Classifications

• • 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
  • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
  • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
  • G01N33/5011—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing antineoplastic activity
• • C—CHEMISTRY; METALLURGY
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  • 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
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
  • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
  • C12N15/1135—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against oncogenes or tumor suppressor genes
• • 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
  • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters
• • 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
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/136—Screening for pharmacological compounds
• • 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
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/154—Methylation markers
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
  • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
  • Y10T436/00—Chemistry: analytical and immunological testing
  • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
  • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
  • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Definitions

• the present invention relates to methods of identifying candidate compounds for the treatment of leukemia and diagnostic methods based on histone methylation.
• HMTases histone methyltransferases
• H3-K4 methyltransferase MLL is frequently translocated in leukemia (Ayton and Cleary (2001 ) Oncogene 20:5695-5707; Milne, et al. (2002) MoI. Ce// 10:1107-1117; Nakamura, et al. (2002) MoI.
• hDOTI L is a histone H3-K79 methyltransferase (Feng et al., (2002) Curr. Biol. 12:1052-1058), and plays an important role in MLL-AF10-mediated leukemogenesis (Okada et al., (2005) Cell 121 :167-78). It was shown that mistargeting of hDOTI L to the Hoxa9 gene by MLL-AF10 results in H3-K79 methylation and Hoxa9 upregulation which contributes to leukemic transformation (Okada et al., (2005) Cell 121 :167-78).
• hDOTIL and MLL-AF10 interaction involves the OM-LZ (octapeptide motif-leucine zipper) region of AF10, required for MLL-AF10-mediated leukemic transformation (DiMartino et al., (2002) Blood 99:3780-5).
• CALM- AF10 fusion appears to be both necessary and sufficient to mediate leukemogenesis in vitro and in vivo; (2) that hDOTIL and its H3-K79 methyltransferase activity are implicated in CALM-AF10 mediated leukemic transformation; and (3) that the Hoxa ⁇ gene is involved in CALM-AF10 mediated transformation.
• the inventors also provide an experimental model where hDOTIL retains nuclear localization of CALM-AF10 through protein-protein interaction. CALM-AF10 in association with hDOT1 L is then recruited to the Hoxa5 promoter to mediate H3-K79 methylation which in turn leads to Hoxa ⁇ upregulation and leukemogenesis.
• Chromosomal translocation is one of the major causes of human cancer, particularly in acute leukemias.
• a translocation of t(10;11 )(p12- 13;q14-q23), which generates the chimeric gene CALM-AF10, is observed in various types of leukemias including T-ALL (T cell acute lymphoid leukemia) and AML (acute myeloid leukemia) (Carlson et al., (2000) Leukemia 14:100- 104; Dreylng et al., (1998) Blood 91 :4662-7).
• CALM clathrin assembly lymphoid myeloid leukemia
• the present invention provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a DOT1 L polypeptide with a CALM-AF10 fusion protein in the presence of a test compound under conditions sufficient for binding of the DOT1L polypeptide to the CALM-AF10 fusion protein; and detecting interaction between the DOT1L polypeptide and the CALM-
• AF10 fusion protein wherein a reduction in interaction between the DOT1 L polypeptide and the CALM-AF10 fusion protein in the presence of the test compound as compared with the level of interaction in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the invention further provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a CALM-AF10 fusion protein with a test compound under conditions sufficient for binding of the test compound to the CALM-AF10 fusion protein; and detecting binding between the test compound and the CALM-AF10 fusion protein, wherein binding of the test compound to the CALM-AF10 fusion protein indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a nucleic acid comprising a HoxA5 promoter region with a CALM polypeptide or CALM-AF10 fusion protein in the presence of a test compound under conditions sufficient for binding of the CALM polypeptide or CALM-AF10 fusion protein to the HoxA5 promoter; and detecting interaction of the CALM polypeptide or CALM-AF10 fusion protein with the HoxA5 promoter, wherein a reduction in interaction between the CALM polypeptide or CALM-AF10 fusion protein with the HoxA5 promoter in the presence of the test compound as compared with the level of interaction in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a nucleic acid comprising a HoxA5 promoter region with a DOT1L polypeptide and a CALM-AF10 fusion protein in the presence of a test compound under conditions sufficient for binding of the DOT1L polypeptide and the CALM-AF10 fusion protein to form a complex and for the complex to bind to the HoxA5 promoter; and detecting interaction of the DOT1 L/CALM-AF10 complex to the HoxA5 promoter, wherein a reduction in interaction of the DOT1L/CALM-AF10 complex with the HoxA5 promoter in the presence of the test compound as compared with the level of interaction in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a nucleic acid comprising a HoxA5 promoter region and/or any other portion of the HoxA5 gene with a test compound under conditions sufficient for the test compound to bind to the HoxA5 promoter region and/or the any other portion of the HoxA5 gene; and detecting binding between the test compound and the HoxA5 promoter and/or the any other portion of the HoxA5 gene, wherein binding between the test compound and the HoxA5 promoter and/or the any other portion of the HoxA5 gene indicates that the test ,P ⁇ ,,n ⁇ - «. tenuously UfJt / " "I IM' ' ( .”I' ...I!.. compound is a candidate compound for the prevention and/or treatment of leukemia.
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the 5 method comprising: contacting a nucleic acid comprising a HoxA ⁇ promoter region with a test compound under conditions sufficient for HoxA ⁇ promoter activity; and detecting HoxA ⁇ promoter activity, wherein a reduction in HoxA ⁇ promoter activity in the presence of the 0 test compound as compared with the level of HoxA ⁇ promoter activity in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of T cell acute ⁇ lymphoid leukemia (T-ALL) or acute myeloid leukemia subtype MO/1 (AML- M0/1 ): contacting a DOT1 L polypeptide with a histone or nucleosome substrate comprising histone H3 in the presence of a test compound; detecting histone H3 lysine 79 (H3-K79) methylation of the substrate 0 under conditions sufficient to provide H3-K79 methylation; wherein an reduction in H3-K79 methylation in the presence of the test compound as compared with the level of H3-K79 methylation in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of T-ALL or AML subtypes ⁇ MO/1.
• T-ALL T cell acute ⁇ lymphoid leukemia
• AML- M0/1 acute myeloid leukemia subtype MO/1
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of T-ALL or AML- M0/1 : contacting a DOT1L polypeptide with AF10 under conditions sufficient 0 for binding of the DO1 L polypeptide to AF10; detecting interaction between the DOT1 L polypeptide and AF10; wherein a reduction in interaction between DOT1 L polypeptide and AF10 in the presence of the test compound as compared with the level of binding in the absence of the test compound indicates that the test compound ⁇ Z» %,$ Wl > •' ' " 1 T- W' llmi. is a candidate compound for the prevention and/or treatment of T-ALL or AML subtypes MO/1.
• the invention also encompasses diagnostic methods.
• the invention provides a method of diagnosing whether a subject has or is at risk for developing leukemia and/or determining the prognosis for the course of the disease, the method comprising: obtaining a biological sample comprising histones (e.g., nucleosomes) from a subject; detecting histone H3 lysine 79 (H3-K79) methylation associated with the HoxA5 gene; wherein an increase in HoxA5-associated H3-K79 methylation in the biological sample as compared with the level of HoxA5-associated H3-K79 methylation in a non-leukemic biological sample is diagnostic that the subject has or is at risk of developing leukemia and/or is prognostic of the course of the disease in the subject.
