WO2016126616A1 - Methods and kits for measuring and quantifying dna double-stranded breaks using gamma-h2ax and h2ax - Google Patents

Methods and kits for measuring and quantifying dna double-stranded breaks using gamma-h2ax and h2ax Download PDF

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WO2016126616A1
WO2016126616A1 PCT/US2016/016000 US2016016000W WO2016126616A1 WO 2016126616 A1 WO2016126616 A1 WO 2016126616A1 US 2016016000 W US2016016000 W US 2016016000W WO 2016126616 A1 WO2016126616 A1 WO 2016126616A1
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biological sample
complex
h2ax
antibody
η2αχ
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Christophe E. REDON
William M. Bonner
Yiping Zhang
Jiuping Ji
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US Department of Health and Human Services
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US Department of Health and Human Services
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6875—Nucleoproteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2522/00—Reaction characterised by the use of non-enzymatic proteins
    • C12Q2522/10—Nucleic acid binding proteins
    • C12Q2522/101—Single or double stranded nucleic acid binding proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2523/00—Reactions characterised by treatment of reaction samples
    • C12Q2523/10—Characterised by chemical treatment
    • C12Q2523/107—Chemical cleaving agents

Definitions

  • nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 1 ,958 Byte ASCII (Text) file named "723004_ST25.TXT,” dated February 1 , 2016.
  • Exposure to ionizing radiation (IR) or other agents may cause DNA double- stranded breaks (DSBs).
  • DNA DSBs may, potentially, damage living cells, tissues, or both, and may result in illness (for example, Acute Radiation Syndrome and cancer), death, or both. Identifying the amount of exposure to a DNA DSB-causing agent may be useful for determining the need for and nature of further testing and/or medical treatment. Accordingly, there is a need for improved methods and kits for measuring the amount of exposure of a host to a DNA DSB-causing agent.
  • An embodiment of the invention provides a method of measuring the amount of exposure of a host to a DNA DSB-causing agent, the method comprising: contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to gamma ( ⁇ )- ⁇ 2 ⁇ and forms a first complex with the ⁇ - ⁇ 2 ⁇ ; contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the positive control biological sample has been exposed to a known amount of the DSB-causing agent; contacting the first and second complexes of the positive control biological sample and the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX
  • Another embodiment of the invention provides a method of quantifying DNA DSBs in a test biological sample, the method comprising: contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a test biological sample with an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ and forms a first complex with the ⁇ - ⁇ 2 ⁇ ; contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the positive control biological sample has a known quantity of DSBs; contacting the first and second complexes of the positive control biological sample and the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex; detecting the
  • kits comprising: at least one substrate; an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ ; an antibody or antigen binding fragment thereof that specifically binds to H2A core protein; an antibody or antigen binding fragment thereof that specifically binds to H2AX; and a detecting agent comprising a label.
  • Still another embodiment of the invention provides a method of testing compounds for ability to cause DNA DSBs in a host, the method comprising: (a)
  • Another embodiment of the invention provides a method of screening test compounds for ability to cause DNA DSBs, the method comprising: (a) dividing a population of test biological samples into more than one test sub-population; (b) treating each test sub- population with a test compound, wherein each test sub-population is treated with a different test compound; (c) contacting (i) a first portion of each treated test sub-population and (ii) a first portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ and forms a first complex with the ⁇ - ⁇ 2 ⁇ ; (d) contacting (i) a second portion of each treated test sub-population and (ii) a second portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein; wherein the control biological sample has not been treated with a test compound; (e) contacting the first and second complexes
  • An embodiment of the invention provides a method of testing compounds for ability to cause DNA DSBs in a host, the method comprising: (a) contacting (i) a first portion of a control biological sample and (ii) a first portion of a host biological sample with an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ and forms a first complex with the ⁇ - ⁇ 2 ⁇ , wherein the host biological sample is from a host which has been administered a test compound; (b) contacting (i) a second portion of the control biological sample and (ii) a second portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the control biological sample has not been exposed to the test compound; (c) contacting the first and second complexes of the control biological sample and the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2
  • Figure 1A is a graph (standard curve) showing the net readout (Relative Light Units (RLU) minus (-) Background (Bkg)) detecting various concentrations of ⁇ - ⁇ 2 ⁇ (pM) using chemiluminescent enzyme-linked immunosorbant assay (ELISA).
  • Samples contained the standard ⁇ 2 ⁇ peptide at zero, 5, 10, 20, 40, 80, 160, 320 and 640 pM.
  • Figure IB is a graph showing the independence of standard curve values on sample composition.
  • a well-characterized and quantified extract was diluted to 10 pM (diamonds), 20 pM (triangles), or 40 pM (circles) ⁇ - ⁇ 2 ⁇ . Aliquots of each dilution were spiked with amounts of the standard ⁇ 2 ⁇ peptide to 5, 10, 20, 40, 80, and 160 pM. After the assay, the readouts were converted to ⁇ 2 ⁇ peptide concentrations. Solid lines represent measured values of ⁇ 2 ⁇ peptide concentrations after subtraction of input extract concentrations. Dashed lines represent measured values of extract concentrations of ⁇ 2 ⁇ after subtraction of input standard concentrations.
  • Figure 2A is a graph (standard curve) showing the net readout (RLU - Bkg) detecting various concentrations of H2AX (pM) using chemiluminescent ELISA.
  • Samples contained the standard H2AX protein at zero, 50, 100, 200, 400, 800, 1600, 3200 and 6400 pM.
  • the background (Bkg) with zero pM standard is about 500,000 RLU.
  • Figure 2B is a graph showing the independence of standard curve values on sample composition.
  • a well-characterized and quantified extract was diluted to 250 pM (diamonds), 500 pM (triangles), or 1000 pM (circles) H2AX. Aliquots of each dilution were spiked with amounts of the standard H2AX protein peptide to zero, 100, 200, 400, 800, 1600 and 3200 pM. After the assay, the readouts were converted to H2AX protein concentrations. Solid lines represent measured values of H2AX protein concentrations after subtraction of input extract concentrations. Dashed lines represent measured values of extract
  • Figures 3A and 3B are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (%) detected in HCT1 16 cells (triangles), MCF7 cells (squares), or THP1 cells (diamonds) that had been treated with various doses of IR (Gy).
  • the region below 10 Gy in Figure 3 A is expanded in Figure 3B.
  • Figure 4A is a graph showing the concentration of ⁇ - ⁇ 2 ⁇ (pM) detected per 1 x 10 7 /mL of THP1 (diamonds) or HCT1 16 (triangles) cancer cells that had been treated with various concentrations of topotecan ( ⁇ ).
  • Figure 4B is a graph showing the percentage (%) of ⁇ - ⁇ 2 ⁇ per total H2AX in HCT1 16 cells (triangles) or THP1 cells (diamonds) that had been treated with various concentrations of topotecan ( ⁇ ).
  • Figure 5 is a graph comparing ⁇ - ⁇ 2 ⁇ (black bars) ( ⁇ - ⁇ 2 ⁇ pM per 1E7 cells/mL) and y-H2AX/Total H2AX (grey bars) (percentage (%) of ⁇ - ⁇ 2 ⁇ per total H2AX) for a selection of cell lines from the NCI60 tumor panel. Bars are arranged in increasing order of ⁇ - ⁇ 2 ⁇ value to demonstrate the effect of normalizing the ⁇ - ⁇ 2 ⁇ value to total H2AX.
  • Figures 6A-6C are graphs showing ⁇ - ⁇ 2 ⁇ (pM) (A), H2AX (pM) (B), and ⁇ - H2AX/Total H2AX (%) (C) values measured at two different dilutions of extract from 1E7 cells/mL THP1 cells, 1 to 25 (dashed line) and 1 to 50 (solid line).
  • Figures 7A-7C are graphs showing the ⁇ - ⁇ 2 ⁇ (pM/ 10 mg protein/mL) (A), total H2AX (pM/10 mg protein/mL) (B) and y-H2AX/Total H2AX (%) (C) values measured in biopsy samples from nude xenograft mice with human breast cancer tumors at various time points (hours) after administration of carrier (control) (diamonds), 7.5 units of irinotecan delivered intravenously (17.5 IV) alone (squares) or in combination with either 50 (triangles) or 6.25 (circles) units of AZD2281 delivered intraperitoneally (IP).
  • Figures 8A-8F are graphs showing the amounts of ⁇ - ⁇ 2 ⁇ ( ⁇ /1 ⁇ 7 cells/mL) (A and D) and total H2AX (pM/lE7 cells/mL) (B and E) and the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (%) (C and F) measured in peripheral blood mononuclear cells in archived blood samples from two patients (Patient A (A-C) and Patient B (D-F)) at various time points (hours) after drug administration.
  • Figures 9A-9F are graphs showing the amounts of ⁇ - ⁇ 2 ⁇ ( ⁇ /1 ⁇ 7 cells/mL) (A and D) and total H2AX (pM/10 mg protein/mL) (B and E) and the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (%) (C and F) measured in archived patient bone marrow samples (A-C) and tumor biopsies (D-F) taken at various time points after drug administration.
  • Figures 9A-9C Bone marrow samples were obtained from patients undergoing treatment before drug
  • FIGS 9D-F Tumor biopsies were obtained before (pre) and after drug administration (post).
  • Figures 1 OA and 10B are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (%) detected in normal human fibroblasts that were exposed to various amounts of ionizing radiation (IR) (Gy). The region below 1 Gy in Figure 10A is expanded in Figure 10B.
  • Figure 1 1 is a graph showing the percentage (%) of ⁇ - ⁇ 2 ⁇ per total H2AX detected in untreated HT29 cells (control) or HT29 cells that were treated with single drugs (CPT, AZD6738 (AZD) or VE821 (VE)), or combinations of CPT plus AZD6738 or VE821.
  • Figures 12A and 12B are graphs showing the percentage (%) of ⁇ - ⁇ 2 ⁇ per total H2AX detected in normal PBMC (diamonds) or PBMC that had been mixed with various numbers of THPl tumor cells (spiked tumor cells) that had not been exposed to IR (squares) or tumor cells that had been exposed to 10 Gy (circles) or 1 Gy (triangles) of IR.
  • THPl tumor cells spikeked tumor cells
  • 10 Gy circles
  • 1 Gy triangles
  • Figures 12C and 12D are graphs showing the percentage (%) of ⁇ - ⁇ 2 ⁇ per total H2AX detected in normal PBMC (diamonds) or PBMC that had been mixed with various numbers of HT29 tumor cells (spiked tumor cells) that were untreated (squares) or treated with ATR inhibitors VE-821 and camptothecin (CPT) (triangles).
  • the region below 10% ⁇ - H2AX per total H2AX in Figure 12C is expanded in Figure 12D.
  • Figure 13 is a graph showing the ratio of ⁇ - ⁇ 2 AX to total H2AX measured in HT29 cells which were treated with the indicated concentrations of camptothecin (CPT) (diamonds) or rhomidepsin (triangles).
  • CPT camptothecin
  • rhomidepsin triangles
  • Figure 14A is a graph showing the quantity of ⁇ - ⁇ 2 ⁇ (pM) measured in the indicated number of cells per well following treatment with CPT at a concentration of 0 ⁇ (vehicle) (asterisks), 0.01 ⁇ (squares), 0.1 ⁇ (triangles) or 1 ⁇ (diamonds).
  • Figure 14B is a graph showing the quantity of total H2AX (pM) measured in the indicated number of cells per well following treatment with CPT at a concentration of 0 ⁇ (vehicle) (asterisks), 0.01 ⁇ (squares), 0.1 ⁇ (triangles) or 1 ⁇ (diamonds).
  • Figure 14C is a graph showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX measured in the indicated number of cells per well following treatment with CPT at a concentration of 0 ⁇ (vehicle) (asterisks), 0.01 ⁇ (squares), 0.1 ⁇ (triangles) or 1 ⁇ (diamonds).
  • Figure 15 is a graph showing the quantity of ⁇ - ⁇ 2 ⁇ per 1x10 HT29 cells/mL (grey bars) or lxl 0 7 MCF7 cells/mL (striped bars) treated with vehicle (control) or the drug CPT, SN38, LMP776, LMP744, LMP400, AZD1775, cisplatin, etoposide, doxorubicin, talazoparib, olaparib, viromostat, erlotinib, or rhomidepsin.
  • Figure 16 is a graph showing the quantity of total H2AX per lxlO 7 HT29 cells/mL (grey bars) or l l 0 7 MCF7 cells/mL (striped bars) treated with vehicle (control) or the drug CPT, SN38, LMP776, LMP744, LMP400, AZD1775, cisplatin, etoposide, doxorubicin, talazoparib, olaparib, viromostat, erlotinib, or rhomidepsin.
  • Figures 17A and 17B are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX measured in HT29 cells (A) or MCF7 cells before (Pre) or after (Post) treatment with camptothecin (grey squares), SN38 (grey diamonds), LMP776 (grey triangles), LMP744 (grey asterisks), LMP400 (grey circles), AZD1775 (grey X), cisplatin (grey -J-), etoposide (black squares), doxorubicin (black diamonds), talazoparib (black triangles), olaparib (black asterisks), viromostat (black circles), erlotinib (black X), or rhomidepsin (black -J-).
  • Figures 18A and 18B are graphs showing the intensity of staining for ⁇ - ⁇ 2 ⁇ using an anti-y-H2AX antibody (microscope immunofluorescence assay (IFA)) (shaded bars) and the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (ELISA immunoassay (IA)) (striped bars) measured in HT29 cells (A) or MCF7 cells (B).
  • IFA microscope immunofluorescence assay
  • IA ELISA immunoassay
  • Figures 19A-19C are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) (B), or the quantity of total H2AX (pM per 1 x 10 7 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 ⁇ SN38 (squares), 1 ⁇ AZD-6738 (triangles), a combination of 0.25 ⁇ SN38 and 1 ⁇ AZD-6738 (X), or a combination of 0.25 ⁇ SN38 and 0.5 ⁇ AZD-6738 (asterisks).
  • Figures 20A-20C are. graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) (B), or the quantity of total H2AX (pM per 1 x 10 7 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 ⁇ SN38 (squares), 1 ⁇ VE-821 (triangles), a combination of 0.25 ⁇ SN38 and 1 ⁇ VE-821 (X), or a combination of 0.25 ⁇ SN38 and 0.5 ⁇ VE-821 (asterisks).
  • Figures 21A-21C are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) (B), or the quantity of total H2AX (pM per 1 x 10 7 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 ⁇ SN38 (squares), 1 ⁇ VE-822 (triangles), a combination of 0.25 ⁇ SN38 and 1 ⁇ VE-822 (X), or a combination of 0.25 ⁇ SN38 and 0.5 ⁇ VE-822 (asterisks).
  • Figures 22A-22C are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) (B), or the quantity of total H2AX (pM per 1 x 10 7 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 ⁇ SN38 (squares), 1 ⁇ Compound-45 (triangles), a combination of 0.25 ⁇ SN38 and 1 ⁇ Compound-45 (X), or a combination of 0.25 ⁇ SN38 and 0.5 ⁇ Compound-45 (asterisks).
  • Figures 23A-23C are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) (B), or the quantity of total H2AX (pM per 1 x 10 7 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 ⁇ SN38 (squares), 1 ⁇ NU-6027 (triangles), a combination of 0.25 ⁇ SN38 and 1 ⁇ NU-6027 (X), or a combination of 0.25 ⁇ SN38 and 0.5 ⁇ NU-6027 (asterisks).
  • Figures 24A-24C are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) per ⁇ g protein (B), or the quantity of total H2AX (pM per ⁇ g protein) (C) measured in cell lysate isolated from A375 xenograft mouse models treated with vehicle (control), CPT-1 1 (7.5 mg/kg), MK4827 (50 mg/kg), M 4827 (12.5 mg/kg), a combination of CPT-1 1 (7.5 mg/kg) and MK4827 (50 mg/kg) administered simultaneously, a combination of CPT-1 1 (7.5 mg/kg) and MK4827 (12.5 mg/kg) administered simultaneously, MK4827 (7.5 mg/kg) administered four hours prior to CPT-1 1 (50 mg/kg), or MK4827 (7.5 mg/kg) administered four hours prior to CPT-1 1 (12.5 mg/kg).
  • Figures 25A-25C are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) per ⁇ g protein (B), or the quantity of total H2AX (pM per ⁇ g protein) (C) measured in cell lysate isolated from A375 xenograft mouse models treated with vehicle (control), CPT-11 (7.5 mg/kg), AZD2281 (50 mg/kg), AZD2281 (6.25 mg/kg), a combination of CPT-11 (7.5 mg/kg) and AZD2281 (50 mg/kg) administered simultaneously, a combination of CPT-1 1 (7.5 mg kg) and AZD2281 (6.25 mg/kg) administered
  • AZD2281 50 mg/kg administered four hours prior to CPT-1 1 (7.5 mg/kg), or AZD2281 (6.25 mg/kg) administered four hours prior to CPT-11 (7.5 mg/kg).
  • Figures 26A-26C are graphs showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX (A), the quantity of ⁇ - ⁇ 2 ⁇ (pM) per ⁇ g protein (B), or the quantity of total H2AX (pM per ⁇ g protein) (C) measured in cell lysate isolated from A375 xenograft mouse models treated with vehicle (control), CPT-1 1 (7.5 mg/kg), ABT888 (50 mg/kg), ABT888 (12.5 mg/kg), a combination of CPT-1 1 (7.5 mg/kg) and ABT888 (50 mg/kg) administered simultaneously, a combination of CPT-11 (7.5 mg/kg) and ABT888 (12.5 mg/kg) administered simultaneously, ABT888 (7.5 mg/kg) administered four hours prior to CPT-11 (50 mg/kg) and, or ABT888 (7.5 mg/kg) administered four hours prior to CPT-1 1 (12.5 mg/kg).
