CDR3 of SEQ ID NO: 2.
  • the single-domain antibody comprises residues 26-33 and 84-96 of SEQ ID NO: 2.
  • the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 2.
  • the single- domain antibody comprises residues 26-33, 45-52, 60-64 and 84-96 of SEQ ID NO: 2.
  • the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 2.
  • the amino acid sequence of the single- domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 2.
  • the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 2.
  • the single-domain antibody comprises at least a portion of SEQ ID NO: 3 or SEQ ID NO: 4, such as one or both of the CDR1 and CDR3 of SEQ ID NO: 3 or SEQ ID NO: 4.
  • SEQ ID NO: 3 or SEQ ID NO: 4 such as one or both of the CDR1 and CDR3 of SEQ ID NO: 3 or SEQ ID NO: 4.
  • the single-domain antibody comprises residues 26-33 and 84-106 of SEQ ID NO: 3, or residues 26-33 and 83-100 of SEQ ID NO: 4.
  • the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 3 or SEQ ID NO: 4.
  • the single-domain antibody comprises residues 26-33, 45-52, 60-64 and 84-106 of SEQ ID NO: 3, or residues 26-33, 45-51, 59-63 and 83-100 of SEQ ID NO: 4.
  • the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 3 or SEQ ID NO: 4.
  • the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 3 or SEQ ID NO: 4.
  • the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 4.
  • the single-domain antibody comprises at least a portion of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9, such as one or both of the CDR1 and CDR3 of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
  • the single-domain antibody comprises residues 26-33 and 84-104 of SEQ ID NO: 5; residues 26-33 and 84-106 of SEQ ID NO: 6; residues 26-33 and 84-103 of SEQ ID NO: 7; residues 26-33 and 84-101 of SEQ ID NO: 8; or residues 26-33 and 84-96 of SEQ ID NO: 9.
  • the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
  • the single-domain antibody comprises residues 26-33, 45-52, 60-64 and 84-104 of SEQ ID NO: 5; residues 26-33, 45-52, 60-64 and 84-106 of SEQ ID NO: 6; residues 26-33, 45-52, 60-64 and 84- 103 of SEQ ID NO: 7; residues 26-33, 45-52, 60-64 and 84-101 of SEQ ID NO: 8; or residues 26- 33, 45-52, 60-64 and 84-96 of SEQ ID NO: 9.
  • the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
  • the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
  • the single- domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
  • the single-domain antibody comprises at least a portion of SEQ ID NO: 10, such as one or more of the CDR1 and CDR3 of SEQ ID NO: 10.
  • the single-domain antibody comprises residues 26-33 and 84-104 of SEQ ID NO: 10.
  • the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 10.
  • the single-domain antibody comprises residues 26-33, 45-52, 60-64 and 84-104 of SEQ ID NO: 10.
  • the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 10.
  • the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 10.
  • the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 10.
  • single-domain antibodies that bind GPC3, PD1, HER2, MERS S protein or SARS S protein, comprising one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 1, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQE ID NO: 9 or SEQ ID NO:
  • the single-domain antibody binds GPC3 and includes residues 1-25, 34- 44, 53-59, 65-83 and 102-110 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
  • the single-domain antibody binds PD1 and includes residues 1-25, 34-44, 53- 59, 65-83 and 97-105 of SEQ ID NO: 2.
  • the single-domain antibody binds HER2 and includes residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 3, or includes residues 1-25, 34-44, 52-58, 64-82 and 101-109 of SEQ ID NO: 4.
  • the single-domain antibody binds MERS S protein and includes residues 1-25, 34-44, 53-59, 65-83 and 105-113 of SEQ ID NO: 5; or includes residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 6; or includes residues 1-25, 34-44, 53-59, 65-83 and 104-112 of SEQ ID NO: 7; or includes residues 1-25, 34-44, 53-59, 65-83 and 102-110 of SEQ ID NO: 8; or includes residues 1-25, 34-44, 53-59, 65-83 and 97-105 of SEQ ID NO: 9.
  • the single-domain antibody binds SARS S protein and includes residues 1-25, 34-44, 53-59, 65-83 and 105-113 of SEQ ID NO: 10.
  • the single-domain antibody is a chimeric, synthetic or humanized antibody.
  • antibody conjugates that include any of the single- domain monoclonal antibodies disclosed herein.
  • Antibody conjugates include, but are not limited to, antibody-drug conjugates (ADCs), chimeric antigen receptors (CARs), antibody-toxin immunoconjugates, multi-specific (such as bispecific or trispecific) antibodies, antibody- nanoparticle conjugations and immunoliposomes.
  • ADCs that include a drug conjugated to a single-domain antibody disclosed herein.
  • the drug is a small molecule.
  • the drug is an anti-microtubule agent, an anti-mitotic agent and/or a cytotoxic agent.
  • ADCs are further discussed herein in section V below.
  • CARs that include a single-domain antibody disclosed herein.
  • the CAR further includes a transmembrane domain and a signaling domain.
  • the CARs further include a signal peptide and/or one or more linker peptides.
  • the cell is a cytotoxic T lymphocyte (CTL). CARs are further discussed in section VI below.
  • Multi-specific antibodies that include a single-domain antibody disclosed herein and a second monoclonal antibody or antigen-binding fragment thereof are further provided.
  • the second monoclonal antibody or antigen-binding fragment thereof specifically binds a component of the T cell receptor, such as CD3, or specifically binds a natural killer (NK) cell activating receptor, such as CD 16.
  • NK natural killer
  • Immunoconjugates that include a single-domain antibody disclosed herein and an effector molecule are also provided by the present disclosure.
  • the effector molecule is a toxin, such as Pseudomonas exotoxin or a variant thereof.
  • the effector molecule is a detectable label, such as a fluorescent, radioactive or enzymatic label.
  • antibody-nanoparticle conjugates that include a nanoparticle conjugated to a single-domain monoclonal antibody disclosed herein.
  • the nanoparticle includes a polymeric nanoparticle, nanosphere, nanocapsule, liposome, dendrimer, polymeric micelle, or niosome (see Fay and Scott, Immunotherapy 3(3):381-394, 2011 for a review of antibody-nanoparticle conjugates).
  • the nanoparticle includes a drug, such as a cytotoxic agent.
  • Antibody-nanoparticle conjugates are further described in section IX.
  • immunoliposomes that include a liposome conjugated to a single- domain antibody disclosed herein.
  • the liposome comprises a drug, such as a cytotoxic agent, for example an anti-cancer agent.
  • Immunoliposomes are further described in section IX.
  • fusion proteins that include a single-domain antibody disclosed herein and a heterologous protein.
  • the heterologous protein is an Fc domain, such as a human Fc domain.
  • compositions that include a disclosed single-domain antibody, ADC, CAR, isolated cell, immunoconjugate, multi- specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate or immunoliposome and a pharmaceutically acceptable carrier.
  • ADC single-domain antibody
  • CAR single-domain antibody
  • isolated cell immunoconjugate
  • multi-specific antibody such as bispecific or trispecific
  • antibody-nanoparticle conjugate or immunoliposome and a pharmaceutically acceptable carrier.
  • nucleic acid molecules encoding the single-domain antibodies, CARs, immunoconjugates and multi- specific (such as bispecific or trispecific) antibodies disclosed herein.
  • the nucleic acid molecules are operably linked to a promoter.
  • vectors that include the nucleic acid molecules disclosed herein. Isolated host cells transformed with the disclosed nucleic acid molecules and vectors are further provided by the present disclosure.
  • the nucleic acid is codon-optimized for expression in bacterial cells.
  • the codon-optimized nucleic acid expresses VNAR clone Fl, mutant F1-Y29C or mutant F1-C96S.
  • the nucleic acid encoding VNAR clone Fl is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 92
  • the nucleic acid encoding mutant F1-Y29C is at least 80%, at least
  • nucleic acid encoding mutant F1-C96S is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 96.
  • the nucleic acid encoding VNAR clone Fl comprises or consists of SEQ ID NO: 92
  • the nucleic acid encoding mutant F1-Y29C comprises or consists of SEQ ID NO: 94
  • the nucleic acid encoding mutant F1-C96S comprises or consists of SEQ ID NO: 96.
  • the single-domain antibodies, ADCs, CARs, isolated cells, immunoconjugates, multi- specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and compositions thereof disclosed herein can be used, for example, in methods of treating a GPC3-positive or HER2-positive cancer in a subject; methods of inhibiting tumor growth or metastasis of a GPC3-positive or HER2-positive cancer in a subject; methods of enhancing an anti-tumor response in a subject; methods of treating a MERS virus infection in a subject; methods of treating a SARS virus infection in a subject; methods of detecting expression of GPC3, HER2 or PD1 in a sample; methods of detecting MERS virus or SARS virus in a sample; methods of diagnosing a subject as having a GPC3-positive or HER2 -positive cancer; and methods of diagnosing a subject as infected with MERS virus or SARS virus.
  • ADCs are compounds comprised of a tumor antigen-specific antibody (or antigen-binding fragment thereof) and a drug, typically a cytotoxic agent, such as an anti-microtubule agent or cross-linking agent. Because ADCs are capable of specifically targeting cancer cells, the drug can be much more potent than agents used for standard chemotherapy.
  • cytotoxic drugs currently used with ADCs have an IC50 that is 100- to 1000-fold more potent than conventional chemotherapeutic agents.
  • Common cytotoxic drugs include anti-microtubule agents, such as maytansinoids and auristatins (such as auristatin E and auristatin F).
  • cytotoxins for use with ADCs include pyrrolobenzodiazepines (PDBs), which covalently bind the minor groove of DNA to form interstrand crosslinks.
  • PDBs pyrrolobenzodiazepines
  • ADCs comprise a 1:2 to 1:4 ratio of antibody to drug (Bander, Clinical Advances in Hematology & Oncology 10(8; suppl 10):3-7, 2012).
  • the antibody and drug can be linked by a cleavable or non-cleavable linker.
  • a linker that is stable in the circulation to prevent systemic release of the cytotoxic drug that could result in significant off-target toxicity.
  • Non-cleavable linkers prevent release of the cytotoxic agent before the ADC is internalized by the target cell.
  • Monoclonal antibodies have one conserved N-linked oligosaccharide chain at the Asn297 residue in the CH2 domain of each heavy chain (Qasba et al. , Biotechnol Prog 24:520-526, 2008).
  • a mutant i,4-galactosyltransferase enzyme (Y289L-Gal-Tl; U.S. Patent Application Publication Nos.
  • 2-keto-galactose is transferred to free GlcNAc residues on the antibody heavy chain to provide a chemical handle for conjugation.
  • the oligosaccharide chain attached to monoclonal antibodies can be classified into three groups based on the terminal galactose residues - fully galactosylated (two galactose residues; IgG- G2), one galactose residue (IgG-Gl) or completely degalactosylated (IgG-GO).
  • Treatment of a monoclonal antibody with i,4-galactosidase converts the antibody to the IgG-GO glycoform.
  • the mutant i,4-galactosyltransferase enzyme is capable of transferring 2-keto-galactose or 2-azido- galactose from their respective UDP derivatives to the GlcNAc residues on the IgG-Gl and IgG-GO glycoforms.
  • the chemical handle on the transferred sugar enables conjugation of a variety of molecules to the monoclonal antibody via the glycan residues (Qasba et al. , Biotechnol Prog 24:520-526, 2008).
  • ADCs that include a drug (such as a cytotoxic agent) conjugated to a monoclonal antibody that binds (such as specifically binds) a tumor or viral antigen.
  • a drug such as a cytotoxic agent
  • the drug is a small molecule.
  • the drug is a cross-linking agent, an anti-microtubule agent and/or anti-mitotic agent, or any cytotoxic agent suitable for mediating killing of tumor cells.
  • cytotoxic agents include, but are not limited to, a PDB, an auristatin, a maytansinoid, dolastatin, calicheamicin, nemorubicin and its derivatives, PNU- 159682, anthracycline, vinca alkaloid, taxane, trichothecene, CC1065, camptothecin, elinafide, a combretastain, a dolastatin, a duocarmycin, an enediyne, a geldanamycin, an indolino- benzodiazepine dimer, a puromycin, a tubulysin, a hemiasterlin, a spliceostatin, or a pladienolide, as well as stereoisomers, isosteres, analogs, and derivatives thereof that have cytotoxic activity.
  • PDB auristatin
  • a maytansinoid dolastatin
  • the ADC comprises a pyrrolobenzodiazepine (PBD).
  • PBD pyrrolobenzodiazepine
  • the natural product anthramycin (a PBD) was first reported in 1965 (Leimgruber et al, J Am Chem Soc, 87:5793-5795, 1965; Leimgruber et al. , JAm Chem Soc, 87:5791-5793, 1965). Since then, a number of PBDs, both naturally-occurring and synthetic analogues, have been reported (Gerratana, Med Res Rev 32(2):254-293, 2012; and U.S. Patent Nos. 6,884,799; 7,049,311; 7,067,511;
  • PDB dimers recognize and bind to specific DNA sequences, and have been shown to be useful as cytotoxic agents. PBD dimers have been conjugated to antibodies and the resulting ADC shown to have anti-cancer properties (see, for example, US 2010/0203007). Exemplary linkage sites on the PBD dimer include the five-membered pyrrolo ring, the tether between the PBD units, and the N10-C11 imine group (see WO 2009/016516; US 2009/304710; US 2010/047257; US 2009/036431; US
  • the ADC comprises an antibody conjugated to one or more maytansinoid molecules.
  • Maytansinoids are derivatives of maytansine, and are mitototic inhibitors which act by inhibiting tubulin polymerization. Maytansine was first isolated from the east African shrub Maytenus serrata (U.S. Patent No. 3,896,111). Subsequently, it was discovered that certain microbes also produce maytansinoids, such as maytansinol and C-3 maytansinol esters (U.S. Patent No. 4,151,042). Synthetic maytansinoids are disclosed, for example, in U.S. Patent Nos.
  • the ADC includes an antibody conjugated to a dolastatin or auristatin, or an analog or derivative thereof (see U.S. Patent Nos. 5,635,483; 5,780,588; 5,767,237; and 6,124,431).
  • Auristatins are derivatives of the marine mollusk compound dolastatin- 10.
  • Dolastatins and auristatins have been shown to interfere with microtubule dynamics, GTP hydrolysis, and nuclear and cellular division (Woyke et al. , Antimicrob Agents and Chemother 45(12):3580-3584, 2001) and have anticancer (U.S. Patent No. 5,663,149) and antifungal activity (Pettit et al. , Antimicrob Agents Chemother 42:2961-2965, 1998).
  • Exemplary dolastatins and auristatins include, but are not limited to, dolastatin 10, auristatin E, auristatin F, auristatin EB (AEB), auristatin EFP (AEFP), MM AD (Monomethyl Auristatin D or monomethyl dolastatin 10), MMAF (Monomethyl Auristatin F or N-methylvaline-valine-dolaisoleuine-dolaproine- phenylalanine), MMAE (Monomethyl Auristatin E or N-methylvaline-valine-dolaisoleuine- dolaproine-norephedrine), 5-benzoylvaleric acid-AE ester (AEVB), and other auristatins (see, for example, U.S. Publication No. 2013/0129753).
  • the ADC comprises an antibody conjugated to one or more calicheamicin molecules.
  • the calicheamicin family of antibiotics, and analogues thereof, are capable of producing double- stranded DNA breaks at sub-picomolar concentrations (Hinman et al, Cancer Res 53:3336-3342, 1993; Lode et al, Cancer Res 58:2925-2928, 1998).
  • Exemplary methods for preparing ADCs with a calicheamicin drug moiety are described in U.S. Patent Nos. 5,712,374; 5,714,586; 5,739,116; and 5,767,285.
  • the ADC comprises an anthracycline.
  • Anthracyclines are antibiotic compounds that exhibit cytotoxic activity. It is believed that anthracyclines can operate to kill cells by a number of different mechanisms, including intercalation of the drug molecules into the DNA of the cell thereby inhibiting DNA-dependent nucleic acid synthesis; inducing production of free radicals which then react with cellular macromolecules to cause damage to the cells; and/or interactions of the drug molecules with the cell membrane.
  • Non-limiting exemplary anthracyclines include doxorubicin, epirubicin, idarubicin, daunomycin, daunorubicin, doxorubicin, epirubicin, nemorubicin, valrubicin and mitoxantrone, and derivatives thereof.
  • PNU- 159682 is a potent metabolite (or derivative) of nemorubicin (Quintieri et al, Clin Cancer Res 11(4): 1608- 1617, 2005).
  • Nemorubicin is a semisynthetic analog of doxorubicin with a 2-methoxymorpholino group on the glycoside amino of doxorubicin (Grandi et al, Cancer Treat Rev 17:133, 1990;
  • the ADC can further include a linker.
  • the linker is a bifunctional or multifunctional moiety that can be used to link one or more drug moieties to an antibody to form an ADC.
  • ADCs are prepared using a linker having reactive functionalities for covalently attaching to the drug and to the antibody. For example, a cysteine thiol of an antibody can form a bond with a reactive functional group of a linker or a drug- linker intermediate to make an ADC.
  • a linker has a functionality that is capable of reacting with a free cysteine present on an antibody to form a covalent bond.
  • functionalities include maleimide, haloacetamides, oc-haloacetyl, activated esters such as succinimide esters, 4-nitrophenyl esters, pentafluorophenyl esters, tetrafluorophenyl esters, anhydrides, acid chlorides, sulfonyl chlorides, isocyanates, and isothiocyanates.
  • a linker has a functionality that is capable of reacting with an electrophilic group present on an antibody.
  • electrophilic groups include, but are not limited to, aldehyde and ketone carbonyl groups.
  • a heteroatom of the reactive functionality of the linker can react with an electrophilic group on an antibody and form a covalent bond to an antibody unit.
  • Non-limiting examples include hydrazide, oxime, amino, hydrazine, thiosemicarbazone, hydrazine carboxylate and arylhydrazide.
  • the linker is a cleavable linker, which facilitates release of the drug.
  • cleavable linkers include acid-labile linkers (for example, comprising hydrazone), protease- sensitive linkers (for example, peptidase- sensitive), photolabile linkers, and disulfide- containing linkers (Chari et al, Cancer Res 52:127-131, 1992; U.S. Patent No. 5,208,020).
  • the ADCs disclosed herein can be used for the treatment of a GPC3- or HER2 -positive cancer alone or in combination with another therapeutic agent and/or in combination with any standard therapy for the treatment of cancer (such as surgical resection of the tumor, chemotherapy or radiation therapy).
  • any standard therapy for the treatment of cancer such as surgical resection of the tumor, chemotherapy or radiation therapy.
  • CARs also known as chimeric T cell receptors, artificial T cell receptors or chimeric immunoreceptors
  • CTLs cytotoxic T lymphocytes
  • CARs include a binding moiety, an extracellular hinge and spacer element, a transmembrane region and an endodomain that performs signaling functions (Cartellieri et al , J Biomed Biotechnol 2010:956304, 2010).
  • the binding moiety is an antigen binding fragment of a monoclonal antibody, such as a scFv, or is a single-domain antibody.
  • the endodomain can consist of a signaling chain having an IT AM, such as CD3 ⁇ or FceRIy.
  • IT AM such as CD3 ⁇ or FceRIy.
  • the endodomain further includes the intracellular portion of at least one additional co- stimulatory domain, such as CD28 and/or CD137.
  • CTLs expressing CARs can be used to target a specific cell type, such as a tumor cell.
  • the monoclonal antibodies disclosed herein can be used to engineer CTLs that express a CAR containing an antigen-binding fragment of an antigen-specific antibody, thereby targeting the engineered CTLs to tumor antigen-expressing tumor cells.
  • Engineered T cells have previously been used for adoptive therapy for some types of cancer (see, for example, Park et al. , Mol Ther 15(4):825-833, 2007).
  • the use of T cells expressing CARs is more universal than standard CTL- based immunotherapy because CTLs expressing CARs are HLA unrestricted and can therefore be used for any patient having a tumor that expresses the target antigen.
  • CARs that include a tumor antigen-specific monoclonal antibody, or antigen-binding fragment thereof, such as a scFv.
  • CTLs expressing CARs comprised of a tumor antigen-specific monoclonal antibody (or antibody binding fragment) can be used for the treatment of cancers that express GPC3 or HER2.
  • the CAR is a bispecific CAR.
  • Multi- specific antibodies are recombinant proteins comprised antigen-binding fragments of two or more different monoclonal antibodies.
  • bispecific antibodies are comprised of antigen-binding fragments of two different monoclonal antibodies.
  • bispecific antibodies bind two different antigens and trispecific antibodies bind three different antigens.
  • Multi-specific antibodies can be used for cancer immunotherapy by simultaneously targeting, for example, both CTLs (such as a CTL receptor component such as CD3) or effector natural killer (NK) cells, and at least one tumor antigen.
  • CTLs such as a CTL receptor component such as CD3
  • NK effector natural killer
  • the antigen-specific monoclonal antibodies disclosed herein can be used to generate multi- specific (such as bispecific or trispecific) antibodies that target both the antigen and CTLs, or target both the antigen and NK cells, thereby providing a means to treat tumor antigen-expressing cancers.
  • Bi-specific T-cell engagers are a type of bispecific monoclonal antibody that are fusions of a first single-chain variable fragment (scFv) that targets a tumor antigen and a second scFv that binds T cells, such as bind CD3 on T cells.
  • scFv single-chain variable fragment
  • a second scFv that binds T cells, such as bind CD3 on T cells.
  • one of the binding moieties of the BiTE (such as one of the scFv molecules) is specific for PD1.
  • Bi-specific killer cell engagers are a type of bispecific monoclonal antibody that are fusions of a first scFv that targets a tumor antigen and a second scFv that binds a NK cell activating receptor, such as CD 16.
  • multi-specific monoclonal antibodies comprising a viral or tumor antigen-specific monoclonal antibody, or antigen-binding fragment thereof.
  • the multi-specific monoclonal antibody further comprises a monoclonal antibody, or antigen-binding fragment thereof, that specifically binds a component of the T cell receptor, such as CD3.
  • the multi-specific monoclonal antibody further comprises a monoclonal antibody, or antigen-binding fragment thereof, that specifically binds a NK cell activating receptor, such as CD16, Ly49, or CD94.
  • the antigen- binding fragments are scFv.
  • Multi- specific antibodies comprising an antigen-specific antibody, or antigen-binding fragment thereof, can be used for the treatment of cancers that express GPC3 or HER2.
  • methods of treating a subject with cancer by selecting a subject with a cancer that expresses GPC3 or HER2, and administering to the subject a therapeutically effective amount of the GPC3- or HER2-targeting multi- specific antibody.
  • the disclosed monoclonal antibodies can be conjugated to a therapeutic agent or effector molecule.
  • Immunoconjugates include, but are not limited to, molecules in which there is a covalent linkage of a therapeutic agent to an antibody.
  • a therapeutic agent is an agent with a particular biological activity directed against a particular target molecule or a cell bearing a target molecule.
  • therapeutic agents can include various drugs such as vinblastine, daunomycin and the like, cytotoxins such as native or modified Pseudomonas exotoxin or diphtheria toxin, encapsulating agents (such as liposomes) that contain pharmacological compositions, radioactive agents such as 125 1, 32 P, 14 C, 3 H and 35 S and other labels, target moieties and ligands.
  • the choice of a particular therapeutic agent depends on the particular target molecule or cell, and the desired biological effect.
  • the therapeutic agent can be a cytotoxin that is used to bring about the death of a particular target cell (such as a tumor cell).
  • the therapeutic agent can be conjugated to a non- lethal pharmacological agent or a liposome containing a non-lethal pharmacological agent.
  • nucleic acids encoding antibodies and conjugates and fusion proteins thereof.
  • Effector molecules can be linked to an antibody of interest using any number of means known to those of skill in the art. Both covalent and noncovalent attachment means may be used.
  • the procedure for attaching an effector molecule to an antibody varies according to the chemical structure of the effector.
  • Polypeptides typically contain a variety of functional groups; such as carboxylic acid (COOH), free amine (-NH 2 ) or sulfhydryl (-SH) groups, which are available for reaction with a suitable functional group on an antibody to result in the binding of the effector molecule.
  • the antibody is derivatized to expose or attach additional reactive functional groups. The derivatization may involve attachment of any of a number of known linker molecules.
  • the linker can be any molecule used to join the antibody to the effector molecule.
  • the linker is capable of forming covalent bonds to both the antibody and to the effector molecule.
  • Suitable linkers are well known to those of skill in the art and include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers, or peptide linkers.
  • the linkers may be joined to the constituent amino acids through their side groups (such as through a disulfide linkage to cysteine) or to the alpha carbon amino and carboxyl groups of the terminal amino acids.
  • immunoconjugates will comprise linkages that are cleavable in the vicinity of the target site.
  • Cleavage of the linker to release the effector molecule from the antibody may be prompted by enzymatic activity or conditions to which the immunoconjugate is subjected either inside the target cell or in the vicinity of the target site.
  • the antibodies or antibody fragments disclosed herein can be derivatized or linked to another molecule (such as another peptide or protein).
  • the antibodies or portion thereof is derivatized such that the binding to the target antigen is not affected adversely by the derivatization or labeling.
  • the antibody can be functionally linked (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another antibody (for example, a bispecific antibody or a diabody), a detection agent, a pharmaceutical agent, and/or a protein or peptide that can mediate association of the antibody or antibody portion with another molecule (such as a streptavidin core region or a polyhistidine tag).
  • One type of derivatized antibody is produced by cross-linking two or more antibodies (of the same type or of different types, such as to create bispecific antibodies).
  • Suitable crosslinkers include those that are heterobifunctional, having two distinctly reactive groups separated by an appropriate spacer (such as m-maleimidobenzoyl-N-hydroxysuccinimide ester) or
  • the antibody can be conjugated with a detectable marker; for example, a detectable marker capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy or diagnostic imaging techniques (such as computed tomography (CT), computed axial tomography (CAT) scans, magnetic resonance imaging (MRI), nuclear magnetic resonance imaging NMRI), magnetic resonance tomography (MTR), ultrasound, fiberoptic examination, and laparoscopic examination).
  • a detectable marker capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy or diagnostic imaging techniques (such as computed tomography (CT), computed axial tomography (CAT) scans, magnetic resonance imaging (MRI), nuclear magnetic resonance imaging NMRI), magnetic resonance tomography (MTR), ultrasound, fiberoptic examination, and laparoscopic examination).
  • CT computed tomography
  • CAT computed axial tomography
  • MRI magnetic resonance imaging
  • NMRI nuclear magnetic resonance imaging NMRI
  • MMR magnetic resonance tomography
  • ultrasound fiberoptic examination
  • useful detectable markers include fluorescent compounds, including fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-l-napthalenesulfonyl chloride, phycoerythrin, lanthanide phosphors and the like.
  • Bioluminescent markers are also of use, such as luciferase, green fluorescent protein (GFP) and yellow fluorescent protein (YFP).
  • GFP green fluorescent protein
  • YFP yellow fluorescent protein
  • An antibody or antigen binding fragment can also be conjugated with enzymes that are useful for detection, such as horseradish peroxidase, ⁇ - galactosidase, luciferase, alkaline phosphatase, glucose oxidase and the like.
  • an antibody or antigen binding fragment When an antibody or antigen binding fragment is conjugated with a detectable enzyme, it can be detected by adding additional reagents that the enzyme uses to produce a reaction product that can be discerned. For example, when the agent horseradish peroxidase is present the addition of hydrogen peroxide and diaminobenzidine leads to a colored reaction product, which is visually detectable.
  • An antibody or antigen binding fragment may also be conjugated with biotin, and detected through indirect measurement of avidin or streptavidin binding. It should be noted that the avidin itself can be conjugated with an enzyme or a fluorescent label.
  • An antibody may be labeled with a magnetic agent, such as gadolinium. Antibodies can also be labeled with lanthanides (such as europium and dysprosium), and manganese.
  • Paramagnetic particles such as superparamagnetic iron oxide are also of use as labels.
  • An antibody may also be labeled with a predetermined polypeptide epitopes recognized by a secondary reporter (such as leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags).
  • labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
  • An antibody can also be labeled with a radiolabeled amino acid.
  • the radiolabel may be used for both diagnostic and therapeutic purposes.
  • the radiolabel may be used to detect expression of a target antigen by x-ray, emission spectra, or other diagnostic techniques.
  • Examples of labels for polypeptides include, but are not limited to, the following radioisotopes or radionucleotides: 3 H, 14 C, 15 N, 35 S, 90 Y, "Tc, i n In, 125 I, 131 I.
  • An antibody can also be derivatized with a chemical group such as polyethylene glycol (PEG), a methyl or ethyl group, or a carbohydrate group. These groups may be useful to improve the biological characteristics of the antibody, such as to increase serum half-life or to increase tissue binding.
  • PEG polyethylene glycol
  • methyl or ethyl group a methyl or ethyl group
  • carbohydrate group a chemical group such as polyethylene glycol (PEG), a methyl or ethyl group, or a carbohydrate group.
  • Toxins can be employed with the monoclonal antibodies described herein to produce immunotoxins.
  • Exemplary toxins include ricin, abrin, diphtheria toxin and subunits thereof, as well as botulinum toxins A through F. These toxins are readily available from commercial sources (for example, Sigma Chemical Company, St. Louis, MO). Contemplated toxins also include variants of the toxins described herein (see, for example, see, U.S. Patent Nos. 5,079,163 and 4,689,401).
  • the toxin is Pseudomonas exotoxin (PE) (U.S. Patent No. 5,602,095).
  • Pseudomonas exotoxin refers to a full-length native (naturally occurring) PE or a PE that has been modified. Such modifications can include, but are not limited to, elimination of domain la, various amino acid deletions in domains lb, II and III, single amino acid substitutions and the addition of one or more sequences at the carboxyl terminus (for example, see Siegall et al. , /. Biol. Chem. 264: 14256-14261, 1989).