• histones e.g., nucleosomes
• the invention provides a method of diagnosing whether a subject has or is at risk for developing leukemia and/or determining the prognosis for the course of the disease, the method comprising determining HoxA5 promoter activity in the subject.
• FIG. 1A-F Knockdown of CALM-AF10 in U937 cells impairs their proliferation and leukemogenesis in vitro and in vivo
• a Top panel depicts the fusion protein and the target region for knockdown. The two arrows indicate the primer position used for RT-PCR. Bottom panel is RT-PCR results evaluating the knockdown efficiency. /?-actin serves as a control.
• V vector control
• KD Knockdown
• b, c Effects of CALM-AF10 knockdown on cell proliferation in RPMI medium (b) and methylcellulose (c). Only colonies having over 50 cells were counted.
• FIGS 2A-F Expression of CALM-AF10 is sufficient to cause mouse bone marrow cell transformation and hDOTIL plays an important role in this process
• a Schematic representation of the retroviral transduction procedures
• b Expression confirmation of the transduced genes by RT-PCR.
• U937 cells serve as a positive control.
• GAPDH serves as a control for equal input RNA in RT-PCR.
• c Serial colony plating assay of bone marrow cells transduced by wild-type and mutant CALM-AF10 with vector control. Presented is the average colony numbers with standard deviations of three independent experiments.
• d Growth curve of the transduced cells in mFTOC culture
• e lmmunophenotyping by FACS of CALM-AF10 transformed cells.
• the cell surface markers used in the analysis are indicated, f, Diagram of the 2nd transduction procedure (left panel), and the effect of wild-type and catalytic-deficient hDOTI L on colony formation of CALM-AF10 transformed cells (right panel).
• FIGS 3A-B Hoxa ⁇ is involved in leukemic transformation by CALM- AF10.
• a Left panel, RT-PCR analysis of the expression of late Hoxa genes and Bmi-1 in wild-type and CALM-AF10 knockdown U937 cells.
• Right panel RT-PCR analysis of expression of late Hoxa genes and Bmi-1 in mouse bone marrow cells derived from second round colonies, and transduced by wild- type and OM-LZ deletion CALM-AF10 mutants.
• Lack of detectable signal for Hoxa9 is not due to primer failure as the same primers detected Hoxa9 expression in MLL-ENL transduced cells (lane 9).
• Nuclei are stained by DAPI (lower panel), d, Quantification of the cells presented in (c).
• N cells expressed in the nucleus.
• FIGS 5A-C CALM-AF10 in association with hDOTIL binds to Hoxa ⁇ both in the promoter and downstream to mediate local H3-K79 methylation.
• a Diagram of the Hoxa ⁇ gene locus and amplicons used for ChIP assays
• b ChIP analysis of the location of CALM-AF10 across the
• FIGS 6A-B CALM-AF10 and hDOTI L interaction is mediated by the OM-LZ region of AF10.
• a Diagram of the constructs used in transfection.
• b Co-immunoprecipitation of CALM-AF10 and hDOTIL in 293T cells. Transfected cells were harvested 36 hours post-transfection. Total cell "MJh&c&sw&M prepared with lysis buffer containing 420 mM KCI. M2 agarose beads were used for immunoprecipitation, and the beads were washed with lysis buffer containing 500 mM KCI. The result was analyzed by Western blotting using hDOTIL (top panel) and Flag (bottom panel) antibodies. In: Input, S: Supernatant, IP: Immunoprecipitate.
• Figures 7A-B Schematic representation of CALM and AF10 proteins. Potential functional motifs, including NES and NLS are indicated. Red arrows indicate the major breakpoint for the CALM-AF10 fusion present in U937 cells. The green arrow indicates breakpoint of AF10 in MLL-AF10 fusion. Numbers represent amino acid position, b, Alignment of a putative NES sequence in CALM. This sequence is conserved in AP180, an endocytotic accessory protein similar to CALM.
• FIG. 8 FACS analysis demonstrating the immunophenotypic differences between CALM-AF10 and MLL-AF10-tranduced bone marrow cells.
• Cells derived from second round colonies of wild-type Hoxa ⁇ bone marrow cells were stained with c-Kit, Gr1 , and CD11 b antibodies before FACS analysis.
• Chromatin structure is important in gene regulation and epigenetic inherence. It is known that post-translational modifications of histones are involved in the establishment and maintenance of higher-order chromatin structure; further, it has been reported that the tails of certain core histones are modified by acetylation, methylation, phosphorylation, ribosylation and ubiquitination.
• the present invention is based, in part, on the first demonstration that (1 ) CALM-AF10 fusion appears to be both necessary and sufficient to mediate leukemogenesis in vitro and in vivo; (2) that hDOTI L and its H3-K79 methyltransferase activity are implicated in CALM-AF10 mediated leukemic transformation; and (3) that the Hoxa ⁇ gene is involved in CALM- AF10 mediated transformation. While not wishing to be limited to any theory of the invention, the inventors also provide an experimental model where '"3 clear localization of CALM-AF10 through protein-protein interaction.
• polypeptide includes both proteins and peptides.
• the polypeptides used in the practice of the present invention are “isolated” polypeptides.
• An “isolated” polypeptide as used herein is a polypeptide that is separated or substantially free from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other ⁇ '"'p ⁇ ypeptici ⁇ s'or nucleic acids commonly found associated with the polypeptide.
• the "isolated" polypeptide is at least about 1%, 5%, 10%, 25%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or more pure (w/w).
• an "isolated" polypeptide indicates that at least about a 5-fold, 10-fold, 25-fold, 100-fold, 1000-fold, 10,000-fold, or more enrichment of the protein (w/w) is achieved as compared with the starting material.
• the nucleic acids used in the present invention are “isolated” nucleic acids.
• an “isolated” nucleic acid means a nucleic acid separated or substantially free from at least some of the other components of the naturally occurring organism, such as for example, the cell structural components or other polypeptides or nucleic acids commonly found associated with the nucleic acid.
• the "isolated” nucleic acid is at least about 1%, 5%, 10%, 25%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or more pure (w/w).
• an "isolated" nucleic acid indicates that at least about a 5- fold, 10-fold, 25-fold, 100-fold, 1000-fold, 10,000-fold, 100,000-fold or more enrichment of the nucleic acid (w/w) is achieved as compared with the starting material.
• expression and grammatical equivalents with reference to a nucleic acid refers to transcription of the nucleic acid and, optionally translation.
• modulate refers to an increase or decrease.
• the term “increase” or “enhance” means an elevation by at least about 25%, 50%, 75%, 2-fold, 3-fold, 5-fold, 10-fold, 15-fold, 20-fold or more.
• the terms “decrease” or “reduce” means a diminishment by at least about 25%, 40%, 50%, 60%, 75%, 80%, 85%, 90%, 95%, 98% or more.
• the indicated activity, substance or other parameter is not detectable.