  • Figure 27A is a graph showing the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX measured by immunoassay (IA) in cells isolated from A375 xenograft mice that were treated with vehicle (control), CPT-1 1 , ABT-888 (ABT), AZD-2281 (AZD), or MK-4827 (MK), a combination of CPT-11 with ABT-888, a combination of CPT-11 with AZD-2281, or a combination of CPT- 1 1 with MK-4827, at the indicated dosages.
  • IA immunoassay
  • Figure 27B is a graph showing the quantity of ⁇ - ⁇ 2 ⁇ measured by
  • IF A immunofluorescence assay
  • Figure 27C is a graph showing PAR inhibition (pg ⁇ g protein/mL) measured by immunoassay (IA) in cells isolated from A375 xenograft mice that were treated with vehicle (control), CPT-1 1 , ABT-888 (ABT), AZD-2281 (AZD), or MK-4827 (MK), a combination of CPT-1 1 with ABT-888, a combination of CPT-1 1 with AZD-2281 , or a combination of CPT- 1 1 with MK-4827, at the indicated dosages.
  • IA immunoassay
  • the methods and kits of the invention provide many advantages. For example, because the inventive methods and kits quantify both ⁇ - ⁇ 2 ⁇ and total H2AX, the inventive methods and kits may provide an accurate biodosimetric measurement of the amount of exposure of a host to a DNA DSB-causing agent. The inventive methods and kits also may provide the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX in a sample independent of any one or more of cell type, cell number, cell viability, cell lysis efficiency, and laboratory operator variability. In the inventive methods and kits, total H2AX may advantageously serve as an internal control that may account for differences in sample quality that may have arisen due to any one or more of specimen collection, storage, shipping, sample processing, extract preparation, and ELIS A testing.
  • inventive methods and kits include any one or more of lower background signals, greater sensitivity, and the ability to test patient tissue samples.
  • the inventive methods and kits may provide a quantitative range of about 100-fold for both ⁇ - ⁇ 2 ⁇ and total H2AX.
  • the inventive methods and kits may also provide a sensitivity of at least about 5 pM for ⁇ - ⁇ 2 ⁇ and at least about 50 pM for total H2AX.
  • the inventive methods and kits may also advantageously measure an actual amount of protein (e.g., actual pictograms) as opposed to merely providing relative values of proteins.
  • inventive methods and kits may employ an immobilized antibody or antigen binding fragment thereof to capture total H2A core protein and ⁇ - ⁇ 2 ⁇ , which may reduce or eliminate the need to purify the antigen from complex mixtures prior to analysis, which may simplify the methods and increase the specificity and sensitivity of the methods.
  • inventive methods and kits may provide a standardized clinical assay that can be used as a biodosimeter.
  • the inventive methods may, advantageously, be completed rapidly (for example, within about one working day, less than about one working day, or more than about one working day).
  • the inventive methods may, advantageously screen agents for the ability to cause DNA DSB after a short treatment with the agent(s) to be screened in vitro (e.g., about 1 hr, less than about 1 hr, more than about 1 hr).
  • the inventive methods may, for example, be suitable for high-throughput screening (for example, about 100 to about 5000 cells per well) and may be carried out using a plate-based immunoassay, for example, a 96/384 plate-based immunoassay.
  • the inventive methods and kits may also be compatible with other, additional assays in order to, for example, further identify potential downstream targets and carry out mechanistic and molecular studies (e.g., PARP1 assays, Topi assays, and LUMINEX protein assays for apoptosis (Invitrogen, Waltham, MA)).
  • WB Western Blot
  • the inventive methods and kits may also be compatible with other, additional assays in order to, for example, further identify potential downstream targets and carry out mechanistic and molecular studies (e.g., PARP1 assays, Topi assays, and LUMINEX protein assays for apoptosis (Invitrogen, Waltham, MA)).
  • inventive methods provide a more comprehensive measurement of DNA DSB because the inventive methods cover ⁇ - ⁇ 2 ⁇ formed by multiple biochemical enzymatic targets and pathways.
  • the inventive methods and kits may also advantageously overcome one or more obstacles to obtaining an accurate biodosimetric measurement using other methods such as those that involve counting "nuclear foci" through a microscope.
  • Nuclear foci refer to areas surrounding the DSB, which may be microscopically detected and counted using an anti-y-H2AX antibody.
  • each focus contains a certain percentage of the total nuclear H2AX, and the total H2AX content may vary from cell type to cell type, methods that involve counting nuclear foci lack the total H2AX value necessary to convert those data into biodosimetric measurements.
  • the inventive methods and kits may be any suitable for a microscope.
  • An embodiment of the invention provides a method of measuring the amount of exposure of a host to a DNA DSB-causing agent.
  • the DNA DSB-causing agent may be any agent that causes DNA DSBs.
  • Non-limiting examples of DNA DSB-causing agents include IR (such as, for example, X-rays and gamma rays), environmental agents such as, for example, ultraviolet (UV) light, reactive oxygen species, mutagenic chemicals, cigarette smoke, and radiation from, for example, cell phones, and drugs such as, for example, anticancer agents (e.g., bleomycin and topotecan).
  • IR such as, for example, X-rays and gamma rays
  • environmental agents such as, for example, ultraviolet (UV) light, reactive oxygen species, mutagenic chemicals, cigarette smoke, and radiation from, for example, cell phones
  • drugs such as, for example, anticancer agents (e.g., bleomycin and topotecan).
  • the method may comprise contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to phosphorylated H2AX (gamma ( ⁇ )- ⁇ 2 ⁇ ) and forms a first complex with the ⁇ - ⁇ 2 ⁇ .
  • the biological samples may comprise any suitable biological sample.
  • the biological samples can comprise any solubilized homogenate or extract from any suitable biological material.
  • suitable biological material include tissues, serum, plasma, urine, sputum, saliva, whole cells, cell lysate, or a fraction of the cell lysates, e.g., a nuclear or cytoplasmic fraction, a whole protein fraction, or an acid extract of histones.
  • the cells can be any cells of the host, e.g., the cells of any organ or tissue, including blood cells or cancer cells.
  • the cells may be hair bulb cells. Hair bulbs contain dividing cells and are believed to be more sensitive to drug effects.
  • the source material may be from any eukaryotic source such as, for example, invertebrates (such as, for example, yeast), and vertebrates.
  • the biological samples comprise cell lysate.
  • the biological samples comprise cell lysate from no more than a single cell type.
  • the biological samples comprise cell lysates from two or more cell types, for example, normal and abnormal tissues, such as those in a tumor biopsy.
  • the biological sample is a cancer cell or a lysate of a cancer cell.
  • the positive control biological sample is preferably identical to the biological sample from the host with the exception that the positive control biological sample has been exposed to a known amount of the DSB-causing agent.
  • the host may be any eukaryote such as, for example, an invertebrate (such as, for example, yeast) or vertebrate. Mammals are the preferred host.
  • the mammalian host may be, for example, of the order Rodentia, such as mice and hamsters, or of the order Logomorpha, such as rabbits.
  • the host may be from the order Carnivora, including Felines (cats) and Canines (dogs).
  • the host may be from the order Artiodactyla, including Bovines (cows) and S wines (pigs) or of the order Perssodactyla, including Equines (horses).
  • the host may be of the order Primates, Ceboids, or Simoids (monkeys) or of the order Anthropoids (humans and apes). Most preferably, the host is a human.
  • anti-y-H2AX antibody The antibody and antigen binding fragment thereof that specifically bind to ⁇ - H2AX are also collectively referred to herein as "anti-y-H2AX antibody” or "anti-y-H2AX antibodies.”
  • the anti-y-H2AX antibody binds to ⁇ - ⁇ 2 ⁇ with measurably higher affinity to ⁇ - ⁇ 2 ⁇ than to other molecules.
  • the anti-y-H2AX antibody may specifically bind to the carboxyl terminus of ⁇ - ⁇ 2 ⁇ (SEQ ID NO: 1 , wherein the serine in the first position of SEQ ID NO: 1 is phosphorylated), and does not bind to the carboxyl terminus of non-phosphorylated H2AX (SEQ ID NO: 3, wherein the serine in the first position of SEQ ID NO: 3 is not phosphorylated).
  • the anti-y-H2AX antibody may specifically bind to ⁇ - ⁇ 2 ⁇ (SEQ ID NO: 2, wherein the serine at position 27 of SEQ ID NO: 2 is phosphorylated), and does not bind to non- phosphorylated H2AX (SEQ ID NO: 4, wherein the serine at position 27 of SEQ ID NO: 3 is not phosphorylated).
  • Suitable anti-y-H2AX antibodies are described in U.S. Patent Nos. 6,884,873 and 6,362,317, each of which is incorporated by reference herein in its entirety.
  • Anti-y-H2AX antibodies are also commercially available (from, for example, Millipore (Billerica, MA)).
  • the contacting may take place in vitro or in vivo with respect to the host, preferably, the contacting is in vitro.
  • Contacting a biological sample with the anti-y-H2AX antibody may comprise physically contacting the biological sample with the anti-y-H2AX antibody such that the anti-y-H2AX antibody binds to ⁇ - ⁇ 2 ⁇ that is present in the sample.
  • the binding of the anti-y-H2AX antibody to the ⁇ - ⁇ 2 ⁇ forms a first complex that comprises the ⁇ - ⁇ 2 ⁇ bound to the anti-y-H2AX antibody.
  • the method may further comprise contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein.
  • the antibody and antigen binding fragment thereof that specifically bind to the H2A core protein are also collectively referred to herein as "anti-H2A core protein antibody” or "anti-H2A core protein antibodies.”
  • the anti-H2A core protein antibody binds to H2A core protein with measurably higher affinity to H2A core protein than to other molecules.
  • the anti-H2A core protein antibody specifically binds to H2A core protein that is present in the sample, such as, for example, H2A1 , H2A2, H2AX (both phosphorylated and non- phosphorylated), and H2AZ.
  • the anti-H2A core protein antibody captures all H2A proteins that are present in the biological sample (total H2A), including H2AX (both phosphorylated and non-phosphorylated).
  • the second complex may comprise anti-H2A core protein antibody bound to phosphorylated or non-phosphorylated H2AX.
  • Anti-H2A core protein antibodies are commercially available from companies such as, for example, Novus (St. Charles, MO).
  • Contacting a biological sample with the anti-H2A core protein antibody may comprise physically contacting the biological sample with the anti-H2A core protein antibody such that the anti-H2A core protein antibody binds to H2A core protein that is present in the sample.
  • the binding of the anti-H2A core protein antibody with the anti-H2A core protein forms a second complex that comprises the H2A core protein bound to the anti-H2A core protein antibody.
  • the contacting of the biological sample(s) with the anti-y-H2AX antibody and the contacting of the biological sample(s) with the anti-H2A core protein antibody may take place simultaneously or in any sequence.
  • a substrate such as, for example, a multi-well plate, is coated with both the anti-y-H2AX antibody and the anti-H2A core protein antibody.
  • the anti-y-H2AX antibody and the anti-H2A core protein antibody are applied to separate wells of a multi-well plate.
  • a biological sample may be added to the coated surfaces of the wells so that the anti-y-H2AX antibody and the anti-H2A core protein antibody specifically bind to their respective antigens simultaneously or sequentially.
  • the anti-y-H2AX antibody and the anti- H2A core protein antibody are coated onto separate substrates. A portion of a biological sample may be added to the coated surface of each substrate so that anti-y-H2AX antibody and the anti-H2A core protein antibody specifically bind to their respective antigens simultaneously or sequentially.
  • the method comprises contacting the biological sample(s) with the anti-y-H2AX antibody prior to contacting of the biological sample(s) with the anti-H2A core protein antibody.
  • the method comprises contacting the biological sample(s) with the anti-y-H2AX antibody after contacting of the biological sample(s) with the anti-H2A core protein antibody.
  • the method comprises washing any unbound anti-y-H2AX antibody and any unbound anti-H2A core protein antibody from the first and second complexes, respectively.
  • the method may further comprise contacting the first and second complexes of the positive control biological sample and the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex.
  • the antibody and antigen binding fragment thereof that specifically bind to H2AX are also collectively referred to herein as "anti-H2AX antibody” or "anti-H2AX antibodies.”
  • the anti-H2AX antibody binds H2AX with measurably higher affinity to H2AX than to other molecules.
  • the anti-H2AX antibody specifically binds to H2AX that is present in the sample, including phosphorylated H2AX and non-phosphorylated H2AX.
  • the anti-H2AX antibody captures all H2AX proteins that are present in the biological sample (total H2AX).
  • Anti-H2AX antibodies for most mammals are commercially available (for example, Abeam (San Francisco, CA)).
  • Contacting the first and second complexes with the anti-H2AX antibody may comprise physically contacting the first and second complexes with the anti-H2AX antibody such that the anti-H2AX antibody binds to any H2AX that is present in the first and second complexes.
  • the binding of the anti-H2AX antibody to the first complex forms a third complex that comprises the H2AX of the first complex bound to the anti-H2AX antibody.
  • the binding of the anti-H2AX antibody to the second complex forms a fourth complex that comprises the H2AX of the second complex bound to the anti-H2AX antibody.
  • the fourth complex comprises the anti-H2AX antibody bound to any phosphorylated or non-phosphorylated H2AX that was captured by the anti-H2A core protein antibody.
  • the contacting of the first and second complexes with the anti-H2AX antibody may take place simultaneously or in any sequence.
  • the method may comprise contacting the first complex with the anti-H2AX antibody prior to contacting the second complex with the anti-H2AX antibody.
  • the method may comprise contacting the first complex with the anti-H2AX antibody after contacting the second complex with the anti-H2AX antibody.
  • the method comprises washing any unbound anti-H2AX antibody from the third and fourth complexes, respectively.
  • the method further comprises detecting the third and fourth complexes in the positive control biological sample and the biological sample from the host.
  • the third and fourth complexes may be detected in any suitable manner known in the art.
  • detecting the third and fourth complexes in the biological samples(s) comprises contacting each of the third and fourth complexes with a detecting agent.
  • the detecting agent may comprise, for example, an antibody or antigen binding fragment thereof that specifically binds to the third and fourth complex, respectively
  • detection antibody detection antibody
  • detection antibodies detection antibodies
  • the third and fourth complexes may be detected using the same detection antibody or different detection antibodies.
  • the detection antibody binds to the third or fourth complex (or both) with measurably higher affinity to the third or fourth complex (or both) than to other molecules.
  • the detection antibody specifically binds to the anti-H2AX antibody.
  • the detection antibody comprises a detectable label.
  • the detectable label may be any suitable detectable label that provides a detectable signal.
  • detectable labels include enzymes (e.g., alkaline phosphatase, horseradish peroxidase), fluorescent molecules (e.g., fluorescein isothiocyanate (FITC), phycoerythrin (PE)), luminescent molecules, dyes, biotin, and element particles (e.g., gold particles).
  • the detectable label is an enzyme
  • the method may further comprise adding a substrate to the third and fourth complexes that is catalyzed by the enzyme to produce a detectable signal.
  • the detectable signal may be amplified and/or visually detected. For example, acetylcholinesterase-catalyzed hydrolysis may be useful for colorimetric detection through gold or silver nanoparticle aggregation.
  • the antibodies for use in the inventive methods can be of any type.
  • any of the antibodies can be of any isotype, e.g., IgA, IgD, IgE, IgG, IgM, etc.
  • Any of the antibodies can be monoclonal or polyclonal.
  • Any of the antibodies can be a naturally-occurring antibody, e.g., an antibody isolated and/or purified from a mammal, e.g., mouse, rabbit, goat, horse, chicken, hamster, human, etc.
  • any of the antibodies can be a genetically-engineered antibody, e.g., a humanized antibody or a chimeric antibody. Any of the antibodies can be in monomelic or polymeric form.
  • the methods may employ an antigen binding fragment of any of the antibodies described herein.
  • the antigen binding fragment can be any portion of the antibody that has at least one antigen binding site.
  • the antigen binding fragment is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
  • a single-chain variable region fragment which is a truncated Fab fragment including the variable (V) domain of an antibody heavy chain linked to a V domain of a light antibody chain via a synthetic peptide, can be generated using routine recombinant DNA technology techniques (see, e.g., Murphy et al. (eds.), Murphy 's
  • disulfide- stabilized variable region fragments can be prepared by recombinant DNA
  • the antigen binding fragment of the antibody that specifically binds to ⁇ - ⁇ 2 ⁇ , H2A core protein, or H2AX is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
  • Fab Fab fragment
  • F(ab')2 fragment diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment
  • scFv single-chain variable region fragment
  • dsFv disulfide-stabilized variable region fragment
  • the method comprises washing any unbound detection antibody from the third and fourth complexes, respectively.
  • the method further comprises quantifying the third and fourth complexes in the positive control biological sample and the biological sample from the host.
  • the third and fourth complexes may be quantified in any suitable manner known in the art.
  • quantifying the third and fourth complexes comprises determining the amount of detectable label present.
  • the method may comprise determining the amount of fluorescence or luminescence provided by the detectable label.
  • the method further comprises determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host; and comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host to determine the amount of exposure of the host to the DNA DSB-causing agent.
  • comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the same in the biological sample from the host provides the amount of exposure of the host to a DNA DSB-causing agent.
  • Another embodiment of the invention provides a method of quantifying DNA DSBs in a test biological sample.
  • the method may comprise contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a test biological sample with an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ and forms a first complex with the ⁇ - ⁇ 2 ⁇ .
