WO2013036867A2 - Compositions and methods for cancer and cancer stem cell detection and elimination - Google Patents

Compositions and methods for cancer and cancer stem cell detection and elimination Download PDF

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WO2013036867A2
WO2013036867A2 PCT/US2012/054307 US2012054307W WO2013036867A2 WO 2013036867 A2 WO2013036867 A2 WO 2013036867A2 US 2012054307 W US2012054307 W US 2012054307W WO 2013036867 A2 WO2013036867 A2 WO 2013036867A2
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stem cell
shh
transcript
jak2
cells
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PCT/US2012/054307
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French (fr)
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WO2013036867A3 (en
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Catriona H. Jamieson
Qingfei JIANG
Kelly A. Frazer
Christian Barrett
Anil Sadarangani
Alice SHIH
Angele COURT
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The Regents Of The University Of California
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Priority to US14/342,384 priority Critical patent/US9611330B2/en
Publication of WO2013036867A2 publication Critical patent/WO2013036867A2/en
Publication of WO2013036867A3 publication Critical patent/WO2013036867A3/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/40—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against enzymes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/713—Double-stranded nucleic acids or oligonucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2/00—Peptides of undefined number of amino acids; Derivatives thereof
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • 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
    • C12N15/1137—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 enzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C12N9/80—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5) acting on amide bonds in linear amides (3.5.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04004—Adenosine deaminase (3.5.4.4)
    • 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
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57426—Specifically defined cancers leukemia
    • 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
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
    • G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
    • G01N2333/4701—Details
    • G01N2333/4703—Regulators; Modulating activity
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the invention relates to oncology, cellular and developmental biology and drug discovery.
  • the invention provides compositions and methods for inhibiting or ablating cancer stem cells.
  • the invention provides compositions and methods for inhibiting the action of double-stranded RNA- specific adenosine deaminases, or ADAR, enzymes.
  • the invention provides compositions and methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition of cell differentiation and/or self- renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, e.g., leukemia or Chronic Myeloid Leukemia (CML).
  • CML Chronic Myeloid Leukemia
  • the invention provides compositions and methods for inhibiting a Sonic Hedgehog (Shh) pathway, e.g., by using a Smoothened (SMO) protein inhibitor.
  • the invention provides compositions and methods for inhibiting a Sonic Hedgehog (Shh) pathway, e.g., by using a Smoothened (SMO) protein inhibitor: to force, stimulate or initiate a dormant cell or a cancer stem cell (e.g., a Chronic Myelogenous Leukemia (CML) stem cell) to cycle so they the cell can more effectively targeted by a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor; as a biomarker of response to chemotherapy; and/or, as a target for drug development.
  • a cancer stem cell e.g., a Chronic Myelogenous Leukemia (CML) stem cell
  • the invention provides compositions and methods for measuring or determining, or predicting, chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance comprising measuring or determining, individually or together, levels or amounts of GLI2 transcript and/or protein (increasing) and/or GLI3 transcript and/or protein (decreasing) as prognostic biomarkers of chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance.
  • CML chronic myelogenous leukemia
  • LSC Leukemic Stem Cell
  • the invention provides compositions and methods for measuring or determining, or predicting, a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, comprising measuring or determining, individually or together, levels or amounts of GLI1 and/or GLI2 transcript and/or protein.
  • Shh Sonic Hedgehog
  • the invention provides compositions and methods for determining or measuring the effectiveness of a treatment, a drug, a therapy or a diet for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
  • the invention provides compositions and methods for determining or predicting a positive response or monitoring a response (predicting a negative or positive response) to a selective JAK2 inhibition therapy, drug or treatment.
  • RNA editing is a post-transcriptional processing mechanism that results in an RNA sequence that is different from that encoded by the genomic DNA and thereby diversifies the gene product and function.
  • the type of RNA editing that is most prevalent in higher eukaryotes converts adenosine residues into inosine (A-to-I editing) in double- stranded RNA (dsRNA) through the action of double-stranded RNA-specific adenosine deaminases, or ADAR, enzymes.
  • ADAR is an enzyme that in humans is encoded by the ADAR gene (ADARl is an acronym for "adenosine deaminase acting on RNA 1").
  • ADARl RNA edits by site- specific deamination of adenosines.
  • the ADARl enzyme destabilizes double stranded RNA through conversion of adenosine to inosine.
  • the ADARl enzyme modifies cellular and viral RNAs, including coding and noncoding RNAs.
  • ADARl is an RNA editing enzyme, required for hematopoiesis.
  • ADARl +/ ⁇ chimeric embryos die before embryonic day 14 with defects in the hematopoietic system.
  • ADARl expression are critical for embryonic erythropoiesis in the liver. Mutations in the ADAR gene have been associated with dyschromatosis symmetrica hereditaria. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. Traditional CML treatment, such as hydroxyurea and imatinib, is a great financial burden on patients. Moreover, they are not efficient at eradicate leukemia cancer stem cells, which often leads to disease progression and relapse. New drugs that target at cancer stem cells are urgently needed for patient care.
  • LSC leukemia stem cells
  • HSC hematopoietic stem cell
  • STAT5a Signal transducer and activator of transcription 5A
  • STAT5a is a protein that in humans is encoded by the ST AT 5 A gene.
  • the protein encoded by this gene is a member of the STAT family of transcription factors.
  • STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators.
  • This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones.
  • Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis.
  • Janus kinase 2 is a human protein that has been implicated in signaling by members of the type II cytokine receptor family (e.g. interferon receptors), the GM-CSF receptor family, and the gpl30 receptor family (e.g., IL-6R), and the single chain receptors such as Epo-R.
  • JAK2 gene fusions with the TEL(ETV6) and PCMl genes have been found in leukemia patients. Mutations in JAK2 have been implicated in
  • the invention provides methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal (or self-renewal capacity) of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, comprising,
  • an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide; and
  • composition comprising (b) administering a sufficient amount of the composition to an individual in need thereof, wherein a sufficient amount comprises the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells.
  • the hematopoietic stem cell or cancer stem cell comprises a cancer stem cell, or a leukemia cell, or a Chronic Myeloid
  • CML Chronic Myeloid Leukemia
  • composition that inhibits or slows the expression of an ADARl gene, an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide comprises:
  • the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA); or
  • inhibitory nucleic acid molecule comprises a ribozyme.
  • the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript comprises a single or doublestranded and/or sense or antisense sequence or subsequence comprising SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3.
  • the antibody inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme comprises an antibody or antigen-binding fragment thereof that specifically binds to a protein as set forth in SEQ ID NO: 3.
  • the polypeptide or peptide inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme comprises a peptide aptamer or an ADARl-binding polypeptide or peptide.
  • composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide is administered in vitro, ex vivo or in vivo.
  • an ADARl gene adenosine deaminase acting on RNA 1
  • an ADARl gene product adenosine deaminase acting on RNA 1
  • ADARl transcript an ADARl polypeptide
  • the invention provides compositions, pharmaceutical compositions or formulations, or equivalents, comprising a composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide, wherein optionally the composition or formulation is formulated for administration in vitro, ex vivo or in vivo.
  • an ADARl gene adenosine deaminase acting on RNA 1
  • an ADARl gene product an ADARl gene product
  • an ADARl transcript an ADARl polypeptide
  • kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
  • the invention provides compositions and methods to detect dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells.
  • CML Chronic Myelogenous Leukemia
  • the invention provides compositions and methods for use therapeutically to force dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells, into cycle so they can be targeted by a therapeutic agent or procedure, e.g., chemotherapy, radiation therapy or targeted tyrosine kinase inhibitors.
  • the invention provides methods for activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle, or initiating cell cycling in a cancer stem cell, or breaking dormancy in a cancer stem cell, or inducing in a stem cell susceptibility to BCR-ABL inhibition, comprising,
  • the invention provides methods for radiosensitization of a cancer stem cell, or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells, or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor, comprising,
  • the cancer stem cell is a hematopoietic cancer stem cell, or the cancer stem cell is a leukemia stem cell, or a Chronic Myeloid Leukemia (CML) stem cell or a Chronic Myeloid Leukemia (CML) stem cell.
  • CML Chronic Myeloid Leukemia
  • CML Chronic Myeloid Leukemia
  • composition that inhibits or slows the expression of an Shh gene, an Shh gene product, an Shh transcript, and/or an Shh polypeptide comprises:
  • an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of a Shh gene or Shh gene transcript (b) a polypeptide, peptide or an antibody inhibitory to the expression of the Shh gene or Shh gene transcript, or activity or expression of the Shh polypeptide;
  • the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the Shh gene or Shh gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA); or
  • inhibitory nucleic acid molecule comprises a ribozyme
  • the composition that inhibits or slows the expression of a Shh gene, a Shh gene product, a Shh transcript, and/or a Shh polypeptide comprises a PF-04449913 (structure illustrated in Figure 17a), or an equivalent thereof, or a bioisostere thereof.
  • the antibody inhibitory to the expression of a Shh gene, a Shh gene product or a Shh transcript, or activity or expression of the Shh polypeptide comprises an antibody or antigen-binding fragment thereof that specifically binds to a Shh protein.
  • the polypeptide or peptide inhibitory to the expression of a Shh gene, a Shh gene product or a Shh transcript, or activity or expression of the Shh protein comprises a peptide aptamer or a Shh protein-binding polypeptide or peptide.
  • the composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide is administered in vitro, ex vivo or in vivo.
  • compositions, pharmaceutical compositions or formulations comprising a composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide, wherein optionally the composition or formulation is formulated for administration in vitro, ex vivo or in vivo.
  • the composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide comprises any composition used to practice a method of the invention, e.g., a PF-04449913 (structure illustrated in Figure 17a), or an equivalent thereof, or a bioisostere thereof.
  • the invention provides arrays or kits comprising a cancer stem cell splice isoform and/or proteome detection platform, wherein the array or kit comprises a sufficient plurality of nucleic acids and/or proteins to detect a dormant cancer stem cell from a non- dormant stem cell or a cancer stem cell transitioning from GO to Gl of the cell cycle.
  • the invention provides methods for determining the effectiveness of a test compound for: activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle; or initiating cell cycling in a cancer stem cell; or breaking dormancy in a cancer stem cell; or radiosensitizing of a cancer stem cell; or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells; inducing in a stem cell susceptibility to BCR-ABL inhibition; or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor, comprising analyzing the cancer stem cell transcript (RNA) splice isoform pattern and/or the proteome before and after contacting the test compound to the stem cell, wherein a change of the cancer stem cell to a non-dormant transcript (RNA) splice isoform pattern and/or the proteome pattern indicates that the test compound is effective for: activating, stimulating or initiating in a cancer stem
  • kits comprising: a composition used to practice a method of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
  • the invention provides compositions and methods to detect dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells.
  • CML Chronic Myelogenous Leukemia
  • the invention provides compositions and methods for use therapeutically to force dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells, into cycle so they can be targeted by a therapeutic agent or procedure, e.g., chemotherapy, radiation therapy or targeted tyrosine kinase inhibitors.
  • the invention provides compositions and methods for measuring or determining, or predicting, chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance, comprising: measuring or determining, individually or together, levels or amounts of GLI2 transcript and/or protein (increasing) and/or GLI3 transcript and/or protein (decreasing) as prognostic biomarkers of chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance, wherein increased or increasing levels of GLI2 transcript and/or protein and/or decreasing levels of GLI3 transcript and/or protein indicate and/or predict chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance.
  • CML chronic myelogenous leukemia
  • the presence of one or both GLI1 and/or GLI2 transcript and/or protein, and/or increased or increasing levels of one or both GLI1 and/or GLI2 transcript and/or protein indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition.
  • Shh Sonic Hedgehog
  • compositions and methods for measuring or determining, or predicting, whether a cancer stem cell has or will transition from GO to Gl of the cell cycle, or has or will initiate cell cycling, or has or will break dormancy, or has been induced to have a susceptibility to BCR-ABL inhibition comprising:
  • the presence of one or both GLI1 and/or GLI2 transcript and/or protein, and/or increased or increasing levels of one or both GLI1 and/or GLI2 transcript and/or protein indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, thereby also indicating or predicting whether a cancer stem cell has or will transition from GO to Gl of the cell cycle, or has or will initiate cell cycling, or has or will break dormancy, or has been induced to have a susceptibility to BCR-ABL inhibition.
  • Sonic Hedgehog Sonic Hedgehog
  • the presence, absence and/or amount of a GLIl, GLI2 and/or GLI3 transcript and/or protein is measured using an array, an immunoassay, an immunoprecipitation, a kit, a polymerase chain reaction (PCR), a qRT-PCR, a nanofluidic assay or device, a nanofluidic proteome assay, a chromatography, a nanoproteomics quantification, an isoelectric focusing assay, or a combination thereof.
  • the invention provides compositions and methods for assessing the eradication of self-renewing cancer stem cells, or Leukemic Stem Cells (LSCs), comprising:
  • the absence of one or both GLIl and/or GLI2 transcript and/or protein, and/or decreasing levels of one or both GLIl and/or GLI2 transcript and/or protein indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, thereby also indicating or predicting an eradication or diminishment of self-renewing cancer stem cells, or Leukemic Stem Cells (LSCs).
  • Shh Sonic Hedgehog
  • LSCs Leukemic Stem Cells
  • the invention provides arrays, immunoassays, kits and the like comprising nucleic acids, proteins or antibodies capable of determining or measuring the presence, absence and/or amount of a GLIl, GLI2 and/or GLI3 transcript and/or protein.