• treat By the term “treat,” “treating” or “treatment of (or grammatically equivalent terms) it is meant that the severity of the subject's condition is reduced or at least partially improved or ameliorated and/or that some alleviation, mitigation or decrease in at least one clinical symptom is achieved ⁇ in. HI . ⁇ ' * st s c S-'-. "S '"a
• treat there "is a " delay in the progression of the condition and/or prevention or delay of the onset of a disease or disorder.
• the term “treat,” “treats,” “treating,” or “treatment of and the like also include prophylactic treatment of the subject (e.g., to prevent the onset of infection or cancer).
• the term “prevent,” “prevents,” or “prevention” are not meant to imply complete abolition of disease and encompasses any type of prophylactic treatment that reduces the incidence of the condition, delays the onset and/or progression of the condition, and/or reduces the symptoms associated with the condition.
• the term “treat,” “treating” or “treatment of (or grammatically equivalent terms) refer to both prophylactic and therapeutic regimens.
• a “treatment effective amount” is an amount that is sufficient to treat (as defined herein) the subject.
• a “diagnostic method”, as used herein, refers to a screening procedure that is carried out to identify those subjects that are affected with and/or at risk for a particular disorder.
• a “prognostic method” refers to a method used to help predict, at least in part, the course of a disease ⁇ e.g., more aggressive or less aggressive).
• a prognostic method may be used to assess the severity of the disease.
• the screening procedure disclosed herein may be carried out to both identify an affected individual, to evaluate the severity of the disease, and/or to predict the future course of the disease. Such methods may be useful in evaluating the possible benefit of therapeutic treatment, what type of treatment to implement, and the like.
• a prognostic method may be carried out on a subject previously diagnosed with a particular disorder when it is desired to gain greater insight into how the disease will progress for that particular subject (e.g., the likelihood that a particular patient will respond favorably to a particular drug treatment, or when it is desired to classify or separate patients into distinct and different sub-populations for the purpose of conducting a clinical trial thereon).
• the present invention provides methods of using the interaction(s) between DOT1 L and/or CALM-AF10 and/or HoxA5 as a target for drug discovery.
• the invention can be practiced with any DOT1 L polypeptide or nucleic acid now known or later discovered.
• DOT1L nucleic acid and polypeptides have previously been described (see, e.g., U.S. Patent Publication No. 2005- 0048634 A1 ; Feng et al., (2002) Curr. Biol.
• the yeast homolog of DOT1 was originally identified as a Disruptor Of Telomeric silencing (the protein and nucleic acid sequences of yeast DOT1 can be found at Accession No. NP_010728).
• the human homolog designated as hDOTI L (human DOT1-like protein), has been cloned and isolated, and determined to be an HMTase.
• the sequences of the hDOTIL nucleic acid and protein have been deposited under GenBank accession number AF509504. Only the approximately 360 N-terminal amino acids of hDOT1 L share significant sequence similarity with the yeast DOT1.
• DOT1 homologs from C. elegans (C. elegans, GenBank Accession number NP_510056 and CAA90610), Drosophila (GenBank Accession No. CG10272 and AAF54122), mouse (GenBank Accession No. XP_125730), Anopheles gambiae (GenBank
• the DOT1 L polypeptide has
• H3-K79 specific HMTase activity By H3-K79 "specific" HMTase activity it is meant that all, or essentially all, of the HMTase activity is directed to H3-K79
• AF10 polypeptides are also known in the art, see, e.g., human AF10 sequence, Gen Bank Accession No. AY598745; mouse AF10 sequence,
• GenBank Accession No. 054826 GenBank Accession No. 054826.
• the present invention can be practiced with any AF 10 polypeptide known now or later determined.
• CALM polypeptide now known in the art or later discovered, see, e.g., GenBank Accession Nos.
• AAB07762 human amino acid
• U45976 human mRNA
• X6877 and NM_031728 rat nucleic acid
• M83985, AAA37587 and AAA37586 mouse amino acid
• S27866 mouse nucleic acid
• XM_595075 and XP_595075 bovine amino acid
• S39150 and XP_595075 bovine nucleic acid
• DOT1L polypeptide encompass functional fragments of the full-length polypeptides and functional equivalents of either of the foregoing that have substantially similar or substantially identical amino acid sequences (at least about 75%, 80%, 85%,
• polypeptide (or nucleic acid) has the same or substantially similar activity with respect to one or more of the biological properties of the native polypeptide (or nucleic acid), e.g., at least about 50%, 75%, 85%, 90%, 95% or 98% or more of the activity of the native polypeptide (or nucleic acid).
• a functional DOT1L polypeptide (including functional fragments and functional equivalents as discussed above) has the same or substantially similar H3-K79 HMTase activity, SAM binding activity, histone and/or nucleosome binding activity, AF10 binding activity, CALM-AF10 fusion protein binding activity, leukemogenic activity and/or any other biological activity of interest as compared with a native DOT1 L polypeptide.
• Methods of assessing DOT1L binding to histones, nucleosomes, nucleic acids or polypeptides can be carried out using standard techniques that will be apparent to those skilled in the art (see the Examples for exemplary methods). Such methods include yeast and mammalian two- hybrid assays and co-immunoprecipitation techniques.
• DOT1L DOT1L
• H3-K79 HMTase and leukemogenic activity can also be evaluated using standard methods known in the art, for example, as described in the Examples below.
• the invention can also be practiced with functional fragments of CALM, AF10, and DOT1L, and functional equivalents thereof.
• functional DOT1 L fragments and functional equivalents thereof comprise the catalytic domain comprising the SAM binding domain (optionally comprising adjacent sequences) and nucleic acids encoding the same.
• Functional DOT1 L fragments and functional equivalents comprising the catalytic domain can optionally further comprise the DOT1 L positively charged region.
• the functional DOT1 L fragment or functional equivalent comprises the DOT1 L leucine rich interaction domain with AFIO.
• the functional DOT1 L fragment or functional equivalent can comprise the leucine zipper region and/or the coiled coil region. In still further embodiments, the functional DOT1 L fragment or functional equivalent comprises the nuclear export signal and/or nuclear localization signal.
• the functional DOT1 L fragment or functional equivalent comprises the N-terminal portion of a DOT1 polypeptide, Wl ⁇ ampifapproximately the N-terminal 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100 amino acids.
• the functional fragment is truncated at the N-terminus, e.g., less than about 100, 85, 75, 60, 50, 35, 20, 15, 10 or 5 amino acids are truncated from the N-terminus.
• the functional DOT1 L fragment or functional equivalent comprises the N-terminal 10 to 100 amino acids, the N-terminal 10 to 70 amino acids, the N-terminal 20 to 50 amino acids or the N-terminal 20 to 40 amino acids.
• the N-terminal 5 to 100, 10 to 75 or 15 to 50 amino acids are truncated from the N-terminus functional DOT1 L fragment or functional equivalent.
• a functional AF10 fragment or functional equivalent has the same or substantially similar DOT1L binding activity, leukemogenic activity and/or any other biological activity of interest as compared with a native AF10 polypeptide.
• the functional AF10 fragment or functional equivalent can comprise the OM-LZ domain, e.g., amino acids 719-800 of AF10 [human AF10 sequence, Accession No. AY598745; mouse AF10 sequence, Accession No. 054826], the PHD sequence, the AT sequence, the C-terminal glutamine-rich region and/or the nuclear localization signal.