  • the test biological sample may be any suitable test biological sample.
  • the test biological sample may be a biological sample from a host, as described herein with respect to other aspects of the invention.
  • the positive control biological sample may also be as described herein with respect to other aspects of the invention except that the positive control biological sample has a known quantity of DSBs.
  • the anti-y-H2AX antibody, the first complex, and the contacting of the anti-y-H2AX antibody with the biological samples may be as described with respect to other aspects of the invention.
  • the method of quantifying DNA DSBs in a test biological sample may further comprise contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein.
  • the anti-H2A core protein antibody, the second complex, and the contacting of the anti-H2A core protein antibody with the biological samples may be as described with respect to other aspects of the invention.
  • the method of quantifying DNA DSBs in a test biological sample further comprises washing any unbound anti-y-H2AX antibody and any unbound anti-H2A core protein antibody from the first and second complexes, respectively.
  • the method of quantifying DNA DSBs in a test biological sample may further comprise contacting the first and second complexes of the positive control biological sample and the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex.
  • the anti-H2AX antibody, the third and fourth complexes, and the contacting of the anti-H2AX antibody with the first and second complexes may be as described herein with respect to other aspects of the invention.
  • the method of quantifying DNA DSBs in a test biological sample further comprises washing any unbound anti-H2AX antibody from the third and fourth complexes, respectively.
  • the method may further comprise comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample to determine the quantity of DSBs in the test biological sample. Because the positive control biological sample has a known quantity of DSBs, comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample provides the quantity of DSBs in the test biological sample.
  • kits that may be useful for measuring the amount of exposure of a host to a DNA DSB-causing agent and/or quantifying DNA DSBs in a test biological sample.
  • the kit may comprise at least one substrate.
  • the kit may comprise one, two, three four, five, six, or more substrates.
  • the kit comprises two substrates, including a first substrate for testing a test biological sample or a biological sample from a host and a second substrate for testing a positive control biological sample.
  • the substrate is a plate, e.g., a multiwell plate.
  • the kit may further comprise an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ , an antibody or antigen binding fragment thereof that specifically binds to H2A core protein, and an antibody or antigen binding fragment thereof that specifically binds to H2AX.
  • the anti-y-H2AX, anti-H2A core protein, and anti-H2AX antibodies and antigen binding fragments thereof may be as described herein with respect to other aspects of the invention.
  • the antigen binding fragment of the antibody that specifically binds to ⁇ - ⁇ 2 ⁇ , H2A core protein, or H2AX is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
  • the anti-y-H2AX and anti-H2A core protein antibody is affixed to the at least one substrate.
  • the kit may comprise a first substrate comprising an anti-y-H2AX antibody affixed thereto and a second substrate comprising an anti-H2A core protein antibody affixed thereto.
  • the kit comprises a single substrate comprising both anti-y-H2AX and anti-H2A core protein antibodies affixed thereto.
  • anti-y-H2AX antibody may be affixed to each of a first set of one or more wells of the multiwell plate and anti-H2A core protein antibody may be affixed to a second set of one or more wells of the multiwell plate.
  • the substrate may be a multiwell plate in which the anti-y-H2AX antibody and the anti-H2A core protein antibody are affixed to separate wells.
  • the kit may further comprise a detecting agent comprising a label.
  • the detecting agent may be a detection antibody as described herein with respect to other aspects of the invention.
  • the detecting agent may be an antibody or antigen binding fragment thereof that specifically binds to the antibody or antigen binding fragment thereof that specifically binds to H2AX.
  • the label may also be as described herein with respect to other aspects of the invention.
  • the label may be an enzyme, a fluorescent molecule, a dye, or biotin.
  • the kit may further comprise a reagent for facilitating the binding of one or more of the anti-y-H2AX antibody, anti-H2A core protein antibody, and anti-H2AX antibody to the ⁇ - ⁇ 2 ⁇ , H2A core protein, and H2AX, respectively.
  • the kit may further comprise a reagent for facilitating detection of the detecting agent (e.g., a substrate that reacts with an enzyme to provide a detectable signal).
  • the kit may further comprise one or more protamines (small nuclear proteins) which may, advantageously, decrease non-specific binding and/or increase signal-to-background ratio.
  • the kit may also comprise other materials and reagents commonly employed in immunochemical test kits.
  • the inventive methods and kits may be useful for monitoring drug therapies, such as anti-cancer therapy, in a patient.
  • Quantifying DNA DSBs or measuring the amount of exposure of a host to a DNA DSB-causing agent according to the inventive methods may, for example, indicate a need to increase or decrease the dosage of the drug, e.g., anti-cancer agent.
  • Another embodiment of the invention provides a method of screening test compounds for ability to cause DNA DSBs.
  • the method may comprise dividing a population of test biological samples into more than one test sub-population.
  • the test biological samples are divided into at least two sub-populations. Dividing the test biological samples into more than one sub-population may be carried out in any suitable manner.
  • the test biological samples may be divided by being placed in different wells of multi-well plates.
  • the test biological sample may be as described herein with respect to other aspects of the invention.
  • the method may further comprise treating each test sub-population with a test compound, wherein each test sub-population is treated with a different test compound.
  • the test compound(s) may, for example, be obtained from a library.
  • the library may comprise any collection of two or more test compounds that is believed to possibly contain one or more compounds that may cause DNA DSBs.
  • Each sub-population may be treated with a different test compound such that the ability of each compound to cause DNA DSBs may be evaluated.
  • the method may further comprise contacting (i) a first portion of each treated test sub-population and (ii) a first portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ and forms a first complex with the ⁇ - ⁇ 2 ⁇ ; contacting (i) a second portion of each treated test sub-population and (ii) a second portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein; and contacting the first and second complexes of the control biological sample and the treated test sub-populations with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex.
  • the antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ ; the antibody or antigen binding fragment thereof that specifically binds to an H2A core protein; the antibody or antigen binding fragment thereof that specifically binds to H2AX; the first, second, third, and fourth complexes; and the contacting may be as described herein with respect to other aspects of the invention.
  • the control biological sample may be identical to the test biological sample with the exception that the control biological sample has not been treated with a test compound.
  • the method may further comprise detecting the third and fourth complexes in the control biological sample and the treated test sub-populations; quantifying the third and fourth complexes in the control biological sample and the treated test sub-populations;
  • determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub-populations.
  • the detecting, quantifying, and determining of the ratio may be carried out as described herein with respect to other aspects of the invention.
  • the method may further comprise comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub- populations, wherein an increase in the ratio in a treated test sub-population as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs.
  • the comparing may be carried out as described herein with respect to other aspects of the invention.
  • Another embodiment of the invention provides a method of testing compounds for ability to cause DNA DSBs in a host.
  • the method may comprise administering a test compound to the host and obtaining a biological sample from the host after the host has been administered the test compound.
  • the host, the biological sample from the host, and the test compounds may be as described herein with respect to other aspects of the invention.
  • the method may further comprise contacting (i) a first portion of a control biological sample and (ii) a first portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ and forms a first complex with the ⁇ - ⁇ 2 ⁇ ; contacting (i) a second portion of the control biological sample and (ii) a second portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the control biological sample has not been exposed to the test compound; and contacting the first and second complexes of the control biological sample and the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex.
  • the antibody or antigen binding fragment thereof that specifically binds to ⁇ - ⁇ 2 ⁇ ; the antibody or antigen binding fragment thereof that specifically binds to an H2A core protein; the antibody or antigen binding fragment thereof that specifically binds to H2AX; the first, second, third, and fourth complexes; and the contacting may be as described herein with respect to other aspects of the invention.
  • the control biological sample may be identical to the biological sample from the host except that the control biological sample has not been exposed to the test compound.
  • the control biological sample may be obtained from a host that has not been administered a test compound or from the host prior to administering a test compound.
  • the method may further comprise detecting the third and fourth complexes in the control biological sample and the host biological sample; quantifying the third and fourth complexes in the control biological sample and the host biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample; and determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample.
  • the detecting, quantifying, and determining of the ratio may be carried out as described herein with respect to other aspects of the invention.
  • the method may further comprise comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample, wherein an increase in the ratio in the host biological sample as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs in the host.
  • the comparing may be carried out as described herein with respect to other aspects of the invention.
  • the methods of screening test compounds for ability to cause DNA DSBs and the methods of testing compounds for ability to cause DNA DSBs in a host may provide many advantages. For example, the methods may be useful for identifying and developing new drugs that cause DNA DSBs, which may be useful for treating any of a variety of different diseases, e.g., cancer.
  • the methods may be useful for testing any one or more of (1) whether alterations of a drug increase the drug's effectiveness for inducing DNA DSBs; (2) the mechanism(s) of drug-induced DNA DSBs and/or drug-induced effects on DNA DSB repair; (3) which cancer types are targeted by a particular drug, (4) whether a drug targets a protein involved in DNA DSB repair, (5) whether a drug targets a cancer associated with a mutated gene, e.g., a gene involved in DNA DSB repair, and (6) the effect of different combinations of drugs on DNA DSB repair.
  • the methods of testing compounds for ability to cause DNA DSBs in a host may be useful for determining whether a drug candidate causes DNA DSBs in tumor-bearing animals and/or cancer patients in clinical trials.
  • any of the inventive methods described herein may further comprise forming any of the complexes described herein in the presence of one or more protamines.
  • the one or more protamines may, advantageously, reduce non-specific binding and/or increase the signal-to-background ratio.
  • This example demonstrates the performance of the ⁇ - ⁇ 2 ⁇ immunoassay.
  • Anti-y-H2AX mouse monoclonal antibody, clone JBW301 (1 ⁇ g/ ⁇ L) Lot# DAM 1567248 (Millipore). Used at 1 :250 dilution.
  • Anti-histone H2AX rabbit polyclonal antibody (1.7 ⁇ g/ ⁇ L) Lot# 778559 (Abeam) Used at 1 :850 dilution.
  • HRP horseradish peroxidase
  • Pierce REACTI-BIND plates (96-well) (Thermo Scientific) were coated with anti- ⁇ - ⁇ 2 ⁇ antibody (Millipore) diluted to a concentration of 4 ⁇ g/mL in 0.1 M pH 9.6 carbonate buffer (Sigma- Aldrich, St. Louis, MO), 100 ⁇ , for 2 hours at 37°C.
  • the ⁇ - H2AX synthetic peptide standard or a whole-cell extract was added to each well and incubated for antigen capture overnight at 4°C.
  • Plates were incubated with 100 ⁇ of 2 ⁇ g/mL anti-histone H2AX rabbit polyclonal antibody (Abeam) diluted in 2% bovine serum albumin (BSA)/phosphate buffered saline (PBS) supplemented with 1 ihlmL mouse serum for 2 hours (h) at 24°C. Subsequently, 100 ⁇ HRP-conjugated affinity-purified goat anti-rabbit (KPL) was added at a final concentration of 1 ⁇ g/mL diluted in 2% BSA/PBS, supplemented with 1 mouse serum, and incubated for 1 hour at 24°C.
  • BSA bovine serum albumin
  • PBS phosphate buffered saline
  • KPL affinity-purified goat anti-rabbit
  • H2AX recombinant standard or whole-cell extract 250 pM, 500 pM, or 1,000 pM was added to each well and incubated for antigen capture overnight at 4°C. Plates were incubated with 100 ⁇ , ⁇ of 2 ⁇ g/mL total anti-histone H2AX rabbit polyclonal antibody (Abeam) diluted in 2% BSA/PBS supplemented with 1 ⁇ ⁇ ⁇ mouse serum for 2 h at 25°C.
  • the Low-C sample contained un-irradiated MCF7 cells diluted 1 :200 from a stock extract of 1E7 cells/mL while the Mid-C sample contained MCF7 cells diluted 1 :50 from the same stock extract.
  • the High-C sample contained SN12C cell extract diluted 1 :50 from a stock of 1 E7 cells/mL.
  • Human breast cancer cell lines HCT 1 16 or MCF 7 were cultured with 10% fetal bovine serum at 37 °C in a 5% C0 2 incubator. The cells were treated with the topoisomerase I inhibitor topotecan, the apoptosis-inducing biomolecule tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), or IR.
  • TNF tumor necrosis factor
  • TRAIL apoptosis-inducing ligand
  • IR apoptosis-inducing ligand
  • the ⁇ - ⁇ 2 ⁇ immunoassay ⁇ - ⁇ 2 ⁇ ELISA was compared with ⁇ - ⁇ 2 ⁇ detection by both Western blot and immunofluorescence assay (IFA).
  • This example demonstrates a method of determining the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX in cancer cells treated with IR or topotecan.
  • THP1 leukemia cells were treated with the various amounts of IR shown in Figures 6A-6C. Extracts at 1 x 10 7 cells/mL were prepared of each irradiated sample, and two dilutions, 1 to 25 (30,000 cells/sample) and 1 to 50 (15,000 cells/sample) were used to measure ⁇ - ⁇ 2 ⁇ (Figure 6A) and total H2AX ( Figure 6B) utilizing the ⁇ - ⁇ 2 ⁇
  • FIGS. 6A-6C show data from the two dilutions (1 :25 and 1 :50). Using the values obtained in Figures 6A- 6B, the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX was calculated and is shown in Figure 6C. As shown in Figure 6C, the assay is independent of sample size.
  • the concentration of total H2AX in the same extract used for the ⁇ 2 ⁇ determination was measured using the H2AX immunoassay of Example 2.
  • the ratio of ⁇ - H2AX to total H2AX was calculated for the HCT1 16 cells, MCF7 cells, and THP1 cells that had been treated with various doses of IR.
  • the results for THP1 are shown in Figure 6B.
  • the ⁇ - ⁇ 2 ⁇ ELISA functioned to determine the concentration of ⁇ - H2AX in extracts of cancer cells treated with IR.
  • the ⁇ - ⁇ 2 ⁇ and total H2AX immunoassays can be used to calculate the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX in cells treated with IR. This value is approximately proportional to the number of DNA DSBs induced per nucleus and can be interpreted in terms of radiosensitivity of the various cell lines while ⁇ 2 ⁇ values alone cannot.
  • Figure 3B shows the region below 10 Gy, the region relevant to human exposures in radiological accidents and cancer treatment.
  • the concentration of total H2AX in 1 x 10 7 HCT116 cells or THP1 cells that had been treated with various concentrations of topotecan was measured using the H2AX immunoassay of Example 2 (H2AX ELISA).
  • H2AX ELISA H2AX immunoassay of Example 2
  • the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX was calculated for the HCT1 16 cells and THP1 cells that had been treated with various concentrations of topotecan.
  • the results are shown in Figure 4B.
  • the ⁇ - ⁇ 2 ⁇ and total H2AX immunoassays can be used to calculate the ratio of ⁇ - ⁇ 2 ⁇ tp total H2AX in cells treated with topotecan. This value more accurately reflects the relative effects of topotecan on different cell lines than ⁇ 2 ⁇ values alone.
  • This example demonstrates a method of determining the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX in various types of cancer cells and tumor panels.
  • the ⁇ - ⁇ 2 ⁇ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 were used to determine the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX in various cancer cell types ( Figure 5 and Table 7) and tumor panels (Table 8). The results are shown in Figure 5 and Tables 7 and 8.
  • Example 1 The ⁇ - ⁇ 2 ⁇ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 were used to determine the ratio of basal concentrations of ⁇ - ⁇ 2 ⁇ to basal concentrations of total H2AX in a panel of 60 cancer cell lines (NCI 60), including six leukemia, nine non-small cell lung carcinoma, seven colon, six central nervous system, nine melanoma, seven ovarian, eight renal, two prostate, and six breast cancer cell lines.
  • NCI 60 cancer cell lines
  • the H2AX as the maximum percentage of total H2A was calculated.
  • the percentage values for H2AX out of total H2A generally agreed with those from other lines of research.
  • Bone marrow and tumor biopsy samples were taken from patients before treatment with drugs and at various time points after treatment. The samples were frozen and stored for later analysis. Cells from the stored samples were extracted and analyzed by the assays of Examples 1 and 2. The results are shown in Figures 9A-9C (bone marrow) and Figures 9D-9F (tumor biopsy). As shown in Figures 9C and 9F, the assays of Examples 1 and 2 can be used to measure the amount of ⁇ - ⁇ 2 ⁇ in archived bone marrow and tumor biopsies. [0122] The assays of Examples 1 and 2 were successfully used to measure the amount of ⁇ - ⁇ 2 ⁇ in the biospecimen types shown in Table 9.
  • Examples 1 and 2 is approximately 0.2 Gy.
  • AZD6738 or VE821 was added at 1 ⁇ , and the cells were cultured for an additional 7 hours. At the end of the eight (8) hour culture, the cells were harvested, extracted, and analyzed using the assays of Examples 1 and 2. The ratio of ⁇ - H2AX to total H2AX was calculated, and the results are shown in Figure 1 1. As shown in Figure 1 1 , the immunoassays of Examples 1 and 2 may be used to detect the synergistic cytotoxicity of drug combinations using the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX as a readout for DNA DSB breaks.
  • HT29 cells were treated with the genotoxic agent camptothecin (CPT) or the non- genotoxic agent rhomidepsin for 1 hour at a concentration of 0 (vehicle) 0.001 , 0.001 , 0.01 , 1 or 10 ⁇ .
  • CPT camptothecin
  • the cells were collected.
  • the ⁇ - ⁇ 2 ⁇ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 were used to determine the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX in the collected cells.
  • the results are shown in Figure 13.
  • DNA DSB as measured by the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX, was detected with CPT treatment as low as 1 nM.
  • no DNA DSB as measured by the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX, was detected following rhomidepsin treatment, even at a concentration as high as 10 ⁇ .
