US20230279147A1 - H1.0k180me2 antibodies, methods of making and uses thereof - Google Patents

H1.0k180me2 antibodies, methods of making and uses thereof Download PDF

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US20230279147A1
US20230279147A1 US18/054,427 US202218054427A US2023279147A1 US 20230279147 A1 US20230279147 A1 US 20230279147A1 US 202218054427 A US202218054427 A US 202218054427A US 2023279147 A1 US2023279147 A1 US 2023279147A1
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antibody
seq
antigen
cdr
amino acid
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Victoria V. Lunyak
James Robert TOLLERVEY
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Aelan Cell Technologies Inc
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Aelan Cell Technologies Inc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/44—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material not provided for elsewhere, e.g. haptens, metals, DNA, RNA, amino acids
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • 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
    • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
    • 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
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • 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

  • Histone proteins are the main protein components of chromatin and double-stranded DNA is wound around histone proteins. Changes in histone proteins can differentially alter access of the transcriptional machinery to some genes while leaving access to other genes intact. Differential chromatin condensation achieved by histone posttranslational modifications (PTMs) underlies packaging of chromatin (Lunyak and Rosenfeld 92008) Hum. Mol. Genet., 17: R28-36; Jenuwein and Allis (2001) Science, 293: 1074-1080). Histone PTMs, for example methylation, can act as an epigenetic code and play critical roles in many aspects of the cellular responses tightly linked to development, injury, disease and aging.
  • PTMs histone posttranslational modifications
  • H1 and H5 Five major families of histones exist: H1, H2A, H2B, H3 and H4. Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1 and H5 are known as the linker histones.
  • Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1 and H5 are known as the linker histones.
  • the large number of H1.0-binding proteins identified by multiple studies in recent years point to an important role for protein-protein interactions of H1.0 and suggests a new paradigm for H1.0 structure and function that extends beyond its effects on chromatin architecture.
  • antibodies that bind a protein comprising an H1.0K180me2 antigen, or a peptide thereof, wherein the antibodies are useful for therapeutics and diagnostics. Also provided are methods of making such antibodies.
  • an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises any one of the CDR-L amino acid sequences of Tables 4, 5, and 6, and comprises any one of the CDR-H amino acid sequences of Tables 7, 8, and 9.
  • an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7.
  • an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8.
  • an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 9.
  • the antibody is chimeric or humanized. In some embodiments, the antibody is a monoclonal antibody. In some embodiments, the antibody is an antigen-binding fragment.
  • the antibody exhibits reduced binding to the H1.0K180me2 protein or peptide, if the protein or peptide comprises residues other than K180 that are methylated. In some embodiments, the antibody does not bind, or only minimally binds, if the H1.0K180me2 protein or peptide comprises methylated lysine residues at lysine residues corresponding to K166, K172, K174, K175, and/or K177 of a human histone H1.0 protein.
  • the antibody is conjugated to a label. In some embodiments, the antibody is attached to solid surface. In some embodiments, the antibody attached a bead, column, resin, or a microplate. In some embodiments, the antibody is conjugated to an agent. In some embodiments, the agent is selected from the group consisting of a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • the agent is selected from the group consisting of a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine,
  • a vector encoding any one of the antibodies provided herein.
  • the vector comprises the nucleic acid of SEQ ID NO: 4 or the nucleic acid of SEQ ID NO: 5.
  • a cell comprising one or more of these vectors.
  • a method of determining whether an individual has, or is at risk of, developing, Alzheimer's disease comprising:
  • a method of determining whether an individual diagnosed with Alzheimer's disease and receiving treatment for the Alzheimer's disease, will benefit from the treatment or will continue to benefit from the treatment comprising:
  • a method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, wherein the individual has not yet started the treatment comprising:
  • a method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment comprising:
  • a method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, wherein the individual has not yet started the treatment comprising:
  • a method of determining whether an individual has been exposed to a DNA damaging agent comprising:
  • a method of determining whether an individual receiving treatment with a rapalogue is responsive to such treatment comprising:
  • the rapalogue is selected from the group consisting of Rapamycin, Sirolimus, Rapamune, Everolimus, RA 001, Afinitor, Zortress, Temsirolimus, CCI-779, Torisel, Ridaforolimus, AP23573, MK-8669, Deforolimus, Zotarolimus, ABT-578, AZD8055, AZD2014, OSI-027, MLN0128, WYE-132, Torin1, PI-103, P7170, PF-04691502, PF-05212384, PKI-587, GNE477, PKI-180, WJD008, XL765, SAR245409, NVP-BEZ235, BGT226, SF1126, GSK2126458, Ku-0063794, WYE-354, NVP-BEZ235, PF-05212384, XL765, Torin 2, WYE-125132, and OSI-027.
  • the increase or decrease in the concentration is above or below a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the biological sample is selected from the group consisting of whole blood, plasma, serum, saliva, urine, synovial fluid, cerebrospinal fluid, bronchial lavage, ascites fluid, bone marrow aspirate, pleural effusion, tissue, cells, a biopsy, interstitial fluid, and lymphatic fluid.
  • a method of treating a methylated H1.0-related disease or condition in an individual comprising administering to the individual a therapeutically effective amount of any one of the antibodies described herein.
  • the disease or condition is selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxic stressor, a disease or condition comprising the accumulation of senescent cells, and a disease or condition accompanied by elevated levels of H1.0K180me2 proteins or peptides.
  • a method of clearing H1.0K180me2 in an individual comprising administering to the individual a therapeutically effective amount of any one of the antibodies described herein.
  • the individual suffers from a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
  • transdermal patch for measuring a concentration of a hypodermal target molecule, comprising:
  • the patch is a transdermal microneedle array patch.
  • the substrate is elastically stretchable.
  • a portable unit for determining whether an individual has been exposed to radiation or a DNA-damaging agent comprising:
  • test strip suitable for a lateral flow assay of an analyte, comprising a sample receiving zone, wherein the sample receiving zone comprises any one of the antibodies described herein.
  • a pharmaceutical composition comprising any of the antibodies provided herein.
  • the pharmaceutical composition may further comprise a pharmaceutically acceptable excipient.
  • kits comprising a therapeutically effective amount of any one of the antibodies provided herein.
  • provided herein is an article of manufacture comprising any one of antibodies or compositions provided herein.
  • provided herein is any one of antibodies or compositions provided herein, for use as a medicament.
  • provided herein is any one of antibodies or compositions provided herein, for use in a method of treatment, wherein the method comprises clearing H1.0K180me2 in an individual; optionally wherein the individual suffers from a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
  • a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
  • FIG. 1 diagrams an exemplary process of generating monoclonal antibodies.
  • FIG. 2 A demonstrates binding efficiency of antibody clones to a H1.0Kme2 peptide (methylated at the residue corresponding to K180 of the human H1.0 protein).
  • FIG. 2 B demonstrates the binding efficiency of antibody clones to an unmodified H1.0 peptide (not methylated).
  • FIG. 2 C provides raw data for the binding of antibody clones to H1.0Kme2 or H1.0 peptide.
  • FIG. 3 shows specificity of antibody clones to H1.0 peptides with 0, 1, or 2 methyl modifications on K180.
  • FIG. 4 A illustrates specific in vitro H1.0K180 methylation by G9A methyltransferase.
  • FIG. 4 B shows methylation sites on H1.0 by G9A determined by LC/MS.
  • FIG. 4 C shows detection of methylation of H1.0K180 by a H1.0K180me2 antibody.
  • FIG. 4 D is an analysis of antibody clone specificity for in vitro methylated H1.0.
  • FIG. 5 A shows a protein sequence alignment between the antibody heavy chains of Clone A (SEQ ID NO: 6) and Clone B (SEQ ID NO: 7).
  • FIG. 5 B shows a protein sequence alignment between the antibody light chains of Clone A (SEQ ID NO: 8) and Clone B (SEQ ID NO: 9).
  • FIG. 5 C shows the DNA (SEQ ID NOs: 4 and 5) and protein sequences (SEQ ID NOs: 6 and 8) for antibody Clone A.
  • FIG. 5 D illustrates an exemplary method for recombinant expression of an antibody.
  • FIG. 6 illustrates various possible modifications to an antibody that can enhance function.
  • FIG. 7 A depicts the sequence of antibody clone A heavy chain (SEQ ID NO: 6) and is annotated with structural information.
  • FIG. 7 B depicts the sequence of antibody clone A light chain (SEQ ID NO: 8) and is annotated with structural information.
  • FIG. 7 C depicts the predicted light chain complementary determining regions (CDR) and framework (FW) regions for antibody Clone A (SEQ ID NOs: 10, 11, 14, 15, 18 and 38-43).
  • FIG. 7 D depicts the predicted heavy chain CDR and FW regions for antibody Clone A (SEQ ID NOs: 20-23, 28-31, 36, 37 and 44-56).
  • FIG. 8 shows an exemplary use of an ELISA for the direct detection of H1.0K180me2 epitope in samples of bodily fluids.
  • FIGS. 9 A- 9 C show age-related accumulation of circulating H1.0K180me2 in the brain tissue and blood serum. Shown are western blot analyses of H1.0K180me2 in mouse ( FIG. 9 A ) and human ( FIG. 9 B ) brain tissue, revealing that its abundance increases with organismal age.
  • FIG. 9 C shows H1.0K180me2 levels in human serum samples normalized by total IgG serum levels. The symbol “a” represents an antibody, in this figure and throughout.
  • FIGS. 10 A- 10 C demonstrate the utility of measurements of serum H1.0K180me2 as biomarkers of Alzheimer's disease.
  • FIG. 10 A shows that serum H1.0K180me2 is decreased in individuals with Alzheimer's disease, when compared to age-matched controls (normalized by serum volume).
  • FIG. 10 B shows that serum H1.0K180me2 is decreased in individuals with Alzheimer's disease, when compared to age-matched controls (normalized by total serum IgG levels).
  • FIG. 10 C shows that serum H1.0K180me2 is decreased in individuals with Alzheimer's disease, when compared to age-matched controls (normalized by total serum protein concentration).
  • FIG. 11 A shows the dimethylation of H1.0K180 (H1.0K180me2) on chromatin immediately after DNA damage, by western blot analysis.
  • FIG. 11 B shows secretion of H1.0K180me2 from after DNA damage.
  • FIGS. 12 A and 12 B show LC-MS/MS analysis ( FIG. 12 A ) and slot blot analysis ( FIG. 12 B ) on hADSCs of SR, acute DNA damage, and genotoxic stress induced senescence, revealing that dimethylated H1.0K180 (H1.0K180me2) is released from chromatin upon genotoxic stress induced senescence ( FIG. 12 A ) and is secreted out of the cells into the extracellular matrix/cellular media ( FIG. 12 B ).
  • FIGS. 13 A- 13 C show the effect of ionizing radiation on H1.0K180me2 levels.
  • FIG. 13 A shows that exposure to ionizing radiation induces increased levels of circulating H1.0K180me2 in mouse serum.
  • FIG. 13 A and FIG. 13 B show a slot blot analysis of the presence ( FIG. 13 A ) and quantification ( FIG. 13 B ) of H1.0K180me2, using antibodies specific for the H1.0K180me2 epitope in the serum.
  • FIG. 13 C shows a western blot analysis of presence of H1.0K180me2 epitope levels, using antibodies specific for the H1.0K180me2 epitope, in mouse serum after X-ray irradiation (7 Gy).
  • FIG. 14 shows a western blot analysis of H1.0K180me2 in SR hADSCs (self renewing human adipose derived stem cells) after bleomycin treatment, revealing that everolimus, a derivative of rapamycin, can act to block H1.0K180me2 appearance upon DNA damage.
  • H1.0K180me2 antibodies are useful for therapeutic and diagnostic uses. These H1.0K180me2 antibodies may be used in the treatment of methylated H1.0-related diseases or conditions in an individual. These H1.0K180me2 antibodies may also be used for detecting replicative senescence, DNA damage, genotoxic stress, radiation exposure, Alzheimer's disease, for monitoring therapeutic regimens, patient stratification, drug screening, and may serve as a marker of biological aging in a system. These compositions and methods are described in detail below.
  • WO 2017/184895 describes compositions and methods related to H1.0 dimethylated proteins; and WO 2017/184873 describes compositions and methods related to the methylation of H1.0 protein.
  • the contents of these publications are incorporated herein by reference in their entirety.
  • antibodies that specifically bind a dimethylated histone H1.0 antigen, wherein the dimethylated histone H1.0 antigen is a histone H1.0 protein or peptide thereof, comprising a dimethylated lysine residue, wherein the lysine residue corresponds to K180 of the full length human histone H1.0 protein (SEQ ID NO: 1), and wherein the dimethylated K180 residue is required for binding.
  • the K180 is represented by K* in SEQ ID NO: 1 of Table 1 below.
  • the dimethylated H1.0 antigen is interchangeably referred to as the H1.0K180me2 antigen or H1.0K180me2 epitope throughout.
  • the H1.0K180me2-containing proteins and peptides are referred to as “H1.0K180me2 proteins” and “H1.0K180me2 peptides” throughout.
  • the terms “anti-H1.0K180me2” or “H1.0K180me2 antibody” or “anti-H1.0K180me2 antibody” interchangeably refer to these antibodies.
  • K180 refers to the residue corresponding to K180 of the human H1.0 protein (SEQ ID NO: 1).
  • K172 refers to the residue corresponding to K172 of the human H1.0 protein
  • K190 refers to the residue corresponding to K190 of the human H1.0 protein, etc.
  • H1.0K180me2 antibodies of the present disclosure bind to human and non-human mammalian H1.0K180me2 antigens.
  • antibody as used herein throughout is in the broadest sense and includes a monoclonal antibody, human antibody, humanized antibody, non-human antibody, chimeric antibody, bispecific antibody, an antigen-binding fragment (e.g Fab fragment, a Fab′2 fragment, a CDR or a ScFv), and other antibody fragments that retain specificity for the H1.0K180me2 antigen.
  • the antibody is a single chain antibody that retains the specificity for the H1.0K180me2 antigen.
  • the antibodies are chimeric human x mouse antibodies, In one exemplary embodiment, the antibodies are chimeric human x rabbit antibodies. In one exemplary embodiment, the antibodies are humanized mouse antibodies. In one exemplary embodiment, the antibodies are humanized rabbit antibodies.
  • the H1.0K180me2 antibodies provided herein are diagnostic antibodies. In some embodiments, the H1.0K180me2 antibodies provided herein are therapeutic antibodies.
  • the H1.0K180me2 antibody is an affinity-purified antibody.
  • the H1.0K180me2 antibody is an isolated antibody.
  • H1.0K180me2 antibodies provided herein may be conjugated to an agent for a variety of purposes including, but not limited to, detection, diagnostics, visualization, quantification, sorting, therapeutics, and for use in biological assays.
  • the H1.0K180me2 antibodies are conjugated to a label, for example a detectable label, a spin label, a colorimetric label, a radioactive label, an enzymatic label, a fluorescent label, or a magnetic label.
  • a label for example a detectable label, a spin label, a colorimetric label, a radioactive label, an enzymatic label, a fluorescent label, or a magnetic label.
  • the H1.0K180me2 antibodies are attached to a solid surface, for example a bead (e.g. a magnetic, glass or plastic bead), column, resin or a microplate.
  • a bead e.g. a magnetic, glass or plastic bead
  • an antibody is coated onto the microplate.
  • the antibodies attached to a solid surface are conjugated to a label; in some embodiments the antibodies attached to as solid surface are antigen-binding fragments.
  • an antibody is conjugated to an effector molecule including, but not limited to, a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • an effector molecule including, but not limited to, a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • H1.0K180me2 antibodies provided herein can bind extracellular H1.0K180me2 and/or intracellular H1.0K180me2.
  • the antibodies provided herein may be of any immunoglobulin type such as IgG, IgA, IgE, IgD, or IgM.
  • the antibody is of the IgG subtype and may be an IgG1 antibody, an IgG2 antibody, an IgG3 antibody, or an IgG4 antibody.
  • the H1.0K180me2 antibody is specific for human H1.0K180me2. In some embodiments, the H1.0K180me2 antibody is cross reactive with H1.0K180me2 from other species.
  • H1.0K180me2 antibodies provided herein are selective for the H1.0K180me2 antigen, e.g. the H1.0K180me2 antibody is selective for dimethylation at residue K180.
  • the H1.0K180me2 antibodies provided herein are specific for the H1.0K180me2 antigen, e.g. the H1.0K180me2 antibody is specific for dimethylation at residue K180, and exhibits little or no binding of an H1.0K180 epitope (unmethylated at K180), H1.0K180me1 epitope (mono-methylated at K180), or an H1.0K180me3 epitope (trimethylated at K180).
  • the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen that comprises an unmethylated K180 residue ( FIG. 4 D ).
  • the antibodies provided herein specifically bind an H1.0K180me2-containing antigen.
  • the H1.0K180me2-containing antigen does not comprise any other lysine residues that are methylated.
  • the H1.0K180me2 antibody does not bind, or only minimally binds if the target H1.0K180me2 antigen comprises additional methylated lysine residues, e.g. where the lysine residues correspond to K166, K172, K174, K175, and/or K177 of a human histone H1.0 protein.
  • the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen that comprises one or more of the following residues: K172me1, K172me2, K172me3, K174me1, K174me2, K174me3, K175me1, K175me2, K175me3, K177me1, K177me2, K177me3, K166me1, K166me2, K166me3, K180me1, and/or K180me3.
  • the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen that comprises a dimethylated K180 residue, but also comprises one or more of the following residues: K172me1, K172me2, K172me3, K174me1, K174me2, K174me3, K175me1, K175me2, K175me3, K177me1, K177me2, K177me3, K166me1, K166me2, K166me3, K180me1, and/or K180me3.
  • the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen when the H1.0K180me2 antibody displays at least 1.5-fold, 2-fold, 2.5-fold, 2.7-fold, 5-fold, or even 10-fold less specificity (binding preference, affinity) for the antigen than for H1.0K180me2-containing antigen that does not comprise any other lysine residues that are methylated.
  • the H1.0K180me2 antibodies of the present disclosure may bind the H1.0K180me2 epitope in any medium.
  • the H1.0K180me2 antibody displays at least 1.5-fold, 2-fold, 2.5-fold, 2.7-fold, 5-fold, or even 10-fold more specificity (binding preference, affinity) for the dimethylated antigen at K180 (H1.0K180me2 antigen), than an unmethylated antigen at K180 (H1.0K180 antigen).
  • the specificity for an H1.0K180me2 antigen is generally at least about 2-fold, about 5-fold, or at least about 10-, 20-, 50-, 10 ⁇ circumflex over ( ) ⁇ 2-, 10 ⁇ circumflex over ( ) ⁇ 3-, 10 ⁇ circumflex over ( ) ⁇ 4, 10 ⁇ circumflex over ( ) ⁇ 5, or 10 ⁇ circumflex over ( ) ⁇ 6-fold over a non-specific target molecule (e.g. a randomly generated molecule lacking the specifically recognized site(s)), over an unmethylated K180 residue, over a trimethylated K180 residue, or over an H1.0 protein methylated at any other residue.
  • a non-specific target molecule e.g. a randomly generated molecule lacking the specifically recognized site(s)
  • the H1.0K180me2 antibody displays at least 1.5-fold, 2-fold, 2.5-fold, 2.7-fold, 5-fold, or even 10-fold more specificity (binding preference, affinity) for the dimethylated antigen at K180 (H1.0K180me2 antigen), than a monomethylated antigen at K180 (H1.0K180me1 antigen).
  • the specificity for an H1.0K180me2 antigen is generally at least about 2-fold, about 5-fold, or at least about 10-, 20-, 50-, 10 ⁇ circumflex over ( ) ⁇ 2-, 10 ⁇ circumflex over ( ) ⁇ 3-, 10 ⁇ circumflex over ( ) ⁇ 4, 10 ⁇ circumflex over ( ) ⁇ 5, or 10 ⁇ circumflex over ( ) ⁇ 6-fold over a non-specific target molecule (e.g. a randomly generated molecule lacking the specifically recognized site(s)), over a monomethylated K180 residue, over a trimethylated K180 residue, or over an H1.0 protein methylated at any other residue.
  • a non-specific target molecule e.g. a randomly generated molecule lacking the specifically recognized site(s)
  • the H1.0K180me2 antibodies provided herein has a dissociation constant (Kd) of range of 0.0001 nM to 1 M.
  • Kd of the antibody may be about 1 ⁇ M, about 100 nM, about 50 nM, about 10 nM, about 5 nM, about 1 nM, about 0.5 nM, about 0.1 nM, about 0.05 nM, about 0.01 nM, about 0.005 nM, about 0.001 nM, about 0.0005 nM, or even about 0.0001 nM.
  • H1.0K180me2 antibodies e.g. monoclonal H1.0K180me2 antibodies, mAb
  • mAb monoclonal H1.0K180me2 antibodies
  • FIG. 6 Part a. shows a glycomodified afucosylated mAb that exhibits enhanced binding to IgG Fc receptors (Fc ⁇ R) as well as increased ADCC.
  • Fc ⁇ R IgG Fc receptors
  • FIG. 6 Part b.
  • the amino acid sequence of a mAb can be modified in the constant region. Such modification can increase binding of the mAb to Fc ⁇ R and also increase ADCC. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • FIG. 6 Part c.
  • a different isotype can be substituted.
  • IgG4 does not induce ADCC to the same degree that IgG1 does.
  • Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • Radio-immunoconjugates can be produced by conjugating a radioactive isotope to a mAb linker. Use of a stable linker will prevent leakage of free radioactive isotope. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • Antibody drug conjugates can be made by conjugating a drug to a mAb with a linker.
  • a cleavable linker or pH-sensitive linker can be used to allow the drug to act separately from the mAb.
  • Such conjugation can targeting of the drug to cell or tissue specified by the antibody and limits toxicity by not circulating freely. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • FIG. 6 Part f.
  • the specificity of mAbs can utilized in the generation of Chimeric Antigen Receptor T cells (CAR-T cells). These can be generate by fusing the DNA that codes for a mAb variable region to the DNA sequence of the internal signaling portion of the T-cell receptor. This chimeric receptor is useful for introducing into T cells for use in adoptive therapy.
  • the antigen binding domains of any the H1.0K180me2 antibodies described herein can be used to generated CAR-T cells.
  • Bispecific antibodies are created by removing the constant region from an antibody and crosslinking the remaining variable region to the isolated variable region of another antibody. Removal of the constant region can result in reduced half-life and requires continuous transfusion of such a crosslinked antibody to achieve desired levels of exposure. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • the H1.0K180me2 antibody comprises the variable domain, complementary binding region, framework regions of Clone A (discussed below). In some embodiments, the H1.0K180me2 antibody is a monoclonal humanized antibody, or antigen-binding fragment thereof, that comprises the CDRs of Clone A (discussed below). In some embodiments the H1.0K180me2 antibody comprises the variable domain, complementary binding region, framework regions of Clone B (discussed below). In some embodiments, the H1.0K180me2 antibody is a monoclonal humanized antibody, or antigen-binding fragment thereof, that comprises the CDRs of Clone B (discussed below).
  • immunoassay formats may be used to select antibodies specifically immunoreactive with H1.0K180me2.
  • solid-phase ELISA immunoassays may be used to select monoclonal antibodies specific to H1.0K180me2 (see, e.g., Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York, for a description of immunoassay formats and conditions that may be used to determine specific immunoreactivity).
  • the antibodies are produced by recombinant cells engineered to express the desired variable heavy (VH) and variable light (VL) and constant domains of the desired antibody (e.g. FIG. 5 D ).
  • VH variable heavy
  • VL variable light
  • the antibodies are produced by hybridomas.
  • any peptide comprising the H1.0K180me2 antigen, optionally linked to the immunogenic carrier is used for immunization using standard protocols.
  • a peptide comprising CAKPVKASKPKKAKPVK(me2)PK is used for immunization using standard protocols ( FIG. 1 ). The quality and titer of generated antibodies may be assessed using techniques known to those in the art.
  • Phase I involves immunizing rabbits against a H1.0K180me2 peptide conjugated to a Keyhole Limpet Hemocyanin (KLH). The titer of the immunization is compared between pre-immunization and post-immunization bleeds. Peripheral Blood Mononuclear Cells (PBMCs) are isolated and were then sorted for positive antigen binding cells by flow cytometry.
  • Phase II total RNA is extracted from cells isolated in Phase 1. RT-PCR of the heavy chain and light chain variable domains of the antibodies is performed and the scFv amplicon is inserted into vectors.
  • scFv vectors are then used to generate a cell surface-display library.
  • the cell surface-display library is panned for at least one round with H1.0K180me2 peptide. This step further selects against unmethylated H1.0K peptide binding. Clones that bind H1.0K180me2 are further selected by flow cytometry and can be subsequently sequenced.
  • Phase IV full length heavy chains and light chains are created to generate full recombinant antibodies. These antibodies can be expressed and purified. The binding of these antibodies to H1.0K180me2 protein can be then validated by ELISA, slot blot, and western blot. This is explained in further detail in Examples 2-4.
  • Exemplary amino acid sequences for unmethylated as well as methylated H1.0 protein are provided in FIG. 4 B as well as Table 1 above. (methylated lysine residues are denoted as (me1/2/3 indicating mono, di, and tri methylation possibilities).
  • compositions described herein also include nucleic acids encoding any of the antibodies disclosed herein, vectors comprising any of the nucleic acids encoding the antibodies, and host cells comprising any such vectors.
  • Table 2 provides exemplary nucleic acid sequences for the antigen-binding fragments of the antibodies provided herein.
  • cells that contain the nucleotides and vectors encoding the antibodies are secreted.
  • antibodies can also be prepared by any of a number of commercial services, e.g. upon provision of the sequences.
  • Tables 3-9 provides amino acid sequences for the antigen-binding fragments of some exemplary H1.0K180me2 antibodies.
  • Table 3 provides exemplary heavy chain variable (VH) and heavy chain light (VL) sequences. Also provided herein are VH and VL sequences that have at least 85%
  • SEQ ID NO: 6 Amino Acid Sequence of the Heavy Chain Variable (VH) Domain of an H1.0K180me2 antibody (Clone A) QSVEESGGRLVTPGTPLTLTCTVSGFSLNNYVMMWVRQAPGEGLEWIAAIT TGGTTYYANWAKGRFTISKTSTTVDLKIISPTTEDTATYFCARDLYGDTSD DIWDAFDPWGPGTLVTVSS
  • SEQ ID NO: 7 Amino Acid Sequence of the Heavy Chain Variable Domain of an H1.0K180me2 antibody (Clone B) QSLEESGGRLVTPGTPLTLTCTASGFSLSDYYTTWVRQAPGQGLEYIGYIS GTGTPYYATWAKGRFTISRTSTTVGLKMTSLTTEDTATYFCARSYPGIDAN N
  • SEQ ID NO: 8 Amino Acid Sequence of the Light Chain Variable (VL) Domain of an H1.0K180me2 antibody (Clone A) DP
  • Tables 4-9 provide exemplary complementary determining region (CDR) sequences (regions 1, 2, and 3) of the antigen-binding domain of the light chain (CDR-L) and the antigen-binding domain of the heavy chain (CDR-H).