• a functional CALM fragment or functional equivalent has the same or substantially similar leukemogenic activity, HoxA5 gene binding activity and/or any other biological activity of interest as compared with a native CALM polypeptide.
• the functional CALM fragment or functional equivalent comprises the putative CRM 1 -dependent NES (nuclear exporting signal) sequence at its C-terminus, the ENTH domain, the HoxA5 gene binding domain and/or the clathrin-binding domain.
• equivalents refers to an amino acid sequence that is altered by one or more amino acids.
• the equivalent may have "conservative" changes, wherein a substituted amino acid has similar structural or chemical properties.
• such changes can be guided by known similarities between amino acids in physical features such as charge density, ihy ⁇ rophobicity/ ⁇ yclroph ilicity, size and configuration, so that amino acids are substituted with other amino acids having essentially the same functional properties.
• Sequence similarity or identity may be determined using standard techniques known in the art, including, but not limited to, the local sequence identity algorithm of Smith & Waterman, Adv. Appl. Math. 2, 482 (1981 ), by the sequence identity alignment algorithm of Needleman & Wunsch, J. MoI. Biol. 48,443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Natl. Acad.
• WU-BLAST-2 uses several search parameters, which are optionally set to the default values. The parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched; however, the values may be adjusted to increase sensitivity.
• identities are scored positively (+1 ) and all forms of sequence variation including gaps are assigned a value of "0", which obviates the need for a weighted scale or parameters as described below for sequence similarity calculations.
• Percent sequence identity can be calculated, for example, by dividing the number of matching identical residues by the total number of residues of the "shorter" sequence in the aligned region and multiplying by 100. The "longer" sequence is the one having the most actual residues in the aligned region.
• the length of the polypeptide fragment is not critical.
• Illustrative functional fragments comprise at least about 80, 100, 200, 300, 400, 500, 600, 700, 800, 1000, 1200, 1400 or more amino acids (optionally, contiguous amino acids) of a full-length polypeptide, e.g., about 80 to 1400 amino acids, about 100 to 1000 amino acids, about 100 to 700 amino acids, or about 200 to 600 amino acids (optionally, contiguous amino acids) of a full-length polypeptide .
• the invention also provides nucleic acids encoding the functional fragments.
• Exemplary nucleic acids encoding functional fragments comprise at least about 250, 300, 400, 500, 600, 700, 800, 1000, 1500, 2000, 2OTOf more nucleotide bases (optionally, contiguous bases) of a nucleic acid encoding a full-length polypeptide, e.g., about 250 to 4000, about 300 to 3000, about 300 to 2000, about 400 to 2000, or about 600 to 1500 nucleotide bases (optionally, contiguous bases).
• the polypeptides can be derived from any species of interest (e.g., mammalian [including but not limited to human, non-human primate such as monkey, mouse, rat, lagomorph, bovine, ovine, caprine, porcine, equine, feline, canine, etc.], insect, yeast, avian, plants, etc.) as well as allelic variations, isoforms, splice variants and the like.
• the amino acid sequences can further be wholly or partially synthetic.
• DOT1 L polypeptide encompass fusion proteins (and nucleic acid sequences encoding the same) comprising the polypeptide (including functional fragments).
• the fusion protein is a non-naturally occurring fusion protein and the afore-mentioned terms do not encompass naturally occurring fusion proteins.
• naturally occurring fusion protein includes those associated with pathological states such as MLL-AF10 or CALM-AF10.
• polypeptide it may be useful to express the polypeptide as a fusion protein that can be recognized by a commercially available antibody (e.g., FLAG motifs) or as a fusion protein that can otherwise be more easily purified (e.g., by addition of a poly-His tail).
• fusion proteins that enhance the stability of the protein may be produced, e.g., fusion proteins comprising maltose binding protein (MBP) or glutathione-S-transferase.
• the fusion protein can comprise a reporter molecule.
• a fusion protein can be generated for use in yeast two-hybrid systems (e.g., GAL4-DOT1 L fusions), as known in the art.
• CALM-AF10 fusion protein encompasses naturally and non- naturally occurring fusion proteins between AF10 and CALM as well as functional fragments and functional equivalents thereof which retain at least one biological activity of CALM-AF10 such as DOT1 L binding, HoxA5 gene binding, leukemogenesis and/or any other biological activity of interest.
• the AF10 and CALM portions of the fusion protein are as described herein for "r ⁇ f6 andBAt ⁇ Ci 'polypeptides.
• a trifusion of DOT1L/CALM-AF10 can be constructed for use in the methods of the invention.
• the present invention can be used in a number of research, diagnostic and/or therapeutic applications.
• the DOT1 L polypeptides, CALM polypeptides, AF10 polypeptides and CALM-AF10 fusion proteins and nucleic acids encoding the same can be used to identify:
• CALM complex regional lung disease 2019
• compounds that bind to and/or modulate e.g., increase or decrease) one or more biological activities of CALM, including but not limited to leukemogenic activity and/or any other biological activity of interest;
• HoxA5 promoter activity e.g., transcription of a nucleic acid operatively associated with the HoxA5 promoter, whether native or heterologous
• DOT1 L/CALM-AF10 e.g., transcription of a nucleic acid operatively associated with the HoxA5 promoter, whether native or heterologous
• CALM-AF10 e.g., CALM-AF10
• CALM e.g., a chimeric construct comprising the HoxA5 promoter operably associated with a transgene, such as a reporter gene).
• the present invention further encompasses methods of identifying compounds for the treatment and/or prevention of leukemia by identifying compounds that bind to and/or modulate the biological activity of a DOT1L polypeptide, CALM polypeptide, AF10 polypeptide, CALM-AF10 fusion protein, DOT1 L/CALM-AF10 trifusion protein, modulate HoxA5 promoter activity and/or modulate the interaction of DOT1 L, CALM, AF10, CALM-AF10 and/or HoxA5.
• the invention provides methods of identifying compounds for the treatment and/or prevention of T cell acute lymphoid leukemia (T-ALL) or acute myeloid leukemia subtype MO/1 (AML- MO/1 ).
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a DOT1L polypeptide with a CALM-AF10 fusion protein in the presence of a test compound under conditions sufficient for binding of the DOT1 L polypeptide to the CALM-AF10 fusion protein; and detecting the level of interaction between the DOT1 L polypeptide and the CALM-AF10 fusion protein, wherein a reduction in interaction between the DOT1 L polypeptide and the CALM-AF10 fusion protein in the presence of the test compound as compared with the level of interaction in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the level of DOT1 L polypeptide interaction with the CALM-AF10 fusion protein can be evaluated by any suitable method, for example, by determining binding between the DOT1 L polypeptide and CALM-AF10 and/or by determining histone H3-K79 methylation of the HoxA5 gene or portion thereof (e.g., all or a functional part of the promoter region, exon 1 , exon 2 and/or the intron between exon 1 and exon 2) and/or by determining HoxA5 promoter activity (e.g., when the promoter is operatively associated with the native " "" ""' sequence,' "' ⁇ "cDNA representing the HoxA5 coding sequence or a heterologous sequence such as a reporter gene).