  • the arrays or kits comprise a composition used to practice a method of the invention, or a composition, and optionally comprising instructions for use thereof.
  • the invention provides compositions and methods for determining or measuring the effectiveness of a treatment, a drug, a therapy or a diet for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells, comprising:
  • a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message determines or predicts that the treatment, drug, therapy or diet will be effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
  • LSC leukemic stem cell
  • the invention provides compositions and methods for selecting a diet, a treatment, a drug or a therapy: to treat or ameliorate a leukemic stem cell (LSC), or, for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells, comprising:
  • the invention determines or predicts that the treatment, drug, therapy or diet will be effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
  • the invention provides compositions and methods for determining or predicting a positive response or monitoring a response (predicting a negative or positive response) to a selective JAK2 inhibition therapy, drug or treatment, comprising
  • a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message determines or predicts that the selective JAK2 inhibition therapy, drug or treatment will be (or is) effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
  • LSC leukemic stem cell
  • the invention provides compositions and methods for assessing the resistance, or relative resistance, of a self-renewing leukemic stem cell (LSC) or cells to a selective JAK2 inhibition therapy, drug or treatment, comprising:
  • an increased amount of, or the presence of, the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message determines or predicts that the self-renewing leukemic stem cell (LSC) or cells will be resistant, or relatively resistant, to a selective JAK2 inhibition therapy, drug or treatment, or
  • a decreased amount of, or lack of, the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message determines or predicts that the self-renewing leukemic stem cell (LSC) or cells will be sensitive or responsive to a selective JAK2 inhibition therapy, drug or treatment.
  • LSC self-renewing leukemic stem cell
  • compositions and methods for distinguishing leukemic progenitors from their normal counterparts comprising:
  • the method detects a cancer stem cell specific JAK/STAT signaling pathway splice isoforms by RNA sequencing, qRT-PCR and/or nanoproteomics.
  • the LSC is a chronic myelogenous or myeloid leukemia (CML) stem cell, or a cancer stem cell in a primary or metastatic niche, or a cancer stem cell in a setting of inflammatory cytokines and interleukins as elaborated in a cancer.
  • CML chronic myelogenous or myeloid leukemia
  • the presence, absence and/or amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message is measured by a procedure or device comprising (or comprising use of): a fluorescent activated cell sorter (FACS), an array, an immunoassay, an immunoprecipitation, a kit, a polymerase chain reaction (PCR), a qRT- PCR, a nanofluidic assay or device, a nanofluidic proteome assay, a chromatography, a nanoproteomics quantification, or an isoelectric focusing assay, or any combination thereof.
  • FACS fluorescent activated cell sorter
  • PCR polymerase chain reaction
  • qRT- PCR qRT- PCR
  • nanofluidic assay or device a nanofluidic proteome assay
  • Figure 1A graphically illustrates data showing that the expression of ADARl pi 50 is increasing as CML progresses from CP to BC; the values were normalized to HPRT; a significant increase of ADARl pl50 expression was observed in CML BC comparing to CML CP.
  • FIG. 5 illustrates representative pictures of GFP+ colonies; as described in detail in Example 1, below.
  • Figure 7 graphically illustrates data showing that ADAR1 expression is significantly positively and negatively correlated with PU1 and GATA1, respectively:
  • Figure 7A mRNA from individual colony formed from sorted CD24+38+Lin- CML patient was measured for expression of ADAR1, PU1, and GATA1 using qRT-PCR;
  • Figure 7B cord blood sorted CD34+38+Lin- cells were transduced with either ORF control or ADAR1 overexpression lentivirus; the expression levels of ADAR1, PU1, and GATA1 were analyzed; as described in detail in Example 1, below.
  • Figure 8a graphically illustrates data where GLI1 and GLI2 transcripts were compared by TaqMan RT-PCR in FACS-purified human cord blood and peripheral blood CD34 + CD38 Lin " PT progenitor cells, chronic phase CML and in blast crisis CML patient samples; and comparative qRT-PCR analysis of GLI3 transcript levels was performed on normal, chronic phase and blast crisis CML cells;
  • Figure 8b graphically illustrates data from a FACS analysis that showed a reduction in leukemic progenitor survival following 7 days of PF-04449913 compared with vehicle (DMSO) treatment in SL/M2 co-cultures;
  • Figure 8c graphically illustrates data from the down regulation of GLI expression, as analyzed by TaqMan RT-PCR in human LSC engrafted bone marrow derived from PF- 04449913 and vehicle treated mice;
  • Figure 8d graphically illustrates data showing spleen size in blast crisis CML LSC engrafted mice after 14 days of treatment with vehicle or PF
  • Figure 9a graphically illustrates data showing the frequency of CD45 + cells in hematopoietic tissues of blast crisis CML engrafted mice
  • Figure 9b graphically illustrates data from a FACS quantitation of common myeloid progenitors (CMP), granulocyte- macrophage progenitors (GMP) and megakaryocyte-erythroid progenitors (MEP) populations within each hematopoietic tissue
  • Figure 9c graphically illustrates data showing a comparison of cell cycle status of human CD45 + blast crisis CML progenitors engrafted mice in the bone marrow and spleen
  • Figure 9d illustrates representative FACS plots comparing Ki67 and 7AAD in bone marrow engrafted viable human CD45 + cells after 14 days of vehicle or PF-04449913 treatment
  • Figure 9c graphically illustrates data from a gene set enrichment analysis for the significantly down-regulated pathway "Regulators of Cell Cycle”
  • Figure 9f graphically illustrates data showing isoform-level
  • Figure 9g graphically illustrates data showing the relative expression of the 75 isoforms in PF-0449913 -treated and in normal cells relative to vehicle treated cells; all figures are also further described, below.
  • FIG. 10a graphically illustrates data showing: Left, Differentiation into CFU-
  • Figure 1 1a schematically illustrates in vivo experiments where RAG2 "/" y c "/” pups were transplanted intrahepatically with 50,000 CD34 + cells within 48 hours of birth; and after 8 to 10 weeks, blast crisis CML engrafted mice were treated daily for 14 days by oral gavage with vehicle, PF-04449913 (100 mg/kg), Dasatinib (50 mg/kg) or combination (PF-04449913 100 mg/kg and Dasatinib 50 mg/kg); and then hematopoietic tissues were FACS analyzed for leukemia engraftment and qRT-PCR for BCR-ABL1 transcripts;
  • Figure 11c graphically
  • Figure 12a schematically illustrates the chemical structure of PF-04449913, a selective smoothened (SMO) antagonist
  • Figure 12b graphically illustrates data from a competition-binding assay using a characterized cyclopamine-competitive SMO antagonist.
  • PF-04449913 competes with the radiolabeled SMO antagonist for binding to human SMO (amino acids 181-787) with an IC50 of 4 nM;
  • Figure 12c graphically illustrates data from a study inhibiting Shh-stimulated luciferase expression using mouse embryonic fibroblasts expressing luciferase under control of an 8X Gli-response element (Gli-Luc MEFs);
  • Figure 12d graphically illustrates data from a study showing dose- dependent inhibition by PF-04449913 in the Gli-Luc MEF reporter assay;
  • Figure 13a graphically illustrates data from a study showing anti -tumor activity of
  • Figure 13b graphically illustrates data from a study showing dose dependent anti-tumor efficacy of PF-04449913 against Ptch+/-p53+/- medulloblastoma allografts
  • Figure 13c graphically illustrates data from a study showing Hh pathway inhibition in PF-04449913 treated Ptch+/-p53+/- medulloblastoma allografts
  • Figure 13d graphically illustrates data from a study showing which genes are significantly down-regulated by PF-04449913 treatment in Ptch +/ ⁇ p53 _/ ⁇ mice
  • Figure 13e graphically illustrates data from a study showing gene signatures are enriched for within the top 31 PF-04449913-downregulated genes in Ptch+/-p53 -/- mice; all figures are also further described, below.
  • Figure 14a graphically illustrates data from a study showing the percentage of weight changes in groups of mice over the course of 14 days of treatment with vehicle, PF-04449913, dasatinib, or a combination thereof;
  • Figure 14b illustrates representative photographs of spleens from no transplant, blast crisis CML engrafted mice treated with vehicle or PF-04449913;
  • Figure 14c graphically illustrates representative FACS plots of blast crisis CML engrafted mice treated with vehicle, PF-04449913, dasatinib, or combination;
  • Figure 15a graphically illustrates heat-map of normalized expression values on log2 scale for 10,573 highly expressed genes in FACS-purified primary blast crisis CML CD34 + CD38 " Lin “ and CD34 + CD38 + Lin " ; RAG2 "/” g-c “/” marrow engrafted blast crisis CML CD34 + CD38 " Lin " and CD34 + CD38 + Lin " ; and normal cord blood CD34 + CD38 " Lin " and CD34 + CD38 + Lin " samples;
  • Figure 15c graphically illustrates a GSEA enrichment plot for the significantly down-regulated pathway (regulation of Cell Cycle);
  • Figure 15d graphically illustrates a cell cycle analysis of bone marrow from blast crisis CML engrafted mice after
  • Figure 16a schematically illustrates a heatmap from unsupervised agglomerative hierarchical clustering of sonic hedgehog (SHH) pathway genes using RNA Seq data from FACS-purified progenitors (CD34 + CD38 + lin " PL) from 8 chronic phase (CP) and 9 blast crisis (BC) patients, 3 normal cord blood (CB) and 3 normal peripheral blood (NPB) sample;
  • Figure 16b graphically illustrates a principal components plot derived from RNA Seq data for 41 genes in the SHH pathway, from 8 chronic phase (CP; black triangles) and 9 blast crisis (BC; red circles) subjects, as well as 3 cord blood normal samples (CB; blue diamonds) and 3 normal peripheral blood (NPB; blue circles);
  • Figure 16c graphically illustrates box plots for GLI2 expression of 7 chronic phase (CP) and 6 blast crisis (BC) non-treated subjects, as well as 3 cord blood normal samples (CB) and 3 normal peripheral blood (NPBc);
  • Figure 16d graphically illustrates quantitative RT-
  • Figure 17a schematically illustrates the chemical structure of PF-04449913, a selective smoothened (SMO) antagonist
  • Figure 18a graphically illustrates a heatmap from unsupervised agglomerative hierarchical clustering of cell cycle pathway genes using RNA Seq data from FACS- purified progenitors (CD34 + CD38 + lin ⁇ PI ⁇ ) from 8 chronic phase (CP) and 9 blast crisis (BC) patients sample;
  • Figure 18b schematically illustrates a network analysis performed on differentially expressed genes between BC and CP revealed CDK IA as a key hub for cell cycle difference;
  • Figure 18c graphically illustrates representative FACS plots comparing Ki67 and 7AAD in bone marrow engrafted viable human CD45 + cells after 14 days of vehicle or PF-04449913 treatment;
  • Figure 18e schematically and graphically illustrates a GSEA enrichment plot for the significantly down-regulated pathway;
  • Figure 18f
  • Figure 19a summarizes the characteristics of patients enrolled in clinical trial NCT01546038;
  • Figure 19b graphically illustrates the clinical response to PF-04449913 in the bone marrow of AML patient samples;
  • Figure 19c illustrates representative FACS cell cycle plots of Ki67 and 7AAD staining of human CD34+CD38- and CD34+ CD38+ cells derived from primary patient samples after 4 weeks (C1D28) of treatment with PF- 04449913 (40mg) on the Phase 1 clinical trial;
  • Figure 19d graphically illustrates cell cycle analysis (peripheral blood-CD45+PI-) from a secondary AML patient that was treated with PF-04449913 (40mg) for 4 weeks on the Phase 1 clinical trial;
  • Figure 19e summarizes the characteristics of patient samples analyzed for their cell cycle study; all figures are also further described, below.
  • Figure 20a schematically illustrates in vivo experiments using RAG2 "/" y c "/” pups that were transplanted intrahepatically with 50,000 CD34 + cells within 48 hours of birth, as discussed in detail, below;
  • FIG. 20e Graph shows percentage of CD34+CD38+lin- cells in the bone marrow; *p ⁇ 0.05 by ANOVA and Tukey post-hoc analysis;
  • Figure 20e graphically illustrates data of myeloid sarcoma count from
  • Figure 21a graphically illustrates data from a competition-binding assay using a characterized cyclopamine-competitive SMO antagonist
  • Figure 21b graphically illustrates data showing that the inhibition of Shh stimulated luciferase expression using mouse embryonic fibroblasts expressing luciferase under control of an 8X GLI-response element (GLI-LUC MEFs)
  • Figure 21c graphically illustrates data showing the dose dependent inhibition by PF-04449913 in the GLI-Luc MEF reporter assay
  • Figure 21d graphically illustrates data showing anti-tumor activity of PF-04449913 against Ptch+A p53+/- medulloblastoma
  • Figure 2 le graphically illustrates data showing the dose dependent anti-tumor efficacy of PF-04449913 against Ptch+/-p53+/- medulloblastoma allografts
  • Figure 21 f graphically illustrates data showing genes significantly down- regulated by PF-04
  • Figure 22 b summarizes the characteristics of patients enrolled and sequenced using the gene expression profile by Affymetrix
  • GENECHIP 1.0 STTM after PF-04449913 treatment for 28 days (C1D28);
  • Figure 23c graphically illustrates data from a FACS quantification of GO (green), Gl (light blue) and G2/S (navy) human CD45 + cells in cord blood engrafted marrow after 14 days of treatment with vehicle (
  • Figure 24 illustrates a mechanism of action analysis using nanoproteonomics
  • CB1000 CB1000 technology to show the nanoproteomics of SAR302503, panels show phospho- JAK2 protein (upper left); total JAK2 protein (upper right); phospho-STAT5A protein (lower right) and 2-microblobulin (lower right) status after vehicle (blue) or selective JAK2 inhibitor (SAR302503; green) treatment; all figures are also further described, below.