  • CDR-L1 a VL CDR1 region
  • CDR-L2 a VL CDR2 region
  • CDR-L3 a VH CDR1 region
  • CDR-H2 referred to as CDR-H2
  • a VH CDR3 region is referred to as CDR-H3.
  • an H1.0K180me2 antibody wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 or SEQ ID NO: 7.
  • an H1.0K180me2 antibody wherein the antibody comprises the light chain variable domain of SEQ ID NO: 8 or SEQ ID NO: 9.
  • an H1.0K180me2 antibody wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 or SEQ ID NO: 7 and the light chain variable domain of SEQ ID NO: 8 or SEQ ID NO: 9.
  • an H1.0K180me2 antibody wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 and comprises the light chain variable domain of SEQ ID NO: 8.
  • a H1.0K180me2 wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 and comprises the light chain variable domain of SEQ ID NO: 9.
  • an H1.0K180me2 antibody wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 7 and comprises the light chain variable domain of SEQ ID NO: 8.
  • an H1.0K180me2 antibody wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 7 and comprises the light chain variable domain of SEQ ID NO: 9.
  • an H1.0K180me2 antibody wherein the antigen-binding region of the antibody comprises:
  • an H1.0K180me2 antibody wherein the antigen-binding region of the antibody comprises:
  • an H1.0K180me2 antibody wherein the antigen-binding region of the antibody comprises: an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises any one of the CDR-L amino acid sequences of Tables 4, 5, and 6, and comprises any one of the CDR-H amino acid sequences of Tables 7, 8, and 9.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO.12, or SEQ ID NO: 13.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L2 of SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO.16, or SEQ ID NO: 17.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L3 of SEQ ID NO: 18 or SEQ ID NO: 19.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO.12, or SEQ ID NO: 13; a CDR-L2 of SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO.16, or SEQ ID NO: 17; and a CDR-L3 of SEQ ID NO: 18 or SEQ ID NO: 19.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10 or SEQ ID NO: 11, the CDR-L2 of SEQ ID NO: 14 or SEQ ID NO: 15, or the CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12 or SEQ ID NO: 13, the CDR-L2 of SEQ ID NO: 16 or SEQ ID NO: 17, or the CDR-L3 of SEQ ID NO: 19.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, or SEQ ID NO: 23; the CDR-H2 of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31; or the CDR-H3 of SEQ ID NO: 36 or SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, CDR-L2 of SEQ ID NO: 14, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, CDR-L2 of SEQ ID NO: 15, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 11, CDR-L2 of SEQ ID NO: 14, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 11, CDR-L2 of SEQ ID NO: 15, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12, CDR-L2 of SEQ ID NO: 14, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12, CDR-L2 of SEQ ID NO: 16, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12, CDR-L2 of SEQ ID NO: 17, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 13, CDR-L2 of SEQ ID NO: 16, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 13, CDR-L2 of SEQ ID NO: 17, and CDR-L3 of SEQ ID NO: 18.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, or SEQ ID NO: 27.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H2 of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H3 of SEQ ID NO: 36 or SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of antibody comprises the CDR-H1 of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, or SEQ ID NO: 27; comprises the CDR-H2 of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35; and comprises the CDR-H3 of SEQ ID NO: 36 or SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 32.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 33.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 34.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 35.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 and comprises the CDR-H2 of SEQ ID NO: 32.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 and comprises the CDR-H2 of SEQ ID NO: 33.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 and comprises the CDR-H2 of SEQ ID NO: 34.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 comprises the CDR-H2 of SEQ ID NO: 35.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 and comprises the CDR-H2 of SEQ ID NO: 32.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 and comprises the CDR-H2 of SEQ ID NO: 33.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 and comprises the CDR-H2 of SEQ ID NO: 34.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 comprises the CDR-H2 of SEQ ID NO: 35.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 27 and comprises the CDR-H2 of SEQ ID NO: 32.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 27 and comprises the CDR-H2 of SEQ ID NO: 33.
  • an H1.K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ TD NO: 27 and comprises the CDR-H2 of SEQ ID NO: 34.
  • an H1.0K180me2 antibody wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ TD NO: 27 comprises the CDR-H2 of SEQ ID NO: 35.
  • Table 10 provides exemplary antibody framework (FW) sequences.
  • VL framework regions are referred to as LRF1, LRF2, and LRF3.
  • VH framework regions are referred to as HRF1, HRF2, HRF3, and HRF4.
  • therapeutic H1.0K180me2 antibodies for the treatment of a methylated H1.0-related disease or condition.
  • a “methylated H1.0-related disease or condition” is one where there is an increase in the levels of H1.0K180me2, an increase in the endogenous dimethylation of a H1.0 protein/peptide substrate at K180, an increase in the release of H1.0K180me2 from the chromatin, an increase in the release of H1.0K180me2 from the nucleus into the cytoplasm, an increase in the cytoplasmic deposition of H1.0K180me2, an increase in the levels of H1.0K180me2 in the extracellular space, an increase in the circulating levels of H1.0K180me2 in a bodily fluid (e.g. serum, urine, saliva, cerebrospinal fluid, etc.), and/or an increase in the level of autoantibodies specific for H1.0K180me2.
  • a bodily fluid e.g. serum, urine, saliva, cerebrospinal fluid, etc.
  • Methylated H1.0-related diseases and conditions include, but are not limited to, age-related pathologies associated with increase of senescent cells, Alzheimer's disease, radiation exposure, exposure to a genotoxic stressor, conditions that comprise the accumulation of senescent cells associated with external and internal stressors, and autoimmune group of diseases and conditions associated with high level of autoantibodies to H1.0K180me2.
  • kits for treating a methylated H1.0-related disease or condition in an individual by binding and clearing H1.0K180me2 comprising administering to the individual a therapeutically effective amount of a therapeutic H1.0K180me2 antibody.
  • an individual refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sport, or pet animals, such as dogs, horses, rabbits, cattle, pigs, hamsters, gerbils, mice, ferrets, rats, cats, and the like. Individuals may be male or female.
  • the individual can be of any age. In some embodiments of the methods described herein, e.g. for the treatment of Alzheimer's disease, the individual is greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • FIG. 9 B During aging, there is increased accumulation of cytoplasmic H1.0K180me2 in the brain tissue of humans, FIG. 9 B . These observations are correlated with an age-related increase of circulating H1.0K180me2 antigen observed in serological tests ( FIG. 9 C ). Additionally, when whole cell lysates of mouse brain samples from 1 month (young) and 24 month (old) mice were compared by western blot analysis with anti-H1.0K180me2, anti-H1.0, anti- ⁇ H2A.X and anti- ⁇ -Actin antibodies, H1.0K180me2 levels increased in the 24 month mouse, correlating with increased levels of ⁇ H2A.X ( FIG. 9 A ).
  • FIGS. 10 A- 10 C show the quantification of H1.0K180me2 levels determined by slot blot analysis in Alzheimer's disease patients and age-matched controls. Quantification of H1.0K180me2 levels was determined by slot blot analysis in Alzheimer's disease patients and age-matched controls.
  • FIG. 10 B shows H1.0K180me2 levels in human serum normalized by total IgG serum levels.
  • FIG. 10 C shows H1.0K180me2 levels in human serum normalized by total protein levels.
  • serum concentrations of H1.0K180me2 are sufficient for identification of Alzheimer's disease patients, the use of serum sample normalization by total IgG ( FIG. 10 B ) or total protein ( FIG. 10 C ) allows for direct comparisons between individuals regardless of variables which may alter overall serum concentration, such as protocol used to obtain serum, operator variability, hydration state of patient and activity state of patient.
  • an H1.0K180me2 antibody e.g. a cell penetrating antibody or a cell clearing antibody
  • H1.0K180me2 dimethylation of H1.0K180 (H1.0K180me2) is observed on chromatin following acute DNA damage with bleomycin, a chemotherapeutic agent ( FIG. 11 A ).
  • SR hADSCs self-renewing human adipose derived stem cells
  • hADSCs treated with DNA damaging agent bleomycin for 2 hours were lysed and fractionated to obtain the chromatin bound fraction.
  • Western blot analysis with an H1.0K180me2 antibody shows methylation of H1.0K180 on the chromatin upon DNA damage ( FIG. 11 A ).
  • H1.0K180me2 is released from the chromatin upon genotoxic stress induced senescence (days after treatment with a DNA damaging agent) ( FIG. 12 A ) and is secreted out of the cells into the extracellular space ( FIG. 12 B ).
  • Chromatin bound H1.0 decreased from ⁇ 60% of total in SR and acute DNA damage, to ⁇ 30% of total upon genotoxic stress induced senescence.
  • Culture media from SR hADSCs treated with bleomycin was collected for slot blot analysis with ⁇ -H1.0 and ⁇ -H1.0K180me2 antibodies to assess secretion of H1.0 to the extracellular matrix (ECM).
  • an H1.0K180me2 antibody e.g. a cell penetrating antibody, or a cell-clearing antibody
  • H1.0K180me2 In the context of radiation exposure, exposure to ionizing radiation induces increased levels of circulating H1.0K180me2 in serum ( FIG. 13 A and FIG. 13 B .
  • the effect of ionizing radiation on H1.0K180me2 levels in serum was examined. Serum was collected from wild-type mice before and either 2 hours or 48 hours after exposure to 7 Gy of ionizing radiation. H1.0K180me2 serum levels 2 hours (mouse 1) or 48 hours (mouse 2) after irradiation were compared to initial levels before treatment using slot blot and immunoblotting with ⁇ -H1.0K180me2 antibody ( FIG. 13 A ). The concentration of H1.0K180me2 in each serum sample was calculated using a standard curve of H1.0K180me2 peptide included in each analysis.
  • Mouse serum albumin was used as a loading control. H1.0K180me2 dot blot bands were quantified and normalized by serum albumin. Relative increases in H1.0K180me2 after irradiation are shown ( FIG. 13 B ). Western blot analysis of equal volumes of mouse serum with ⁇ -H1.0K180me2 antibody also showed increased H1.0K180me2 after irradiation ( FIG. 13 C ).
  • an H1.0K180me2 antibody e.g. a cell penetrating antibody or a cell clearing antibody
  • antibodies that recognize and selectively and/or specifically bind to the H1.0K180me2 epitope, and may be used for therapeutics.
  • the therapeutic antibody is a neutralizing antibody, and the antibody neutralizes one or more biological activities of H1.0K180me2.
  • the antibody may bind extracellular H1.0K180me2 and neutralize any binding or signaling activity it may possess.
  • the antibody may clear or block H1.0K180me2 in a cell, or a sample.
  • the antibody may clear the cells comprising H1.0K180me2.
  • the therapeutic antibody may clear senescent cells. In some embodiments, the antibody may clear cells/tissue or protein products that give rise to the symptom of Alzheimer's disease. In some embodiments, the antibody may clear cells damaged by radiation damage, DNA damaging agents, and other genotoxins. In some embodiments, the antibody is a cell-penetrating antibody. In other embodiments, the affected cells' membranes are comprised and allow for entry of the therapeutic H1.0K180me2 antibodies provided herein.
  • the therapeutic antibody provided herein has antibody-dependent cellular cytotoxicity (ADCC) activity.
  • ADCC antibody-dependent cellular cytotoxicity
  • Effector cells bearing Fc gamma receptors (Fc ⁇ R or FCGR) on their cell surface including cytotoxic T-cells, natural killer (NK) cells, macrophages, neutrophils, eosinophils, dendritic cells, or monocytes, recognize and bind the Fc region of antibodies bound to the target-cells. Such binding may trigger the activation of intracellular signaling pathways leading to cell death.
  • the therapeutic antibody has complement-dependent cytotoxicity (CDC) activity.
  • CDC complement-dependent cytotoxicity
  • Antibody-induced CDC is mediated through the proteins of the classical complement cascade and is triggered by binding of the complement protein Clq to the antibody.
  • Antibody Fc region binding to Clq may induce activation of the complement cascade.
  • the therapeutic antibody has antibody-dependent cellular phagocytosis (ADCP) activity.
  • ADCP antibody-dependent cellular phagocytosis
  • Phagocytic cells bearing Fc receptors on their cell surface including monocytes and macrophages, recognize and bind the Fc region of antibodies bound to target-cells.
  • phagocytosis of the target cell may be initiated.
  • the therapeutic antibodies may form an immune complex.
  • an immune complex may be a cell expressing or extruding H1.0K180me2 antigen, covered by antibodies.
  • any of the therapeutic H1.0K180me2 antibodies provided herein may be administered in combination with other known drugs/treatments for the diseases which manifest in H1.0 methylation.
  • any of the therapeutic H1.0K180me2 antibodies may be administered in combination with the administration of an Alzheimer's disease preventive drug or regimen which include, but are not limited to, APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, A ⁇ aggregation inhibitors, A ⁇ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins,
  • H1.0K180me2 antibodies described herein may be carried out intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally.
  • An effective amount of the therapeutic may be administered for the treatment of the disease or condition manifesting in H1.0 methylation.
  • the appropriate dosage of the therapeutic may be determined based on the type of disease or disorder to be treated, the type of the therapeutic antibody, the severity and course of the disease or condition, the clinical condition of the individual, the individual's clinical history and response to the treatment, and the discretion of the attending physician.
  • any one of the H1.0K180me2 antibodies provided herein is administered intravenously.
  • normal dosage amounts may vary from about 1 ng/kg up to about 1000 mg/kg of an individual's body weight or more per day, depending upon the route of administration.
  • the treatment may be sustained until a desired suppression of symptoms is achieved.
  • Dosage regimens may be useful, depending on the pattern of pharmacokinetic decay that the physician wishes to achieve. For example, dosing an individual from one to twenty-one times a week is provided herein.
  • dosing frequency is three times per day, twice per day, once per day, once every other day, once weekly, once every two weeks, once every four weeks, once every five weeks, once every six weeks, once every seven weeks, once every eight weeks, once every nine weeks, once every ten weeks, or once monthly, once every two months, once every three months, or longer. Progress of the therapy is may be monitored by conventional techniques and assays. The dosing regimen may vary over time independently of the dose used.
  • compositions comprising therapeutic H1.0K180me2 antibodies including pharmaceutical compositions comprising any one or more of the therapeutic antibodies described herein.
  • the pharmaceutical compositions may further comprise one or more pharmaceutically acceptable excipients.
  • the composition is sterile.
  • kits comprising therapeutic H1.0K180me2 antibody compositions described herein.
  • the kits further contain a component selected from any of secondary antibodies, reagents for immunohistochemistry analysis, pharmaceutically acceptable excipient and instruction manual and any combination thereof.
  • the kit comprises any one or more of the therapeutic compositions described herein, with one or more pharmaceutically acceptable excipients.
  • the present application also provides articles of manufacture comprising any one of the therapeutic compositions or kits described herein.
  • articles of manufacture include vials (e.g. sealed vials).
  • H1.0K180me2 antibodies that specifically bind the H1.0K180me2 antigen, useful for diagnostics.
  • the H1.0K180me2 antibodies provided herein require dimethylation of the K180 residue for binding.
  • H1.0K180me2 antibodies are discussed in more detail in the preceding Section I(A).
  • FIG. 8 depicts the exemplary use of an ELISA for the direct detection of H1.0K180me2 epitope in samples of bodily fluids.
  • an antibody specific to an H1.0K180me2 epitope is provided, and is immobilized (coated) on a microplate.
  • a clinical sample containing an H1.0K180me2 epitope for quantification is provided.
  • the sample is added to the microplate, and the H1.0K180me2 epitope binds to the immobilized antibodies. Unbound materials are washed away.
  • Detection antibodies are then added, for example an HRP or any other labelled antibodies. These detection antibodies bind the capture epitope. Unbound detection antibodies are washed away.
  • a detection substrate solution is added, and a fluorophore or color change is measured. This is then quantified against a standard curve to report levels of H1.0K180me2 epitope in the clinical sample.
  • H1.0K180me2 may be useful for detecting replicative senescence, DNA damage, genotoxic stress, radiation exposure, Alzheimer's disease, and biological aging.
  • the quantification may also useful for monitoring therapeutic regimens, drug screening, and stratification of patients as responders or non-responders to drug treatments aimed to restore cell viability, prevent DNA damage, increase cellular metabolism and autophagy, inhibit cellular senescence and block insoluble protein waste accumulation in cellular cytoplasm.
  • H1.0K180me2 may be detected and quantified in vivo, in vitro, ex vivo, in situ, or in a cell-free system.
  • quantification may involve contacting a biological sample in vitro with an antibody as disclosed herein, and determining the concentration and/or subcellular localization of a protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody.
  • H1.0K180me2 may be detected by any number of methods well known to those of skill in the art.
  • the H1.0K180me2 antibodies provided herein are readily used in a variety of immunoassays. These immunoassays include, but are not limited to enzyme-linked immunosorbent assay (ELISA), Western blot, radioimmunoassay (RIA), flow cytometry, lateral flow immunoassay, slot blot, magnetic immunoassay, a radioimmunoassay, indirect immunofluorescence assay, direct immunofluorescence assay, surround Optical Fiber Immunoassay (SOFIA), spectrophotometry, radiography, electrophoresis, immunoelectrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, fluid or gel precipitation reactions, immunodiffusion, spectrometry, mass spectrometry, quantitative mass-spectrometry, any type of multiplex assay
  • the H1.0K180me2 antibodies provided herein may be conjugated to a label (e.g. conjugated to a label) for example a detectable label, a spin label, a colorimetric label, a radioactive label, an enzymatic label, a fluorescent label, or a magnetic label.
  • a label e.g. conjugated to a label
  • a detectable label for example a detectable label, a spin label, a colorimetric label, a radioactive label, an enzymatic label, a fluorescent label, or a magnetic label.
  • the H1.0K180me2 antibodies provided herein may be conjugated to a detectable label.
  • the detectable group may be any material having a detectable physical or chemical property, for example detectable by spectroscopic, photochemical, biochemical, immunochemical, fluorescent, electrical, optical or chemical methods.
  • Useful labels in the present disclosure include, but are not limited to, magnetic beads (e.g.
  • DYNABEADS® fluorescent dyes (e.g., fluorescein isothiocyanate, red, rhodamine, and the like), radiolabels (e.g., 3H, 125I, 35S, 14C, or 32P), enzymes (e.g., LacZ, CAT, horseradish peroxidase, alkaline phosphatase and others, commonly used as detectable enzymes, either as marker gene products or in an ELISA), biotin, avidin, or streptavidin and colorimetric labels such as colloidal gold colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads, and nanoparticles.
  • biotin is the label.
  • the labels provided herein may be coupled directly or indirectly to the desired component of the assay according to methods well known in the art. As indicated above, a wide variety of labels may be used, with the choice of label depending on the sensitivity required, ease of conjugation of the compound, stability requirements, available instrumentation, and disposal provisions. Labels are often attached by indirect methods. Generally, a ligand molecule (e.g., biotin) is covalently bound to the molecule. The ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound.
  • a ligand molecule e.g., biotin
  • an anti-ligand e.g., streptavidin
  • ligands and anti-ligands may be used. Where a ligand has a natural anti-ligand, for example, biotin, it may be used in conjunction with the labeled, naturally occurring anti-ligands. Alternatively, any haptenic or antigenic compound may be used in combination with an antibody. Components can also be conjugated directly to signal-generating compounds, e.g., by conjugation with an enzyme or fluorophore. Enzymes of interest as labels include, but are not limited to, hydrolases, phosphatases, esterases, glycosidases, or oxitranscription factoreductases, and peroxidases.
  • Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc.
  • Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol.
  • detecting labels are well known to those of skill in the art.
  • methods for detection include a scintillation counter or photographic film as in autoradiography.
  • the label is a fluorescent label, it may be detected by exciting the fluorochrome with the appropriate wavelength of light and detecting the resulting fluorescence, e.g., by microscopy, visual inspection, via photographic film, by the use of electronic detectors such as charge coupled devices (CCDs) or photomultipliers and the like.
  • CCDs charge coupled devices
  • enzymatic labels may be detected by providing appropriate substrates for the enzyme and detecting the resulting reaction product.
  • simple colorimetric labels may be detected simply by observing the color associated with the label. Thus, in various dipstick assays, conjugated gold often appears pink, while various conjugated beads appear the color of the bead.
  • the concentration of H1.0K180me2 in a particular fraction may be quantified, for example quantification of H1.0K180me2 in an intra-cellular fraction, in a soluble and chromatin bound fraction, or in a cytoplasmic fraction.
  • an increase in the concentration of H1.0K180me2 in a cytoplasm fraction is indicative of a senescent state of the cells.
  • intact cells, cells in culture, or cells in slice culture are imaged to visualize the localization of an H1.0K180me2.
  • an increase in a non-nuclear sub-localization of H1.0K180me2 is indicative of a senescent state.
  • release of H1.0K180me2 into the cytosol or extracellular matrix is indicative of a senescent state.
  • Detection may be carried out on any biological sample.
  • biological samples include, but are not limited to whole blood, plasma, serum, saliva, urine, feces, synovial fluid, cerebrospinal fluid, bronchial lavage, ascites fluid, bone marrow aspirate, pleural effusion, tissue, cells, a biopsy, interstitial fluid, lymphatic fluid, or fractions thereof derived from the individual.
  • the biological sample comprises cells and the cells are in culture, in a suspension, on a slide, in intact tissue, or in preparation ready for a FACs analysis.
  • Biological samples are obtained from individuals.
  • an individual refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sport, or pet animals, such as dogs, horses, rabbits, cattle, pigs, hamsters, gerbils, mice, ferrets, rats, cats, and the like.
  • Individuals may be male or female. In some embodiments, the individual is a female. In some embodiments, the individual is a male.
  • the individual may be of any age. In some embodiments where detection of Alzheimer's disease is carried, the individual can be greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • Biological samples are obtained according to standard methods well known to those of skill in the art.
  • the sample is optionally pretreated as necessary by dilution in an appropriate buffer solution or concentrated, if desired.
  • Any of a number of standard aqueous buffer solutions, employing one of a variety of buffers, such as phosphate, Tris, or the like, at physiological pH may be used.
  • H1.0K180me2 protein or peptide may be used in tandem, for example, as a positive control or as competitor in a competitive immunoassay, and may be labeled or not, depending on the format of the assay to be carried out.
  • control i.e. reference control
  • the relative comparison may allow, for example, for the determination of whether an individual has, or is at risk of developing a disease (e.g. Alzheimer's disease) or whether the individual is responsive, or may be responsive to a particular treatment (e.g. an Alzheimer's disease treatment; or a treatment with a rapalogue).
  • Controls may be age-matched controls; sex-matched controls; age- and sex-matched controls; healthy controls; unmanipulated controls; or a reference standard representing a compilation of reference standards.
  • the comparisons can also be made to a sample from the same individual prior to a treatment (e.g.
  • the comparisons can also be made to a sample from the same individual from an unaffected area, for example from an unaffected tissue.
  • the sensitivity, specificity, positive and negative predictive values (PPV and NPV) as well as positive and negative likelihood ratios (PLR and NLR)) can be calculated for each diagnostic test design.
  • the statistical methods help to predict the presence or absence of disease in the patients.
  • Sensitivity is generally the probability that the test result will be positive when disease is present (true positive rate).
  • Specificity is generally the probability that a test result will be negative when the disease is not present (true negative rate).
  • the positive predictive value generally is the probability that the disease is present when the test is positive, accounting for the pre-test prevalence of the disease (e.g. pre-test prevalence for Alzheimer's disease is 10%).
  • the negative predictive value is generally the probability that the disease is not present when the test is negative, accounting for the pre-test prevalence of AD as 10% (Prince, M. J., Am J Epidemiol, 1996).
  • the positive likelihood ratio (LR+ or PLR) is generally the probability of a person who has the disease testing positive divided by the probability of a person who does not have the disease testing positive.
  • Positive likelihood ratios generally indicate how much to increase the probability of the disease, if the test is positive.
  • a PLR>1 indicates an increase probability that the target disorder is present
  • a PLR ⁇ 1 indicates a decreased probability that the target disorder is present
  • the negative likelihood ratio (LR- or NLR) is generally the probability of a person who has the disease testing negative divided by the probability of a person who does not have the disease testing negative.
  • Negative likelihood ratios (NLR) generally indicate how much to decrease the probability of the disease, if the test is negative.
  • the comparison will be made to a threshold level established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the ROC curve, thresholds and areas under the curve (AUC) are shown for each of the test's designs provided herein.
  • the diagnostic methods provided herein may be used for confirmatory tests, e.g. to definitively confirm that an individual has a disease, e.g. Alzheimer's disease.
  • the diagnostic methods provided herein may be used for their predictive value (for testing, screening), e.g. to determine the likelihood that an individual will develop a disease, e.g. Alzheimer's disease.
  • the diagnostics may involve computation of likelihood ratios.
  • the diagnostic methods provided herein may be used as a companion diagnostic.
  • the diagnostics may involve computation of positive predictive values (PPV) and negative predictive values (NPV).
  • the diagnostic methods provided herein may be used to establish a diagnostic odds ratio (OR).
  • the diagnostic may involved computation of sensitivity and specificity and is a measure of the effectiveness of a diagnostic test.
  • H1.0K180me2 antibodies provided herein are useful for a variety of diagnostic purposes, discussed below.
  • H1.0K180me2 antibodies to determine H1.0K180me2 levels
  • H1.0K180me2 antibodies for use in the screening of individuals for Alzheimer's disease, for use in identifying whether individuals are at risk for developing Alzheimer's disease, for use in estimating the likelihood of whether individuals will develop Alzheimer's disease, for use in the diagnosis of Alzheimer's disease, for use in the early detection of Alzheimer's disease, for use in the prognosis of Alzheimer's disease, for selecting individuals who may respond to an Alzheimer's disease treatment with an Alzheimer's disease drug or regimen for use in treatment selection/determining treatment options for those diagnosed with Alzheimer's disease, for use in monitoring the treatment of those diagnosed with Alzheimer's disease and receiving ongoing treatment with an Alzheimer's disease drug or regimen, or for use in screening for Alzheimer's disease drugs and regimens.