• HoxA5 promoter activity e.g., when the promoter is operatively associated with the native " "" ""' sequence,' "' ⁇ "cDNA representing the HoxA5 coding sequence or a heterologous sequence such as a reporter gene.
• the level of DOT1L polypeptide interaction with the CALM-AF10 fusion protein can also be evaluated by determining nuclear localization of CALM-AF10. Binding between two or more components can be determined directly or indirectly (e.g., by detecting a biological action or consequence that results from binding of the components).
• a reporter gene can encode any suitable reporter molecule known in the art, including polypeptides and nontranslated RNA such as RNAi and antisense RNA that result in a detectable change in a cell or organism.
• the reporter molecule is a polypeptide, such as an enzyme (e.g., Green Fluorescent Protein, ⁇ - glucuronidase, ⁇ -galactosidase, luciferase, etc.).
• the invention also provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a CALM polypeptide or CALM-AF10 fusion protein with a test compound under conditions sufficient for binding of the test compound to the CALM polypeptide or CALM-AF10 fusion protein; and detecting the level of binding between the test compound and the CALM polypeptide or CALM-AF10 fusion protein, wherein binding of the test compound to the CALM polypeptide or CALM-AF10 fusion protein indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the invention also provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a nucleic acid comprising all or a portion of the HoxA5 gene (e.g., comprising all or a functional part of the promoter region, exon 1 , exon 2 and/or the intron between exons 1 and 2) with a CALM polypeptide, AF10 polypeptide, DOT1 L polypeptide or CALM-AF10 fusion protein in the presence of a test compound under conditions sufficient for binding of the CALM polypeptide, AF10 polypeptide, DOT1L polypeptide or CALM-AF10 fusion protein to the all or portion of the HoxA5 gene; and detecting the level of interaction of the CALM polypeptide, AF10 polypeptide, or CALM-AF10 fusion protein with the all or portion of the HoxA5 gene, wherein a reduction in interaction between the CALM polypeptide, AF10 polypeptide, DOT
• Exemplary regions of the HoxA5 gene that can interact with DOT1L/CALM-AF10 are shown in Figure 5A. Interaction between the CALM polypeptide, AF10 polypeptide, DOT1 L polypeptide or CALM-AF10 fusion protein with the HoxA5 gene or portion thereof can be evaluated by any suitable method, including but not limited to determining binding of the CALM polypeptide, AF10 polypeptide, DOT1L polypeptide or CALM-AF10 fusion protein to the HoxA5 gene or portion thereof and/or by determining H3-K79 methylation of the HoxA5 gene or portion thereof (e.g., all or a functional part of the HoxA5 promoter) and/or by determining HoxA5 promoter activity (e.g., when the promoter is operatively associated with the native sequence, a cDNA representing the HoxA5 coding sequence or a heterologous sequence such as a reporter gene).
• any suitable method including but not limited to determining binding of the CALM
• the method is carried out in a cell- based system, wherein the cells comprise a recombinant nucleic acid comprising a HoxA5 promoter operatively associated with a nucleic acid encoding a reporter molecule (e.g., a polypeptide such as an enzyme).
• the cell can be a leukemic cell that comprises a CALM-AF10 fusion protein or, alternatively, can be a cell that has been modified to produce a CALM-AF10 fusion protein.
• One or more candidate compounds can be added to the cell, and binding of CALM-AF10 to HoxA5 as indicated by the level of HoxA5 promoter activity can be evaluated by determining the expression of the reporter molecule (e.g., enzymatic activity).
• the invention also provides a method of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising: contacting a nucleic acid comprising all or a portion of the HoxA5 gene (as described above) with a DOT1 L polypeptide and a CALM-AF10 fusion protein in the presence of a test compound under conditions sufficient for binding of the DOT1L polypeptide and the CALM-AF10 fusion protein to form a complex and for the complex to bind to the HoxA5 promoter; and detecting the level of interaction of the DOT1 L/CALM-AF10 fusion protein complex to the HoxA5 promoter, wherein a reduction in interaction of the DOT1 L/CALM-AF10 fusion protein complex with
• a DOT1 L-CALM-AF 10 trifusion protein can be substituted for DOT1L and CALM-AF10 in the foregoing method.
• Interaction between the DOT1 L/CALM-AF10 complex and HoxA5 gene or portion thereof can be evaluated by any suitable method, including but not limited to determining binding of the complex to the HoxA5 gene or portion thereof or by determining H3-K79 methylation of the HoxA5 gene or portion thereof (e.g., the HoxA5 promoter) or by determining HoxA5 promoter activity (e.g., when the promoter is operatively associated with the native sequence, a cDNA representing the HoxA5 coding sequence or a heterologous sequence such as a reporter gene).
• any suitable method including but not limited to determining binding of the complex to the HoxA5 gene or portion thereof or by determining H3-K79 methylation of the HoxA5 gene or portion thereof (e.g., the HoxA5 promoter) or by determining HoxA5 promoter activity (e.g., when the promoter is operatively associated with the native sequence, a cDNA representing the HoxA5 coding
• the invention also provides methods of identifying a candidate compound for the prevention and/or treatment of leukemia, the method comprising identifying compounds that bind to and/or modulate HoxA5 promoter activity (e.g., by down-regulating expression of the HoxA5 gene or a chimeric construct comprising a HoxA5 promoter operably associated with a transgene, such as a reporter gene).
• the method comprises: contacting a nucleic acid comprising all or a functional part of the HoxA5 promoter region and/or any other region of the HoxA5 gene (e.g., exon 1 , exon 2 or the intron between exon 1 and exon2) with a test compound under conditions sufficient for the test compound to bind to the all or functional part of the HoxA5 promoter region and/or the any other region of the HoxA5 gene that is present in the nucleic acid; and between the test compound and the all or a functional part of the HoxA ⁇ promoter and/or the any other region of the HoxA ⁇ gene present in the nucleic acid, wherein binding indicates that the test compound is a candidate compound for the prevention and/or treatment 5 of leukemia.
• a test compound comprising all or a functional part of the HoxA5 promoter region and/or any other region of the HoxA5 gene (e.g., exon 1 , exon 2 or the intron between exon 1 and exon2) with
• identifying a candidate compound for the prevention and/or treatment of leukemia comprise: contacting a nucleic acid comprising all or a functional part the HoxA5 promoter region with a test compound under conditions sufficient for HoxA ⁇ promoter activity; and
• test compound detecting the level of HoxA ⁇ promoter activity, wherein a reduction in HoxA ⁇ promoter activity in the presence of the test compound as compared with the level of HoxA ⁇ promoter activity in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• the test compound is a candidate compound for the prevention and/or treatment of leukemia.
• HoxA ⁇ promoter activity can be determined as described herein.