  • Example 1 demonstrates that the ⁇ - ⁇ 2 ⁇ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 provide a detectable signal of DNA DSB with as few as 160 cells when the cells are treated with a genotoxic agent at a concentration of 0.01 ⁇ or higher in vitro.
  • HT29 were treated with CPT for 1 hour at a concentration of 0 ⁇ (vehicle), 0.01 ⁇ , 0.1 ⁇ or 1 ⁇ .
  • the cells were collected and further diluted to 5000, 2500, 1250, 625, 312, or 156 cells per assay.
  • the ⁇ - ⁇ 2 ⁇ immunoassay of Example 1 was used to quantitate ⁇ - ⁇ 2 ⁇ ( Figure 14A) in the collected cells.
  • the total H2AX immunoassay of Example 2 was used to quantitate total H2AX ( Figure 14B) in the collected cells.
  • the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX in the collected cells was determined ( Figure 14C). As shown in Figure 14C, the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX provided a detectable signal of DNA DSB with as few as 160 cells when the cells were treated with CPT at a concentration of 0.01 ⁇ or higher.
  • the immunoassays of Examples 1 and 2 were tested for the ability to screen genotoxic agents, ⁇ - H2AX is a sensitive and early signal of any one or more of DNA DSB, DNA repair, and apoptosis, any one or more of which may lead to tumor killing. Therefore, the immunoassays of Examples 1 and 2 were used for high throughput screening of potential agents for genotoxins and therapeutics.
  • the genotoxic agents included Topi inhibitors, Top2 inhibitors, DNA crosslink formers, and blockers of one or more of DNA replication, DNA repair, and the cell cycle, as shown in Table 10.
  • HT29 or MCF7 cells were plated overnight and separately treated with vehicle (control) or the drug CPT, SN38, LMP776, LMP744, LMP400, AZD1775, cisplatin, etoposide, doxorubicin, talazoparib, olaparib, viromostat, erlotinib, or rhomidepsin under the conditions shown in Table 10.
  • Table 10 also indicates whether each drug is a genotoxic agent ("yes"), a non-genotoxic agent ("no"), or whether it is unknown whether the drug is a genotoxic agent ("?”).
  • the ⁇ - ⁇ 2 ⁇ immunoassay of Example 1 was used to quantitate ⁇ - H2AX ( Figure 15) per lxlO 7 collected cells.
  • the total H2AX immunoassay of Example 2 was used to quantitate total H2AX ( Figure 16) per lxlO 7 collected cells.
  • the ratio of ⁇ - H2AX to total H2AX in the HT29 cells ( Figure 17A) and the MCF7 cells ( Figure 17B) was determined.
  • DNA DSB as measured by the ratio of ⁇ - H2AX to total H2AX, was detected with genotoxic agent treatment.
  • no DNA DSB as measured by the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX, was detected following non- genotoxic agent treatment.
  • This example compares the detection of DNA DSB using a microscope immunofluorescence assay (IF A) to the detection of DNA DSB using the immunoassays (IA) of Examples 1 and 2.
  • the ⁇ - ⁇ 2 ⁇ in the cells treated as described in Example 14 was quantified by staining using a labeled anti-y-H2AX antibody and measuring the intensity of the staining observed through a microscope (immunofluorescence microscope assay (IF A)).
  • IF A immunofluorescence microscope assay
  • the quantity of ⁇ - ⁇ 2 ⁇ measured by staining intensity was compared to the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX measured by the immunoassays (IA) of Examples 1 and 2.
  • the results are shown in Figure 18A (HT29) and Figure 18B (MCF7).
  • MCF7 cells were treated with vehicle (control), SN38 (0.25 ⁇ ), ataxia- telangiectasia, a rad3-related protein (ATR) inhibitor (ATRi) (1 ⁇ ), a combination of SN38 (0.25 ⁇ ) and the ARTi (1 ⁇ ), or a combination of SN38 (0.25 ⁇ ) and the ARTi (0.5 ⁇ ).
  • the ATR inhibitor was AZD-6738, VE-821 , VE-822, Compound-45, or NU-6027.
  • the treated cells were quantified for ⁇ - ⁇ 2 ⁇ and total H2AX using the immunoassays of Examples 1 and 2, respectively, and the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX was determined.
  • A375 xenograft mouse models were treated with vehicle (control), CPT-11 alone, a PARP inhibitor alone, a combination of CPT-11 and the PARP inhibitor (PARPi) administered simultaneously, or a combination of CPT-1 1 and the PARPi, wherein the PARPi is administered four hours before CPT-1 1 is administered.
  • CPT-1 1 is a modified version of CPT, also referred to as ironotecan (CAMPTOSAR).
  • the PARP inhibitor was ABT-888, AZD-2281 , or MK-4827. The dosages are shown in Figures 24A-24C, Figures 25A-25C, and Figures 26A-26C.
  • This example compares the detection of DNA DSB using a microscope immunofluorescence assay (IF A) to the detection of DNA DSB using the immunoassays (IA) of Examples 1 and 2.
  • A375 xenograft mouse models were treated with vehicle (control), camptothecin- 1 1 (CPT-11) alone, a PARP inhibitor alone, or a combination of CPT-1 1 and the PARP inhibitor at the dosages indicated in Figures 27A-27C.
  • the PARP inhibitor was ABT-888, AZD-2281, or MK-4827.
  • Cells from the treated mice were quantified for ⁇ - ⁇ 2 ⁇ and total H2AX using the immunoassays of Examples 1 and 2, respectively, and the ratio of ⁇ - ⁇ 2 ⁇ to total H2AX was determined. The results are shown in Figure 27A.

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Abstract

Disclosed are methods of measuring the amount of exposure of a host to a DNA double-stranded break (DSB)-causing agent by determining the ratio of the quantity of γ-H2AX to the quantity of total H2AX in a biological sample from the host as compared to the ratio of the quantity of γ-H2AX to the quantity of total H2AX in a positive control biological sample that has been exposed to a known amount of a DSB-causing agent. Related kits and methods of quantifying DSBs in a test biological sample are also disclosed.

Description

METHODS AND KITS FOR MEASURING AND QUANTIFYING DNA DOUBLE- STRANDED BREAKS USING GAMMA-H2AX AND H2AX
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This patent application claims the benefit of U.S. Provisional Patent Application No. 62/1 10,764, filed February 2, 2015, which is incorporated by reference in its entirety herein.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED
ELECTRONICALLY
[0002] Incorporated by reference in its entirety herein is a computer-readable
nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 1 ,958 Byte ASCII (Text) file named "723004_ST25.TXT," dated February 1 , 2016.
BACKGROUND OF THE INVENTION
[0003] Exposure to ionizing radiation (IR) or other agents may cause DNA double- stranded breaks (DSBs). DNA DSBs may, potentially, damage living cells, tissues, or both, and may result in illness (for example, Acute Radiation Syndrome and cancer), death, or both. Identifying the amount of exposure to a DNA DSB-causing agent may be useful for determining the need for and nature of further testing and/or medical treatment. Accordingly, there is a need for improved methods and kits for measuring the amount of exposure of a host to a DNA DSB-causing agent.
BRIEF SUMMARY OF THE INVENTION
[0004] An embodiment of the invention provides a method of measuring the amount of exposure of a host to a DNA DSB-causing agent, the method comprising: contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to gamma (γ)-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ; contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the positive control biological sample has been exposed to a known amount of the DSB-causing agent; contacting the first and second complexes of the positive control biological sample and the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex; detecting the third and fourth complexes in the positive control biological sample and the biological sample from the host; quantifying the third and fourth complexes in the positive control biological sample and the biological sample from the host; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host; and comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host to determine the amount of exposure of the host to the DNA DSB-causing agent.
[0005] Another embodiment of the invention provides a method of quantifying DNA DSBs in a test biological sample, the method comprising: contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a test biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ; contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the positive control biological sample has a known quantity of DSBs; contacting the first and second complexes of the positive control biological sample and the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex; detecting the third and fourth complexes in the positive control biological sample and the test biological sample; quantifying the third and fourth complexes in the positive control biological sample and the test biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample; and comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample to determine the quantity of DSBs in the test biological sample.
[0006] Another embodiment of the invention provides a kit comprising: at least one substrate; an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ; an antibody or antigen binding fragment thereof that specifically binds to H2A core protein; an antibody or antigen binding fragment thereof that specifically binds to H2AX; and a detecting agent comprising a label.
[0007] Still another embodiment of the invention provides a method of testing compounds for ability to cause DNA DSBs in a host, the method comprising: (a)
administering a test compound to a host; (b) obtaining a biological sample from the host after the host has been administered the test compound; (c) contacting (i) a first portion of a control biological sample and (ii) a first portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ; (d) contacting (i) a second portion of the control biological sample and (ii) a second portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the control biological sample has not been exposed to the test compound; (e) contacting the first and second complexes of the control biological sample and the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex; (f) detecting the third and fourth complexes in the control biological sample and the host biological sample; (g) quantifying the third and fourth complexes in the control biological sample and the host biological sample; (h) detemiining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample; (i) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample; and (j) comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample, wherein an increase in the ratio in the host biological sample as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs in the host.
[0008] Another embodiment of the invention provides a method of screening test compounds for ability to cause DNA DSBs, the method comprising: (a) dividing a population of test biological samples into more than one test sub-population; (b) treating each test sub- population with a test compound, wherein each test sub-population is treated with a different test compound; (c) contacting (i) a first portion of each treated test sub-population and (ii) a first portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ; (d) contacting (i) a second portion of each treated test sub-population and (ii) a second portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein; wherein the control biological sample has not been treated with a test compound; (e) contacting the first and second complexes of the control biological sample and the treated test sub-populations with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex; (f) detecting the third and fourth complexes in the control biological sample and the treated test sub-populations; (g) quantifying the third and fourth complexes in the control biological sample and the treated test sub-populations; (h) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample; (i) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub-populations; and (j) comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub-populations, wherein an increase in the ratio in a treated test sub-population as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs.
[0009] An embodiment of the invention provides a method of testing compounds for ability to cause DNA DSBs in a host, the method comprising: (a) contacting (i) a first portion of a control biological sample and (ii) a first portion of a host biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ, wherein the host biological sample is from a host which has been administered a test compound; (b) contacting (i) a second portion of the control biological sample and (ii) a second portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the control biological sample has not been exposed to the test compound; (c) contacting the first and second complexes of the control biological sample and the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex; (d) detecting the third and fourth complexes in the control biological sample and the host biological sample; (e) quantifying the third and fourth complexes in the control biological sample and the host biological sample; (f) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample; and (g) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample; (h) comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample, wherein an increase in the ratio in the host biological sample as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs in the host.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
[0010] Figure 1A is a graph (standard curve) showing the net readout (Relative Light Units (RLU) minus (-) Background (Bkg)) detecting various concentrations of γ-Η2ΑΧ (pM) using chemiluminescent enzyme-linked immunosorbant assay (ELISA). Samples contained the standard γΗ2ΑΧ peptide at zero, 5, 10, 20, 40, 80, 160, 320 and 640 pM. The
background (Bkg) with zero pM standard is about 500,000 RLU.
[0011] Figure IB is a graph showing the independence of standard curve values on sample composition. A well-characterized and quantified extract was diluted to 10 pM (diamonds), 20 pM (triangles), or 40 pM (circles) γ-Η2ΑΧ. Aliquots of each dilution were spiked with amounts of the standard γΗ2ΑΧ peptide to 5, 10, 20, 40, 80, and 160 pM. After the assay, the readouts were converted to γΗ2ΑΧ peptide concentrations. Solid lines represent measured values of γΗ2ΑΧ peptide concentrations after subtraction of input extract concentrations. Dashed lines represent measured values of extract concentrations of γΗ2ΑΧ after subtraction of input standard concentrations. [0012] Figure 2A is a graph (standard curve) showing the net readout (RLU - Bkg) detecting various concentrations of H2AX (pM) using chemiluminescent ELISA. Samples contained the standard H2AX protein at zero, 50, 100, 200, 400, 800, 1600, 3200 and 6400 pM. The background (Bkg) with zero pM standard is about 500,000 RLU.
[0013] Figure 2B is a graph showing the independence of standard curve values on sample composition. A well-characterized and quantified extract was diluted to 250 pM (diamonds), 500 pM (triangles), or 1000 pM (circles) H2AX. Aliquots of each dilution were spiked with amounts of the standard H2AX protein peptide to zero, 100, 200, 400, 800, 1600 and 3200 pM. After the assay, the readouts were converted to H2AX protein concentrations. Solid lines represent measured values of H2AX protein concentrations after subtraction of input extract concentrations. Dashed lines represent measured values of extract
concentrations of H2AX after subtraction of input standard concentrations.
[0014] Figures 3A and 3B are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (%) detected in HCT1 16 cells (triangles), MCF7 cells (squares), or THP1 cells (diamonds) that had been treated with various doses of IR (Gy). The region below 10 Gy in Figure 3 A is expanded in Figure 3B.
[0015] Figure 4A is a graph showing the concentration of γ-Η2ΑΧ (pM) detected per 1 x 107 /mL of THP1 (diamonds) or HCT1 16 (triangles) cancer cells that had been treated with various concentrations of topotecan (μΜ).
[0016] Figure 4B is a graph showing the percentage (%) of γ-Η2ΑΧ per total H2AX in HCT1 16 cells (triangles) or THP1 cells (diamonds) that had been treated with various concentrations of topotecan (μΜ).
[0017] Figure 5 is a graph comparing γ-Η2ΑΧ (black bars) (γ-Η2ΑΧ pM per 1E7 cells/mL) and y-H2AX/Total H2AX (grey bars) (percentage (%) of γ-Η2ΑΧ per total H2AX) for a selection of cell lines from the NCI60 tumor panel. Bars are arranged in increasing order of γ-Η2ΑΧ value to demonstrate the effect of normalizing the γ-Η2ΑΧ value to total H2AX.
[0018] Figures 6A-6C are graphs showing γ-Η2ΑΧ (pM) (A), H2AX (pM) (B), and γ- H2AX/Total H2AX (%) (C) values measured at two different dilutions of extract from 1E7 cells/mL THP1 cells, 1 to 25 (dashed line) and 1 to 50 (solid line).
[0019] Figures 7A-7C are graphs showing the γ-Η2ΑΧ (pM/ 10 mg protein/mL) (A), total H2AX (pM/10 mg protein/mL) (B) and y-H2AX/Total H2AX (%) (C) values measured in biopsy samples from nude xenograft mice with human breast cancer tumors at various time points (hours) after administration of carrier (control) (diamonds), 7.5 units of irinotecan delivered intravenously (17.5 IV) alone (squares) or in combination with either 50 (triangles) or 6.25 (circles) units of AZD2281 delivered intraperitoneally (IP).
[0020] Figures 8A-8F are graphs showing the amounts of γ-Η2ΑΧ (ρΜ/1Ε7 cells/mL) (A and D) and total H2AX (pM/lE7 cells/mL) (B and E) and the ratio of γ-Η2ΑΧ to total H2AX (%) (C and F) measured in peripheral blood mononuclear cells in archived blood samples from two patients (Patient A (A-C) and Patient B (D-F)) at various time points (hours) after drug administration.
[0021] Figures 9A-9F are graphs showing the amounts of γ-Η2ΑΧ (ρΜ/1Ε7 cells/mL) (A and D) and total H2AX (pM/10 mg protein/mL) (B and E) and the ratio of γ-Η2ΑΧ to total H2AX (%) (C and F) measured in archived patient bone marrow samples (A-C) and tumor biopsies (D-F) taken at various time points after drug administration. Figures 9A-9C: Bone marrow samples were obtained from patients undergoing treatment before drug
administration (0), and 4 hours (hr) after drug administration on day 1 (Dl 4) and day 4 (D4 4). Figures 9D-F: Tumor biopsies were obtained before (pre) and after drug administration (post).
[0022] Figures 1 OA and 10B are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (%) detected in normal human fibroblasts that were exposed to various amounts of ionizing radiation (IR) (Gy). The region below 1 Gy in Figure 10A is expanded in Figure 10B.
[0023] Figure 1 1 is a graph showing the percentage (%) of γ-Η2ΑΧ per total H2AX detected in untreated HT29 cells (control) or HT29 cells that were treated with single drugs (CPT, AZD6738 (AZD) or VE821 (VE)), or combinations of CPT plus AZD6738 or VE821.
[0024] Figures 12A and 12B are graphs showing the percentage (%) of γ-Η2ΑΧ per total H2AX detected in normal PBMC (diamonds) or PBMC that had been mixed with various numbers of THPl tumor cells (spiked tumor cells) that had not been exposed to IR (squares) or tumor cells that had been exposed to 10 Gy (circles) or 1 Gy (triangles) of IR. The region below 10% γ-Η2ΑΧ per total H2AX in Figure 12A is expanded in Figure 12B.
[0025] Figures 12C and 12D are graphs showing the percentage (%) of γ-Η2ΑΧ per total H2AX detected in normal PBMC (diamonds) or PBMC that had been mixed with various numbers of HT29 tumor cells (spiked tumor cells) that were untreated (squares) or treated with ATR inhibitors VE-821 and camptothecin (CPT) (triangles). The region below 10% γ- H2AX per total H2AX in Figure 12C is expanded in Figure 12D. [0026] Figure 13 is a graph showing the ratio of γ-Η2 AX to total H2AX measured in HT29 cells which were treated with the indicated concentrations of camptothecin (CPT) (diamonds) or rhomidepsin (triangles).
[0027] Figure 14A is a graph showing the quantity of γ-Η2ΑΧ (pM) measured in the indicated number of cells per well following treatment with CPT at a concentration of 0 μΜ (vehicle) (asterisks), 0.01 μΜ (squares), 0.1 μΜ (triangles) or 1 μΜ (diamonds).