  • Alzheimer's disease patients displayed lower concentrations of H1.0K180me2 than healthy age-matched healthy controls, indicating that H1.0K180me2 concentrations may effectively segregate patients with Alzheimer's disease from healthy individuals ( FIG. 10 A ). Although serum concentrations of H1.0K180me2 were sufficient for identification of Alzheimer's disease patients, the use of a serum sample normalization by total IgG ( FIG. 10 B ) or total protein ( FIG. 10 C ) allowed for direct comparisons between individuals regardless of variables which may alter overall serum concentration, such as protocol used to obtain serum, operator variability, hydration state of patient and activity state of patient.
  • H1.0K180me2 serum levels were elevated in healthy aged individuals relative to healthy younger individuals, while patients with Alzheimer's disease exhibited significantly lower normalized serum levels of H1.0K180me2 relative to healthy aged, individuals (>60 years) ( FIG. 10 B, 10 C ).
  • H1.0K180me2 Levels More specifically, in some embodiments, provided herein are methods using an H1.0K180me2 antibody, to determine H1.0K180me2 levels, for screening an individual for Alzheimer's disease, for identifying an individual is at risk for developing Alzheimer's disease, estimating the likelihood of whether an individual will develop Alzheimer's disease, for determining whether an individual has Alzheimer's disease, for detecting the early signs of Alzheimer's disease in an individual, and for use in the prognosis of Alzheimer's disease in an individual, the method comprising: (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of H1.0K180me2 in the sample that binds the antibody, wherein a decrease in the concentration relative to a control indicates that the individual has Alzheimer's disease, is at risk of developing Alzheimer's disease, or has a greater likelihood of developing Alzheimer's disease, and wherein an increase or no change in the concentration relative to a control may indicate that the individual does not have Alzheimer
  • a control includes, but is not limited to, a healthy control (e.g. age-matched, sex-matched), a reference standard representing a compilation of healthy controls, or a control sample from the same individual isolated earlier in time.
  • a healthy control e.g. age-matched, sex-matched
  • a reference standard representing a compilation of healthy controls
  • the concentration of circulating H1.0K180me2 is determined.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the method further comprises treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual has, or is at risk of developing, Alzheimer's disease.
  • observational studies include, but are not limited to: (a) Cross-sectional design (single time-point design, or delayed cross-sectional)—testing of one or few specimens/samples per patient that are collected at a single time-point; (b) Longitudinal design—testing of multiple specimens/samples per patient that are collected over an extended period of time (e.g.
  • the methods provided herein are intended for the diagnosis of Alzheimer's disease, wherein the methods may be used to determine, verify or confirm a patient's clinical condition as a sole determinant.
  • this type of testing also includes sole confirmatory assays (to verify results of previous testing) and sole exclusion assays (to rule out a particular condition).
  • the methods provided herein are intended to provide an “aid-to-diagnostic” of Alzheimer's disease, wherein the methods may be used to provide additional information to assist in the determination or verification of a patient's clinical status.
  • the test is not necessarily the sole determinant but may be used to evaluate a patient's current state.
  • the methods provided herein are intended for the screening of Alzheimer's disease, wherein the methods may be used to determine the status of a disease, disorder or other physiological state in an asymptomatic individual. Depending on the nature of the condition and the targeted patient population, the screening methods may be used routinely or may be restricted to “at risk” patients. In this context the methods described herein used to evaluate a patient's current state.
  • the methods provided herein are intended to determine the predisposition to Alzheimer's disease, wherein the methods described herein may be used to determine the likelihood of disease onset (e.g. assessing the risk of developing the disease in future) in pre-symptomatic patients, where for patients at sufficient risk (as determined by test results), preventive interventions may be taken.
  • the methods provided herein are intended for the prognosis of Alzheimer's disease, wherein the methods described herein may be used to measure factors linked to a clinical outcome, irrespective of treatment.
  • the methods described herein may be used to estimate the natural progression of a disease (e.g. outcome in the absence of treatment), or to the methods described herein are designed to evaluate a patient's future state.
  • the methods provided herein are intended for determination of physiological status of aging population (“aging clock”) wherein the methods described herein may be used to evaluate the physiological state of an individual for the purpose of identifying a human condition or characteristic of aging or risk of Alzheimer's disease with aging.
  • the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used to increase confidence in the Alzheimer's disease screening, diagnosis, or detection.
  • the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used in conjunction with other Cerebrospinal Fluids (CSF) tests including but not limited to the measurement of A ⁇ 42 , T-tau, p-tau, A ⁇ 42 /T-tau ratio, and A ⁇ 42 /p-tau.
  • CSF Cerebrospinal Fluids
  • the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used in conjunction with assessment of cognitive status tests, for example the MMSE (mini-mental state examination), GDS (global deterioration rate), and CDR (clinical, Dementia rating) tests.
  • MMSE mini-mental state examination
  • GDS global deterioration rate
  • CDR clinical, Dementia rating
  • the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used in conjunction with neuroimaging.
  • the levels of H1.0K180me2 may be normalized against total IgG in the biological sample or normalized against total protein in the biological sample. In some embodiments of the methods described herein, the concentration of H1.0K180me2 may be determined as a relative ratio to non-methylated, labeled, synthetic H1.0 peptide.
  • the individual is greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • H1.0K180me2 antibodies to determine H1.0K180me2 levels, for use in methods for selecting individuals who may respond to an Alzheimer's disease treatment with an Alzheimer's disease drug or regimen, for use in treatment selection/determining treatment options for those diagnosed with Alzheimer's disease, for use in monitoring the treatment of those diagnosed with Alzheimer's disease and receiving ongoing treatment with an Alzheimer's disease drug or regimen, or for use in screening for Alzheimer's disease drugs and regimens.
  • these Alzheimer's disease drugs and regimens/treatments include, but are not limited to, treatment with APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, A ⁇ aggregation inhibitors, A ⁇ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, or ultrasound therapy.
  • APP synthesis Inhibitors
  • APP synthesis inhibitors (+phenserine), beta-secretase inhibitors (MK-8931, E2609, LY2811376, LY2886721, PF-05297909, gamma-secretase inhibitors and modulators (semegacestat LY450139, avagacestat BMS-708163, PF-3084014, ELND006, tarenflurbil, CHF5074), A ⁇ aggregation inhibitors (tramiprosate (3APS), clioquinol (PBT1), PBT2, ELND005 (scyllo-inositol), PQ912), A ⁇ immunotherapy (GSK933776, AN1802+QS21, ACC-001, Alzheimer's disease-106, Bapineuzumab, Solanezumab, Gantenerumab (R04909832), Ponezumab (PF-04360365), MABT5102A (crenezumab), BAN2401, Intra-
  • a method using an H1.0K180me2 antibody for determining whether an individual diagnosed with Alzheimer's disease receiving ongoing treatment, will benefit or continue to benefit from the ongoing treatment comprising: (a) providing a biological sample from the individual who is receiving ongoing treatment; (b) contacting the biological sample with an H1.0K180me2 antibody; (c) determining the concentration of H1.0K180me2 in the sample that binds the antibody; and (d) selecting an individual who will benefit or continue benefit from treatment, wherein an increase in the concentration relative to a control indicates that the individual will benefit or continue to benefit from treatment, and wherein a decrease or no change in the concentration relative to a control may indicate that the individual will not likely benefit or not continue to benefit from or be responsive to the treatment.
  • a control includes, but is not limited to, samples from individuals with Alzheimer's disease not receiving a treatment, or a control sample from the same individual isolated earlier in time prior to the start of treatment.
  • the concentration of circulating H1.0K180me2 is determined.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the method comprises: (a) providing a biological sample from the individual, before the individual is treated for Alzheimer's disease; (b) contacting the biological sample with a candidate treatment; (c) contacting the biological sample with an H1.0K180me2 antibody; (d) determining the concentration and/or subcellular localization of H1.0K180me2 in the sample that binds the antibody; and (e) selecting an individual who may benefit from the treatment, wherein an increase in the concentration relative to a control or a decrease in cytoplasmic subcellular localization indicates that the individual may benefit from a treatment and wherein an decrease or no change in the concentration relative to a control or an increase or no change in cytoplasmic subcellular localization may indicate that the individual will not benefit from a treatment.
  • the method comprises: (a) administering to the individual the candidate treatment; (b) providing a biological sample from the individual, after administration of the treatment; (c) contacting the biological sample with an H1.0K180me2 antibody; (d) determining the concentration and/or subcellular localization of H1.0K180me2 in the sample that binds the antibody; and (e) selecting an individual who may benefit from the treatment, wherein an increase in the concentration relative to a control or a decrease in cytoplasmic subcellular localization indicates that the individual may benefit from a treatment and wherein an decrease or no change in the concentration relative to a control or an increase or no change in cytoplasmic subcellular localization may indicate that the individual will not benefit from a treatment.
  • a control can include, but is not limited to, samples from healthy individuals, or contacting the biological sample with a placebo treatment.
  • the concentration of circulating H1.0K180me2 is determined.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the methods provided herein are useful for ensuring that the H1.0K180me2 levels remain within physiological levels or within an established therapeutic drug range.
  • the methods provided herein are useful for the monitoring of Alzheimer's disease, wherein the methods described may be used to measure the H1.0K180me2 levels for the purpose of adjusting treatments/interventions as required. In related embodiments, the methods provided herein are useful for monitoring the effects of an Alzheimer's disease drug or nutritional regiment or life style adjustment in an individual receiving such treatment.
  • the methods provided herein are useful for monitoring the clinical performance in any observational or interventional clinical study for Alzheimer's disease, wherein (a) an observational study refers is a study in which test results obtained during the study are not used for patient management and do not impact treatment decisions; and (b) an interventional study is a study in which test results obtained during the study may influence patient management decisions and may be used to guide treatments.
  • the methods provided herein are useful for serial measurement, whereby multiple determinations are taken over time.
  • These types of monitoring methods may be used for the detection/assessment of disease progression/regression, disease recurrence, minimum residual disease, response/resistance to treatment, and/or adverse effects due to treatment.
  • These types of monitoring methods may be designed to evaluate changes in an individual's state.
  • the methods provided herein are useful for prediction of Alzheimer's disease treatment response or reaction, wherein the methods described herein may be used to measure factors that determine the likelihood of patient responses or adverse reactions to a specific therapy. Described herein are predictive methods designed specifically for use as companion diagnostics.
  • the levels of H1.0K180me2 may be normalized against total IgG in the biological sample or normalized against total protein in the biological sample. In some embodiments of the methods described herein, the concentration of H1.0K180me2 may be determined as a relative ratio to non-methylated, labeled, synthetic H1.0 peptide.
  • the individual is greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • the methods may be used for screening for new Alzheimer's disease drugs and regimens.
  • H1.0K180me2 antibodies for use in detecting senescence.
  • senescence is associated with replicative senescence (REP-SEN), genotoxic stress-induced senescence and radiation-induced senescence.
  • REP-SEN replicative senescence
  • genotoxic stress-induced senescence genotoxic stress-induced senescence
  • radiation-induced senescence genotoxic stress-induced senescence
  • the method for the detection of senescence involves the direct detection of H1.0K180me2.
  • the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the biological sample comprises senescent cells.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the methods may be used for identifying individuals that have undergone senescence induced by a genotoxin.
  • the genotoxic stress-induced senescence is a result of exposure of the individual to a DNA damaging agent, drug or toxin, for example radiation, UV-light, bleomycin and any other genotoxic drugs including but not limited to Trazodone, Etotifen, Cephalexin, Nisoldipme, CGS 15943, Clotrimazole, 5-Nonyltryptamine, Doxepin, Pergolide, Paroxetine, Resveratrol, Quercetin, Honokiol, 7-nitroindazole, Megestrol, Fluvoxamine, Etoposide, Veliparib, Rucaparib, Olaparib, Camptothecin, or Terbinafine and chemotherapeutic drugs in general.
  • the methods are useful for identifying senescence in individuals undergoing chemotherapy treatments to ensure that the chemotherapy is effective.
  • the chemotherapeutic agent in these embodiments may be selected from the group consisting of Alemtuzumab (Campath), Alitretinoin (Panretin), Allopurinol (Zyloprim), Altretamine, (Hexalen), Amifostine (Ethyol), Anastrozole (Arimidex), Arsenic Trioxide (Trisenox), Asparaginase (Elspar), BCG Live (TICE BCG), Bexarotene (Targretin), Bleomycin (Blenoxane), Busulfan Intravenous (Busulfex), Busulfan Oral (Myleran), Calusterone (Methosarb), Capecitabine (Xeloda), Streptozocin (Zanosar), Tale (Sclerosol), Tamoxifen (Nolvadex), Temozolomide (Temodar
  • H1.0K180me2 antibodies for use in detecting DNA damage, for example acute DNA damage.
  • H1.0K180me2 dimethylation of H1.0K180 (H1.0K180me2) is observed on chromatin following acute DNA damage with bleomycin, a chemotherapeutic agent ( FIG. 11 A ). Also as described above, in the context of genotoxic stress, H1.0K180me2 is released from the chromatin upon genotoxic stress induced senescence (days after treatment with a DNA damaging agent) ( FIG. 12 A ) and is secreted out of the cells into the extracellular space ( FIG. 12 B ).
  • the method for the detection DNA damage involves the direct detection of H1.0K180me2.
  • the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the biological sample has undergone DNA damage.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the DNA damage is a result of exposure of the cells or an individual to a DNA damaging agent, drug or toxin, for example radiation, bleomycin or other DNA-damaging agents (e.g. chemotherapeutic drugs discussed above).
  • a DNA damaging agent for example radiation, bleomycin or other DNA-damaging agents (e.g. chemotherapeutic drugs discussed above).
  • the method is useful for determining DNA damage within 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 45 minutes, 60 minutes, 75 minutes, 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 24 hours, 48 hours, 3 days, 4 days, or up to 5 days of such exposure to a genotoxin or DNA damaging agent.
  • a portable unit for the detection of DNA damage can comprise a sample collection unit, a reader, and an assay module comprising an H1.0K180me2 antibody.
  • H1.0K180me2 antibodies for use in detecting radiation exposure.
  • H1.0K180me2 In the context of radiation exposure, exposure to ionizing radiation induces increased levels of circulating H1.0K180me2 in serum ( FIG. 13 A and FIG. 13 B .
  • the effect of ionizing radiation on H1.0K180me2 levels in serum was examined. Serum was collected from wild-type mice before and either 2 hours or 48 hours after exposure to 7 Gy of ionizing radiation. H1.0K180me2 serum levels 2 hours (mouse 1) or 48 hours (mouse 2) after irradiation were compared to initial levels before treatment using slot blot and immunoblotting with ⁇ -H1.0K180me2 antibody ( FIG. 13 A ). The concentration of H1.0K180me2 in each serum sample was calculated using a standard curve of H1.0K180me2 peptide included in each analysis.
  • Mouse serum albumin was used as a loading control. H1.0K180me2 dot blot bands were quantified and normalized by serum albumin. Relative increases in H1.0K180me2 after irradiation are shown ( FIG. 13 B ). Western blot analysis of equal volumes of mouse serum with ⁇ -H1.0K180me2 antibody also showed increased H1.0K180me2 after irradiation ( FIG. 13 C ).
  • the method for the detection of radiation exposure involves the direct detection of H1.0K180me2.
  • the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that radiation exposure has occurred.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the change in the concentration of the H1.0K170me2 antigen after 2 hrs after 7Gy X-ray exposure is from 12 umol/L to 21 umol/L, and from 26 umol/L to 35 umol/L after 48 hrs.
  • the method is useful for determining radiation exposure within 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 45 minutes, 60 minutes, 75 minutes, 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 24 hrs, 48 hrs, 3 days, 4 days, or up to 5 days of such exposure.
  • the method is useful determining such exposure in a field situation, for example in a combat zone, with military personnel.
  • a portable unit for the detection of radiation damage can comprise a sample collection unit, a reader, and an assay module comprising an H1.0K180me2 antibody.
  • rapamycin The mammalian target of rapamycin (mTOR) has emerged as a promising therapeutic target. Rapamycin and some rapamycin derivatives, rapamycin analogs, and other mTOR inhibitors are FDA-approved drugs for treatment of certain disease states.
  • H1.0K180me2 may be useful for the screening of an individual's responsiveness to rapamycin, rapamycin derivatives, rapamycin analogs, and other mTOR inhibitors, referred to collectively as “rapalogues,” and may be useful for monitoring rapalogue-based therapeutic regimens.
  • rapalogues mTOR inhibitors
  • the inventors have also found that the detection of H1.0K180me2 may be useful for drug screening purposes, for the screening of additional rapalogues. Specifically, it is shown here that a rapamycin derivative and immunosuppressant, everolimus, blocks the appearance of H1.0K180me2 upon DNA damage ( FIG. 14 ).
  • rapalogues include FDA-approved rapalogues, and those rapalogues presently undergoing clinical trials.
  • FDA-approved rapalogues include Rapamycin, Sirolimus, Rapamune, Everolimus, RAD001, Afinitor, Zortress, Temsirolimus, CCI-779, Torisel, Ridaforolimus, AP23573, MK-8669, Deforolimus, Zotarolimus, and ABT-578.
  • Rapalogues AZD8055, AZD2014, OSI-027, MLN0128, WYE-132, Torin1, PI-103, P7170, PF-04691502, PF-05212384, PKI-587, GNE477, PKI-180, WJD008, XL765, SAR245409, NVP-BEZ235, BGT226, SF1126, GSK2126458, Ku-0063794, WYE-354, NVP-BEZ235, PF-05212384, XL765, Torin 2, WYE-125132, and OSI-027.
  • rapalogue-based treatment ongoing in an individual diagnosed with cancer, an immunodeficiency, diabetes, arthritis, Alzheimer's disease and other neurodegenerative diseases, cardiovascular disease, an autoimmune disease, and other age related pathologies.
  • a method of determining whether an individual receiving treatment with a rapalogue is responsive to such treatment comprising: (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; (b) determining the concentration and/or localization of H1.0K180me2 in the sample that binds the antibody; and (c) determining whether the individual is responsive to treatment, wherein a decrease in the concentration established or a change in the localization relative to a control indicates that the individual is responsive to the rapalogue.
  • it is determined that the rapalogue treatment is not effective, or needs to be modified if there is an increase in the extracellular concentration of the H1.0K180me2 relative to a control.
  • the method further comprises using the information to modify the treatment type, course, duration, and/or dosage.
  • the concentration of circulating H1.0K180me2 is determined.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • this method comprises providing a biological sample from the individual; treating the sample with a rapalogue in vitro, ex vivo, in slice culture, or in tissue culture; and determining the concentration and/or subcellular localization of H1.0K180me2 in the sample.
  • the concentration of the H1.0K180me2 is determined, by measuring the concentration of H1.0K180me2 in the sample using an H1.0K180me2 antibody. In some embodiments it is determined that the rapalogue treatment may not be effective, if there is an increase in the cytoplasmic or extracellular concentration of the H1.0K180me2 relative to a control. In some embodiments it is determined that the rapalogue treatment may not be effective, if there is an increase in the cytoplasmic localization of the H1.0K180me2 relative to a control. In some embodiments, the decrease is relative to an age-matched control that is not diagnosed disease for which the individual may receive a rapalogue treatment.
  • the treatment may be effective, if there is a decrease in the cytoplasmic or extracellular concentration of the H1.0K180me2 protein relative to a control.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • the methods provided herein further comprises using the information to modify the treatment type, course, duration, and/or dosage.
  • provided herein is the use of the detection of H1.0K180me2 to monitor for the ability for new rapalogues to be identified (drug screening applications).
  • H1.0K180me2 antibodies for use in detecting biological aging.
  • biological aging markers or biomarkers of aging are expected to find many uses in biological research since age is a fundamental characteristic of most organisms.
  • Accurate measures of biological age by aging markers are useful for testing the age-related diseases theories of biological aging, such as (i) diagnosing various age related diseases and for defining cancer subtypes, (ii) predicting/prognosticating the onset of various diseases, and serving as (iii) surrogate markers for evaluating therapeutic interventions including rejuvenation approaches.
  • the method for the detection of biological aging involves the direct detection of H1.0K180me2.
  • the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the biological sample is from an individual that has experienced biological aging.
  • the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • kits useful for the detection of H1.0K180me2 comprises one or more H1.0K180me2 antibodies as described herein.
  • the antibodies can optionally include instructional materials for carrying out any of the methods described herein. While the instructional materials typically comprise written or printed materials, they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated herein. Such media include, but are not limited to, electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media can include addresses to internet sites that provide such instructional materials.
  • kits may also include additional components to facilitate the particular application for which the kit is designed.
  • the kit may additionally contain reagents for detecting the label (e.g., enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels, and the like).
  • the kits may additionally include buffers and other reagents routinely used for the practice of a particular method.
  • kits useful in an immunoassay to detect H1.0K180me2 may include an H1.0K180me2 protein or peptide.
  • This peptide may be employed, for example, as a positive control or as competitor in a competitive immunoassay, and may be labeled or not, depending on the format of the assay to be carried out.
  • kits useful in an immunoassay to detect H1.0K180me2, in addition to an anti-H1.0K180me2 peptide may include an H1.0K180me2 antibody.
  • This antibody may be employed, for example, as a positive control or as competitor in a competitive immunoassay, and may be labeled or not, depending on the format of the assay to be carried out.
  • transdermal patches for measuring a concentration of a hypodermal target H1.0K180me2 proteins and peptides, comprising: a substrate comprising an H1.0K180me2 antibody; and a plurality of microneedles.
  • the patches are transdermal microneedle array patches.
  • the substrate of the patches is elastically stretchable.
  • kits comprising patches which comprise the antibodies or peptides provided herein, and optionally, instructions for use.
  • the patch is useful for detecting and measuring the concentration of H1.0K180me2 in a biological sample, for the purpose of detecting replicative senescence, DNA damage, genotoxic stress, radiation exposure, and Alzheimer's disease, useful for monitoring therapeutic regimens, and useful for drug screening.
  • the unit may comprise a sample collection unit, a reader, and an assay module comprising an H1.0K180me2 antibody.
  • lateral flow strips or test strips suitable for a lateral flow assay of an analyte, comprising a sample receiving zone, wherein the sample receiving zone comprises either an H1.0K180me2 antibody.
  • antibody is conjugated to a label.
  • the invention may be defined by reference to the following enumerated, illustrative embodiments.
  • Embodiment 1 An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises:
  • Embodiment 2 An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises:
  • Embodiment 3 An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises any one of the CDR-L amino acid sequences of Tables 4, 5, and 6, and comprises any one of the CDR-H amino acid sequences of Tables 7, 8, and 9.
  • Embodiment 4 The antibody of embodiment 1, wherein the antigen-binding domain of the antibody comprises
  • Embodiment 5 The antibody of embodiment 1, wherein the antigen-binding domain of the antibody comprises
  • Embodiment 6 An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • Embodiment 7 An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7.
  • Embodiment 8 An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • Embodiment 9 The antibody of embodiment 8, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8.
  • Embodiment 10 The antibody of embodiment 8, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 9.
  • Embodiment 11 The antibody of any one of embodiments ito 10, wherein the antibody is chimeric or humanized.
  • Embodiment 12 The antibody of any one of embodiments 1 to 10, wherein the antibody is a monoclonal antibody.
  • Embodiment 13 The antibody of any one of embodiments 1 to 10, wherein the antibody is an antigen-binding fragment.
  • Embodiment 14 The antibody of any one of embodiments 1 to 13, wherein the antibody exhibits reduced binding to the H1.0K180me2 protein or peptide, if the protein or peptide comprises residues other than K180 that are methylated.
  • Embodiment 16 The antibody of any one of any one of embodiments 1 to 15, wherein the antibody is conjugated to a label.
  • Embodiment 17 The antibody of any one of embodiment 16, wherein the antibody is attached to solid surface.
  • Embodiment 18 The antibody of embodiment 17, wherein the antibody attached a bead, column, resin, or a microplate.
  • Embodiment 19 The antibody of any one of any one of embodiments 1 to 15, wherein the antibody is conjugated to an agent.
  • Embodiment 20 The antibody of embodiment 19, wherein the agent is selected from the group consisting of a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • the agent is selected from the group consisting of a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • Embodiment 21 A method of determining whether an individual has, or is at risk of, developing, Alzheimer's disease, comprising:
  • Embodiment 22 The method of embodiment 21, further comprising treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual has, or is at risk of developing, Alzheimer's disease.
  • Embodiment 23 A method of determining whether an individual diagnosed with Alzheimer's disease and receiving treatment for the Alzheimer's disease, will benefit from the treatment or will continue to benefit from the treatment, the method comprising:
  • Embodiment 24 The method of embodiment 23, further comprising treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual will benefit or continue to benefit from the treatment.
  • Embodiment 25 A method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, wherein the individual has not yet started the treatment, the method comprising:
  • Embodiment 27 The method of any one of embodiments 25-26, wherein the treatment is selected from the group consisting of APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, A ⁇ aggregation inhibitors, A ⁇ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, and ultrasound therapy.
  • Embodiment 28 A method of determining whether an individual has been exposed to a DNA damaging agent, comprising:
  • Embodiment 29 The method of embodiment 28, wherein the DNA damaging agent is radiation.
  • Embodiment 30 A method of determining whether an individual receiving treatment with a rapalogue is responsive to such treatment, comprising:
  • Embodiment 31 The method of embodiment 30, wherein the decrease is below a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • Embodiment 32 The method of embodiment 30, wherein the rapalogue is selected from the group consisting of Rapamycin, Sirolimus, Rapamune, Everolimus, RA 001, Afinitor, Zortress, Temsirolimus, CCI-779, Torisel, Ridaforolimus, AP23573, MK-8669, Deforolimus, Zotarolimus, ABT-578, AZD8055, AZD2014, OSI-027, MLN0128, WYE-132, Torin1, PI-103, P7170, PF-04691502, PF-05212384, PKI-587, GNE477, PKI-180, WJD008, XL765, SAR245409, NVP-BEZ235, BGT226, SF1126, GSK2126458, Ku-0063794, WYE-354, NVP-BEZ235, PF-05212384, XL765, Torin 2, WYE-125132,
  • Embodiment 33 The method of any one of embodiments 21 to 32, wherein the increase or decrease in the concentration is above or below a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • Embodiment 34 The method of any one of embodiments 21 to 33, wherein the biological sample is selected from the group consisting of whole blood, plasma, serum, saliva, urine, synovial fluid, cerebrospinal fluid, bronchial lavage, ascites fluid, bone marrow aspirate, pleural effusion, tissue, cells, a biopsy, interstitial fluid, and lymphatic fluid.