  • Figure 25A graphically illustrates RNA-seq-based expression levels of isoforms involved in the Jak/Stat pathway, in vehicle-treated (blue) and SAR302503 -treated (red) blast crisis CML sorted progenitors;
  • Figure 25B graphically illustrates specific isoform expression after treatment with SAR302503 (JAK2 inhibitor) and dasatinib (BCR-ABL inhibitor), relative to vehicle treatment; all figures are also further described, below.
  • CML Chronic Myeloid Leukemia
  • compositions and methods of the invention can slow or inhibit RNA editing by, e.g., inhibiting or slowing the expression of or the activity of an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide.
  • ADARl is an RNA editing enzyme, required for hematopoiesis; and levels of ADARl were assessed in isolated human normal and cancer stem cells (CSC) at various times during the progression of CML. Data described herein demonstrates a crucial role for ADARl in both cell differentiation and self-renewal of hematopoietic stem cells.
  • the invention provides compositions and methods that target, or inhibit ADARl, and treat or ameliorate diseases and conditions responsive to the inhibition of cell differentiation and/or self-renewal of hematopoietic stem cells, such as cancer, e.g., CML.
  • the invention provides a model for the development of therapeutics for treating CML patients, as well as for diagnosing and monitoring CML patients.
  • ADARl expression in vitro transduction of lentiviral ADARl pi 50 changes normal and chronic phase progenitors to a preferred differentiation to a GMP (Granulocyte- macrophage progenitor) population found in the leukemia stem cells in CML; and ADARl knockdown (shRNA) leads to a universal (blast and chronic phase) decrease of self-renewal capacity.
  • GMP Granulocyte- macrophage progenitor
  • ADARl is significantly upregulated in cancer stem cell population as CML progresses from chronic phase to blast crisis, the final phase of the disease, and because ADARl deletion in CML patient sample reduces cancer stem cell renewal capacity, the compositions and methods of the invention are effective for diagnosing, treating and ameliorate diseases and conditions responsive to the inhibition of cell differentiation and/or self-renewal of hematopoietic stem cells, such as cancer, e.g., CML.
  • the invention provides compositions and methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, e.g., leukemia or Chronic Myeloid Leukemia (CML), comprising use of polypeptides, e.g., antibodies, and/or peptides, e.g., aptamers, that inhibit or slow the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl enzyme.
  • an ADARl gene adenosine deaminase acting on RNA 1
  • ADARl gene product an ADARl transcript
  • ADARl enzyme an ADARl enzyme
  • Polypeptides and peptides used to practice the invention can comprise a recombinant protein, a synthetic protein, a peptidomimetic, a non-natural peptide, or a combination thereof.
  • Peptides and proteins used to practice the invention can be recombinantly expressed in vitro or in vivo.
  • the peptides and polypeptides used to practice the invention can be made and isolated using any method known in the art.
  • Polypeptide and peptides used to practice the invention can also be synthesized, whole or in part, using chemical methods well known in the art. See e.g., Caruthers (1980) Nucleic Acids Res. Symp.
  • peptide synthesis can be performed using various solid-phase techniques (see e.g., Roberge (1995) Science 269:202; Merrifield (1997) Methods Enzymol. 289:3-13) including any automated polypeptide synthesis process known in the art.
  • Antibodies see e.g., Roberge (1995) Science 269:202; Merrifield (1997) Methods Enzymol. 289:3-13) including any automated polypeptide synthesis process known in the art.
  • compositions and methods of the invention comprise use of antibodies to inhibit or slow the expression of or the activity of: an ADAR1 gene (adenosine deaminase acting on RNA 1), an ADAR1 gene product, an AD AR1 transcript, and/or an ADAR1 enzyme.
  • an ADAR1 gene adenosine deaminase acting on RNA 1
  • an ADAR1 gene product adenosine deaminase acting on RNA 1
  • ADAR1 gene product an ADAR1 gene product
  • AD AR1 transcript an ADAR1 enzyme
  • an antibody for practicing the invention can comprise a peptide or polypeptide derived from, modeled after or substantially encoded by an ADAR1 gene (SEQ ID NO: 1) or transcript (SEQ ID NO:2), or a peptide or polypeptide derived from, modeled after a protein as set forth in SEQ ID NO:3, or subsequences thereof, or immunogenic fragments thereof, capable of specifically binding an antigen or epitope, see, e.g. Fundamental Immunology, Third Edition, W.E. Paul, ed., Raven Press, N.Y. (1993); Wilson (1994) J. Immunol. Methods 175:267-273; Yarmush (1992) J. Biochem. Biophys. Methods 25:85-97.
  • an antibody for practicing the invention includes antigen-binding portions, i.e., "antigen binding sites,” (e.g., fragments, subsequences, complementarity determining regions (CDRs)) that retain capacity to bind antigen (e.g., a Bcl-2 family protein, or immunogenic fragments thereof) including (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al, (1989) Nature 341 :544-546), which consists of a VH domain; and (vi
  • Antibodies also can be generated in vitro, e.g., using recombinant antibody binding site expressing phage display libraries, in addition to the traditional in vivo methods using animals. See, e.g., Hoogenboom (1997) Trends Biotechnol. 15:62-70; Katz (1997) Annu. Rev. Biophys. Biomol. Struct. 26:27-45.
  • antibodies used to practice this invention comprise
  • antibodies used to practice this invention are matured antibodies having nanomolar or even picomolar affinities for the target antigen, e.g., a targeted transcriptional activating factor.
  • Affinity matured antibodies can be produced by procedures known in the art.
  • antibodies used to practice this invention are designed to bind to, or affinity matured to bind to, a polypeptide encoded by SEQ ID NO: l, or subsequences thereof:
  • antibodies used to practice this invention are designed to bind to, or affinity matured to bind to, a polypeptide encoded by SEQ ID NO:2, or subsequences thereof:
  • antibodies used to practice this invention are designed to bind to, or affinity matured to bind to, a polypeptide SEQ ID NO:3, or subsequences thereof:
  • compositions and methods of the invention use nucleic acids for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal of hematopoietic stem cells or cancer stem cells.
  • compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the ADAR1 gene (e.g., SEQ ID NO: l) or an ADAR1 gene transcript (e.g., SEQ ID NO:2).
  • compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADAR1 gene or ADAR1 gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA), or a ribozyme.
  • dsRNA double-stranded RNA
  • siRNA small interfering RNA
  • miRNA microRNA
  • shRNA short hairpin RNA
  • nucleic acids of the invention are made, isolated and/or manipulated by, e.g., cloning and expression of cDNA libraries, amplification of message or genomic DNA by PCR, and the like.
  • RNA, iRNA, antisense nucleic acid, cDNA, genomic DNA, vectors, viruses or hybrids thereof can be isolated from a variety of sources, genetically engineered, amplified, and/or expressed/ generated recombinantly. Recombinant polypeptides generated from these nucleic acids can be individually isolated or cloned and tested for a desired activity. Any recombinant expression system can be used, including e.g. bacterial, fungal, mammalian, yeast, insect or plant cell expression systems.
  • nucleic acids used to practice this invention can be synthesized in vitro by well-known chemical synthesis techniques, as described in, e.g., Adams (1983) J. Am. Chem. Soc. 105:661; Belousov (1997) Nucleic Acids Res. 25:3440-3444; Frenkel (1995) Free Radic. Biol. Med. 19:373-380; Blommers (1994) Biochemistry 33 :7886- 7896; Narang (1979) Meth. Enzymol. 68:90; Brown (1979) Meth. Enzymol. 68: 109; Beaucage (1981) Tetra. Lett. 22: 1859; U.S. Patent No. 4,458,066.
  • nucleic acids used to practice this invention such as, e.g., subcloning, labeling probes (e.g., random-primer labeling using Klenow polymerase, nick translation, amplification), sequencing, hybridization and the like are well described in the scientific and patent literature, see, e.g., Sambrook, ed.,
  • MOLECULAR CLONING A LABORATORY MANUAL (2ND ED.), Vols. 1-3, Cold Spring Harbor Laboratory, (1989); CURRENT PROTOCOLS IN MOLECULAR
  • BIOLOGY Ausubel, ed. John Wiley & Sons, Inc., New York (1997); LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY: HYBRIDIZATION WITH NUCLEIC ACID PROBES, Part I. Theory and Nucleic Acid Preparation, Tijssen, ed. Elsevier, N.Y. (1993).
  • Another useful means of obtaining and manipulating nucleic acids used to practice the methods of the invention is to clone from genomic samples, and, if desired, screen and re-clone inserts isolated or amplified from, e.g., genomic clones or cDNA clones.
  • Sources of nucleic acid used in the methods of the invention include genomic or cDNA libraries contained in, e.g., mammalian artificial chromosomes (MACs), see, e.g., U.S. Patent Nos. 5,721, 118; 6,025,155; human artificial chromosomes, see, e.g., Rosenfeld (1997) Nat. Genet.
  • MACs mammalian artificial chromosomes
  • yeast artificial chromosomes YAC
  • bacterial artificial chromosomes BAC
  • P I artificial chromosomes see, e.g., Woon (1998) Genomics 50:306-316
  • P l-derived vectors PACs
  • cosmids recombinant viruses, phages or plasmids.
  • Nucleic acids or nucleic acid sequences used to practice this invention can be an oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin.
  • PNA peptide nucleic acid
  • nucleic acids or “nucleic acid sequences” including oligonucleotide, nucleotide, polynucleotide, or any fragment of any of these; and include DNA or RNA (e.g., mRNA, rRNA, tRNA, iRNA) of genomic or synthetic origin which may be single-stranded or double-stranded; and can be a sense or antisense strand, or a peptide nucleic acid (PNA), or any DNA-like or RNA-like material, natural or synthetic in origin, including, e.g., iRNA, ribonucleoproteins (e.g., e.g., double stranded iRNAs, e.g., iRNPs).
  • DNA or RNA e.g., mRNA, rRNA, tRNA, iRNA
  • PNA peptide nucleic acid
  • nucleic acids i.e., oligonucleotides, containing known analogues of natural nucleotides.
  • Compounds use to practice this invention include nucleic-acid-like structures with synthetic backbones, see e.g., Mata (1997) Toxicol. Appl. Pharmacol. 144: 189-197; Strauss-Soukup (1997) Biochemistry 36:8692-8698; Straussense Nucleic Acid Drug Dev 6: 153- 156.
  • oligonucleotides including a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands that may be chemically synthesized.
  • Compounds use to practice this invention include synthetic oligonucleotides having no 5' phosphate, and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase.
  • a synthetic oligonucleotide can ligate to a fragment that has not been dephosphorylated.
  • compounds used to practice this invention include genes or any segment of DNA or RNA involved in producing a polypeptide chain; it can include regions preceding and following the coding region (leader and trailer) as well as, where applicable, intervening sequences (introns) between individual coding segments (exons).
  • "Operably linked” can refer to a functional relationship between two or more nucleic acid (e.g., DNA or RNA) segments. In alternative aspects, it can refer to the functional relationship of transcriptional regulatory sequence to a transcribed sequence.
  • a promoter can be operably linked to a coding sequence, such as a nucleic acid used to practice this invention, if it stimulates or modulates the transcription of the coding sequence in an appropriate host cell or other expression system.
  • promoter transcriptional regulatory sequences can be operably linked to a transcribed sequence where they can be physically contiguous to the transcribed sequence, i.e., they can be cz ' s-acting.
  • transcriptional regulatory sequences such as enhancers, need not be physically contiguous or located in close proximity to the coding sequences whose transcription they enhance.
  • the invention comprises use of "expression cassettes" comprising a nucleotide sequence used to practice this invention, which can be capable of affecting expression of the nucleic acid, e.g., a structural gene or a transcript (e.g., encoding a DRP or antibody) in a host compatible with such sequences.
  • Expression cassettes can include at least a promoter operably linked with the polypeptide coding sequence or inhibitory sequence; and, in one aspect, with other sequences, e.g., transcription termination signals. Additional factors necessary or helpful in effecting expression may also be used, e.g., enhancers.
  • expression cassettes used to practice this invention also include plasmids, expression vectors, recombinant viruses, any form of recombinant "naked DNA" vector, and the like.
  • a "vector" used to practice this invention can comprise a nucleic acid that can infect, transfect, transiently or permanently transduce a cell.
  • a vector used to practice this invention can be a naked nucleic acid, or a nucleic acid complexed with protein or lipid.
  • vectors used to practice this invention can comprise viral or bacterial nucleic acids and/or proteins, and/or membranes (e.g., a cell membrane, a viral lipid envelope, etc.).
  • vectors used to practice this invention can include, but are not limited to replicons (e.g., RNA replicons, bacteriophages) to which fragments of DNA may be attached and become replicated.
  • Vectors thus include, but are not limited to RNA, autonomous self-replicating circular or linear DNA or RNA (e.g., plasmids, viruses, and the like, see, e.g., U.S. Patent No. 5,217,879), and can include both the expression and non-expression plasmids.
  • the vector used to practice this invention can be stably replicated by the cells during mitosis as an autonomous structure, or can be incorporated within the host's genome.