• the present invention further provides methods of identifying
• the invention provides a method of identifying a candidate compound for the prevention and/or treatment of T-
• the method comprising: contacting a DOT1 L polypeptide with a histone or nucleosome substrate comprising histone H3 in the presence of a test compound; detecting the level of H3-K79 methylation of the substrate under conditions sufficient to provide H3-K79 methylation, wherein an inhibition of H3-K79 methylation in the presence of the test
• test compound as compared with the level of H3-K79 methylation in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of T-ALL or AML subtypes MO/1. -•'" S S ⁇ !'.'. * *!" "2 "'.'.'Ji
• Thetnvention further provides a method of identifying a candidate compound for the prevention and/or treatment of T-ALL or AML subtypes MO/1, comprising: contacting a DOT1L polypeptide with AF10; detecting the level of binding between the DOT1 L polypeptide and AF10 under conditions sufficient for binding therebetween, wherein a reduction in binding between DOT1L polypeptide and AF10 in the presence of the test compound as compared with the level of binding in the absence of the test compound indicates that the test compound is a candidate compound for the prevention and/or treatment of T-ALL or AML subtypes MO/1.
• Methods of assessing binding to polypeptides and nucleic acids can be carried out using standard techniques that will be apparent to those skilled in the art (see the Examples for exemplary methods). Such methods include yeast and mammalian two-hybrid assays and co-immunoprecipitation techniques. Other activities such as H3-K79 HMTase and leukemogenic activity can also be evaluated using standard methods known in the art, for example, as described in the Examples below.
• HoxA5 promoter activity can also be evaluated by any method known in the art, for example, by detecting expression or activity of a reporter gene operably associated with the HoxA5 promoter, by detecting HoxA5 transcripts (e.g., by RT-PCR) and/or the HoxA5 protein product.
• the screening methods of the invention can be carried out in a cell- based or cell-free system.
• the assay can be performed in a whole animal (including transgenic non-human animals).
• the polypeptide(s) can be added directly to the cell or can be produced from a nucleic acid in the cell.
• the nucleic acid can be endogenous to the cell or can be foreign (e.g., a genetically modified cell).
• test compounds include small organic compounds (i.e., non-oligomers), oligomers or combinations thereof, and inorganic molecules.
• Suitable organic molecules can include but are not limited to polypeptides (including enzymes, antibodies and Fab 1 fragments), carbohydrates, lipids, coenzymes, and nucleic acid molecules (including DNA, RNA and chimerics " ancf " analogs thereof) and nucleotides and nucleotide analogs.
• the compound is an antisense nucleic acid, an siRNA or a ribozyme that inhibits production of a target polypeptide.
• Non-oligomers include a wide variety of organic molecules, such as heterocyclics, aromatics, alicyclics, aliphatics and combinations thereof, comprising steroids, antibiotics, enzyme inhibitors, ligands, hormones, drugs, alkaloids, opioids, terpenes, porphyrins, toxins, catalysts, as well as combinations thereof.
• Oligomers include oligopeptides, oligonucleotides, oligosaccharides, polylipids, polyesters, polyamides, polyurethanes, polyureas, polyethers, and poly (phosphorus derivatives), e.g.
• oligomers may be obtained from combinatorial libraries in accordance with known techniques.
• a compound library e.g., a combinatorial chemical compound library (e.g., benzodiazepine libraries as described in U.S. Patent No. 5,288,514; phosphonate ester libraries as described in U.S. Patent No. 5,420,328, pyrrolidine libraries as described in U.S. Patent Nos. 5,525,735 and 5,525,734, and diketopiperazine and diketomorpholine libraries as described in U.S. Patent No. 5,817,751 ), a polypeptide library, a cDNA library, a library of antisense nucleic acids, and the like, or an arrayed collection of compounds such as polypeptide and nucleic acid arrays.
• a combinatorial chemical compound library e.g., benzodiazepine libraries as described in U.S. Patent No. 5,288,514; phosphonate ester libraries as described in U.S. Patent No. 5,420,328, pyrrolidine libraries as described in U.S
• the invention also encompasses compounds identified by the screening methods described above.
• the invention provides methods of treating a subject afflicted with or at risk for leukemia (e.g., T-ALL or AML subtypes MO/1 ) by administering a treatment effective amount of an inhibitory nucleic acid (e.g., RNAi such as siRNA) or an antibody (e.g., monoclonal antibody) directed against HoxA5, CALM, AF10, CALM-AF10 and/or DOT1L.
• an inhibitory nucleic acid e.g., RNAi such as siRNA
• an antibody e.g., monoclonal antibody directed against HoxA5, CALM, AF10, CALM-AF10 and/or DOT1L.
• the antibody can be a monoclonal or polyclonal antibody including antibody fragments.
• the antibody and antibody fragment is not limited to any particular form and can be a bispecific, humanized, or chimerized antibody or antibody fragment and can further be a Fab fragment, single chain antibody, and the like.
• Suitable subject for practicing the present invention include avian and mammalian subject, with mammalian subjects including but not limited to humans, non-human primates, mice, rats, sheep, pigs, cattle, goats, rabbits, horses, dogs, cats, and the like.
• the invention encompasses diagnostic methods for assessing whether a subject has or is at risk for leukemia and/or prognostic methods for predicting the future course of leukemia in a subject by assessing H3-K79 histone methylation of HoxA5, wherein an increase in H3-K79 methylation of HoxA5 as compared with a normal (e.g., non-leukemic) subject is diagnostic of leukemia and/or prognostic of the course of the disease.
• a normal e.g., non-leukemic
• the level of H3-K79 methylation and, optionally, the level of H3-K4 methylation of the HoxA5 gene are determined (e.g., the HoxA5 promoter, exon 1 , exon 2 and/or the intron between exon 1 and 2), wherein an increase in H3-K79 methylation and, optionally, a reduction in H3-K4 methylation as compared with a normal (e.g., non-leukemic) subject is diagnostic of leukemia and/or prognostic of the course of the disease.
• the invention further provides a method of diagnosing whether a subject has or is at risk for developing leukemia and/or determining the prognosis for the course of the disease, the method comprising determining HoxA5 promoter activity in the subject, where upregulation (i.e., increased activity) of HoxA5 promoter activity as compared with HoxA5 promoter activity in a control (e.g., healthy) subject indicates that the subject has or is at risk for developing leukemia.
• HoxA5 promoter activity can be determined by any method known in the art.
• the method can further comprise obtaining a biological sample from the subject and determining the HoxA5 promoter activity in the biological sample (e.g., by increased expression of a nucleic acid operatively associated with the HoxA5 promoter, whether native or heterologous).
• ⁇ e ' exemplary method of diagnosing whether a subject has or is at risk for developing leukemia and/or determining the prognosis for the course of the disease comprises: obtaining a biological sample comprising the HoxA ⁇ gene from a subject; detecting the level of H3-K79 methylation of the HoxA ⁇ 5 gene in the biological sample; wherein an elevation in H3-K79 methylation of the HoxA5 gene in the biological sample as compared with the level of H3- K79 methylation in a non-leukemic biological sample is diagnostic that the subject has or is at risk of developing leukemia and/or prognostic of the course of the disease in the subject.
• the method can optionally further 0 include determination of the level of H3-K4 methylation of the HoxA ⁇ gene, wherein a decrease in H3-K4 methylation of the HoxA ⁇ gene in the biological sample as compared with a non-leukemic sample is diagnostic that the subject has or is at risk of developing leukemia and/or prognostic of the course of the disease in the subject.
• the foregoing diagnostic methods of the invention are practiced as a diagnostic and/or prognostic method for T- ALL or AML subtypes MO/1.