  • the biological sample is selected from the group consisting of whole blood, plasma, serum, saliva, urine, synovial fluid, cerebrospinal fluid, bronchial lavage, ascites fluid, bone marrow aspirate, pleural effusion, tissue, cells, a biopsy, interstitial fluid, and lymphatic fluid.
  • Embodiment 35 A transdermal patch for measuring a concentration of a hypodermal target molecule, comprising:
  • Embodiment 36 The patch of embodiment 35, wherein the patch is a transdermal microneedle array patch.
  • Embodiment 37 The patch of embodiment 35, wherein the substrate is elastically stretchable.
  • Embodiment 38 A portable unit for determining whether an individual has been exposed to radiation or a DNA-damaging agent, comprising:
  • Embodiment 39 A test strip suitable for a lateral flow assay of an analyte, comprising a sample receiving zone, wherein the sample receiving zone comprises the antibody of any one of embodiments 1 to 18.
  • Embodiment 40 A method of treating a methylated H1.0-related disease or condition in an individual comprising administering to the individual a therapeutically effective amount of the antibody of any one of embodiments 1 to 20.
  • Embodiment 41 The method of embodiment 40, wherein the disease or condition is selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxic stressor, a disease or condition comprising the accumulation of senescent cells, and a disease or condition accompanied by elevated levels of H1.0K180me2 proteins or peptides.
  • Embodiment 42 A method of clearing H1.0K180me2 in an individual comprising administering to the individual a therapeutically effective amount of the antibody of any one of embodiments 1 to 20.
  • Embodiment 43 The method of embodiment 42, wherein the individual suffers from a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
  • a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
  • Embodiment 44 A pharmaceutical composition comprising the antibody of any one of embodiments 1 to 20, and a pharmaceutically acceptable excipient.
  • Embodiment 45 A kit comprising any one of therapeutically effective amount of the antibody of any one of embodiments 1 to 18.
  • Embodiment 46 An article of manufacture comprising any one of the compositions of embodiments of embodiments 1 to 20, and 35 to 45.
  • Embodiment 47 A vector encoding an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, comprising the nucleic acid of SEQ ID NO: 4.
  • Embodiment 48 A vector encoding an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, comprising the nucleic acid of SEQ ID NO: 5.
  • Embodiment 49 A cell comprising the vector of any one of embodiments 47 to 48.
  • phase I two New Zealand rabbits were immunized for antibody production. Injections were administered subcutaneously (SQ) as emulsions of Keyhole Limpet Hemocyanin (KLH)-conjugated H1.0K180me2 peptide (KLH-CAKPVKASKPKKAKPVK(me2)PK (SEQ ID NO: 72)) in Complete Freund's Adjuvant (CFA) or Incomplete Freund's Adjuvant (IFA).
  • KLH Keyhole Limpet Hemocyanin
  • CFA Complete Freund's Adjuvant
  • IFA Incomplete Freund's Adjuvant
  • Boosters consisted of 0.25 mg antigen in IFA at 4 SQ sites. Rabbits were bled at week 6 and at week 8. The titer of the immunization was assessed using ELISA by comparing pre- and post-immunization bleeds. Once an appropriate ELISA positive titer was recorded toward the immunizing antigen, peripheral blood mononuclear cells (PBMCs) were collected from one or both rabbits. B-cells were subsequently isolated by flow cytometry sorting using a dual-screening protocol which ensured only rabbit lgG and antigen-specific B-cells were isolated.
  • PBMCs peripheral blood mononuclear cells
  • scFv single-chain variable fragment
  • Phase III consisted of multiple rounds of library screening to increase the specificity of the library towards H1.0K180me2. This was done by panning and flow cytometry to isolate scFv domains exhibiting the highest specificity to biotin-conjugated H1.0K180me2 peptide (Biotin-CAKPVKASKPKKAKPVK(me2)PK (SEQ ID NO: 73)), whilst selecting against scFv domains exhibiting specificity towards unmethylated H1.0 peptide (Biotin-CAKPVKASKPKKAKPVKPK (SEQ ID NO: 74)).
  • the scFv domains with the highest specificity for H1.0K180me2 were sequenced by Sanger sequencing, before being moved on to phase IV.
  • phase IV full-length IgG heavy-chain and light-chain clones were generated incorporating the scFv domains, followed by expression of compete, full-length recombinant rabbit monoclonal IgG antibodies.
  • These antibodies were then validated for specificity to H1.0K180me2 using ELISA, slot blot immunoassay, and western blot.
  • 5 distinct antibody clones were created, sorted below A through E in order of their specificity for H1.0K180me2:
  • Phases I-IV are summarized in the Table 11 below.
  • the specificity of the recombinant rabbit anti-H1.0K180me2 monoclonal IgG antibody clones for H1.0K180me2 peptide was determined using ELISA in FIG. 2 A .
  • Wells were coated with H1.0K180me2 peptide; 50 ul of peptide solution (5 ug/ml) was used to coat each well.
  • 100 ul of each clone antibody was added to wells in a 2 ⁇ dilution series. Curves for each peptide were generated by plotting antibody concentration against measured O.D at 450 nm.
  • FIG. 2 C provides raw data for ELISA plot generation of FIGS. 2 A and 2 B .
  • Clones D and E were both able to detect H1.0K180me1 peptide in addition to H1.0K180me2, suggesting a lack of antibody specificity for H1.0K180me2.
  • FIG. 4 A shows an overview of the in vitro methylation approach.
  • the methylation reaction comprised recombinant G9A (methyltransferase), an unlabeled methyl donor (S-Adenosyl-L-Methionine), and recombinant human H1.0 protein, which were incubated at 37° C. for 1 hour.
  • G9A is capable of methylating full-length H1.0 protein, including the addition of K180me2.
  • H1.0K180me2 can subsequently be identified using an anti-H1.0K180me2 rabbit polyclonal antibody to confirm methylation.
  • FIG. 4 B displays the sequence of full-length H1.0 protein, and the number of “me” circles represents the methylation state of the lysine residue (mono- or di-methylated).
  • G9A specifically methylates several C-terminal lysine residues, including H1.0K180me2.
  • FIG. 4 C demonstrates an in-vitro methylation assay of recombinant full-length histone H1.0 with increasing amounts of G9A, and detection with rabbit anti-H1.0K180me2 polyclonal antibody.
  • the top panel exhibits increased H1.0K180 methylation with increasing G9A concentration.
  • FIG. 4 D shows an analysis of clone specificity for in vitro methylated H1.0.
  • Clone A is capable of recognizing in vitro methylated H1.0, with minimal non-specific binding to unmethylated full length H1.0 in the absence of G9A protein. All other clones recognize unmethylated H1.0 and show no specificity for methylated full-length H1.0.
  • FIG. 5 A is an EMBOSS NEEDLE (Li W. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Research [6 Apr. 2015, 43(W1):W580-4) pairwise sequence alignment of the heavy chain variable domain protein sequences of clones A and B. The heavy chain sequences share 61% identity and 70% similarity.
  • FIG. 5 B is an EMBOSS NEEDLE pairwise sequence alignment of the light chain variable domain protein sequences of clones A and B.
  • the light chain sequences share 83% identity and 88% similarity.
  • FIG. 5 C provides DNA and protein sequences of the light and heavy chain variable domains for Clone A (RW24).
  • FIG. 5 D is a schematic representation of one method of construction of full length light and heavy chain expression vectors incorporating the variable domain DNA sequences, in order to create full-length recombinant IgG antibodies.
  • Example 6 Mapping Framework and CDR Regions of Clone a Heavy Chain with Chothia Predictive Software
  • FIGS. 7 A and 7 B Shown in FIGS. 7 A and 7 B (left panel) are the analyses of clone A heavy chain and clone A light chain with Chothia, a program that predicts antibody architecture. Each residue of the heavy chain or light chain is displayed in the top box, and a residue number is assigned by Chothia in the box below each corresponding residue. Shown in light gray are predicted framework regions of the clone A heavy chain or light chain. Show in dark gray are the predicted CDRs. Stars indicated predicted CK2 phosporylation sites. Arrows indicate unusual residues for each location.
  • FIG. 7 B shows a distribution of residues that are predicted to be in position L1 for all Chothia predictions performed.
  • L1 position is aspartate, which has the greatest relative frequency for all amino acids predicted to be in position L1.
  • FIG. 7 C depicts the predicted light chain complementary determining regions and framework regions for antibody Clone A, using the Chothia, AbM, Kabat, and Contact algorithms/numbering schemes.
  • FIG. 7 D depicts the predicted heavy chain complementary determining regions and framework regions for antibody Clone A, using the Chothia, AbM, Kabat, and Contact algorithms/numbering schemes.

Abstract

Provided herein are antibodies that specifically bind a protein comprising an H1.0K180me2 antigen or a peptide thereof, methods of making such antibodies, and methods of using such antibodies for therapeutics and diagnostics.

Description

    CROSS-REFERENCE TO RELATED APPLICATIONS
  • This application claims priority to U.S. Provisional Application Ser. No. 62/577,041, filed on Oct. 25, 2017, the contents of which are incorporated herein by reference in its entirety.
    • DESCRIPTION OF THE TEXT FILE SUBMITTED ELECTRONICALLY
  • The contents of the text file submitted electronically herewith are incorporated herein by reference in their entirety: A computer readable format copy of the Sequence Listing (filename: ALNC_010_01WO_SeqList_ST25.txt, date recorded: Oct. 23, 2018, file size 27 kilobytes).
    • BACKGROUND
  • Cellular chromatin is a dynamic polymer, capable of many configurations, and prone to remodeling and restructuring as it receives physiologically relevant input. Histone proteins are the main protein components of chromatin and double-stranded DNA is wound around histone proteins. Changes in histone proteins can differentially alter access of the transcriptional machinery to some genes while leaving access to other genes intact. Differential chromatin condensation achieved by histone posttranslational modifications (PTMs) underlies packaging of chromatin (Lunyak and Rosenfeld 92008) Hum. Mol. Genet., 17: R28-36; Jenuwein and Allis (2001) Science, 293: 1074-1080). Histone PTMs, for example methylation, can act as an epigenetic code and play critical roles in many aspects of the cellular responses tightly linked to development, injury, disease and aging.
  • Five major families of histones exist: H1, H2A, H2B, H3 and H4. Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1 and H5 are known as the linker histones. The large number of H1.0-binding proteins identified by multiple studies in recent years point to an important role for protein-protein interactions of H1.0 and suggests a new paradigm for H1.0 structure and function that extends beyond its effects on chromatin architecture.
  • There is a need to detect H1.0 methylation in various cellular contexts; and sensitive assays are needed to differentiate among the various types of cellular contexts, as they relate to the development of disease, response to injury, and response to therapeutic regimens. There is also a need to therapeutically address methylated H1.0-related diseases and conditions. Provided herein are methods and compositions for this purpose.
    • SUMMARY
  • Provided herein are antibodies that bind a protein comprising an H1.0K180me2 antigen, or a peptide thereof, wherein the antibodies are useful for therapeutics and diagnostics. Also provided are methods of making such antibodies.
  • Accordingly, in one aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises:
      • (a) any one of the CDR-L1 amino acid sequences of Table 4;
      • (b) any one of the CDR-L2 amino acid sequences of Table 5; and
      • (c) any one of the CDR-L3 amino acid sequences of Table 6.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises:
      • (a) any one of the CDR-H1 amino acid sequences of Table 7;
      • (b) any one of the CDR-H2 amino acid sequences of Table 8; and
      • (c) any one of the CDR-H3 amino acid sequences of Table 9.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises any one of the CDR-L amino acid sequences of Tables 4, 5, and 6, and comprises any one of the CDR-H amino acid sequences of Tables 7, 8, and 9.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the H1.0K180me2 antibody comprises:
      • (a) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11;
      • (b) a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 14 or SEQ ID NO: 15; and
      • (c) a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 18.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the H1.0K180me2 antibody comprises:
      • (a) a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22 or SEQ ID NO: 23;
      • (b) a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30 or SEQ ID NO: 31; and
      • (c) a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 36 or SEQ ID NO: 37.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8.
  • In another aspect, provided herein is an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 9.
  • In some embodiments, the antibody is chimeric or humanized. In some embodiments, the antibody is a monoclonal antibody. In some embodiments, the antibody is an antigen-binding fragment.
  • In some embodiments, the antibody exhibits reduced binding to the H1.0K180me2 protein or peptide, if the protein or peptide comprises residues other than K180 that are methylated. In some embodiments, the antibody does not bind, or only minimally binds, if the H1.0K180me2 protein or peptide comprises methylated lysine residues at lysine residues corresponding to K166, K172, K174, K175, and/or K177 of a human histone H1.0 protein.
  • In some embodiments, the antibody is conjugated to a label. In some embodiments, the antibody is attached to solid surface. In some embodiments, the antibody attached a bead, column, resin, or a microplate. In some embodiments, the antibody is conjugated to an agent. In some embodiments, the agent is selected from the group consisting of a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • In another aspect, provided herein is a vector encoding any one of the antibodies provided herein. In some embodiments, the vector comprises the nucleic acid of SEQ ID NO: 4 or the nucleic acid of SEQ ID NO: 5. In a related aspect, provided herein is a cell comprising one or more of these vectors.
  • In another aspect, provided herein is a method of determining whether an individual has, or is at risk of, developing, Alzheimer's disease, comprising:
      • (a) contacting a biological sample from the individual with the any one of the antibodies described herein; and
      • (b) determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody, wherein a decrease in the concentration relative to a control indicates that the individual has, or is at risk of developing, Alzheimer's disease. In some embodiments, the method further comprises treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual has, or is at risk of developing, Alzheimer's disease.
  • In another aspect, provided herein is a method of determining whether an individual diagnosed with Alzheimer's disease and receiving treatment for the Alzheimer's disease, will benefit from the treatment or will continue to benefit from the treatment, the method comprising:
      • (a) contacting a biological sample from the individual with the any one of the antibodies described herein; and
      • (b) determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • (c) determining that the individual will benefit from the treatment or will continue to benefit from the treatment if there is an increase in the concentration, relative to a control. In some embodiments, the method further comprises treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual will benefit or continue to benefit from the treatment.
  • In another aspect, provided herein is a method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, wherein the individual has not yet started the treatment, the method comprising:
      • (a) administering to the individual a candidate treatment;
      • (b) contacting a biological sample from the individual after administration of the candidate treatment with the any one of the antibodies described herein; and
      • (c) determining the concentration and/or subcellular localization of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • (d) determining that the individual will benefit from the candidate treatment if there is an increase in the concentration or an decrease in cytoplasmic subcellular localization, relative to a control. In some embodiments, the treatment is selected from the group consisting of APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, Aβ aggregation inhibitors, Aβ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, and ultrasound therapy.
  • In another aspect, provided herein is a method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, the method comprising:
      • (a) providing a biological sample obtained from the individual after administration of the candidate treatment;
      • (b) contacting the biological sample from the individual with the any one of the antibodies described herein; and
      • (c) determining the concentration and/or subcellular localization of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • (d) determining that the individual will benefit from the candidate treatment if there is an increase in the concentration or an decrease in cytoplasmic subcellular localization, relative to a control. In some embodiments, the treatment is selected from the group consisting of APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, Aβ aggregation inhibitors, Aβ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, and ultrasound therapy.
  • In another aspect, provided herein is a method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, wherein the individual has not yet started the treatment, the method comprising:
      • (a) contacting a biological sample from the individual with a candidate treatment;
      • (b) contacting a biological sample from the individual with the any one of the antibodies described herein;
      • (c) determining the concentration and/or subcellular localization of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • (d) determining that the individual will benefit from the candidate treatment if there is an increase in the concentration relative to a control or an decrease in cytoplasmic subcellular localization, relative to a control. In some embodiments, the treatment is selected from the group consisting of APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, Aβ aggregation inhibitors, Aβ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, and ultrasound therapy.
  • In another aspect, provided herein is a method of determining whether an individual has been exposed to a DNA damaging agent, comprising:
      • (a) contacting a biological sample from the individual with the any one of the antibodies described herein; and
      • (b) determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the individual has been exposed to a DNA damaging agent. In some embodiments, the DNA damaging agent is radiation.
  • In another aspect, provided herein is a method of determining whether an individual receiving treatment with a rapalogue is responsive to such treatment, comprising:
      • (a) contacting a biological sample from the individual with the any one of the antibodies described herein;
      • (b) determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • (c) determining whether the individual is responsive to treatment, wherein a decrease in the concentration relative to a control indicates that the individual is responsive.
  • In some embodiments, the rapalogue is selected from the group consisting of Rapamycin, Sirolimus, Rapamune, Everolimus, RA 001, Afinitor, Zortress, Temsirolimus, CCI-779, Torisel, Ridaforolimus, AP23573, MK-8669, Deforolimus, Zotarolimus, ABT-578, AZD8055, AZD2014, OSI-027, MLN0128, WYE-132, Torin1, PI-103, P7170, PF-04691502, PF-05212384, PKI-587, GNE477, PKI-180, WJD008, XL765, SAR245409, NVP-BEZ235, BGT226, SF1126, GSK2126458, Ku-0063794, WYE-354, NVP-BEZ235, PF-05212384, XL765, Torin 2, WYE-125132, and OSI-027.
  • In some embodiments of any one of the diagnostic methods provided herein, the increase or decrease in the concentration is above or below a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity. In some embodiments, the biological sample is selected from the group consisting of whole blood, plasma, serum, saliva, urine, synovial fluid, cerebrospinal fluid, bronchial lavage, ascites fluid, bone marrow aspirate, pleural effusion, tissue, cells, a biopsy, interstitial fluid, and lymphatic fluid.
  • In another aspect, provided herein is a method of treating a methylated H1.0-related disease or condition in an individual comprising administering to the individual a therapeutically effective amount of any one of the antibodies described herein. In some embodiments, the disease or condition is selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxic stressor, a disease or condition comprising the accumulation of senescent cells, and a disease or condition accompanied by elevated levels of H1.0K180me2 proteins or peptides.
  • In another aspect, provided herein is a method of clearing H1.0K180me2 in an individual comprising administering to the individual a therapeutically effective amount of any one of the antibodies described herein. In some embodiments, the individual suffers from a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
  • In another aspect, provided herein is a transdermal patch for measuring a concentration of a hypodermal target molecule, comprising:
      • (a) a substrate comprising the any one of the antibodies described herein; and
      • (b) a plurality of microneedles.
  • In some embodiments, the patch is a transdermal microneedle array patch. In some embodiments, the substrate is elastically stretchable.
  • In another aspect, provided herein is a portable unit for determining whether an individual has been exposed to radiation or a DNA-damaging agent, comprising:
      • (a) a sample collection unit;
      • (b) a reader;
      • (c) an assay module comprising any one of the antibodies described herein; and
      • (d) a plurality of microneedles.
  • In another aspect, provided herein is a test strip suitable for a lateral flow assay of an analyte, comprising a sample receiving zone, wherein the sample receiving zone comprises any one of the antibodies described herein.
  • In another aspect, provided herein is a pharmaceutical composition comprising any of the antibodies provided herein. The pharmaceutical composition may further comprise a pharmaceutically acceptable excipient.
  • In another aspect, provided herein is a kit comprising a therapeutically effective amount of any one of the antibodies provided herein.
  • In another aspect, provided herein is an article of manufacture comprising any one of antibodies or compositions provided herein.
  • In another aspect, provided herein is any one of antibodies or compositions provided herein, for use as a medicament.
  • In another aspect, provided herein is any one of antibodies or compositions provided herein, for use in the treatment of a methylated H1.0-related disease or condition; optionally wherein the disease or condition is selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxic stressor, a disease or condition comprising the accumulation of senescent cells, and a disease or condition accompanied by elevated levels of H1.0K180me2 proteins or peptides.
  • In another aspect, provided herein is any one of antibodies or compositions provided herein, for use in a method of treatment, wherein the method comprises clearing H1.0K180me2 in an individual; optionally wherein the individual suffers from a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1 diagrams an exemplary process of generating monoclonal antibodies.
  • FIG. 2A demonstrates binding efficiency of antibody clones to a H1.0Kme2 peptide (methylated at the residue corresponding to K180 of the human H1.0 protein). FIG. 2B demonstrates the binding efficiency of antibody clones to an unmodified H1.0 peptide (not methylated). FIG. 2C provides raw data for the binding of antibody clones to H1.0Kme2 or H1.0 peptide.
  • FIG. 3 shows specificity of antibody clones to H1.0 peptides with 0, 1, or 2 methyl modifications on K180.
  • FIG. 4A illustrates specific in vitro H1.0K180 methylation by G9A methyltransferase. FIG. 4B shows methylation sites on H1.0 by G9A determined by LC/MS.
  • FIG. 4C shows detection of methylation of H1.0K180 by a H1.0K180me2 antibody. FIG. 4D is an analysis of antibody clone specificity for in vitro methylated H1.0.
  • FIG. 5A shows a protein sequence alignment between the antibody heavy chains of Clone A (SEQ ID NO: 6) and Clone B (SEQ ID NO: 7). FIG. 5B shows a protein sequence alignment between the antibody light chains of Clone A (SEQ ID NO: 8) and Clone B (SEQ ID NO: 9). FIG. 5C shows the DNA (SEQ ID NOs: 4 and 5) and protein sequences (SEQ ID NOs: 6 and 8) for antibody Clone A. FIG. 5D illustrates an exemplary method for recombinant expression of an antibody.
  • FIG. 6 illustrates various possible modifications to an antibody that can enhance function.
  • FIG. 7A depicts the sequence of antibody clone A heavy chain (SEQ ID NO: 6) and is annotated with structural information. FIG. 7B depicts the sequence of antibody clone A light chain (SEQ ID NO: 8) and is annotated with structural information. FIG. 7C depicts the predicted light chain complementary determining regions (CDR) and framework (FW) regions for antibody Clone A (SEQ ID NOs: 10, 11, 14, 15, 18 and 38-43). FIG. 7D depicts the predicted heavy chain CDR and FW regions for antibody Clone A (SEQ ID NOs: 20-23, 28-31, 36, 37 and 44-56).
  • FIG. 8 shows an exemplary use of an ELISA for the direct detection of H1.0K180me2 epitope in samples of bodily fluids.
  • FIGS. 9A-9C show age-related accumulation of circulating H1.0K180me2 in the brain tissue and blood serum. Shown are western blot analyses of H1.0K180me2 in mouse (FIG. 9A) and human (FIG. 9B) brain tissue, revealing that its abundance increases with organismal age. FIG. 9C shows H1.0K180me2 levels in human serum samples normalized by total IgG serum levels. The symbol “a” represents an antibody, in this figure and throughout.
  • FIGS. 10A-10C demonstrate the utility of measurements of serum H1.0K180me2 as biomarkers of Alzheimer's disease. FIG. 10A shows that serum H1.0K180me2 is decreased in individuals with Alzheimer's disease, when compared to age-matched controls (normalized by serum volume). FIG. 10B shows that serum H1.0K180me2 is decreased in individuals with Alzheimer's disease, when compared to age-matched controls (normalized by total serum IgG levels). FIG. 10C shows that serum H1.0K180me2 is decreased in individuals with Alzheimer's disease, when compared to age-matched controls (normalized by total serum protein concentration).
  • FIG. 11A shows the dimethylation of H1.0K180 (H1.0K180me2) on chromatin immediately after DNA damage, by western blot analysis. FIG. 11B shows secretion of H1.0K180me2 from after DNA damage.
  • FIGS. 12A and 12B show LC-MS/MS analysis (FIG. 12A) and slot blot analysis (FIG. 12B) on hADSCs of SR, acute DNA damage, and genotoxic stress induced senescence, revealing that dimethylated H1.0K180 (H1.0K180me2) is released from chromatin upon genotoxic stress induced senescence (FIG. 12A) and is secreted out of the cells into the extracellular matrix/cellular media (FIG. 12B).
  • FIGS. 13A-13C show the effect of ionizing radiation on H1.0K180me2 levels. FIG. 13A shows that exposure to ionizing radiation induces increased levels of circulating H1.0K180me2 in mouse serum. FIG. 13A and FIG. 13B show a slot blot analysis of the presence (FIG. 13A) and quantification (FIG. 13B) of H1.0K180me2, using antibodies specific for the H1.0K180me2 epitope in the serum. FIG. 13C shows a western blot analysis of presence of H1.0K180me2 epitope levels, using antibodies specific for the H1.0K180me2 epitope, in mouse serum after X-ray irradiation (7 Gy).
  • FIG. 14 shows a western blot analysis of H1.0K180me2 in SR hADSCs (self renewing human adipose derived stem cells) after bleomycin treatment, revealing that everolimus, a derivative of rapamycin, can act to block H1.0K180me2 appearance upon DNA damage.
    •  DETAILED DESCRIPTION
  • Provided herein are H1.0K180me2 antibodies. These antibodies are useful for therapeutic and diagnostic uses. These H1.0K180me2 antibodies may be used in the treatment of methylated H1.0-related diseases or conditions in an individual. These H1.0K180me2 antibodies may also be used for detecting replicative senescence, DNA damage, genotoxic stress, radiation exposure, Alzheimer's disease, for monitoring therapeutic regimens, patient stratification, drug screening, and may serve as a marker of biological aging in a system. These compositions and methods are described in detail below.
  • WO 2017/184895 describes compositions and methods related to H1.0 dimethylated proteins; and WO 2017/184873 describes compositions and methods related to the methylation of H1.0 protein. The contents of these publications are incorporated herein by reference in their entirety.
  • I. H1.0K180me2 Antibodies that Bind to Histone H1.0K180me2 Proteins and Peptides
  • A. H1.0K180me2 Antibodies
  • Provided herein are antibodies that specifically bind a dimethylated histone H1.0 antigen, wherein the dimethylated histone H1.0 antigen is a histone H1.0 protein or peptide thereof, comprising a dimethylated lysine residue, wherein the lysine residue corresponds to K180 of the full length human histone H1.0 protein (SEQ ID NO: 1), and wherein the dimethylated K180 residue is required for binding. The K180 is represented by K* in SEQ ID NO: 1 of Table 1 below.