  • promoters used to practice this invention include all sequences capable of driving transcription of a coding sequence in a cell, e.g., a mammalian cell such as a brain cell.
  • promoters used in the constructs of the invention include cz ' s-acting transcriptional control elements and regulatory sequences that are involved in regulating or modulating the timing and/or rate of transcription of a gene.
  • a promoter used to practice this invention can be a cz ' s-acting transcriptional control element, including an enhancer, a promoter, a transcription terminator, an origin of replication, a chromosomal integration sequence, 5' and 3 ' untranslated regions, or an intronic sequence, which are involved in transcriptional regulation.
  • These cis-acting sequences typically interact with proteins or other biomolecules to carry out (turn on/off, regulate, modulate, etc.) transcription.
  • Constutive promoters used to practice this invention can be those that drive expression continuously under most environmental conditions and states of development or cell differentiation.
  • “Inducible” or “regulatable” promoters used to practice this invention can direct expression of the nucleic acid of the invention under the influence of environmental conditions or developmental conditions.
  • compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the ADAR1 gene (e.g., SEQ ID NO: l) or a ADARl gene transcript (e.g., SEQ ID NO:2).
  • ADAR1 gene e.g., SEQ ID NO: l
  • ADARl gene transcript e.g., SEQ ID NO:2
  • compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADAR1 gene or ADAR1 gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA), or a ribozyme.
  • dsRNA double-stranded RNA
  • siRNA small interfering RNA
  • miRNA microRNA
  • shRNA short hairpin RNA
  • Naturally occurring or synthetic nucleic acids can be used as antisense oligonucleotides.
  • the antisense oligonucleotides can be of any length; for example, in alternative aspects, the antisense oligonucleotides are between about 5 to 100, about 10 to 80, about 15 to 60, about 18 to 40. The optimal length can be determined by routine screening.
  • the antisense oligonucleotides can be present at any concentration. The optimal concentration can be determined by routine screening.
  • a wide variety of synthetic, non-naturally occurring nucleotide and nucleic acid analogues are known which can address this potential problem.
  • peptide nucleic acids containing non-ionic backbones, such as N-(2-aminoethyl) glycine units can be used.
  • Antisense oligonucleotides having phosphorothioate linkages can also be used, as described in WO 97/03211 ; WO 96/39154; Mata (1997) Toxicol. Appl. Pharmacol. 144: 189-197; Antisense Therapeutics, ed. Agrawal (Humana Press, Totowa, N.J., 1996).
  • Antisense oligonucleotides having synthetic DNA backbone analogues provided by the invention can also include phosphoro-dithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3'-N-carbamate, and morpholino carbamate nucleic acids.
  • RNA interference RNA interference
  • the invention provides RNAi inhibitory nucleic acid molecules capable of decreasing or inhibiting expression of one or a set of ADAR1 transcripts or proteins, e.g., the transcript (mRNA, message) SEQ ID NO:2 or isoform or isoforms thereof.
  • the RNAi molecule comprises a double-stranded RNA (dsRNA) molecule.
  • the RNAi molecule can comprise a double-stranded RNA (dsRNA) molecule, e.g., siRNA, miRNA (microRNA) and/or short hairpin RNA (shRNA) molecules.
  • the RNAi is about 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. While the invention is not limited by any particular mechanism of action, the RNAi can enter a cell and cause the degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to double-stranded RNA (dsRNA), mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi).
  • ssRNA single-stranded RNA
  • dsRNA double-stranded RNA
  • RNAi RNA interference
  • RNAi e.g., siRNA for inhibiting transcription and/or miRNA to inhibit translation
  • siRNA for inhibiting transcription and/or miRNA to inhibit translation
  • dsRNA double-stranded RNA
  • short interfering RNA short interfering RNA
  • intracellular introduction of the RNAi is by internalization of a target cell specific ligand bonded to an RNA binding protein comprising an RNAi (e.g., microRNA) is adsorbed.
  • a target cell specific ligand bonded to an RNA binding protein comprising an RNAi (e.g., microRNA) is adsorbed.
  • the ligand can be specific to a unique target cell surface antigen.
  • the ligand can be spontaneously internalized after binding to the cell surface antigen. If the unique cell surface antigen is not naturally internalized after binding to its ligand, internalization can be promoted by the
  • the invention provides lipid- based formulations for delivering, e.g., introducing nucleic acids of the invention as nucleic acid-lipid particles comprising an RNAi molecule to a cell, see .g., U.S. Patent App. Pub. No. 20060008910.
  • RNAi molecules e.g., siRNA and/or miRNA
  • Methods for making and using RNAi molecules, e.g., siRNA and/or miRNA, for selectively degrade RNA are well known in the art, see, e.g., U.S. Patent No. 6,506,559; 6,51 1,824; 6,515,109; 6,489,127.
  • an inhibitory polynucleotide e.g., a duplex siRNA of the invention
  • a regulatory region e.g., promoter, enhancer, silencer, splice donor, acceptor, etc.
  • the sense and antisense strands of the targeted portion of the targeted IRES can be transcribed as two separate RNA strands that will anneal together, or as a single RNA strand that will form a hairpin loop and anneal with itself.
  • a construct targeting a portion of a gene e.g., an NADPH oxidase enzyme coding sequence or transcriptional activation sequence, is inserted between two promoters (e.g., mammalian, viral, human, tissue specific, constitutive or other type of promoter) such that transcription occurs bidirectionally and will result in complementary RNA strands that may subsequently anneal to form an inhibitory siRNA of the invention.
  • promoters e.g., mammalian, viral, human, tissue specific, constitutive or other type of promoter
  • a targeted portion of a gene, coding sequence, promoter or transcript can be designed as a first and second antisense binding region together on a single expression vector; for example, comprising a first coding region of a targeted gene in sense orientation relative to its controlling promoter, and wherein the second coding region of the gene is in antisense orientation relative to its controlling promoter. If transcription of the sense and antisense coding regions of the targeted portion of the targeted gene occurs from two separate promoters, the result may be two separate RNA strands that may subsequently anneal to form a gene-inhibitory siRNA used to practice this invention.
  • transcription of the sense and antisense targeted portion of the targeted gene is controlled by a single promoter, and the resulting transcript will be a single hairpin RNA strand that is self-complementary, i.e., forms a duplex by folding back on itself to create a gene- inhibitory siRNA molecule.
  • a spacer e.g., of nucleotides, between the sense and antisense coding regions of the targeted portion of the targeted gene can improve the ability of the single strand RNA to form a hairpin loop, wherein the hairpin loop comprises the spacer.
  • the spacer comprises a length of nucleotides of between about 5 to 50 nucleotides.
  • the sense and antisense coding regions of the siRNA can each be on a separate expression vector and under the control of its own promoter.
  • the invention provides ribozymes capable of binding and inhibiting, e.g., decreasing or inhibiting, expression of one or a set of ADAR1 transcripts or proteins, e.g., SEQ ID NO: 1 or SEQ ID NO:2, or isoform or isoforms thereof.
  • ribozymes can inhibit a gene's activity by, e.g., targeting a genomic DNA or an mRNA (a message, a transcript).
  • Strategies for designing ribozymes and selecting a gene-specific antisense sequence for targeting are well described in the scientific and patent literature, and the skilled artisan can design such ribozymes using the novel reagents of the invention.
  • Ribozymes act by binding to a target RNA through the target RNA binding portion of a ribozyme which is held in close proximity to an enzymatic portion of the RNA that cleaves the target RNA.
  • the ribozyme recognizes and binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cleave and inactivate the target RNA. Cleavage of a target RNA in such a manner will destroy its ability to direct synthesis of an encoded protein if the cleavage occurs in the coding sequence. After a ribozyme has bound and cleaved its RNA target, it can be released from that RNA to bind and cleave new targets repeatedly.
  • kits comprising compositions and/or instructions for practicing methods of the invention.
  • kits, cells, vectors and the like can also be provided.
  • the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
  • the invention provides compositions and methods to detect dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells.
  • CML Chronic Myelogenous Leukemia
  • the invention provides compositions and methods for use to, e.g., therapeutically, initiate, stimulate or force a dormant cancer stem cell, e.g., a Chronic Myelogenous Leukemia (CML) stem cell, into cycle so that it can be targeted by a therapeutic agent or procedure, e.g., chemotherapy, radiation therapy or targeted tyrosine kinase inhibitors, or any agent or procedure that targets dividing cells.
  • a therapeutic agent or procedure e.g., chemotherapy, radiation therapy or targeted tyrosine kinase inhibitors, or any agent or procedure that targets dividing cells.
  • compositions and methods comprising or comprising use of sonic hedgehog inhibitors, e.g., inhibitors of
  • SMO Smoothened
  • a stem cell e.g., a cancer stem cell, a transition from GO to Gl of the cell cycle, thereby sensitizing the stem cells to agents that target dividing cells.
  • RNA sequencing performed on FACS-purified human progenitors from PF-04449913 treated blast crisis LSC engrafted mice demonstrated greater Shh gene splice isoform concordance with normal progenitors than vehicle treated controls.
  • RNA sequencing revealed significantly decreased cell cycle regulatory gene expression and splice isoform analysis demonstrated reversion toward a normal splice isoform signature for many cell cycle regulatory genes.
  • PF-04449913 synergized with BCR-ABL inhibition to reduce blast crisis LSC survival and self-renewal in concert with increased expression of Shh pathway regulators.
  • the invention also provides novel stem cell, e.g., LSC, splice isoform detection platforms, e.g., as kits of the invention, to assess the efficacy of Shh inhibitor-mediated sensitization.
  • stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify "conversion" of a stem cell to a "normal cell", or to determine or define a molecularly targeted therapy for dormant cancer stem cell elimination strategies that ultimately avert relapse.
  • stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify compounds or treatments that can successfully inhibit Shh expression.
  • compositions and methods of the invention can be used synergistically to sensitize dormant stem cells, e.g., LSC, to therapeutic agents that target dividing cells including e.g., tyrosine kinase inhibitors, chemotherapy.
  • compositions and methods of the invention can be used sensitize, e.g., radiosensitize, a cancer stem cell, e.g., a LSC and other cancer stem cell populations, through cell cycle induction or stimulation.
  • RNA isoform pattern of a leukemic cancer stem cell reverting to the pattern of a normal cell.
  • this RNA isoform pattern can be used as a biomarker of response to chemotherapy and a target for drug development, e.g., successful or effective inhibition of Shh give a particular, detectable RNA isoform pattern.
  • the invention provides splice isoform detection kits or arrays for stem cells, e.g., LSC stem cells.
  • the invention provides nanoproteomic detection kits or arrays for stem cells (to determine an altered proteome caused by an altered RNA splicing pattern, or alternatively spliced transcripts) to determine a response to a stem cell therapy, e.g., a LSC targeted therapy.
  • kits comprising compositions and/or instructions for practicing methods of the invention.
  • kits, cells, vectors and the like can also be provided.
  • the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
  • compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the Shh or a Shh gene transcript.
  • compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the Shh gene or Shh gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA), or a ribozyme.
  • dsRNA double-stranded RNA
  • siRNA small interfering RNA
  • miRNA microRNA
  • shRNA short hairpin RNA
  • Naturally occurring or synthetic nucleic acids can be used as antisense oligonucleotides.
  • the antisense oligonucleotides can be of any length; for example, in alternative aspects, the antisense oligonucleotides are between about 5 to 100, about 10 to 80, about 15 to 60, about 18 to 40. The optimal length can be determined by routine screening.
  • the antisense oligonucleotides can be present at any concentration. The optimal concentration can be determined by routine screening.
  • a wide variety of synthetic, non-naturally occurring nucleotide and nucleic acid analogues are known which can address this potential problem.
  • PNAs peptide nucleic acids
  • non-ionic backbones such as N-(2-aminoethyl) glycine units
  • Antisense oligonucleotides having phosphorothioate linkages can also be used, as described in WO 97/03211 ; WO 96/39154; Mata (1997) Toxicol. Appl. Pharmacol.
  • Antisense oligonucleotides having synthetic DNA backbone analogues provided by the invention can also include phosphoro-dithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3 '-N -carbamate, and morpholino carbamate nucleic acids.
  • RNA interference RNA interference
  • the invention provides RNAi inhibitory nucleic acid molecules capable of decreasing or inhibiting expression of one or a set oiShh transcripts or proteins, e.g., the transcript (mRNA, message) or isoform or isoforms thereof.
  • the RNAi molecule comprises a double-stranded RNA (dsRNA) molecule.
  • the RNAi molecule can comprise a double-stranded RNA (dsRNA) molecule, e.g., siRNA, miRNA (microRNA) and/or short hairpin RNA (shRNA) molecules.
  • the RNAi is about 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. While the invention is not limited by any particular mechanism of action, the RNAi can enter a cell and cause the degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to double-stranded RNA (dsRNA), mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi).
  • ssRNA single-stranded RNA
  • dsRNA double-stranded RNA
  • RNAi RNA interference
  • RNAi e.g., siRNA for inhibiting transcription and/or miRNA to inhibit translation
  • siRNA for inhibiting transcription and/or miRNA to inhibit translation
  • dsRNA double-stranded RNA
  • short interfering RNA short interfering RNA
  • intracellular introduction of the RNAi is by internalization of a target cell specific ligand bonded to an RNA binding protein comprising an RNAi (e.g., microRNA) is adsorbed.
  • the ligand can be specific to a unique target cell surface antigen.