  • PE employed with the monoclonal antibodies described herein can include the native sequence, cytotoxic fragments of the native sequence, and conservatively modified variants of native PE and its cytotoxic fragments.
  • Cytotoxic fragments of PE include those which are cytotoxic with or without subsequent proteolytic or other processing in the target cell. Cytotoxic fragments of PE include PE40, PE38, and PE35.
  • Cytotoxic fragments of PE include PE40, PE38, and PE35.
  • PE-LR protease-resistant PE variants and PE variants with reduced immunogenicity
  • PE-LR protease-resistant PE variants and PE variants with reduced immunogenicity
  • PE-LR protease-resistant PE variants and PE variants with reduced immunogenicity
  • PE-LR protease-resistant PE variants and PE variants with reduced immunogenicity
  • PE-LR protease-resistant PE variants and PE variants with reduced immunogenicity
  • the PE is a variant that is resistant to lysosomal degradation, such as PE- LR (Weldon et al , Blood 113(16):3792-3800, 2009; PCT Publication No. WO 2009/032954).
  • the PE is a variant designated PE-LR/6X (PCT Publication No. WO 2011/032022).
  • the PE variant is PE with reducing immunogenicity.
  • the PE is a variant designated PE-LR/8M (PCT Publication No. WO 2011/032022).
  • Modification of PE may occur in any previously described variant, including cytotoxic fragments of PE (for example, PE38, PE-LR and PE-LR/8M).
  • Modified PEs may include any substitution(s), such as for one or more amino acid residues within one or more T-cell epitopes and/or B cell epitopes of PE, or deletion of one or more T-cell and/or B-cell epitopes (see, for example, U.S. Patent Application Publication No. 2015/0099707).
  • Contemplated forms of PE also include deimmunized forms of PE, for example versions with domain II deleted (for example, PE24).
  • Deimmunized forms of PE are described in, for example, PCT Publication Nos. WO 2005/052006, WO 2007/016150, WO 2007/014743, WO 2007/031741, WO 2009/32954, WO 2011/32022, WO 2012/154530, and WO 2012/170617.
  • the antibodies described herein can also be used to target any number of different diagnostic or therapeutic compounds to cells expressing the tumor or viral antigen on their surface.
  • an antibody of the present disclosure can be attached directly or via a linker to a drug that is to be delivered directly to cells expressing cell-surface antigen. This can be done for therapeutic, diagnostic or research purposes.
  • Therapeutic agents include such compounds as nucleic acids, proteins, peptides, amino acids or derivatives, glycoproteins, radioisotopes, lipids, carbohydrates, or recombinant viruses.
  • Nucleic acid therapeutic and diagnostic moieties include antisense nucleic acids, derivatized oligonucleotides for covalent cross-linking with single or duplex DNA, and triplex forming oligonucleotides.
  • the molecule linked to an antibody can be an encapsulation system, such as a nanoparticle, liposome or micelle that contains a therapeutic composition such as a drug, a nucleic acid (for example, an antisense nucleic acid), or another therapeutic moiety that is preferably shielded from direct exposure to the circulatory system.
  • a therapeutic composition such as a drug, a nucleic acid (for example, an antisense nucleic acid), or another therapeutic moiety that is preferably shielded from direct exposure to the circulatory system.
  • Means of preparing liposomes attached to antibodies are well known to those of skill in the art (see, for example, U.S. Patent No. 4,957,735; Connor et al, Pharm. Ther. 28:341-365, 1985).
  • Antibodies described herein can also be covalently or non-covalently linked to a detectable label.
  • Detectable labels suitable for such use include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
  • Useful labels include magnetic beads, fluorescent dyes (for example, fluorescein isothiocyanate, Texas red, rhodamine, green fluorescent protein, and the like), radiolabels (for example, 3 H, 125 1, 35 S, 14 C, or 32 P), enzymes (such as horseradish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (such as polystyrene, polypropylene, latex, and the like) beads.
  • fluorescent dyes for example, fluorescein isothiocyanate, Texas red, rhodamine, green fluorescent protein, and the like
  • radiolabels for example, 3 H, 125 1,
  • radiolabels may be detected using photographic film or scintillation counters
  • fluorescent markers may be detected using a photodetector to detect emitted illumination
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
  • the single-domain monoclonal antibodies disclosed herein can be conjugated to a variety of different types of nanoparticles to deliver cytotoxic agents or other anti-cancer agents directly to tumor cells via binding of the antibody to a tumor specific antigen expressed on the surface of tumor cells.
  • the use of nanoparticles reduces off-target side effects and can also improve drug bioavailability and reduce the dose of a drug required to achieve a therapeutic effect.
  • Nanoparticle formulations can be tailored to suit the drug that is to be carried or encapsulated within the nanoparticle. For example, hydrophobic molecules can be incorporated inside the core of a nanoparticle, while hydrophilic drugs can be carried within an aqueous core protected by a polymeric or lipid shell.
  • nanoparticles include, but at not limited to, nanospheres, nanocapsules, liposomes, dendrimers, polymeric micelles, niosomes, and polymeric nanoparticles (Fay and Scott, Immunotherapy 3(3):381-394, 2011).
  • Liposomes are currently one of the most common types of nanoparticles used for drug delivery.
  • An antibody conjugated to a liposome is often referred to as an "immunoliposome.”
  • the liposomal component of an immunoliposome is typically a lipid vesicle of one or more concentric phospholipid bilayers.
  • the phospholipids are composed of a hydrophilic head group and two hydrophobic chains to enable encapsulation of both hydrophobic and hydrophilic drugs.
  • Conventional liposomes are rapidly removed from the circulation via macrophages of the reticuloendothelial system (RES). To generate long-circulating liposomes, the composition, size and charge of the liposome can be modulated.
  • RES reticuloendothelial system
  • the surface of the liposome may also be modified, such as with a glycolipid or sialic acid.
  • a glycolipid or sialic acid for example, the inclusion of polyethylene glycol (PEG) significantly increases circulation half-life.
  • PEG polyethylene glycol
  • Niosomes are non-ionic surfactant-based vesicles having a structure similar to liposomes.
  • the membranes of niosomes are composed only of nonionic surfactants, such as poly glyceryl- alkyl ethers or N-palmitoylglucosamine.
  • Niosomes range from small, unilalamellar to large, multilamellar particles. These nanoparticles are monodisperse, water-soluble, chemically stable, have low toxicity, are biodegradable and non-immunogenic, and increase bioavailability of encapsulated drugs.
  • Dendrimers include a range of branched polymer complexes. These nanoparticles are water-soluble, biocompatible and are sufficiently non-immunogenic for human use. Generally, dendrimers consist of an initiator core, surrounded by a layer of a selected polymer that is grafted to the core, forming a branched macromolecular complex. Dendrimers are typically produced using polymers such as poly(amidoamine) or poly(L-lysine). Dendrimers have been used for a variety of therapeutic and diagnostic applications, including for the delivery of DNA, RNA, bioimaging contrast agents and chemotherapeutic agents.
  • Polymeric micelles are composed of aggregates of amphiphilic co-polymers (consisting of both hydrophilic and hydrophobic monomer units) assembled into hydrophobic cores, surrounded by a corona of hydrophilic polymeric chains exposed to the aqueous environment.
  • the polymers used to prepare polymeric micelles are heterobifunctional copolymers composed of a hydrophilic block of PEG, poly(vinyl pyrrolidone) and hydrophobic poly(L-lactide) or poly(L- lysine) that forms the particle core.
  • Polymeric micelles can be used to carry drugs that have poor solubility. These nanoparticles have been used to encapsulate a number of anti-cancer drugs, including doxorubicin and camptothecin. Cationic micelles have also been developed to carry DNA or RNA molecules.
  • Nanospheres consist of a solid matrix of polymer, while nanocapsules contain an aqueous core.
  • the formulation selected typically depends on the solubility of the therapeutic agent to be carried/encapsulated; poorly water-soluble drugs are more readily encapsulated within a nanospheres, while water- soluble and labile drugs, such as DNA and proteins, are more readily encapsulated within nanocapsules.
  • the polymers used to produce these nanoparticles include, for example, poly(acrylamide), poly(ester), poly(alkylcyanoacrylates), poly(lactic acid) (PLA), poly(glycolic acids) (PGA), and poly(D,L-lactic-co-glycolic acid) (PLGA).
  • Antibodies can be conjugated to a suitable nanoparticle according to standard methods known in the art.
  • conjugation can be either covalent or non-covalent.
  • the nanoparticle is a liposome
  • the antibody is attached to a sterically stabilized, long circulation liposome via a PEG chain.
  • Coupling of antibodies or antibody fragments to a liposome can also involve thioester bonds, for example by reaction of thiols and maleimide groups.
  • Cross-linking agents can be used to create sulfhydryl groups for attachment of antibodies to nanoparticles (Paszko and Senge, Curr Med Chem
  • compositions include one or more of the disclosed single-domain antibodies that bind (for example specifically bind) GPC3, HER2, PD1, MERS virus S protein or SARS virus S protein, in a carrier.
  • Compositions comprising ADCs, CARs (and CTLs comprising CARs), multi- specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and immunoconjugates are also provided.
  • the compositions can be prepared in unit dosage forms for administration to a subject. The amount and timing of administration are at the discretion of the treating clinician to achieve the desired outcome.
  • immunoliposome or immunoconjugate can be formulated for systemic or local (such as intra- tumor) administration.
  • the antibody is formulated for parenteral administration, such as intravenous administration.
  • compositions for administration can include a solution of the antibody, ADC, CAR, CTL, multi-specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate, immunoliposome or immunoconjugate in a pharmaceutically acceptable carrier, such as an aqueous carrier.
  • a pharmaceutically acceptable carrier such as an aqueous carrier.
  • aqueous carriers can be used, for example, buffered saline and the like.
  • These solutions are sterile and generally free of undesirable matter.
  • These compositions may be sterilized by conventional, well known sterilization techniques.
  • the compositions may contain
  • auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like.
  • concentration of antibody in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the subject's needs.
  • a typical pharmaceutical composition for intravenous administration includes about 0.1 to
  • antibody or ADC, CAR, multi-specific antibody, antibody-nanoparticle conjugate, or immunoconjugate
  • Dosages from 0.1 up to about 100 mg per subject per day may be used, particularly if the agent is administered to a secluded site and not into the circulatory or lymph system, such as into a body cavity or into a lumen of an organ.
  • Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remington's Pharmaceutical Science, 19th ed., Mack Publishing Company, Easton, PA (1995).
  • Antibodies may be provided in lyophilized form and rehydrated with sterile water before administration, although they are also provided in sterile solutions of known concentration. The antibody solution is then added to an infusion bag containing 0.9% sodium chloride, USP, and in some cases administered at a dosage of from 0.5 to 15 mg/kg of body weight.
  • an infusion bag containing 0.9% sodium chloride, USP, and in some cases administered at a dosage of from 0.5 to 15 mg/kg of body weight.
  • Antibodies, ADCs, CARs, multi-specific (such as bispecific or trispecific) antibodies, antibody- nanoparticle conjugates, immunoliposomes or immunoconjugates can be administered by slow infusion, rather than in an intravenous push or bolus.
  • a higher loading dose is administered, with subsequent, maintenance doses being administered at a lower level.
  • an initial loading dose of 4 mg/kg may be infused over a period of some 90 minutes, followed by weekly maintenance doses for 4-8 weeks of 2 mg/kg infused over a 30 minute period if the previous dose was well tolerated.
  • Controlled release parenteral formulations can be made as implants, oily injections, or as particulate systems.
  • protein delivery systems see, Banga, A.J.,
  • Particulate systems include, for example, microspheres, microparticles, microcapsules, nanocapsules, nanospheres, and nanoparticles.
  • Microcapsules contain the therapeutic protein, such as a cytotoxin or a drug, as a central core. In microspheres the therapeutic is dispersed throughout the particle. Particles, microspheres, and microcapsules smaller than about 1 ⁇ are generally referred to as nanoparticles, nanospheres, and nanocapsules, respectively. Capillaries have a diameter of approximately 5 ⁇ so that only nanoparticles are administered intravenously. Microparticles are typically around 100 ⁇ in diameter and are administered subcutaneously or intramuscularly. See, for example, Kreuter, J., Colloidal Drug Delivery Systems, J. Kreuter, ed., Marcel Dekker, Inc., New York, NY, pp. 219-342 (1994); and Tice & Tabibi, Treatise on Controlled Drug Delivery, A. Kydonieus, ed., Marcel Dekker, Inc. New York, NY, pp. 315-339, (1992).
  • the therapeutic protein such as a cytotoxin or a
  • Polymers can be used for ion-controlled release of the antibody-based compositions disclosed herein.
  • Various degradable and nondegradable polymeric matrices for use in controlled drug delivery are known in the art (Langer, Accounts Chem. Res. 26:537-542, 1993).
  • the block copolymer, polaxamer 407 exists as a viscous yet mobile liquid at low temperatures but forms a semisolid gel at body temperature. It has been shown to be an effective vehicle for formulation and sustained delivery of recombinant interleukin-2 and urease (Johnston et al, Pharm. Res. 9:425-434, 1992; and Pec et al, J. Parent. Set Tech. 44(2):58-65, 1990).
  • hydroxyapatite has been used as a microcarrier for controlled release of proteins (Ijntema et al. , Int. J. Pharm.112:215-224, 1994).
  • liposomes are used for controlled release as well as drug targeting of the lipid-capsulated drug (Betageri et al, Liposome Drug Delivery Systems, Technomic Publishing Co., Inc., Lancaster, PA (1993)).
  • Numerous additional systems for controlled delivery of therapeutic proteins are known (see U.S. Patent Nos. 5,055,303; 5,188,837; 4,235,871 ; 4,501,728; 4,837,028; 4,957,735; 5,019,369; 5,055,303;
  • the antibodies, compositions, CARs (and CTLs expressing CARs), ADCs, multi- specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and immunoconjugates disclosed herein can be administered to slow or inhibit the growth of tumor cells or inhibit the metastasis of tumor cells, such as GPC3-positive or HER2 -positive cancers.
  • a therapeutically effective amount of a composition is administered to a subject in an amount sufficient to inhibit growth, replication or metastasis of cancer cells, or to inhibit a sign or a symptom of the cancer.
  • Suitable subjects may include those diagnosed with a cancer that expresses GPC3, such as, but not limited to, hepatocellular carcinoma (HCC), melanoma, squamous cell carcinoma of the lung or ovarian clear cell carcinoma, or with a cancer that expresses HER2, for example breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma or head and neck carcinoma.
  • GPC3 hepatocellular carcinoma
  • melanoma melanoma
  • HER2 hepatocellular carcinoma
  • breast cancer gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon
  • a method of treating a GPC3-positive cancer in a subject by administering to the subject a therapeutically effective amount of a GPC3 -specific antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi- specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate, immunoconjugate, immunoliposome or composition disclosed herein.
  • a method of inhibiting tumor growth or metastasis of a GPC3- positive cancer in a subject by administering to the subject a therapeutically effective amount of a GPC3-specific antibody, ADC, CAR (e.g.
  • the GPC3-positive cancer is HCC, melanoma, squamous cell carcinoma of the lung or ovarian clear cell carcinoma.
  • Also provided herein is a method of treating a HER2 -positive cancer in a subject by administering to the subject a therapeutically effective amount of a HER2-specific antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi- specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate, immunoconjugate, immunoliposome or composition disclosed herein. Also provided herein is a method of inhibiting tumor growth or metastasis of a HER2- positive cancer in a subject by administering to the subject a therapeutically effective amount of a HER2-specific antibody, ADC, CAR (e.g.
  • the HER2-positive cancer is breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma or head and neck carcinoma.
  • a method of enhancing an anti-tumor response in a subject comprising administering to the subject a PD1 -specific single-domain monoclonal antibody disclosed herein.
  • the subject has melanoma, lung cancer, bladder cancer, breast cancer, Hodgkin' s lymphoma, renal cancer, head and neck cancer, gastric cancer, glioblastoma, colorectal cancer or Merkel cell carcinoma.
  • Also provided herein is a method of treating a MERS virus infection in a subject by administering to the subject a MERS virus-specific single-domain monoclonal antibody disclosed herein.
  • a method of treating a SARS virus infection in a subject by administering the subject a SARS virus-specific single-domain monoclonal antibody disclosed herein is also provided.
  • a therapeutically effective amount of a single-domain antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi-specific (such as bispecific or trispecific) antibody, immunoconjugate, immunoliposome or composition disclosed herein will depend upon the severity of the disease, the type of disease, and the general state of the patient's health.
  • a therapeutically effective amount of the antibody-based composition is that which provides either subjective relief of a symptom(s) or an objectively identifiable improvement as noted by the clinician or other qualified observer.
  • immunoconjugates multi-specific (such as bispecific or trispecific) antibodies, antibody- nanoparticle conjugates, immunoliposomes and compositions disclosed herein can also be accompanied by administration of other anti-cancer agents or therapeutic treatments (such as surgical resection of a tumor).
  • Any suitable anti-cancer agent can be administered in combination with the antibodies, compositions and immunoconjugates disclosed herein.
  • Exemplary anti-cancer agents include, but are not limited to, chemotherapeutic agents, such as, for example, mitotic inhibitors, alkylating agents, anti-metabolites, intercalating antibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes, topoisomerase inhibitors, anti-survival agents, biological response modifiers, anti-hormones (e.g. anti-androgens) and anti-angiogenesis agents.
  • Other anti-cancer treatments include radiation therapy and other antibodies that specifically target cancer cells.
  • alkylating agents include nitrogen mustards (such as
  • mechlorethamine cyclophosphamide, melphalan, uracil mustard or chlorambucil
  • alkyl sulfonates such as busulfan
  • nitrosoureas such as carmustine, lomustine, semustine, streptozocin, or dacarbazine
  • Non-limiting examples of antimetabolites include folic acid analogs (such as methotrexate), pyrimidine analogs (such as 5-FU or cytarabine), and purine analogs, such as mercaptopurine or thioguanine.
  • folic acid analogs such as methotrexate
  • pyrimidine analogs such as 5-FU or cytarabine
  • purine analogs such as mercaptopurine or thioguanine.
  • Non-limiting examples of natural products include vinca alkaloids (such as vinblastine, vincristine, or vindesine), epipodophyllotoxins (such as etoposide or teniposide), antibiotics (such as dactinomycin, daunorubicin, doxorubicin, bleomycin, plicamycin, or mitomycin C), and enzymes (such as L-asparaginase).
  • vinca alkaloids such as vinblastine, vincristine, or vindesine
  • epipodophyllotoxins such as etoposide or teniposide
  • antibiotics such as dactinomycin, daunorubicin, doxorubicin, bleomycin, plicamycin, or mitomycin C
  • enzymes such as L-asparaginase
  • miscellaneous agents include platinum coordination complexes (such as cis-diamine-dichloroplatinum II also known as cisplatin), substituted ureas (such as hydroxyurea), methyl hydrazine derivatives (such as procarbazine), and adrenocrotical suppressants (such as mitotane and aminoglutethimide).
  • platinum coordination complexes such as cis-diamine-dichloroplatinum II also known as cisplatin
  • substituted ureas such as hydroxyurea
  • methyl hydrazine derivatives such as procarbazine
  • adrenocrotical suppressants such as mitotane and aminoglutethimide
  • Non- limiting examples of hormones and antagonists include adrenocorticosteroids (such as prednisone), progestins (such as hydroxyprogesterone caproate, medroxyprogesterone acetate, and magestrol acetate), estrogens (such as diethylstilbestrol and ethinyl estradiol), antiestrogens (such as tamoxifen), and androgens (such as testerone proprionate and fluoxymesterone).
  • adrenocorticosteroids such as prednisone
  • progestins such as hydroxyprogesterone caproate, medroxyprogesterone acetate, and magestrol acetate
  • estrogens such as diethylstilbestrol and ethinyl estradiol
  • antiestrogens such as tamoxifen
  • androgens such as testerone proprionate and fluoxymesterone
  • chemotherapy drugs examples include Adriamycin, Alkeran, Ara-C, BiCNU, Busulfan, CCNU, Carboplatinum, Cisplatinum, Cytoxan, Daunorubicin, DTIC, 5-FU, Fludarabine, Hydrea, Idarubicin, Ifosfamide, Methotrexate, Mithramycin, Mitomycin, Mitoxantrone, Nitrogen Mustard, Taxol (or other taxanes, such as docetaxel), Velban, Vincristine, VP- 16, while some more newer drugs include Gemcitabine (Gemzar), Herceptin, Irinotecan (Camptosar, CPT-11),
  • Leustatin Leustatin, Navelbine, Rituxan STI-571, Taxotere, Topotecan (Hycamtin), Xeloda (Capecitabine), Zevelin and calcitriol.
  • Non- limiting examples of immunomodulators that can be used include AS- 101 (Wyeth- Ayerst Labs.), bropirimine (Upjohn), gamma interferon (Genentech), GM-CSF (granulocyte macrophage colony stimulating factor; Genetics Institute), IL-2 (Cetus or Hoffman-LaRoche), human immune globulin (Cutter Biological), IMREG (from Imreg of New Jersey, La.), SK&F 106528, and TNF (tumor necrosis factor; Genentech).
  • Another common treatment for some types of cancer is surgical treatment, for example surgical resection of the cancer or a portion of it.
  • surgical treatment for example surgical resection of the cancer or a portion of it.
  • radiotherapy for example administration of radioactive material or energy (such as external beam therapy) to the tumor site to help eradicate the tumor or shrink it prior to surgical resection.
  • anti-MERS virus S protein or anti-SARS virus S protein antibodies can also be accompanied by administration of other therapeutic agents, such as anti- viral agents or
  • Anti-viral gents include, for example, ribavirin, protease inhibitors (e.g. lopinavir-ritonavir), human interferons (e.g. IFN-oc or IFN-b), human gamma
  • Immunomodulatory therapy can include, for example, corticosteroids, thymosin alpha 1, etanercept, infliximab, cyclophosphamide, azathioprine, cyclosporin and thalidomide.
  • GPC3, HER2, PD1, MERS virus S protein or SARS S protein expression is detected in a biological sample.
  • the sample can be any sample, including, but not limited to, tissue from biopsies, autopsies and pathology specimens. Biological samples also include sections of tissues, for example, frozen sections taken for histological purposes. Biological samples further include body fluids, such as blood, serum, plasma, sputum, spinal fluid or urine. A biological sample is typically obtained from a mammal, such as a human or non-human primate.
  • a method of determining if a subject has a GPC3-positive cancer by contacting a sample from the subject with a GPC3-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample identifies the subject as having a GPC3-positive cancer.
  • Also provided herein is a method of determining if a subject has a HER2 -positive cancer by contacting a sample from the subject with a HER2-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample identifies the subject as having a HER2 -positive cancer.
  • a method of confirming a diagnosis of a GPC3-positive cancer in a subject by contacting a sample from a subject diagnosed with a GPC3-positive cancer with a GPC3-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample confirms the diagnosis of a GPC3 -positive cancer in the subject.
  • a method of confirming a diagnosis of a HER2-positive cancer in a subject by contacting a sample from a subject diagnosed with a HER2-positive cancer with a HER2-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample confirms the diagnosis of a HER2 -positive cancer in the subject.
  • the single-domain monoclonal antibody is directly labeled.
  • the methods further include contacting a second antibody that specifically binds the monoclonal antibody with the sample; and detecting the binding of the second antibody.
  • An increase in binding of the second antibody to the sample as compared to binding of the second antibody to a control sample detects a GPC3- or HER2 -positive cancer in the subject or confirms the diagnosis of a GPC3- or HER2 -positive cancer in the subject.
  • the cancer is HCC, melanoma, squamous cell carcinoma of the lung or ovarian clear cell carcinoma, or any other type of cancer that expresses GPC3.
  • the cancer is breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma or head and neck carcinoma, or any other type of cancer that expresses HER2.
  • control sample is a sample from a subject without cancer.
  • sample is a blood or tissue sample.
  • kits for diagnosing a subject as infected with MERS virus by contacting a sample obtained from the subject with a MERS virus S protein-specific single- domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample diagnoses the subject as infected with MERS virus.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample diagnoses the subject as infected with SARS virus.
  • a method of detecting MERS virus in a sample by contacting the sample with a MERS virus S protein-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample detects MERS virus in the sample.
  • a method of detecting SARS virus in a sample by contacting the sample with a SARS virus S protein-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample.
  • An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample detects SARS virus in the sample.
  • the antibody that binds In some embodiments of the methods of diagnosis and detection, the antibody that binds
  • the antibody that binds (for example specifically binds) GPC3, HER2, PD1, MERS virus S protein or SARS S protein (the first antibody) is unlabeled and a second antibody or other molecule that can bind the antibody that specifically binds GPC3, HER2, PD1, MERS virus S protein or SARS S protein is labeled.
  • a second antibody is chosen that is able to specifically bind the specific species and class of the first antibody.
  • the first antibody is a human IgG
  • the secondary antibody may be an anti-human-IgG.
  • Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.
  • Suitable labels for the antibody or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase.
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin.
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin.
  • a non- limiting exemplary luminescent material is luminol; a non-limiting exemplary a magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include 125 I, 131 1, 35 S or 3 H.
  • GPC3, HER2, PDl, MERS virus S protein or SARS S protein can be assayed in a biological sample by a competition immunoassay utilizing GPC3, HER2, PDl, MERS virus S protein or SARS S protein standards labeled with a detectable substance and an unlabeled antibody that specifically binds GPC3, HER2, PDl , MERS virus S protein or SARS S protein.
  • the biological sample, the labeled GPC3, HER2, PDl, MERS virus S protein or SARS S protein standards and the antibody that specifically bind GPC3, HER2, PDl, MERS virus S protein or SARS S protein are combined and the amount of labeled GPC3, HER2, PDl, MERS virus S protein or SARS S protein standard bound to the unlabeled antibody is determined.
  • the amount of GPC3, HER2, PDl, MERS virus S protein or SARS S protein in the biological sample is inversely proportional to the amount of labeled GPC3, HER2, PDl , MERS virus S protein or SARS S protein standard bound to the antibody that specifically binds GPC3, HER2, PDl , MERS virus S protein or SARS S protein.
  • the antibody that specifically binds GPC3, HER2, PDl, MERS virus S protein or SARS S protein may be used to detect the production of GPC3, HER2, PDl, MERS virus S protein or SARS S protein in cells in cell culture.
  • the antibody can be used to detect the amount of GPC3, HER2, PDl, MERS virus S protein or SARS S protein in a biological sample, such as a tissue sample, or a blood or serum sample.
  • the GPC3, HER2, PDl , MERS virus S protein or SARS S protein is cell-surface GPC3, HER2, PDl , MERS virus S protein or SARS S protein.
  • the GPC3, HER2, PDl, MERS virus S protein or SARS S protein is soluble (e.g. in a cell culture supernatant or in a body fluid sample, such as a blood or serum sample).
  • a kit is provided for detecting GPC3, HER2, PDl, MERS virus S protein or SARS S protein in a biological sample, such as a blood sample or tissue sample. For example, to confirm a cancer diagnosis in a subject, a biopsy can be performed to obtain a tissue sample for histological examination.
  • Kits for detecting a polypeptide will typically comprise a monoclonal antibody that specifically binds GPC3, HER2, PDl, MERS virus S protein or SARS S protein, such as any of the single-domain antibodies disclosed herein.
  • the antibody is labeled (for example, with a fluorescent, radioactive, or an enzymatic label).
  • kits in one embodiment, includes instructional materials disclosing means of use of an antibody that binds GPC3, HER2, PDl, MERS virus S protein or SARS S protein.
  • the instructional materials may be written, in an electronic form (such as a computer diskette or compact disk) or may be visual (such as video files).
  • the kits may also include additional components to facilitate the particular application for which the kit is designed.
  • the kit may additionally contain means of detecting a label (such as enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels such as a secondary antibody, or the like).
  • the kits may additionally include buffers and other reagents routinely used for the practice of a particular method. Such kits and appropriate contents are well known to those of skill in the art.
  • the diagnostic kit comprises an immunoassay.
  • the method of detecting GPC3, HER2, PDl, MERS virus S protein or SARS S protein in a biological sample generally includes the steps of contacting the biological sample with an antibody which specifically reacts, under immunologically reactive conditions, to GPC3, HER2, PDl, MERS virus S protein or SARS S protein.
  • the antibody is allowed to specifically bind under immunologically reactive conditions to form an immune complex, and the presence of the immune complex (bound antibody) is detected directly or indirectly.
  • the antibodies disclosed herein can also be utilized in immunoassays such as but not limited to radioimmunoassays (RIAs), ELISA, or immunohistochemical assays.
  • the antibodies can also be used for fluorescence activated cell sorting (FACS).
  • FACS employs a plurality of color channels, low angle and obtuse light-scattering detection channels, and impedance channels, among other more sophisticated levels of detection, to separate or sort cells (see U.S. Patent No. 5,
  • any of the single-domain monoclonal antibodies that bind GPC3, HER2, PDl, MERS virus S protein or SARS S protein, as disclosed herein, can be used in these assays.
  • the antibodies can be used in a conventional immunoassay, including, without limitation, an ELISA, an RIA, FACS, tissue immunohistochemistry, Western blot or immunoprecipitation.