  • TABLE 1
    Full length H1.0 Protein Amino Acid Sequence
    SEQ ID NO: 1
      1 MTENSTSAPAAKPKRAKASK KSTDHPKYSD MIVAAIQAEK NRAGSSRQSI QKYIKSHYKV
     61 GENADSQIKL SIKRLVTTGV LKQTKGVGAS GSFRLAKSDE PKKSVAFKKT KKEIKKVATP
    121 KKASKPKKAA SKAPTKKPKA TPVKKAKKKL AATPKKAKKP KTVKAKPVKA SKPKKAKPV K*
    181 PKAKSSAKRA GKKK (SEQ ID NO: 1)
    Histone H1.0 Protein Amino Acid Sequence with exemplary points of
    methylation indicated
    SEQ ID NO: 2
    MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYKVGENADSQI
    KLSIKRLVTTGVLKQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVATPKKASKPKKAASKAPTKKPK
    ATPVKKAKKKLAATPK(me1/2/3)KAKKPKTVKPVK(me1/2/3)ASK(me1/2/3)PKK(me1/2/3)AKP
    VK(me1/2/3)PKAKSSAKRAGKKK
  • The dimethylated H1.0 antigen is interchangeably referred to as the H1.0K180me2 antigen or H1.0K180me2 epitope throughout. The H1.0K180me2-containing proteins and peptides are referred to as “H1.0K180me2 proteins” and “H1.0K180me2 peptides” throughout. The terms “anti-H1.0K180me2” or “H1.0K180me2 antibody” or “anti-H1.0K180me2 antibody” interchangeably refer to these antibodies.
  • As above, use of the term “K180” herein refers to the residue corresponding to K180 of the human H1.0 protein (SEQ ID NO: 1). Similarly, the term “K172”, refers to the residue corresponding to K172 of the human H1.0 protein, the term “K190” refers to the residue corresponding to K190 of the human H1.0 protein, etc.
  • The H1.0K180me2 antibodies of the present disclosure bind to human and non-human mammalian H1.0K180me2 antigens.
  • The term “antibody” as used herein throughout is in the broadest sense and includes a monoclonal antibody, human antibody, humanized antibody, non-human antibody, chimeric antibody, bispecific antibody, an antigen-binding fragment (e.g Fab fragment, a Fab′2 fragment, a CDR or a ScFv), and other antibody fragments that retain specificity for the H1.0K180me2 antigen. In some embodiments, the antibody is a single chain antibody that retains the specificity for the H1.0K180me2 antigen. In one exemplary embodiment, the antibodies are chimeric human x mouse antibodies, In one exemplary embodiment, the antibodies are chimeric human x rabbit antibodies. In one exemplary embodiment, the antibodies are humanized mouse antibodies. In one exemplary embodiment, the antibodies are humanized rabbit antibodies.
  • In some embodiments, the H1.0K180me2 antibodies provided herein are diagnostic antibodies. In some embodiments, the H1.0K180me2 antibodies provided herein are therapeutic antibodies.
  • In some embodiments, the H1.0K180me2 antibody is an affinity-purified antibody.
  • In some embodiments, the H1.0K180me2 antibody is an isolated antibody.
  • The H1.0K180me2 antibodies provided herein may be conjugated to an agent for a variety of purposes including, but not limited to, detection, diagnostics, visualization, quantification, sorting, therapeutics, and for use in biological assays.
  • In some embodiments, the H1.0K180me2 antibodies are conjugated to a label, for example a detectable label, a spin label, a colorimetric label, a radioactive label, an enzymatic label, a fluorescent label, or a magnetic label.
  • In some embodiments, the H1.0K180me2 antibodies are attached to a solid surface, for example a bead (e.g. a magnetic, glass or plastic bead), column, resin or a microplate. In some embodiments, an antibody is coated onto the microplate. In some embodiments, the antibodies attached to a solid surface are conjugated to a label; in some embodiments the antibodies attached to as solid surface are antigen-binding fragments.
  • In some embodiments, an antibody is conjugated to an effector molecule including, but not limited to, a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • The H1.0K180me2 antibodies provided herein can bind extracellular H1.0K180me2 and/or intracellular H1.0K180me2.
  • The antibodies provided herein may be of any immunoglobulin type such as IgG, IgA, IgE, IgD, or IgM. In some embodiments, the antibody is of the IgG subtype and may be an IgG1 antibody, an IgG2 antibody, an IgG3 antibody, or an IgG4 antibody.
  • Provided herein are antibodies specific for the H1.0K180me2 antigen from any species. In some embodiments, the H1.0K180me2 antibody is specific for human H1.0K180me2. In some embodiments, the H1.0K180me2 antibody is cross reactive with H1.0K180me2 from other species.
  • The H1.0K180me2 antibodies provided herein are selective for the H1.0K180me2 antigen, e.g. the H1.0K180me2 antibody is selective for dimethylation at residue K180.
  • The H1.0K180me2 antibodies provided herein are specific for the H1.0K180me2 antigen, e.g. the H1.0K180me2 antibody is specific for dimethylation at residue K180, and exhibits little or no binding of an H1.0K180 epitope (unmethylated at K180), H1.0K180me1 epitope (mono-methylated at K180), or an H1.0K180me3 epitope (trimethylated at K180). In some embodiments, the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen that comprises an unmethylated K180 residue (FIG. 4D).
  • The antibodies provided herein specifically bind an H1.0K180me2-containing antigen. In some embodiments, the H1.0K180me2-containing antigen does not comprise any other lysine residues that are methylated.
  • In some embodiments, the H1.0K180me2 antibody does not bind, or only minimally binds if the target H1.0K180me2 antigen comprises additional methylated lysine residues, e.g. where the lysine residues correspond to K166, K172, K174, K175, and/or K177 of a human histone H1.0 protein.
  • In some embodiments, the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen that comprises one or more of the following residues: K172me1, K172me2, K172me3, K174me1, K174me2, K174me3, K175me1, K175me2, K175me3, K177me1, K177me2, K177me3, K166me1, K166me2, K166me3, K180me1, and/or K180me3.
  • In some embodiments, the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen that comprises a dimethylated K180 residue, but also comprises one or more of the following residues: K172me1, K172me2, K172me3, K174me1, K174me2, K174me3, K175me1, K175me2, K175me3, K177me1, K177me2, K177me3, K166me1, K166me2, K166me3, K180me1, and/or K180me3.
  • In some embodiments, the H1.0K180me2 antibody does not bind, or only minimally binds, an antigen when the H1.0K180me2 antibody displays at least 1.5-fold, 2-fold, 2.5-fold, 2.7-fold, 5-fold, or even 10-fold less specificity (binding preference, affinity) for the antigen than for H1.0K180me2-containing antigen that does not comprise any other lysine residues that are methylated.
  • The H1.0K180me2 antibodies of the present disclosure may bind the H1.0K180me2 epitope in any medium.
  • In some embodiments, the H1.0K180me2 antibody displays at least 1.5-fold, 2-fold, 2.5-fold, 2.7-fold, 5-fold, or even 10-fold more specificity (binding preference, affinity) for the dimethylated antigen at K180 (H1.0K180me2 antigen), than an unmethylated antigen at K180 (H1.0K180 antigen). (FIG. 2A-2B) In some embodiments the specificity for an H1.0K180me2 antigen is generally at least about 2-fold, about 5-fold, or at least about 10-, 20-, 50-, 10{circumflex over ( )}2-, 10{circumflex over ( )}3-, 10{circumflex over ( )}4, 10{circumflex over ( )}5, or 10{circumflex over ( )}6-fold over a non-specific target molecule (e.g. a randomly generated molecule lacking the specifically recognized site(s)), over an unmethylated K180 residue, over a trimethylated K180 residue, or over an H1.0 protein methylated at any other residue.
  • In some embodiments, the H1.0K180me2 antibody displays at least 1.5-fold, 2-fold, 2.5-fold, 2.7-fold, 5-fold, or even 10-fold more specificity (binding preference, affinity) for the dimethylated antigen at K180 (H1.0K180me2 antigen), than a monomethylated antigen at K180 (H1.0K180me1 antigen). (FIG. 3 ) In some embodiments the specificity for an H1.0K180me2 antigen is generally at least about 2-fold, about 5-fold, or at least about 10-, 20-, 50-, 10{circumflex over ( )}2-, 10{circumflex over ( )}3-, 10{circumflex over ( )}4, 10{circumflex over ( )}5, or 10{circumflex over ( )}6-fold over a non-specific target molecule (e.g. a randomly generated molecule lacking the specifically recognized site(s)), over a monomethylated K180 residue, over a trimethylated K180 residue, or over an H1.0 protein methylated at any other residue.
  • In certain embodiments, the H1.0K180me2 antibodies provided herein has a dissociation constant (Kd) of range of 0.0001 nM to 1 M. For example, Kd of the antibody may be about 1 μM, about 100 nM, about 50 nM, about 10 nM, about 5 nM, about 1 nM, about 0.5 nM, about 0.1 nM, about 0.05 nM, about 0.01 nM, about 0.005 nM, about 0.001 nM, about 0.0005 nM, or even about 0.0001 nM.
  • The structure of H1.0K180me2 antibodies (e.g. monoclonal H1.0K180me2 antibodies, mAb) may be modified to function in desired contexts, exemplary embodiments shown in FIG. 6 .
  • FIG. 6 , Part a. shows a glycomodified afucosylated mAb that exhibits enhanced binding to IgG Fc receptors (FcγR) as well as increased ADCC. Expression of mAbs in cell lines lacking fucosylation enzymes can be used to produce afucosylated mAbs. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • FIG. 6 , Part b. The amino acid sequence of a mAb can be modified in the constant region. Such modification can increase binding of the mAb to FcγR and also increase ADCC. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • FIG. 6 , Part c. When ADCC is not the desired mechanism, a different isotype can be substituted. IgG4 does not induce ADCC to the same degree that IgG1 does. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • FIG. 6 , Part d. Radio-immunoconjugates can be produced by conjugating a radioactive isotope to a mAb linker. Use of a stable linker will prevent leakage of free radioactive isotope. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • FIG. 6 , Part e. Antibody drug conjugates can be made by conjugating a drug to a mAb with a linker. A cleavable linker or pH-sensitive linker can be used to allow the drug to act separately from the mAb. Such conjugation can targeting of the drug to cell or tissue specified by the antibody and limits toxicity by not circulating freely. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • FIG. 6 , Part f. The specificity of mAbs can utilized in the generation of Chimeric Antigen Receptor T cells (CAR-T cells). These can be generate by fusing the DNA that codes for a mAb variable region to the DNA sequence of the internal signaling portion of the T-cell receptor. This chimeric receptor is useful for introducing into T cells for use in adoptive therapy. The antigen binding domains of any the H1.0K180me2 antibodies described herein can be used to generated CAR-T cells.
  • FIG. 6 , Part g. Bispecific antibodies are created by removing the constant region from an antibody and crosslinking the remaining variable region to the isolated variable region of another antibody. Removal of the constant region can result in reduced half-life and requires continuous transfusion of such a crosslinked antibody to achieve desired levels of exposure. Any of the H1.0K180me2 antibodies described herein can be modified in this manner.
  • In some embodiments the H1.0K180me2 antibody comprises the variable domain, complementary binding region, framework regions of Clone A (discussed below). In some embodiments, the H1.0K180me2 antibody is a monoclonal humanized antibody, or antigen-binding fragment thereof, that comprises the CDRs of Clone A (discussed below). In some embodiments the H1.0K180me2 antibody comprises the variable domain, complementary binding region, framework regions of Clone B (discussed below). In some embodiments, the H1.0K180me2 antibody is a monoclonal humanized antibody, or antigen-binding fragment thereof, that comprises the CDRs of Clone B (discussed below).
  • B. Generation of H1.0K180me2 Antibodies
  • A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with H1.0K180me2. For example, solid-phase ELISA immunoassays may be used to select monoclonal antibodies specific to H1.0K180me2 (see, e.g., Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York, for a description of immunoassay formats and conditions that may be used to determine specific immunoreactivity).
  • Production of the antibodies provided herein may be by any method known to those with skill in the art. For example, in some embodiments, the antibodies are produced by recombinant cells engineered to express the desired variable heavy (VH) and variable light (VL) and constant domains of the desired antibody (e.g. FIG. 5D). In some embodiments the antibodies are produced by hybridomas.
  • In some embodiments, any peptide comprising the H1.0K180me2 antigen, optionally linked to the immunogenic carrier, is used for immunization using standard protocols. In an exemplary embodiment, a peptide comprising CAKPVKASKPKKAKPVK(me2)PK (SEQ ID NO: 3), optionally linked to an immunogenic carrier, is used for immunization using standard protocols (FIG. 1 ). The quality and titer of generated antibodies may be assessed using techniques known to those in the art.
  • An exemplary method for developing a monoclonal antibody is illustrated in FIG. 1 as four distinct phases. As the figure describes, Phase I involves immunizing rabbits against a H1.0K180me2 peptide conjugated to a Keyhole Limpet Hemocyanin (KLH). The titer of the immunization is compared between pre-immunization and post-immunization bleeds. Peripheral Blood Mononuclear Cells (PBMCs) are isolated and were then sorted for positive antigen binding cells by flow cytometry. In Phase II, total RNA is extracted from cells isolated in Phase 1. RT-PCR of the heavy chain and light chain variable domains of the antibodies is performed and the scFv amplicon is inserted into vectors. These scFv vectors are then used to generate a cell surface-display library. In Phase III, the cell surface-display library is panned for at least one round with H1.0K180me2 peptide. This step further selects against unmethylated H1.0K peptide binding. Clones that bind H1.0K180me2 are further selected by flow cytometry and can be subsequently sequenced. In Phase IV, full length heavy chains and light chains are created to generate full recombinant antibodies. These antibodies can be expressed and purified. The binding of these antibodies to H1.0K180me2 protein can be then validated by ELISA, slot blot, and western blot. This is explained in further detail in Examples 2-4. Exemplary amino acid sequences for unmethylated as well as methylated H1.0 protein are provided in FIG. 4B as well as Table 1 above. (methylated lysine residues are denoted as (me1/2/3 indicating mono, di, and tri methylation possibilities).
  • The inventive compositions described herein also include nucleic acids encoding any of the antibodies disclosed herein, vectors comprising any of the nucleic acids encoding the antibodies, and host cells comprising any such vectors. Table 2 provides exemplary nucleic acid sequences for the antigen-binding fragments of the antibodies provided herein. Also provided herein are cells that contain the nucleotides and vectors encoding the antibodies. In some embodiments the antibodies are secreted.
  • TABLE 2
    Exemplary H1.0K180me2 Antibody Nucleic
    Acid Sequences
    SEQ ID NO: 4: Clone A heavy chain variable
    domain (VH)
    cagtcggtggaggagtccgggggtcgcctggtcacgcctgggacacccctg
    acactcacctgcacggtctctggattctccctcaataactatgtgatgatg
    tgggtccgccaggctccaggggaggggctggaatggatcgctgccattact
    actggcggtaccacatactacgegaactgggcgaaaggccgattcaccatc
    tccaaaacctcgaccacggtggatctgaaaatcatcagtccgacaaccgag
    gacacggccacctatttctgcgccagagatetttatggtgatactagtgat
    gatatttgggatgcttttgatccctggggcccaggcaccctggtcaccgtc
    tcctcag
    SEQ ID NO: 5: Clone A light chain variable
    domain (VL)
    Gaccctgtgctgacccagactccatcgtccgtgtctgcagctgtgggaggc
    acagtcaccatcagttgccagtccagtgagagtgtttataagaataacaac
    ttagcctggtatcagcagaaaccagggcagcctcccaagctcctgatctat
    tctgcatccactctggcatctggggtcccatcgcggttcaaaggcagtgga
    tctgggacacagtcactctcaccatcagtggcgtgcagtgtgacgatgctg
    ccacttactactgtctaggagtatatagtgatatttttgctttc
  • Those of skill in the art understand that antibodies can also be prepared by any of a number of commercial services, e.g. upon provision of the sequences.
  • Tables 3-9 provides amino acid sequences for the antigen-binding fragments of some exemplary H1.0K180me2 antibodies.
  • Table 3 provides exemplary heavy chain variable (VH) and heavy chain light (VL) sequences. Also provided herein are VH and VL sequences that have at least 85%
  • TABLE 3
    Exemplary H1.0K180me2 antibody VH and VL sequences
    SEQ ID NO: 6: Amino Acid Sequence of the Heavy
    Chain Variable (VH) Domain of an H1.0K180me2
    antibody (Clone A)
    QSVEESGGRLVTPGTPLTLTCTVSGFSLNNYVMMWVRQAPGEGLEWIAAIT
    TGGTTYYANWAKGRFTISKTSTTVDLKIISPTTEDTATYFCARDLYGDTSD
    DIWDAFDPWGPGTLVTVSS
    SEQ ID NO: 7: Amino Acid Sequence of the Heavy
    Chain Variable Domain of an H1.0K180me2 antibody
    (Clone B)
    QSLEESGGRLVTPGTPLTLTCTASGFSLSDYYTTWVRQAPGQGLEYIGYIS
    GTGTPYYATWAKGRFTISRTSTTVGLKMTSLTTEDTATYFCARSYPGIDAN
    N
    SEQ ID NO: 8: Amino Acid Sequence of the Light
    Chain Variable (VL) Domain of an H1.0K180me2
    antibody (Clone A)
    DPVLTQTPSSVSAAVGGTVTISCQSSESVYKNNNLAWYQQKPGQPPKLLIY
    SASTLASGVPSRFKGSGSGTQFTLTISGVQCDDAATYYCLGVYSDIFAF
    SEQ ID NO: 9: Amino Acid Sequence of the Light
    Chain Variable Domain of an H1.0K180me2 antibody
    (Clone B)
    AQVLTQTPSSVSAAVGGTVTISCQSSQSVYNNNYLGWYQQKPGQPPKLLIY
    LASTLASGVPSRFKGSGSGTQFTLTISDLECDDAATYYCGGDYDVYIAAF
  • Tables 4-9 provide exemplary complementary determining region (CDR) sequences ( regions 1, 2, and 3) of the antigen-binding domain of the light chain (CDR-L) and the antigen-binding domain of the heavy chain (CDR-H). As referred to below, a VL CDR1 region is referred to as CDR-L1; a VL CDR2 region is referred to as CDR-L2; a VL CDR3 region is referred to as CDR-L3; a VH CDR1 region is referred to as CDR-H1; a VH CDR2 region is referred to as CDR-H2; and a VH CDR3 region is referred to as CDR-H3.
  • TABLE 4
    Exemplary H1.0K180me2 antibody CDR-L1 sequences
       SEQ ID NO: 10: Amino Acid Sequence of CDR-L1
    QSSESVYKNNNLA
    SEQ ID NO: 11: Amino Acid Sequence of CDR-L1
    YKNNNLAWY
    SEQ ID NO: 12: Amino Acid Sequence of CDR-L1
    QSSQSVYNNNYLG
    SEQ ID NO: 13: Amino Acid Sequence of CDR-L1
    YNNNYLGWY
  • TABLE 5
    Exemplary H1.0K180me2 antibody CDR-L2 sequences
       SEQ ID NO: 14: Amino Acid Sequence of CDR-L2
    SASTLAS
    SEQ ID NO: 15: Amino Acid Sequence of CDR-L2
    LLIYSASTLA
    SEQ ID NO: 16: Amino Acid Sequence of CDR-L2
    LASTLAS
    SEQ ID NO: 17: Amino Acid Sequence of CDR-L2
    LLIYLASTLA
  • TABLE 6
    Exemplary H1.0K180me2 antibody CDR-L3 sequences
       SEQ ID NO: 18: Amino Acid Sequence of CDR-L3
    LGVYSDIFAF
    SEQ ID NO: 19: Amino Acid Sequence of CDR-L3
    GGDYDVYIAA
  • TABLE 7
    Exemplary H1.0K180me2 antibody CDR-H1 sequences
       SEQ ID NO: 20: Amino Acid Sequence of CDR-H1
    GFSLNNY
    SEQ ID NO: 21: Amino Acid Sequence of CDR-H1
    GFSLNNYVMM
    SEQ ID NO: 22: Amino Acid Sequence of CDR-H1
    NYVMM
    SEQ ID NO: 23: Amino Acid Sequence of CDR-H1
    NNYVMM
    SEQ ID NO: 24: Amino Acid Sequence of CDR-H1
    GFSLSDY
    SEQ ID NO: 25: Amino Acid Sequence of CDR-H1
    GFSLSDYYTT
    SEQ ID NO: 26: Amino Acid Sequence of CDR-H1
    DYYTT
    SEQ ID NO: 27: Amino Acid Sequence of CDR-H1
    SDYYTT
  • TABLE 8
    Exemplary H1.0K180me2 antibody CDR-H2 sequences
        SEQ ID NO: 28: Amino Acid Sequence of CDR-H2
    TTGGT
    SEQ ID NO: 29: Amino Acid Sequence of CDR-H2
    AITTGGTTY
    SEQ ID NO: 30: Amino Acid Sequence of CDR-H2
    AITTGGTTYYANWAKG
    SEQ ID NO: 31: Amino Acid Sequence of CDR-H2
    WIAAITTGGTTY
    SEQ ID NO: 32: Amino Acid Sequence of CDR-H2
    SGTGT
    SEQ ID NO: 33: Amino Acid Sequence of CDR-H2
    YISGTGTPY
    SEQ ID NO: 34: Amino Acid Sequence of CDR-H2
    YISGTGTPYYATWAKG
    SEQ ID NO: 35: Amino Acid Sequence of CDR-H2
    YIGYISGTGTPY
  • TABLE 9
    Exemplary H1.0K180me2 antibody CDR-H3 sequences
        SEQ ID NO: 36: Amino Acid Sequence of CDR-H3
    DLYGDTSDDIWDAFDP
    SEQ ID NO: 37: Amino Acid Sequence of CDR-H3
    ARDLYGDTSDDIWDAFD
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 or SEQ ID NO: 7.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antibody comprises the light chain variable domain of SEQ ID NO: 8 or SEQ ID NO: 9.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 or SEQ ID NO: 7 and the light chain variable domain of SEQ ID NO: 8 or SEQ ID NO: 9.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 and comprises the light chain variable domain of SEQ ID NO: 8.
  • In some embodiments, provided herein is a H1.0K180me2, wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 6 and comprises the light chain variable domain of SEQ ID NO: 9.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 7 and comprises the light chain variable domain of SEQ ID NO: 8.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antibody comprises the heavy chain variable domain of SEQ ID NO: 7 and comprises the light chain variable domain of SEQ ID NO: 9.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antigen-binding region of the antibody comprises:
      • (a) any one of the CDR-L1 amino acid sequences of Table 4;
      • (b) any one of the CDR-L2 amino acid sequences of Table 5; and
      • (c) any one of the CDR-L3 amino acid sequences of Table 6.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antigen-binding region of the antibody comprises:
      • (a) any one of the CDR-H1 amino acid sequences of Table 7;
      • (b) any one of the CDR-H2 amino acid sequences of Table 8; and
      • (c) any one of the CDR-H3 amino acid sequences of Table 9.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the antigen-binding region of the antibody comprises: an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises any one of the CDR-L amino acid sequences of Tables 4, 5, and 6, and comprises any one of the CDR-H amino acid sequences of Tables 7, 8, and 9.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO.12, or SEQ ID NO: 13.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L2 of SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO.16, or SEQ ID NO: 17.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L3 of SEQ ID NO: 18 or SEQ ID NO: 19.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO.12, or SEQ ID NO: 13; a CDR-L2 of SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO.16, or SEQ ID NO: 17; and a CDR-L3 of SEQ ID NO: 18 or SEQ ID NO: 19.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10 or SEQ ID NO: 11, the CDR-L2 of SEQ ID NO: 14 or SEQ ID NO: 15, or the CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12 or SEQ ID NO: 13, the CDR-L2 of SEQ ID NO: 16 or SEQ ID NO: 17, or the CDR-L3 of SEQ ID NO: 19.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, or SEQ ID NO: 23; the CDR-H2 of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, or SEQ ID NO: 31; or the CDR-H3 of SEQ ID NO: 36 or SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, CDR-L2 of SEQ ID NO: 14, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 10, CDR-L2 of SEQ ID NO: 15, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 11, CDR-L2 of SEQ ID NO: 14, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 11, CDR-L2 of SEQ ID NO: 15, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12, CDR-L2 of SEQ ID NO: 14, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12, CDR-L2 of SEQ ID NO: 16, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 12, CDR-L2 of SEQ ID NO: 17, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 13, CDR-L2 of SEQ ID NO: 16, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the light chain of the antibody comprises the CDR-L1 of SEQ ID NO: 13, CDR-L2 of SEQ ID NO: 17, and CDR-L3 of SEQ ID NO: 18.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, or SEQ ID NO: 27.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H2 of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H3 of SEQ ID NO: 36 or SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of antibody comprises the CDR-H1 of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23 SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, or SEQ ID NO: 27; comprises the CDR-H2 of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, or SEQ ID NO: 35; and comprises the CDR-H3 of SEQ ID NO: 36 or SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 36.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 20 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21, and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 21 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 22 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 28 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 comprises the CDR-H2 of SEQ ID NO: 29 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 30 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 23 and comprises the CDR-H2 of SEQ ID NO: 31 and comprises the CDR-H3 of SEQ ID NO: 37.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 32.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 33.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 34.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 24 and comprises the CDR-H2 of SEQ ID NO: 35.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 and comprises the CDR-H2 of SEQ ID NO: 32.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 and comprises the CDR-H2 of SEQ ID NO: 33.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 and comprises the CDR-H2 of SEQ ID NO: 34.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 25 comprises the CDR-H2 of SEQ ID NO: 35.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 and comprises the CDR-H2 of SEQ ID NO: 32.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 and comprises the CDR-H2 of SEQ ID NO: 33.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 and comprises the CDR-H2 of SEQ ID NO: 34.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 26 comprises the CDR-H2 of SEQ ID NO: 35.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 27 and comprises the CDR-H2 of SEQ ID NO: 32.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ ID NO: 27 and comprises the CDR-H2 of SEQ ID NO: 33.
  • In some embodiments, provided herein is an H1.K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ TD NO: 27 and comprises the CDR-H2 of SEQ ID NO: 34.
  • In some embodiments, provided herein is an H1.0K180me2 antibody, wherein the heavy chain of the antibody comprises the CDR-H1 of SEQ TD NO: 27 comprises the CDR-H2 of SEQ ID NO: 35.
  • Table 10 provides exemplary antibody framework (FW) sequences. As referred to below, VL framework regions are referred to as LRF1, LRF2, and LRF3. Likewise, VH framework regions are referred to as HRF1, HRF2, HRF3, and HRF4.