  • the ligand can be spontaneously internalized after binding to the cell surface antigen. If the unique cell surface antigen is not naturally internalized after binding to its ligand, internalization can be promoted by the incorporation of an arginine-rich peptide, or other membrane permeable peptide, into the structure of the ligand or RNA binding protein or attachment of such a peptide to the ligand or RNA binding protein.
  • the invention provides lipid- based formulations for delivering, e.g., introducing nucleic acids of the invention as nucleic acid-lipid particles comprising an RNAi molecule to a cell, see .g., U.S. Patent App. Pub. No. 20060008910.
  • RNAi molecules e.g., siRNA and/or miRNA
  • Methods for making and using RNAi molecules, e.g., siRNA and/or miRNA, for selectively degrade RNA are well known in the art, see, e.g., U.S. Patent No. 6,506,559; 6,51 1,824; 6,515,109; 6,489,127.
  • an inhibitory polynucleotide e.g., a duplex siRNA of the invention
  • a regulatory region e.g., promoter, enhancer, silencer, splice donor, acceptor, etc.
  • the sense and antisense strands of the targeted portion of the targeted IRES can be transcribed as two separate RNA strands that will anneal together, or as a single RNA strand that will form a hairpin loop and anneal with itself.
  • a construct targeting a portion of a gene e.g., a Shh coding sequence or transcriptional activation sequence
  • two promoters e.g., mammalian, viral, human, tissue specific, constitutive or other type of promoter
  • a targeted portion of a gene, coding sequence, promoter or transcript can be designed as a first and second antisense binding region together on a single expression vector; for example, comprising a first coding region of a targeted gene in sense orientation relative to its controlling promoter, and wherein the second coding region of the gene is in antisense orientation relative to its controlling promoter. If transcription of the sense and antisense coding regions of the targeted portion of the targeted gene occurs from two separate promoters, the result may be two separate RNA strands that may subsequently anneal to form a gene-inhibitory siRNA used to practice this invention.
  • transcription of the sense and antisense targeted portion of the targeted gene is controlled by a single promoter, and the resulting transcript will be a single hairpin RNA strand that is self-complementary, i.e., forms a duplex by folding back on itself to create a gene- inhibitory siRNA molecule.
  • a spacer e.g., of nucleotides, between the sense and antisense coding regions of the targeted portion of the targeted gene can improve the ability of the single strand RNA to form a hairpin loop, wherein the hairpin loop comprises the spacer.
  • the spacer comprises a length of nucleotides of between about 5 to 50 nucleotides.
  • the sense and antisense coding regions of the siRNA can each be on a separate expression vector and under the control of its own promoter.
  • compositions and methods of the invention comprise use of ribozymes capable of binding and inhibiting, e.g., decreasing or inhibiting, expression of one or a set oiShh transcripts or proteins, or isoform or isoforms thereof.
  • ribozymes can inhibit a gene's activity by, e.g., targeting a genomic DNA or an mRNA (a message, a transcript).
  • Strategies for designing ribozymes and selecting a gene-specific antisense sequence for targeting are well described in the scientific and patent literature, and the skilled artisan can design such ribozymes using the novel reagents of the invention.
  • Ribozymes act by binding to a target RNA through the target RNA binding portion of a ribozyme which is held in close proximity to an enzymatic portion of the RNA that cleaves the target RNA.
  • the ribozyme recognizes and binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cleave and inactivate the target RNA. Cleavage of a target RNA in such a manner will destroy its ability to direct synthesis of an encoded protein if the cleavage occurs in the coding sequence. After a ribozyme has bound and cleaved its RNA target, it can be released from that RNA to bind and cleave new targets repeatedly.
  • the invention also provides bioisosteres of compounds used to practice the invention, e.g., compounds having a structure as set forth in Figure 17a, or PF-04449913.
  • the invention provides compositions that inhibit or slow the expression of a Shh gene, a Shh gene product, a Shh transcript, and/or a Shh polypeptide comprising a PF-04449913, or an equivalent thereof, or a bioisostere thereof.
  • bioisosteres of the invention are compounds of the invention comprising one or more substituent and/or group replacements with a substituent and/or group having substantially similar physical or chemical properties which produce substantially similar biological properties to a compound of the invention, or stereoisomer, racemer or isomer thereof.
  • the purpose of exchanging one bioisostere for another is to enhance the desired biological or physical properties of a compound without making significant changes in chemical structures.
  • bioisosteres of compounds of the invention are made by replacing one or more hydrogen atom(s) with one or more fluorine and/or deuterium atom(s), e.g., at a site of metabolic oxidation; this may prevent metabolism (catabolism) from taking place.
  • fluorine atom or deuterium is similar in size to the hydrogen atom the overall topology of the molecule is not significantly affected, leaving the desired biological activity unaffected. However, with a blocked pathway for metabolism, the molecule may have a longer half-life or be less toxic, and the like.
  • this invention compositions and methods to analyze or measure biomarkers in human leukemia cells to predict the amount of blastic transformation, the severity of the disease, the progress (e.g., regression) of the disease in light of a particular treatment or drug administration.
  • this invention compositions and methods to analyze or measure biomarkers which are predictors of response to selective Sonic Hedgehog (Shh) inhibition.
  • compositions and methods of the invention measure GLI1 and GLI2 transcript and/or GLI1 and GLI2 protein levels to predict a response to selective Shh inhibition, where GLI1 and GLI2 presence is a positive predictor of a response to selective Shh inhibition.
  • GLI1 and/or GLI2 are used as predictive biomarkers, individually or together, of a response to an inhibitor of the Sonic Hedgehog (shh) pathway, including inhibitors of Smoothened (SMO), an integral membrane protein mediator of Hedgehog signaling (see e.g., Shi et al. (2011) Development, Epub 2011 Aug 18; Su, et al. (2011) Sci. Signal. Jul 5;4(180):ra43). Both qRT-PCR and nanoproteomics confirmed these functional biomarkers.
  • SMO Smoothened
  • compositions and methods of the invention measure
  • GLI2 increasing
  • GLI3 decreasing
  • CML chronic myelogenous leukemia
  • LSC Leukemic Stem Cell
  • tyrosine kinase inhibitor resistance Both qRT-PCR and nanoproteomics confirmed these functional biomarkers.
  • compositions and methods comprising or comprising use of sonic hedgehog inhibitors, e.g., inhibitors of
  • SMO Smoothened
  • RNA sequencing performed on FACS-purified human progenitors from PF-04449913 treated blast crisis LSC engrafted mice demonstrated greater Shh gene splice isoform concordance with normal progenitors than vehicle treated controls.
  • RNA sequencing revealed significantly decreased cell cycle regulatory gene expression and splice isoform analysis demonstrated reversion toward a normal splice isoform signature for many cell cycle regulatory genes.
  • PF-04449913 synergized with BCR-ABL inhibition to reduce blast crisis LSC survival and self-renewal in concert with increased expression of Shh pathway regulators.
  • the invention also provides novel stem cell, e.g., LSC, splice isoform detection platforms, e.g., as kits of the invention, to assess the efficacy of Shh inhibitor-mediated sensitization.
  • stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify "conversion" of a stem cell to a "normal cell", or to determine or define a molecularly targeted therapy for dormant cancer stem cell elimination strategies that ultimately avert relapse.
  • stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify compounds or treatments that can successfully inhibit Shh expression.
  • compositions and methods of the invention can be used synergistically to sensitize dormant stem cells, e.g., LSC, to therapeutic agents that target dividing cells including e.g., tyrosine kinase inhibitors, chemotherapy.
  • compositions and methods of the invention can be used sensitize, e.g., radiosensitize, a cancer stem cell, e.g., a LSC and other cancer stem cell populations, through cell cycle induction or stimulation.
  • RNA isoform pattern of a leukemic cancer stem cell reverting to the pattern of a normal cell.
  • this RNA isoform pattern can be used as a biomarker of response to chemotherapy and a target for drug development, e.g., successful or effective inhibition of Shh give a particular, detectable RNA isoform pattern.
  • the invention provides splice isoform detection kits or arrays for stem cells, e.g., LSC stem cells.
  • the invention provides nanoproteomic detection kits or arrays for stem cells (to determine an altered proteome caused by an altered RNA splicing pattern, or alternatively spliced transcripts) to determine a response to a stem cell therapy, e.g., a LSC targeted therapy.
  • biomarkers of the invention can be detected using arrays, microarrays, proteomic arrays and the like, e.g., as described by: Oehler, et al, (2009) Blood, "The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data", Oct 8; 114(15):3292-8. Epub 2009 Aug 4; Fan, et al., Nature Medicine, May 2009, "Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens," Volume 15, Number 5: 566-571; OTSieill, et al, Proc. Natl. Acad. Sci. USA, Oct 2006, "Isoelectric focusing technology quantifies protein signaling in 25 cells", Volume 103, Number 44: 16153-16158.
  • kits comprising compositions and/or instructions for practicing methods of the invention.
  • kits, cells, vectors and the like can also be provided.
  • the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
  • the invention provides compositions and methods for determining the pattern of alternatively spliced transcripts and their protein products to, e.g., distinguish leukemic progenitors from their normal counterparts, e.g., by
  • the pattern of alternatively spliced Stat5a specific splice isoforms is used as a novel leukemic stem cell (LSC) identification marker.
  • LSC leukemic stem cell
  • the invention provides compositions and methods to assess LSC specific responses to targeted agents such as JAK2 inhibitors, e.g., Stat5a specific splice isoforms can be used as biomarkers of response to JAK2 inhibition.
  • JAK2 inhibitors e.g., Stat5a specific splice isoforms
  • one or both phosphoStat5a and phospho-JAK2 are used as biomarker or biomarkers of a response to a selective JAK2 inhibition, e.g., when selective JAK2 inhibition is used as a clinical treatment or when selective JAK2 inhibitors are tested in in vitro, in animals, or in clinical trials.
  • phosphoStat5a and phospho-JAK2 are used as biomarker or biomarkers of a response to a selective JAK2 inhibition, e.g., when selective JAK2 inhibition is used as a clinical treatment or when selective JAK2 inhibitors are tested in in vitro, in animals, or in clinical trials.
  • both signatures of response are quantitatively measured; and if the alternative spliced forms do not decrease, the self- renewing LSC are resistant to treatment; and, if STAT5a isoforms are decreased or inhibited, LSC self-renewal capacity is decreased.
  • RNA-seq that will provide functional LSC markers and will help to determine if different therapies will target this specific population.
  • Our invention is the first to analyze specific isoform expression of STAT5 as a paradigm for human leukemia stem cell identification and to identify splice isoforms that predict cancer stem cell response.
  • reductions in phosphoStat5a and/or phosphoJAK2 proteins are positive predictors of response to selective JAK2 inhibition.
  • Both qRT-PCR confirmed decreases in transcripts and nanoproteomics confirmed decreases in these alternatively spliced proteins as functional biomarkers of response.
  • the invention provides compositions and methods that comprise use of splice isoform specific qPCR, and equivalents, and/or nanoproteomics, to detect isoforms that sustain LSC self-renewal, including Stat5a isoforms and other pathway LSC specific splice isoforms in a prognostic kit for cancer stem cells (CSC).
  • CSC cancer stem cells
  • the invention provides compositions and methods that comprise use of splice isoforms such as Stat5a isoforms as predictors of LSC response to selective JAK2 inhibition.
  • the invention provides compositions and methods that comprise use of splice isoform patterns by qPCR and nanoproteomics to predict response to CSC targeted therapy.
  • the invention provides compositions and methods to detect cancer stem cell specific JAK/STAT signaling pathway splice isoforms by R A sequencing, qRT-PCR and nanoproteomics, validated in CML, but applicable to cancer stem cells in the primary and metastatic niches, particularly in the setting of inflammatory cytokines and interleukins elaborated in cancer.
  • biomarkers, or alternatively spliced forms, used to practice the invention can be detected using e.g., arrays, microarrays, proteomic arrays and the like, e.g., as described by: Oehler, et al, (2009) Blood, "The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data", Oct 8; 1 14(15):3292-8. Epub 2009 Aug 4; Fan, et al, Nature Medicine, May 2009,
  • Figure 24 Nanoproteomic SAR302503 mechanism of action analysis. Sorted progenitors from mice spleen that where treated where analyzed using nanoproteonomics (CB 1000) technology. Panels shows phospho-JAK2 protein (upper left); total JAK2 protein (upper right); phospho-STAT5A protein (lower right) and p2-microblobulin (lower right) status after vehicle (blue) or selective JAK2 inhibitor (SAR302503; green) treatment.
  • CB 1000 nanoproteonomics
  • Figure 25 Identification and quantification of transcript isoforms in LSC treated with vehicle or a selective JAK2 inhibitor.
  • A) RNA-seq-based expression levels of isoforms involved in the Jak/Stat pathway, in vehicle-treated (blue) and SAR302503- treated (red) blast crisis CML sorted progenitors.
  • kits comprising compositions and/or instructions for practicing methods of the invention.
  • kits, cells, vectors and the like can also be provided.
  • the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
  • Example 1 Inhibiting ADAR Enzyme to Decrease in Self-Renewal Capacity or Stem
  • This example provides data demonstrating that the methods and compositions of the invention are effective for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells.
  • ADAR1 may also play a role in self-renewal, as a significant of decrease in self-renewal capacity was observed in shRNA transducer chronic phase progenitors.
  • the data shown herein illustrates a crucial role for ADAR1 in both cell differentiation and self-renewal of hematopoietic stem cells.