  • Antigen-specific VNAR domains have previously been generated from the immune repertoire of a number of different shark species, including the nurse shark (Ginglymostoma cirratum) (Dooley et al, Mol Immunol 40:25-33, 2003), the wobbegong shark (Orectolobus maculatus) (Nuttall et al, Mol Immunol 38:313-326, 2001 ; Liu et al, BMC Biotechnol 7:78, 2007), the spiny dogfish (Squalus acanthias) (Miiller et al , MAbs 4:673-685, 2012; Liu et al. , Mol
  • Target-specific clones have generally been isolated using different display technologies, such as phage display (Dooley et al , Mol Immunol 40:25-33, 2003; Nuttall et al , Mol Immunol 38:313-326, 2001) or ribosome display (Kopsidas et al , Immunol Lett 107: 163- 168, 2006).
  • display technologies such as phage display (Dooley et al , Mol Immunol 40:25-33, 2003; Nuttall et al , Mol Immunol 38:313-326, 2001) or ribosome display (Kopsidas et al , Immunol Lett 107: 163- 168, 2006).
  • FIG. 1 An overview of the process used to generate the VNAR antibody library is illustrated in FIG. 1.
  • a naive shark antibody library was constructed with an approximate size of 1.2 x 10 10 .
  • Sequencing of twenty-five randomly picked colonies demonstrated that 72% of the clones were type II VNAR (FIGS. 2A-2B).
  • the CDR3 length distribution of the selected clones was analyzed and determined to range from 9 to 24 amino acids, with the average length being 18 amino acids (FIG. 2C).
  • VNAR sequences for each shark and each primer combination were separately PCR amplified from the cDNA product (FIG. 8).
  • the 12 PCR fractions from the six sharks were evenly pooled to ensure every group of VNAR was equally represented in the library.
  • the vector backbone fragment was prepared by PCR.
  • the amplified VNAR fragment was assembled with the vector backbone by overlap extension PCR using a VNAR-specific forward primer and a vector backbone-specific reverse primer.
  • the assembled PCR product was self-ligated with T4 DNA ligase, and transformed into TGI to make the library.
  • the method disclosed herein for generating a VNAR antibody library differs from standard methods (which use conventional digestion and ligation) by utilizing overlap extension PCR and a self-ligation method (FIG. 1). This approach is far more efficient than the common digestion/ligation method.
  • the library disclosed herein contains 1.2 x 10 10 individual clones, which is much larger than previously reported VNAR libraries.
  • the method includes providing complementary DNA (cDNA) generated from RNA isolated from lymphocytes of one or more cartilaginous fish; providing a vector backbone comprising a vector junction sequence; amplifying VNAR nucleic acid from the cDNA by polymerase chain reaction (PCR) using a VNAR-specific forward primer and at least one reverse primer comprising VNAR-specific sequence and the vector junction sequence to generate VNAR nucleic acid sequences comprising the vector junction sequence; assembling the VNAR nucleic acid sequences comprising the vector junction sequence and the vector backbone comprising the vector junction sequence by overlapping extension PCR using the VNAR-specific forward primer and a vector backbone-specific reverse primer, thereby producing linear VNAR vectors; and maintaining the linear VNAR vectors under conditions to permit self-ligation, thereby producing a library of VNAR vectors.
  • cDNA complementary DNA
  • PCR polymerase chain reaction
  • the method further includes the step of obtaining RNA from immune cells, such as lymphocytes, of one or more cartilaginous fish. In some examples, the method further includes the step of generating cDNA from the isolated RNA using RT-PCR.
  • the method further includes the step of generating the vector backbone comprising the vector junction sequence by PCR amplification of the vector backbone using a primer that includes the vector junction sequence.
  • the method further includes the step of transforming the library of VNAR vectors into isolated host cells, such as isolated bacterial cells. Competent bacterial cells suitable for generating a phage display library are well-known in the art.
  • the one or more cartilaginous fish are of the species Ginglymostoma cirratum, Orectolobus maculatus, Squalus acanthias, Triakis scyUiurn or Chiloscyllium plagiosum.
  • the one or more cartilaginous fish are of the species Ginglymostoma cirratum (nurse shark).
  • the VNAR-specific forward primer is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 88.
  • the VNAR- specific forward primer comprises or consists of SEQ ID NO: 88.
  • the at least one reverse primer is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 89, is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 90, or both.
  • the at least one reverse primer comprises or consists of SEQ ID NO: 89, SEQ ID NO: 90, or both.
  • the vector-backbone specific reverse primer is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 92.
  • the vector- backbone specific reverse primer comprises or consists of SEQ ID NO: 92.
  • the vector backbone containing the vector junction sequence is prepared by PCR amplification of the vector using a forward primer at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 91 and a reverse primer at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 92.
  • the vector backbone containing the vector junction sequence is prepared by PCR amplification of the vector using a forward primer comprising or consisting of SEQ ID NO: 91 and the vector-backbone specific reverse primer comprising or consisting of SEQ ID NO: 92.
  • self-ligation is catalyzed by T4 DNA ligase.
  • GPC3 -negative A431 cells (a human epithelial carcinoma cell line) were engineered to express high levels of GPC3 by transfection with a plasmid encoding full-length GPC3. Both A431 and the stably transfected cells (Gl) were maintained in DMEM.
  • YP7 a previously described GPC3 mouse antibody, recognizes a C-terminal epitope (amino acids 510-560) of GPC3 (Phung et al, mAbs 4:592-599, 2012).
  • YP7 was used in the competitive phage ELISA as a blocker for measuring the binding of GPC3-F1 monoclonal phage to the GPC3 peptide 511-560.
  • the vector backbone fragment was prepared by PCR with forward primer IgNARComb3x- F: AGTGGCCAGGCCGGCCACC (SEQ ID NO: 91), and reverse primer IgNARComb3x-R: GGCCGCCTGGGCCACGGTA (SEQ ID NO: 92).
  • the amplified VNAR fragment was assembled with the vector backbone by over-lapping extension PCR using primer IgNAR-F and
  • the assembled PCR product was self-ligated with T4 DNA ligase, and transformed into TGI to make the library. Phage display and panning method
  • Library bacterial stock was inoculated into 2.5 liters of 2XYT media containing 2% glucose, 100 ⁇ g/ml ampicillin, and cultured at 37°C with shaking (250 rpm). When the cells reached mid-log phase (OD 6 oo between 0.4-0.8), super-infection was performed by adding helper phage M13K07 at 5 x 10 9 pfu/ml. After one hour of continued growth, the cells were resuspended in 2.5 liters of 2XYT media containing 100 ⁇ g/ml ampicillin and 50 ⁇ g/ml kanamycin, and incubated at 25°C overnight. After the cells were centrifuged and filtered with a 0.22 ⁇ membrane, the supernatant was stored at 4°C for panning.
  • a 96-well Maxisorb ELISA plate (Nunc/Thermo Fisher Scientific, Rochester, NY) was used to capture various antigens (100 ⁇ g/ml) in phosphate buffered saline (PBS) at 4°C overnight. After the coating buffer was decanted, the plate was treated with blocking buffer (2% bovine serum albumin (BSA) in PBST) at room temperature for 1 hour. Then 30 ⁇ pre -blocked phage supernatant (typically contained 10 10 -10 n cfu) in 30 ⁇ blocking buffer was added per well for 1 hour at room temperature to allow binding. After four washes with PBS containing 0.05% Tween-20, bound phages were eluted with 100 mM triethylamine. After four rounds of panning, single colonies were picked and identified by using phage ELISA methods.
  • BSA bovine serum albumin
  • the coding sequence of the GPC3 binder was cloned into expression vector pVRC8400.
  • the resultant vector was used to transfect HEK293 cells.
  • the volumetric titer of the secreted VNAR-IIFC in batch culturing was about 30 mg/L. Purification was carried out with protein A column (GE healthcare Life Sciences, Pittsburg, PA) according to the manufacturer's instructions.
  • the antigen proteins were used to coat a 96-well plate at 5 ⁇ g/ml in PBS buffer, 50 ⁇ /well, at 4°C overnight. After the plate was blocked with 2% BSA in PBST buffer, 25 ⁇ pre-blocked phage supernatant (typically 10 10 -10 n cfu) were added to the plate. Binding was detected by horseradish peroxidase (HRP) -conjugated mouse anti-M13 antibody (GE healthcare Life Sciences, Pittsburg, PA). The cut-off value for a positive binder was set at 5 as the ratio of antigen binding versus background in OD450 reading is > 3.
  • HRP horseradish peroxidase
  • phage FACS 25 ⁇ phage supernatant (approximately 10 10 phages) were pre- blocked with FACS buffer (5% BSA in PBS) for 1 hour on ice, then mixed with 10 6 Gl cell suspension and incubated for 1 hour on ice. The binding was detected by a mouse anti-M13 primary antibody and phycoerythrin conjugated goat-anti-mouse secondary antibody (Sigma- Aldrich).
  • the structural models of PE38 and mPE24 were generated by molecular modeling using I- TASSER (available online at zhanglab.ccmb.med.umich.edu/I-TASSER). Molecular models were viewed and analyzed using Chimera (available online at cgl.ucsf.edu/chimera).
  • Example 2 Phage-displayed shark single-domain antibody library to identify high-affinity binders to tumor and viral antigens
  • This example describes the construction of a shark VNAR antibody phage library and the identification of antibodies that bind to specific tumor and viral antigens.
  • FIG. 1 An overview of the process is illustrated in FIG. 1.
  • a naive shark antibody library was constructed with an approximate size of 1.2 x 10 10 . From here, twenty five colonies were randomly picked from the library and sequenced (FIG. 2A). The result showed that 72% of the clones are type II VNAR (FIG. 2B). The CDR3 length distribution was analyzed and determined to range from 9 to 24 amino acids, with the average length being 18 amino acids (FIG. 2C). Screening of VNAR binders to different targets
  • tumor biomarkers and virus antigen proteins were arbitrarily chosen as selection targets. These included a synthetic GPC3 peptide (amino acids 511-560), the recombinant extracellular domains of HER2 and PD1, the recombinant spike proteins of the MERS and SARS viruses, and recombinant Pseudomonas exotoxin PE38.
  • binders to all of the listed targets were identified by monoclonal phage ELISA (FIG. 3). These binders were named GPC3-F1, HER2-A6, PD1-A1, MERS -A3, MERS-A7, MERS-A8, MERS-B4, MERS -B 5, SARS-01, and PE38-B6.
  • hFc and rFc binders were identified as a result of using GPC3-hFc and GPC3-rFc fusion proteins as selection agents; these were named hFc or rFc binders hFc-05, hFc-48, hFc/rFc-04, hFc/rFc-03, hFc/rFc-02, hFc/rFc-01, hFc/rFc-28, hFc/rFc-10, hFc/rFc-21, rFc/tiFc-03, and rFc/tiFc-11.
  • Glypican-3 is a liver cancer antigen that has been associated with hepatocellular carcinoma.
  • GPC3 specific human antibodies HN3 and HS20, and a mouse antibody YP7 were previously generated (Feng and Ho, FEBS Lett 588:377-382, 2014).
  • the mouse antibody YP7 was generated by immunizing mice with the synthetic GPC3 peptide 511-560. Using this same peptide as the selection agent, a shark binder (named GPC3-F1) was successfully discovered (FIG. 3). Phage FACS confirmed that this clone binds GPC3 over-expressing Gl cells (FIG. 5A).
  • VNAR sequence was cloned from the phage, and a VNAR-IIFC fusion protein was made in HEK293 cells.
  • the transient expression level was about 20 mg/L.
  • the cellular binding of the purified GPC3Fl-hFc on HepG2 and Gl cells was confirmed (FIG. 5B).
  • the binding affinity was measured on Gl cells, and the Kd value was calculated to be 124 nM (FIG. 5C). Since the Fl clone was selected using the same peptide that was used to generate the mouse monoclonal antibody YP7 (Phung et al , mAbs 4:592-599, 2012), it was investigated whether they recognize the same epitope.
  • the PE38-B6 binder was selected using a 38 kD truncated form of PE that contains domain II and the catalytic domain III.
  • the further truncated form of PE is a 24 kD fragment (PE24) that only retains domain III with the removal of human/mouse B cell epitopes (Liu et al. , Proc Natl Acad Sci USA 109:11782-11787, 2012; Alewine et al, Mol Cancer Ther 13:2653-2661, 2014).
  • a phage ELISA was conducted and it was determined that the PE38-B6 clone binds the wild type PE38, but not mPE24 (FIG. 6A).
  • shark VNAR domain antibodies have been suggested as a new class of target binding proteins that can be used in therapeutic, diagnostic and other biotechnological applications.
  • there are only fourteen specific targets with shark binders that have been developed and reported (Kovaleva et al, Expert Opin Biol Ther 14:1527-1539, 2014; Ohtani et al, Fish Shellfish Immunol 34:724-728, 2013; Camacho-Villegas et al, mAbs 5:80-85, 2013; Muller et al, mAbs 4:673-685, 2012; Walsh et al, Virology 411:132-141, 2011; Goodchild et al, Mol Immunol 48:2027-2037, 2011; Ohtani et al , Mar Biotechnol 15:56-62, 2013; Nuttall et al, FEBS Lett 516:80-6, 2002; Liu et al, Mol Immunol 44:1775-1783, 2007; Doo
  • VNAR library To develop the VNAR library disclosed herein, immune cells were collected from a group of six naive nurse sharks. Using one forward primer and two reverse primers, the VNAR fragments for each shark and each primer combination were separately PCR amplified (FIG. 8). The 12 PCR fractions from the six sharks were evenly pooled to ensure every group of VNAR was equally represented in the library. Instead of using conventional digestion and ligation method, overlapping PCR and a self-ligation method were used to make the library (FIG. 1). This approach is far more efficient than the common digestion/ligation method. The library contains 1.2 x 10 10 individual clones, which is much larger than previously reported shark libraries.
  • a panel of tumor and virus antigen proteins were used as targets to successfully discover binders of interest.
  • a binder for every antigen was identified, which indicates that the phage display library is an efficient route to generate shark binders even when naive sharks are used.
  • Type II VNAR was found to be the major type in both the library and in the selected binders
  • the CDRs control the antibody binding specificity.
  • the framework of shark VNAR may also contribute its binding specificity.
  • hFc-05 and hFc-48 have an almost identical sequence except for 3 consecutive amino acid changes in FR1 (QTI and RSV, respectively).
  • the clone hFc-05 was shown to only bind hFc with no cross-reactivity to rFc and mFc.
  • the hFc-48 clone retained its ability to bind hFc, but was also shown to bind mouse serum IgGs equally well. This phenomenon indicated that the framework structure influences the binding specificity.
  • the studies disclosed herein indicate that a large phage-displayed naive library is a very efficient route to generate shark VNAR binders.
  • the shark library approach provides a powerful platform to isolate high affinity binders to tumor and viral antigens.
  • VNAR clone GPC3-F1 does not belong to any known type of VNAR because it contains three cysteine residues instead of two cysteines (found in Type IV VNAR) or four cysteines (found in Type II VNAR).
  • TWO mutants of GPC-F1 were engineered to resemble a Type II or Type IV VNAR.
  • F1-Y29C introduces a cysteine residue into CDR1 to generate a Type II VNAR and F1-C96S removes a cysteine residue from CDR3 to generate a Type IV VNAR.
  • the amino acid sequences of Fl, F1-Y29C and F1-C96S are provided below, along with codon-optimized (for expression in bacterial cells) nucleic acid sequences encoding each VNAR.

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Abstract

The antigen binding region of immunoglobulin new antigen receptor (IgNAR) antibodies found in cartilaginous fish is composed solely of a heavy chain, which makes it one of the smallest immunoglobulins in the animal kingdom. The reduced size allows the variable region (VNAR domain) of this immunoglobulin to bind poorly exposed epitopes in target proteins. Construction of a naive phage-displayed VNAR antibody library from six adult nurse sharks is described. Isolation and characterization of a panel of binders from the VNAR library is also described. The VNAR antibodies bind a variety of tumor antigens, including glypican-3 (GPC3), HER2 and PDl, and viral antigens, including the spike protein of Middle East respiratory syndrome (MERS) virus and severe acute respiratory syndrome (SARS) virus.

Description

VARIABLE NEW ANTIGEN RECEPTOR (VNAR) ANTIBODIES AND ANTIBODY CONJUGATES TARGETING TUMOR AND VIRAL ANTIGENS
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application No. 62/334, 194, filed
May 10, 2016, which is herein incorporated by reference in its entirety.
FIELD
This disclosure concerns the construction of a phage display variable new antigen receptor (VNAR) antibody library and the identification of antibody clones from the VNAR library that bind tumor and viral antigens.
BACKGROUND
Classical IgG has become essential to many modern day biotechnologies and therapeutics. For example, flow cytometry and enzyme-linked immunosorbent assay (ELISA) would not be possible without the advancement of antibody production techniques. The use of IgG in new applications can be limited by the size of the immunoglobulin, in particular the size of the binding domain. IgG is best described as a heterodimeric homodimer, which means it consists of two copies of both a heavy chain and a light chain. The antibody has two identical antigen binding regions (Fab) which are determined by the interaction of the heavy chain variable domain (VH) with one light chain variable domain (VL). This requirement for two separate variable domains limits the minimal size of protein products, with dual domain single chain Fv (scFv) fragments having a molecular weight of about 30 kD. This and other limitations have stimulated an interest in exploring alternative immunoglobulin proteins, such as the shark VNAR (variable domain of the IgNAR, or new antigen receptor) and the camelid VHH domain antibodies, both of which can be isolated as soluble, stable, monomeric binding domains (Wesolowski et al. , Med Microbiol immunol 198: 157- 174, 2009). VNAR and VHH domain antibodies range from 12- 15 kD in size, which is about half the size of the smallest scFv binding unit.
Sharks and other cartilaginous fish (rays, skates, and chimaeras) are the phylogenetically oldest living organisms that use antibodies as part of their adaptive immune system. These fish produce three different isotypes of antibodies, IgM, IgW and IgNAR (immunoglobulin new antigen receptor) (Rumfelt et al , BMC Immunol 5:8, 2004; Rumfelt et al , J Immunol 173 : 1129-1 139, 2004). IgNAR antibodies are homodimeric proteins containing only heavy chains with an antigen binding region at the end of the each heavy chain. This class of antibody serves as the major component of the fish' s humoral immune response (Feige et al. , Proc Natl Acad Sci USA
111 :8155-8160, 2014). Shark VNAR domains share similar, desirable features to the camelid VHH domains, which are well characterized and currently being used in clinical trials. Even though less is known about the VNAR antibodies, they have the potential to be used as biological therapeutics based on several factors, including (i) their small size and potential to penetrate dense tissues inaccessible to IgG (Irving et al. , J Immunol Methods 248:31-45, 2001); (ii) their propensity to bind in protein clefts and hidden enzyme active sites (Stanfield et al. , Science 305: 1770-1773, 2004); (iii) their solubility and robustness in harsh conditions (Simmons et al. , / Immunol Methods 315: 171-184, 2006); and their ability for high-affinity (up to sub-nanomolar) binding.
Additionally, these antibodies have the ability to bind a wide range of antigens, despite the nature of their single domain architecture (Fennell et al. , J Mol Biol 400: 155-170, 2010).
SUMMARY
Disclosed herein are single-domain monoclonal antibodies selected from a naive shark VNAR antibody library that specifically bind a tumor or viral antigen. Also disclosed is an efficient method of producing a highly diverse VNAR antibody library using overlap extension PCR.
Provided herein are single-domain monoclonal antibodies that bind, such as specifically bind, glypican-3 (GPC3), programmed cell death 1 (PD1), HER2, Middle East respiratory syndrome (MERS) virus spike protein or severe respiratory syndrome (SARS) virus spike protein. Also provided are antibody conjugates that include the single-domain monoclonal antibodies disclosed herein, including antibody-drug conjugates (ADCs), chimeric antigen receptors (CARs), immunoconjugates (such as antibody-toxin conjugates), multi-specific (such as bispecific or trispecific) antibodies, and antibody-nanoparticle conjugates. Further provided are fusion proteins that include the disclosed single-domain monoclonal antibodies and a heterologous protein.
Compositions that include the antibodies, antibody conjugates and fusion proteins disclosed herein are also provided by the present disclosure. Also provided are nucleic acid molecules and vectors encoding the disclosed single-domain monoclonal antibodies and conjugates thereof.
Also provided herein are methods of treating a GPC3 -positive or HER2 -positive cancer in a subject; methods of inhibiting tumor growth or metastasis of a GPC3-positive or HER2-positive cancer in a subject; methods of enhancing an anti-tumor response in a subject; methods of treating a MERS virus infection in a subject; methods of treating a SARS virus infection in a subject;
methods of detecting expression of GPC3, HER2 or PD1 in a sample; and methods of detecting MERS virus or SARS virus in a sample, using the disclosed single-domain monoclonal antibodies and conjugates and compositions thereof. Further provided herein are methods of generating a VNAR library. In some embodiments, the method includes providing complementary DNA (cDNA) generated from RNA isolated from lymphocytes of one or more cartilaginous fish; providing a vector backbone comprising a vector junction sequence; amplifying VNAR nucleic acid from the cDNA by polymerase chain reaction (PCR) using a VNAR-specific forward primer and at least one reverse primer comprising VNAR- specific sequence and the vector junction sequence to generate VNAR nucleic acid sequences comprising the vector junction sequence; assembling the VNAR nucleic acid sequences comprising the vector junction sequence and the vector backbone comprising the vector junction sequence by overlap extension PCR using the VNAR-specific forward primer and a vector backbone-specific reverse primer, thereby producing linear VNAR vectors; and maintaining the linear VNAR vectors under conditions to permit self-ligation.
The foregoing and other objects, features, and advantages of the invention will become more apparent from the following detailed description, which proceeds with reference to the accompanying figures.
BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 is a schematic outline for generating the shark VNAR library disclosed herein.
FIGS. 2A-2C provide a sequence alignment and characterization of randomly picked clones from the VNAR library. (FIG. 2A) Sequence alignment of HEL-5A7 (SEQ ID NO: 11) and 25 randomly sequenced clones (SEQ ID NOs: 12-36). (FIG. 2B) Statistical analysis of the types of clones. (FIG. 2C) CDR3 length distribution of the clones.
FIG. 3 is a series of graphs showing identification of the binders by phage ELISA.
Monoclonal phage ELISA was carried out to identify the binders to GPC3, Her2, PDl, Middle East respiratory syndrome (MERS) virus spike (S) protein, severe acute respiratory syndrome (SARS) virus S protein, PE38 and human Fc (hFc) (or rabbit Fc - rFc).
FIGS. 4A-4C provide a sequence alignment of the identified binders and analysis of the binders. (FIG. 4A) Sequence alignment of the identified binders (SEQ ID NOs: 1-10 and 37-47). (FIG. 4B) VNAR type analysis of the binders. (FIG. 4C) CDR3 length of the binders.
FIGS. 5A-5D are flow cytometry plots and graphs showing characterization of the GPC3 binder. (FIG. 5A) Phage flow cytometry showing the GPC3-F1 clone binding GPC3-positive Gl cells. PD1-A1, which binds PDl antigen, was used as the phage control. (FIG. 5B) Purified GPC3-Fl-hFc fusion protein binds GPC3-positive HepG2 and Gl cells. (FIG. 5C) The cell binding affinity of GPC3-Fl-hFc (KD 124 nM) was measured by flow cytometry on Gl cells. (FIG. 5D) Epitope mapping of GPC3-F1 showing its epitope is not competitive with YP7 (generated by immunizing mice using the same GPC3 peptide 511-560).
FIG. 6A shows the results of a phage ELISA demonstrating binding of the PE clone to PE38, but not mPE24.
FIG. 6B shows structural models of PE38 and PE24. Seven B-cell epitopes (indicated by balls) were mutated.
FIG. 7 is a graph showing binding specificity of the hFc binders.
FIG. 8 shows PCR amplification of VNAR fragments using primer pair IgNAR-F/IgNAR-Rl
(top panels) and primer pair IgNAR-F/IgNAR-R2 (bottom panels).
FIGS. 9A-9J provide sequence alignments of each VNAR antibody with the four most closely related sequences identified by Basic Local Alignment Search Tool (BLAST). (FIG. 9A)
GPC3-F1 (SEQ ID NOs: 1 and 48-51). (FIG. 9B) PD1-A1 (SEQ ID NOs: 2 and 52-55). (FIG. 9C)
HER2-A6 (SEQ ID NOs: 3 and 56-59). (FIG. 9D) HER2-B7 (SEQ ID NOs: 4 and 60-63). (FIG.
9E) MERS-A3 (SEQ ID NOs: 5 and 64-67). (FIG. 9F) MERS-A7 (SEQ ID NOs: 6 and 68-71). (FIG. 9G) MERS-A8 (SEQ ID NOs: 7 and 72-75). (FIG. 9H) MERS-B4 (SEQ ID NOs: 8 and 76-
79). (FIG. 91) MERS-B5 (SEQ ID NOs: 9 and 80-83). (FIG. 9J) SARS-01 (SEQ ID NOs: 10 and
84-87).
SEQUENCE LISTING
The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. The Sequence Listing is submitted as an ASCII text file, created on May 8, 2017, 94.4 KB, which is incorporated by reference herein. In the accompanying sequence listing:
SEQ ID NO: 1 is the amino acid sequence of VNAR clone GPC3-F1.
SEQ ID NO: 2 is the amino acid sequence of VNAR clone PD1-A1.
SEQ ID NO: 3 is the amino acid sequence of VNAR clone HER2-A6.
SEQ ID NO: 4 is the amino acid sequence of VNAR clone HER2-B7.
SEQ ID NO: 5 is the amino acid sequence of VNAR clone MERS-A3.
SEQ ID NO: 6 is the amino acid sequence of VNAR clone MERS-A7.
SEQ ID NO: 7 is the amino acid sequence of VNAR clone MERS-A8.
SEQ ID NO: 8 is the amino acid sequence of VNAR clone MERS-B4.
SEQ ID NO: 9 is the amino acid sequence of VNAR clone MERS-B5. SEQ ID NO: 10 is the amino acid sequence of VNAR clone SARS-01.
SEQ ID NO: 11 is the amino acid sequence of VNAR antibody HEL-5A7.
SEQ ID NOs: 12-36 are the amino acid sequences of randomly sequenced clones from the shark VNAR library (shown in FIG. 2).
SEQ ID NOs: 37-47 are the amino acid sequences of VNAR clones that bind hFc or hFc/rFc (shown in FIG. 4).
SEQ ID NOs: 48-87 are the amino acid sequences of VNAR antibodies identified during BLAST searches (shown in FIGS. 9A-9J).
SEQ ID NOs: 88-92 are primer sequences.
SEQ ID NO: 93 is a codon-optimized nucleotide sequence encoding VNAR clone GPC3-F1. SEQ ID NO: 94 is a codon-optimized nucleotide sequence encoding VNAR mutant Fl-
Y29C.
SEQ ID NO: 95 is the amino acid sequence of VNAR mutant F1-Y29C.
SEQ ID NO: 96 is a codon-optimized nucleotide sequence encoding VNAR mutant Fl-
C96S.
SEQ ID NO: 97 is the amino acid sequence of VNAR mutant F1-C96S.
DETAILED DESCRIPTION
I. Abbreviations
ADC antibody-drug conjugate
ADCC antibody-dependent cellular cytotoxicity
BSA bovine serum albumin
CAR chimeric antigen receptor
CCA cholangiocarcinoma
CCC clear cell carcinoma
cDNA complementary DNA
CDR complementarity determining region
ELISA enzyme-linked immunosorbent assay
FACS fluorescence activated cell sorting
FR framework
GPC-3 glypican-3
HCC hepatocellular carcinoma
hFc human Fc
IgNAR immunoglobulin new antigen receptor MERS Middle East respiratory syndrome
mFc mouse Fc
PCR polymerase chain reaction
PD1 programmed cell death protein 1
PE Pseudomonas exotoxin
PFU plaque forming units
rFc rabbit Fc
SARS severe acute respiratory syndrome
scFv single chain variable fragment
VH variable heavy domain
VL variable light domain
VNAR variable domain of the immunoglobulin new antigen receptor
II. Terms and Methods
Unless otherwise noted, technical terms are used according to conventional usage.
Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632- 02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).
In order to facilitate review of the various embodiments of the disclosure, the following explanations of specific terms are provided:
Antibody: A polypeptide ligand comprising at least one variable region that recognizes and binds (such as specifically recognizes and specifically binds) an epitope of an antigen.
Mammalian immunoglobulin molecules are composed of a heavy (H) chain and a light (L) chain, each of which has a variable region, termed the variable heavy (VH) region and the variable light (VL) region, respectively. Together, the VH region and the VL region are responsible for binding the antigen recognized by the antibody. There are five main heavy chain classes (or isotypes) of mammalian immunoglobulin, which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE. Antibody isotypes not found in mammals include IgX, IgY, IgW and IgNAR. IgY is the primary antibody produced by birds and reptiles, and has some functionally similar to mammalian IgG and IgE. IgW and IgNAR antibodies are produced by cartilaginous fish, while IgX antibodies are found in amphibians. Antibody variable regions contain "framework" regions and hypervariable regions, known as "complementarity determining regions" or "CDRs." The CDRs are primarily responsible for binding to an epitope of an antigen. The framework regions of an antibody serve to position and align the CDRs in three-dimensional space. The amino acid sequence boundaries of a given CDR can be readily determined using any of a number of well-known numbering schemes, including those described by Kabat et al. {Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991; the "Kabat" numbering scheme), Chothia et al. (see
Chothia and Lesk, J Mol Biol 196:901-917, 1987; Chothia et al , Nature 342:877, 1989; and Al- Lazikani et al, (JMB 273,927-948, 1997; the "Chothia" numbering scheme), and the
ImMunoGeneTics (IMGT) database (see, Lefranc, Nucleic Acids Res 29:207-9, 2001; the "IMGT" numbering scheme). The Kabat and IMGT databases are maintained online.