  • TABLE 10
    Exemplary H1.0K180me2 antibody framework
    (FW) sequences
    Clone A Sequences
       SEQ ID NO: 38: Amino Acid Sequence of LRF1
    DPVLTQTPSSVSAAVGGTVTISC
    SEQ ID NO: 39: Amino Acid Sequence of LRF1
    DPVLTQTPSSVSAAVGGTVTISCQSSESV
    SEQ ID NO: 40: Amino Acid Sequence of LRF2
    WYQQKPGQPPKLLIY
    SEQ ID NO: 41: Amino Acid Sequence of LRF2
    QQKPGQPPK
    SEQ ID NO: 42: Amino Acid Sequence of LRF3
    GVPSRFKGSGSGTQFTLTISGVQCDDAATYYC
    SEQ ID NO: 43: Amino Acid Sequence of LRF3
    SGVPSRFKGSGSGTQFTLTISGVQCDDAATYYC
    SEQ ID NO: 44: Amino Acid Sequence of HFR1
    QSVEESGGRLVTPGTPLTLTCTVS
    SEQ ID NO: 45: Amino Acid Sequence of HFR1
    QSVEESGGRLVTPGTPLTLTCTVSGFSLN
    SEQ ID NO: 46: Amino Acid Sequence of HFR1
    QSVEESGGRLVTPGTPLTLTCTVSGFSL
    SEQ ID NO: 47: Amino Acid Sequence of HFR2
    VMMWVRQAPGEGLEWIAAI
    SEQ ID NO: 48: Amino Acid Sequence of HFR2
    WVRQAPGEGLEWIA
    SEQ ID NO: 49: Amino Acid Sequence of HFR2
    WVRQAPGEGLE
    SEQ ID NO: 50: Amino Acid Sequence of HFR3
    TYYANWAKGRFTISKTSTTVDLKIISPTTEDTATYFCAR
    SEQ ID NO: 51: Amino Acid Sequence of HFR3
    YANWAKGRFTISKTSTTVDLKIISPTTEDTATYFCAR
    SEQ ID NO: 52: Amino Acid Sequence of HFR3
    RFTISKTSTTVDLKIISPTTEDTATYFCAR
    SEQ ID NO: 53: Amino Acid Sequence of HFR3
    YANWAKGRFTISKTSTTVDLKIISPTTEDTATYFC
    SEQ ID NO: 54: Amino Acid Sequence of HFR4
    WGPGTLVTVSS
    SEQ ID NO: 55: Amino Acid Sequence of HFR4
    PWGPGTLVTVSS
    Clone B Sequences
    SEQ ID NO: 56: Amino Acid Sequence of LRF1
    AQVLTQTPSSVSAAVGGTVTISC
    SEQ ID NO: 57: Amino Acid Sequence of LRF1
    AQVLTQTPSSVSAAVGGTVTISCQSSQSV
    SEQ ID NO: 58: Amino Acid Sequence of LRF2
    WYQQKPGQPPKLLIY
    SEQ ID NO: 59: Amino Acid Sequence of LRF2
    QQKPGQPPK
    SEQ ID NO: 60: Amino Acid Sequence of LRF3
    GVPSRFKGSGSGTQFTLTISDLECDDAATYYC
    SEQ ID NO: 61: Amino Acid Sequence of LRF3
    SGVPSRFKGSGSGTQFTLTISDLECDDAATYYC
    SEQ ID NO: 62: Amino Acid Sequence of HFR1
    QSLEESGGRLVTPGTPLTLTCTAS
    SEQ ID NO: 63: Amino Acid Sequence of HFR1
    QSLEESGGRLVTPGTPLTLTCTASGFSLS
    SEQ ID NO: 64: Amino Acid Sequence of HFR1
    QSLEESGGRLVTPGTPLTLTCTASGFSL
    SEQ ID NO: 65: Amino Acid Sequence of HFR2
    YTTWVRQAPGQGLEYIGYI
    SEQ ID NO: 66: Amino Acid Sequence of HFR2
    WVRQAPGQGLEYIG
    SEQ ID NO: 67: Amino Acid Sequence of HFR2
    WVRQAPGQGLE
    SEQ ID NO: 68: Amino Acid Sequence of HFR3
    PYYATWAKGRFTISRTSTTVGLKMTSLTTEDTATYFCAR
    SEQ ID NO: 69: Amino Acid Sequence of HFR3
    YATWAKGRFTISRTSTTVGLKMTSLTTEDTATYFCAR
    SEQ ID NO: 70: Amino Acid Sequence of HFR3
    RFTISRTSTTVGLKMTSLTTEDTATYFCAR
    SEQ ID NO: 71: Amino Acid Sequence of HFR3
    YATWAKGRFTISRTSTTVGLKMTSLTTEDTATYFC
    • II. Therapeutic Uses of H1.0K180Me2 Antibody
  • A. Treatment of Methylated H1.0-Related Diseases and Conditions
  • Provided herein are therapeutic H1.0K180me2 antibodies for the treatment of a methylated H1.0-related disease or condition.
  • As used herein, a “methylated H1.0-related disease or condition” is one where there is an increase in the levels of H1.0K180me2, an increase in the endogenous dimethylation of a H1.0 protein/peptide substrate at K180, an increase in the release of H1.0K180me2 from the chromatin, an increase in the release of H1.0K180me2 from the nucleus into the cytoplasm, an increase in the cytoplasmic deposition of H1.0K180me2, an increase in the levels of H1.0K180me2 in the extracellular space, an increase in the circulating levels of H1.0K180me2 in a bodily fluid (e.g. serum, urine, saliva, cerebrospinal fluid, etc.), and/or an increase in the level of autoantibodies specific for H1.0K180me2.
  • Methylated H1.0-related diseases and conditions include, but are not limited to, age-related pathologies associated with increase of senescent cells, Alzheimer's disease, radiation exposure, exposure to a genotoxic stressor, conditions that comprise the accumulation of senescent cells associated with external and internal stressors, and autoimmune group of diseases and conditions associated with high level of autoantibodies to H1.0K180me2.
  • Provided herein are methods of treating a methylated H1.0-related disease or condition in an individual by binding and clearing H1.0K180me2 comprising administering to the individual a therapeutically effective amount of a therapeutic H1.0K180me2 antibody.
  • As used herein, an individual refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sport, or pet animals, such as dogs, horses, rabbits, cattle, pigs, hamsters, gerbils, mice, ferrets, rats, cats, and the like. Individuals may be male or female.
  • The individual can be of any age. In some embodiments of the methods described herein, e.g. for the treatment of Alzheimer's disease, the individual is greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • Turning to the methylated H1.0-related diseases and conditions more specifically, exemplary indications are presented below.
    • Alzheimer's Disease
  • During aging, there is increased accumulation of cytoplasmic H1.0K180me2 in the brain tissue of humans, FIG. 9B. These observations are correlated with an age-related increase of circulating H1.0K180me2 antigen observed in serological tests (FIG. 9C). Additionally, when whole cell lysates of mouse brain samples from 1 month (young) and 24 month (old) mice were compared by western blot analysis with anti-H1.0K180me2, anti-H1.0, anti-γH2A.X and anti-β-Actin antibodies, H1.0K180me2 levels increased in the 24 month mouse, correlating with increased levels of γH2A.X (FIG. 9A).
  • However in individuals diagnosed with Alzheimer's disease, there is a drop in the circulating levels of the H1.0K180me2 antigen observed serological ELISA tests when comparing a control population (no Alzheimer's disease pathology) with a reference control (diagnosed Alzheimer's disease patients) (FIGS. 10A-10C). FIG. 10A shows the quantification of H1.0K180me2 levels determined by slot blot analysis in Alzheimer's disease patients and age-matched controls. Quantification of H1.0K180me2 levels was determined by slot blot analysis in Alzheimer's disease patients and age-matched controls. FIG. 10B shows H1.0K180me2 levels in human serum normalized by total IgG serum levels. FIG. 10C shows H1.0K180me2 levels in human serum normalized by total protein levels. Although serum concentrations of H1.0K180me2 are sufficient for identification of Alzheimer's disease patients, the use of serum sample normalization by total IgG (FIG. 10B) or total protein (FIG. 10C) allows for direct comparisons between individuals regardless of variables which may alter overall serum concentration, such as protocol used to obtain serum, operator variability, hydration state of patient and activity state of patient.
  • Thus in the context of Alzheimer's disease, treatment with a therapeutically effective amount of an H1.0K180me2 antibody (e.g. a cell penetrating antibody or a cell clearing antibody) is provided.
    • DNA Damage and Genotoxic Stress
  • In the context of DNA damaging agents, dimethylation of H1.0K180 (H1.0K180me2) is observed on chromatin following acute DNA damage with bleomycin, a chemotherapeutic agent (FIG. 11A). To assess the relationship between H1.0K180 methylation and DNA damage, SR hADSCs (self-renewing human adipose derived stem cells) and hADSCs treated with DNA damaging agent bleomycin for 2 hours were lysed and fractionated to obtain the chromatin bound fraction. Western blot analysis with an H1.0K180me2 antibody shows methylation of H1.0K180 on the chromatin upon DNA damage (FIG. 11A). Upon treatment of SR hADSCs with bleomycin to induce DNA double-strand breaks, H1.0K180me2 localized to the cytoplasm.
  • By slot blot immunoassay, it was found that the presence of H1.0K180me2 was detected in the conditioned medium of hADSCs in a time course dependent manner after genotoxic insult imposed by bleomycin, with maximal H1.0K180me2 secretion detected within 48 hours (FIG. 11B). This signifies secretion out of the cells. An increase in DNA fragmentation factor (DFFB/DFF40/CAD) secretion upon GSI-SEN was seen, in a similar manner, with H1.0K180me2 starting 48 hours after treatment (FIG. 11B). None of the protein is secreted in measurable quantities upon onset of acute DNA damage (ADD).
  • In the context of genotoxic stress, H1.0K180me2 is released from the chromatin upon genotoxic stress induced senescence (days after treatment with a DNA damaging agent) (FIG. 12A) and is secreted out of the cells into the extracellular space (FIG. 12B). As shown in FIG. 12A, Chromatin bound H1.0 decreased from ˜60% of total in SR and acute DNA damage, to ˜30% of total upon genotoxic stress induced senescence. Culture media from SR hADSCs treated with bleomycin was collected for slot blot analysis with α-H1.0 and α-H1.0K180me2 antibodies to assess secretion of H1.0 to the extracellular matrix (ECM). Secreted H1.0 was detectable in the cell culture media, and after 24 hours of bleomycin treatment, secreted H1.0K180me2 was also readily detected (FIG. 12B). These results confirmed that methylated H1.0K180 is released from chromatin upon genotoxic stress induced senescence and is secreted into the ECM.
  • Thus in the context of DNA damage and genotoxic stress, treatment with a therapeutically effective amount of an H1.0K180me2 antibody (e.g. a cell penetrating antibody, or a cell-clearing antibody) is provided.
    • Radiation Exposure
  • In the context of radiation exposure, exposure to ionizing radiation induces increased levels of circulating H1.0K180me2 in serum (FIG. 13A and FIG. 13B. The effect of ionizing radiation on H1.0K180me2 levels in serum was examined. Serum was collected from wild-type mice before and either 2 hours or 48 hours after exposure to 7 Gy of ionizing radiation. H1.0K180me2 serum levels 2 hours (mouse 1) or 48 hours (mouse 2) after irradiation were compared to initial levels before treatment using slot blot and immunoblotting with α-H1.0K180me2 antibody (FIG. 13A). The concentration of H1.0K180me2 in each serum sample was calculated using a standard curve of H1.0K180me2 peptide included in each analysis. Mouse serum albumin was used as a loading control. H1.0K180me2 dot blot bands were quantified and normalized by serum albumin. Relative increases in H1.0K180me2 after irradiation are shown (FIG. 13B). Western blot analysis of equal volumes of mouse serum with α-H1.0K180me2 antibody also showed increased H1.0K180me2 after irradiation (FIG. 13C).
  • Thus in the context of radiation exposure, treatment with a therapeutically effective amount of an H1.0K180me2 antibody (e.g. a cell penetrating antibody or a cell clearing antibody) is provided.
  • B. Therapeutic H1.0K180me2 Antibodies
  • As discussed in the above Section (I)(A), provided herein are antibodies that recognize and selectively and/or specifically bind to the H1.0K180me2 epitope, and may be used for therapeutics.
  • In some embodiments, the therapeutic antibody is a neutralizing antibody, and the antibody neutralizes one or more biological activities of H1.0K180me2. For example, the antibody may bind extracellular H1.0K180me2 and neutralize any binding or signaling activity it may possess. In some embodiments, the antibody may clear or block H1.0K180me2 in a cell, or a sample. In some embodiments, the antibody may clear the cells comprising H1.0K180me2.
  • In some embodiments, the therapeutic antibody may clear senescent cells. In some embodiments, the antibody may clear cells/tissue or protein products that give rise to the symptom of Alzheimer's disease. In some embodiments, the antibody may clear cells damaged by radiation damage, DNA damaging agents, and other genotoxins. In some embodiments, the antibody is a cell-penetrating antibody. In other embodiments, the affected cells' membranes are comprised and allow for entry of the therapeutic H1.0K180me2 antibodies provided herein.
  • In some embodiments, the therapeutic antibody provided herein has antibody-dependent cellular cytotoxicity (ADCC) activity. Effector cells bearing Fc gamma receptors (FcγR or FCGR) on their cell surface, including cytotoxic T-cells, natural killer (NK) cells, macrophages, neutrophils, eosinophils, dendritic cells, or monocytes, recognize and bind the Fc region of antibodies bound to the target-cells. Such binding may trigger the activation of intracellular signaling pathways leading to cell death.
  • In some embodiments, the therapeutic antibody has complement-dependent cytotoxicity (CDC) activity. Antibody-induced CDC is mediated through the proteins of the classical complement cascade and is triggered by binding of the complement protein Clq to the antibody. Antibody Fc region binding to Clq may induce activation of the complement cascade.
  • In some embodiments, the therapeutic antibody has antibody-dependent cellular phagocytosis (ADCP) activity. Phagocytic cells bearing Fc receptors on their cell surface, including monocytes and macrophages, recognize and bind the Fc region of antibodies bound to target-cells. Upon binding of the Fc receptor to the antibody-bound target cell, phagocytosis of the target cell may be initiated.
  • In some embodiments, the therapeutic antibodies may form an immune complex. For example, an immune complex may be a cell expressing or extruding H1.0K180me2 antigen, covered by antibodies.
  • C. Combination Therapies
  • The administration of any of the therapeutic H1.0K180me2 antibodies provided herein may be administered in combination with other known drugs/treatments for the diseases which manifest in H1.0 methylation.
  • In the context of Alzheimer's disease prevention, any of the therapeutic H1.0K180me2 antibodies may be administered in combination with the administration of an Alzheimer's disease preventive drug or regimen which include, but are not limited to, APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, Aβ aggregation inhibitors, Aβ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, and ultrasound therapy.
  • E. Administration of the Therapeutic H1.0K180me2 Antibodies
  • In vivo administration of the therapeutic H1.0K180me2 antibodies described herein may be carried out intravenously, intramuscularly, subcutaneously, topically, orally, transdermally, intraperitoneally, intraorbitally, by implantation, by inhalation, intrathecally, intraventricularly, or intranasally. An effective amount of the therapeutic may be administered for the treatment of the disease or condition manifesting in H1.0 methylation. The appropriate dosage of the therapeutic may be determined based on the type of disease or disorder to be treated, the type of the therapeutic antibody, the severity and course of the disease or condition, the clinical condition of the individual, the individual's clinical history and response to the treatment, and the discretion of the attending physician. In an exemplary embodiment, any one of the H1.0K180me2 antibodies provided herein is administered intravenously.
  • For in vivo administration of the therapeutic H1.0K180me2 antibodies described herein, normal dosage amounts may vary from about 1 ng/kg up to about 1000 mg/kg of an individual's body weight or more per day, depending upon the route of administration. For repeated administrations over several days or longer, depending on the severity of the methylated H1.0-related disease or condition to be treated, the treatment may be sustained until a desired suppression of symptoms is achieved. Dosage regimens may be useful, depending on the pattern of pharmacokinetic decay that the physician wishes to achieve. For example, dosing an individual from one to twenty-one times a week is provided herein. In certain embodiments, dosing frequency is three times per day, twice per day, once per day, once every other day, once weekly, once every two weeks, once every four weeks, once every five weeks, once every six weeks, once every seven weeks, once every eight weeks, once every nine weeks, once every ten weeks, or once monthly, once every two months, once every three months, or longer. Progress of the therapy is may be monitored by conventional techniques and assays. The dosing regimen may vary over time independently of the dose used.
  • E. Pharmaceutical Compositions
  • The present application provides compositions comprising therapeutic H1.0K180me2 antibodies including pharmaceutical compositions comprising any one or more of the therapeutic antibodies described herein. The pharmaceutical compositions may further comprise one or more pharmaceutically acceptable excipients. In some embodiments the composition is sterile.
  • F. Therapeutic Kits and Articles of Manufacture
  • The present application provides kits comprising therapeutic H1.0K180me2 antibody compositions described herein. In some embodiments, the kits further contain a component selected from any of secondary antibodies, reagents for immunohistochemistry analysis, pharmaceutically acceptable excipient and instruction manual and any combination thereof. In some embodiments, the kit comprises any one or more of the therapeutic compositions described herein, with one or more pharmaceutically acceptable excipients.
  • The present application also provides articles of manufacture comprising any one of the therapeutic compositions or kits described herein. Examples of an article of manufacture include vials (e.g. sealed vials).
    • III. Diagnostic Uses of H1.0K180Me2 Antibody
  • A. Detection of the H1.0K180Me2 Antigen
  • Provided herein are antibodies that specifically bind the H1.0K180me2 antigen, useful for diagnostics. The H1.0K180me2 antibodies provided herein require dimethylation of the K180 residue for binding. H1.0K180me2 antibodies are discussed in more detail in the preceding Section I(A).
  • FIG. 8 depicts the exemplary use of an ELISA for the direct detection of H1.0K180me2 epitope in samples of bodily fluids. In this exemplary scheme, an antibody specific to an H1.0K180me2 epitope is provided, and is immobilized (coated) on a microplate. A clinical sample containing an H1.0K180me2 epitope for quantification is provided. The sample is added to the microplate, and the H1.0K180me2 epitope binds to the immobilized antibodies. Unbound materials are washed away. Detection antibodies are then added, for example an HRP or any other labelled antibodies. These detection antibodies bind the capture epitope. Unbound detection antibodies are washed away. A detection substrate solution is added, and a fluorophore or color change is measured. This is then quantified against a standard curve to report levels of H1.0K180me2 epitope in the clinical sample.
  • Provided herein are assays for the detection and quantification of the concentration of H1.0K180me2. Such quantification may be useful for detecting replicative senescence, DNA damage, genotoxic stress, radiation exposure, Alzheimer's disease, and biological aging. The quantification may also useful for monitoring therapeutic regimens, drug screening, and stratification of patients as responders or non-responders to drug treatments aimed to restore cell viability, prevent DNA damage, increase cellular metabolism and autophagy, inhibit cellular senescence and block insoluble protein waste accumulation in cellular cytoplasm. Depending on the application, H1.0K180me2 may be detected and quantified in vivo, in vitro, ex vivo, in situ, or in a cell-free system. For instance, quantification may involve contacting a biological sample in vitro with an antibody as disclosed herein, and determining the concentration and/or subcellular localization of a protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody.
  • H1.0K180me2 may be detected by any number of methods well known to those of skill in the art. The H1.0K180me2 antibodies provided herein are readily used in a variety of immunoassays. These immunoassays include, but are not limited to enzyme-linked immunosorbent assay (ELISA), Western blot, radioimmunoassay (RIA), flow cytometry, lateral flow immunoassay, slot blot, magnetic immunoassay, a radioimmunoassay, indirect immunofluorescence assay, direct immunofluorescence assay, surround Optical Fiber Immunoassay (SOFIA), spectrophotometry, radiography, electrophoresis, immunoelectrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, fluid or gel precipitation reactions, immunodiffusion, spectrometry, mass spectrometry, quantitative mass-spectrometry, any type of multiplex assay, and any type of microfluidic assay.
  • The H1.0K180me2 antibodies provided herein may be conjugated to a label (e.g. conjugated to a label) for example a detectable label, a spin label, a colorimetric label, a radioactive label, an enzymatic label, a fluorescent label, or a magnetic label.
  • The H1.0K180me2 antibodies provided herein may be conjugated to a detectable label. The detectable group may be any material having a detectable physical or chemical property, for example detectable by spectroscopic, photochemical, biochemical, immunochemical, fluorescent, electrical, optical or chemical methods. Useful labels in the present disclosure include, but are not limited to, magnetic beads (e.g. DYNABEADS®), fluorescent dyes (e.g., fluorescein isothiocyanate, red, rhodamine, and the like), radiolabels (e.g., 3H, 125I, 35S, 14C, or 32P), enzymes (e.g., LacZ, CAT, horseradish peroxidase, alkaline phosphatase and others, commonly used as detectable enzymes, either as marker gene products or in an ELISA), biotin, avidin, or streptavidin and colorimetric labels such as colloidal gold colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads, and nanoparticles. In an exemplary embodiment, biotin is the label.
  • The labels provided herein may be coupled directly or indirectly to the desired component of the assay according to methods well known in the art. As indicated above, a wide variety of labels may be used, with the choice of label depending on the sensitivity required, ease of conjugation of the compound, stability requirements, available instrumentation, and disposal provisions. Labels are often attached by indirect methods. Generally, a ligand molecule (e.g., biotin) is covalently bound to the molecule. The ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound. A number of ligands and anti-ligands may be used. Where a ligand has a natural anti-ligand, for example, biotin, it may be used in conjunction with the labeled, naturally occurring anti-ligands. Alternatively, any haptenic or antigenic compound may be used in combination with an antibody. Components can also be conjugated directly to signal-generating compounds, e.g., by conjugation with an enzyme or fluorophore. Enzymes of interest as labels include, but are not limited to, hydrolases, phosphatases, esterases, glycosidases, or oxitranscription factoreductases, and peroxidases. Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc. Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol.
  • Methods of detecting labels are well known to those of skill in the art. Thus, for example, where the label is a radioactive label, methods for detection include a scintillation counter or photographic film as in autoradiography. Where the label is a fluorescent label, it may be detected by exciting the fluorochrome with the appropriate wavelength of light and detecting the resulting fluorescence, e.g., by microscopy, visual inspection, via photographic film, by the use of electronic detectors such as charge coupled devices (CCDs) or photomultipliers and the like. Similarly, enzymatic labels may be detected by providing appropriate substrates for the enzyme and detecting the resulting reaction product. Finally, simple colorimetric labels may be detected simply by observing the color associated with the label. Thus, in various dipstick assays, conjugated gold often appears pink, while various conjugated beads appear the color of the bead.
  • Upon detection, the concentration of H1.0K180me2 in a particular fraction may be quantified, for example quantification of H1.0K180me2 in an intra-cellular fraction, in a soluble and chromatin bound fraction, or in a cytoplasmic fraction. For example, an increase in the concentration of H1.0K180me2 in a cytoplasm fraction is indicative of a senescent state of the cells. In some embodiments intact cells, cells in culture, or cells in slice culture are imaged to visualize the localization of an H1.0K180me2. For example, an increase in a non-nuclear sub-localization of H1.0K180me2 is indicative of a senescent state. In some embodiments release of H1.0K180me2 into the cytosol or extracellular matrix is indicative of a senescent state.
  • Detection may be carried out on any biological sample. Biological samples include, but are not limited to whole blood, plasma, serum, saliva, urine, feces, synovial fluid, cerebrospinal fluid, bronchial lavage, ascites fluid, bone marrow aspirate, pleural effusion, tissue, cells, a biopsy, interstitial fluid, lymphatic fluid, or fractions thereof derived from the individual. In some embodiments, the biological sample comprises cells and the cells are in culture, in a suspension, on a slide, in intact tissue, or in preparation ready for a FACs analysis.
  • Biological samples are obtained from individuals. As used herein, an individual refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sport, or pet animals, such as dogs, horses, rabbits, cattle, pigs, hamsters, gerbils, mice, ferrets, rats, cats, and the like. Individuals may be male or female. In some embodiments, the individual is a female. In some embodiments, the individual is a male.
  • In the diagnostic methods provided herein, the individual may be of any age. In some embodiments where detection of Alzheimer's disease is carried, the individual can be greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • Biological samples are obtained according to standard methods well known to those of skill in the art. The sample is optionally pretreated as necessary by dilution in an appropriate buffer solution or concentrated, if desired. Any of a number of standard aqueous buffer solutions, employing one of a variety of buffers, such as phosphate, Tris, or the like, at physiological pH may be used.
  • The direct detection methods described herein may be used to quantify the concentration of H1.0K180me2 in the biological sample. In some embodiments, an H1.0K180me2 protein or peptide may be used in tandem, for example, as a positive control or as competitor in a competitive immunoassay, and may be labeled or not, depending on the format of the assay to be carried out.
  • One of skill will appreciate that in some embodiments, it may be necessary to compare the determined concentrations of the H1.0K180me2 antigen to a control (i.e. reference control). The relative comparison may allow, for example, for the determination of whether an individual has, or is at risk of developing a disease (e.g. Alzheimer's disease) or whether the individual is responsive, or may be responsive to a particular treatment (e.g. an Alzheimer's disease treatment; or a treatment with a rapalogue). Controls may be age-matched controls; sex-matched controls; age- and sex-matched controls; healthy controls; unmanipulated controls; or a reference standard representing a compilation of reference standards. The comparisons can also be made to a sample from the same individual prior to a treatment (e.g. with an Alzheimer's disease treatment or rapalogue treatment) or prior to an exposure to a genotoxin, DNA-damaging agent, or radiation, for example. The comparisons can also be made to a sample from the same individual from an unaffected area, for example from an unaffected tissue.
  • One of skill will appreciate that it is often desirable to reduce non-specific binding in immunoassays and during analyte detection. Where the assay involves H1.0K180me2 antibodies immobilized on a solid substrate, it may be desirable to minimize the amount of non-specific binding to the substrate. Methods of reducing such non-specific binding are known to those of skill in the art. Typically, this involves coating the substrate with a proteinaceous composition. In some embodiments, protein compositions such as bovine serum albumin (BSA), nonfat powdered milk, and gelatin may be utilized.
  • The sensitivity, specificity, positive and negative predictive values (PPV and NPV) as well as positive and negative likelihood ratios (PLR and NLR)) can be calculated for each diagnostic test design. The statistical methods help to predict the presence or absence of disease in the patients.
  • Sensitivity is generally the probability that the test result will be positive when disease is present (true positive rate).
  • Specificity is generally the probability that a test result will be negative when the disease is not present (true negative rate).
  • The positive predictive value (PPV) generally is the probability that the disease is present when the test is positive, accounting for the pre-test prevalence of the disease (e.g. pre-test prevalence for Alzheimer's disease is 10%).
  • The negative predictive value (NPV) is generally the probability that the disease is not present when the test is negative, accounting for the pre-test prevalence of AD as 10% (Prince, M. J., Am J Epidemiol, 1996).