[0028] Figure 14B is a graph showing the quantity of total H2AX (pM) measured in the indicated number of cells per well following treatment with CPT at a concentration of 0 μΜ (vehicle) (asterisks), 0.01 μΜ (squares), 0.1 μΜ (triangles) or 1 μΜ (diamonds).
[0029] Figure 14C is a graph showing the ratio of γ-Η2ΑΧ to total H2AX measured in the indicated number of cells per well following treatment with CPT at a concentration of 0 μΜ (vehicle) (asterisks), 0.01 μ (squares), 0.1 μΜ (triangles) or 1 μΜ (diamonds).
[0030] Figure 15 is a graph showing the quantity of γ-Η2ΑΧ per 1x10 HT29 cells/mL (grey bars) or lxl 07 MCF7 cells/mL (striped bars) treated with vehicle (control) or the drug CPT, SN38, LMP776, LMP744, LMP400, AZD1775, cisplatin, etoposide, doxorubicin, talazoparib, olaparib, viromostat, erlotinib, or rhomidepsin.
[0031] Figure 16 is a graph showing the quantity of total H2AX per lxlO7 HT29 cells/mL (grey bars) or l l 07 MCF7 cells/mL (striped bars) treated with vehicle (control) or the drug CPT, SN38, LMP776, LMP744, LMP400, AZD1775, cisplatin, etoposide, doxorubicin, talazoparib, olaparib, viromostat, erlotinib, or rhomidepsin.
[0032] Figures 17A and 17B are graphs showing the ratio of γ-Η2ΑΧ to total H2AX measured in HT29 cells (A) or MCF7 cells before (Pre) or after (Post) treatment with camptothecin (grey squares), SN38 (grey diamonds), LMP776 (grey triangles), LMP744 (grey asterisks), LMP400 (grey circles), AZD1775 (grey X), cisplatin (grey -J-), etoposide (black squares), doxorubicin (black diamonds), talazoparib (black triangles), olaparib (black asterisks), viromostat (black circles), erlotinib (black X), or rhomidepsin (black -J-).
[0033] Figures 18A and 18B are graphs showing the intensity of staining for γ-Η2ΑΧ using an anti-y-H2AX antibody (microscope immunofluorescence assay (IFA)) (shaded bars) and the ratio of γ-Η2ΑΧ to total H2AX (ELISA immunoassay (IA)) (striped bars) measured in HT29 cells (A) or MCF7 cells (B).
[0034] Figures 19A-19C are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) (B), or the quantity of total H2AX (pM per 1 x 107 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 μΜ SN38 (squares), 1 μΜ AZD-6738 (triangles), a combination of 0.25 μΜ SN38 and 1 μΜ AZD-6738 (X), or a combination of 0.25 μΜ SN38 and 0.5 μΜ AZD-6738 (asterisks).
[0035] Figures 20A-20C are. graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) (B), or the quantity of total H2AX (pM per 1 x 107 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 μΜ SN38 (squares), 1 μΜ VE-821 (triangles), a combination of 0.25 μΜ SN38 and 1 μΜ VE-821 (X), or a combination of 0.25 μΜ SN38 and 0.5 μΜ VE-821 (asterisks).
[0036] Figures 21A-21C are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) (B), or the quantity of total H2AX (pM per 1 x 107 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 μΜ SN38 (squares), 1 μΜ VE-822 (triangles), a combination of 0.25 μΜ SN38 and 1 μΜ VE-822 (X), or a combination of 0.25 μΜ SN38 and 0.5 μΜ VE-822 (asterisks).
[0037] Figures 22A-22C are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) (B), or the quantity of total H2AX (pM per 1 x 107 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 μΜ SN38 (squares), 1 μΜ Compound-45 (triangles), a combination of 0.25 μΜ SN38 and 1 μΜ Compound-45 (X), or a combination of 0.25 μΜ SN38 and 0.5 μΜ Compound-45 (asterisks).
[0038] Figures 23A-23C are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) (B), or the quantity of total H2AX (pM per 1 x 107 cells/mL) (C) measured at various time points following treatment of MCF7 cells with vehicle (diamonds), 0.25 μΜ SN38 (squares), 1 μΜ NU-6027 (triangles), a combination of 0.25 μΜ SN38 and 1 μΜ NU-6027 (X), or a combination of 0.25 μΜ SN38 and 0.5 μΜ NU-6027 (asterisks).
[0039] Figures 24A-24C are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) per μg protein (B), or the quantity of total H2AX (pM per μg protein) (C) measured in cell lysate isolated from A375 xenograft mouse models treated with vehicle (control), CPT-1 1 (7.5 mg/kg), MK4827 (50 mg/kg), M 4827 (12.5 mg/kg), a combination of CPT-1 1 (7.5 mg/kg) and MK4827 (50 mg/kg) administered simultaneously, a combination of CPT-1 1 (7.5 mg/kg) and MK4827 (12.5 mg/kg) administered simultaneously, MK4827 (7.5 mg/kg) administered four hours prior to CPT-1 1 (50 mg/kg), or MK4827 (7.5 mg/kg) administered four hours prior to CPT-1 1 (12.5 mg/kg).
[0040] Figures 25A-25C are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) per μg protein (B), or the quantity of total H2AX (pM per μg protein) (C) measured in cell lysate isolated from A375 xenograft mouse models treated with vehicle (control), CPT-11 (7.5 mg/kg), AZD2281 (50 mg/kg), AZD2281 (6.25 mg/kg), a combination of CPT-11 (7.5 mg/kg) and AZD2281 (50 mg/kg) administered simultaneously, a combination of CPT-1 1 (7.5 mg kg) and AZD2281 (6.25 mg/kg) administered
simultaneously, AZD2281 (50 mg/kg) administered four hours prior to CPT-1 1 (7.5 mg/kg), or AZD2281 (6.25 mg/kg) administered four hours prior to CPT-11 (7.5 mg/kg).
[0041] Figures 26A-26C are graphs showing the ratio of γ-Η2ΑΧ to total H2AX (A), the quantity of γ-Η2ΑΧ (pM) per μg protein (B), or the quantity of total H2AX (pM per μg protein) (C) measured in cell lysate isolated from A375 xenograft mouse models treated with vehicle (control), CPT-1 1 (7.5 mg/kg), ABT888 (50 mg/kg), ABT888 (12.5 mg/kg), a combination of CPT-1 1 (7.5 mg/kg) and ABT888 (50 mg/kg) administered simultaneously, a combination of CPT-11 (7.5 mg/kg) and ABT888 (12.5 mg/kg) administered simultaneously, ABT888 (7.5 mg/kg) administered four hours prior to CPT-11 (50 mg/kg) and, or ABT888 (7.5 mg/kg) administered four hours prior to CPT-1 1 (12.5 mg/kg).
[0042] Figure 27A is a graph showing the ratio of γ-Η2ΑΧ to total H2AX measured by immunoassay (IA) in cells isolated from A375 xenograft mice that were treated with vehicle (control), CPT-1 1 , ABT-888 (ABT), AZD-2281 (AZD), or MK-4827 (MK), a combination of CPT-11 with ABT-888, a combination of CPT-11 with AZD-2281, or a combination of CPT- 1 1 with MK-4827, at the indicated dosages.
[0043] Figure 27B is a graph showing the quantity of γ-Η2ΑΧ measured by
immunofluorescence assay (IF A) microscopy in cells isolated from A375 xenograft mice that were treated with vehicle (control), CPT-1 1 , ABT-888 (ABT), AZD-2281 (AZD), or MK- 4827 (MK), a combination of CPT-1 1 with ABT-888, a combination of CPT-1 1 with AZD- 2281, or a combination of CPT-1 1 with MK-4827, at the indicated dosages.
[0044] Figure 27C is a graph showing PAR inhibition (pg^g protein/mL) measured by immunoassay (IA) in cells isolated from A375 xenograft mice that were treated with vehicle (control), CPT-1 1 , ABT-888 (ABT), AZD-2281 (AZD), or MK-4827 (MK), a combination of CPT-1 1 with ABT-888, a combination of CPT-1 1 with AZD-2281 , or a combination of CPT- 1 1 with MK-4827, at the indicated dosages.
DETAILED DESCRIPTION OF THE INVENTION
[0045] The methods and kits of the invention provide many advantages. For example, because the inventive methods and kits quantify both γ-Η2ΑΧ and total H2AX, the inventive methods and kits may provide an accurate biodosimetric measurement of the amount of exposure of a host to a DNA DSB-causing agent. The inventive methods and kits also may provide the ratio of γ-Η2ΑΧ to total H2AX in a sample independent of any one or more of cell type, cell number, cell viability, cell lysis efficiency, and laboratory operator variability. In the inventive methods and kits, total H2AX may advantageously serve as an internal control that may account for differences in sample quality that may have arisen due to any one or more of specimen collection, storage, shipping, sample processing, extract preparation, and ELIS A testing. Other advantages that may be provided by the inventive methods and kits include any one or more of lower background signals, greater sensitivity, and the ability to test patient tissue samples. The inventive methods and kits may provide a quantitative range of about 100-fold for both γ-Η2ΑΧ and total H2AX. The inventive methods and kits may also provide a sensitivity of at least about 5 pM for γ-Η2ΑΧ and at least about 50 pM for total H2AX. The inventive methods and kits may also advantageously measure an actual amount of protein (e.g., actual pictograms) as opposed to merely providing relative values of proteins. In addition, the inventive methods and kits may employ an immobilized antibody or antigen binding fragment thereof to capture total H2A core protein and γ-Η2ΑΧ, which may reduce or eliminate the need to purify the antigen from complex mixtures prior to analysis, which may simplify the methods and increase the specificity and sensitivity of the methods. Moreover, the inventive methods and kits may provide a standardized clinical assay that can be used as a biodosimeter. The inventive methods may, advantageously, be completed rapidly (for example, within about one working day, less than about one working day, or more than about one working day). The inventive methods may, advantageously screen agents for the ability to cause DNA DSB after a short treatment with the agent(s) to be screened in vitro (e.g., about 1 hr, less than about 1 hr, more than about 1 hr). The inventive methods may, for example, be suitable for high-throughput screening (for example, about 100 to about 5000 cells per well) and may be carried out using a plate-based immunoassay, for example, a 96/384 plate-based immunoassay. Because the cell extract employed in the inventive methods may also be used for additional, conventional immunoassays such as, for example Western Blot (WB), the inventive methods and kits may also be compatible with other, additional assays in order to, for example, further identify potential downstream targets and carry out mechanistic and molecular studies (e.g., PARP1 assays, Topi assays, and LUMINEX protein assays for apoptosis (Invitrogen, Waltham, MA)). Without being bound to a particular theory or mechanism, it is also believed that because γ-Η2ΑΧ forms at a biological endpoint as opposed to an intermediate biochemical step, the inventive methods provide a more comprehensive measurement of DNA DSB because the inventive methods cover γ-Η2ΑΧ formed by multiple biochemical enzymatic targets and pathways.
[0046] The inventive methods and kits may also advantageously overcome one or more obstacles to obtaining an accurate biodosimetric measurement using other methods such as those that involve counting "nuclear foci" through a microscope. "Nuclear foci" refer to areas surrounding the DSB, which may be microscopically detected and counted using an anti-y-H2AX antibody. However, because each focus contains a certain percentage of the total nuclear H2AX, and the total H2AX content may vary from cell type to cell type, methods that involve counting nuclear foci lack the total H2AX value necessary to convert those data into biodosimetric measurements. The inventive methods and kits may
advantageously overcome one or more of these obstacles.
[0047] An embodiment of the invention provides a method of measuring the amount of exposure of a host to a DNA DSB-causing agent. The DNA DSB-causing agent may be any agent that causes DNA DSBs. Non-limiting examples of DNA DSB-causing agents include IR (such as, for example, X-rays and gamma rays), environmental agents such as, for example, ultraviolet (UV) light, reactive oxygen species, mutagenic chemicals, cigarette smoke, and radiation from, for example, cell phones, and drugs such as, for example, anticancer agents (e.g., bleomycin and topotecan).
[0048] In response to DSB formation, cells phosphorylate the histone protein H2AX. In this regard, the method may comprise contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to phosphorylated H2AX (gamma (γ)-Η2ΑΧ) and forms a first complex with the γ-Η2ΑΧ.
[0049] The biological samples (from the host and the positive control biological sample) may comprise any suitable biological sample. The biological samples can comprise any solubilized homogenate or extract from any suitable biological material. Non-limiting examples include tissues, serum, plasma, urine, sputum, saliva, whole cells, cell lysate, or a fraction of the cell lysates, e.g., a nuclear or cytoplasmic fraction, a whole protein fraction, or an acid extract of histones. If the sample comprises whole cells, the cells can be any cells of the host, e.g., the cells of any organ or tissue, including blood cells or cancer cells. In an embodiment of the invention, the cells may be hair bulb cells. Hair bulbs contain dividing cells and are believed to be more sensitive to drug effects. In an embodiment of the invention, the source material may be from any eukaryotic source such as, for example, invertebrates (such as, for example, yeast), and vertebrates. Preferably, the biological samples comprise cell lysate. In an embodiment of the invention, the biological samples comprise cell lysate from no more than a single cell type. In another embodiment of the invention, the biological samples comprise cell lysates from two or more cell types, for example, normal and abnormal tissues, such as those in a tumor biopsy. In an embodiment of the invention, the biological sample is a cancer cell or a lysate of a cancer cell. Regardless of the origin or composition of the biological sample from the host, the positive control biological sample is preferably identical to the biological sample from the host with the exception that the positive control biological sample has been exposed to a known amount of the DSB-causing agent.
[0050] The host may be any eukaryote such as, for example, an invertebrate (such as, for example, yeast) or vertebrate. Mammals are the preferred host. The mammalian host may be, for example, of the order Rodentia, such as mice and hamsters, or of the order Logomorpha, such as rabbits. The host may be from the order Carnivora, including Felines (cats) and Canines (dogs). The host may be from the order Artiodactyla, including Bovines (cows) and S wines (pigs) or of the order Perssodactyla, including Equines (horses). The host may be of the order Primates, Ceboids, or Simoids (monkeys) or of the order Anthropoids (humans and apes). Most preferably, the host is a human.
[0051] The antibody and antigen binding fragment thereof that specifically bind to γ- H2AX are also collectively referred to herein as "anti-y-H2AX antibody" or "anti-y-H2AX antibodies." The anti-y-H2AX antibody binds to γ-Η2ΑΧ with measurably higher affinity to γ-Η2ΑΧ than to other molecules. In an embodiment of the invention, the anti-y-H2AX antibody may specifically bind to the carboxyl terminus of γ-Η2ΑΧ (SEQ ID NO: 1 , wherein the serine in the first position of SEQ ID NO: 1 is phosphorylated), and does not bind to the carboxyl terminus of non-phosphorylated H2AX (SEQ ID NO: 3, wherein the serine in the first position of SEQ ID NO: 3 is not phosphorylated). In an embodiment of the invention, the anti-y-H2AX antibody may specifically bind to γ-Η2ΑΧ (SEQ ID NO: 2, wherein the serine at position 27 of SEQ ID NO: 2 is phosphorylated), and does not bind to non- phosphorylated H2AX (SEQ ID NO: 4, wherein the serine at position 27 of SEQ ID NO: 3 is not phosphorylated). Suitable anti-y-H2AX antibodies are described in U.S. Patent Nos. 6,884,873 and 6,362,317, each of which is incorporated by reference herein in its entirety. Anti-y-H2AX antibodies are also commercially available (from, for example, Millipore (Billerica, MA)).
[0052] While the contacting may take place in vitro or in vivo with respect to the host, preferably, the contacting is in vitro. Contacting a biological sample with the anti-y-H2AX antibody may comprise physically contacting the biological sample with the anti-y-H2AX antibody such that the anti-y-H2AX antibody binds to γ-Η2ΑΧ that is present in the sample. The binding of the anti-y-H2AX antibody to the γ-Η2ΑΧ forms a first complex that comprises the γ-Η2ΑΧ bound to the anti-y-H2AX antibody.
[0053] The method may further comprise contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein. The antibody and antigen binding fragment thereof that specifically bind to the H2A core protein are also collectively referred to herein as "anti-H2A core protein antibody" or "anti-H2A core protein antibodies." The anti-H2A core protein antibody binds to H2A core protein with measurably higher affinity to H2A core protein than to other molecules. In an embodiment of the invention, the anti-H2A core protein antibody specifically binds to H2A core protein that is present in the sample, such as, for example, H2A1 , H2A2, H2AX (both phosphorylated and non- phosphorylated), and H2AZ. In this regard, the anti-H2A core protein antibody captures all H2A proteins that are present in the biological sample (total H2A), including H2AX (both phosphorylated and non-phosphorylated). Accordingly, the second complex may comprise anti-H2A core protein antibody bound to phosphorylated or non-phosphorylated H2AX. Anti-H2A core protein antibodies are commercially available from companies such as, for example, Novus (St. Charles, MO).
[0054] Contacting a biological sample with the anti-H2A core protein antibody may comprise physically contacting the biological sample with the anti-H2A core protein antibody such that the anti-H2A core protein antibody binds to H2A core protein that is present in the sample. The binding of the anti-H2A core protein antibody with the anti-H2A core protein forms a second complex that comprises the H2A core protein bound to the anti-H2A core protein antibody.