A "single-domain antibody" refers to an antibody having a single domain (a variable domain) that is capable of specifically binding an antigen, or an epitope of an antigen, in the absence of an additional antibody domain. Single-domain antibodies include, for example, VNAR antibodies, camelid VHH antibodies, VH domain antibodies and VL domain antibodies. VNAR antibodies are produced by cartilaginous fish, such as nurse sharks, wobbegong sharks, spiny dogfish and bamboo sharks. Camelid VHH antibodies are produced by several species including camel, llama, alpaca, dromedary, and guanaco, which produce heavy chain antibodies that are naturally devoid of light chains.
A "monoclonal antibody" is an antibody produced by a single clone of lymphocytes or by a cell into which the coding sequence of a single antibody has been transfected. Monoclonal antibodies are produced by methods known to those of skill in the art. Monoclonal antibodies include humanized monoclonal antibodies.
A "chimeric antibody" has framework residues from one species, such as human, and CDRs (which generally confer antigen binding) from another species, such as a VNAR that specifically binds a tumor or viral antigen.
A "humanized" antibody is an immunoglobulin including a human framework region and one or more CDRs from a non-human (for example a shark, mouse, rabbit, rat, or synthetic) immunoglobulin. The non-human immunoglobulin providing the CDRs is termed a "donor," and the human immunoglobulin providing the framework is termed an "acceptor." In one embodiment, all CDRs are from the donor immunoglobulin in a humanized immunoglobulin. Constant regions need not be present, but if they are, they must be substantially identical to human immunoglobulin constant regions, i.e. , at least about 85-90%, such as about 95% or more identical. Hence, all parts of a humanized immunoglobulin, except possibly the CDRs, are substantially identical to corresponding parts of natural human immunoglobulin sequences. A humanized antibody binds to the same antigen as the donor antibody that provides the CDRs. Humanized or other monoclonal antibodies can have additional conservative amino acid substitutions which have substantially no effect on antigen binding or other immunoglobulin functions. Methods of humanizing shark VNAR antibodies has been previously described (Kovalenko et al. , / Biol Chem 288(24): 17408-17419, 2013).
Antibody-drug conjugate (ADC): A molecule that includes an antibody (or antigen- binding fragment of an antibody) conjugated to a drug, such as a cytotoxic agent. ADCs can be used to specifically target a drug to cancer cells through specific binding of the antibody to a tumor antigen expressed on the cell surface. Exemplary drugs for use with ADCs include anti- microtubule agents (such as maytansinoids, auristatin E and auristatin F) and interstrand crosslinking agents (e.g. , pyrrolobenzodiazepines; PDBs).
Anti-microtubule agent: A type of drug that blocks cell growth by stopping mitosis. Anti-microtubule agents, also referred to as "anti-mitotic agents," are used to treat cancer.
Binding affinity: Affinity of an antibody for an antigen. In one embodiment, affinity is calculated by a modification of the Scatchard method described by Frankel et al. (Mol. Immunol. , 16: 101-106, 1979). In another embodiment, binding affinity is measured by an antigen/antibody dissociation rate. In another embodiment, binding affinity is measured by a competition radioimmunoassay. In another embodiment, binding affinity is measured by ELISA. An antibody that "specifically binds" an antigen is an antibody that binds the antigen with high affinity and does not significantly bind other unrelated antigens.
Bispecific antibody: A recombinant protein that includes antigen-binding fragments of two different monoclonal antibodies, and is thereby capable of binding two different antigens. In some embodiments, bispecific antibodies are used for cancer immunotherapy by simultaneously targeting, for example, both CTLs (such as a CTL receptor component such as CD3) or effector natural killer (NK) cells, and a tumor antigen. Similarly, a multi-specific antibody is a recombinant protein that includes antigen-binding fragments of at least two different monoclonal antibodies, such as two, three or four different monoclonal antibodies.
Breast cancer: A type of cancer that forms in the tissues of the breast, typically in the ducts and lobules. In some embodiments, a patient with breast cancer is node -positive, meaning the breast cancer has spread to the lymph nodes.
Cartilaginous fish: A class of fish that have a skeleton made of cartilage, instead of bone. These fish also have paired fins, paired nostrils, scales and a two-chambered heart. Cartilaginous fish are in the class Chondrichthyes, and include sharks, skates, rays and chimaeras (also known as ghost sharks). In some embodiments herein, the cartilaginous fish is a shark, such as a shark of the species Ginglymostoma cirratum, Orectolobus maculatus, Squalus acanthias, Triakis scyUium or Chiloscyllium plagiosum.
Chemotherapeutic agent: Any chemical agent with therapeutic usefulness in the treatment of diseases characterized by abnormal cell growth. Such diseases include tumors, neoplasms, and cancer as well as diseases characterized by hyperplastic growth, such as psoriasis. In one embodiment, a chemotherapeutic agent is a radioactive compound. One of skill in the art can readily identify a chemotherapeutic agent of use (see for example, Slapak and Kufe, Principles of Cancer Therapy, Chapter 86 in Harrison's Principles of Internal Medicine, 14th edition; Perry et al, Chemotherapy, Ch. 17 in Abeloff, Clinical Oncology 2nd ed., © 2000 Churchill Livingstone, Inc; Baltzer, L., Berkery, R. (eds.): Oncology Pocket Guide to Chemotherapy, 2nd ed. St. Louis, Mosby-Year Book, 1995; Fischer, D.S., Knobf, M.F., Durivage, H.J. (eds): The Cancer
Chemotherapy Handbook, 4th ed. St. Louis, Mosby-Year Book, 1993). Combination
chemotherapy is the administration of more than one agent to treat cancer. One example is the administration of an antibody (or immunoconjugate or ADC) that binds a tumor antigen used in combination with a radioactive or chemical compound.
Chimeric antigen receptor (CAR): A chimeric molecule that includes an antigen-binding portion (such as a single domain antibody) and a signaling domain, such as a signaling domain from a T cell receptor (e.g. CD3ζ). Typically, CARs are comprised of an antigen-binding moiety, a transmembrane domain and an endodomain. The endodomain typically includes a signaling chain having an immunoreceptor tyrosine-based activation motif (IT AM), such as CD3ζ or FceRIy. In some instances, the endodomain further includes the intracellular portion of at least one additional co-stimulatory domain, such as CD28 and/or CD137.
Codon-optimized: A "codon-optimized" nucleic acid refers to a nucleic acid sequence that has been altered such that the codons are optimal for expression in a particular system (such as a particular species or group of species). For example, a nucleic acid sequence can be optimized for expression in mammalian cells or in a particular mammalian species (such as human cells). In another example, a nucleic acid sequence is optimized for expression in bacterial cells, such as for production of protein (such as an antibody or immunotoxin). Codon optimization does not alter the amino acid sequence of the encoded protein.
Complementarity determining region (CDR): A region of hypervariable amino acid sequence that defines the binding affinity and specificity of an antibody.
Conservative variant: "Conservative" amino acid substitutions are those substitutions that do not substantially affect or decrease the affinity of a protein. For example, a monoclonal antibody that specifically binds a target antigen can include at most about 1, at most about 2, at most about 5, at most about 10, or at most about 15 conservative substitutions and specifically bind the target antigen. The term "conservative variant" also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid, provided that the antibody specifically binds the target antigen. Non-conservative substitutions are those that reduce an activity or binding to the target antigen.
Conjugate: In the context of the present disclosure, a "conjugate" is an antibody or antibody fragment (such as an antigen-binding fragment) covalently linked to an effector molecule or a second protein (such as a second antibody). The effector molecule can be, for example, a drug, toxin, therapeutic agent, detectable label, protein, nucleic acid, lipid, nanoparticle, carbohydrate or recombinant virus. An antibody conjugate is often referred to as an "immunoconjugate." When the conjugate comprises an antibody linked to a drug (e.g. , a cytotoxic agent), the conjugate is often referred to as an "antibody-drug conjugate" or "ADC." Other antibody conjugates include, for example, multi-specific (such as bispecific or trispecific) antibodies and chimeric antigen receptors (CARs).
Contacting: Placement in direct physical association; includes both in solid and liquid form.
Cytotoxic agent: Any drug or compound that kills cells.
Cytotoxicity: The toxicity of a molecule, such as an immunotoxin, to the cells intended to be targeted, as opposed to the cells of the rest of an organism. In one embodiment, in contrast, the term "toxicity" refers to toxicity of an immunotoxin to cells other than those that are the cells intended to be targeted by the targeting moiety of the immunotoxin, and the term "animal toxicity" refers to toxicity of the immunotoxin to an animal by toxicity of the immunotoxin to cells other than those intended to be targeted by the immunotoxin.
Degenerate variant: In the context of the present disclosure, a "degenerate variant" refers to a polynucleotide encoding a polypeptide or an antibody that includes a sequence that is degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon. Therefore, all degenerate nucleotide sequences are included as long as the amino acid sequence of the polypeptide or antibody encoded by the nucleotide sequence is unchanged.
Diagnostic: Identifying the presence or nature of a pathologic condition, such as, but not limited to, cancer. Diagnostic methods differ in their sensitivity and specificity. The "sensitivity" of a diagnostic assay is the percentage of diseased individuals who test positive (percent of true positives). The "specificity" of a diagnostic assay is one minus the false positive rate, where the false positive rate is defined as the proportion of those without the disease who test positive. While a particular diagnostic method may not provide a definitive diagnosis of a condition, it suffices if the method provides a positive indication that aids in diagnosis. "Prognostic" is the probability of development (e.g., severity) of a pathologic condition, such as cancer or metastasis.
Drug: Any compound used to treat, ameliorate or prevent a disease or condition in a subject. In some embodiments herein, the drug is an anti-cancer agent, for example a cytotoxic agent, such as an anti-mitotic or anti-microtubule agent.
Effector molecule: The portion of an antibody conjugate (or immunoconjugate) that is intended to have a desired effect on a cell to which the conjugate is targeted. Effector molecules are also known as effector moieties (EMs), therapeutic agents, diagnostic agents, or similar terms. Therapeutic agents (or drugs) include such compounds as small molecules, nucleic acids, proteins, peptides, amino acids or derivatives, glycoproteins, radioisotopes, lipids, nanoparticles, carbohydrates, or recombinant viruses. Nucleic acid therapeutic and diagnostic moieties include antisense nucleic acids, derivatized oligonucleotides for covalent cross-linking with single or duplex DNA, and triplex forming oligonucleotides. Alternatively, the effector molecule can be contained within an encapsulation system, such as a nanoparticle, liposome or micelle, which is conjugated to the antibody. Encapsulation shields the effector molecule from direct exposure to the circulatory system. Means of preparing liposomes attached to antibodies are well known to those of skill in the art (see, for example, U.S. Patent No. 4,957,735; and Connor et al , Pharm Ther 28:341-365, 1985). Diagnostic agents or moieties include radioisotopes and other detectable labels (e.g. , fluorophores, chemiluminescent agents, and enzymes). Radioactive isotopes include 35 S, nC, 13N, 150, 18F, 19F, 99mTc, 1311, 3H, 14C, 15N, 90Y, 99Tc, i nIn and 125I.
Epitope: An antigenic determinant. These are particular chemical groups or peptide sequences on a molecule that are antigenic, i.e. that elicit a specific immune response. An antibody specifically binds a particular antigenic epitope on a polypeptide.
Framework region: Amino acid sequences interposed between CDRs. The framework regions serve to hold the CDRs in an appropriate orientation for antigen binding.
Fusion protein: A protein comprising at least a portion of two different (heterologous) proteins.
Glypican-3 (GPC3): A member of the glypican family of heparan sulfate (HS) proteoglycans that are attached to the cell surface by a glycosylphosphatidylinositol anchor (Filmus and Selleck, / Clin Invest 108:497-501, 2001). The GPC3 gene codes for a core protein of approximately 70 kD, which can be cleaved by furin to produce an N-terminal 40 kD fragment and a C-terminal 30 kD fragment. Two HS chains are attached on the C-terminal portion of GPC3. GPC3 and other glypican family proteins play a role in cell division and cell growth regulation.
GPC3 is highly expressed in HCC and some other human cancers including melanoma, squamous cell carcinomas of the lung, and clear cell carcinomas of the ovary (Ho and Kim, Eur J Cancer
47(3):333-338, 2011), but is not expressed in normal tissues. GPC3 is also known as SGB, DGSX, MXR7, SDYS, SGBS, OCI-5, SGBS1 and GTR2-2.
There are four known isoforms of human GPC3 (isoforms 1-4). Nucleic acid and amino acid sequences of the four isoforms of GPC3 are known, including GenBank Accession numbers:
NM_001164617 and NP_001158089 (isoform 1); NM_004484 and NP_004475 (isoform 2);
NM_001164618 and NP_001158090 (isoform 3); and NM_001164619 and NP_001158091 (isoform 4). In some embodiments of the present disclosure, the antibodies disclosed herein bind one or more of the four human GPC3 isoforms, or a conservative variant thereof.
GPC3-positive cancer: A cancer that overexpresses GPC3. Examples of GPC3-positive cancers include, but are not limited to, HCC, melanoma, squamous cell carcinoma of the lung and ovarian clear cell carcinoma.
Hepatocellular carcinoma (HCC): A primary malignancy of the liver typically occurring in patients with inflammatory livers resulting from viral hepatitis, liver toxins or hepatic cirrhosis
(often caused by alcoholism). HCC is also called malignant hepatoma.
HER2: A member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. This protein has no ligand binding domain of its own and therefore cannot bind growth factors. However, it does bind tightly to other ligand-bound EGF receptor family members to form a heterodimer, stabilizing ligand binding and enhancing kinase-mediated activation of downstream signaling pathways, such as those involving mitogen-activated protein kinase and phosphatidylinositol-3 kinase. Amplification and/or overexpression of the HER2 gene has been reported in numerous cancers, including breast and ovarian tumors. For example, amplification of the HER2 genes has been reported in approximately 20-25% of primary breast cancers. HER2 is also known as v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene, epidermal growth factor receptor 2 (EGFR2), ERBB2 and Her-2/neu.
HER2-positive cancer: A cancer that overexpresses HER2. Examples of HER2-positive cancers include, but are not limited to, breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma and head and neck carcinoma.
Heterologous: Originating from a separate genetic source or species. Immune response: A response of a cell of the immune system, such as a B cell, T cell, or monocyte, to a stimulus. In one embodiment, the response is specific for a particular antigen (an "antigen-specific response"). In one embodiment, an immune response is a T cell response, such as a CD4+ response or a CD8+ response. In another embodiment, the response is a B cell response, and results in the production of antigen-specific antibodies.
Immunoconjugate: A covalent linkage of an effector molecule to an antibody or functional fragment thereof. The effector molecule can be a detectable label or an immunotoxin. Specific, non-limiting examples of toxins include, but are not limited to, abrin, ricin, Pseudomonas exotoxin (PE, such as PE35, PE37, PE38, and PE40), diphtheria toxin (DT), botulinum toxin, or modified toxins thereof, or other toxic agents that directly or indirectly inhibit cell growth or kill cells. For example, PE and DT are highly toxic compounds that typically bring about death through liver toxicity. PE and DT, however, can be modified into a form for use as an
immunotoxin by removing the native targeting component of the toxin (such as the domain la of PE and the B chain of DT) and replacing it with a different targeting moiety, such as an antibody. A "chimeric molecule" is a targeting moiety, such as a ligand or an antibody, conjugated (coupled) to an effector molecule. The term "conjugated" or "linked" refers to making two polypeptides into one contiguous polypeptide molecule. In one embodiment, an antibody is joined to an effector molecule. In another embodiment, an antibody joined to an effector molecule is further joined to a lipid or other molecule to a protein or peptide to increase its half-life in the body. The linkage can be either by chemical or recombinant means. In one embodiment, the linkage is chemical, wherein a reaction between the antibody moiety and the effector molecule has produced a covalent bond formed between the two molecules to form one molecule. A peptide linker (short peptide sequence) can optionally be included between the antibody and the effector molecule. Because immunoconjugates were originally prepared from two molecules with separate functionalities, such as an antibody and an effector molecule, they are also sometimes referred to as "chimeric molecules." The term "chimeric molecule," as used herein, therefore refers to a targeting moiety, such as a ligand or an antibody, conjugated (coupled) to an effector molecule.
Immunoglobulin new antigen receptor (IgNAR) antibody: One of the three isotypes of immunoglobulin molecules produced by cartilaginous fish. IgNAR antibodies are homodimers of one variable new antigen receptor (VNAR) domain and five constant new antigen receptor (CNAR) domains (Roux <?i al , Proc Natl Acad Sci USA 95: 11804- 11809, 1998). IgNAR antibodies are a major component of the immune system of cartilaginous fish. Immunoliposome: A liposome with antibodies or antibody fragments conjugated to its surface. Immunoliposomes can carry cytotoxic agents or other drugs to antibody-targeted cells, such as tumor cells.
Interstrand crosslinking agent: A type of cytotoxic drug capable of binding covalently between two strands of DNA, thereby preventing DNA replication and/or transcription.
Isolated: An "isolated" biological component, such as a nucleic acid, protein (including antibodies) or organelle, has been substantially separated or purified away from other biological components in the environment (such as a cell) in which the component naturally occurs, i.e. , other chromosomal and extra-chromosomal DNA and RNA, proteins and organelles. Nucleic acids and proteins that have been "isolated" include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
Label: A detectable compound or composition that is conjugated directly or indirectly to another molecule, such as an antibody or a protein, to facilitate detection of that molecule.
Specific, non-limiting examples of labels include fluorescent tags, enzymatic linkages, and radioactive isotopes. In one example, a "labeled antibody" refers to incorporation of another molecule in the antibody. For example, the label is a detectable marker, such as the incorporation of a radiolabeled amino acid or attachment to a polypeptide of biotinyl moieties that can be detected by marked avidin (for example, streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or colorimetric methods). Various methods of labeling polypeptides and glycoproteins are known in the art and may be used. Examples of labels for polypeptides include, but are not limited to, the following: radioisotopes or radionucleotides (such as 35S, nC, 13N, 150, 18F, 19F, 99mTc, 1311, 3H, 14C, 15N, 90Y, 99Tc, i nIn and 125I), fluorescent labels (such as fluorescein isothiocyanate (FITC), rhodamine, lanthanide phosphors), enzymatic labels (such as horseradish peroxidase, beta-galactosidase, luciferase, alkaline phosphatase),
chemiluminescent markers, biotinyl groups, predetermined polypeptide epitopes recognized by a secondary reporter (such as a leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags), or magnetic agents, such as gadolinium chelates. In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
Linker: In some cases, a linker is a peptide within an antibody binding fragment (such as an Fv fragment) which serves to indirectly bond the variable heavy chain to the variable light chain. "Linker" can also refer to a peptide serving to link a targeting moiety, such as an antibody, to an effector molecule, such as a cytotoxin or a detectable label. The terms "conjugating," "joining," "bonding" or "linking" refer to making two
polypeptides into one contiguous polypeptide molecule, or to covalently attaching a radionuclide, drug or other molecule to a polypeptide, such as an antibody or antibody fragment. In the specific context, the terms include reference to joining a ligand, such as an antibody moiety, to an effector molecule. The linkage can be either by chemical or recombinant means. "Chemical means" refers to a reaction between the antibody moiety and the effector molecule such that there is a covalent bond formed between the two molecules to form one molecule.
Liver cancer: A type of cancer than forms in the tissues of the liver. Types of liver cancers include, for example, hepatocellular carcinoma (HCC), cholangiocarcinoma (also known as bile duct cancer), angiosarcoma and hepatoblastoma.
Lung cancer: Cancer that forms in tissues of the lung, usually in the cells lining air passages. The two main types are small cell lung cancer and non-small cell lung cancer. These types are diagnosed based on how the cells look under a microscope.
Mammal: This term includes both human and non-human mammals. Similarly, the term "subject" includes both human and veterinary subjects.
Melanoma: A form of cancer that originates in melanocytes (cells that make the pigment melanin). Melanocytes are found primary in the skin, but are also present in the bowel and eye. Melanoma in the skin includes superficial spreading melanoma, nodular melanoma, acral lentiginous melanoma, and lentigo maligna (melanoma). Any of the above types may produce melanin or can be amelanotic. Similarly, any subtype may show desmoplasia (dense fibrous reaction with neurotropism) which is a marker of aggressive behavior and a tendency to local recurrence. Other melanomas include clear cell sarcoma, mucosal melanoma and uveal melanoma.
Middle East respiratory syndrome (MERS) virus: A coronavirus that was first reported in Saudi Arabia in 2012. This virus causes a severe, acute respiratory illness characterized by fever, cough and shortness of breath. MERS virus, which is also known as MERS-CoV, causes death in about 30-40% of infected patients. The spike (S) protein of MERS virus is a type I membrane glycoprotein that assembles into trimers that constitute the spikes on the surface of the enveloped coronavirus particle. The S protein mediates virus entry into cells by binding cellular receptor dipeptidyl peptidase 4 (DPP4) and is responsible for membrane fusion.
Neoplasia, malignancy, cancer or tumor: A neoplasm is an abnormal growth of tissue or cells that results from excessive cell division. Neoplastic growth can produce a tumor. The amount of a tumor in an individual is the "tumor burden" which can be measured as the number, volume, or weight of the tumor. A tumor that does not metastasize is referred to as "benign." A tumor that invades the surrounding tissue and/or can metastasize is referred to as "malignant." Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein-coding regions, in the same reading frame.
Ovarian cancer: Cancer that forms in tissues of the ovary. Most ovarian cancers are either ovarian epithelial carcinomas (cancer that begins in the cells on the surface of the ovary) or malignant germ cell tumors (cancer that begins in egg cells).
Ovarian clear cell carcinoma: A distinct histopathologic subtype of epithelial ovarian cancer with an incidence of less than 5% of all ovarian malignancies. When viewed under a microscope, the insides of the cells of this type of tumor appear clear.
Overlap extension PCR: A type of PCR that can be used to insert specific mutations into a nucleic acid or to recombine two DNA sequences. By modifying the sequences incorporated into the 5' ends of primers used to PCR amplify a nucleic acid sequence, any pair of PCR products can be made to share a common sequence at one end. The common sequence allows strands from two different fragments to hybridize to one another, forming an overlap. Extension of this overlap by DNA polymerase yields a recombinant molecule (Horton et al, BioTechniques 54(3):129-133, 2013). Overlap extension PCR is also known as "splicing by overlap extension" or "SOEing." Pharmaceutical agent: A chemical compound or composition capable of inducing a desired therapeutic or prophylactic effect when properly administered to a subject or a cell.
Pharmaceutically acceptable carriers: The pharmaceutically acceptable carriers of use are conventional. Remington' s Pharmaceutical Sciences, by E.W. Martin, Mack Publishing Co., Easton, PA, 15th Edition, 1975, describes compositions and formulations suitable for
pharmaceutical delivery of the antibodies and conjugates disclosed herein.
In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (such as powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate. Preventing, treating or ameliorating a disease: "Preventing" a disease refers to inhibiting the full development of a disease. "Treating" refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition after it has begun to develop, such as a reduction in tumor burden or a decrease in the number of size of metastases.
"Ameliorating" refers to the reduction in the number or severity of signs or symptoms of a disease, such as cancer.
Programmed cell death protein 1 (PD1): A cell surface receptor that belongs to the immunoglobulin superfamily. PD1 is expressed on T cells and pro-B cells and binds two ligands - PD-L1 and PD-L2. PD1 functions as an immune checkpoint and plays an important role in down- regulating the immune system by preventing the activation of T cells. PD-L1 is highly expressed in several cancers. Antibodies targeting PD1 can block the interaction between PD1 and PD-L1, thereby enhancing T cell responses important for antitumor immune activity.
Purified: The term purified does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified peptide preparation is one in which the peptide or protein is more enriched than the peptide or protein is in its natural environment within a cell. In one embodiment, a preparation is purified such that the protein or peptide represents at least 50% of the total peptide or protein content of the preparation. Substantial purification denotes purification from other proteins or cellular components. A substantially purified protein is at least 60%, 70%, 80%, 90%, 95% or 98% pure. Thus, in one specific, non-limiting example, a substantially purified protein is 90% free of other proteins or cellular components.
Pyrrolobenzodiazepine (PBD): A class of sequence- selective DNA minor-groove binding crosslinking agents originally discovered in Streptomyces species. PDBs are significantly more potent than systemic chemotherapeutic drugs. The mechanism of action of PBDs is associated with their ability to form an adduct in the minor groove of DNA, thereby interfering with DNA processing. In the context of the present disclosure, PBDs include naturally produced and isolated PBDs, chemically synthesized naturally occurring PBDs, and chemically synthesized non-naturally occurring PBDs. PBDs also include monomeric, dimeric and hybrid PBDs (for a review see Gerratana, Med Res Rev 32(2):254-293, 2012).
Recombinant: A recombinant nucleic acid or protein is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or by the artificial manipulation of isolated segments of nucleic acids, for example, by genetic engineering techniques. Sample (or biological sample): A biological specimen containing genomic DNA, RNA (including mRNA), protein, or combinations thereof, obtained from a subject. Examples include, but are not limited to, peripheral blood, tissue, cells, urine, saliva, tissue biopsy, fine needle aspirate, surgical specimen, and autopsy material. In one example, a sample includes a tumor biopsy.
Sequence identity: The similarity between amino acid or nucleic acid sequences is expressed in terms of the similarity between the sequences, otherwise referred to as sequence identity. Sequence identity is frequently measured in terms of percentage identity (or similarity or homology); the higher the percentage, the more similar the two sequences are. Homologs or variants of a polypeptide or nucleic acid molecule will possess a relatively high degree of sequence identity when aligned using standard methods.
Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith and Waterman, Adv. Appl. Math. 2:482, 1981; Needleman and Wunsch, /. Mol. Biol. 48:443, 1970; Pearson and Lipman, Proc. Natl. Acad. Set U.S.A. 85:2444, 1988; Higgins and Sharp, Gene 73:237, 1988; Higgins and Sharp, CABIOS 5: 151, 1989; Corpet et al. , Nucleic Acids Research 16: 10881, 1988; and Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85:2444, 1988. Altschul et al. , Nature Genet. 6: 119, 1994, presents a detailed consideration of sequence alignment methods and homology calculations.
The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., J. Mol. Biol.
215:403, 1990) is available from several sources, including the National Center for Biotechnology Information (NCBI, Bethesda, MD) and on the internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. A description of how to determine sequence identity using this program is available on the NCBI website on the internet.
Homologs and variants of an antibody that specifically binds a target antigen or a fragment thereof are typically characterized by possession of at least about 75%, for example at least about 80%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity counted over the full length alignment with the amino acid sequence of the antibody using the NCBI Blast 2.0, gapped blastp set to default parameters. For comparisons of amino acid sequences of greater than about 30 amino acids, the Blast 2 sequences function is employed using the default BLOSUM62 matrix set to default parameters, (gap existence cost of 11, and a per residue gap cost of 1). When aligning short peptides (fewer than around 30 amino acids), the alignment should be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties). Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, such as at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% sequence identity. When less than the entire sequence is being compared for sequence identity, homologs and variants will typically possess at least 80% sequence identity over short windows of 10-20 amino acids, and may possess sequence identities of at least 85% or at least 90% or 95% depending on their similarity to the reference sequence. Methods for determining sequence identity over such short windows are available at the NCBI website on the internet. One of skill in the art will appreciate that these sequence identity ranges are provided for guidance only; it is entirely possible that strongly significant homologs could be obtained that fall outside of the ranges provided.
Severe acute respiratory syndrome (SARS) virus: A coronavirus that causes a severe and acute respiratory illness characterized by muscle pain, headache, fever, cough, dyspnea and pneumonia. SARS virus, which is also known as SARS-CoV, was first described in 2003 following an outbreak in Asia. The spike (S) protein of SARS virus is composed of two subunits, SI and S2. The S 1 subunit contains a receptor-binding domain that engages with the host cell receptor angiotensin-converting enzyme 2 (ACE2), while the S2 subunit mediates fusion between the viral and host cell membranes.
Small molecule: A molecule, typically with a molecular weight less than about 1000 Daltons, or in some embodiments, less than about 500 Daltons, wherein the molecule is capable of modulating, to some measurable extent, an activity of a target molecule.
Subject: Living multi-cellular vertebrate organisms, a category that includes both human and veterinary subjects, including human and non-human mammals.
Squamous cell carcinoma: A type of cancer that originates in squamous cells, thin, flat cells that form the surface of the skin, eyes, various internal organs, and the lining of hollow organs and ducts of some glands. Squamous cell carcinoma is also referred to as epidermoid carcinoma. One type of squamous cell carcinoma is squamous cell carcinoma of the lung.
Synthetic: Produced by artificial means in a laboratory, for example a synthetic nucleic acid or protein (for example, an antibody) can be chemically synthesized in a laboratory.
Therapeutically effective amount: A quantity of a specific substance sufficient to achieve a desired effect in a subject being treated. For instance, this can be the amount necessary to inhibit or suppress growth of a tumor, or inhibit a viral infection. In one embodiment, a therapeutically effective amount is the amount necessary to eliminate, reduce the size, or prevent metastasis of a tumor. When administered to a subject, a dosage will generally be used that will achieve target tissue concentrations (for example, in tumors) that has been shown to achieve a desired in vitro effect. Toxin: An agent that directly or indirectly inhibits the growth of and/or kills cells. Toxins include, for example, Pseudomonas exotoxin (PE, such as PE35, PE37, PE38 and PE40), diphtheria toxin (DT), botulinum toxin, abrin, ricin, saporin, restrictocin or gelonin, or modified toxins thereof. For example, PE and DT are highly toxic compounds that typically bring about death through liver toxicity. PE and DT, however, can be modified into a form for use as an
immunotoxin by removing the native targeting component of the toxin (such as domain la of PE or the B chain of DT) and replacing it with a different targeting moiety, such as an antibody.