• One exemplary method of diagnosing whether a subject has or is at risk for developing T-ALL or AML-M0/1 and/or determining the prognosis for 0 the course of the disease comprises: obtaining a biological sample comprising histones (e.g., nucleosomes) from a subject; detecting the level of H3-K79 methylation in the biological sample; wherein an increase in H3-K79 methylation in the biological sample as compared with the level of H3-K79 methylation in a non-leukemic biological sample is diagnostic that the subject ⁇ has or is at risk of developing T-ALL or AML-M0/1 and/or prognostic of the course of the disease in the subject.
• histones e.g., nucleosomes
• the method can optionally further include determination of the level of H3-K4 methylation, wherein a decrease in H3-K4 methylation in the biological sample as compared with a non-leukemic sample is diagnostic that the subject has or is at risk of developing T-ALL or 0 AML-M0/1 and/or prognostic of the course of the disease in the subject.
• the invention provides a method of diagnosing whether a subject has or is at risk for developing T-ALL or AML-M0/1 and/or determining the prognosis for the course of the disease, the method comprising: obtaining a biological sample " " "'" ' '”com'p ⁇ srng"'H ⁇ sfones (e.g., nucleosomes) from a subject; detecting the level of H3-K79 methylation associated with one or more HoxA genes (e.g., the HoxA9 gene) in the biological sample; wherein an increase in HoxA gene- associated H3-K79 methylation (e.g., associated with the HoxA9 gene) in the 5 biological sample as compared with the level in a non-leukemic biological sample is diagnostic that the subject has or is at risk of developing T-ALL or AML-M0/1 and/or prognostic of the course of the disease in the subject.
• the method can optionally further include determination of the level of H3
• a decrease in HoxA gene associated H3-K4 methylation in the biological sample as compared with a non-leukemic sample is diagnostic that the subject has or is at risk of developing T-ALL or AML-M0/1 and/or prognostic of the course of the disease in the subject.
• any mammalian subject including but not limited to human, non-human primate, cattle, sheep, goat, cat, dog, pig, horse, rat, mouse, rabbit or guinea pig subjects.
• the subject has or is believed to be at risk of developing leukemia.
• the subject is an animal model of leukemia.
• Any suitable biological sample can be used including cell or tissue
• the biological sample is a B cell or bone marrow sample.
• the biological sample is a histone or nucleosome preparation comprising histone H3 (e.g., obtained from B cells or
• cells or tissue are removed from a subject, cultured and histones or nucleosomes prepared from the cultured cells or tissue.
• non-leukemic biological sample it is meant a suitable control sample that is indicative of a normal subject (i.e., not having or at risk for 'cfev'ii ⁇ pingl ⁇ ufcenriia).
• the sample can be isolated from a normal subject or, in some instances (e.g., a nucleosome preparation), can be isolated from cultured cells.
• CALM-AF10 knockdown in U937 cells and transplantation DNA encoding 21 bp-shRNA (5'- ATC AGG AGC ACA GAG CTG TGA -3'; SEQ ID NO:3) that targets the junction of CALM and AF10 was subcloned into pMSCV-puro with an H1 RNA promoter. Transduced cells were selected by puromycin (0.5 ⁇ g/ml) and cloned by limiting dilution. Knockdown efficiency was evaluated by RT-PCR. Five to ten week old NOD/SCI D mice were irradiated (300 rad).
• CALM-AF10 was cloned from U937 cells by RT-PCR. Wild-type and OM-LZ deletion mutant CALM-AF10 were subcloned into pMSCV-neo in the downstream of a Flag-tag.
• Retrovirus preparation, transduction, and colony assays were performed as previously described (Okada et al., (2005) Ce//121 :167-78). In the experiments presented in Fig. was added to the methylcellulose until the 3rd round to prevent the growth of untransduced cells. Colonies on methylcellulose were picked and further cultured in mFTOC (10% FBS in RPM11640, 1mM MEM sodium pyruvate, 1% MEM non-essential amino acid, 1OmM HEPES, pH. 7.3, 5x10 5 M 2-mercaptoethanol) with 5 ng/ml mlL-3 (Peprotech). Transduction of DOT1L with Blasticidin-resistant retrovirus was described previously (Okada et al., (2005) Ce//121 : 167-78).
• U937 cells were maintained in RPMI 1640 supplemented with 10% fetal calf serum.
• 293T or U2OS cell were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum.
• Transfection was performed by using Fugene6 (Roche). Twenty- four hours after transfection, U2OS cells were fixed with 3% paraformaldehyde and permiabilized with 0.1% Triton X-100 for 5 min.
• Flag M2 Sigma
• hDOTI L Okada et al., (2005) Ce//121 : 167-78 antibodies were used as primary antibodies for immunostaining.
• DAPI was used for nuclear staining.
• 293T cells were harvested 36 hours after transfection, and washed with ice-cold phosphate-buffered saline (PBS) before being lysed with lysis buffer (50 mM Hepes-KOH [pH 7.9], 420 mM KCI, 0.1 mM EDTA [pH 8.0], 5 mM MgCI2, 20% glycerol, 1 mM DTT, 1 mM phenylmethylsulfonyl fluoride, 1 ⁇ g of aprotinin/ml, 0.5 ⁇ g of leupeptin/ml, and 0.7 ⁇ g of pepstatin/ml).
• PBS ice-cold phosphate-buffered saline
• RNA 10 or colonies of mouse bone marrow cells derived from second and third round of wild-type or mutant CALM-AF10 transduced cells using RNeasy (Qiagen). Up to 1 ⁇ g of total RNA was treated with RNase-free DNase I, and applied for reverse transcription using ImProm-ll (Promega) according to manufacturer's protocol. Half a microliter of cDNA from the 20 ⁇ l RT reaction was used as
• CALM-AF10 ⁇ '-TATACAGCCAGCCTGTCATG -3' (SEQ ID NO:4), CALM-
• ChIP assay Cell preparation, immunoprecipitation, and PCR were described previously (Okada et al., (2005) Ce//121 :167-78). Antibodies were obtained as follows; anti-3mK4 (Abeam), anti-2mK9 (Upstate), and anti- 25 2mK79 (Feng et al., (2002) Curr. Biol. 12:1052-1058). Primer sequences and detailed PCR conditions are available upon request.
• hDOT1 L may also play an important role in CALM-AF10- mediated leukemia.
• CALM-AF10-mediated leukemic transformation depends on functional hDOTI L.
• hDOTI L a methylcellulose colony serial plating assay was used (Fig. 2a).
• hDOTI L can interact with CALM-AF10 and the interaction is dependent on the OM-LZ region of AF10 (Fig. 6).
• Fig. 6 we performed the colony serial plating assay by transduction of mouse bone marrow cells with wild-type or a deletion CALM-AF10 mutant that lacked the hDOTI L interaction region OM-LZ.
• RT-PCR analysis confirmed expression of both fusion proteins in cells derived from the second round of colonies (Fig. 2b, lanes 1 and 2). Although the colony numbers did not increase in the third round of plating when compared with the second round in bone marrow cells expressing CALM-AF10 (Fig. 2c, middle columns), the cells were able to proliferate continuously in mFTOC (mouse fetal thymus organ culture) media supplemented with mlL-3 for more than 6 months (Fig. 2d and data not shown).