  • The positive likelihood ratio (LR+ or PLR) is generally the probability of a person who has the disease testing positive divided by the probability of a person who does not have the disease testing positive. Positive likelihood ratios (PLR) generally indicate how much to increase the probability of the disease, if the test is positive. A PLR>1 indicates an increase probability that the target disorder is present, a PLR<1 indicates a decreased probability that the target disorder is present, and a PLR=1 means that test does not change the probability of the disease.
  • The negative likelihood ratio (LR- or NLR) is generally the probability of a person who has the disease testing negative divided by the probability of a person who does not have the disease testing negative. Negative likelihood ratios (NLR) generally indicate how much to decrease the probability of the disease, if the test is negative.
  • In some embodiments, the comparison will be made to a threshold level established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity. The ROC curve, thresholds and areas under the curve (AUC) are shown for each of the test's designs provided herein.
  • In some embodiments, the diagnostic methods provided herein may be used for confirmatory tests, e.g. to definitively confirm that an individual has a disease, e.g. Alzheimer's disease.
  • In other embodiments, the diagnostic methods provided herein may be used for their predictive value (for testing, screening), e.g. to determine the likelihood that an individual will develop a disease, e.g. Alzheimer's disease. In such embodiments, the diagnostics may involve computation of likelihood ratios.
  • In other embodiments, the diagnostic methods provided herein may be used as a companion diagnostic. In such embodiments, the diagnostics may involve computation of positive predictive values (PPV) and negative predictive values (NPV).
  • In some embodiments, the diagnostic methods provided herein may be used to establish a diagnostic odds ratio (OR). In such embodiments, the diagnostic may involved computation of sensitivity and specificity and is a measure of the effectiveness of a diagnostic test.
  • The H1.0K180me2 antibodies provided herein are useful for a variety of diagnostic purposes, discussed below.
  • B. Detection of Alzheimer's Disease
  • Provided herein are H1.0K180me2 antibodies (to determine H1.0K180me2 levels), for use in the screening of individuals for Alzheimer's disease, for use in identifying whether individuals are at risk for developing Alzheimer's disease, for use in estimating the likelihood of whether individuals will develop Alzheimer's disease, for use in the diagnosis of Alzheimer's disease, for use in the early detection of Alzheimer's disease, for use in the prognosis of Alzheimer's disease, for selecting individuals who may respond to an Alzheimer's disease treatment with an Alzheimer's disease drug or regimen for use in treatment selection/determining treatment options for those diagnosed with Alzheimer's disease, for use in monitoring the treatment of those diagnosed with Alzheimer's disease and receiving ongoing treatment with an Alzheimer's disease drug or regimen, or for use in screening for Alzheimer's disease drugs and regimens.
  • Alzheimer's disease patients displayed lower concentrations of H1.0K180me2 than healthy age-matched healthy controls, indicating that H1.0K180me2 concentrations may effectively segregate patients with Alzheimer's disease from healthy individuals (FIG. 10A). Although serum concentrations of H1.0K180me2 were sufficient for identification of Alzheimer's disease patients, the use of a serum sample normalization by total IgG (FIG. 10B) or total protein (FIG. 10C) allowed for direct comparisons between individuals regardless of variables which may alter overall serum concentration, such as protocol used to obtain serum, operator variability, hydration state of patient and activity state of patient. For example, it was observed that H1.0K180me2 serum levels were elevated in healthy aged individuals relative to healthy younger individuals, while patients with Alzheimer's disease exhibited significantly lower normalized serum levels of H1.0K180me2 relative to healthy aged, individuals (>60 years) (FIG. 10B, 10C).
  • Exemplary Methods, H1.0K180me2 Levels: More specifically, in some embodiments, provided herein are methods using an H1.0K180me2 antibody, to determine H1.0K180me2 levels, for screening an individual for Alzheimer's disease, for identifying an individual is at risk for developing Alzheimer's disease, estimating the likelihood of whether an individual will develop Alzheimer's disease, for determining whether an individual has Alzheimer's disease, for detecting the early signs of Alzheimer's disease in an individual, and for use in the prognosis of Alzheimer's disease in an individual, the method comprising: (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of H1.0K180me2 in the sample that binds the antibody, wherein a decrease in the concentration relative to a control indicates that the individual has Alzheimer's disease, is at risk of developing Alzheimer's disease, or has a greater likelihood of developing Alzheimer's disease, and wherein an increase or no change in the concentration relative to a control may indicate that the individual does not have Alzheimer's disease, is not at risk of developing Alzheimer's disease, or does not have a greater likelihood of developing Alzheimer's disease. A control includes, but is not limited to, a healthy control (e.g. age-matched, sex-matched), a reference standard representing a compilation of healthy controls, or a control sample from the same individual isolated earlier in time. In some embodiments, the concentration of circulating H1.0K180me2 is determined. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity. In some embodiments, the method further comprises treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual has, or is at risk of developing, Alzheimer's disease.
  • In related embodiments, the methods provided herein are used in observational studies. Examples of observational studies include, but are not limited to: (a) Cross-sectional design (single time-point design, or delayed cross-sectional)—testing of one or few specimens/samples per patient that are collected at a single time-point; (b) Longitudinal design—testing of multiple specimens/samples per patient that are collected over an extended period of time (e.g. weeks, months, years); (c) Retrospective design—testing of previously collected specimens for which the analyte status and the patient's clinical status is known (characterized specimens) prior to the commencement of the study; (d) Prospective design—testing of specimens collected before or during the study but for which both the analyte status and the patient's clinical status are established during the study; and (e) Prospective-retrospective design—testing of previously collected specimens for which the clinical status is known but the analyte status is unknown and will be established during the study.
  • In related embodiments, the methods provided herein are intended for the diagnosis of Alzheimer's disease, wherein the methods may be used to determine, verify or confirm a patient's clinical condition as a sole determinant. In these embodiments, this type of testing also includes sole confirmatory assays (to verify results of previous testing) and sole exclusion assays (to rule out a particular condition).
  • In related embodiments, the methods provided herein are intended to provide an “aid-to-diagnostic” of Alzheimer's disease, wherein the methods may be used to provide additional information to assist in the determination or verification of a patient's clinical status. The test is not necessarily the sole determinant but may be used to evaluate a patient's current state.
  • In related embodiments, the methods provided herein are intended for the screening of Alzheimer's disease, wherein the methods may be used to determine the status of a disease, disorder or other physiological state in an asymptomatic individual. Depending on the nature of the condition and the targeted patient population, the screening methods may be used routinely or may be restricted to “at risk” patients. In this context the methods described herein used to evaluate a patient's current state.
  • In related embodiments, the methods provided herein are intended to determine the predisposition to Alzheimer's disease, wherein the methods described herein may be used to determine the likelihood of disease onset (e.g. assessing the risk of developing the disease in future) in pre-symptomatic patients, where for patients at sufficient risk (as determined by test results), preventive interventions may be taken.
  • In related embodiments, the methods provided herein are intended for the prognosis of Alzheimer's disease, wherein the methods described herein may be used to measure factors linked to a clinical outcome, irrespective of treatment. The methods described herein may be used to estimate the natural progression of a disease (e.g. outcome in the absence of treatment), or to the methods described herein are designed to evaluate a patient's future state.
  • In related embodiments, the methods provided herein are intended for determination of physiological status of aging population (“aging clock”) wherein the methods described herein may be used to evaluate the physiological state of an individual for the purpose of identifying a human condition or characteristic of aging or risk of Alzheimer's disease with aging.
  • In related embodiments, the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used to increase confidence in the Alzheimer's disease screening, diagnosis, or detection.
  • In related embodiments, the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used in conjunction with other Cerebrospinal Fluids (CSF) tests including but not limited to the measurement of Aβ42, T-tau, p-tau, Aβ42/T-tau ratio, and Aβ42/p-tau.
  • In related embodiments, the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used in conjunction with assessment of cognitive status tests, for example the MMSE (mini-mental state examination), GDS (global deterioration rate), and CDR (clinical, Dementia rating) tests.
  • In related embodiments, the quantification of H1.0K180me2 antigen and/or quantification of H1.0K180me2 autoantibodies may be used in conjunction with neuroimaging.
  • In some embodiments of the methods described herein, the levels of H1.0K180me2 may be normalized against total IgG in the biological sample or normalized against total protein in the biological sample. In some embodiments of the methods described herein, the concentration of H1.0K180me2 may be determined as a relative ratio to non-methylated, labeled, synthetic H1.0 peptide.
  • In embodiments of the methods described herein, the individual is greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • C. Companion Diagnostics for Alzheimer's Disease
  • Also provided herein are H1.0K180me2 antibodies (to determine H1.0K180me2 levels), for use in methods for selecting individuals who may respond to an Alzheimer's disease treatment with an Alzheimer's disease drug or regimen, for use in treatment selection/determining treatment options for those diagnosed with Alzheimer's disease, for use in monitoring the treatment of those diagnosed with Alzheimer's disease and receiving ongoing treatment with an Alzheimer's disease drug or regimen, or for use in screening for Alzheimer's disease drugs and regimens.
  • In these embodiments, these Alzheimer's disease drugs and regimens/treatments include, but are not limited to, treatment with APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, Aβ aggregation inhibitors, Aβ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, or ultrasound therapy. More specifically, APP synthesis inhibitors (+phenserine), beta-secretase inhibitors (MK-8931, E2609, LY2811376, LY2886721, PF-05297909, gamma-secretase inhibitors and modulators (semegacestat LY450139, avagacestat BMS-708163, PF-3084014, ELND006, tarenflurbil, CHF5074), Aβ aggregation inhibitors (tramiprosate (3APS), clioquinol (PBT1), PBT2, ELND005 (scyllo-inositol), PQ912), Aβ immunotherapy (GSK933776, AN1802+QS21, ACC-001, Alzheimer's disease-106, Bapineuzumab, Solanezumab, Gantenerumab (R04909832), Ponezumab (PF-04360365), MABT5102A (crenezumab), BAN2401, Intravenous immunoglobulin, gantenerumab (R1450 or R04909832)), anti-tau drugs (lithium, Tideglusib (NP031112), LMTX (methylene blue)), cholinesterase inhibitors (Razadyne® (galantamine), Exelon® (rivastigmine), and Aricept® (donepezil)), an N-methyl D-aspartate (NMDA) antagonists (Aricept® and Namzaric®, a combination of Namenda® and donepezil), atypical antipsychotics (olanzapine, quetiapine, risperidone), blockers of protein S-nitrosylation, agonist at the glucagon-like peptide-1 receptor, rapamycin and rapalogues, endocannabinoid and cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants (Vitamin E, vitamin C, α-lipoic acid, coenzyme Q), anti-inflammatory molecules and drugs, drugs controlling control of glutamate homeostasis, autophagic inducers, hormones and hormonal regulators, statins, insulin and insulin carriers including intranasal insulin, long acting insulin and thalidomide), Ramipril, resveratrol, multifunctional nanocarriers, vitamins and nutritional supplements, small RNA molecules, peptides, and ultrasound therapy. In some embodiments, the Alzheimer's disease drugs and regimens are pending FDA-approval, selected from a list of FDA-registered clinical trials for drug approval, which may be obtained on the world wide web address of the U.S. Food and Drug Administration.
  • Exemplary Methods, H1.0K180me2 Levels: In some embodiments, provided herein is a method using an H1.0K180me2 antibody for determining whether an individual diagnosed with Alzheimer's disease receiving ongoing treatment, will benefit or continue to benefit from the ongoing treatment, comprising: (a) providing a biological sample from the individual who is receiving ongoing treatment; (b) contacting the biological sample with an H1.0K180me2 antibody; (c) determining the concentration of H1.0K180me2 in the sample that binds the antibody; and (d) selecting an individual who will benefit or continue benefit from treatment, wherein an increase in the concentration relative to a control indicates that the individual will benefit or continue to benefit from treatment, and wherein a decrease or no change in the concentration relative to a control may indicate that the individual will not likely benefit or not continue to benefit from or be responsive to the treatment. A control includes, but is not limited to, samples from individuals with Alzheimer's disease not receiving a treatment, or a control sample from the same individual isolated earlier in time prior to the start of treatment. In some embodiments, the concentration of circulating H1.0K180me2 is determined. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • Also provided herein is a method using an H1.0K180me2 antibody for use in treatment selection for an individual diagnosed with Alzheimer's disease, for determining treatment options for an individual diagnosed with Alzheimer's disease, and for determining whether who may benefit from a particular treatment. In some embodiments, the method comprises: (a) providing a biological sample from the individual, before the individual is treated for Alzheimer's disease; (b) contacting the biological sample with a candidate treatment; (c) contacting the biological sample with an H1.0K180me2 antibody; (d) determining the concentration and/or subcellular localization of H1.0K180me2 in the sample that binds the antibody; and (e) selecting an individual who may benefit from the treatment, wherein an increase in the concentration relative to a control or a decrease in cytoplasmic subcellular localization indicates that the individual may benefit from a treatment and wherein an decrease or no change in the concentration relative to a control or an increase or no change in cytoplasmic subcellular localization may indicate that the individual will not benefit from a treatment. In another embodiment, the method comprises: (a) administering to the individual the candidate treatment; (b) providing a biological sample from the individual, after administration of the treatment; (c) contacting the biological sample with an H1.0K180me2 antibody; (d) determining the concentration and/or subcellular localization of H1.0K180me2 in the sample that binds the antibody; and (e) selecting an individual who may benefit from the treatment, wherein an increase in the concentration relative to a control or a decrease in cytoplasmic subcellular localization indicates that the individual may benefit from a treatment and wherein an decrease or no change in the concentration relative to a control or an increase or no change in cytoplasmic subcellular localization may indicate that the individual will not benefit from a treatment. A control can include, but is not limited to, samples from healthy individuals, or contacting the biological sample with a placebo treatment. In some embodiments, the concentration of circulating H1.0K180me2 is determined. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • In related embodiments, the methods provided herein are useful for ensuring that the H1.0K180me2 levels remain within physiological levels or within an established therapeutic drug range.
  • In related embodiments, the methods provided herein are useful for the monitoring of Alzheimer's disease, wherein the methods described may be used to measure the H1.0K180me2 levels for the purpose of adjusting treatments/interventions as required. In related embodiments, the methods provided herein are useful for monitoring the effects of an Alzheimer's disease drug or nutritional regiment or life style adjustment in an individual receiving such treatment.
  • In related embodiments, the methods provided herein are useful for monitoring the clinical performance in any observational or interventional clinical study for Alzheimer's disease, wherein (a) an observational study refers is a study in which test results obtained during the study are not used for patient management and do not impact treatment decisions; and (b) an interventional study is a study in which test results obtained during the study may influence patient management decisions and may be used to guide treatments.
  • In related embodiments, the methods provided herein are useful for serial measurement, whereby multiple determinations are taken over time. These types of monitoring methods may be used for the detection/assessment of disease progression/regression, disease recurrence, minimum residual disease, response/resistance to treatment, and/or adverse effects due to treatment. These types of monitoring methods may be designed to evaluate changes in an individual's state.
  • In related embodiments, the methods provided herein are useful for prediction of Alzheimer's disease treatment response or reaction, wherein the methods described herein may be used to measure factors that determine the likelihood of patient responses or adverse reactions to a specific therapy. Described herein are predictive methods designed specifically for use as companion diagnostics.
  • In some embodiments of the methods described herein, the levels of H1.0K180me2 may be normalized against total IgG in the biological sample or normalized against total protein in the biological sample. In some embodiments of the methods described herein, the concentration of H1.0K180me2 may be determined as a relative ratio to non-methylated, labeled, synthetic H1.0 peptide.
  • In embodiments of the methods described herein, the individual is greater than 50 years old. In some embodiments of the method described herein, the individual is less than 50 years old. In some embodiments, of the methods described herein, the individual is at least 50 years old, is at least 55 years old, is at least 60 years old, is at least 65 years old, is at least 70 years old, is at least 75 years old, or is at least 80 years old. In an exemplary embodiment, the individual is at least 60 years old.
  • In related embodiments, the methods may be used for screening for new Alzheimer's disease drugs and regimens.
  • D. Detection of Senescence
  • Provided herein are H1.0K180me2 antibodies, for use in detecting senescence. As provided herein, senescence is associated with replicative senescence (REP-SEN), genotoxic stress-induced senescence and radiation-induced senescence.
  • Generally the method for the detection of senescence involves the direct detection of H1.0K180me2. For direct detection of H1.0K180me2, the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the biological sample comprises senescent cells. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • In some embodiments, the methods may be used for identifying individuals that have undergone senescence induced by a genotoxin. In some embodiments the genotoxic stress-induced senescence is a result of exposure of the individual to a DNA damaging agent, drug or toxin, for example radiation, UV-light, bleomycin and any other genotoxic drugs including but not limited to Trazodone, Etotifen, Cephalexin, Nisoldipme, CGS 15943, Clotrimazole, 5-Nonyltryptamine, Doxepin, Pergolide, Paroxetine, Resveratrol, Quercetin, Honokiol, 7-nitroindazole, Megestrol, Fluvoxamine, Etoposide, Veliparib, Rucaparib, Olaparib, Camptothecin, or Terbinafine and chemotherapeutic drugs in general.
  • In some embodiments, the methods are useful for identifying senescence in individuals undergoing chemotherapy treatments to ensure that the chemotherapy is effective. The chemotherapeutic agent in these embodiments may be selected from the group consisting of Alemtuzumab (Campath), Alitretinoin (Panretin), Allopurinol (Zyloprim), Altretamine, (Hexalen), Amifostine (Ethyol), Anastrozole (Arimidex), Arsenic Trioxide (Trisenox), Asparaginase (Elspar), BCG Live (TICE BCG), Bexarotene (Targretin), Bleomycin (Blenoxane), Busulfan Intravenous (Busulfex), Busulfan Oral (Myleran), Calusterone (Methosarb), Capecitabine (Xeloda), Streptozocin (Zanosar), Tale (Sclerosol), Tamoxifen (Nolvadex), Temozolomide (Temodar), Teniposide, VM-26 (Vumon), Testolactone (Teslac), Thioguanine, 6-TG (Thioguanine), Thiotepa (Thioplex), and Topotecan (Hycamtin).
  • E. Detection of DNA Damage
  • Provided herein are H1.0K180me2 antibodies, for use in detecting DNA damage, for example acute DNA damage.
  • As described above, in the context of DNA damaging agents, dimethylation of H1.0K180 (H1.0K180me2) is observed on chromatin following acute DNA damage with bleomycin, a chemotherapeutic agent (FIG. 11A). Also as described above, in the context of genotoxic stress, H1.0K180me2 is released from the chromatin upon genotoxic stress induced senescence (days after treatment with a DNA damaging agent) (FIG. 12A) and is secreted out of the cells into the extracellular space (FIG. 12B).
  • Generally the method for the detection DNA damage involves the direct detection of H1.0K180me2. For direct detection of H1.0K180me2, the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the biological sample has undergone DNA damage. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • In some embodiments the DNA damage is a result of exposure of the cells or an individual to a DNA damaging agent, drug or toxin, for example radiation, bleomycin or other DNA-damaging agents (e.g. chemotherapeutic drugs discussed above).
  • In some embodiments, the method is useful for determining DNA damage within 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 45 minutes, 60 minutes, 75 minutes, 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 24 hours, 48 hours, 3 days, 4 days, or up to 5 days of such exposure to a genotoxin or DNA damaging agent.
  • In some embodiments, provided herein is a portable unit for the detection of DNA damage. The unit can comprise a sample collection unit, a reader, and an assay module comprising an H1.0K180me2 antibody.
  • F. Detection of Radiation Exposure
  • Provided herein are H1.0K180me2 antibodies, for use in detecting radiation exposure.
  • In the context of radiation exposure, exposure to ionizing radiation induces increased levels of circulating H1.0K180me2 in serum (FIG. 13A and FIG. 13B. The effect of ionizing radiation on H1.0K180me2 levels in serum was examined. Serum was collected from wild-type mice before and either 2 hours or 48 hours after exposure to 7 Gy of ionizing radiation. H1.0K180me2 serum levels 2 hours (mouse 1) or 48 hours (mouse 2) after irradiation were compared to initial levels before treatment using slot blot and immunoblotting with α-H1.0K180me2 antibody (FIG. 13A). The concentration of H1.0K180me2 in each serum sample was calculated using a standard curve of H1.0K180me2 peptide included in each analysis. Mouse serum albumin was used as a loading control. H1.0K180me2 dot blot bands were quantified and normalized by serum albumin. Relative increases in H1.0K180me2 after irradiation are shown (FIG. 13B). Western blot analysis of equal volumes of mouse serum with α-H1.0K180me2 antibody also showed increased H1.0K180me2 after irradiation (FIG. 13C).
  • Generally the method for the detection of radiation exposure involves the direct detection of H1.0K180me2. For direct detection of H1.0K180me2, the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that radiation exposure has occurred. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity. In one exemplary embodiment, the change in the concentration of the H1.0K170me2 antigen after 2 hrs after 7Gy X-ray exposure is from 12 umol/L to 21 umol/L, and from 26 umol/L to 35 umol/L after 48 hrs.
  • In some embodiments, the method is useful for determining radiation exposure within 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 45 minutes, 60 minutes, 75 minutes, 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 24 hrs, 48 hrs, 3 days, 4 days, or up to 5 days of such exposure.
  • In some embodiments, the method is useful determining such exposure in a field situation, for example in a combat zone, with military personnel.
  • In some embodiments, provided herein is a portable unit for the detection of radiation damage. The unit can comprise a sample collection unit, a reader, and an assay module comprising an H1.0K180me2 antibody.
  • G. H1.0K180me2 and Rapalogues
  • The mammalian target of rapamycin (mTOR) has emerged as a promising therapeutic target. Rapamycin and some rapamycin derivatives, rapamycin analogs, and other mTOR inhibitors are FDA-approved drugs for treatment of certain disease states.
  • The inventors have found that the detection of H1.0K180me2 may be useful for the screening of an individual's responsiveness to rapamycin, rapamycin derivatives, rapamycin analogs, and other mTOR inhibitors, referred to collectively as “rapalogues,” and may be useful for monitoring rapalogue-based therapeutic regimens. The inventors have also found that the detection of H1.0K180me2 may be useful for drug screening purposes, for the screening of additional rapalogues. Specifically, it is shown here that a rapamycin derivative and immunosuppressant, everolimus, blocks the appearance of H1.0K180me2 upon DNA damage (FIG. 14 ). It has also been observed that treatment with a rapalogue, prior to, or in parallel with a genotoxic stress exposure, may reduce the effect of the genotoxic stressor, as evidenced by a change in the concentration and/or subcellular localization of H1.0K180me2.
  • As used herein, rapalogues include FDA-approved rapalogues, and those rapalogues presently undergoing clinical trials. FDA-approved rapalogues include Rapamycin, Sirolimus, Rapamune, Everolimus, RAD001, Afinitor, Zortress, Temsirolimus, CCI-779, Torisel, Ridaforolimus, AP23573, MK-8669, Deforolimus, Zotarolimus, and ABT-578. Other Rapalogues AZD8055, AZD2014, OSI-027, MLN0128, WYE-132, Torin1, PI-103, P7170, PF-04691502, PF-05212384, PKI-587, GNE477, PKI-180, WJD008, XL765, SAR245409, NVP-BEZ235, BGT226, SF1126, GSK2126458, Ku-0063794, WYE-354, NVP-BEZ235, PF-05212384, XL765, Torin 2, WYE-125132, and OSI-027.
  • Generally provided herein is a method for monitoring the effects of a rapalogue-based treatment ongoing in an individual diagnosed with cancer, an immunodeficiency, diabetes, arthritis, Alzheimer's disease and other neurodegenerative diseases, cardiovascular disease, an autoimmune disease, and other age related pathologies.
  • Thus, in some embodiments, provided herein is a method of determining whether an individual receiving treatment with a rapalogue is responsive to such treatment, comprising: (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; (b) determining the concentration and/or localization of H1.0K180me2 in the sample that binds the antibody; and (c) determining whether the individual is responsive to treatment, wherein a decrease in the concentration established or a change in the localization relative to a control indicates that the individual is responsive to the rapalogue. In some embodiments, it is determined that the rapalogue treatment is not effective, or needs to be modified if there is an increase in the extracellular concentration of the H1.0K180me2 relative to a control. In some embodiments it is determined that the rapalogue treatment is not effective, or needs to be modified if there is an increase in the cytoplasmic localization of the H1.0K180me2 relative to a control. In some embodiments, the decrease is relative to an age-matched control that is not diagnosed with the relevant disease for which the rapalogue is being administered. In some embodiments it is determined that the treatment is effective, and should be continued if there is a decrease in the extracellular or cytoplasmic concentration of the H1.0K180me2 protein relative to a control. In some embodiments, the method further comprises using the information to modify the treatment type, course, duration, and/or dosage. In some embodiments, the concentration of circulating H1.0K180me2 is determined. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • In some embodiments, provided herein is a method for selecting an individual, diagnosed with or suspected of having cancer, an immunodeficiency, diabetes, Alzheimer's disease or other neurodegenerative diseases, cardiovascular disease, an autoimmune disease, arthritis, and other age related pathologies, who may benefit from rapalogue treatment, or to determine whether an individual may respond to treatment with a rapalogue. In some embodiments, this method comprises providing a biological sample from the individual; treating the sample with a rapalogue in vitro, ex vivo, in slice culture, or in tissue culture; and determining the concentration and/or subcellular localization of H1.0K180me2 in the sample. In some embodiments, the concentration of the H1.0K180me2 is determined, by measuring the concentration of H1.0K180me2 in the sample using an H1.0K180me2 antibody. In some embodiments it is determined that the rapalogue treatment may not be effective, if there is an increase in the cytoplasmic or extracellular concentration of the H1.0K180me2 relative to a control. In some embodiments it is determined that the rapalogue treatment may not be effective, if there is an increase in the cytoplasmic localization of the H1.0K180me2 relative to a control. In some embodiments, the decrease is relative to an age-matched control that is not diagnosed disease for which the individual may receive a rapalogue treatment. In some embodiments it is determined that the treatment may be effective, if there is a decrease in the cytoplasmic or extracellular concentration of the H1.0K180me2 protein relative to a control. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • In some embodiments, the methods provided herein further comprises using the information to modify the treatment type, course, duration, and/or dosage.
  • In other embodiments, provided herein is the use of the detection of H1.0K180me2 to monitor for the ability for new rapalogues to be identified (drug screening applications).
  • H. Detection of Biological Aging
  • Provided herein are H1.0K180me2 antibodies, for use in detecting biological aging. As provided herein, biological aging markers or biomarkers of aging are expected to find many uses in biological research since age is a fundamental characteristic of most organisms.