Variable new antigen receptor (VNAR): The single variable domain of the
immunoglobulin new antigen receptor (IgNAR) antibody found in cartilaginous fish. VNAR antibodies are comprised of only two CDRs (CDRl and CDR3), but also contain two other hypervariable (HV) regions, referred to as the HV2 and HV4 regions. The CDRs and HV regions are surrounded by framework (FW) regions in the following N-terminal to C-terminal order: FW1- CDR1 -FW2-HV2-FW3 a-HV4-FW3b-CDR3 -FW4.
Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. The singular terms "a," "an," and "the" include plural referents unless context clearly indicates otherwise. "Comprising A or B" means including A, or B, or A and B. It is further to be understood that all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for description. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.
III. Introduction
The VNAR domain, like other variable domains has an immunoglobulin fold that contains β sheets held together by two canonical cysteine residues. In addition to the cysteines found in framework region (FR) 1 and 3b, the CDR3 can have one or two additional cysteines that form disulfide bonds with CDRl or other framework regions. IgNAR are classified into four types based on the number and positioning of non-canonical cysteines in the VNAR domain. Type I VNAR domains contain two cysteine residues in CDR3 that form two extra disulfide bonds with FR2 and FR4. Type II VNAR domains have one non-canonical cysteine in CDR3 that forms a disulfide bond with a non-canonical cysteine in CDR1. Type III VNAR domains form a disulfide bond in CDR3 and FR2, and type IV domains have no additional disulfide bonds. While type I VNAR usually have flatter antigen binding regions and CDR3 regions that average 21 amino acids long, type II are usually shorter with an average of 15 amino acids and have a protruding CDR3 that enables binding to pockets and grooves (Barelle et αΙ. , Αάν Exp Med Biol 655:49-62, 2009). The canonical CDR2 loop in classical IgG is missing in VNAR and is replaced with a short stretch of highly diverse amino acids, termed hypervariable region 2 (HV2) (Stanfield et al , Science 305: 1770-1773, 2004).
Additionally, there is a second hypervariable region, named HV4, which is inserted in the middle of FR3, therefore breaking FR3 into FR3a and FR3b.
Shark VNAR domains have many unique and advantageous properties that are absent from conventional IgG. First, sharks are evolutionarily distant from mammals on the tree of life, so sharks have the ability to generate high affinity binders to structurally conservative mammalian drug targets. These may include heparan sulfate proteoglycans, G-protein coupled receptors, ion channels, cytokines and tumor antigens that exhibit poor immunogenicity in mice and rabbits.
Second, conventional IgG antibodies have intrinsic drawbacks that can be overcome by shark VNAR domains. For example, the antigen binding region of conventional antibodies can be restricted in its ability to access certain epitopes, for example functional clefts of enzymes (Wesolowski et al , Med Microbiol immunol 198: 157-174, 2009; Barelle et al. , Adv Exp Med Biol 655:49-62, 2009; Nuttall and Walsh, Curr Opin Pharmacol 8:609-615, 2008). Like the camel VHH CDR3, IgNAR CDR3 is, on average, much longer (ranging from 9 to 26 amino acids) than the mouse or human counterpart. This can potentially lead to a larger diversity of structures that can interact with more diversified antigens (Diaz et al , Immunogenetics 54:501-512, 2002). Similarly, the longer CDR3 region in shark antibodies possess the extraordinary capacity to form long finger- like extensions that can probe proteins for hidden epitopes (Wesolowski et al. , Med Microbiol immunol 198: 157- 174, 2009). Third, conventional antibodies often have poor tissue penetration ability due to their large size (Mordenti et al, Toxicol Pathol 27:536-544, 1999). Whole IgG have a molecular weight of about 150 kD, while the molecular weight of Fab or scFv fragments is around 25 kD. As mentioned above, VNAR domains can be as small as 12-15 kD for their total weight. Finally, shark VNAR domain antibodies have structural advantages including high solubility, thermal and chemical stability, refolding capacity, and are easily expressed in E.coli systems (Wesolowski et al , Med Microbiol immunol 198: 157-174, 2009). Sharks enrich their blood with urea to prevent osmotic loss of water in the marine environment, so their antibody structure has evolved over millennia to become particularly stable (Feige et al , Proc Natl Acad Sci USA 111 :8155-8160, 2014). Phage display technology has been used in several shark VNAR engineering studies. These utilized VNAR libraries derived from naive sharks (Liu et al , Mol Immunol 44: 1775-1783, 2007) or immunized sharks (Stanfield et al , J Mol Biol 367:358-372, 2007; Dooley et al , Mol Immunol 40:25-33, 2003; Dooley and Flajnik, Eur J Immunol 35:936-945, 2005; Dooley et al , Proc Natl Acad Sci USA 103: 1846-1851, 2006), and synthetic/semisynthetic libraries created in the lab (Shao et al , Mol Immunol 44:656-665, 2007; Liu et al , BMC Biotechnol 7:78, 2007; Nuttall et al , Mol Immunol 38:313-326, 2001 ; Nuttall et al , Eur J Biochem 270:3543-3554, 2003; Nuttall et al , Proteins 55: 187-197, 2004). These studies generated VNAR binders to a variety of antigens with the affinity ranging from micromolar to low nanomolar levels. The present disclosure describes the construction of a large phage-displayed naive shark VNAR library from six sharks. To demonstrate the usefulness of the library, several rounds of panning were used to identify strong binders to important tumor and viral antigens. These included antigens associated with liver and breast cancers, as well as antigens from SARS virus and MERS virus. IV. Shark VNAR Antibodies Specific for Tumor and Viral Antigens
Disclosed herein are single-chain monoclonal antibodies that are specific for a tumor antigen (GPC3, PD1 or HER2), or a viral antigen (MERS virus spike protein or SARS virus spike protein). The disclosed antibodies were isolated from a naive shark VNAR phage display library. The disclosed antibodies can be used in a variety of compositions and conjugates, including chimeric antigen receptors, antibody-drug conjugates, immunoconjugates (e.g. conjugates comprising a toxin, such as PE), multi-specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and pharmaceutical compositions. The antibodies, conjugates and compositions disclosed herein can be used, for example, for the diagnosis and treatment of various types of cancer (such as GPC- or HER2-expressing cancers) or the diagnosis and treatment of MERS virus or SARS virus.
Shark VNAR antibodies include a complementarity determining region (CDR) 1 and a CDR3 that contribute to antigen-specific binding. VNAR antibodies also include two hypervariable region (HV) regions, referred to as HV2 and HV4. Provided in the table below are the amino acid sequences of 10 VNAR antibody clones identified from the shark VNAR phage display library disclosed herein. Also provided are two mutants of clone GPC-Fl , which each have a single amino acid substitution relative to the wild-type clone; the amino acid substitution is shown in bold. Residues that comprise the CDR1, HV2, HV4 and CDR3 regions are listed in the table and are indicated by underline. VNAR Sequence CDR1 HV2 HV4 CDR3 SEQ ID Clone residues residues residues residues NO:
GPC3-F1 ARVDQTPKTITKETGESLTINCV 26-33 45-52 60-64 84-101 1
LRDTSYALGSTYWYRKKLGST
NEESISKGGRYVETVNSGSKSFS
LRINDLTVEDSGTYRCKVSAGIR
IYSSYCSRDVYGGGTVVTVN
F1-Y29C ARVDQTPKTITKETGESLTINCV 26-33 45-52 60-64 84-101 95
LRDTS CALGSTYWYRKKLGST NEESISKGGRYVETVNSGSKSFS LRINDLTVEDSGTYRCKVSAGIR IYSSYCSRDVYGGGTVVTVN
F1-C96S ARVDQTPKTITKETGESLTINCV 26-33 45-52 60-64 84-101 97
LRDTSYALGSTYWYRKKLGST
NEESISKGGRYVETVNSGSKSFS
LRINDLTVEDSGTYRCKVSAGIR
IYSSYSSRDVYGGGTVVTVN
PD1-A1 ARVDQTPQTITKETGESLTINCV 26-33 45-52 60-64 84-96 2
LRDTKCPLSSTYWHROKSGPAN
EERIRFGGRYVETKNSGSKSFSL
RINDLTAEDSGTYRCKAFCPDA
SELVVYGGGTVVTVN
HER2-A6 ARVDQTPQTITKETGESLTINCV 26-33 45-52 60-64 84-106 3
LRDSNCALPSTYWYRKKSGSTN
EOIISKGGRYVETVNSGTKSFSL
RINDLTVFSOWHVSMVGRIPGP
WSGIAMTGFRKLMDVYGGGTV
VTVN
HER2-B7 ARVDQTPQTITKETGESVTITCV 26-33 45-51 59-63 83-100 4
LRDSDCTLPGTWWYLRRNGSP
OIGISNGGRYVETVNSRSKSFSL
RINDLTVEDSGTYRCKVFGITDI
HSSDCRLHLYGGGTAVTVN VNAR Sequence CDR1 HV2 HV4 CDR3 SEQ ID Clone residues residues residues residues NO:
MERS-A3 ARVDQTPQTITKETGESLTINCV 26-33 45-52 60-64 84-104 5
LRHSNCALWNTHWYRKKSGSV NEESISKGGRYVETVNSGSKSFS LRENDLSVEDSGTYRCKVDANG MGRYDCWENWYRDPYGGGTA VTVN
MERS-A7 ARVDQTPQRITKETGESLTINCV 26-33 45-52 60-64 84-106 6
LRVRDCVPSSTYWYHKKSGST
NEENIGKGGRYVETVNSGSKSF
SLRINDLTVEDSGTYRCKVFGR
PS S S W YGNCHOMDSGG AYGGG
TVVTVN
MERS-A8 ARVDQTPRSVTKETGESLTINC 26-33 45-52 60-64 84-103 7
VLRDASYALGSTCWYRKKSGS
TNEESISKGGRYVETVNSGSKSF
SLRINDLTVEDGGTYRCGVGR
WCGWTVCDVGALOAACGDGT
VVTVN
MERS-B4 ARVDQTPQTITKETGESLTINCV 26-33 45-52 60-64 84-101 8
LRDSDCALSSTYWYRKKSGSTN
EESISLAGRYVERVNSRSKSFSL
RINDLTVEDSGTYRCEVHLSWY
TRFDCGTGDVYGGGTVVTVN
MERS-B5 ARVDQTPQTITKETGESLTINCV 26-33 45-52 60-64 84-96 9
LRDSNCALSSTYWYRKKSGSRN EENISKGGRYVETVNSGTKSFSL RINDLTVEDSGTYRCKVPPIRWS CPAIYGGGTVVTVN
SARS-01 ARVDQTPQTITKETGESLTINCV 26-33 45-52 60-64 84-104 10
LRDSNCALSSTYWYRKKSGSTN EESISKGGRYVETVNSGSKSFSL RINDLTVEDSGTYRCNVFSWGY SCPSTAPLGNYDVYGGGTVVTV
N The CDRs and HV regions of a VNAR antibody are surrounded by framework (FW) regions in the following N-terminal to C-terminal order: FWl-CDRl-FW2-HV2-FW3a-HV4-FW3b- CDR3-FW4. The table below provides the amino acid residues of the FW regions for each VNAR disclosed herein.
Figure imgf000027_0001
Provided herein are single-domain antibodies that bind GPC3. In some embodiments, the single-domain antibody comprises at least a portion of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97, such as one or both of the CDRl and CDR3 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97. In particular embodiments, the single-domain antibody comprises residues 26-33 and 84- 101 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97. In some examples, the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97. In particular examples, the single-domain antibody comprises residues 26-33, 45-52, 60- 64 and 84-101 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97. In some examples, the single-domain antibody further comprises one or more of the FWl, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97. In specific examples, the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97. In particular non-limiting examples, the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
Provided herein are single-domain antibodies that bind PD-1. In some embodiments, the single-domain antibody comprises at least a portion of SEQ ID NO: 2, such as one or both of the CDR1 and CDR3 of SEQ ID NO: 2. In particular embodiments, the single-domain antibody comprises residues 26-33 and 84-96 of SEQ ID NO: 2. In some examples, the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 2. In some examples, the single- domain antibody comprises residues 26-33, 45-52, 60-64 and 84-96 of SEQ ID NO: 2. In some examples, the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 2. In specific examples, the amino acid sequence of the single- domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 2. In particular non-limiting examples, the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 2.
Provided herein are single-domain antibodies that bind HER2. In some embodiments, the single-domain antibody comprises at least a portion of SEQ ID NO: 3 or SEQ ID NO: 4, such as one or both of the CDR1 and CDR3 of SEQ ID NO: 3 or SEQ ID NO: 4. In particular
embodiments, the single-domain antibody comprises residues 26-33 and 84-106 of SEQ ID NO: 3, or residues 26-33 and 83-100 of SEQ ID NO: 4. In some examples, the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 3 or SEQ ID NO: 4. In some examples, the single-domain antibody comprises residues 26-33, 45-52, 60-64 and 84-106 of SEQ ID NO: 3, or residues 26-33, 45-51, 59-63 and 83-100 of SEQ ID NO: 4. In some examples, the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 3 or SEQ ID NO: 4. In specific examples, the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 3 or SEQ ID NO: 4. In particular non-limiting examples, the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 4.
Provided herein are single-domain antibodies that bind MERS virus spike protein. In some embodiments, the single-domain antibody comprises at least a portion of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9, such as one or both of the CDR1 and CDR3 of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9. In particular embodiments, the single-domain antibody comprises residues 26-33 and 84-104 of SEQ ID NO: 5; residues 26-33 and 84-106 of SEQ ID NO: 6; residues 26-33 and 84-103 of SEQ ID NO: 7; residues 26-33 and 84-101 of SEQ ID NO: 8; or residues 26-33 and 84-96 of SEQ ID NO: 9. In some examples, the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9. In some examples, the single-domain antibody comprises residues 26-33, 45-52, 60-64 and 84-104 of SEQ ID NO: 5; residues 26-33, 45-52, 60-64 and 84-106 of SEQ ID NO: 6; residues 26-33, 45-52, 60-64 and 84- 103 of SEQ ID NO: 7; residues 26-33, 45-52, 60-64 and 84-101 of SEQ ID NO: 8; or residues 26- 33, 45-52, 60-64 and 84-96 of SEQ ID NO: 9. In some examples, the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9. In specific examples, the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9. In particular non-limiting examples, the single- domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
Provided herein are single-domain antibodies that bind SARS virus spike protein. In some embodiments, the single-domain antibody comprises at least a portion of SEQ ID NO: 10, such as one or more of the CDR1 and CDR3 of SEQ ID NO: 10. In particular embodiments, the single- domain antibody comprises residues 26-33 and 84-104 of SEQ ID NO: 10. In some examples, the single-domain antibody further comprises the HV2 and/or HV4 of SEQ ID NO: 10. In some examples, the single-domain antibody comprises residues 26-33, 45-52, 60-64 and 84-104 of SEQ ID NO: 10. In some examples, the single-domain antibody further comprises one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 10. In specific examples, the amino acid sequence of the single-domain antibody is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 10. In particular non-limiting examples, the single-domain antibody comprises or consists of the amino acid sequence of SEQ ID NO: 10.
Also provided herein are single-domain antibodies that bind GPC3, PD1, HER2, MERS S protein or SARS S protein, comprising one or more of the FW1, FW2, FW3a, FW3b and FW4 of SEQ ID NO: 1, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQE ID NO: 9 or SEQ ID NO:
10. In particular examples, the single-domain antibody binds GPC3 and includes residues 1-25, 34- 44, 53-59, 65-83 and 102-110 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97. In other particular examples, the single-domain antibody binds PD1 and includes residues 1-25, 34-44, 53- 59, 65-83 and 97-105 of SEQ ID NO: 2. In other particular examples, the single-domain antibody binds HER2 and includes residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 3, or includes residues 1-25, 34-44, 52-58, 64-82 and 101-109 of SEQ ID NO: 4. In other particular examples, the single-domain antibody binds MERS S protein and includes residues 1-25, 34-44, 53-59, 65-83 and 105-113 of SEQ ID NO: 5; or includes residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 6; or includes residues 1-25, 34-44, 53-59, 65-83 and 104-112 of SEQ ID NO: 7; or includes residues 1-25, 34-44, 53-59, 65-83 and 102-110 of SEQ ID NO: 8; or includes residues 1-25, 34-44, 53-59, 65-83 and 97-105 of SEQ ID NO: 9. In yet other particular examples, the single-domain antibody binds SARS S protein and includes residues 1-25, 34-44, 53-59, 65-83 and 105-113 of SEQ ID NO: 10.
In some embodiments, the single-domain antibody is a chimeric, synthetic or humanized antibody.
The present disclosure also provides antibody conjugates that include any of the single- domain monoclonal antibodies disclosed herein. Antibody conjugates include, but are not limited to, antibody-drug conjugates (ADCs), chimeric antigen receptors (CARs), antibody-toxin immunoconjugates, multi-specific (such as bispecific or trispecific) antibodies, antibody- nanoparticle conjugations and immunoliposomes.
Provided herein are ADCs that include a drug conjugated to a single-domain antibody disclosed herein. In some embodiments, the drug is a small molecule. In some embodiments, the drug is an anti-microtubule agent, an anti-mitotic agent and/or a cytotoxic agent. ADCs are further discussed herein in section V below.
Also provided herein are CARs that include a single-domain antibody disclosed herein. In some embodiments, the CAR further includes a transmembrane domain and a signaling domain. In some examples, the CARs further include a signal peptide and/or one or more linker peptides. Also provided are isolated cells expressing a CAR disclosed herein. In some embodiments, the cell is a cytotoxic T lymphocyte (CTL). CARs are further discussed in section VI below.
Multi- specific (such as bispecific or trispecific) antibodies that include a single-domain antibody disclosed herein and a second monoclonal antibody or antigen-binding fragment thereof are further provided. In some embodiments, the second monoclonal antibody or antigen-binding fragment thereof specifically binds a component of the T cell receptor, such as CD3, or specifically binds a natural killer (NK) cell activating receptor, such as CD 16. Multi-specific antibodies are discussed in greater detail in section VII below.
Immunoconjugates that include a single-domain antibody disclosed herein and an effector molecule are also provided by the present disclosure. In some embodiments, the effector molecule is a toxin, such as Pseudomonas exotoxin or a variant thereof. In other embodiments, the effector molecule is a detectable label, such as a fluorescent, radioactive or enzymatic label.
Immunoconjugates are discussed in greater detail in section VIII below.
Also provided herein are antibody-nanoparticle conjugates that include a nanoparticle conjugated to a single-domain monoclonal antibody disclosed herein. In some embodiments, the nanoparticle includes a polymeric nanoparticle, nanosphere, nanocapsule, liposome, dendrimer, polymeric micelle, or niosome (see Fay and Scott, Immunotherapy 3(3):381-394, 2011 for a review of antibody-nanoparticle conjugates). In some examples, the nanoparticle includes a drug, such as a cytotoxic agent. Antibody-nanoparticle conjugates are further described in section IX.
Further provided are immunoliposomes that include a liposome conjugated to a single- domain antibody disclosed herein. In some embodiments, the liposome comprises a drug, such as a cytotoxic agent, for example an anti-cancer agent. Immunoliposomes are further described in section IX.
Also provided herein are fusion proteins that include a single-domain antibody disclosed herein and a heterologous protein. In some embodiments, the heterologous protein is an Fc domain, such as a human Fc domain.
Further provided herein are compositions that include a disclosed single-domain antibody, ADC, CAR, isolated cell, immunoconjugate, multi- specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate or immunoliposome and a pharmaceutically acceptable carrier. Compositions and methods of their use are discussed further in section X below.
Also provided herein are isolated nucleic acid molecules encoding the single-domain antibodies, CARs, immunoconjugates and multi- specific (such as bispecific or trispecific) antibodies disclosed herein. In some embodiments, the nucleic acid molecules are operably linked to a promoter. Further provided are vectors that include the nucleic acid molecules disclosed herein. Isolated host cells transformed with the disclosed nucleic acid molecules and vectors are further provided by the present disclosure.
In some embodiments, the nucleic acid is codon-optimized for expression in bacterial cells. In some examples, the codon-optimized nucleic acid expresses VNAR clone Fl, mutant F1-Y29C or mutant F1-C96S. In some examples, the nucleic acid encoding VNAR clone Fl is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 92, the nucleic acid encoding mutant F1-Y29C is at least 80%, at least
85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 94 and/or the nucleic acid encoding mutant F1-C96S is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 96. In specific non-limiting examples, the nucleic acid encoding VNAR clone Fl comprises or consists of SEQ ID NO: 92, the nucleic acid encoding mutant F1-Y29C comprises or consists of SEQ ID NO: 94 and/or the nucleic acid encoding mutant F1-C96S comprises or consists of SEQ ID NO: 96.
The single-domain antibodies, ADCs, CARs, isolated cells, immunoconjugates, multi- specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and compositions thereof disclosed herein can be used, for example, in methods of treating a GPC3-positive or HER2-positive cancer in a subject; methods of inhibiting tumor growth or metastasis of a GPC3-positive or HER2-positive cancer in a subject; methods of enhancing an anti-tumor response in a subject; methods of treating a MERS virus infection in a subject; methods of treating a SARS virus infection in a subject; methods of detecting expression of GPC3, HER2 or PD1 in a sample; methods of detecting MERS virus or SARS virus in a sample; methods of diagnosing a subject as having a GPC3-positive or HER2 -positive cancer; and methods of diagnosing a subject as infected with MERS virus or SARS virus. V. Antibody-Drug Conjugates (ADCs)
ADCs are compounds comprised of a tumor antigen- specific antibody (or antigen-binding fragment thereof) and a drug, typically a cytotoxic agent, such as an anti-microtubule agent or cross-linking agent. Because ADCs are capable of specifically targeting cancer cells, the drug can be much more potent than agents used for standard chemotherapy. The most common cytotoxic drugs currently used with ADCs have an IC50 that is 100- to 1000-fold more potent than conventional chemotherapeutic agents. Common cytotoxic drugs include anti-microtubule agents, such as maytansinoids and auristatins (such as auristatin E and auristatin F). Other cytotoxins for use with ADCs include pyrrolobenzodiazepines (PDBs), which covalently bind the minor groove of DNA to form interstrand crosslinks. In many instances, ADCs comprise a 1:2 to 1:4 ratio of antibody to drug (Bander, Clinical Advances in Hematology & Oncology 10(8; suppl 10):3-7, 2012).
The antibody and drug can be linked by a cleavable or non-cleavable linker. However, in some instances, it is desirable to have a linker that is stable in the circulation to prevent systemic release of the cytotoxic drug that could result in significant off-target toxicity. Non-cleavable linkers prevent release of the cytotoxic agent before the ADC is internalized by the target cell.
Once in the lysosome, digestion of the antibody by lysosomal proteases results in the release of the cytotoxic agent (Bander, Clinical Advances in Hematology & Oncology 10(8; suppl 10):3-7, 2012).
One method for site- specific and stable conjugation of a drug to a monoclonal antibody is via glycan engineering. Monoclonal antibodies have one conserved N-linked oligosaccharide chain at the Asn297 residue in the CH2 domain of each heavy chain (Qasba et al. , Biotechnol Prog 24:520-526, 2008). Using a mutant i,4-galactosyltransferase enzyme (Y289L-Gal-Tl; U.S. Patent Application Publication Nos. 2007/0258986 and 2006/0084162, herein incorporated by reference), 2-keto-galactose is transferred to free GlcNAc residues on the antibody heavy chain to provide a chemical handle for conjugation. The oligosaccharide chain attached to monoclonal antibodies can be classified into three groups based on the terminal galactose residues - fully galactosylated (two galactose residues; IgG- G2), one galactose residue (IgG-Gl) or completely degalactosylated (IgG-GO). Treatment of a monoclonal antibody with i,4-galactosidase converts the antibody to the IgG-GO glycoform. The mutant i,4-galactosyltransferase enzyme is capable of transferring 2-keto-galactose or 2-azido- galactose from their respective UDP derivatives to the GlcNAc residues on the IgG-Gl and IgG-GO glycoforms. The chemical handle on the transferred sugar enables conjugation of a variety of molecules to the monoclonal antibody via the glycan residues (Qasba et al. , Biotechnol Prog 24:520-526, 2008).
Provided herein are ADCs that include a drug (such as a cytotoxic agent) conjugated to a monoclonal antibody that binds (such as specifically binds) a tumor or viral antigen. In some embodiments, the drug is a small molecule. In some examples, the drug is a cross-linking agent, an anti-microtubule agent and/or anti-mitotic agent, or any cytotoxic agent suitable for mediating killing of tumor cells. Exemplary cytotoxic agents include, but are not limited to, a PDB, an auristatin, a maytansinoid, dolastatin, calicheamicin, nemorubicin and its derivatives, PNU- 159682, anthracycline, vinca alkaloid, taxane, trichothecene, CC1065, camptothecin, elinafide, a combretastain, a dolastatin, a duocarmycin, an enediyne, a geldanamycin, an indolino- benzodiazepine dimer, a puromycin, a tubulysin, a hemiasterlin, a spliceostatin, or a pladienolide, as well as stereoisomers, isosteres, analogs, and derivatives thereof that have cytotoxic activity.
In some embodiments, the ADC comprises a pyrrolobenzodiazepine (PBD). The natural product anthramycin (a PBD) was first reported in 1965 (Leimgruber et al, J Am Chem Soc, 87:5793-5795, 1965; Leimgruber et al. , JAm Chem Soc, 87:5791-5793, 1965). Since then, a number of PBDs, both naturally-occurring and synthetic analogues, have been reported (Gerratana, Med Res Rev 32(2):254-293, 2012; and U.S. Patent Nos. 6,884,799; 7,049,311; 7,067,511;
7,265,105; 7,511,032; 7,528,126; and 7,557,099). As one example, PDB dimers recognize and bind to specific DNA sequences, and have been shown to be useful as cytotoxic agents. PBD dimers have been conjugated to antibodies and the resulting ADC shown to have anti-cancer properties (see, for example, US 2010/0203007). Exemplary linkage sites on the PBD dimer include the five-membered pyrrolo ring, the tether between the PBD units, and the N10-C11 imine group (see WO 2009/016516; US 2009/304710; US 2010/047257; US 2009/036431; US
2011/0256157; and WO 2011/130598).
In some embodiments, the ADC comprises an antibody conjugated to one or more maytansinoid molecules. Maytansinoids are derivatives of maytansine, and are mitototic inhibitors which act by inhibiting tubulin polymerization. Maytansine was first isolated from the east African shrub Maytenus serrata (U.S. Patent No. 3,896,111). Subsequently, it was discovered that certain microbes also produce maytansinoids, such as maytansinol and C-3 maytansinol esters (U.S. Patent No. 4,151,042). Synthetic maytansinoids are disclosed, for example, in U.S. Patent Nos.
4,137,230; 4,248,870; 4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016; 4,308,268;
4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821; 4,322,348; 4,331,598; 4,361,650;
4,364,866; 4,424,219; 4,450,254; 4,362,663; and 4,371,533.
In some embodiments, the ADC includes an antibody conjugated to a dolastatin or auristatin, or an analog or derivative thereof (see U.S. Patent Nos. 5,635,483; 5,780,588; 5,767,237; and 6,124,431). Auristatins are derivatives of the marine mollusk compound dolastatin- 10.
Dolastatins and auristatins have been shown to interfere with microtubule dynamics, GTP hydrolysis, and nuclear and cellular division (Woyke et al. , Antimicrob Agents and Chemother 45(12):3580-3584, 2001) and have anticancer (U.S. Patent No. 5,663,149) and antifungal activity (Pettit et al. , Antimicrob Agents Chemother 42:2961-2965, 1998). Exemplary dolastatins and auristatins include, but are not limited to, dolastatin 10, auristatin E, auristatin F, auristatin EB (AEB), auristatin EFP (AEFP), MM AD (Monomethyl Auristatin D or monomethyl dolastatin 10), MMAF (Monomethyl Auristatin F or N-methylvaline-valine-dolaisoleuine-dolaproine- phenylalanine), MMAE (Monomethyl Auristatin E or N-methylvaline-valine-dolaisoleuine- dolaproine-norephedrine), 5-benzoylvaleric acid-AE ester (AEVB), and other auristatins (see, for example, U.S. Publication No. 2013/0129753).
In some embodiments, the ADC comprises an antibody conjugated to one or more calicheamicin molecules. The calicheamicin family of antibiotics, and analogues thereof, are capable of producing double- stranded DNA breaks at sub-picomolar concentrations (Hinman et al, Cancer Res 53:3336-3342, 1993; Lode et al, Cancer Res 58:2925-2928, 1998). Exemplary methods for preparing ADCs with a calicheamicin drug moiety are described in U.S. Patent Nos. 5,712,374; 5,714,586; 5,739,116; and 5,767,285.
In some embodiments, the ADC comprises an anthracycline. Anthracyclines are antibiotic compounds that exhibit cytotoxic activity. It is believed that anthracyclines can operate to kill cells by a number of different mechanisms, including intercalation of the drug molecules into the DNA of the cell thereby inhibiting DNA-dependent nucleic acid synthesis; inducing production of free radicals which then react with cellular macromolecules to cause damage to the cells; and/or interactions of the drug molecules with the cell membrane. Non-limiting exemplary anthracyclines include doxorubicin, epirubicin, idarubicin, daunomycin, daunorubicin, doxorubicin, epirubicin, nemorubicin, valrubicin and mitoxantrone, and derivatives thereof. For example, PNU- 159682 is a potent metabolite (or derivative) of nemorubicin (Quintieri et al, Clin Cancer Res 11(4): 1608- 1617, 2005). Nemorubicin is a semisynthetic analog of doxorubicin with a 2-methoxymorpholino group on the glycoside amino of doxorubicin (Grandi et al, Cancer Treat Rev 17:133, 1990;
Ripamonti et al, Br J Cancer 65:703-707, 1992).