  • This example provides data demonstrating that the methods and compositions of the invention are effective for: inducing in a stem cell susceptibility to BCR-ABL inhibition; activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle; or initiating cell cycling in a cancer stem cell; or breaking dormancy in a cancer stem cell; or radiosensitizing of a cancer stem cell; or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells; or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor.
  • SONIC HEDHEGOG TARGETS AS BIOMARKERS OF PROGNOSIS AND RESPONSE FOR HUMAN CHRONIC MYELOGENOUS LEUKEMIA
  • This example provides data demonstrating that the methods and compositions of the invention are effective for measuring or determining, or predicting, chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance, and for measuring or determining, or predicting, a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted
  • Shh inhibition or a selective Shh inhibition, comprising measuring or determining, individually or together, levels or amounts of GLIl and/or GLI2 transcript and/or protein.
  • Shh signaling in maintenance of dormancy.
  • human blast crisis LSC harbor enhanced expression of the Shh transcriptional activator, GLI2, and decreased expression of a transcriptional repressor, GLI3.
  • PF-04449913 Treatment of human blast crisis LSC engrafted RAG2 "/" yc "/” mice with a novel selective Shh inhibitor, PF-04449913 (see Figure 17a, Supplementary Figure la), reduced leukemic burden in a niche- dependent manner commensurate with GLI downregulation.
  • Full transcriptome R A sequencing performed on FACS-purified human progenitors from PF-04449913 treated blast crisis LSC engrafted mice demonstrated greater Shh gene splice isoform concordance with normal progenitors than vehicle treated controls.
  • RNA sequencing after the Shh inhibition revealed significantly decreased cell cycle regulatory gene expression and splice isoform analysis demonstrated reversion toward a normal splice isoform signature for many cell cycle regulatory genes.
  • cell cycle FACS analysis showed that selective Shh inhibition permitted dormant blast crisis LSC to enter the cell cycle while normal progenitor cell cycle status was unaffected.
  • PF-04449913 synergized with BCR-ABL inhibition to reduce blast crisis LSC survival and self-renewal in concert with increased expression of Shh pathway regulators.
  • Shh signaling links human blast crisis LSC quiescence and self-renewal and whether these traits can be uncoupled with a therapeutic Shh antagonist, as a strategy to enhance sensitivity to BCR-ABL1 tyrosine kinase inhibitors (TKI).
  • TKI BCR-ABL1 tyrosine kinase inhibitors
  • Supplementary Table 1 shows CML patient and normal sample characteristics.
  • Shh pathway gene isoforms that adopted a pattern similar to normal progenitors after Shh inhibitor treatment included pathway regulators such as SUFU, ARRB1, BTRC, CSKN1G1, FBXW1 1, and PRKACB.
  • FACS analysis revealed that Shh inhibitor responses were more robust in extramedullary than medullary niches (Supplementary Fig. 3 c, d) suggesting that resistant LSC were more prominent in the marrow perhaps as a consequence of quiescence induction.
  • hematopoietic stem cell fate decisions 10 10 .
  • RNA sequencing derived predictive biomarkers of CSC response and selective Shh pathway inhibition as a strategy to invoke cycling of dormant LSC thereby sensitizing them to BCR-ABL inhibitors and obviating therapeutic resistance.
  • This approach may also provide a viable strategy for CSC eradication in other refractory malignancies.
  • the SOLiDTM Total RNA-Seq kit (Applied Biosystems part # 4445374) was used to prepare libraries from normal and blast crisis CML samples, which were sequenced on Solid v.3 plus instruments.
  • Gene isoform models were developed by first combining the isoform models from June 2011 versions of REFSEQTM n , UCSC Known Genes 12 , and ENSEMBLTM 13 and then creating a nonredundant set of models using the
  • CUFFCOMPARETM program from version 0.9.3 of the CUFFLINKSTM software package 14 . Then, we mapped RNA-seq reads to the nucleotide sequences of the isoform models using BWA 15 with default parameters and then translated the alignment coordinates in hgl9/GRCh37 human genome reference sequence coordinates using a custom script.
  • mice Equal numbers of primary normal or blast crisis CML CD34 + cells were transplanted intrahepatically into neonatal RAG2 "/" yc "/” mice to form primagrafts, according to established methods l ' 3 . At 8-12 weeks post-transplant, mice were treated with PF-04449913, Dasatinib, a combination of PF-04449913 and Dasatinib, or drug vehicle for 14 days followed by FACS analysis of human hematopoietic engraftment in hematopoietic tissues.
  • ctccagactgtccacagcat (SEQ ID NO:4)
  • BCR-ABL Reverse ccctgaggctcaaagtcaga (SEQ ID NO:5)
  • HPRT Forward cgtcttgctcgagatgtgatg (SEQ ID NO:6)
  • HPRT Reverse HPRT Reverse:
  • tttatagccccccttgagcac SEQ ID NO:7. Relative levels of mRNA were determined according to standard curves. All values were then normalized to HPRT or RPL27 values from the same sample.
  • TAQMANTM primer/probe sets (ABI) for FoxMl (Mm00514924_ml), Glil (Mm00494645_ml), Gli2 (Mm01293117_ml), Mycn (Mm00476449_ml), Ptchl (Mm00436026_ml), Ptch2 (Mm00436047_ml), Sfrpl (Mm00489161_ml), Smo (MmOl 162710_ml) and mouse GAPDH (4352339E), on the ABI 7900HT instrument. Target gene expression levels were normalized to mouse GAPDH and calibrated to vehicle treated mice to yield the relative quantitation (RQ) value.
  • RQ relative quantitation
  • Nanofluidic phospho-proteomic immunoassay (NPI) experiments were performed with the NANOPRO 1000TM instrument (Cell Biosciences) and all samples were run in triplicate at least.
  • the FIREFLYTM system first performed a charge-based separation (isoelectric focusing). Predicted pis were calculated with SCANSITETM. Each sample was run on a panel of different pH gradients (pH 5-8) to optimize the resolution of different peak patterns. After separation and photo-activated in-capillary immobilization, GLI-2 was detected using GLI2-specific antibody (Abeam). A 2-microglubulin-specific antibody 2 ⁇ ; Upstate) was used to normalize the amount of loaded protein. The peaks were quantified by calculating the area under the curve (AUC).
  • mice were treated daily by oral gavage with vehicle (50% 1,2 Propandiol , 50% HBSS or methylcellulose), PF-04449913 (100 mg/kg dissolved in vehicle), Dasatinib (50 mg/kg dissolved in vehicle), combination of PF-04449913 (100 mg/kg) and dasatinib (50mg/kg).
  • vehicle 50% 1,2 Propandiol , 50% HBSS or methylcellulose
  • PF-04449913 100 mg/kg dissolved in vehicle
  • Dasatinib 50 mg/kg dissolved in vehicle
  • combination of PF-04449913 100 mg/kg
  • dasatinib 50mg/kg
  • mice at 7-10 weeks were irradiated sublethally and transplanted with 100K CD34 + human cord blood cells via retro-orbital injection. Eight weeks after transplantation of cord blood cells, the mice were treated for 14 days with either vehicle, or PF-04449913 via oral gavage.
  • mice bone marrow stromal cell lines M2-10B4 (M2) and SL/SL (SL) were provided by StemCell Technologies on behalf of Dr. Donna Hogge in the Terry Fox Laboratory (Vancouver, British Colombia).
  • M2-10B4 M2-10B4
  • SL/SL SL
  • the cell lines were treated with mitomycin-C (1 mg/ml) and plated in a 1 : 1 mixture in total concentration of 100,000/ml.
  • 10,000-20,000 CD34 + blast crisis CML or normal cells were then plated on adherent SL/M2 stromal cells, cultured for 7 days, and analyzed by FACS as described previously 19 .
  • OP9M2 stromal cells (20 Gray on a Saxon-Markl irradiator) were co-cultured with 50,000 human CD34 + cord blood.
  • OP9M2 stroma was grown in AlphaMem from Gibco with 20% Hyclone FBS, 1% pen strep glutamine and supplemented with cytokines: 50ug/ml SCF, lOug/ml thrombopoietin, and lOug/ml Flt3.
  • Membranes were prepared from a stable cell line created in HEK293FlpIn-TetR cells (Invitrogen) using Flp recombinase-mediated insertion of the pSecTag-FRT/V5-His vector containing a cDNA encoding amino acids 181-787 of human Smo fused to the murine Igk leader sequence to produce a cell surface expressed Smo 181-781 protein. LacZ-negative cells were analyzed for binding a well characterized cyclopamine- competitive tritiated Smo antagonist 22 . The tritiated ligand was prepared using Crabtree's catalyst and tritium gas.
  • the labeled material was purified by RP HPLC (53.1 Ci/mmol specific activity at 99% purity).
  • ⁇ of assay buffer was added to all the wells of a 96 well GF/B filter plate (Millipore MULTISCREEN- HTS-FBTM cat# MSFBN6B50) . The plates were counted in a TOPCOU TTM
  • Microarray data were RMA normalized using BIOCONDUCTOR AFFYTM package. Differentially expressed genes were identified based on joint thresholds oft- test pvalue ⁇ 0.01 and fold change >2. Their human orthologs were mapped using HOMOLOGENE BUILD 62TM. They were compared with curated gene sets from a variety of pathway/signature databases and enrichment P-value was determined using hypergeometric statistics calculated with MATLABTM. More specifically, the probability of observing at least (k) genes from a gene set is given by where (f) is size of the gene set, (n) is the # of differentially expressed genes, (g) is the total number of unique human ortholog genes of mouse probes on the microarray.
  • the obs/exp ratio was calculated as k/(f*n/g).
  • b FACS quantitation of common myeloid progenitors (CMP), granulocyte-macrophage progenitors (GMP) and megakaryocyte-erythroid progenitors (MEP) populations within each hematopoietic tissue, c.
  • CMP common myeloid progenitors
  • GMP granulocyte-macrophage progenitors
  • MEP megakaryocyte-erythroid progenitors
  • 110 isoforms of 51 genes were significantly differentially expressed in either PF-04449913 -treated or normal cells when compared to vehicle-treated cells.
  • the expression level of treated and normal isoforms followed the same directional change (concordant) when compared to vehicle-treated cells, g.
  • a significant concordance was observed in the relative expression of the 75 isoforms in PF-0449913-treated and in normal cells relative to vehicle treated cells.
  • DMSO vehicle
  • PF-04449913 PF-04449913
  • FIG. 1 1 Schematic of in vivo experiments.
  • RAG2 "/" y c "/” pups were transplanted intrahepatically with 50,000 CD34 + cells within 48 hours of birth.
  • blast crisis CML engrafted mice were treated daily for 14 days by oral gavage with vehicle, PF-04449913 (100 mg/kg), Dasatinib (50 mg/kg) or combination (PF-04449913 100 mg/kg and Dasatinib 50 mg/kg).
  • Hematopoietic tissues were FACS analyzed for leukemia engraftment and qRT-PCR for BCR-ABLl transcripts
  • SMO selective smoothened
  • Figure 13 (Supplementary Figure 2): PF-04449913 Inhibits Shh Signaling in Ptch +/" p53 +/"
  • Figure 14 (Supplementary Figure 3): LSC Responses to Shh Inhibition are Niche Dependent: Fig. 14a. Percentage of weight changes in each treatment group of mice over the course of 14 days of treatment, b. Representative photographs of spleens from no transplant, blast crisis CML engrafted mice treated with vehicle or PF-04449913. c.
  • Figure 15 (Supplementary Figure 4): Decreased Cell Cycle Regulator Expression
  • Fig. 15a Heat-map of normalized expression values on log2 scale for 10,573 highly expressed genes in FACS-purified primary blast crisis CML CD34 + CD38 " Lin " and CD34 + CD38 + Lin " (SOLiD RNAseq gene count per million reads >1 in all the 6 samples); RAG2 "/” g-c “/” marrow engrafted blast crisis CML CD34 + CD38 " Lin " and CD34 + CD38 + Lin " ; and normal cord blood CD34 + CD38 " Lin " and
  • GSEA Gene set enrichment analysis
  • the "Regulation of Cell Cycle” pathway was significantly down-regulated in human progenitors from PF-04449913 treated mice; 7 of 8 investigated pathways decreased. Table columns are pathway name, number of genes (pathway size), nominal p-value; FDR adjusted q- value and adjusted p-value controlling for the family -wise error rate.
  • FIG. 16 SHH Pathway Gene Expression Pattern Portends BC Transformation. Using the SHH pathway allowed us to distinguish CML CP from BC and normal counterparts, demonstrating that this pathway is activated with disease progression.
  • SHH sonic hedgehog
  • Figure 17 Figure 2. Selective SHH Inhibition Reduces BC LSC Burden in Selective Niches.
  • SHH pathway inhibitor on AML and CML samples and observed a decrease in survival after treatment.
  • GLI2 as a biomarker of response.
  • PF-04449913 Chemical structure of PF-04449913, a selective smoothened (SMO) antagonist
  • CFU Colony forming unit
  • Figure 18 SHH PATHWAY Inhibition Induces Cycling of Dormant BC LSC.
  • b Network analysis performed on differentially expressed genes between BC and CP revealed CDKN1A as a key hub for cell cycle difference, c.
  • FIG. 19 SHH Inhibition in clinical samples. We tested the effects of SHH pathway inhibition in a clinical study and observed similar results to what we observed in our preclinical model.
  • FIG. 20 SHH Inhibitor Induced cell cycle activation Enhances BC LSC TKI Sensitivity. Using our preclinical model, we demonstrated that using SHH pathway inhibitor in combination with current therapy is the best possible route for curative treatment.