• mFTOC mouse fetal thymus organ culture
• CALM-AF10 fusion protein is sufficient to transform progenitor bone marrow cells and that the hDOTI L interaction region is required for the transformation capacity of CALM-AF10.
• CALM-AF10-mediated leukemic transformation involves Hoxa5 upregulation. Having established the role of hDOT1 L in CALM-AF10- mediated leukemic transformation, we attempted to identify the relevant target genes. cDNA microarray studies have revealed that overexpression of late Hoxa genes and Bmi-1 is a characteristic of leukemias involving CALM-AF10 and some MLL-fusion proteins (Dik et al., (2005) Leukemia 19:1948-57; Drabkin et al., (2002) Leukemia 16:186-95; Souler et al., (2005) Blood
• Hoxa ⁇ was significantly upregulated in " " '” " ' “”mouse bone "marrow cells transduced by CALM-AF10 when compared with cells transduced by the OM-LZ deletion mutant (Fig. 3a, compare lanes 5 and 6), suggesting that hDOTIL plays a role in Hoxa ⁇ upregulation.
• Hoxa ⁇ upregulation may play a key role in the transformation process.
• To determine whether Hoxa ⁇ is necessary for CALM-AF 10-mediated leukemic transformation we performed colony replating assays using bone marrow cells isolated from Hoxa ⁇ knockout mice. In parallel, we also analyzed the effect of Hoxa ⁇ knockout on the transformation capability of MLL-AF10.
• CALM-AF10 Nuclear localization of CALM-AF10 depends on its ability to interact with hDOTIL.
• CALM is a cytoplasmic protein known to function in
• clathrin assembly (Tebar et al., (1999) MoI. Biol. Cell. 10:2687-702; Meyrholz et al., (200 ⁇ ) Traffic 6:122 ⁇ -34). It contains a putative CRM 1 -dependent NES (nuclear exporting signal) sequence at its C-terminus, which is retained in the CALM-AF10 fusion protein (Vecchi et al., (2001 ) J. Cell. Biol. 153:1511-7). (Fig. 7).
• AF10 is a nuclear protein with its NLS (nuclear
• CALM-AF10 2 ⁇ localization signal retained in the CALM-AF 10 fusion protein (Fig. 7).
• CALM-AF10 may directly or indirectly contribute to Hoxa ⁇ upregulation.
• FIG. 4a nuclear distribution-in wild-type, but not in mutant, CALM-AF10 transfected cells is also noticeable (Figs. 4a, b).
• CALM exhibited a mesh-like cytoplasmic distribution (Fig. 4a) which is characteristic of clathrin-related proteins (Tebar et al., (1999) MoI Biol. Cell 10:2687-702).
• CALM-AF10 when CALM-AF10 is co-expressed with hDOTI L, CALM-AF10 becomes localized to the nucleus (Figs. 4c, 4d, left columns). High resolution analysis of the proteins indicates that they colocalize in the nucleus (Fig. 4e). Importantly, this change in CALM-AF10 localization depends on its ability to interact with hDOTI L since co-expression of hDOTI L with a CALM-AF10 mutant that lacks the OM-LZ region has no effect on the localization of the fusion protein (Figs. 4c, 4d, middle columns). In addition, hDOTI L did not affect CALM localization (Figs. 4c, 4d, right panels).
• Upregulation of Hoxa5 is concomitant with CALM-AF10 binding and H3-K79 methylation.
• CALM-AF10 can localize to the nucleus and interact with hDOTIL raises the possibility that Hoxa ⁇ might be a direct target of CALM-AF10.
• Fig. 5b results shown in Fig. 5b demonstrate that the fusion proteins bind to a region covered by amplicons e-g (Fig. 5b, lanes 5-7). The observed binding is specific, as no signal is observed in a parallel ChIP experiment using cells transduced by an empty vector.
• CALM-AF10 fusion in certain leukemia patients has provided circumstantial evidence indicating CALM-AF10 might possess oncogenic capability.
• CALM-AF10 fusion is both necessary and sufficient for leukemogenesis (Figs. 1 and 2).
• Figs. 1 and 2 we demonstrate that CALM-AF10 fusion is both necessary and sufficient for leukemogenesis.
• Figs. 2c CALM-AF10 lacking the hDOTI L interaction domain loses its transformation capability (Fig. 2c).
• overexpression of an enzymatically inactive form of hDOTIL suppressed proliferation of CALM- AF10 transformed cells (Fig. 2f).
• hDOT1 L contributes to CALM-AF10-mediated leukemic transformation by preventing nuclear export of CALM-AF10 and by methylation of H3-K79 at the Hoxa ⁇ gene which contributes to its activation.
• Hoxa ⁇ is required specifically for CALM-AF10 mediated leukemic transformation because bone marrow cells derived from Hoxa ⁇ null mice, while not affecting transformation by MLL-AF10, cannot be transformed by CALM-AF10 (Fig. 3b).
• our studies not only establish CALM-AF10 as a cause of leukemic transformation, but also reveal Hoxa ⁇ and hDOTI L as important players in a leukemogenesis process that involves CALM-AF10 fusion.
• hDOT1 L also contributes to leukemogenesis by MLL-AF10 (Okada et al., (200 ⁇ ) CeIh 21 : 167-78).
• MLL-AF10 alkada et al., (200 ⁇ ) CeIh 21 : 167-78.
• leukemogenesis mediated by MLL-AF10 and CALM-AF10 both involve hDOTI L and Hox gene activation, the underlying mechanisms are not the same.
• Hoxa ⁇ does not appear to play a key role in MLL-AF10-mediated leukemic transformation (Fig. 3b).
• Hoxa9 upregulation through hDOTIL-mediated H3-K79 methylation appears to be a key event in MLL-AF10-mediated leukemic transformation (Okada et al., (200 ⁇ ) Ce//121 :167-78). It worth noting that while Hoxa9 overexpression has been observed in a number of leukemias, its overexpression is not always transformation (So et al., (2004) S/ooc/ 103:3192-9). This highlights the importance of distinguishing overexpressed Hoxa genes necessary for leukemic transformation from those not essential for transformation. A second difference lies in their distinct immunophenotypes.
• CALM-AF10 transformed bone marrow cells are mainly lineage- uncommitted progenitors (positive only for c-Kit), the cells transformed by MLL-AF10 tend to differentiate into myeloid lineage with expression of lineage markers (Fig. 2e, Fig. 8) (Okada et al., (2005) Ce//121 : 167-78).
• lineage markers Fig. 2e, Fig. 8
• This observation is consistent with the fact that leukemia patients with CALM-AF10 0 often develop hematologic malignancy of multi-lineages, an indication that the leukemic cells have originated from a very early stage of hematopoietic development (Kobayashi et al., (1997) Genes Chromosomes Cancer 20:253- 9).
• Hoxa genes Up-regulation of different Hoxa genes might be linked to these phenotypical differences. For example, constitutive expression of Hoxa ⁇ in 5 human CD34 + cells prevents differentiation toward erythrocytes and increases myelopoiesis (Crooks et al., (1999) Blood 94:519-28).

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