In some embodiments, the ADC can further include a linker. In some examples, the linker is a bifunctional or multifunctional moiety that can be used to link one or more drug moieties to an antibody to form an ADC. In some embodiments, ADCs are prepared using a linker having reactive functionalities for covalently attaching to the drug and to the antibody. For example, a cysteine thiol of an antibody can form a bond with a reactive functional group of a linker or a drug- linker intermediate to make an ADC.
In some examples, a linker has a functionality that is capable of reacting with a free cysteine present on an antibody to form a covalent bond. Exemplary linkers with such reactive
functionalities include maleimide, haloacetamides, oc-haloacetyl, activated esters such as succinimide esters, 4-nitrophenyl esters, pentafluorophenyl esters, tetrafluorophenyl esters, anhydrides, acid chlorides, sulfonyl chlorides, isocyanates, and isothiocyanates.
In some examples, a linker has a functionality that is capable of reacting with an electrophilic group present on an antibody. Examples of such electrophilic groups include, but are not limited to, aldehyde and ketone carbonyl groups. In some cases, a heteroatom of the reactive functionality of the linker can react with an electrophilic group on an antibody and form a covalent bond to an antibody unit. Non-limiting examples include hydrazide, oxime, amino, hydrazine, thiosemicarbazone, hydrazine carboxylate and arylhydrazide.
In some examples, the linker is a cleavable linker, which facilitates release of the drug. Examples of cleavable linkers include acid-labile linkers (for example, comprising hydrazone), protease- sensitive linkers (for example, peptidase- sensitive), photolabile linkers, and disulfide- containing linkers (Chari et al, Cancer Res 52:127-131, 1992; U.S. Patent No. 5,208,020).
The ADCs disclosed herein can be used for the treatment of a GPC3- or HER2 -positive cancer alone or in combination with another therapeutic agent and/or in combination with any standard therapy for the treatment of cancer (such as surgical resection of the tumor, chemotherapy or radiation therapy). VI. Chimeric Antigen Receptors (CARs)
The disclosed monoclonal antibodies can also be used to produce CARs (also known as chimeric T cell receptors, artificial T cell receptors or chimeric immunoreceptors) and/or cytotoxic T lymphocytes (CTLs) engineered to express CARs. Generally, CARs include a binding moiety, an extracellular hinge and spacer element, a transmembrane region and an endodomain that performs signaling functions (Cartellieri et al , J Biomed Biotechnol 2010:956304, 2010). In many instances, the binding moiety is an antigen binding fragment of a monoclonal antibody, such as a scFv, or is a single-domain antibody. Several different endodomains have been used to generate CARs. For example, the endodomain can consist of a signaling chain having an IT AM, such as CD3ζ or FceRIy. In some instances, the endodomain further includes the intracellular portion of at least one additional co- stimulatory domain, such as CD28 and/or CD137.
CTLs expressing CARs can be used to target a specific cell type, such as a tumor cell.
Thus, the monoclonal antibodies disclosed herein can be used to engineer CTLs that express a CAR containing an antigen-binding fragment of an antigen-specific antibody, thereby targeting the engineered CTLs to tumor antigen-expressing tumor cells. Engineered T cells have previously been used for adoptive therapy for some types of cancer (see, for example, Park et al. , Mol Ther 15(4):825-833, 2007). The use of T cells expressing CARs is more universal than standard CTL- based immunotherapy because CTLs expressing CARs are HLA unrestricted and can therefore be used for any patient having a tumor that expresses the target antigen.
Accordingly, provided herein are CARs that include a tumor antigen- specific monoclonal antibody, or antigen-binding fragment thereof, such as a scFv. Also provided are isolated nucleic acid molecules and vectors encoding the CARs, and host cells, such as CTLs, expressing the CARs. CTLs expressing CARs comprised of a tumor antigen-specific monoclonal antibody (or antibody binding fragment) can be used for the treatment of cancers that express GPC3 or HER2.
In some embodiments herein, the CAR is a bispecific CAR.
VII. Multi-specific Antibodies
Multi- specific antibodies are recombinant proteins comprised antigen-binding fragments of two or more different monoclonal antibodies. For example, bispecific antibodies are comprised of antigen-binding fragments of two different monoclonal antibodies. Thus, bispecific antibodies bind two different antigens and trispecific antibodies bind three different antigens. Multi-specific antibodies can be used for cancer immunotherapy by simultaneously targeting, for example, both CTLs (such as a CTL receptor component such as CD3) or effector natural killer (NK) cells, and at least one tumor antigen. The antigen-specific monoclonal antibodies disclosed herein can be used to generate multi- specific (such as bispecific or trispecific) antibodies that target both the antigen and CTLs, or target both the antigen and NK cells, thereby providing a means to treat tumor antigen-expressing cancers.
Bi-specific T-cell engagers (BiTEs) are a type of bispecific monoclonal antibody that are fusions of a first single-chain variable fragment (scFv) that targets a tumor antigen and a second scFv that binds T cells, such as bind CD3 on T cells. In some embodiments herein, one of the binding moieties of the BiTE (such as one of the scFv molecules) is specific for PD1.
Bi-specific killer cell engagers (BiKEs) are a type of bispecific monoclonal antibody that are fusions of a first scFv that targets a tumor antigen and a second scFv that binds a NK cell activating receptor, such as CD 16.
Provided herein are multi- specific, such as trispecific or bispecific, monoclonal antibodies comprising a viral or tumor antigen-specific monoclonal antibody, or antigen-binding fragment thereof. In some embodiments, the multi-specific monoclonal antibody further comprises a monoclonal antibody, or antigen-binding fragment thereof, that specifically binds a component of the T cell receptor, such as CD3. In other embodiments, the multi-specific monoclonal antibody further comprises a monoclonal antibody, or antigen-binding fragment thereof, that specifically binds a NK cell activating receptor, such as CD16, Ly49, or CD94. In some examples, the antigen- binding fragments are scFv. Also provided are isolated nucleic acid molecules and vectors encoding the multi-specific antibodies, and host cells comprising the nucleic acid molecules or vectors. Multi- specific antibodies comprising an antigen-specific antibody, or antigen-binding fragment thereof, can be used for the treatment of cancers that express GPC3 or HER2. Thus, provided herein are methods of treating a subject with cancer by selecting a subject with a cancer that expresses GPC3 or HER2, and administering to the subject a therapeutically effective amount of the GPC3- or HER2-targeting multi- specific antibody.
VIII. Immunoconjugates
The disclosed monoclonal antibodies can be conjugated to a therapeutic agent or effector molecule. Immunoconjugates include, but are not limited to, molecules in which there is a covalent linkage of a therapeutic agent to an antibody. A therapeutic agent is an agent with a particular biological activity directed against a particular target molecule or a cell bearing a target molecule. One of skill in the art will appreciate that therapeutic agents can include various drugs such as vinblastine, daunomycin and the like, cytotoxins such as native or modified Pseudomonas exotoxin or diphtheria toxin, encapsulating agents (such as liposomes) that contain pharmacological compositions, radioactive agents such as 1251, 32P, 14C, 3H and 35S and other labels, target moieties and ligands.
The choice of a particular therapeutic agent depends on the particular target molecule or cell, and the desired biological effect. Thus, for example, the therapeutic agent can be a cytotoxin that is used to bring about the death of a particular target cell (such as a tumor cell). Conversely, where it is desired to invoke a non- lethal biological response, the therapeutic agent can be conjugated to a non- lethal pharmacological agent or a liposome containing a non-lethal pharmacological agent.
With the therapeutic agents and antibodies described herein, one of skill can readily construct a variety of clones containing functionally equivalent nucleic acids, such as nucleic acids which differ in sequence but which encode the same effector moiety or antibody sequence. Thus, the present disclosure provides nucleic acids encoding antibodies and conjugates and fusion proteins thereof.
Effector molecules can be linked to an antibody of interest using any number of means known to those of skill in the art. Both covalent and noncovalent attachment means may be used. The procedure for attaching an effector molecule to an antibody varies according to the chemical structure of the effector. Polypeptides typically contain a variety of functional groups; such as carboxylic acid (COOH), free amine (-NH2) or sulfhydryl (-SH) groups, which are available for reaction with a suitable functional group on an antibody to result in the binding of the effector molecule. Alternatively, the antibody is derivatized to expose or attach additional reactive functional groups. The derivatization may involve attachment of any of a number of known linker molecules. The linker can be any molecule used to join the antibody to the effector molecule. The linker is capable of forming covalent bonds to both the antibody and to the effector molecule. Suitable linkers are well known to those of skill in the art and include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers, or peptide linkers. Where the antibody and the effector molecule are polypeptides, the linkers may be joined to the constituent amino acids through their side groups (such as through a disulfide linkage to cysteine) or to the alpha carbon amino and carboxyl groups of the terminal amino acids.
In some circumstances, it is desirable to free the effector molecule from the antibody when the immunoconjugate has reached its target site. Therefore, in these circumstances,
immunoconjugates will comprise linkages that are cleavable in the vicinity of the target site.
Cleavage of the linker to release the effector molecule from the antibody may be prompted by enzymatic activity or conditions to which the immunoconjugate is subjected either inside the target cell or in the vicinity of the target site.
In view of the large number of methods that have been reported for attaching a variety of radiodiagnostic compounds, radiotherapeutic compounds, labels (such as enzymes or fluorescent molecules), drugs, toxins, and other agents to antibodies one skilled in the art will be able to determine a suitable method for attaching a given agent to an antibody or other polypeptide.
The antibodies or antibody fragments disclosed herein can be derivatized or linked to another molecule (such as another peptide or protein). In general, the antibodies or portion thereof is derivatized such that the binding to the target antigen is not affected adversely by the derivatization or labeling. For example, the antibody can be functionally linked (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another antibody (for example, a bispecific antibody or a diabody), a detection agent, a pharmaceutical agent, and/or a protein or peptide that can mediate association of the antibody or antibody portion with another molecule (such as a streptavidin core region or a polyhistidine tag).
One type of derivatized antibody is produced by cross-linking two or more antibodies (of the same type or of different types, such as to create bispecific antibodies). Suitable crosslinkers include those that are heterobifunctional, having two distinctly reactive groups separated by an appropriate spacer (such as m-maleimidobenzoyl-N-hydroxysuccinimide ester) or
homobifunctional (such as disuccinimidyl suberate). Such linkers are commercially available.
The antibody can be conjugated with a detectable marker; for example, a detectable marker capable of detection by ELISA, spectrophotometry, flow cytometry, microscopy or diagnostic imaging techniques (such as computed tomography (CT), computed axial tomography (CAT) scans, magnetic resonance imaging (MRI), nuclear magnetic resonance imaging NMRI), magnetic resonance tomography (MTR), ultrasound, fiberoptic examination, and laparoscopic examination). Specific, non-limiting examples of detectable markers include fluorophores, chemiluminescent agents, enzymatic linkages, radioactive isotopes and heavy metals or compounds (for example super paramagnetic iron oxide nanocrystals for detection by MRI). For example, useful detectable markers include fluorescent compounds, including fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-l-napthalenesulfonyl chloride, phycoerythrin, lanthanide phosphors and the like. Bioluminescent markers are also of use, such as luciferase, green fluorescent protein (GFP) and yellow fluorescent protein (YFP). An antibody or antigen binding fragment can also be conjugated with enzymes that are useful for detection, such as horseradish peroxidase, β- galactosidase, luciferase, alkaline phosphatase, glucose oxidase and the like. When an antibody or antigen binding fragment is conjugated with a detectable enzyme, it can be detected by adding additional reagents that the enzyme uses to produce a reaction product that can be discerned. For example, when the agent horseradish peroxidase is present the addition of hydrogen peroxide and diaminobenzidine leads to a colored reaction product, which is visually detectable. An antibody or antigen binding fragment may also be conjugated with biotin, and detected through indirect measurement of avidin or streptavidin binding. It should be noted that the avidin itself can be conjugated with an enzyme or a fluorescent label. An antibody may be labeled with a magnetic agent, such as gadolinium. Antibodies can also be labeled with lanthanides (such as europium and dysprosium), and manganese.
Paramagnetic particles such as superparamagnetic iron oxide are also of use as labels. An antibody may also be labeled with a predetermined polypeptide epitopes recognized by a secondary reporter (such as leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
An antibody can also be labeled with a radiolabeled amino acid. The radiolabel may be used for both diagnostic and therapeutic purposes. For instance, the radiolabel may be used to detect expression of a target antigen by x-ray, emission spectra, or other diagnostic techniques. Examples of labels for polypeptides include, but are not limited to, the following radioisotopes or radionucleotides: 3H, 14C, 15N, 35S, 90Y, "Tc, i nIn, 125I, 131I.
An antibody can also be derivatized with a chemical group such as polyethylene glycol (PEG), a methyl or ethyl group, or a carbohydrate group. These groups may be useful to improve the biological characteristics of the antibody, such as to increase serum half-life or to increase tissue binding.
Toxins can be employed with the monoclonal antibodies described herein to produce immunotoxins. Exemplary toxins include ricin, abrin, diphtheria toxin and subunits thereof, as well as botulinum toxins A through F. These toxins are readily available from commercial sources (for example, Sigma Chemical Company, St. Louis, MO). Contemplated toxins also include variants of the toxins described herein (see, for example, see, U.S. Patent Nos. 5,079,163 and 4,689,401). In one embodiment, the toxin is Pseudomonas exotoxin (PE) (U.S. Patent No. 5,602,095). As used herein "Pseudomonas exotoxin" refers to a full-length native (naturally occurring) PE or a PE that has been modified. Such modifications can include, but are not limited to, elimination of domain la, various amino acid deletions in domains lb, II and III, single amino acid substitutions and the addition of one or more sequences at the carboxyl terminus (for example, see Siegall et al. , /. Biol. Chem. 264: 14256-14261, 1989).
PE employed with the monoclonal antibodies described herein can include the native sequence, cytotoxic fragments of the native sequence, and conservatively modified variants of native PE and its cytotoxic fragments. Cytotoxic fragments of PE include those which are cytotoxic with or without subsequent proteolytic or other processing in the target cell. Cytotoxic fragments of PE include PE40, PE38, and PE35. For additional description of PE and variants thereof, see for example, U.S. Patent Nos. 4,892,827; 5,512,658; 5,602,095; 5,608,039; 5,821,238; and 5,854,044; U.S. Patent Application Publication No. 2015/0099707; PCT Publication Nos. WO 99/51643 and WO 2014/052064; Pai et al, Proc. Natl. Acad. Sci. USA 88:3358-3362, 1991 ; Kondo et al. , J. Biol. Chem. 263:9470-9475, 1988; Pastan et al , Biochim. Biophys. Acta 1333:C1-C6, 1997.
Also contemplated herein are protease-resistant PE variants and PE variants with reduced immunogenicity, such as, but not limited to PE-LR, PE-6X, PE-8X, PE-LR/6X and PE-LR/8X (see, for example, Weldon et al. , Blood 113(16):3792-3800, 2009; Onda et al. , Proc Natl Acad Sci USA 105(32): 11311-11316, 2008; and PCT Publication Nos. WO 2007/016150, WO 2009/032954 and WO 2011/032022, which are herein incorporated by reference).
In some examples, the PE is a variant that is resistant to lysosomal degradation, such as PE- LR (Weldon et al , Blood 113(16):3792-3800, 2009; PCT Publication No. WO 2009/032954). In other examples, the PE is a variant designated PE-LR/6X (PCT Publication No. WO 2011/032022). In other examples, the PE variant is PE with reducing immunogenicity. In yet other examples, the PE is a variant designated PE-LR/8M (PCT Publication No. WO 2011/032022).
Modification of PE may occur in any previously described variant, including cytotoxic fragments of PE (for example, PE38, PE-LR and PE-LR/8M). Modified PEs may include any substitution(s), such as for one or more amino acid residues within one or more T-cell epitopes and/or B cell epitopes of PE, or deletion of one or more T-cell and/or B-cell epitopes (see, for example, U.S. Patent Application Publication No. 2015/0099707).
Contemplated forms of PE also include deimmunized forms of PE, for example versions with domain II deleted (for example, PE24). Deimmunized forms of PE are described in, for example, PCT Publication Nos. WO 2005/052006, WO 2007/016150, WO 2007/014743, WO 2007/031741, WO 2009/32954, WO 2011/32022, WO 2012/154530, and WO 2012/170617.
The antibodies described herein can also be used to target any number of different diagnostic or therapeutic compounds to cells expressing the tumor or viral antigen on their surface. Thus, an antibody of the present disclosure can be attached directly or via a linker to a drug that is to be delivered directly to cells expressing cell-surface antigen. This can be done for therapeutic, diagnostic or research purposes. Therapeutic agents include such compounds as nucleic acids, proteins, peptides, amino acids or derivatives, glycoproteins, radioisotopes, lipids, carbohydrates, or recombinant viruses. Nucleic acid therapeutic and diagnostic moieties include antisense nucleic acids, derivatized oligonucleotides for covalent cross-linking with single or duplex DNA, and triplex forming oligonucleotides.
Alternatively, the molecule linked to an antibody can be an encapsulation system, such as a nanoparticle, liposome or micelle that contains a therapeutic composition such as a drug, a nucleic acid (for example, an antisense nucleic acid), or another therapeutic moiety that is preferably shielded from direct exposure to the circulatory system. Means of preparing liposomes attached to antibodies are well known to those of skill in the art (see, for example, U.S. Patent No. 4,957,735; Connor et al, Pharm. Ther. 28:341-365, 1985).
Antibodies described herein can also be covalently or non-covalently linked to a detectable label. Detectable labels suitable for such use include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels include magnetic beads, fluorescent dyes (for example, fluorescein isothiocyanate, Texas red, rhodamine, green fluorescent protein, and the like), radiolabels (for example, 3H, 1251, 35S, 14C, or 32P), enzymes (such as horseradish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (such as polystyrene, polypropylene, latex, and the like) beads.
Means of detecting such labels are well known to those of skill in the art. Thus, for example, radiolabels may be detected using photographic film or scintillation counters, fluorescent markers may be detected using a photodetector to detect emitted illumination. Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
IX. Antibody-Nanoparticle Conjugates
The single-domain monoclonal antibodies disclosed herein can be conjugated to a variety of different types of nanoparticles to deliver cytotoxic agents or other anti-cancer agents directly to tumor cells via binding of the antibody to a tumor specific antigen expressed on the surface of tumor cells. The use of nanoparticles reduces off-target side effects and can also improve drug bioavailability and reduce the dose of a drug required to achieve a therapeutic effect. Nanoparticle formulations can be tailored to suit the drug that is to be carried or encapsulated within the nanoparticle. For example, hydrophobic molecules can be incorporated inside the core of a nanoparticle, while hydrophilic drugs can be carried within an aqueous core protected by a polymeric or lipid shell. Examples of nanoparticles include, but at not limited to, nanospheres, nanocapsules, liposomes, dendrimers, polymeric micelles, niosomes, and polymeric nanoparticles (Fay and Scott, Immunotherapy 3(3):381-394, 2011).
Liposomes are currently one of the most common types of nanoparticles used for drug delivery. An antibody conjugated to a liposome is often referred to as an "immunoliposome." The liposomal component of an immunoliposome is typically a lipid vesicle of one or more concentric phospholipid bilayers. In some cases, the phospholipids are composed of a hydrophilic head group and two hydrophobic chains to enable encapsulation of both hydrophobic and hydrophilic drugs. Conventional liposomes are rapidly removed from the circulation via macrophages of the reticuloendothelial system (RES). To generate long-circulating liposomes, the composition, size and charge of the liposome can be modulated. The surface of the liposome may also be modified, such as with a glycolipid or sialic acid. For example, the inclusion of polyethylene glycol (PEG) significantly increases circulation half-life. Liposomes for use as drug delivery agents, including for preparation of immunoliposomes, have been described in the art (see, for example, Paszko and Senge, Curr Med Chem 19(31)5239-5277, 2012; Immordino et al, Int J Nanomedicine 1(3):297- 315, 2006; U.S. Patent Application Publication Nos. 2011/0268655; 2010/00329981).
Niosomes are non-ionic surfactant-based vesicles having a structure similar to liposomes.
The membranes of niosomes are composed only of nonionic surfactants, such as poly glyceryl- alkyl ethers or N-palmitoylglucosamine. Niosomes range from small, unilalamellar to large, multilamellar particles. These nanoparticles are monodisperse, water-soluble, chemically stable, have low toxicity, are biodegradable and non-immunogenic, and increase bioavailability of encapsulated drugs.
Dendrimers include a range of branched polymer complexes. These nanoparticles are water-soluble, biocompatible and are sufficiently non-immunogenic for human use. Generally, dendrimers consist of an initiator core, surrounded by a layer of a selected polymer that is grafted to the core, forming a branched macromolecular complex. Dendrimers are typically produced using polymers such as poly(amidoamine) or poly(L-lysine). Dendrimers have been used for a variety of therapeutic and diagnostic applications, including for the delivery of DNA, RNA, bioimaging contrast agents and chemotherapeutic agents.
Polymeric micelles are composed of aggregates of amphiphilic co-polymers (consisting of both hydrophilic and hydrophobic monomer units) assembled into hydrophobic cores, surrounded by a corona of hydrophilic polymeric chains exposed to the aqueous environment. In many cases, the polymers used to prepare polymeric micelles are heterobifunctional copolymers composed of a hydrophilic block of PEG, poly(vinyl pyrrolidone) and hydrophobic poly(L-lactide) or poly(L- lysine) that forms the particle core. Polymeric micelles can be used to carry drugs that have poor solubility. These nanoparticles have been used to encapsulate a number of anti-cancer drugs, including doxorubicin and camptothecin. Cationic micelles have also been developed to carry DNA or RNA molecules.
Polymeric nanoparticles include both nanospheres and nanocapsules. Nanospheres consist of a solid matrix of polymer, while nanocapsules contain an aqueous core. The formulation selected typically depends on the solubility of the therapeutic agent to be carried/encapsulated; poorly water-soluble drugs are more readily encapsulated within a nanospheres, while water- soluble and labile drugs, such as DNA and proteins, are more readily encapsulated within nanocapsules. The polymers used to produce these nanoparticles include, for example, poly(acrylamide), poly(ester), poly(alkylcyanoacrylates), poly(lactic acid) (PLA), poly(glycolic acids) (PGA), and poly(D,L-lactic-co-glycolic acid) (PLGA).
Antibodies, including single-domain antibodies, can be conjugated to a suitable nanoparticle according to standard methods known in the art. For example, conjugation can be either covalent or non-covalent. In some embodiments in which the nanoparticle is a liposome, the antibody is attached to a sterically stabilized, long circulation liposome via a PEG chain. Coupling of antibodies or antibody fragments to a liposome can also involve thioester bonds, for example by reaction of thiols and maleimide groups. Cross-linking agents can be used to create sulfhydryl groups for attachment of antibodies to nanoparticles (Paszko and Senge, Curr Med Chem
19(31)5239-5277, 2012). X. Compositions and Methods of Use
Compositions are provided that include one or more of the disclosed single-domain antibodies that bind (for example specifically bind) GPC3, HER2, PD1, MERS virus S protein or SARS virus S protein, in a carrier. Compositions comprising ADCs, CARs (and CTLs comprising CARs), multi- specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and immunoconjugates are also provided. The compositions can be prepared in unit dosage forms for administration to a subject. The amount and timing of administration are at the discretion of the treating clinician to achieve the desired outcome. The antibody, ADC, CAR, CTL, multi-specific antibody, antibody-nanoparticle conjugate,
immunoliposome or immunoconjugate can be formulated for systemic or local (such as intra- tumor) administration. In one example, the antibody is formulated for parenteral administration, such as intravenous administration.
The compositions for administration can include a solution of the antibody, ADC, CAR, CTL, multi-specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate, immunoliposome or immunoconjugate in a pharmaceutically acceptable carrier, such as an aqueous carrier. A variety of aqueous carriers can be used, for example, buffered saline and the like. These solutions are sterile and generally free of undesirable matter. These compositions may be sterilized by conventional, well known sterilization techniques. The compositions may contain
pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like. The concentration of antibody in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the subject's needs.
A typical pharmaceutical composition for intravenous administration includes about 0.1 to
10 mg of antibody (or ADC, CAR, multi-specific antibody, antibody-nanoparticle conjugate, or immunoconjugate) per subject per day. Dosages from 0.1 up to about 100 mg per subject per day may be used, particularly if the agent is administered to a secluded site and not into the circulatory or lymph system, such as into a body cavity or into a lumen of an organ. Actual methods for preparing administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remington's Pharmaceutical Science, 19th ed., Mack Publishing Company, Easton, PA (1995).
Antibodies (or other therapeutic molecules) may be provided in lyophilized form and rehydrated with sterile water before administration, although they are also provided in sterile solutions of known concentration. The antibody solution is then added to an infusion bag containing 0.9% sodium chloride, USP, and in some cases administered at a dosage of from 0.5 to 15 mg/kg of body weight. Considerable experience is available in the art in the administration of antibody drugs, which have been marketed in the U.S. since the approval of RITUXAN™ in 1997. Antibodies, ADCs, CARs, multi-specific (such as bispecific or trispecific) antibodies, antibody- nanoparticle conjugates, immunoliposomes or immunoconjugates can be administered by slow infusion, rather than in an intravenous push or bolus. In one example, a higher loading dose is administered, with subsequent, maintenance doses being administered at a lower level. For example, an initial loading dose of 4 mg/kg may be infused over a period of some 90 minutes, followed by weekly maintenance doses for 4-8 weeks of 2 mg/kg infused over a 30 minute period if the previous dose was well tolerated.
Controlled release parenteral formulations can be made as implants, oily injections, or as particulate systems. For a broad overview of protein delivery systems see, Banga, A.J.,
Therapeutic Peptides and Proteins: Formulation, Processing, and Delivery Systems, Technomic Publishing Company, Inc., Lancaster, PA, (1995). Particulate systems include, for example, microspheres, microparticles, microcapsules, nanocapsules, nanospheres, and nanoparticles.
Microcapsules contain the therapeutic protein, such as a cytotoxin or a drug, as a central core. In microspheres the therapeutic is dispersed throughout the particle. Particles, microspheres, and microcapsules smaller than about 1 μιη are generally referred to as nanoparticles, nanospheres, and nanocapsules, respectively. Capillaries have a diameter of approximately 5 μιη so that only nanoparticles are administered intravenously. Microparticles are typically around 100 μιη in diameter and are administered subcutaneously or intramuscularly. See, for example, Kreuter, J., Colloidal Drug Delivery Systems, J. Kreuter, ed., Marcel Dekker, Inc., New York, NY, pp. 219-342 (1994); and Tice & Tabibi, Treatise on Controlled Drug Delivery, A. Kydonieus, ed., Marcel Dekker, Inc. New York, NY, pp. 315-339, (1992).
Polymers can be used for ion-controlled release of the antibody-based compositions disclosed herein. Various degradable and nondegradable polymeric matrices for use in controlled drug delivery are known in the art (Langer, Accounts Chem. Res. 26:537-542, 1993). For example, the block copolymer, polaxamer 407, exists as a viscous yet mobile liquid at low temperatures but forms a semisolid gel at body temperature. It has been shown to be an effective vehicle for formulation and sustained delivery of recombinant interleukin-2 and urease (Johnston et al, Pharm. Res. 9:425-434, 1992; and Pec et al, J. Parent. Set Tech. 44(2):58-65, 1990).
Alternatively, hydroxyapatite has been used as a microcarrier for controlled release of proteins (Ijntema et al. , Int. J. Pharm.112:215-224, 1994). In yet another aspect, liposomes are used for controlled release as well as drug targeting of the lipid-capsulated drug (Betageri et al, Liposome Drug Delivery Systems, Technomic Publishing Co., Inc., Lancaster, PA (1993)). Numerous additional systems for controlled delivery of therapeutic proteins are known (see U.S. Patent Nos. 5,055,303; 5,188,837; 4,235,871 ; 4,501,728; 4,837,028; 4,957,735; 5,019,369; 5,055,303;
5,514,670; 5,413,797; 5,268,164; 5,004,697; 4,902,505; 5,506,206; 5,271,961 ; 5,254,342 and 5,534,496).
A. Therapeutic Methods
The antibodies, compositions, CARs (and CTLs expressing CARs), ADCs, multi- specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and immunoconjugates disclosed herein can be administered to slow or inhibit the growth of tumor cells or inhibit the metastasis of tumor cells, such as GPC3-positive or HER2 -positive cancers. In these applications, a therapeutically effective amount of a composition is administered to a subject in an amount sufficient to inhibit growth, replication or metastasis of cancer cells, or to inhibit a sign or a symptom of the cancer. Suitable subjects may include those diagnosed with a cancer that expresses GPC3, such as, but not limited to, hepatocellular carcinoma (HCC), melanoma, squamous cell carcinoma of the lung or ovarian clear cell carcinoma, or with a cancer that expresses HER2, for example breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma or head and neck carcinoma. Provided herein is a method of treating a GPC3-positive cancer in a subject by administering to the subject a therapeutically effective amount of a GPC3 -specific antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi- specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate, immunoconjugate, immunoliposome or composition disclosed herein. Also provided herein is a method of inhibiting tumor growth or metastasis of a GPC3- positive cancer in a subject by administering to the subject a therapeutically effective amount of a GPC3-specific antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi-specific (such as bispecific or trispecific) antibody, immunoconjugate, antibody-nanoparticle conjugate, immunoliposome or composition disclosed herein. In some embodiments, the GPC3-positive cancer is HCC, melanoma, squamous cell carcinoma of the lung or ovarian clear cell carcinoma.