[0055] The contacting of the biological sample(s) with the anti-y-H2AX antibody and the contacting of the biological sample(s) with the anti-H2A core protein antibody may take place simultaneously or in any sequence. In an embodiment of the invention, a substrate such as, for example, a multi-well plate, is coated with both the anti-y-H2AX antibody and the anti-H2A core protein antibody. Preferably, the anti-y-H2AX antibody and the anti-H2A core protein antibody are applied to separate wells of a multi-well plate. A biological sample may be added to the coated surfaces of the wells so that the anti-y-H2AX antibody and the anti-H2A core protein antibody specifically bind to their respective antigens simultaneously or sequentially. In an embodiment of the invention, the anti-y-H2AX antibody and the anti- H2A core protein antibody are coated onto separate substrates. A portion of a biological sample may be added to the coated surface of each substrate so that anti-y-H2AX antibody and the anti-H2A core protein antibody specifically bind to their respective antigens simultaneously or sequentially. In an embodiment of the invention, the method comprises contacting the biological sample(s) with the anti-y-H2AX antibody prior to contacting of the biological sample(s) with the anti-H2A core protein antibody. In another embodiment of the invention, the method comprises contacting the biological sample(s) with the anti-y-H2AX antibody after contacting of the biological sample(s) with the anti-H2A core protein antibody.
[0056] In an embodiment of the invention, the method comprises washing any unbound anti-y-H2AX antibody and any unbound anti-H2A core protein antibody from the first and second complexes, respectively.
[0057] The method may further comprise contacting the first and second complexes of the positive control biological sample and the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex. The antibody and antigen binding fragment thereof that specifically bind to H2AX are also collectively referred to herein as "anti-H2AX antibody" or "anti-H2AX antibodies." The anti-H2AX antibody binds H2AX with measurably higher affinity to H2AX than to other molecules. In an embodiment of the invention, the anti-H2AX antibody specifically binds to H2AX that is present in the sample, including phosphorylated H2AX and non-phosphorylated H2AX. In this regard, the anti-H2AX antibody captures all H2AX proteins that are present in the biological sample (total H2AX). Anti-H2AX antibodies for most mammals are commercially available (for example, Abeam (San Francisco, CA)).
[0058] Contacting the first and second complexes with the anti-H2AX antibody may comprise physically contacting the first and second complexes with the anti-H2AX antibody such that the anti-H2AX antibody binds to any H2AX that is present in the first and second complexes. The binding of the anti-H2AX antibody to the first complex forms a third complex that comprises the H2AX of the first complex bound to the anti-H2AX antibody. The binding of the anti-H2AX antibody to the second complex forms a fourth complex that comprises the H2AX of the second complex bound to the anti-H2AX antibody. In this regard, the fourth complex comprises the anti-H2AX antibody bound to any phosphorylated or non-phosphorylated H2AX that was captured by the anti-H2A core protein antibody.
[0059] The contacting of the first and second complexes with the anti-H2AX antibody may take place simultaneously or in any sequence. In an embodiment of the invention, the method may comprise contacting the first complex with the anti-H2AX antibody prior to contacting the second complex with the anti-H2AX antibody. In another embodiment of the invention, the method may comprise contacting the first complex with the anti-H2AX antibody after contacting the second complex with the anti-H2AX antibody.
[0060] In an embodiment of the invention, the method comprises washing any unbound anti-H2AX antibody from the third and fourth complexes, respectively.
[0061] The method further comprises detecting the third and fourth complexes in the positive control biological sample and the biological sample from the host. The third and fourth complexes may be detected in any suitable manner known in the art. In an
embodiment of the invention, detecting the third and fourth complexes in the biological samples(s) comprises contacting each of the third and fourth complexes with a detecting agent. The detecting agent may comprise, for example, an antibody or antigen binding fragment thereof that specifically binds to the third and fourth complex, respectively
(hereinafter referred to collectively as "detection antibody" or "detection antibodies"). The third and fourth complexes may be detected using the same detection antibody or different detection antibodies. The detection antibody binds to the third or fourth complex (or both) with measurably higher affinity to the third or fourth complex (or both) than to other molecules. In an embodiment of the invention, the detection antibody specifically binds to the anti-H2AX antibody.
[0062] In an embodiment of the invention, the detection antibody comprises a detectable label. The detectable label may be any suitable detectable label that provides a detectable signal. Non-limiting examples of detectable labels include enzymes (e.g., alkaline phosphatase, horseradish peroxidase), fluorescent molecules (e.g., fluorescein isothiocyanate (FITC), phycoerythrin (PE)), luminescent molecules, dyes, biotin, and element particles (e.g., gold particles). When the detectable label is an enzyme, the method may further comprise adding a substrate to the third and fourth complexes that is catalyzed by the enzyme to produce a detectable signal. In an embodiment of the invention, the detectable signal may be amplified and/or visually detected. For example, acetylcholinesterase-catalyzed hydrolysis may be useful for colorimetric detection through gold or silver nanoparticle aggregation.
[0063] The antibodies for use in the inventive methods, including the anti-y-H2AX antibody, the anti-H2A core protein antibody, the anti-H2AX antibody, and the detection antibody, can be of any type. For instance, any of the antibodies can be of any isotype, e.g., IgA, IgD, IgE, IgG, IgM, etc. Any of the antibodies can be monoclonal or polyclonal. Any of the antibodies can be a naturally-occurring antibody, e.g., an antibody isolated and/or purified from a mammal, e.g., mouse, rabbit, goat, horse, chicken, hamster, human, etc. Alternatively, any of the antibodies can be a genetically-engineered antibody, e.g., a humanized antibody or a chimeric antibody. Any of the antibodies can be in monomelic or polymeric form.
[0064] In an embodiment of the invention, the methods may employ an antigen binding fragment of any of the antibodies described herein. The antigen binding fragment can be any portion of the antibody that has at least one antigen binding site. In an embodiment, the antigen binding fragment is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv). A single-chain variable region fragment (scFv), which is a truncated Fab fragment including the variable (V) domain of an antibody heavy chain linked to a V domain of a light antibody chain via a synthetic peptide, can be generated using routine recombinant DNA technology techniques (see, e.g., Murphy et al. (eds.), Murphy 's
Immunobiology, 8th Ed., Garland Science, New York, NY (2014)). Similarly, disulfide- stabilized variable region fragments (dsFv) can be prepared by recombinant DNA
technology. In an embodiment of the invention, the antigen binding fragment of the antibody that specifically binds to γ-Η2ΑΧ, H2A core protein, or H2AX is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv). The antigen binding fragments that may be useful in the methods of the invention, however, are not limited to these exemplary types of antibody fragments.
[0065] In an embodiment of the invention, the method comprises washing any unbound detection antibody from the third and fourth complexes, respectively.
[0066] The method further comprises quantifying the third and fourth complexes in the positive control biological sample and the biological sample from the host. The third and fourth complexes may be quantified in any suitable manner known in the art. In an embodiment of the invention, quantifying the third and fourth complexes comprises determining the amount of detectable label present. For example, the method may comprise determining the amount of fluorescence or luminescence provided by the detectable label.
[0067] The method further comprises determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host; and comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host to determine the amount of exposure of the host to the DNA DSB-causing agent. Because the positive control biological sample was exposed to a known amount of a DNA DSB-causing agent, comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the same in the biological sample from the host provides the amount of exposure of the host to a DNA DSB-causing agent.
[0068] Another embodiment of the invention provides a method of quantifying DNA DSBs in a test biological sample. The method may comprise contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a test biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ. The test biological sample may be any suitable test biological sample. For example, the test biological sample may be a biological sample from a host, as described herein with respect to other aspects of the invention. In an embodiment, the positive control biological sample may also be as described herein with respect to other aspects of the invention except that the positive control biological sample has a known quantity of DSBs. The anti-y-H2AX antibody, the first complex, and the contacting of the anti-y-H2AX antibody with the biological samples may be as described with respect to other aspects of the invention.
[0069] The method of quantifying DNA DSBs in a test biological sample may further comprise contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein. The anti-H2A core protein antibody, the second complex, and the contacting of the anti-H2A core protein antibody with the biological samples may be as described with respect to other aspects of the invention.
[0070] In an embodiment of the invention, the method of quantifying DNA DSBs in a test biological sample further comprises washing any unbound anti-y-H2AX antibody and any unbound anti-H2A core protein antibody from the first and second complexes, respectively.
[0071] The method of quantifying DNA DSBs in a test biological sample may further comprise contacting the first and second complexes of the positive control biological sample and the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex. The anti-H2AX antibody, the third and fourth complexes, and the contacting of the anti-H2AX antibody with the first and second complexes may be as described herein with respect to other aspects of the invention.
[0072] In an embodiment of the invention, the method of quantifying DNA DSBs in a test biological sample further comprises washing any unbound anti-H2AX antibody from the third and fourth complexes, respectively.
[0073] The method of quantifying DNA DSBs in a test biological sample may further comprise detecting the third and fourth complexes in the positive control biological sample and the test biological sample; quantifying the third and fourth complexes in the positive control biological sample and the test biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample; and determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample. Detecting the third and fourth complexes, quantifying the third and fourth complexes, and determining the ratio of the quantity of the third complex to the quantity of the fourth complex may be carried out as described herein with respect to other aspects of the invention.
[0074] The method may further comprise comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample to determine the quantity of DSBs in the test biological sample. Because the positive control biological sample has a known quantity of DSBs, comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample provides the quantity of DSBs in the test biological sample.
[0075] Another embodiment of the invention provides a kit that may be useful for measuring the amount of exposure of a host to a DNA DSB-causing agent and/or quantifying DNA DSBs in a test biological sample. The kit may comprise at least one substrate. For example, the kit may comprise one, two, three four, five, six, or more substrates. Preferably, the kit comprises two substrates, including a first substrate for testing a test biological sample or a biological sample from a host and a second substrate for testing a positive control biological sample. In an embodiment of the invention, the substrate is a plate, e.g., a multiwell plate.
[0076] The kit may further comprise an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ, an antibody or antigen binding fragment thereof that specifically binds to H2A core protein, and an antibody or antigen binding fragment thereof that specifically binds to H2AX. The anti-y-H2AX, anti-H2A core protein, and anti-H2AX antibodies and antigen binding fragments thereof may be as described herein with respect to other aspects of the invention. In an embodiment of the invention, the antigen binding fragment of the antibody that specifically binds to γ-Η2ΑΧ, H2A core protein, or H2AX is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
[0077] In an embodiment of the invention, the anti-y-H2AX and anti-H2A core protein antibody is affixed to the at least one substrate. For example, the kit may comprise a first substrate comprising an anti-y-H2AX antibody affixed thereto and a second substrate comprising an anti-H2A core protein antibody affixed thereto. In an embodiment of the invention, the kit comprises a single substrate comprising both anti-y-H2AX and anti-H2A core protein antibodies affixed thereto. For example, when the substrate is a multiwell plate, anti-y-H2AX antibody may be affixed to each of a first set of one or more wells of the multiwell plate and anti-H2A core protein antibody may be affixed to a second set of one or more wells of the multiwell plate. In this regard, the substrate may be a multiwell plate in which the anti-y-H2AX antibody and the anti-H2A core protein antibody are affixed to separate wells.
[0078] The kit may further comprise a detecting agent comprising a label. The detecting agent may be a detection antibody as described herein with respect to other aspects of the invention. In this regard, the detecting agent may be an antibody or antigen binding fragment thereof that specifically binds to the antibody or antigen binding fragment thereof that specifically binds to H2AX. The label may also be as described herein with respect to other aspects of the invention. For example, the label may be an enzyme, a fluorescent molecule, a dye, or biotin.
[0079] The kit may further comprise a reagent for facilitating the binding of one or more of the anti-y-H2AX antibody, anti-H2A core protein antibody, and anti-H2AX antibody to the γ-Η2ΑΧ, H2A core protein, and H2AX, respectively. The kit may further comprise a reagent for facilitating detection of the detecting agent (e.g., a substrate that reacts with an enzyme to provide a detectable signal). The kit may further comprise one or more protamines (small nuclear proteins) which may, advantageously, decrease non-specific binding and/or increase signal-to-background ratio. The kit may also comprise other materials and reagents commonly employed in immunochemical test kits.
[0080] Because many drugs, such as anti-cancer agents, cause DNA DSBs, the inventive methods and kits may be useful for monitoring drug therapies, such as anti-cancer therapy, in a patient. Quantifying DNA DSBs or measuring the amount of exposure of a host to a DNA DSB-causing agent according to the inventive methods may, for example, indicate a need to increase or decrease the dosage of the drug, e.g., anti-cancer agent.
[0081] Another embodiment of the invention provides a method of screening test compounds for ability to cause DNA DSBs. The method may comprise dividing a population of test biological samples into more than one test sub-population. In an embodiment, the test biological samples are divided into at least two sub-populations. Dividing the test biological samples into more than one sub-population may be carried out in any suitable manner. For example, the test biological samples may be divided by being placed in different wells of multi-well plates. The test biological sample may be as described herein with respect to other aspects of the invention.
[0082] The method may further comprise treating each test sub-population with a test compound, wherein each test sub-population is treated with a different test compound. The test compound(s) may, for example, be obtained from a library. The library may comprise any collection of two or more test compounds that is believed to possibly contain one or more compounds that may cause DNA DSBs. Each sub-population may be treated with a different test compound such that the ability of each compound to cause DNA DSBs may be evaluated.
[0083] The method may further comprise contacting (i) a first portion of each treated test sub-population and (ii) a first portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ; contacting (i) a second portion of each treated test sub-population and (ii) a second portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein; and contacting the first and second complexes of the control biological sample and the treated test sub-populations with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex. The antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ; the antibody or antigen binding fragment thereof that specifically binds to an H2A core protein; the antibody or antigen binding fragment thereof that specifically binds to H2AX; the first, second, third, and fourth complexes; and the contacting may be as described herein with respect to other aspects of the invention. The control biological sample may be identical to the test biological sample with the exception that the control biological sample has not been treated with a test compound.
[0084] The method may further comprise detecting the third and fourth complexes in the control biological sample and the treated test sub-populations; quantifying the third and fourth complexes in the control biological sample and the treated test sub-populations;
determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample; and determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub-populations. The detecting, quantifying, and determining of the ratio may be carried out as described herein with respect to other aspects of the invention.
[0085] The method may further comprise comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub- populations, wherein an increase in the ratio in a treated test sub-population as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs. The comparing may be carried out as described herein with respect to other aspects of the invention.
[0086] Another embodiment of the invention provides a method of testing compounds for ability to cause DNA DSBs in a host. The method may comprise administering a test compound to the host and obtaining a biological sample from the host after the host has been administered the test compound. The host, the biological sample from the host, and the test compounds may be as described herein with respect to other aspects of the invention.
[0087] The method may further comprise contacting (i) a first portion of a control biological sample and (ii) a first portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ; contacting (i) a second portion of the control biological sample and (ii) a second portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein, wherein the control biological sample has not been exposed to the test compound; and contacting the first and second complexes of the control biological sample and the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex. The antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ; the antibody or antigen binding fragment thereof that specifically binds to an H2A core protein; the antibody or antigen binding fragment thereof that specifically binds to H2AX; the first, second, third, and fourth complexes; and the contacting may be as described herein with respect to other aspects of the invention. The control biological sample may be identical to the biological sample from the host except that the control biological sample has not been exposed to the test compound. For example, the control biological sample may be obtained from a host that has not been administered a test compound or from the host prior to administering a test compound.
[0088] The method may further comprise detecting the third and fourth complexes in the control biological sample and the host biological sample; quantifying the third and fourth complexes in the control biological sample and the host biological sample; determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample; and determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample. The detecting, quantifying, and determining of the ratio may be carried out as described herein with respect to other aspects of the invention.
[0089] The method may further comprise comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample, wherein an increase in the ratio in the host biological sample as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs in the host. The comparing may be carried out as described herein with respect to other aspects of the invention.
[0090] The methods of screening test compounds for ability to cause DNA DSBs and the methods of testing compounds for ability to cause DNA DSBs in a host may provide many advantages. For example, the methods may be useful for identifying and developing new drugs that cause DNA DSBs, which may be useful for treating any of a variety of different diseases, e.g., cancer. The methods may be useful for testing any one or more of (1) whether alterations of a drug increase the drug's effectiveness for inducing DNA DSBs; (2) the mechanism(s) of drug-induced DNA DSBs and/or drug-induced effects on DNA DSB repair; (3) which cancer types are targeted by a particular drug, (4) whether a drug targets a protein involved in DNA DSB repair, (5) whether a drug targets a cancer associated with a mutated gene, e.g., a gene involved in DNA DSB repair, and (6) the effect of different combinations of drugs on DNA DSB repair. The methods of testing compounds for ability to cause DNA DSBs in a host may be useful for determining whether a drug candidate causes DNA DSBs in tumor-bearing animals and/or cancer patients in clinical trials.
[0091] Any of the inventive methods described herein may further comprise forming any of the complexes described herein in the presence of one or more protamines. The one or more protamines may, advantageously, reduce non-specific binding and/or increase the signal-to-background ratio.
[0092] The following examples further illustrate the invention but, of course, should 'not be construed as in any way limiting its scope.
EXAMPLE 1
This example demonstrates the performance of the γ-Η2ΑΧ immunoassay.
Materials:
Anti-y-H2AX (Serl 39) mouse monoclonal antibody, clone JBW301 (1 μg/μL) Lot# DAM 1567248 (Millipore). Used at 1 :250 dilution.
Anti-histone H2AX rabbit polyclonal antibody (1.7 μg/μL) Lot# 778559 (Abeam) Used at 1 :850 dilution.