  • There can be differences between chronological and biological age. Some individuals age more rapidly, while others, due to good habits, genes and/or lack of environmental stressors, age more slowly making them healthier and “younger looking” longer. Being able to track one's biological age may help to modify life style (similar to tracking body mass index) or help to deploy antiaging procedures.
  • Accurate measures of biological age by aging markers are useful for testing the age-related diseases theories of biological aging, such as (i) diagnosing various age related diseases and for defining cancer subtypes, (ii) predicting/prognosticating the onset of various diseases, and serving as (iii) surrogate markers for evaluating therapeutic interventions including rejuvenation approaches.
  • Generally the method for the detection of biological aging involves the direct detection of H1.0K180me2. For direct detection of H1.0K180me2, the method generally comprises (a) contacting a biological sample from the individual with an H1.0K180me2 antibody; and (b) determining the concentration of the H1.0K180me2 antigen in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the biological sample is from an individual that has experienced biological aging. In some embodiments, the change in the concentration is relative to a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • I. Diagnostic Kits and Articles of Manufacture
  • Provided herein are kits useful for the detection of H1.0K180me2. In some embodiments, the kit comprises one or more H1.0K180me2 antibodies as described herein. In certain embodiments, the antibodies. In addition, the kits can optionally include instructional materials for carrying out any of the methods described herein. While the instructional materials typically comprise written or printed materials, they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated herein. Such media include, but are not limited to, electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media can include addresses to internet sites that provide such instructional materials.
  • The kits may also include additional components to facilitate the particular application for which the kit is designed. Thus, for example, where a kit contains an anti-H1.0K180me2 that is labeled, the kit may additionally contain reagents for detecting the label (e.g., enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels, and the like). The kits may additionally include buffers and other reagents routinely used for the practice of a particular method.
  • An exemplary kit useful in an immunoassay to detect H1.0K180me2 may include an H1.0K180me2 protein or peptide. This peptide may be employed, for example, as a positive control or as competitor in a competitive immunoassay, and may be labeled or not, depending on the format of the assay to be carried out.
  • Another exemplary kit useful in an immunoassay to detect H1.0K180me2, in addition to an anti-H1.0K180me2 peptide, may include an H1.0K180me2 antibody. This antibody may be employed, for example, as a positive control or as competitor in a competitive immunoassay, and may be labeled or not, depending on the format of the assay to be carried out.
  • Also provided herein are transdermal patches for measuring a concentration of a hypodermal target H1.0K180me2 proteins and peptides, comprising: a substrate comprising an H1.0K180me2 antibody; and a plurality of microneedles. In some embodiments, the patches are transdermal microneedle array patches. In some embodiments, the substrate of the patches is elastically stretchable. In some embodiments, provided herein are kits comprising patches which comprise the antibodies or peptides provided herein, and optionally, instructions for use. In some embodiments, the patch is useful for detecting and measuring the concentration of H1.0K180me2 in a biological sample, for the purpose of detecting replicative senescence, DNA damage, genotoxic stress, radiation exposure, and Alzheimer's disease, useful for monitoring therapeutic regimens, and useful for drug screening.
  • Also provided herein is a portable unit, for detection, for example for the detection of DNA damage or radiation exposure. The unit may comprise a sample collection unit, a reader, and an assay module comprising an H1.0K180me2 antibody.
  • Also provided herein are lateral flow strips or test strips suitable for a lateral flow assay of an analyte, comprising a sample receiving zone, wherein the sample receiving zone comprises either an H1.0K180me2 antibody. In some embodiments, antibody is conjugated to a label.
    • ENUMERATED EMBODIMENTS
  • The invention may be defined by reference to the following enumerated, illustrative embodiments.
  • Embodiment 1. An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises:
      • any one of the CDR-L1 amino acid sequences of Table 4;
      • any one of the CDR-L2 amino acid sequences of Table 5; and
      • any one of the CDR-L3 amino acid sequences of Table 6.
  • Embodiment 2. An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises:
      • any one of the CDR-H1 amino acid sequences of Table 7;
      • any one of the CDR-H2 amino acid sequences of Table 8; and
      • any one of the CDR-H3 amino acid sequences of Table 9.
  • Embodiment 3. An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises any one of the CDR-L amino acid sequences of Tables 4, 5, and 6, and comprises any one of the CDR-H amino acid sequences of Tables 7, 8, and 9.
  • Embodiment 4. The antibody of embodiment 1, wherein the antigen-binding domain of the antibody comprises
      • a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11;
      • a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 14 or SEQ ID NO: 15; and
      • a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 18.
  • Embodiment 5. The antibody of embodiment 1, wherein the antigen-binding domain of the antibody comprises
      • a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22 or SEQ ID NO: 23;
      • a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30 or SEQ ID NO: 31; and
      • a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 36 or SEQ ID NO: 37.
  • Embodiment 6. An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • Embodiment 7. An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7.
  • Embodiment 8. An antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 or SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO: 9.
  • Embodiment 9. The antibody of embodiment 8, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 6 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 8.
  • Embodiment 10. The antibody of embodiment 8, wherein the heavy chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 7 and the light chain variable domain of the antibody comprises the amino acid sequence of SEQ ID NO: 9.
  • Embodiment 11. The antibody of any one of embodiments ito 10, wherein the antibody is chimeric or humanized.
  • Embodiment 12. The antibody of any one of embodiments 1 to 10, wherein the antibody is a monoclonal antibody.
  • Embodiment 13. The antibody of any one of embodiments 1 to 10, wherein the antibody is an antigen-binding fragment.
  • Embodiment 14. The antibody of any one of embodiments 1 to 13, wherein the antibody exhibits reduced binding to the H1.0K180me2 protein or peptide, if the protein or peptide comprises residues other than K180 that are methylated.
  • 15. The antibody of any one of embodiments 1 to 14, wherein the antibody does not bind, or only minimally binds, if the H1.0K180me2 protein or peptide comprises methylated lysine residues at lysine residues corresponding to K166, K172, K174, K175, and/or K177 of a human histone H1.0 protein.
  • Embodiment 16. The antibody of any one of any one of embodiments 1 to 15, wherein the antibody is conjugated to a label.
  • Embodiment 17. The antibody of any one of embodiment 16, wherein the antibody is attached to solid surface.
  • Embodiment 18. The antibody of embodiment 17, wherein the antibody attached a bead, column, resin, or a microplate.
  • Embodiment 19. The antibody of any one of any one of embodiments 1 to 15, wherein the antibody is conjugated to an agent.
  • Embodiment 20. The antibody of embodiment 19, wherein the agent is selected from the group consisting of a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
  • Embodiment 21. A method of determining whether an individual has, or is at risk of, developing, Alzheimer's disease, comprising:
      • contacting a biological sample from the individual with the antibody of any one of embodiments 1 to 18; and
      • determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody, wherein a decrease in the concentration relative to a control indicates that the individual has, or is at risk of developing, Alzheimer's disease.
  • Embodiment 22. The method of embodiment 21, further comprising treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual has, or is at risk of developing, Alzheimer's disease.
  • Embodiment 23. A method of determining whether an individual diagnosed with Alzheimer's disease and receiving treatment for the Alzheimer's disease, will benefit from the treatment or will continue to benefit from the treatment, the method comprising:
      • contacting a biological sample from the individual with the antibody of any one of embodiments 1 to 18; and
      • determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • determining that the individual will benefit from the treatment or will continue to benefit from the treatment if there is an increase in the concentration, relative to a control.
  • Embodiment 24. The method of embodiment 23, further comprising treating the individual with an Alzheimer's disease drug or regimen if it is determined that the individual will benefit or continue to benefit from the treatment.
  • Embodiment 25. A method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, wherein the individual has not yet started the treatment, the method comprising:
      • administering to the individual a candidate treatment;
      • contacting a biological sample from the individual after administration of the candidate treatment with the antibody of any one of embodiments 1 to 18; and
      • determining the concentration and/or subcellular localization of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • determining that the individual will benefit from the candidate treatment if there is an increase in the concentration or an decrease in cytoplasmic subcellular localization, relative to a control.
  • 26. A method of determining whether an individual diagnosed with Alzheimer's disease will benefit from a candidate treatment, wherein the individual has not yet started the treatment, the method comprising:
      • contacting a biological sample from the individual with a candidate treatment;
      • contacting a biological sample from the individual with the antibody of any one of embodiments 1 to 18;
      • determining the concentration and/or subcellular localization of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • determining that the individual will benefit from the candidate treatment if there is an increase in the concentration relative to a control or an decrease in cytoplasmic subcellular localization, relative to a control.
  • Embodiment 27. The method of any one of embodiments 25-26, wherein the treatment is selected from the group consisting of APP synthesis Inhibitors, beta-secretase inhibitors, gamma-secretase inhibitors and modulators, Aβ aggregation inhibitors, Aβ immunotherapy, Cholesterol-lowering drugs, Anti-tau drugs, cholinesterase inhibitors, N-methyl D-aspartate (NMDA) antagonists, atypical antipsychotics, blockers of protein S-nitrosylation, glucagon-like peptide-1 receptor agonists, rapamycin, rapalogues, endocannabinoids, cannabionoids, neuroprotectors, molecules controlling calcium influx, antioxidants, anti-inflammatory drugs, drugs controlling control of glutamate homeostasis, autophagy inducers, hormones, hormonal regulators, statins, insulin, insulin carriers, multifunctional nanocarriers, vitamins, nutritional supplements, small RNA molecules, peptides, and ultrasound therapy.
  • Embodiment 28. A method of determining whether an individual has been exposed to a DNA damaging agent, comprising:
      • contacting a biological sample from the individual with the antibody of any one of embodiments 1 to 18; and
      • determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody, wherein an increase in the concentration relative to a control indicates that the individual has been exposed to a DNA damaging agent.
  • Embodiment 29. The method of embodiment 28, wherein the DNA damaging agent is radiation.
  • Embodiment 30. A method of determining whether an individual receiving treatment with a rapalogue is responsive to such treatment, comprising:
      • contacting a biological sample from the individual with the antibody of any one of embodiments 1 to 18;
      • determining the concentration of the protein comprising an H1.0K180me2 antigen or a peptide thereof in the sample that binds the antibody; and
      • determining whether the individual is responsive to treatment, wherein a decrease in the concentration relative to a control indicates that the individual is responsive.
  • Embodiment 31. The method of embodiment 30, wherein the decrease is below a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • Embodiment 32. The method of embodiment 30, wherein the rapalogue is selected from the group consisting of Rapamycin, Sirolimus, Rapamune, Everolimus, RA 001, Afinitor, Zortress, Temsirolimus, CCI-779, Torisel, Ridaforolimus, AP23573, MK-8669, Deforolimus, Zotarolimus, ABT-578, AZD8055, AZD2014, OSI-027, MLN0128, WYE-132, Torin1, PI-103, P7170, PF-04691502, PF-05212384, PKI-587, GNE477, PKI-180, WJD008, XL765, SAR245409, NVP-BEZ235, BGT226, SF1126, GSK2126458, Ku-0063794, WYE-354, NVP-BEZ235, PF-05212384, XL765, Torin 2, WYE-125132, and OSI-027.
  • Embodiment 33. The method of any one of embodiments 21 to 32, wherein the increase or decrease in the concentration is above or below a threshold established by a Receiver Operating Characteristic curve analysis for optimal specificity and sensitivity.
  • Embodiment 34. The method of any one of embodiments 21 to 33, wherein the biological sample is selected from the group consisting of whole blood, plasma, serum, saliva, urine, synovial fluid, cerebrospinal fluid, bronchial lavage, ascites fluid, bone marrow aspirate, pleural effusion, tissue, cells, a biopsy, interstitial fluid, and lymphatic fluid.
  • Embodiment 35. A transdermal patch for measuring a concentration of a hypodermal target molecule, comprising:
      • a substrate comprising the antibody of any one of embodiments 1 to 18; and
      • a plurality of microneedles.
  • Embodiment 36. The patch of embodiment 35, wherein the patch is a transdermal microneedle array patch.
  • Embodiment 37. The patch of embodiment 35, wherein the substrate is elastically stretchable.
  • Embodiment 38. A portable unit for determining whether an individual has been exposed to radiation or a DNA-damaging agent, comprising:
      • a sample collection unit;
      • a reader;
      • an assay module comprising the antibody of any one of embodiments 1 to 18; and
      • a plurality of microneedles.
  • Embodiment 39. A test strip suitable for a lateral flow assay of an analyte, comprising a sample receiving zone, wherein the sample receiving zone comprises the antibody of any one of embodiments 1 to 18.
  • Embodiment 40. A method of treating a methylated H1.0-related disease or condition in an individual comprising administering to the individual a therapeutically effective amount of the antibody of any one of embodiments 1 to 20.
  • Embodiment 41. The method of embodiment 40, wherein the disease or condition is selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxic stressor, a disease or condition comprising the accumulation of senescent cells, and a disease or condition accompanied by elevated levels of H1.0K180me2 proteins or peptides.
  • Embodiment 42. A method of clearing H1.0K180me2 in an individual comprising administering to the individual a therapeutically effective amount of the antibody of any one of embodiments 1 to 20.
  • Embodiment 43. The method of embodiment 42, wherein the individual suffers from a disease or condition selected from the group consisting of Alzheimer's disease, radiation exposure, exposure to a genotoxin, exposure to a DNA damaging agent, and a condition comprising the accumulation of senescent cells.
  • Embodiment 44. A pharmaceutical composition comprising the antibody of any one of embodiments 1 to 20, and a pharmaceutically acceptable excipient.
  • Embodiment 45. A kit comprising any one of therapeutically effective amount of the antibody of any one of embodiments 1 to 18.
  • Embodiment 46. An article of manufacture comprising any one of the compositions of embodiments of embodiments 1 to 20, and 35 to 45.
  • Embodiment 47. A vector encoding an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, comprising the nucleic acid of SEQ ID NO: 4.
  • Embodiment 48. A vector encoding an antibody that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, comprising the nucleic acid of SEQ ID NO: 5.
  • Embodiment 49. A cell comprising the vector of any one of embodiments 47 to 48.
  • The following examples are included for illustrative purposes and are not intend to limit the scope of the invention.
    • EXAMPLES Example 1: Recombinant Antibody Development Pipeline
  • The antibody development pipeline shown in FIG. 1 was split into four phases (Phase I-IV). In phase I, two New Zealand rabbits were immunized for antibody production. Injections were administered subcutaneously (SQ) as emulsions of Keyhole Limpet Hemocyanin (KLH)-conjugated H1.0K180me2 peptide (KLH-CAKPVKASKPKKAKPVK(me2)PK (SEQ ID NO: 72)) in Complete Freund's Adjuvant (CFA) or Incomplete Freund's Adjuvant (IFA). Initial immunization was performed with 0.5 mg of antigen ((KLH)-conjugated H1.0K180me2 peptide) in CFA at 10 SQ sites. 6 subsequent booster immunizations were performed at routine intervals over a 10-11 week period. Boosters consisted of 0.25 mg antigen in IFA at 4 SQ sites. Rabbits were bled at week 6 and at week 8. The titer of the immunization was assessed using ELISA by comparing pre- and post-immunization bleeds. Once an appropriate ELISA positive titer was recorded toward the immunizing antigen, peripheral blood mononuclear cells (PBMCs) were collected from one or both rabbits. B-cells were subsequently isolated by flow cytometry sorting using a dual-screening protocol which ensured only rabbit lgG and antigen-specific B-cells were isolated.
  • During phase II, total RNA was isolated from the sorted, antigen-positive B-cells. This was followed by creation of a single-chain variable fragment (scFv) surface-display library by reverse transcription-polymerase chain reaction (RT-PCR). This scFv library represents all the variable domain regions of the rabbit IgG antibodies capable of binding the H1.0K180me2 antigen.
  • Phase III consisted of multiple rounds of library screening to increase the specificity of the library towards H1.0K180me2. This was done by panning and flow cytometry to isolate scFv domains exhibiting the highest specificity to biotin-conjugated H1.0K180me2 peptide (Biotin-CAKPVKASKPKKAKPVK(me2)PK (SEQ ID NO: 73)), whilst selecting against scFv domains exhibiting specificity towards unmethylated H1.0 peptide (Biotin-CAKPVKASKPKKAKPVKPK (SEQ ID NO: 74)).
  • The scFv domains with the highest specificity for H1.0K180me2 were sequenced by Sanger sequencing, before being moved on to phase IV. During phase IV, full-length IgG heavy-chain and light-chain clones were generated incorporating the scFv domains, followed by expression of compete, full-length recombinant rabbit monoclonal IgG antibodies. These antibodies were then validated for specificity to H1.0K180me2 using ELISA, slot blot immunoassay, and western blot. In total, 5 distinct antibody clones were created, sorted below A through E in order of their specificity for H1.0K180me2:
      • (a) Clone A (RW24)
      • (b) Clone B (RW6)
      • (c) Clone C (RW37)
      • (d) Clone D (RW28)
      • (e) Clone E (RW36)
  • Phases I-IV are summarized in the Table 11 below.
  • TABLE 11
    H1.0K180me2 Monoclonal Antibody -
    Exemplary Development Pipeline
    Devel-
    opment
    Stage Description
    Phase Immunization of rabbits with KLH conjugated peptide. Isolation
    I of rabbit peripheral blood mononuclear cells (PBMCs) from the
    animal(s) with the highest ELISA-positive titer, with subsequent
    screening and sorting of antigen-positive, and IgG-positive B
    cells
    Phase Total RNA isolation from sorted, antigen-positive B cells, and
    II preparation of surface-display library.
    Phase Multi-round screening of display-library by flow cytometry and
    III panning.
    Phase Generation of candidate full-length Heavy-chain and Light-chain
    IV clones, expression of full-length and complete recombinant
    rabbit monoclonal antibodies, and validation.
    • Example 2: Analysis of Antibody Titer for Rabbit Antibody Clones by ELISA
  • The specificity of the recombinant rabbit anti-H1.0K180me2 monoclonal IgG antibody clones for H1.0K180me2 peptide was determined using ELISA in FIG. 2A. Wells were coated with H1.0K180me2 peptide; 50 ul of peptide solution (5 ug/ml) was used to coat each well. 100 ul of each clone antibody was added to wells in a 2× dilution series. Curves for each peptide were generated by plotting antibody concentration against measured O.D at 450 nm. In order to directly compare the binding efficiencies of the different clones, a threshold cut-off was selected that intersected the linear range of each of the clone titration curves (horizontal dashed line at O.D. 1.5). The concentration of antibody required to meet the threshold O.D was compared for each clone, and given in the figure legend. Clone A (RW24) has the highest binding affinity for H1.0K180me2 peptide.
  • The non-specific binding of the antibody clones to unmodified H1.0 peptide was also determined by ELISA as above in FIG. 2B. Clones D (RW28) and E (RW36) both bound to unmodified H1.0 peptide with high affinity. At the threshold concentration calculated above, Clone A (RW24) was 20× more efficient at binding H1.0K180me2 peptide than unmodified H1.0 peptide, Clone B (RW6): 23×, Clone C (RW37): 22×, Clone D (RW28): 2×, Clone E (RW36): 5×.
  • FIG. 2C provides raw data for ELISA plot generation of FIGS. 2A and 2B.
    • Example 3: Analysis of Specificity of Rabbit Antibody Clones by Slot Blot
  • The specificity of the above generated recombinant rabbit anti-H1.0K180me2 monoclonal IgG antibody clones was determined using slot blot analysis as shown in FIG. 3 . Histone H1.0 peptides (unmodified, K180me1, K180me2) were transferred to membranes using a vacuum-manifold slot blot in a dilution series (100 pmol, 50 pmol, 25 pmol). The membranes were then immunoblotted using the antibody clones to identify potential cross-reactivity with unmodified or mono-methylated H1.0 peptide. Clones A, B and C are highly specific for H1.0K180me2, even in low concentrations. No cross-reactivity with either unmodified or H1.0K180me1 peptides was observed for these clones. Clones D and E were both able to detect H1.0K180me1 peptide in addition to H1.0K180me2, suggesting a lack of antibody specificity for H1.0K180me2.
    • Example 4: Analysis of Specificity of Antibody Clones by In Vitro Methylated H1.0K180me2
  • FIG. 4A shows an overview of the in vitro methylation approach. The methylation reaction comprised recombinant G9A (methyltransferase), an unlabeled methyl donor (S-Adenosyl-L-Methionine), and recombinant human H1.0 protein, which were incubated at 37° C. for 1 hour. During this incubation, G9A is capable of methylating full-length H1.0 protein, including the addition of K180me2. H1.0K180me2 can subsequently be identified using an anti-H1.0K180me2 rabbit polyclonal antibody to confirm methylation.
  • In order to identify the precise locations of methylation by G9A on full-length H1.0 protein, the above reaction was subsequently analyzed by LC-MS, and sites of methylation were identified. FIG. 4B displays the sequence of full-length H1.0 protein, and the number of “me” circles represents the methylation state of the lysine residue (mono- or di-methylated). In the presence of recombinant, full-length H1.0, G9A specifically methylates several C-terminal lysine residues, including H1.0K180me2.
  • FIG. 4C demonstrates an in-vitro methylation assay of recombinant full-length histone H1.0 with increasing amounts of G9A, and detection with rabbit anti-H1.0K180me2 polyclonal antibody. The top panel exhibits increased H1.0K180 methylation with increasing G9A concentration.
  • FIG. 4D shows an analysis of clone specificity for in vitro methylated H1.0. Clone A is capable of recognizing in vitro methylated H1.0, with minimal non-specific binding to unmethylated full length H1.0 in the absence of G9A protein. All other clones recognize unmethylated H1.0 and show no specificity for methylated full-length H1.0.
    • Example 5: Sequence Analysis of Clones a (RW24) and B (RW6)
  • Clones of interest were sequenced.
  • FIG. 5A is an EMBOSS NEEDLE (Li W. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Research [6 Apr. 2015, 43(W1):W580-4) pairwise sequence alignment of the heavy chain variable domain protein sequences of clones A and B. The heavy chain sequences share 61% identity and 70% similarity.
  • FIG. 5B is an EMBOSS NEEDLE pairwise sequence alignment of the light chain variable domain protein sequences of clones A and B. The light chain sequences share 83% identity and 88% similarity.
  • FIG. 5C provides DNA and protein sequences of the light and heavy chain variable domains for Clone A (RW24).
  • FIG. 5D is a schematic representation of one method of construction of full length light and heavy chain expression vectors incorporating the variable domain DNA sequences, in order to create full-length recombinant IgG antibodies.
    • Example 6: Mapping Framework and CDR Regions of Clone a Heavy Chain with Chothia Predictive Software
  • Shown in FIGS. 7A and 7B (left panel) are the analyses of clone A heavy chain and clone A light chain with Chothia, a program that predicts antibody architecture. Each residue of the heavy chain or light chain is displayed in the top box, and a residue number is assigned by Chothia in the box below each corresponding residue. Shown in light gray are predicted framework regions of the clone A heavy chain or light chain. Show in dark gray are the predicted CDRs. Stars indicated predicted CK2 phosporylation sites. Arrows indicate unusual residues for each location.
  • FIG. 7B (right panel) shows a distribution of residues that are predicted to be in position L1 for all Chothia predictions performed. In the example of clone A light chain, L1 position is aspartate, which has the greatest relative frequency for all amino acids predicted to be in position L1.
  • FIG. 7C depicts the predicted light chain complementary determining regions and framework regions for antibody Clone A, using the Chothia, AbM, Kabat, and Contact algorithms/numbering schemes.
  • FIG. 7D depicts the predicted heavy chain complementary determining regions and framework regions for antibody Clone A, using the Chothia, AbM, Kabat, and Contact algorithms/numbering schemes.

Claims (16)

1-52. (canceled)
53. An antibody or antigen-binding fragment thereof that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the antigen-binding domain of the antibody comprises:
(a) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 13;
(b) a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 16 or SEQ ID NO: 17;
(c) a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 19;
(d) a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26 or SEQ ID NO: 27; and
(d) a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34 or SEQ ID NO: 35.
54. An antibody or antigen-binding fragment thereof that specifically binds a protein comprising an H1.0K180me2 antigen or a peptide thereof, wherein the heavy chain variable domain of the antibody or antigen-binding fragment thereof comprises at least 85% of the amino acid sequence of SEQ ID NO: 7 and the light chain variable domain of the antibody or antigen-binding fragment thereof comprises at least 85% the amino acid sequence of SEQ ID NO: 9.
55. The antibody or antigen-binding fragment thereof of claim 54, wherein the heavy chain variable domain of the antibody or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 7 and the light chain variable domain of the antibody or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 9.
56. The antibody or antigen-binding fragment thereof of claim 53, wherein the antibody is chimeric or humanized.
57. The antibody or antigen-binding fragment thereof of claim 53, wherein the antibody is a monoclonal antibody.
58. The antibody or antigen-binding fragment thereof of claim 53, wherein the antibody or antigen-binding fragment thereof does not bind, or only minimally binds, if the H1.0K180me2 protein or peptide comprises methylated lysine residues at lysine residues corresponding to K166, K172, K174, K175, and/or K177 of a human histone H1.0 protein.
59. The antibody or antigen-binding fragment thereof of claim 53, wherein the antibody or antigen-binding fragment thereof is conjugated to a label.
60. The antibody or antigen-binding fragment thereof of claim 53, wherein the antibody or antigen-binding fragment thereof is attached to a solid surface.
61. The antibody of claim 60, wherein the antibody or antigen-binding fragment thereof is attached to a bead, column, resin, or a microplate.
62. The antibody or antigen-binding fragment thereof of claim 53, wherein the antibody or antigen-binding fragment thereof is conjugated to an agent.
63. The antibody or antigen-binding fragment thereof of claim 62, wherein the agent is selected from the group consisting of a radionuclide, a cytotoxin, a chemotherapeutic agent, a drug, a pro-drug, a toxin, an enzyme, an immunomodulator, a pro-apoptotic agent, a cytokine, a hormone, an oligonucleotide, an antisense molecule, a siRNA, and a second antibody.
64. The antibody or antigen-binding fragment thereof of claim 53, wherein the heavy chain variable domain of the antibody or antigen-binding fragment thereof comprises the amino acid sequence of SEQ ID NO: 7.
65. A pharmaceutical composition comprising the antibody or antibody-binding fragment thereof of claim 53, and a pharmaceutically acceptable excipient.
66. A kit comprising a therapeutically effective amount of the antibody or antibody-binding fragment thereof of claim 53.
67. The article of manufacture of claim 66, wherein the article of manufacture is a transdermal patch or a transdermal microneedle array patch.
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