Also provided herein is a method of treating a HER2 -positive cancer in a subject by administering to the subject a therapeutically effective amount of a HER2-specific antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi- specific (such as bispecific or trispecific) antibody, antibody-nanoparticle conjugate, immunoconjugate, immunoliposome or composition disclosed herein. Also provided herein is a method of inhibiting tumor growth or metastasis of a HER2- positive cancer in a subject by administering to the subject a therapeutically effective amount of a HER2-specific antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi-specific (such as bispecific or trispecific) antibody, immunoconjugate, antibody-nanoparticle conjugate, immunoliposome or composition disclosed herein. In some embodiments, the HER2-positive cancer is breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma or head and neck carcinoma.
Further provided herein is a method of enhancing an anti-tumor response in a subject, comprising administering to the subject a PD1 -specific single-domain monoclonal antibody disclosed herein. In some embodiments, the subject has melanoma, lung cancer, bladder cancer, breast cancer, Hodgkin' s lymphoma, renal cancer, head and neck cancer, gastric cancer, glioblastoma, colorectal cancer or Merkel cell carcinoma.
Also provided herein is a method of treating a MERS virus infection in a subject by administering to the subject a MERS virus-specific single-domain monoclonal antibody disclosed herein. A method of treating a SARS virus infection in a subject by administering the subject a SARS virus-specific single-domain monoclonal antibody disclosed herein is also provided.
A therapeutically effective amount of a single-domain antibody, ADC, CAR (e.g. a CTL expressing a CAR), multi-specific (such as bispecific or trispecific) antibody, immunoconjugate, immunoliposome or composition disclosed herein will depend upon the severity of the disease, the type of disease, and the general state of the patient's health. A therapeutically effective amount of the antibody-based composition is that which provides either subjective relief of a symptom(s) or an objectively identifiable improvement as noted by the clinician or other qualified observer.
Administration of the GPC3-, HER2 or PDl-specific antibodies, ADCs, CARs,
immunoconjugates, multi-specific (such as bispecific or trispecific) antibodies, antibody- nanoparticle conjugates, immunoliposomes and compositions disclosed herein can also be accompanied by administration of other anti-cancer agents or therapeutic treatments (such as surgical resection of a tumor). Any suitable anti-cancer agent can be administered in combination with the antibodies, compositions and immunoconjugates disclosed herein. Exemplary anti-cancer agents include, but are not limited to, chemotherapeutic agents, such as, for example, mitotic inhibitors, alkylating agents, anti-metabolites, intercalating antibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes, topoisomerase inhibitors, anti-survival agents, biological response modifiers, anti-hormones (e.g. anti-androgens) and anti-angiogenesis agents. Other anti-cancer treatments include radiation therapy and other antibodies that specifically target cancer cells.
Non-limiting examples of alkylating agents include nitrogen mustards (such as
mechlorethamine, cyclophosphamide, melphalan, uracil mustard or chlorambucil), alkyl sulfonates (such as busulfan), nitrosoureas (such as carmustine, lomustine, semustine, streptozocin, or dacarbazine).
Non-limiting examples of antimetabolites include folic acid analogs (such as methotrexate), pyrimidine analogs (such as 5-FU or cytarabine), and purine analogs, such as mercaptopurine or thioguanine.
Non-limiting examples of natural products include vinca alkaloids (such as vinblastine, vincristine, or vindesine), epipodophyllotoxins (such as etoposide or teniposide), antibiotics (such as dactinomycin, daunorubicin, doxorubicin, bleomycin, plicamycin, or mitomycin C), and enzymes (such as L-asparaginase).
Non- limiting examples of miscellaneous agents include platinum coordination complexes (such as cis-diamine-dichloroplatinum II also known as cisplatin), substituted ureas (such as hydroxyurea), methyl hydrazine derivatives (such as procarbazine), and adrenocrotical suppressants (such as mitotane and aminoglutethimide).
Non- limiting examples of hormones and antagonists include adrenocorticosteroids (such as prednisone), progestins (such as hydroxyprogesterone caproate, medroxyprogesterone acetate, and magestrol acetate), estrogens (such as diethylstilbestrol and ethinyl estradiol), antiestrogens (such as tamoxifen), and androgens (such as testerone proprionate and fluoxymesterone). Examples of the most commonly used chemotherapy drugs include Adriamycin, Alkeran, Ara-C, BiCNU, Busulfan, CCNU, Carboplatinum, Cisplatinum, Cytoxan, Daunorubicin, DTIC, 5-FU, Fludarabine, Hydrea, Idarubicin, Ifosfamide, Methotrexate, Mithramycin, Mitomycin, Mitoxantrone, Nitrogen Mustard, Taxol (or other taxanes, such as docetaxel), Velban, Vincristine, VP- 16, while some more newer drugs include Gemcitabine (Gemzar), Herceptin, Irinotecan (Camptosar, CPT-11),
Leustatin, Navelbine, Rituxan STI-571, Taxotere, Topotecan (Hycamtin), Xeloda (Capecitabine), Zevelin and calcitriol.
Non- limiting examples of immunomodulators that can be used include AS- 101 (Wyeth- Ayerst Labs.), bropirimine (Upjohn), gamma interferon (Genentech), GM-CSF (granulocyte macrophage colony stimulating factor; Genetics Institute), IL-2 (Cetus or Hoffman-LaRoche), human immune globulin (Cutter Biological), IMREG (from Imreg of New Orleans, La.), SK&F 106528, and TNF (tumor necrosis factor; Genentech).
Another common treatment for some types of cancer is surgical treatment, for example surgical resection of the cancer or a portion of it. Another example of a treatment is radiotherapy, for example administration of radioactive material or energy (such as external beam therapy) to the tumor site to help eradicate the tumor or shrink it prior to surgical resection.
Administration of the anti-MERS virus S protein or anti-SARS virus S protein antibodies, ADCs, CARs, immunoconjugates, multi-specific (such as bispecific or trispecific) antibodies, antibody-nanoparticle conjugates, immunoliposomes and compositions disclosed herein can also be accompanied by administration of other therapeutic agents, such as anti- viral agents or
immunomodulatory therapy. Anti-viral gents include, for example, ribavirin, protease inhibitors (e.g. lopinavir-ritonavir), human interferons (e.g. IFN-oc or IFN-b), human gamma
immunoglobulins and convalescent plasma. Immunomodulatory therapy can include, for example, corticosteroids, thymosin alpha 1, etanercept, infliximab, cyclophosphamide, azathioprine, cyclosporin and thalidomide.
B. Methods for Diagnosis and Detection
Methods are provided herein for detecting GPC3, HER2, PD1, MERS virus S protein or SARS S protein in vitro or in vivo. In some cases, GPC3, HER2, PD1, MERS virus S protein or SARS S protein expression is detected in a biological sample. The sample can be any sample, including, but not limited to, tissue from biopsies, autopsies and pathology specimens. Biological samples also include sections of tissues, for example, frozen sections taken for histological purposes. Biological samples further include body fluids, such as blood, serum, plasma, sputum, spinal fluid or urine. A biological sample is typically obtained from a mammal, such as a human or non-human primate. Provided herein is a method of determining if a subject has a GPC3-positive cancer by contacting a sample from the subject with a GPC3-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample identifies the subject as having a GPC3-positive cancer.
Also provided herein is a method of determining if a subject has a HER2 -positive cancer by contacting a sample from the subject with a HER2-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample identifies the subject as having a HER2 -positive cancer.
In another embodiment, provided is a method of confirming a diagnosis of a GPC3-positive cancer in a subject by contacting a sample from a subject diagnosed with a GPC3-positive cancer with a GPC3-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample confirms the diagnosis of a GPC3 -positive cancer in the subject.
In another embodiment, provided is a method of confirming a diagnosis of a HER2-positive cancer in a subject by contacting a sample from a subject diagnosed with a HER2-positive cancer with a HER2-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample confirms the diagnosis of a HER2 -positive cancer in the subject.
In some examples of the disclosed methods, the single-domain monoclonal antibody is directly labeled.
In some examples, the methods further include contacting a second antibody that specifically binds the monoclonal antibody with the sample; and detecting the binding of the second antibody. An increase in binding of the second antibody to the sample as compared to binding of the second antibody to a control sample detects a GPC3- or HER2 -positive cancer in the subject or confirms the diagnosis of a GPC3- or HER2 -positive cancer in the subject.
In some cases, the cancer is HCC, melanoma, squamous cell carcinoma of the lung or ovarian clear cell carcinoma, or any other type of cancer that expresses GPC3.
In some cases, the cancer is breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma or head and neck carcinoma, or any other type of cancer that expresses HER2.
In some examples, the control sample is a sample from a subject without cancer. In particular examples, the sample is a blood or tissue sample.
Further provided herein are methods of diagnosing a subject as infected with MERS virus by contacting a sample obtained from the subject with a MERS virus S protein-specific single- domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample diagnoses the subject as infected with MERS virus.
Also provided herein are methods of diagnosing a subject as infected with SARS virus by contacting a sample obtained from the subject with a SARS virus S protein- specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample diagnoses the subject as infected with SARS virus.
In another embodiment, provided is a method of detecting MERS virus in a sample by contacting the sample with a MERS virus S protein- specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample detects MERS virus in the sample.
In another embodiment, provided is a method of detecting SARS virus in a sample by contacting the sample with a SARS virus S protein-specific single-domain monoclonal antibody disclosed herein; and detecting binding of the antibody to the sample. An increase in binding of the antibody to the sample as compared to binding of the antibody to a control sample detects SARS virus in the sample.
In some embodiments of the methods of diagnosis and detection, the antibody that binds
(for example specifically binds) GPC3, HER2, PD1, MERS virus S protein or SARS S protein is directly labeled with a detectable label. In another embodiment, the antibody that binds (for example, specifically binds) GPC3, HER2, PD1, MERS virus S protein or SARS S protein (the first antibody) is unlabeled and a second antibody or other molecule that can bind the antibody that specifically binds GPC3, HER2, PD1, MERS virus S protein or SARS S protein is labeled. As is well known to one of skill in the art, a second antibody is chosen that is able to specifically bind the specific species and class of the first antibody. For example, if the first antibody is a human IgG, then the secondary antibody may be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.
Suitable labels for the antibody or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials. Non-limiting examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase. Non-limiting examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin. Non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin. A non- limiting exemplary luminescent material is luminol; a non-limiting exemplary a magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include 125I, 1311, 35S or 3H.
In an alternative embodiment, GPC3, HER2, PDl, MERS virus S protein or SARS S protein can be assayed in a biological sample by a competition immunoassay utilizing GPC3, HER2, PDl, MERS virus S protein or SARS S protein standards labeled with a detectable substance and an unlabeled antibody that specifically binds GPC3, HER2, PDl , MERS virus S protein or SARS S protein. In this assay, the biological sample, the labeled GPC3, HER2, PDl, MERS virus S protein or SARS S protein standards and the antibody that specifically bind GPC3, HER2, PDl, MERS virus S protein or SARS S protein are combined and the amount of labeled GPC3, HER2, PDl, MERS virus S protein or SARS S protein standard bound to the unlabeled antibody is determined. The amount of GPC3, HER2, PDl, MERS virus S protein or SARS S protein in the biological sample is inversely proportional to the amount of labeled GPC3, HER2, PDl , MERS virus S protein or SARS S protein standard bound to the antibody that specifically binds GPC3, HER2, PDl , MERS virus S protein or SARS S protein.
The immunoassays and methods disclosed herein can be used for a number of purposes. In one embodiment, the antibody that specifically binds GPC3, HER2, PDl, MERS virus S protein or SARS S protein may be used to detect the production of GPC3, HER2, PDl, MERS virus S protein or SARS S protein in cells in cell culture. In another embodiment, the antibody can be used to detect the amount of GPC3, HER2, PDl, MERS virus S protein or SARS S protein in a biological sample, such as a tissue sample, or a blood or serum sample. In some examples, the GPC3, HER2, PDl , MERS virus S protein or SARS S protein is cell-surface GPC3, HER2, PDl , MERS virus S protein or SARS S protein. In other examples, the GPC3, HER2, PDl, MERS virus S protein or SARS S protein is soluble (e.g. in a cell culture supernatant or in a body fluid sample, such as a blood or serum sample). In one embodiment, a kit is provided for detecting GPC3, HER2, PDl, MERS virus S protein or SARS S protein in a biological sample, such as a blood sample or tissue sample. For example, to confirm a cancer diagnosis in a subject, a biopsy can be performed to obtain a tissue sample for histological examination. Kits for detecting a polypeptide will typically comprise a monoclonal antibody that specifically binds GPC3, HER2, PDl, MERS virus S protein or SARS S protein, such as any of the single-domain antibodies disclosed herein. In a further embodiment, the antibody is labeled (for example, with a fluorescent, radioactive, or an enzymatic label).
In one embodiment, a kit includes instructional materials disclosing means of use of an antibody that binds GPC3, HER2, PDl, MERS virus S protein or SARS S protein. The instructional materials may be written, in an electronic form (such as a computer diskette or compact disk) or may be visual (such as video files). The kits may also include additional components to facilitate the particular application for which the kit is designed. Thus, for example, the kit may additionally contain means of detecting a label (such as enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels such as a secondary antibody, or the like). The kits may additionally include buffers and other reagents routinely used for the practice of a particular method. Such kits and appropriate contents are well known to those of skill in the art.
In one embodiment, the diagnostic kit comprises an immunoassay. Although the details of the immunoassays may vary with the particular format employed, the method of detecting GPC3, HER2, PDl, MERS virus S protein or SARS S protein in a biological sample generally includes the steps of contacting the biological sample with an antibody which specifically reacts, under immunologically reactive conditions, to GPC3, HER2, PDl, MERS virus S protein or SARS S protein. The antibody is allowed to specifically bind under immunologically reactive conditions to form an immune complex, and the presence of the immune complex (bound antibody) is detected directly or indirectly.
The antibodies disclosed herein can also be utilized in immunoassays such as but not limited to radioimmunoassays (RIAs), ELISA, or immunohistochemical assays. The antibodies can also be used for fluorescence activated cell sorting (FACS). FACS employs a plurality of color channels, low angle and obtuse light-scattering detection channels, and impedance channels, among other more sophisticated levels of detection, to separate or sort cells (see U.S. Patent No. 5,
061,620). Any of the single-domain monoclonal antibodies that bind GPC3, HER2, PDl, MERS virus S protein or SARS S protein, as disclosed herein, can be used in these assays. Thus, the antibodies can be used in a conventional immunoassay, including, without limitation, an ELISA, an RIA, FACS, tissue immunohistochemistry, Western blot or immunoprecipitation. XI. Method for Constructing a Phage-Displayed Shark VNAR Antibody Library
Antigen-specific VNAR domains have previously been generated from the immune repertoire of a number of different shark species, including the nurse shark (Ginglymostoma cirratum) (Dooley et al, Mol Immunol 40:25-33, 2003), the wobbegong shark (Orectolobus maculatus) (Nuttall et al, Mol Immunol 38:313-326, 2001 ; Liu et al, BMC Biotechnol 7:78, 2007), the spiny dogfish (Squalus acanthias) (Miiller et al , MAbs 4:673-685, 2012; Liu et al. , Mol
Immunol 44: 1775-1783, 2007; Liu et al , BMC Biotechnol 7:78, 2007), the banded houndshark (Triakis scyUium) (Ohtani et al. Mar Biotechnol 15:56-62, 2013; Ohtani et al . Fish Shellfish Immunol 34:724-728, 2013) and the bamboo shark (Chiloscyllium plagiosum) (Zielonka et al , J Biotechnol 191 :236-245, 2014). Target- specific clones have generally been isolated using different display technologies, such as phage display (Dooley et al , Mol Immunol 40:25-33, 2003; Nuttall et al , Mol Immunol 38:313-326, 2001) or ribosome display (Kopsidas et al , Immunol Lett 107: 163- 168, 2006).
Disclosed herein is an efficient method of producing a highly diverse VNAR antibody library using overlap extension PCR. An overview of the process used to generate the VNAR antibody library is illustrated in FIG. 1. Using overlap extension PCR, followed by a self-ligation step, a naive shark antibody library was constructed with an approximate size of 1.2 x 1010. Sequencing of twenty-five randomly picked colonies demonstrated that 72% of the clones were type II VNAR (FIGS. 2A-2B). The CDR3 length distribution of the selected clones was analyzed and determined to range from 9 to 24 amino acids, with the average length being 18 amino acids (FIG. 2C).
To generate the VNAR antibody library disclosed herein, total RNA was isolated from whole blood cells of six naive nurse sharks (Ginglymostoma cirratum) and total RNA was reverse- transcribed into cDNA. Using one forward primer and two reverse primers, the VNAR sequences for each shark and each primer combination were separately PCR amplified from the cDNA product (FIG. 8). The 12 PCR fractions from the six sharks were evenly pooled to ensure every group of VNAR was equally represented in the library. The vector backbone fragment was prepared by PCR. The amplified VNAR fragment was assembled with the vector backbone by overlap extension PCR using a VNAR-specific forward primer and a vector backbone-specific reverse primer. The assembled PCR product was self-ligated with T4 DNA ligase, and transformed into TGI to make the library.
The method disclosed herein for generating a VNAR antibody library differs from standard methods (which use conventional digestion and ligation) by utilizing overlap extension PCR and a self-ligation method (FIG. 1). This approach is far more efficient than the common digestion/ligation method. The library disclosed herein contains 1.2 x 1010 individual clones, which is much larger than previously reported VNAR libraries.
Provided herein is a method of generating an immunoglobulin new antigen receptor variable domain (VNAR) library. In some embodiments, the method includes providing complementary DNA (cDNA) generated from RNA isolated from lymphocytes of one or more cartilaginous fish; providing a vector backbone comprising a vector junction sequence; amplifying VNAR nucleic acid from the cDNA by polymerase chain reaction (PCR) using a VNAR-specific forward primer and at least one reverse primer comprising VNAR-specific sequence and the vector junction sequence to generate VNAR nucleic acid sequences comprising the vector junction sequence; assembling the VNAR nucleic acid sequences comprising the vector junction sequence and the vector backbone comprising the vector junction sequence by overlapping extension PCR using the VNAR-specific forward primer and a vector backbone-specific reverse primer, thereby producing linear VNAR vectors; and maintaining the linear VNAR vectors under conditions to permit self-ligation, thereby producing a library of VNAR vectors.
In some embodiments, the method further includes the step of obtaining RNA from immune cells, such as lymphocytes, of one or more cartilaginous fish. In some examples, the method further includes the step of generating cDNA from the isolated RNA using RT-PCR.
In some embodiments, the method further includes the step of generating the vector backbone comprising the vector junction sequence by PCR amplification of the vector backbone using a primer that includes the vector junction sequence.
In some embodiments, the method further includes the step of transforming the library of VNAR vectors into isolated host cells, such as isolated bacterial cells. Competent bacterial cells suitable for generating a phage display library are well-known in the art.
In some embodiments, the one or more cartilaginous fish are of the species Ginglymostoma cirratum, Orectolobus maculatus, Squalus acanthias, Triakis scyUiurn or Chiloscyllium plagiosum. In particular examples, the one or more cartilaginous fish are of the species Ginglymostoma cirratum (nurse shark).
In some examples of the method, the VNAR-specific forward primer is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 88. In specific examples, the VNAR- specific forward primer comprises or consists of SEQ ID NO: 88.
In some examples, the at least one reverse primer is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 89, is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 90, or both. In specific examples, the at least one reverse primer comprises or consists of SEQ ID NO: 89, SEQ ID NO: 90, or both. In some examples, the vector-backbone specific reverse primer is at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 92. In specific examples, the vector- backbone specific reverse primer comprises or consists of SEQ ID NO: 92.
In some examples, the vector backbone containing the vector junction sequence is prepared by PCR amplification of the vector using a forward primer at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 91 and a reverse primer at least 80%, at least 85%, at least 90%, or at least 95% identical to SEQ ID NO: 92. In specific examples, the vector backbone containing the vector junction sequence is prepared by PCR amplification of the vector using a forward primer comprising or consisting of SEQ ID NO: 91 and the vector-backbone specific reverse primer comprising or consisting of SEQ ID NO: 92.
In some embodiments, self-ligation is catalyzed by T4 DNA ligase.
The following examples are provided to illustrate certain particular features and/or embodiments. These examples should not be construed to limit the disclosure to the particular features or embodiments described.
EXAMPLES
Example 1: Materials and Methods
This examples describes the materials and experimental procedures used for the studies described in Example 2.
Cell lines
Hepatocellular carcinoma (HCC) cell line HepG2, which is GPC3 positive, was maintained as an adherent monolayer culture in DMEM medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (HyClone, Logan, UT), 1% L-glutamine, and 1% penicillin- streptomycin (Invitrogen) in a 5% incubator at 37°C. Cells were harvested and the media were changed twice a week. GPC3 -negative A431 cells (a human epithelial carcinoma cell line) were engineered to express high levels of GPC3 by transfection with a plasmid encoding full-length GPC3. Both A431 and the stably transfected cells (Gl) were maintained in DMEM.
Protein reagents
YP7, a previously described GPC3 mouse antibody, recognizes a C-terminal epitope (amino acids 510-560) of GPC3 (Phung et al, mAbs 4:592-599, 2012). YP7 was used in the competitive phage ELISA as a blocker for measuring the binding of GPC3-F1 monoclonal phage to the GPC3 peptide 511-560. The recombinant extracellular domain of Her2 (Cat. 10004-H08H) and PDl (Cat. 10377-H08H), the S-protein of MERS (Cat. 40069-V08B) and SARS (Cat. 40150- V08B2), were purchased from Sino Biological (Beijing, China). The recombinant PE38 and PE24 were made according to the published methods (Gao et al, Nat Commun 6:6536, 2015). The recombinant GPC3-hFc was made as previously published (Feng et al, Proc Natl Acad Sci USA 110:E1083- E1091, 2013).
DNA oligos and construction of the library
Total RNA was isolated from whole blood cells of 6 nurse sharks using the TRIZOL™ reagent (Thermo Fisher Scientific, Grand Island, NY) according to the manufacturer's instructions. Total RNA was reverse-transcribed into cDNA using the SUPERSCRIPT™ III First-Strand Synthesis System (Thermo Fisher Scientific) according to the manufacturer's instructions. One forward primer and two reverse primers were synthesized to PCR amplify the VNAR sequence from the cDNA product:
Forward primer IgNAR-F: GCTCGAGTGACCAAACACCG (SEQ ID NO: 88)
Reverse primer IgNAR-Rl:
GGTGGCCGGCCTGGCCACTATTCACAGTCACGGCAGTGCCAT (SEQ ID NO: 89)
Reverse primer IgNAR-R2:
GGTGGCCGGCCTGGCCACTATTCACAGTCACGACAGTGCCACC (SEQ ID NO: 90).
The vector backbone fragment was prepared by PCR with forward primer IgNARComb3x- F: AGTGGCCAGGCCGGCCACC (SEQ ID NO: 91), and reverse primer IgNARComb3x-R: GGCCGCCTGGGCCACGGTA (SEQ ID NO: 92). The amplified VNAR fragment was assembled with the vector backbone by over-lapping extension PCR using primer IgNAR-F and
IgNARComb3x-R. The assembled PCR product was self-ligated with T4 DNA ligase, and transformed into TGI to make the library. Phage display and panning method
Library bacterial stock was inoculated into 2.5 liters of 2XYT media containing 2% glucose, 100 μg/ml ampicillin, and cultured at 37°C with shaking (250 rpm). When the cells reached mid-log phase (OD6oo between 0.4-0.8), super-infection was performed by adding helper phage M13K07 at 5 x 109 pfu/ml. After one hour of continued growth, the cells were resuspended in 2.5 liters of 2XYT media containing 100 μg/ml ampicillin and 50 μg/ml kanamycin, and incubated at 25°C overnight. After the cells were centrifuged and filtered with a 0.22 μιη membrane, the supernatant was stored at 4°C for panning.
For panning, a 96-well Maxisorb ELISA plate (Nunc/Thermo Fisher Scientific, Rochester, NY) was used to capture various antigens (100 μg/ml) in phosphate buffered saline (PBS) at 4°C overnight. After the coating buffer was decanted, the plate was treated with blocking buffer (2% bovine serum albumin (BSA) in PBST) at room temperature for 1 hour. Then 30 μΐ pre -blocked phage supernatant (typically contained 1010-10n cfu) in 30 μΐ blocking buffer was added per well for 1 hour at room temperature to allow binding. After four washes with PBS containing 0.05% Tween-20, bound phages were eluted with 100 mM triethylamine. After four rounds of panning, single colonies were picked and identified by using phage ELISA methods.
GPC3 VNAR-IIFC expression and purification
The coding sequence of the GPC3 binder was cloned into expression vector pVRC8400. The resultant vector was used to transfect HEK293 cells. The volumetric titer of the secreted VNAR-IIFC in batch culturing was about 30 mg/L. Purification was carried out with protein A column (GE healthcare Life Sciences, Pittsburg, PA) according to the manufacturer's instructions.
Phage ELISA
The antigen proteins were used to coat a 96-well plate at 5 μg/ml in PBS buffer, 50 μΐ/well, at 4°C overnight. After the plate was blocked with 2% BSA in PBST buffer, 25 μΐ pre-blocked phage supernatant (typically 1010-10n cfu) were added to the plate. Binding was detected by horseradish peroxidase (HRP) -conjugated mouse anti-M13 antibody (GE healthcare Life Sciences, Pittsburg, PA). The cut-off value for a positive binder was set at 5 as the ratio of antigen binding versus background in OD450 reading is > 3.
Flow cytometry method
Cells were harvested in cell dissociation solution (Invitrogen, Carlsbad, CA), washed, and resuspended in ice cold PBS containing 5% BSA. One million cells per ml were incubated with 10 μg/mL of GPC3Fl-hFc and human IgG (hlgG) isotype control (Sigma- Aldrich, St. Louis, MO). Binding was detected with goat anti-human IgG conjugated with phycoerythrin (Sigma- Aldrich). The fluorescence associated with the live cells was measured using a FACS Calibur (BD
Biosciences, Franklin Lakes, NJ). For the cellular binding affinity measurement, various amounts of antibody were incubated with Gl cells. The geomean values were associated with corresponding concentration, and KD value was determined by using the software Prism 5.0 (GraphPad Software, Inc., La Jolla, CA) using two-sites binding (hyperbola) method.
For the phage FACS, 25 μΐ phage supernatant (approximately 1010 phages) were pre- blocked with FACS buffer (5% BSA in PBS) for 1 hour on ice, then mixed with 106 Gl cell suspension and incubated for 1 hour on ice. The binding was detected by a mouse anti-M13 primary antibody and phycoerythrin conjugated goat-anti-mouse secondary antibody (Sigma- Aldrich).
Structural Modeling of the PE38 and mPE24 toxins
The structural models of PE38 and mPE24 were generated by molecular modeling using I- TASSER (available online at zhanglab.ccmb.med.umich.edu/I-TASSER). Molecular models were viewed and analyzed using Chimera (available online at cgl.ucsf.edu/chimera).
Statistical analysis
All statistical analyses were conducted using GraphPad Prism5 (GraphPad Software, Inc., La Jolla, CA). Differences between groups were analyzed using the two-tailed Student's t test of means. HN3 binding curves were plotted using non-linear least square fit. Kr> values were calculated by using two sites binding (hyperbola) method.
Example 2: Phage-displayed shark single-domain antibody library to identify high-affinity binders to tumor and viral antigens
This example describes the construction of a shark VNAR antibody phage library and the identification of antibodies that bind to specific tumor and viral antigens.
Constructing of the phage library
An overview of the process is illustrated in FIG. 1. Using over-lapping extension PCR, followed by a self-ligation step, a naive shark antibody library was constructed with an approximate size of 1.2 x 1010. From here, twenty five colonies were randomly picked from the library and sequenced (FIG. 2A). The result showed that 72% of the clones are type II VNAR (FIG. 2B). The CDR3 length distribution was analyzed and determined to range from 9 to 24 amino acids, with the average length being 18 amino acids (FIG. 2C). Screening of VNAR binders to different targets
To evaluate the usefulness of the library, a variety of tumor biomarkers and virus antigen proteins were arbitrarily chosen as selection targets. These included a synthetic GPC3 peptide (amino acids 511-560), the recombinant extracellular domains of HER2 and PD1, the recombinant spike proteins of the MERS and SARS viruses, and recombinant Pseudomonas exotoxin PE38.
After 4 rounds of panning, specific binders to all of the listed targets were identified by monoclonal phage ELISA (FIG. 3). These binders were named GPC3-F1, HER2-A6, PD1-A1, MERS -A3, MERS-A7, MERS-A8, MERS-B4, MERS -B 5, SARS-01, and PE38-B6. While performing the panning, a number of hFc and rFc binders were identified as a result of using GPC3-hFc and GPC3-rFc fusion proteins as selection agents; these were named hFc or rFc binders hFc-05, hFc-48, hFc/rFc-04, hFc/rFc-03, hFc/rFc-02, hFc/rFc-01, hFc/rFc-28, hFc/rFc-10, hFc/rFc-21, rFc/tiFc-03, and rFc/tiFc-11. Sequence analysis showed that most of these 21 binders were type II VNAR (86%) (FIG. 4). The CDR3 length distribution was heavily biased toward 18 amino acids (52%). Before selection, the abundance of CDR3s of 18-amino acids was also high (about 20%) (FIG. 2C).