Goat anti-rabbit horseradish peroxidase (HRP)-conjugated polyclonal antibody Lot# 101008. Used at 1 : 1000 dilution. • γ-Η2ΑΧ peptide standard, lyophilized powder (custom preparation from
Invitrogen (Waltham, MA), synthetic peptide:
AVLLPKKTSATVGPKAPSGGK ATQASQEY), wherein the serine at position
27 is phosphorylated (SEQ ID NO: 2).
[0095] Pierce REACTI-BIND plates (96-well) (Thermo Scientific) were coated with anti- γ-Η2ΑΧ antibody (Millipore) diluted to a concentration of 4 μg/mL in 0.1 M pH 9.6 carbonate buffer (Sigma- Aldrich, St. Louis, MO), 100 μίΛνεΙΙ, for 2 hours at 37°C. The γ- H2AX synthetic peptide standard or a whole-cell extract was added to each well and incubated for antigen capture overnight at 4°C. Plates were incubated with 100 μίΛνεΙΙ of 2 μg/mL anti-histone H2AX rabbit polyclonal antibody (Abeam) diluted in 2% bovine serum albumin (BSA)/phosphate buffered saline (PBS) supplemented with 1 ihlmL mouse serum for 2 hours (h) at 24°C. Subsequently, 100 μίΛνεΙΙ HRP-conjugated affinity-purified goat anti-rabbit (KPL) was added at a final concentration of 1 μg/mL diluted in 2% BSA/PBS, supplemented with 1
Figure imgf000026_0001
mouse serum, and incubated for 1 hour at 24°C. Finally, 100 μίΛνεΙΙ of freshly prepared SUPERSIGNAL ELISA Pico chemiluminescent substrate (Thermo Scientific, Waltham, MA) was added to the plate and immediately read on a TECAN INFINITE M200 plate reader (Tecan Group Ltr., Maennedorf, Switzerland). A standard curve was generated by plotting the RLU (relative light unit) values that were obtained for a range of concentrations of the γ-Η2ΑΧ standard peptide (Figure 1 A). The average γ-Η2ΑΧ concentration for each cell extract was then determined using the standard curve (Figure IB).
EXAMPLE 2
[0096] This example demonstrates the performance of the total H2AX immunoassay.
[0097] Materials:
• anti-H2A core protein HIST1H2AC monoclonal antibody, 4F10 (Novus, Cat#:
H00008334-M01), Lot# D8231-4F10. Used at 1 :250 dilution.
• anti-histone H2AX rabbit polyclonal antibody (Abeam, Cat#: abl 0475), Lot# 778559. Used at 1 :850 dilution.
• Goat anti-rabbit HRP-conjugated polyclonal antibody (KPL, Cat#: 074-15-061), Lot# 120504. Used at 1 : 1000 dilution. • Total H2AX recombinant standard, lyophilized powder (Axxora, Cat#: ALX-201- 176-M005), Lot# LI 6677. Used standard stock concentration at 33000 pM.
[0098] Pierce REACTI-BIND plates (96-well) were coated with total anti-H2A core protein HIST1H2AC monoclonal antibody (Novus, St. Charles, MO) diluted to a
concentration of 4 μ^ιτιΐ. in 0.1 M pH 9.6 carbonate buffer (Sigma- Aldrich), 100 μίΛνεΙΙ, for 2 hours at 37°C. A total H2AX recombinant standard or whole-cell extract (250 pM, 500 pM, or 1,000 pM) was added to each well and incubated for antigen capture overnight at 4°C. Plates were incubated with 100 μΙ,ΛνεΙΙ of 2 μg/mL total anti-histone H2AX rabbit polyclonal antibody (Abeam) diluted in 2% BSA/PBS supplemented with 1 μΏ ύ^ mouse serum for 2 h at 25°C. Subsequently, 100 μΐ ννεΐΐ HRP-conjugated affinity-purified goat anti-rabbit (KPL, Inc., Gaithersburg, MD) was added at a final concentration of 1 μg/mL diluted in 2% BSA/PBS, supplemented with 1 μΙ7ηι11 mouse serum, and incubated for 1 hour at 25°C. Protamines were added to decrease non-specific binding and to increase the signal to background ratio. Finally, 100 μΙ,ΛνεΙΙ of freshly prepared SUPERSIGNAL ELISA Pico chemiluminescent substrate (Themio Scientific) was added to the plate and immediately read on a TECAN INFINITE M200 plate reader. A standard curve was generated by plotting the RLU values that were obtained for a range of concentrations of the H2AX standard peptide (Figure 2A). The average total H2AX concentration for each cell extract was then determined using the standard curve (Figure 2B).
EXAMPLE 3
[0099] This example demonstrates the parameters and controls of the assays of Examples 1 and 2.
[0100] Inter-assay precision was measured by running three replicates of (a) a total H2AX standard and assay controls, as described in Example 2 (Table 1) and (b) a γ-Η2ΑΧ standard and assay controls, as described in Example 1 (Table 2). All three runs for the total H2AX immunoassay passed the inter-assay acceptance criteria (% coefficient of variation (CV) < 25%) with a range from 6 to 21 % for the standards and 2.2 to 7.3% for the controls. All three runs for the γ-Η2ΑΧ immunoassay passed the inter-assay acceptance criteria (% CV < 25%) with a range from 1-12%. The results in Tables 1 and 2 are summarized in Table 3. TABLE 1
H2AX Standard Average RLU Standard Deviation
% CV (pM) (n=3) (SD)
50 865,720 184,054 21
100 1,063,562 168,332 16
200 1,418,546 218,046 15
400 2,298,028 327,995 14
800 4,611 161 370,373 8
1600 10,482,498 851,476 8
3200 26,055,096 1,696,172 7
6400 59,158,022 3,389,425 6
Assay Control Average pM (n=3) SD %CV
Low Control 216.1 15.8 7.3
Medium Control 844.8 49.3 5.8
High Control 2337.0 51.0 2.2
TABLE 2
Figure imgf000029_0001
TABLE 3
Figure imgf000029_0002
[0101] Readout ranges were prepared for the lot of tumor cell lines to be used as controls (C) during development of the total H2AX assay (Table 4) and the γ-Η2ΑΧ assay (Table 5). For γ-Η2ΑΧ, the Low-C sample contained un-irradiated MCF7 cells while the High-C sample contained MCF7 cells that were irradiated at 10 Gy and frozen 30 minutes later. Extracts of both were prepared at 1E7 cells/mL and diluted 1 :3. The Mid-C sample was a mixture containing 70%> Low-C and 30% High-C.
[0102] For total H2AX, the Low-C sample contained un-irradiated MCF7 cells diluted 1 :200 from a stock extract of 1E7 cells/mL while the Mid-C sample contained MCF7 cells diluted 1 :50 from the same stock extract. The High-C sample contained SN12C cell extract diluted 1 :50 from a stock of 1 E7 cells/mL.
TABLE 4
Figure imgf000030_0001
EXAMPLE 4
[0103] This example demonstrates the preclinical testing of the γ-Η2ΑΧ immunoassay of Example 1.
[0104] Human breast cancer cell lines HCT 1 16 or MCF 7 (ATCC) were cultured with 10% fetal bovine serum at 37 °C in a 5% C02 incubator. The cells were treated with the topoisomerase I inhibitor topotecan, the apoptosis-inducing biomolecule tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), or IR. The γ-Η2ΑΧ immunoassay (γ-Η2ΑΧ ELISA) was compared with γ-Η2ΑΧ detection by both Western blot and immunofluorescence assay (IFA).
[0105] The ELISA detected changes in γ-Η2ΑΧ in HCT1 16 cell cultures induced by a variety of treatments in vitro and was overall highly correlated to both IFA and Western blot following treatment with topotecan or TRAIL (Table 6). With the less active treatment of IR, only a modest correlation between ELISA and Western blot was observed, but the high correlation with IFA remained. TABLE 6
Figure imgf000031_0001
EXAMPLE 5
[0106] This example demonstrates a method of determining the ratio of γ-Η2ΑΧ to total H2AX in cancer cells treated with IR or topotecan.
[0107] THP1 leukemia cells were treated with the various amounts of IR shown in Figures 6A-6C. Extracts at 1 x 107 cells/mL were prepared of each irradiated sample, and two dilutions, 1 to 25 (30,000 cells/sample) and 1 to 50 (15,000 cells/sample) were used to measure γ-Η2ΑΧ (Figure 6A) and total H2AX (Figure 6B) utilizing the γ-Η2ΑΧ
immunoassay of Example 1 and the total H2AX immunoassay of Example 2. Figures 6A-6C show data from the two dilutions (1 :25 and 1 :50). Using the values obtained in Figures 6A- 6B, the ratio of γ-Η2ΑΧ to total H2AX was calculated and is shown in Figure 6C. As shown in Figure 6C, the assay is independent of sample size.
[0108] The concentration of γ-Η2ΑΧ in 1 x 107 HCT1 16 cells, MCF7 cells, or THP1 leukemia cells that had been treated with various doses of IR was measured using the γ- H2AX immunoassay of Example 1 (γ-Η2ΑΧ ELISA). The results for THP1 are shown in Figure 6A. As shown in Figure 6 A, the γ-Η2ΑΧ ELISA functioned to determine the concentration of γ-Η2ΑΧ in extracts of cancer cells treated with IR.
[0109] The concentration of total H2AX in the same extract used for the γΗ2ΑΧ determination was measured using the H2AX immunoassay of Example 2. The ratio of γ- H2AX to total H2AX was calculated for the HCT1 16 cells, MCF7 cells, and THP1 cells that had been treated with various doses of IR. The results for THP1 are shown in Figure 6B. As shown in Figure 6B, the γ-Η2ΑΧ ELISA functioned to determine the concentration of γ- H2AX in extracts of cancer cells treated with IR.
[0110] As shown in Figures 3A and 3B, the γ-Η2ΑΧ and total H2AX immunoassays can be used to calculate the ratio of γ-Η2ΑΧ to total H2AX in cells treated with IR. This value is approximately proportional to the number of DNA DSBs induced per nucleus and can be interpreted in terms of radiosensitivity of the various cell lines while γΗ2ΑΧ values alone cannot. Figure 3B shows the region below 10 Gy, the region relevant to human exposures in radiological accidents and cancer treatment.
[0111] The concentration of γ-Η2ΑΧ in extracts of HCT1 16 or THP 1 cells that had been treated with various concentrations of topotecan was measured using the γ-Η2ΑΧ ELISA. The results are shown in Figure 4A. As shown in Figure 4A, the γ-Η2ΑΧ ELISA functioned to determine the concentration of γ-Η2ΑΧ in 1 x 107 cancer cells treated with topotecan.
[0112] The concentration of total H2AX in 1 x 107 HCT116 cells or THP1 cells that had been treated with various concentrations of topotecan was measured using the H2AX immunoassay of Example 2 (H2AX ELISA). The ratio of γ-Η2ΑΧ to total H2AX was calculated for the HCT1 16 cells and THP1 cells that had been treated with various concentrations of topotecan. The results are shown in Figure 4B. As shown in Figure 4B, the γ-Η2ΑΧ and total H2AX immunoassays can be used to calculate the ratio of γ-Η2ΑΧ tp total H2AX in cells treated with topotecan. This value more accurately reflects the relative effects of topotecan on different cell lines than γΗ2ΑΧ values alone.
EXAMPLE 6
[0113] This example demonstrates a method of determining the ratio of γ-Η2ΑΧ to total H2AX in various types of cancer cells and tumor panels. [0114] The γ-Η2ΑΧ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 were used to determine the ratio of γ-Η2ΑΧ to total H2AX in various cancer cell types (Figure 5 and Table 7) and tumor panels (Table 8). The results are shown in Figure 5 and Tables 7 and 8.
TABLE 7
Cell Line γΗ2ΑΧ Total H2AX yH2AX/Total
(ρΜ/1Ε7 Cells) (pM/lE7 Cells) H2AX
(%)
NCI/ADR-RJES 207 39631 0.52
Ovarian
SF-268 3837 461520 0.83
CNS
SR 2921 56153 5.20
Leukemia
HL-60 1759 26993 6.52
Leukemia
NCI60 Average 952 +/- 727 72026 +/- 62214 1.55 +/- 1.17 +/- SD
TABLE 8
Tumor Panels yH2AX/Total H2A X (%) Standard Deviation (%)
CNS 1.13 0.75
Ovarian 1.18 0.63
Melanoma 1.21 0.28
NSCLC 1.41 0.84
Renal 1.50 0.85
Prostate 1.51 0.21
Breast 1.67 1.39
Colon 1.76 1.25
Leukemia 2.86 2.48
Average 1.55 1.17
[0115] The γ-Η2ΑΧ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 were used to determine the ratio of basal concentrations of γ-Η2ΑΧ to basal concentrations of total H2AX in a panel of 60 cancer cell lines (NCI 60), including six leukemia, nine non-small cell lung carcinoma, seven colon, six central nervous system, nine melanoma, seven ovarian, eight renal, two prostate, and six breast cancer cell lines.
Assuming that all cell lines have 6 x 109 base pairs of DNA and that all are in the Gl phase of the cell cycle (both of which are approximations), the H2AX as the maximum percentage of total H2A was calculated. The percentage values for H2AX out of total H2A generally agreed with those from other lines of research.
[0116] These data showed that the basal concentrations of γ-Η2ΑΧ and total H2AX varied nearly 20 fold among the different cell types and were dependent on tumor type and cell line. The γ-Η2ΑΧ/Η2ΑΧ ratios ranged from 0.52% in an ovarian cell line (NC1/ADR- RES) to 6.52% in a leukemia cell-line (HL-60). Without being bound by a particular theory or mechanism, it is believed that the underlying cause of the variability may be linked to any one or more of chromosomal polyploidy, chromosomal amplification, genotypes and mutations related to DNA replication, and repair and cell cycle controls. It is also believed that unique patterns of γ-Η2ΑΧ to total H2AX ratio changes due to treatment with IR or DNA-damaging drugs may reveal new targets for drug discovery and development. EXAMPLE 7
[0117] This example demonstrates that the assays of Examples 1 and 2 can be used to measure the amount of γ-Η2ΑΧ induced by cancer drugs.
[0118] Nude mice containing tumors of the human breast carcinoma cell line MX1 were treated with various combinations of two cancer drugs, irinotecan and AZD2281. Irinotecan (7.5 units) was delivered intravenously (17.5 IV) alone or in combination with either 50 or 6.25 units of AZD2281 delivered intraperitoneally (IP). The control was the carrier for the drugs. At 6 hours post treatment, the tumors were biopsied. The biopsies were solubilized and prepared at 10 mg protein/mL. The solubilized, prepared biopsy samples were assayed for γ-Η2ΑΧ (Figure 7A) and total H2AX (Figure 7B) at various time points after
administration, and the respective ratios of γΗ2ΑΧ to total H2AX were calculated (Figure 7C). As shown in Figure 7C, irinotecan alone induced γ-Η2ΑΧ modestly, while the combinations with AZD2281 induced substantially more γ-Η2ΑΧ, particularly at 4 hours after administration.
EXAMPLE 8
[0119] This example demonstrates that the assays of Examples 1 and 2 can be used to measure the amount of γ-Η2ΑΧ in archived patient peripheral blood mononuclear cells (PBMCs), bone marrow, and tumor biopsy samples.
[0120] Blood samples were taken from patients before treatment with drugs and at various time points after treatment. The blood samples were frozen and stored for later analysis. PBMCs from the stored samples were extracted and analyzed using the assays of Examples 1 and 2. The results are shown in Figures 8A-8C (Patient A) and Figures 8D-8F (Patient B). As shown in Figures 8C and 8F, Patient A had a modest increase in γ-Η2ΑΧ levels, while patient B did not.
[0121] Bone marrow and tumor biopsy samples were taken from patients before treatment with drugs and at various time points after treatment. The samples were frozen and stored for later analysis. Cells from the stored samples were extracted and analyzed by the assays of Examples 1 and 2. The results are shown in Figures 9A-9C (bone marrow) and Figures 9D-9F (tumor biopsy). As shown in Figures 9C and 9F, the assays of Examples 1 and 2 can be used to measure the amount of γ-Η2ΑΧ in archived bone marrow and tumor biopsies. [0122] The assays of Examples 1 and 2 were successfully used to measure the amount of γ-Η2ΑΧ in the biospecimen types shown in Table 9.
TABLE 9
Figure imgf000036_0001
EXAMPLE 9
[0123] This example demonstrates that the sensitivity of the combined assays of
Examples 1 and 2 is approximately 0.2 Gy.
[0124] Cultures of normal human fibroblasts (NHFs) were exposed to the amounts of radiation shown in Figure 10A. The exposed cells were permitted to recover for 30 minutes, then analyzed for γ-Η2ΑΧ and H2AX using the assays of Examples 1 and 2. The ratio of γ- H2AX to total H2AX was calculated, and the results are shown in Figures 10A and 10B. As shown in Figure 10B, the sensitivity of the assay was approximately 0.2 Gy.
EXAMPLE 10
[0125] This example demonstrates that the assays of Examples 1 and 2 may detect approximately 10,000 tumor cells in 0.25 mL of blood.
[0126] Normal blood (250 ί) was left unmixed (PBMC) or mixed (spiked) with different numbers of THP1 tumor cells that had been treated with various doses of IR, then analyzed using the assays of Examples 1 and 2. The ratio of γ-Η2ΑΧ to total H2AX was calculated, and the results are shown in Figures 12A and 12B. As shown in Figures 12A and 12B, approximately 10,000 tumor cells in 0.25 mL of blood could be detected.