  • Graph shows percentage of CD34+CD38+lin- cells in the bone marrow; *p ⁇ 0.05 by ANOVA and Tukey post-hoc analysis d.
  • Graph shows normalized BCR- ABL expression (HPRT) +/- SEM; *p ⁇ 0.05 by ANOVA and Tukey post-hoc analysis e.
  • Figure 21 (supplementary Figure 1): PF-04449913 chemical properties and Inhibition of Shh Signaling in a Ptch +/" p53 +/" Tumor model. This figure summarizes the effect of inhibiting the SHH pathway in a different preclinical mouse model.
  • a. Competition-binding assay using a characterized cyclopamine-competitive SMO antagonist. PF-04449913 competes with the radiolabeled SMO antagonist for binding to human SMO (amino acids 181-787) with an IC50 of 4 nM (4.3 nM +/- 5.2 nM, N 5). b. Inhibition of Shh stimulated luciferase expression using mouse embryonic fibroblasts expressing luciferase under control of an 8X GLI-response element (GLI-LUC MEFs). c.
  • Hierarchical clustering was performed on Z-score transformed data using correlation similarity metric and centroid linkage method, g. Hh pathway inhibition in PF-04449913 treated Ptch+/-p53+/- medulloblastoma allografts.
  • Ptch+/-p53+/- allograft bearing SCID-bg female mice were dosed orally once a day for six days with 100 mg/kg of PF- 04449913 or vehicle.
  • Expression levels of FoxMl, GUI, GH2, Mycn, Ptchl, Ptch2, Sfrpl and Smo were determined by qRT-PCR.
  • the vehicle-treated levels for each gene were normalized to 100%.
  • Figure 22 (supplementary Figure 2): Cell cycle analysis in clinical samples - this data supports the effect of these clinical study.
  • SAM Significance Analysis of Microarrays
  • FIG 23 (supplementary Figure 3): SHH Inhibition Spares Normal Human Hematopoietic Progenitors. We did not observe a toxic effect on the normal counterparts analyzed; thus, a clear therapeutic index for the use of SHH inhibition was demonstrated. a. Differentiation into CFU-Mix (purple), BFU-E (red), CFU-G (orange), CFU-M (yellow), CFU-GM (blue) of normal cord blood progenitors was assessed in

Abstract

In alternative embodiments, the invention provides compositions and methods for inhibiting or ablating cancer stem cells. In alternative embodiments, the invention provides compositions and methods for inhibiting the action of double-stranded RNA-specific adenosine deaminases, or ADAR, enzymes. In alternative embodiments, the invention provides compositions and methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, e.g., leukemia or Chronic Myeloid Leukemia (CML). In alternative embodiments, the invention provides compositions and methods for inhibiting a Sonic Hedgehog (Shh) pathway, e.g., by using a Smoothened (SMO) protein inhibitor. In alternative embodiments, the invention provides compositions and methods for measuring or determining, or predicting, chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance. In alternative embodiments, the invention provides compositions and methods for determining or measuring the effectiveness of a treatment, a drug, a therapy or a diet for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.

Description

COMPOSITIONS AND METHODS FOR CANCER AND CANCER STEM CELL DETECTION AND ELIMINATION
RELATED APPLICATIONS
This Patent Convention Treaty (PCT) International Application claims benefit of priority to U.S. Provisional Patent Application Serial No. ("USSN") 61/532,417, filed September 08, 2011 ; USSN 61/537, 157, filed September 21, 2011 ; USSN 61/537,161, filed September 21, 201 1; and USSN 61/537, 185, filed September 21, 2011. The aforementioned applications are expressly incorporated herein by reference in their entirety and for all purposes.
TECHNICAL FIELD
This invention relates to oncology, cellular and developmental biology and drug discovery. In alternative embodiments, the invention provides compositions and methods for inhibiting or ablating cancer stem cells. In alternative embodiments, the invention provides compositions and methods for inhibiting the action of double-stranded RNA- specific adenosine deaminases, or ADAR, enzymes. In alternative embodiments, the invention provides compositions and methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition of cell differentiation and/or self- renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, e.g., leukemia or Chronic Myeloid Leukemia (CML).
In alternative embodiments, the invention provides compositions and methods for inhibiting a Sonic Hedgehog (Shh) pathway, e.g., by using a Smoothened (SMO) protein inhibitor. In alternative embodiments, the invention provides compositions and methods for inhibiting a Sonic Hedgehog (Shh) pathway, e.g., by using a Smoothened (SMO) protein inhibitor: to force, stimulate or initiate a dormant cell or a cancer stem cell (e.g., a Chronic Myelogenous Leukemia (CML) stem cell) to cycle so they the cell can more effectively targeted by a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor; as a biomarker of response to chemotherapy; and/or, as a target for drug development.
In alternative embodiments, the invention provides compositions and methods for measuring or determining, or predicting, chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance comprising measuring or determining, individually or together, levels or amounts of GLI2 transcript and/or protein (increasing) and/or GLI3 transcript and/or protein (decreasing) as prognostic biomarkers of chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance. In alternative embodiments, the invention provides compositions and methods for measuring or determining, or predicting, a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, comprising measuring or determining, individually or together, levels or amounts of GLI1 and/or GLI2 transcript and/or protein.
In alternative embodiments, the invention provides compositions and methods for determining or measuring the effectiveness of a treatment, a drug, a therapy or a diet for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells. In alternative embodiments, the invention provides compositions and methods for determining or predicting a positive response or monitoring a response (predicting a negative or positive response) to a selective JAK2 inhibition therapy, drug or treatment.
BACKGROUND
RNA editing is a post-transcriptional processing mechanism that results in an RNA sequence that is different from that encoded by the genomic DNA and thereby diversifies the gene product and function. The type of RNA editing that is most prevalent in higher eukaryotes converts adenosine residues into inosine (A-to-I editing) in double- stranded RNA (dsRNA) through the action of double-stranded RNA-specific adenosine deaminases, or ADAR, enzymes.
ADAR is an enzyme that in humans is encoded by the ADAR gene (ADARl is an acronym for "adenosine deaminase acting on RNA 1"). ADARl RNA edits by site- specific deamination of adenosines. The ADARl enzyme destabilizes double stranded RNA through conversion of adenosine to inosine. The ADARl enzyme modifies cellular and viral RNAs, including coding and noncoding RNAs. ADARl is an RNA editing enzyme, required for hematopoiesis. ADARl+/~chimeric embryos die before embryonic day 14 with defects in the hematopoietic system. Regulated levels of ADARl expression are critical for embryonic erythropoiesis in the liver. Mutations in the ADAR gene have been associated with dyschromatosis symmetrica hereditaria. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. Traditional CML treatment, such as hydroxyurea and imatinib, is a great financial burden on patients. Moreover, they are not efficient at eradicate leukemia cancer stem cells, which often leads to disease progression and relapse. New drugs that target at cancer stem cells are urgently needed for patient care.
Studies suggested that leukemia stem cells (LSC) promote therapeutic resistance, relapse and disease progression, the leading causes of leukemia mortality, as a result of enhanced survival and self-renewal combined with a propensity to become dormant in supportive microenvironments. Therapies capable of breaking LSC quiescence while sparing normal hematopoietic stem cell (HSC) function have remained elusive. In chronic myeloid leukemia (CML) mouse models, Sonic hedgehog (Shh) pathway activation promotes LSC maintenance. However, the comparative role of Shh signaling in human normal HSC and LSC quiescence induction and self-renewal had not been determined.
Signal transducer and activator of transcription 5A (STAT5a) is a protein that in humans is encoded by the ST AT 5 A gene. The protein encoded by this gene is a member of the STAT family of transcription factors. In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo- or heterodimers that translocate to the cell nucleus where they act as transcription activators. This protein is activated by, and mediates the responses of many cell ligands, such as IL2, IL3, IL7 GM-CSF, erythropoietin, thrombopoietin, and different growth hormones. Activation of this protein in myeloma and lymphoma associated with a TEL/JAK2 gene fusion is independent of cell stimulus and has been shown to be essential for the tumorigenesis.
Janus kinase 2 (JAK2) is a human protein that has been implicated in signaling by members of the type II cytokine receptor family (e.g. interferon receptors), the GM-CSF receptor family, and the gpl30 receptor family (e.g., IL-6R), and the single chain receptors such as Epo-R. JAK2 gene fusions with the TEL(ETV6) and PCMl genes have been found in leukemia patients. Mutations in JAK2 have been implicated in
myeloproliferative disorders. SUMMARY
RNA EDITING AS A NOVEL CANCER STEM CELL TARGET
In alternative embodiments, the invention provides methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal (or self-renewal capacity) of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, comprising,
(a) providing a composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide; and
(b) administering a sufficient amount of the composition to an individual in need thereof, wherein a sufficient amount comprises the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells.
In alternative embodiments of the methods, the hematopoietic stem cell or cancer stem cell comprises a cancer stem cell, or a leukemia cell, or a Chronic Myeloid
Leukemia (CML) cell, a leukemia stem cell, or a Chronic Myeloid Leukemia (CML) stem cell.
In alternative embodiments of the methods, the composition that inhibits or slows the expression of an ADARl gene, an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide comprises:
(a) an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript;
(b) a polypeptide, peptide or an antibody inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme;
(c) the method of (a), wherein the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA); or
(d) the method of (a) or (c), wherein inhibitory nucleic acid molecule comprises a ribozyme. In alternative embodiments of the methods, the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript comprises a single or doublestranded and/or sense or antisense sequence or subsequence comprising SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3.
In alternative embodiments of the methods, the antibody inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme comprises an antibody or antigen-binding fragment thereof that specifically binds to a protein as set forth in SEQ ID NO: 3.
In alternative embodiments of the methods, the polypeptide or peptide inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme comprises a peptide aptamer or an ADARl-binding polypeptide or peptide.
In alternative embodiments of the methods, the composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide is administered in vitro, ex vivo or in vivo.
In alternative embodiments, the invention provides compositions, pharmaceutical compositions or formulations, or equivalents, comprising a composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide, wherein optionally the composition or formulation is formulated for administration in vitro, ex vivo or in vivo.
In alternative embodiments, the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
COMPOSITIONS AND METHODS FOR DORMANT CANCER STEM CELL DETECTION AND ELIMINATION
In alternative embodiments, the invention provides compositions and methods to detect dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells. In alternative embodiments, the invention provides compositions and methods for use therapeutically to force dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells, into cycle so they can be targeted by a therapeutic agent or procedure, e.g., chemotherapy, radiation therapy or targeted tyrosine kinase inhibitors.
In alternative embodiments, the invention provides methods for activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle, or initiating cell cycling in a cancer stem cell, or breaking dormancy in a cancer stem cell, or inducing in a stem cell susceptibility to BCR-ABL inhibition, comprising,
(a) providing a composition that inhibits a Sonic Hedgehog (Shh), or providing a Smoothened (SMO) protein inhibitor (Smoothened (SMO) is an integral membrane protein mediator, a of Hedgehog signaling); and
(b) administering an effective amount of the Sonic Hedgehog (Shh) inhibitor or the Smoothened (SMO) protein inhibitor to the cancer stem cell, thereby activating, stimulating or initiating in the cancer stem cell a transition from GO to Gl of the cell cycle, or initiating cell cycling in the cancer stem cell, inducing in the stem cell susceptibility to BCR-ABL inhibition, or breaking dormancy in the stem cell.
In alternative embodiments, the invention provides methods for radiosensitization of a cancer stem cell, or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells, or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor, comprising,
(a) providing a composition that inhibits a Sonic Hedgehog (Shh), or providing a Smoothened (SMO) protein inhibitor; and
(b) administering an effective amount of the Sonic Hedgehog (Shh) inhibitor or the Smoothened (SMO) protein inhibitor to the cancer stem cell, thereby radiosensitizing the cancer stem cell, or sensitizing the cancer stem cell to a treatment or protocol that targets dividing cells, or sensitizing the cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor.
In alternative embodiments of the methods, the cancer stem cell is a hematopoietic cancer stem cell, or the cancer stem cell is a leukemia stem cell, or a Chronic Myeloid Leukemia (CML) stem cell or a Chronic Myeloid Leukemia (CML) stem cell.
In alternative embodiments of the methods, the composition that inhibits or slows the expression of an Shh gene, an Shh gene product, an Shh transcript, and/or an Shh polypeptide comprises:
(a) an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of a Shh gene or Shh gene transcript; (b) a polypeptide, peptide or an antibody inhibitory to the expression of the Shh gene or Shh gene transcript, or activity or expression of the Shh polypeptide;
(c) the method of (a), wherein the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the Shh gene or Shh gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA); or
(d) the method of (a) or (c), wherein inhibitory nucleic acid molecule comprises a ribozyme.
In alternative embodiments of the methods, the composition that inhibits or slows the expression of a Shh gene, a Shh gene product, a Shh transcript, and/or a Shh polypeptide comprises a PF-04449913 (structure illustrated in Figure 17a), or an equivalent thereof, or a bioisostere thereof.
In alternative embodiments of the methods, the antibody inhibitory to the expression of a Shh gene, a Shh gene product or a Shh transcript, or activity or expression of the Shh polypeptide, comprises an antibody or antigen-binding fragment thereof that specifically binds to a Shh protein.
In alternative embodiments of the methods, the polypeptide or peptide inhibitory to the expression of a Shh gene, a Shh gene product or a Shh transcript, or activity or expression of the Shh protein comprises a peptide aptamer or a Shh protein-binding polypeptide or peptide.