Binding properties of the GPC3-F1 clone
Glypican-3 (GPC3) is a liver cancer antigen that has been associated with hepatocellular carcinoma. GPC3 specific human antibodies HN3 and HS20, and a mouse antibody YP7, were previously generated (Feng and Ho, FEBS Lett 588:377-382, 2014). The mouse antibody YP7 was generated by immunizing mice with the synthetic GPC3 peptide 511-560. Using this same peptide as the selection agent, a shark binder (named GPC3-F1) was successfully discovered (FIG. 3). Phage FACS confirmed that this clone binds GPC3 over-expressing Gl cells (FIG. 5A). Then, the VNAR sequence was cloned from the phage, and a VNAR-IIFC fusion protein was made in HEK293 cells. The transient expression level was about 20 mg/L. The cellular binding of the purified GPC3Fl-hFc on HepG2 and Gl cells was confirmed (FIG. 5B). The binding affinity was measured on Gl cells, and the Kd value was calculated to be 124 nM (FIG. 5C). Since the Fl clone was selected using the same peptide that was used to generate the mouse monoclonal antibody YP7 (Phung et al , mAbs 4:592-599, 2012), it was investigated whether they recognize the same epitope. A competitive phage ELISA showed that the YP7 antibody barely inhibits the GPC3-F1 from binding to the same immunogen peptide (FIG. 5D). This indicates that the epitope of GPC3-F1 is different from YP7. Binding properties of the PE38-B6 clone
The PE38-B6 binder was selected using a 38 kD truncated form of PE that contains domain II and the catalytic domain III. The further truncated form of PE (mPE24) is a 24 kD fragment (PE24) that only retains domain III with the removal of human/mouse B cell epitopes (Liu et al. , Proc Natl Acad Sci USA 109:11782-11787, 2012; Alewine et al, Mol Cancer Ther 13:2653-2661, 2014). A phage ELISA was conducted and it was determined that the PE38-B6 clone binds the wild type PE38, but not mPE24 (FIG. 6A). This indicates that the PE38-B6 clone recognizes the wild type Pseudomonas exotoxin but not the variant with the removal of human/mouse B-cell epitopes. To determine if this was due to a conformational change, the protein folding was predicted by using the I-TASSER program (FIG. 6B). Domain III appears to fold in similar manor with or without the presence of domain II. This observation suggests that the responsible epitope can be found in domain II.
Binding properties of the hFc binders
While most of the hFc binders cross-react with rabbit Fc (rFc) or mouse Fc (mFc), the clone hFc-05 specifically binds hFc without exhibiting cross reactivity (FIG. 7). This indicates that shark antibodies can discriminate between highly similar antigen conformations. When comparing clone hFc-05 to clone hFc-48, only 3 consecutive variations were found in the middle of framework 1 (QTI and RSV, respectively) (FIG. 4). This slight variation in hFc-48 led to its cross-reactivity with mouse IgGs, indicating the framework also regulates the shark antibody binding specificity.
Diagnostic and Therapeutic Applications
In recent years, shark VNAR domain antibodies have been suggested as a new class of target binding proteins that can be used in therapeutic, diagnostic and other biotechnological applications. However, there are only fourteen specific targets with shark binders that have been developed and reported (Kovaleva et al, Expert Opin Biol Ther 14:1527-1539, 2014; Ohtani et al, Fish Shellfish Immunol 34:724-728, 2013; Camacho-Villegas et al, mAbs 5:80-85, 2013; Muller et al, mAbs 4:673-685, 2012; Walsh et al, Virology 411:132-141, 2011; Goodchild et al, Mol Immunol 48:2027-2037, 2011; Ohtani et al , Mar Biotechnol 15:56-62, 2013; Nuttall et al, FEBS Lett 516:80-6, 2002; Liu et al, Mol Immunol 44:1775-1783, 2007; Dooley et al, Mol Immunol 40:25- 33, 2003; Shao et al, Mol Immunol 44:656-665, 2007; Liu et al , BMC Biotechnol 7:78, 2007; Nuttall et al, Mol Immunol 38:313-326, 2001; Nuttall et al, Eur J Biochem 270:3543-3554, 2003; Nuttall et al, Proteins 55:187-197, 2004), none of which are tumor antigens. Semi-synthetic libraries have shown limited sequence diversity, because they are generated by CDR3 randomization based on one specific VNAR sequence. Prior to the present disclosure, a large VNAR library produced from multiple animals had not been reported.
To develop the VNAR library disclosed herein, immune cells were collected from a group of six naive nurse sharks. Using one forward primer and two reverse primers, the VNAR fragments for each shark and each primer combination were separately PCR amplified (FIG. 8). The 12 PCR fractions from the six sharks were evenly pooled to ensure every group of VNAR was equally represented in the library. Instead of using conventional digestion and ligation method, overlapping PCR and a self-ligation method were used to make the library (FIG. 1). This approach is far more efficient than the common digestion/ligation method. The library contains 1.2 x 1010 individual clones, which is much larger than previously reported shark libraries. To challenge the utility of the library, a panel of tumor and virus antigen proteins were used as targets to successfully discover binders of interest. A binder for every antigen was identified, which indicates that the phage display library is an efficient route to generate shark binders even when naive sharks are used.
Type II VNAR was found to be the major type in both the library and in the selected binders
(over 70% in both cases). In a similar study that used hen egg lysozyme to immunize nurse sharks followed by phage display, it was found 80% of the clones in the immunized library and the two antigen binders were type I (Dooley et al, Mol Immunol 40:25-33, 2003). In terms of the CDR3 length, 18 amino acids was dominant in both the library and the binders.
The CDRs control the antibody binding specificity. However the framework of shark VNAR may also contribute its binding specificity. It was found that hFc-05 and hFc-48 have an almost identical sequence except for 3 consecutive amino acid changes in FR1 (QTI and RSV, respectively). The clone hFc-05 was shown to only bind hFc with no cross-reactivity to rFc and mFc. The hFc-48 clone on the other hand, retained its ability to bind hFc, but was also shown to bind mouse serum IgGs equally well. This phenomenon indicated that the framework structure influences the binding specificity.
The studies disclosed herein indicate that a large phage-displayed naive library is a very efficient route to generate shark VNAR binders. The shark library approach provides a powerful platform to isolate high affinity binders to tumor and viral antigens.
Example 3: Mutants of VNAR clone GPC-F1
VNAR clone GPC3-F1 does not belong to any known type of VNAR because it contains three cysteine residues instead of two cysteines (found in Type IV VNAR) or four cysteines (found in Type II VNAR). TWO mutants of GPC-F1 were engineered to resemble a Type II or Type IV VNAR. F1-Y29C introduces a cysteine residue into CDR1 to generate a Type II VNAR and F1-C96S removes a cysteine residue from CDR3 to generate a Type IV VNAR. The amino acid sequences of Fl, F1-Y29C and F1-C96S are provided below, along with codon-optimized (for expression in bacterial cells) nucleic acid sequences encoding each VNAR.
Fl-WT (3 Cys)
gctcgagtggaccaaacaccgaaaacaataacaaaggagacgggcgaatcactgaccatcaactgtgtcctacgagatactagctatgcattg ggcagcacgtactggtatcgaaaaaaattgggctcaacaaacgaggagagcatatcgaaaggtggacgatatgttgaaacagttaacagcgg atcaaagtccttttctttgagaattaatgatctaacagttgaagacagtggcacgtatcgatgcaaggtatccgctggtatccggatatatagctcat actgttctagggatgtatacggaggtggcactgtcgtgactgtgaat (SEQ ID NO: 93)
ARVDQTPKTITKETGESLTINCVLRDTSYALGSTYWYRKKLGSTNEESISKGGRYVETVNS GSKSFSLRINDLTVEDSGTYRCKVSAGIRIYSSYCSRDVYGGGTVVTVN (SEQ ID NO: 1) F1-Y29C (Type II)
gcgcgtgttgaccaaaccccgaaaaccattaccaaagagaccggcgagagcctgaccattaactgcgttctgcgtgataccagctGcgcgct gggtagcacctactggtatcgtaagaaactgggcagcaccaacgaggaaagcatcagcaagggtggccgttacgtggaaaccgttaacagc ggtagcaagagcttcagcctgcgtatcaacgacctgaccgtggaagatagcggtacctatcgttgcaaggttagcgcgggcattcgtatctaca gcagctattgcagccgtgatgtttatggtggtggtaccgttgtgaccgtgaat (SEQ ID NO: 94)
ARVDQTPKTITKETGESLTINCVLRDTSCALGSTYWYRKKLGSTNEESISKGGRYVETVNS GSKSFSLRINDLTVEDSGTYRCKVSAGIRIYSSYCSRDVYGGGTVVTVN (SEQ ID NO: 95)
F1-C96S (Type IV)
gcgcgtgttgaccaaaccccgaaaaccattaccaaagagaccggcgagagcctgaccattaactgcgttctgcgtgataccagctacgcgctg ggtagcacctactggtatcgtaagaaactgggcagcaccaacgaggaaagcatcagcaagggtggccgttacgtggaaaccgttaacagcg gtagcaagagcttcagcctgcgtatcaacgacctgaccgtggaagatagcggtacctatcgttgcaaggttagcgcgggcattcgtatctacag cagctatAgcagccgtgatgtttatggtggtggtaccgttgtgaccgtgaat (SEQ ID NO: 96) ARVDQTPKTITKETGESLTINCVLRDTSYALGSTYWYRKKLGSTNEESISKGGRYVETVNS GSKSFSLRINDLTVEDSGTYRCKVSAGIRIYSSYSSRDVYGGGTVVTVN (SEQ ID NO: 97) In view of the many possible embodiments to which the principles of the disclosed invention may be applied, it should be recognized that the illustrated embodiments are only preferred examples of the invention and should not be taken as limiting the scope of the invention. Rather, the scope of the invention is defined by the following claims. We therefore claim as our invention all that comes within the scope and spirit of these claims.

Claims

1. A single-domain monoclonal antibody that binds glypican-3 (GPC3), comprising a complementarity determining region (CDR) 1 and a CDR3, wherein the monoclonal antibody comprises the CDRl and CDR3 sequences of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
2. The single-domain monoclonal antibody of claim 1, wherein the CDRl and CDR3 sequences are respectively set forth as residues 26-33 and 84-101 of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
3. The single-domain monoclonal antibody of claim 1 or claim 2, further comprising a hypervariable region (HV) 2 and a HV4, wherein the monoclonal antibody comprises the HV2 and HV4 sequences of SEQ ID NO: 1.
4. The single-domain monoclonal antibody of claim 3, wherein the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 1.
5. The single-domain monoclonal antibody of any one of claims 1-4, further comprising a framework region 1 (FW1), a FW2, a FW3a, a FW3b, a FW4, or any combination thereof, of SEQ ID NO : 1.
6. The single-domain monoclonal antibody of claim 5, wherein the FW1, the FW2, the FW3a, the FW3b and the FW4 respectively comprise residues 1-25, 34-44, 53-59, 65-83 and 102- 110 of SEQ ID NO: 1.
7. The single-domain monoclonal antibody of any one of claims 1-6, comprising the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 95 or SEQ ID NO: 97.
8. A single-domain monoclonal antibody that binds programmed cell death protein 1 (PD1), comprising a complementarity determining region (CDR) 1 and a CDR3, wherein the monoclonal antibody comprises the CDRl and CDR3 sequences of SEQ ID NO: 2.
9. The single-domain monoclonal antibody of claim 8, wherein the CDRl and CDR3 sequences are respectively set forth as residues 26-33 and 84-96 of SEQ ID NO: 2.
10. The single-domain monoclonal antibody of claim 8 or claim 9, further comprising a hypervariable region (HV) 2 and a HV4, wherein the monoclonal antibody comprises the HV2 and HV4 sequences of SEQ ID NO: 2.
11. The single-domain monoclonal antibody of claim 10, wherein the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 2.
12. The single-domain monoclonal antibody of any one of claims 8-11, further comprising a FWl, a FW2, a FW3a, a FW3b, a FW4, or any combination thereof, of SEQ ID NO: 2.
13. The single-domain monoclonal antibody of claim 12, wherein the FWl, the FW2, the FW3a, the FW3b and the FW4 respectively comprise residues 1-25, 34-44, 53-59, 65-83 and 97-105 of SEQ ID NO: 2.
14. The single-domain monoclonal antibody of any one of claims 8-13, comprising the amino acid sequence of SEQ ID NO: 2.
15. A single-domain monoclonal antibody that binds HER2, comprising a
complementarity determining region (CDR) 1 and a CDR3, wherein the monoclonal antibody comprises the CDR1 and CDR3 sequences of SEQ ID NO: 3 or SEQ ID NO: 4.
16. The single-domain monoclonal antibody of claim 15, wherein the CDR1 and CDR3 sequences are respectively set forth as residues 26-33 and 84-106 of SEQ ID NO: 3; or the CDR1 and CDR3 sequences are respectively set forth as residues 26-33 and 83-100 of SEQ ID NO: 4.
17. The single-domain monoclonal antibody of claim 15 or claim 16, further comprising a hypervariable region (HV) 2 and a HV4, wherein the monoclonal antibody comprises the HV2 and HV4 sequences of SEQ ID NO: 3 or SEQ ID NO: 4.
18. The single-domain monoclonal antibody of claim 17, wherein the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 3; or the HV2 and HV4 sequences are respectively set forth as residues 45-51 and 59-63 of SEQ ID NO: 4.
19. The single-domain monoclonal antibody of any one of claims 15-18, further comprising a FW1, a FW2, a FW3a, a FW3b, a FW4, or any combination thereof, of SEQ ID NO: 3 or SEQ ID NO: 4.
20. The single-domain monoclonal antibody of claim 19, wherein the FW1, the FW2, the FW3a, the FW3b and the FW4 respectively comprise residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 3, or residues 1-25, 34-44, 52-58, 64-82 and 101-109 of SEQ ID NO: 4.
21. The single-domain monoclonal antibody of any one of claims 15-20, comprising the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 4.
22. A single-domain monoclonal antibody that binds Middle East respiratory syndrome (MERS) virus spike protein, comprising a complementarity determining region (CDR) 1 and a CDR3, wherein the monoclonal antibody comprises the CDRl and CDR3 sequences of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
23. The single-domain monoclonal antibody of claim 22, wherein the CDRl and CDR3 sequences are respectively set forth as residues 26-33 and 84-104 of SEQ ID NO: 5; the CDRl and CDR3 sequences are respectively set forth as residues 26-33 and 84-106 of SEQ ID NO: 6; the
CDRl and CDR3 sequences are respectively set forth as residues 26-33 and 84-103 of SEQ ID NO: 7; the CDRl and CDR3 sequences are respectively set forth as residues 26-33 and 84-101 of SEQ ID NO: 8; or the CDRl and CDR3 sequences are respectively set forth as residues 26-33 and 84-96 of SEQ ID NO: 9.
24. The single-domain monoclonal antibody of claim 22 or claim 23, further comprising a hypervariable region (HV) 2 and a HV4, wherein the monoclonal antibody comprises the HV2 and HV4 sequences of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
25. The single-domain monoclonal antibody of claim 24, wherein the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 5; the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 6; the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 7; the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 8; or the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 9.
26. The single-domain monoclonal antibody of any one of claims 22-25, further comprising a FW1, a FW2, a FW3a, a FW3b, a FW4, or any combination thereof, of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
27. The single-domain monoclonal antibody of claim 26, wherein the FW1, the FW2, the FW3a, the FW3b and the FW4 respectively comprise residues 1-25, 34-44, 53-59, 65-83 and
105-113 of SEQ ID NO: 5; residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 6; residues 1-25, 34-44, 53-59, 65-83 and 104-112 of SEQ ID NO: 7; residues 1-25, 34-44, 53-59, 65- 83 and 102-110 of SEQ ID NO: 8; or residues 1-25, 34-44, 53-59, 65-83 and 97-105 of SEQ ID NO: 9.
28. The single-domain monoclonal antibody of any one of claims 22-27, comprising the amino acid sequence of SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8 or SEQ ID NO: 9.
29. A single-domain monoclonal antibody that binds severe respiratory syndrome
(SARS) virus spike protein, comprising a complementarity determining region (CDR) 1 and a CDR3, wherein the monoclonal antibody comprises the CDR1 and CDR3 sequences of SEQ ID NO: 10.
30. The single-domain monoclonal antibody of claim 29, wherein the CDR1 and CDR3 sequences are respectively set forth as residues 26-33 and 84-104 of SEQ ID NO: 10.
31. The single-domain monoclonal antibody of claim 29 or claim 30, further comprising a hypervariable region (HV) 2 and a HV4, wherein the monoclonal antibody comprises the HV2 and HV4 sequences of SEQ ID NO: 10.
32. The single-domain monoclonal antibody of claim 31 , wherein the HV2 and HV4 sequences are respectively set forth as residues 45-52 and 60-64 of SEQ ID NO: 10.
33. The single-domain monoclonal antibody of any one of claims 29-32, further comprising a FW1, a FW2, a FW3a, a FW3b, a FW4, or any combination thereof, of SEQ ID NO: 10. 34. The single-domain monoclonal antibody of claim 33, wherein the FW1, the FW2, the FW3a, the FW3b and the FW4 respectively comprise residues 1-25,
34-44, 53-59, 65-83 and 105-113 of SEQ ID NO: 10.
35. The single-domain monoclonal antibody of any one of claims 29-34, comprising the amino acid sequence of SEQ ID NO: 10.
36. A single-domain monoclonal antibody that binds glypican-3 (GPC3), programmed cell death protein 1 (PDl), HER2, Middle East respiratory syndrome (MERS) virus spike protein, or severe acute respiratory syndrome (SARS) virus spike protein, comprising a framework region 1 (FW1), a FW2, a FW3a, a FW3b, a FW4, or any combination thereof, of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9 or SEQ ID NO: 10.
37. The single-domain monoclonal antibody of claim 36, wherein:
the single-domain antibody binds GPC3 and comprises residues 1-25, 34-44, 53-59, 65-83 and 102-110 of SEQ ID NO: 1;
the single-domain antibody binds PDl and comprises residues 1-25, 34-44, 53-59, 65-83 and 97-105 of SEQ ID NO: 2;
the single-domain antibody binds HER2 and comprises residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 3, or comprises residues 1-25, 34-44, 52-58, 64-82 and 101-109 of SEQ ID NO: 4;
the single-domain antibody binds MERS spike protein and comprises residues 1-25, 34-44, 53-59, 65-83 and 105-113 of SEQ ID NO: 5, comprises residues 1-25, 34-44, 53-59, 65-83 and 107-115 of SEQ ID NO: 6, comprises residues 1-25, 34-44, 53-59, 65-83 and 104-112 of SEQ ID NO: 7, comprises residues 1-25, 34-44, 53-59, 65-83 and 102-110 of SEQ ID NO: 8, or comprises residues 1-25, 34-44, 53-59, 65-83 and 97-105 of SEQ ID NO: 9; or
the single-domain antibody binds SARS spike protein and comprises residues 1-25, 34-44, 53-59, 65-83 and 105-113 of SEQ ID NO: 10.
38. The single-domain monoclonal antibody of any one of claims 1-37, wherein the antibody is chimeric, synthetic or humanized.
39. An antibody-drug conjugate (ADC) comprising a drug conjugated to the single- domain monoclonal antibody of any one of claims 1-38.
40. The ADC of claim 39, wherein the drug is a small molecule.
41. The ADC of claim 39 or claim 40, wherein the drug is an anti-microtubule agent, an anti-mitotic agent and/or a cytotoxic agent.
42. A chimeric antigen receptor (CAR) comprising the single-domain monoclonal antibody of any one of claims 1-38.
43. An isolated cell expressing the CAR of claim 42.
44. The isolated cell of claim 43, which is a cytotoxic T lymphocyte (CTL).
45. An immunoconjugate comprising the single-domain monoclonal antibody of any of claims 1-38 and an effector molecule.
46. The immunoconjugate of claim 45, wherein the effector molecule is a toxin or a detectable label.
47. The immunoconjugate of claim 46, wherein the toxin is a Pseudomonas exotoxin or a variant thereof.
48. The immunoconjugate of claim 46, wherein the detectable label comprises a fluorophore, an enzyme or a radioisotope.
49. A multi-specific antibody comprising the single-domain monoclonal antibody of any of claims 1-38 and a second monoclonal antibody or antigen-binding fragment thereof.
50. The multi- specific antibody of claim 49, wherein the second monoclonal antibody or antigen-binding fragment thereof specifically binds a component of the T cell receptor or a natural killer (NK) cell activating receptor.
51. An antibody-nanoparticle conjugate, comprising a nanoparticle conjugated to the single-domain monoclonal antibody of any one of claims 1-38.
52. The antibody-nanoparticle conjugate of claim 51, wherein the nanoparticle comprises a polymeric nanoparticle, nanosphere, nanocapsule, liposome, dendrimer, polymeric micelle, or niosome.
53. The antibody-nanoparticle conjugate of claim 51 or claim 52, wherein the nanoparticle comprises a cytotoxic agent.
54. A fusion protein comprising the single-domain monoclonal antibody of any one of claims 1-38 and a heterologous protein.
55. The fusion protein of claim 54, wherein the heterologous protein comprising an Fc domain.
56. A composition comprising the single-domain monoclonal antibody, ADC, CAR, isolated cell, immunoconjugate, multi- specific antibody, antibody-nanoparticle conjugate or fusion protein of any one of claims 1-55 and a pharmaceutically acceptable carrier.
57. A nucleic acid molecule encoding the single-domain monoclonal antibody, CAR, immunoconjugate, multi-specific antibody or fusion protein of any one of claims 1-38, 42, 45-50, 54 and 55.
58. The nucleic acid molecule of claim 57, operably linked to a promoter.
59. A vector comprising the nucleic acid molecule of claim 57 or claim 58.
60. A method of treating a GPC3 -positive cancer in a subject, comprising administering to the subject the single-domain monoclonal antibody of any one of claims 1-7, or administering to the subject an ADC, CAR, immunoconjugate, multi- specific antibody, antibody-nanoparticle conjugate or fusion protein comprising the single-domain monoclonal antibody of any one of claims 1-7.
61. A method of inhibiting tumor growth or metastasis of a GPC3 -positive cancer in a subject, comprising administering to the subject the single-domain monoclonal antibody of any one of claims 1-7, or administering to the subject an ADC, CAR, immunoconjugate, multi- specific antibody, antibody-nanoparticle conjugate or fusion protein comprising the single-domain monoclonal antibody of any one of claims 1-7.
62. The method of claim 60 or claim 61, wherein the GPC3-positive cancer is hepatocellular carcinoma (HCC), melanoma, squamous cell carcinoma of the lung or ovarian clear cell carcinoma.
63. A method of detecting expression of GPC3 in a sample, comprising:
contacting the sample with the single-domain monoclonal antibody of any of claims 1-7; and
detecting binding of the antibody to the sample, thereby detecting expression of GPC3 in the sample.
64. The method of claim 63, wherein the single-domain monoclonal antibody is directly labeled.
65. The method of claim 3 further comprising:
contacting the single-domain monoclonal antibody with a second antibody, and detecting the binding of the second antibody to the single-domain monoclonal antibody, thereby detecting expression of GPC3 in the sample.
66. The method of any one of claims 63-65, wherein the sample is obtained from a subject suspected of having a GPC3-positive cancer.
67. The method of any one of claims 63-65, wherein the sample is a tumor biopsy.
68. A method of treating a HER2-positive cancer in a subject, comprising administering to the subject the single-domain monoclonal antibody of any one of claims 15-21, or administering to the subject an ADC, CAR, immunoconjugate, multi- specific antibody, antibody-nanoparticle conjugate or fusion protein comprising the single-domain monoclonal antibody of any one of claims 15-21.
69. A method of inhibiting tumor growth or metastasis of a HER2 -positive cancer in a subject, comprising administering to the subject the single-domain monoclonal antibody of any one of claims 15-21, or administering to the subject an ADC, CAR, immunoconjugate, multi-specific antibody, antibody-nanoparticle conjugate or fusion protein comprising the single-domain monoclonal antibody of any one of claims 15-21.
70. The method of claim 68 or claim 69, wherein the HER2-positive cancer is breast cancer, gastric cancer, esophageal cancer, ovarian cancer, endometrial cancer, stomach cancer, uterine cancer, pancreatic cancer, prostate cancer, bladder cancer, colon cancer, salivary gland carcinoma, renal adenocarcinoma, mammary gland carcinoma, non-small cell lung carcinoma or head and neck carcinoma.
71. A method of detecting expression of HER2 in a sample, comprising:
contacting the sample with the single-domain monoclonal antibody of any of claims 15-21; and
detecting binding of the antibody to the sample, thereby detecting expression of HER2 in the sample.
72. The method of claim 71, wherein the single-domain monoclonal antibody is directly labeled.
73. The method of claim 71, further comprising:
contacting the single-domain monoclonal antibody with a second antibody, and detecting the binding of the second antibody to the single-domain monoclonal antibody, thereby detecting expression of HER2 in the sample.
74. The method of any one of claims 71-73, wherein the sample is obtained from a subject suspected of having a HER2 -positive cancer.
75. The method of any one of claims 71-73, wherein the sample is a tumor biopsy.
76. A method of enhancing an anti-tumor response in a subject, comprising
administering to the subject the single-domain monoclonal antibody of any one of claims 8-14, or administering to the subject a CAR or multi-specific antibody comprising the single-domain monoclonal antibody of any one of claims 8-14.
77. The method of claim 76, wherein the subject has melanoma, lung cancer, bladder cancer, breast cancer, Hodgkin' s lymphoma, renal cancer, head and neck cancer, gastric cancer, glioblastoma, colorectal cancer or Merkel cell carcinoma.
78. A method of detecting expression of PD-1 in a sample, comprising:
contacting the sample with the single-domain monoclonal antibody of any of claims 8-14; and
detecting binding of the antibody to the sample, thereby detecting expression of PD-1 in the sample.
79. The method of claim 78, wherein the single-domain monoclonal antibody is directly labeled.
80. The method of claim 78, further comprising:
contacting the single-domain monoclonal antibody with a second antibody, and detecting the binding of the second antibody to the single-domain monoclonal antibody, thereby detecting expression of PD-1 in the sample.
81. A method of treating a MERS virus infection in a subject, comprising administering to the subject the single-domain monoclonal antibody of any one of claims 22-28.
82. A method of detecting MERS virus in a sample, comprising:
contacting the sample with the single-domain monoclonal antibody of any of claims 22-28; and
detecting binding of the antibody to the sample, thereby detecting expression of MERS virus in the sample.
83. The method of claim 82, wherein the single-domain monoclonal antibody is directly labeled.
84. The method of claim 82, further comprising:
contacting the single-domain monoclonal antibody with a second antibody, and
detecting the binding of the second antibody to the single-domain monoclonal antibody, thereby detecting expression of MERS virus in the sample.
85. A method of treating a SARS virus infection in a subject, comprising administering to the subject the single-domain monoclonal antibody of any one of claims 29-35.
86. A method of detecting SARS virus in a sample, comprising:
contacting the sample with the single-domain monoclonal antibody of any of claims 29-35; and
detecting binding of the antibody to the sample, thereby detecting expression of SARS virus in the sample.
87. The method of claim 86, wherein the single-domain monoclonal antibody is directly labeled.
88. The method of claim 86, further comprising:
contacting the single-domain monoclonal antibody with a second antibody, and
detecting the binding of the second antibody to the single-domain monoclonal antibody, thereby detecting expression of SARS virus in the sample.
89. A method of generating an immunoglobulin new antigen receptor variable domain (VNAR) library, comprising:
providing complementary DNA (cDNA) generated from RNA isolated from lymphocytes of one or more cartilaginous fish;
providing a vector backbone comprising a vector junction sequence;
amplifying VNAR nucleic acid from the cDNA by polymerase chain reaction (PCR) using a VNAR-specific forward primer and at least one reverse primer comprising VNAR-specific sequence and the vector junction sequence to generate VNAR nucleic acid sequences comprising the vector junction sequence;
assembling the VNAR nucleic acid sequences comprising the vector junction sequence and the vector backbone comprising the vector junction sequence by overlap extension PCR using the VNAR-specific forward primer and a vector backbone-specific reverse primer, thereby producing linear VNAR vectors; and
maintaining the linear VNAR vectors under conditions to permit self-ligation, thereby producing a library of VNAR vectors.
90. The method of claim 89, further comprising transforming the library of VNAR vectors into isolated host cells.
91. The method of claim 90, wherein the host cells are bacterial cells.
92. The method of any one of claims 89-91, wherein the one or more cartilaginous fish are of the species Ginglymostoma cirratum, Orectolobus maculatus, Squalus acanthias, Triakis scyllium or Chiloscyllium plagiosum.
93. The method of any one of claims 89-92, wherein the one or more cartilaginous fish are of the species Ginglymostoma cirratum.
94. The method of claim 93, wherein the VNAR-specific forward primer comprises SEQ ID NO: 88.
95. The method of claim 93 or claim 94, wherein the at least one reverse primer comprises SEQ ID NO: 89, SEQ ID NO: 90, or both.
96. The method of any one of claims 93-95, wherein the vector-backbone specific reverse primer comprises SEQ ID NO: 92.
97. The method of any one of claims 89-96, wherein the vector backbone comprising the vector junction sequence is prepared by PCR amplification of the vector using a forward primer comprising SEQ ID NO: 91 and the vector-backbone specific reverse primer comprising SEQ ID NO: 92.
98. The method of any one of claims 89-97, wherein self-ligation is catalyzed by T4 DNA ligase.
99. A nucleic acid molecule encoding the single-domain monoclonal antibody of any one of claims 1-7.
100. The nucleic acid molecule of claim 99, wherein the nucleic acid molecule is codon- optimized for expression in bacterial cells.
101. The nucleic acid molecule of claim 100, comprising the nucleotide sequence of SEQ ID NO: 93, SEQ ID NO: 94 or SEQ ID NO: 96.
102. The nucleic acid molecule of any one of claims 99-101, operably linked to a promoter.
103. A vector comprising the nucleic acid molecule of any one of claims 99-102.
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