[0127] Normal blood (250 μί) was unmixed or mixed (spiked) with different numbers of HT29 human colorectal adenocarcinoma tumor cells that were untreated or treated with ATR inhibitors VE-821 and camptothecin (CPT), then analyzed using the assays of Examples 1 and 2. The ratio of γ-Η2ΑΧ to total H2AX was calculated, and the results are shown in Figures 12C and 12D. As shown in Figures 12C and 12D, approximately 10,000 tumor cells in 0.25 mL of blood could be detected.
EXAMPLE 11
[0128] This example demonstrates that the immunoassays of Examples 1 and 2 may be used to detect the synergistic cytotoxicity of drug combinations using the ratio of γ-Η2ΑΧ to total H2AX as readout for DNA DSB breaks.
[0129] Cultured HT29 cells were treated with a single drug (CPT, AZD6738 (AZD) or VE821 (VE)), or combination of CPT plus AZD6738 or VE821. For single drug treatment, CPT (1 μΜ) was added into the culture media for a one (1) hour treatment, then washed twice. Medium (without drug) was added, and the cells were cultured for an additional seven (7) hour culture. For AZD6738 or VE821 treatment, drug (1 μΜ) was added to the culture medium and the cells were cultured for a total of eight (8) hours without changing the media. For combination of CPT with ATR inhibitor treatment, HT29 was first treated with CPT at 1 μΜ for 1 hour, then washed twice. AZD6738 or VE821 was added at 1 μΜ, and the cells were cultured for an additional 7 hours. At the end of the eight (8) hour culture, the cells were harvested, extracted, and analyzed using the assays of Examples 1 and 2. The ratio of γ- H2AX to total H2AX was calculated, and the results are shown in Figure 1 1. As shown in Figure 1 1 , the immunoassays of Examples 1 and 2 may be used to detect the synergistic cytotoxicity of drug combinations using the ratio of γ-Η2ΑΧ to total H2AX as a readout for DNA DSB breaks.
EXAMPLE 12
[0130] This example demonstrates that the immunoassays of Examples 1 and 2 detect DNA DSB in cells that have been treated with a genotoxic agent in vitro at a concentration as low as 1 nM.
[0131] HT29 cells were treated with the genotoxic agent camptothecin (CPT) or the non- genotoxic agent rhomidepsin for 1 hour at a concentration of 0 (vehicle) 0.001 , 0.001 , 0.01 , 1 or 10 μΜ. The cells were collected. The γ-Η2ΑΧ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 were used to determine the ratio of γ-Η2ΑΧ to total H2AX in the collected cells. The results are shown in Figure 13. DNA DSB, as measured by the ratio of γ-Η2ΑΧ to total H2AX, was detected with CPT treatment as low as 1 nM. In contrast, no DNA DSB, as measured by the ratio of γ-Η2ΑΧ to total H2AX, was detected following rhomidepsin treatment, even at a concentration as high as 10 μΜ.
EXAMPLE 13
[0132] This example demonstrates that the γ-Η2ΑΧ immunoassay of Example 1 and the total H2AX immunoassay of Example 2 provide a detectable signal of DNA DSB with as few as 160 cells when the cells are treated with a genotoxic agent at a concentration of 0.01 μΜ or higher in vitro.
[0133] HT29 were treated with CPT for 1 hour at a concentration of 0 μΜ (vehicle), 0.01 μΜ, 0.1 μΜ or 1 μΜ. The cells were collected and further diluted to 5000, 2500, 1250, 625, 312, or 156 cells per assay. The γ-Η2ΑΧ immunoassay of Example 1 was used to quantitate γ-Η2ΑΧ (Figure 14A) in the collected cells. The total H2AX immunoassay of Example 2 was used to quantitate total H2AX (Figure 14B) in the collected cells. The ratio of γ-Η2ΑΧ to total H2AX in the collected cells was determined (Figure 14C). As shown in Figure 14C, the ratio of γ-Η2ΑΧ to total H2AX provided a detectable signal of DNA DSB with as few as 160 cells when the cells were treated with CPT at a concentration of 0.01 μΜ or higher.
EXAMPLE 14
[0134] This example demonstrates that the immunoassays of Examples 1 and 2 detect DNA DSB in cells following treatment with a genotoxic agent in vitro.
[0135] The immunoassays of Examples 1 and 2 were tested for the ability to screen genotoxic agents, γ- H2AX is a sensitive and early signal of any one or more of DNA DSB, DNA repair, and apoptosis, any one or more of which may lead to tumor killing. Therefore, the immunoassays of Examples 1 and 2 were used for high throughput screening of potential agents for genotoxins and therapeutics. The genotoxic agents included Topi inhibitors, Top2 inhibitors, DNA crosslink formers, and blockers of one or more of DNA replication, DNA repair, and the cell cycle, as shown in Table 10.
[0136] HT29 or MCF7 cells were plated overnight and separately treated with vehicle (control) or the drug CPT, SN38, LMP776, LMP744, LMP400, AZD1775, cisplatin, etoposide, doxorubicin, talazoparib, olaparib, viromostat, erlotinib, or rhomidepsin under the conditions shown in Table 10. Table 10 also indicates whether each drug is a genotoxic agent ("yes"), a non-genotoxic agent ("no"), or whether it is unknown whether the drug is a genotoxic agent ("?"). The γ-Η2ΑΧ immunoassay of Example 1 was used to quantitate γ- H2AX (Figure 15) per lxlO7 collected cells. The total H2AX immunoassay of Example 2 was used to quantitate total H2AX (Figure 16) per lxlO7 collected cells. The ratio of γ- H2AX to total H2AX in the HT29 cells (Figure 17A) and the MCF7 cells (Figure 17B) was determined. As shown in Figures 17A and 17B, DNA DSB, as measured by the ratio of γ- H2AX to total H2AX, was detected with genotoxic agent treatment. In contrast, no DNA DSB, as measured by the ratio of γ-Η2ΑΧ to total H2AX, was detected following non- genotoxic agent treatment.
TABLE 10
Figure imgf000039_0001
EXAMPLE 15
[0137] This example compares the detection of DNA DSB using a microscope immunofluorescence assay (IF A) to the detection of DNA DSB using the immunoassays (IA) of Examples 1 and 2.
[0138] The presence of γ-Η2ΑΧ in the cells treated as described in Example 14 was confirmed by staining using a labeled anti-y-H2AX antibody and observing the intensity of the staining through a microscope. No staining was observed in the cells treated with vehicle. Staining was observed in the cells treated with, for example, 10 nM, 100 nM, 1 μΜ, and 10 μΜ CPT. The staining intensity increased as the concentration of CPT used to treat the cells increased.
[0139] The γ-Η2ΑΧ in the cells treated as described in Example 14 was quantified by staining using a labeled anti-y-H2AX antibody and measuring the intensity of the staining observed through a microscope (immunofluorescence microscope assay (IF A)). The quantity of γ-Η2ΑΧ measured by staining intensity was compared to the ratio of γ-Η2ΑΧ to total H2AX measured by the immunoassays (IA) of Examples 1 and 2. The results are shown in Figure 18A (HT29) and Figure 18B (MCF7).
EXAMPLE 16
[0140] This example demonstrates that the immunoassays of Examples 1 and 2 can be used to detect DNA DSB induced by the treatment of cells in vitro with drugs.
[0141] MCF7 cells were treated with vehicle (control), SN38 (0.25 μΜ), ataxia- telangiectasia, a rad3-related protein (ATR) inhibitor (ATRi) (1 μΜ), a combination of SN38 (0.25 μΜ) and the ARTi (1 μΜ), or a combination of SN38 (0.25 μΜ) and the ARTi (0.5 μΜ). The ATR inhibitor was AZD-6738, VE-821 , VE-822, Compound-45, or NU-6027. The treated cells were quantified for γ-Η2ΑΧ and total H2AX using the immunoassays of Examples 1 and 2, respectively, and the ratio of γ-Η2ΑΧ to total H2AX was determined. The results are shown in Figures 19A-19C (AZD-6738), Figures 20A-20C (VE-821), Figures 21A-21C (VE-822), Figures 22A-22C (Compound-45), and Figures 23A-23C (NU-6027). To independently confirm the presence of γ-Η2ΑΧ, cells were concentrated by cytospin, and the cell lysate was stained using anti-y-H2AX antibody. The stain was observed through a microscope. More intense staining was observed in the lysate from cells treated with a combination of SN38 and ATRi as compared to that from cells treated with SN38 or ATRi alone. No stain was observed in the lysate of cells treated with vehicle. Accordingly, the γ- H2AX antibody independently confirmed the presence of γ-Η2ΑΧ in the treated cells.
[0142] As shown in Figures 19A-19C, Figures 20A-20C, Figures 21A-21 C, Figures 22A- 22C, and Figures 23A-23C, treatment with ATRi alone did not significantly induce formation of γ-Η2ΑΧ. However, some combinations of the To i inhibitor SN38 with the ATRi led to synergistic induction of DNA DSB. Among the five ATR inhibitors evaluated in
combination with the Topi inhibitor SN38, VE-822 and AZD-6738 were observed to have the highest synergy for γ-Η2ΑΧ induction, while NU-6027 showed none. EXAMPLE 17
[0143] This example demonstrates that the immunoassays of Examples 1 and 2 can be used to detect DNA DSB induced by treating tumor-bearing mice with drugs in vivo.
[0144] A375 xenograft mouse models were treated with vehicle (control), CPT-11 alone, a PARP inhibitor alone, a combination of CPT-11 and the PARP inhibitor (PARPi) administered simultaneously, or a combination of CPT-1 1 and the PARPi, wherein the PARPi is administered four hours before CPT-1 1 is administered. CPT-1 1 is a modified version of CPT, also referred to as ironotecan (CAMPTOSAR). The PARP inhibitor was ABT-888, AZD-2281 , or MK-4827. The dosages are shown in Figures 24A-24C, Figures 25A-25C, and Figures 26A-26C. Cells from the treated mice were quantified for γ-Η2ΑΧ and total H2AX using the immunoassays of Examples 1 and 2, respectively, and the ratio of γ-Η2ΑΧ to total H2AX was determined. The results are shown in Figures 24A-24C
(MK4827), Figures 25A-25C (AZD2281), and Figures 26A-26C (ABT888).
[0145] As shown in Figures 24A-24C, Figures 25A-25C, and Figures 26A-26C, combinations of CPT-11 with ABT-888, AZD-2281 or MK-4827 caused synergistic induction of γ-Η2ΑΧ, which indicates DNA DSB, in A375 xenografts in vivo.
EXAMPLE 18
[0146] This example compares the detection of DNA DSB using a microscope immunofluorescence assay (IF A) to the detection of DNA DSB using the immunoassays (IA) of Examples 1 and 2.
[0147] A375 xenograft mouse models were treated with vehicle (control), camptothecin- 1 1 (CPT-11) alone, a PARP inhibitor alone, or a combination of CPT-1 1 and the PARP inhibitor at the dosages indicated in Figures 27A-27C. The PARP inhibitor was ABT-888, AZD-2281, or MK-4827. Cells from the treated mice were quantified for γ-Η2ΑΧ and total H2AX using the immunoassays of Examples 1 and 2, respectively, and the ratio of γ-Η2ΑΧ to total H2AX was determined. The results are shown in Figure 27A.
[0148] The γ-Η2ΑΧ in the cells from the treated mice was quantified by staining using a labeled anti-y-H2AX antibody and counting the nuclear foci through a microscope. The results are shown in Figure 27B. The ratio of γ-Η2ΑΧ to total H2AX shown in Figure 27A was comparable to the microscopy data, shown in Figure 27B. PARP inhibition was confirmed by PAR ELISA (Figure 27C). [0149] All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.
[0150] The use of the terms "a" and "an" and "the" and "at least one" and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The use of the term "at least one" followed by a list of one or more items (for example, "at least one of A and B") is to be construed to mean one item selected from the listed items (A or B) or any combination of two or more of the listed items (A and B), unless otherwise indicated herein or clearly
contradicted by context. The terms "comprising," "having," "including," and "containing" are to be construed as open-ended terms (i.e., meaning "including, but not limited to,") unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., "such as") provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
[0151] Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

Claims

CLAIM(S):
1. A method of measuring the amount of exposure of a host to a DNA double- stranded break (DSB)-causing agent, the method comprising:
contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ;
contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein,
wherein the positive control biological sample has been exposed to a known amount of the D SB-causing agent;
contacting the first and second complexes of the positive control biological sample and the biological sample from the host with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex;
detecting the third and fourth complexes in the positive control biological sample and the biological sample from the host;
quantifying the third and fourth complexes in the positive control biological sample and the biological sample from the host;
determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample;
determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host; and
comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the biological sample from the host to determine the amount of exposure of the host to the DNA DSB-causing agent.
2. The method of claim 1 , wherein the DNA DSB-causing agent is ionizing radiation
(IR).
3. The method of claim 1 , wherein the DNA DSB-causing agent is a drug.
4. The method of claim 1, wherein the DNA DSB-causing agent is an anti-cancer agent.
5. A method of quantifying DNA DSBs in a test biological sample, the method comprising:
contacting (i) a first portion of a positive control biological sample and (ii) a first portion of a test biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ;
contacting (i) a second portion of the positive control biological sample and (ii) a second portion of the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein,
wherein the positive control biological sample has a known quantity of DSBs; contacting the first and second complexes of the positive control biological sample and the test biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex;
detecting the third and fourth complexes in the positive control biological sample and the test biological sample;
quantifying the third and fourth complexes in the positive control biological sample and the test biological sample;
determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample;
determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample; and
comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the positive control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the test biological sample to determine the quantity of DSBs in the test biological sample.
6. A method of testing compounds for ability to cause DNA DSBs in a host, the method comprising:
(a) contacting (i) a first portion of a control biological sample and (ii) a first portion of a host biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ, wherein the host biological sample is from a host which has been administered a test compound;
(b) contacting (i) a second portion of the control biological sample and (ii) a second portion of the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein,
wherein the control biological sample has not been exposed to the test compound;
(c) contacting the first and second complexes of the control biological sample and the host biological sample with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex;
(d) detecting the third and fourth complexes in the control biological sample and the host biological sample;
(e) quantifying the third and fourth complexes in the control biological sample and the host biological sample;
(f) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample; and
(g) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample;
(h) comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the host biological sample,
wherein an increase in the ratio in the host biological sample as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs in the host.
7. The method of any one of claims 1 -6, wherein the biological samples comprise cell lysates from no more than a single cell type.
8. The method of any one of claims 1 -6, wherein the biological samples comprise cell lysates from two or more cell types.
9. A method of screening test compounds for ability to cause DNA DSBs, the method comprising:
(a) dividing a population of test biological samples into more than one test sub- population;
(b) treating each test sub-population with a test compound, wherein each test sub- population is treated with a different test compound;
(c) contacting (i) a first portion of each treated test sub-population and (ii) a first portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ and forms a first complex with the γ-Η2ΑΧ;
(d) contacting (i) a second portion of each treated test sub-population and (ii) a second portion of a control biological sample with an antibody or antigen binding fragment thereof that specifically binds to an H2A core protein and forms a second complex with the H2A core protein;
wherein the control biological sample has not been treated with a test compound;
(e) contacting the first and second complexes of the control biological sample and the treated test sub-populations with an antibody or antigen binding fragment thereof that specifically binds to H2AX and forms a third complex with H2AX in the first complex and forms a fourth complex with H2AX in the second complex;
(f) detecting the third and fourth complexes in the control biological sample and the treated test sub-populations;
(g) quantifying the third and fourth complexes in the control biological sample and the treated test sub-populations;
(h) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample;
(i) determining a ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub-populations; and (j) comparing the ratio of the quantity of the third complex to the quantity of the fourth complex in the control biological sample to the ratio of the quantity of the third complex to the quantity of the fourth complex in the treated test sub-populations,
wherein an increase in the ratio in a treated test sub-population as compared to the ratio in the control biological sample indicates that the test compound has the ability to cause DNA DSBs.
10. The method of any one of claims 1-9, wherein the antigen binding fragment of the antibody that specifically binds to γ-Η2ΑΧ is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide- stabilized variable region fragment (dsFv).
1 1. The method of any one of claims 1-10, wherein the antigen binding fragment of the antibody that specifically binds to the H2A core protein is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
12. The method of any one of claims 1-1 1 , wherein the antigen binding fragment of the antibody that specifically binds to H2AX is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide- stabilized variable region fragment (dsFv).
13. A kit comprising:
at least one substrate;
an antibody or antigen binding fragment thereof that specifically binds to γ-Η2ΑΧ; an antibody or antigen binding fragment thereof that specifically binds to H2A core protein;
an antibody or antigen binding fragment thereof that specifically binds to H2AX; and a detecting agent comprising a label.
14. The kit according to claim 13, wherein the detecting agent is an antibody or antigen binding fragment thereof that specifically binds to the antibody or antigen binding fragment thereof that specifically binds to H2AX.
15. The kit according to claim 13 or 14, wherein the label is an enzyme.
16. The kit according to claim 13 or 14, wherein the label is a fluorescent molecule.
17. The kit according to claim 13 or 14, wherein the label is a dye.
18. The kit according to claim 13 or 16, wherein the label is biotin.
19. The kit according to any one of claims 13-18, wherein the antigen binding fragment of the antibody that specifically binds to γ-Η2ΑΧ is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
20. The kit according to any one of claims 13-19, wherein the antigen binding fragment of the antibody that specifically binds to the H2A core protein is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
21. The kit according to any one of claims 13-20, wherein the antigen binding fragment of the antibody that specifically binds to H2AX is a Fab fragment (Fab), F(ab')2 fragment, diabody, triabody, tetrabody, single-chain variable region fragment (scFv), or disulfide-stabilized variable region fragment (dsFv).
22. The kit according to any one of claims 13-21 , wherein the substrate is a multiwell plate.
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