In alternative embodiments of the methods, the composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide is administered in vitro, ex vivo or in vivo.
The invention provides compositions, pharmaceutical compositions or formulations comprising a composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide, wherein optionally the composition or formulation is formulated for administration in vitro, ex vivo or in vivo. In alternative embodiments, the composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide comprises any composition used to practice a method of the invention, e.g., a PF-04449913 (structure illustrated in Figure 17a), or an equivalent thereof, or a bioisostere thereof. The invention provides arrays or kits comprising a cancer stem cell splice isoform and/or proteome detection platform, wherein the array or kit comprises a sufficient plurality of nucleic acids and/or proteins to detect a dormant cancer stem cell from a non- dormant stem cell or a cancer stem cell transitioning from GO to Gl of the cell cycle.
The invention provides methods for determining the effectiveness of a test compound for: activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle; or initiating cell cycling in a cancer stem cell; or breaking dormancy in a cancer stem cell; or radiosensitizing of a cancer stem cell; or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells; inducing in a stem cell susceptibility to BCR-ABL inhibition; or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor, comprising analyzing the cancer stem cell transcript (RNA) splice isoform pattern and/or the proteome before and after contacting the test compound to the stem cell, wherein a change of the cancer stem cell to a non-dormant transcript (RNA) splice isoform pattern and/or the proteome pattern indicates that the test compound is effective for: activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle; or initiating cell cycling in a cancer stem cell; or breaking dormancy in a cancer stem cell; or radiosensitizing of a cancer stem cell; or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells; inducing in a stem cell susceptibility to BCR-ABL inhibition; or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor, wherein optionally the analyzing comprises use of an array or a kit of the invention.
The invention provides kits comprising: a composition used to practice a method of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
SONIC HEDHEGOG TARGETS AS BIOMARKERS OF PROGNOSIS AND RESPONSE FOR HUMAN CHRONIC MYELOGENOUS LEUKEMIA
In alternative embodiments, the invention provides compositions and methods to detect dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells. In alternative embodiments, the invention provides compositions and methods for use therapeutically to force dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells, into cycle so they can be targeted by a therapeutic agent or procedure, e.g., chemotherapy, radiation therapy or targeted tyrosine kinase inhibitors.
In alternative embodiments, the invention provides compositions and methods for measuring or determining, or predicting, chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance, comprising: measuring or determining, individually or together, levels or amounts of GLI2 transcript and/or protein (increasing) and/or GLI3 transcript and/or protein (decreasing) as prognostic biomarkers of chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance, wherein increased or increasing levels of GLI2 transcript and/or protein and/or decreasing levels of GLI3 transcript and/or protein indicate and/or predict chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance.
In alternative embodiments, the invention provides compositions and methods for measuring or determining, or predicting, a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, comprising:
measuring or determining, individually or together, levels or amounts of GLI1 and/or GLI2 transcript and/or protein,
wherein the presence of one or both GLI1 and/or GLI2 transcript and/or protein, and/or increased or increasing levels of one or both GLI1 and/or GLI2 transcript and/or protein indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition.
In alternative embodiments, the invention provides compositions and methods for measuring or determining, or predicting, whether a cancer stem cell has or will transition from GO to Gl of the cell cycle, or has or will initiate cell cycling, or has or will break dormancy, or has been induced to have a susceptibility to BCR-ABL inhibition, comprising:
measuring or determining, individually or together, levels or amounts of GLI1 and/or GLI2 transcript and/or protein,
wherein the presence of one or both GLI1 and/or GLI2 transcript and/or protein, and/or increased or increasing levels of one or both GLI1 and/or GLI2 transcript and/or protein, indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, thereby also indicating or predicting whether a cancer stem cell has or will transition from GO to Gl of the cell cycle, or has or will initiate cell cycling, or has or will break dormancy, or has been induced to have a susceptibility to BCR-ABL inhibition.
In alternative embodiments, for methods of the invention, the presence, absence and/or amount of a GLIl, GLI2 and/or GLI3 transcript and/or protein is measured using an array, an immunoassay, an immunoprecipitation, a kit, a polymerase chain reaction (PCR), a qRT-PCR, a nanofluidic assay or device, a nanofluidic proteome assay, a chromatography, a nanoproteomics quantification, an isoelectric focusing assay, or a combination thereof.
In alternative embodiments, the invention provides compositions and methods for assessing the eradication of self-renewing cancer stem cells, or Leukemic Stem Cells (LSCs), comprising:
measuring or determining, individually or together, levels or amounts of GLIl and/or GLI2 transcript and/or protein,
wherein the absence of one or both GLIl and/or GLI2 transcript and/or protein, and/or decreasing levels of one or both GLIl and/or GLI2 transcript and/or protein, indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, thereby also indicating or predicting an eradication or diminishment of self-renewing cancer stem cells, or Leukemic Stem Cells (LSCs).
In alternative embodiments, the invention provides arrays, immunoassays, kits and the like comprising nucleic acids, proteins or antibodies capable of determining or measuring the presence, absence and/or amount of a GLIl, GLI2 and/or GLI3 transcript and/or protein. In alternative embodiments, the arrays or kits comprise a composition used to practice a method of the invention, or a composition, and optionally comprising instructions for use thereof.
SPLICED ISOFORM BIOMARKERS TO ASSESS RESPONSES TO CANCER STEM CELL TARGETED THERAPIES
In alternative embodiments, the invention provides compositions and methods for determining or measuring the effectiveness of a treatment, a drug, a therapy or a diet for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells, comprising:
(a) determining or measuring the amount of an alternatively spliced
phosphoStat5a and/or a phospho-JAK2;
(b) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(c) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the treatment, drug, therapy or diet will be effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
In alternative embodiments, the invention provides compositions and methods for selecting a diet, a treatment, a drug or a therapy: to treat or ameliorate a leukemic stem cell (LSC), or, for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells, comprising:
(a) applying, contacting or administering a diet, a treatment, a drug or a therapy to a LSC cell or a cell population or subpopulation, and
(b) (i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2;
(ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the treatment, drug, therapy or diet will be effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells. In alternative embodiments, the invention provides compositions and methods for determining or predicting a positive response or monitoring a response (predicting a negative or positive response) to a selective JAK2 inhibition therapy, drug or treatment, comprising
(a) applying, contacting or administering a diet, a treatment, a drug or a therapy to a LSC cell or a cell population or subpopulation, and
(b) (i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2;
(ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the selective JAK2 inhibition therapy, drug or treatment will be (or is) effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
In alternative embodiments, the invention provides compositions and methods for assessing the resistance, or relative resistance, of a self-renewing leukemic stem cell (LSC) or cells to a selective JAK2 inhibition therapy, drug or treatment, comprising:
(i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2;
(ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein an increased amount of, or the presence of, the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the self-renewing leukemic stem cell (LSC) or cells will be resistant, or relatively resistant, to a selective JAK2 inhibition therapy, drug or treatment, or
a decreased amount of, or lack of, the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the self-renewing leukemic stem cell (LSC) or cells will be sensitive or responsive to a selective JAK2 inhibition therapy, drug or treatment.
In alternative embodiments, the invention provides compositions and methods for distinguishing leukemic progenitors from their normal counterparts, comprising:
(i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2;
(ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein the presence of the alternatively spliced phosphoStat5a and/or a phospho- JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, distinguishes the leukemic progenitors from their normal counterparts.
In alternative embodiments of methods of the invention, the method detects a cancer stem cell specific JAK/STAT signaling pathway splice isoforms by RNA sequencing, qRT-PCR and/or nanoproteomics.
In alternative embodiments of methods of the invention, the LSC is a chronic myelogenous or myeloid leukemia (CML) stem cell, or a cancer stem cell in a primary or metastatic niche, or a cancer stem cell in a setting of inflammatory cytokines and interleukins as elaborated in a cancer.
In alternative embodiments of methods of the invention, the presence, absence and/or amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, is measured by a procedure or device comprising (or comprising use of): a fluorescent activated cell sorter (FACS), an array, an immunoassay, an immunoprecipitation, a kit, a polymerase chain reaction (PCR), a qRT- PCR, a nanofluidic assay or device, a nanofluidic proteome assay, a chromatography, a nanoproteomics quantification, or an isoelectric focusing assay, or any combination thereof.
The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.
All publications, patents, patent applications cited herein are hereby expressly incorporated by reference for all purposes.
DESCRIPTION OF DRAWINGS
RNA EDITING AS A NOVEL CANCER STEM CELL TARGET
Figure 1A graphically illustrates data showing that the expression of ADARl pi 50 is increasing as CML progresses from CP to BC; the values were normalized to HPRT; a significant increase of ADARl pl50 expression was observed in CML BC comparing to CML CP. Figure IB graphically illustrates data showing the ratio of ADARl isoforms (pl50/pl 10) increases from normal cord blood; qRT-PCR of ADARl isoform mRNA in FACS sorted CD34+38+lin- cells from normal cord blood (n=8), CML CP (n=6) and CML BC (n=7); as described in detail in Example 1, below.
Figures 2A and 2B graphically illustrate data showing that an increase in ADARl expression is driven by Bcr-Abl in CML BC patients; Bcr-Abl and ADARl expression were analyzed in CML CP (n = 6) and CML BC (n = 4); a positive correlation is observed in only CML BC instead of CML CP; as described in detail in Example 1, below.
Figure 3 graphically illustrates data showing that knock down of ADARl leads to increase of Bfu-E colonies and decrease of Macrophage (M) colonies in CML CP (n=3) and BC (n=l) but not in normal cord blood (n=3); sorted CD34+38+Lin- cells from normal cord blood, CML CP and BC patients were transduced with either shADARl or shControl lentivirus. *, <0.05, **, <0.005; ***, <0.0001 ; for CML CP p = 0.0037, p = 0.0001, (n = 3); for CML BC (n = l), p = 0.0167, p = 0.0030; as described in detail in Example 1, below.
Figure 4 graphically illustrates data showing lentiviral overexpression of ADARl leads to decrease of Bfu-E colonies in normal cord blood (n=3); sorted CD34+38+Lin- cells from normal cord blood were transduced with either ORF control or ADAR1 overexpression lentivirus. *, p<0.05. p=0.029; as described in detail in Example 1, below.
Figure 5 illustrates representative pictures of GFP+ colonies; as described in detail in Example 1, below.
Figure 6 graphically illustrates data showing that ADAR1 knockdown leads to a universal decrease of self-renewal capacity; individual colonies from FACS sorted CD34+38+lin- cord Blood (n=4), CML CP (n=3), and CML BC (n=l) were replated in to 96 well-plates and replate efficiency was observed after 14 days. *, p<0.05; as described in detail in Example 1, below.
Figure 7 graphically illustrates data showing that ADAR1 expression is significantly positively and negatively correlated with PU1 and GATA1, respectively: Figure 7A: mRNA from individual colony formed from sorted CD24+38+Lin- CML patient was measured for expression of ADAR1, PU1, and GATA1 using qRT-PCR; Figure 7B: cord blood sorted CD34+38+Lin- cells were transduced with either ORF control or ADAR1 overexpression lentivirus; the expression levels of ADAR1, PU1, and GATA1 were analyzed; as described in detail in Example 1, below.
COMPOSITIONS AND METHODS FOR DORMANT CANCER STEM CELL DETECTION AND ELIMINATION
SONIC HEDHEGOG TARGETS AS BIOMARKERS OF PROGNOSIS AND RESPONSE FOR HUMAN CHRONIC MYELOGENOUS LEUKEMIA
Figure 8a graphically illustrates data where GLI1 and GLI2 transcripts were compared by TaqMan RT-PCR in FACS-purified human cord blood and peripheral blood CD34+CD38 Lin"PT progenitor cells, chronic phase CML and in blast crisis CML patient samples; and comparative qRT-PCR analysis of GLI3 transcript levels was performed on normal, chronic phase and blast crisis CML cells; Figure 8b graphically illustrates data from a FACS analysis that showed a reduction in leukemic progenitor survival following 7 days of PF-04449913 compared with vehicle (DMSO) treatment in SL/M2 co-cultures; Figure 8c graphically illustrates data from the down regulation of GLI expression, as analyzed by TaqMan RT-PCR in human LSC engrafted bone marrow derived from PF- 04449913 and vehicle treated mice; Figure 8d graphically illustrates data showing spleen size in blast crisis CML LSC engrafted mice after 14 days of treatment with vehicle or PF-04449913; Figure 8e illustrates images of an immunofluorescence analysis of splenic sections from no transplant or LSC engrafted mice treated with vehicle or PF-04449913: Photomicrographs of sections stained with DAPI (upper panel) and antibodies specific for human CD45 (upper middle panel), human GLI (lower middle panel) and the merged image (lower panel); Figure 8f graphically illustrates data from isoform-level transcriptome measurements of Shh pathway genes in vehicle-treated and PF-04449913- treated CML BC LSC and in normal CD34+CD38+Lin" FACS-purified progenitors; Figure 8g in tabular format presents data showing a significant concordance was observed in the relative expression of the 50 isoforms in PF-0449913 -treated and in normal cells relative to vehicle treated cells; Figure 8h graphically illustrates data of nanoproteomic (CB1000) traces of total GLI protein after vehicle and PF-04449913 treatment; and, Figure 8i graphically illustrates the quantification of GLI protein expression in splenic CD34+ cells derived from vehicle (n=3) or PF-04449913 treated LSC engrafted mice; all figures are also further described, below.
Figure 9a graphically illustrates data showing the frequency of CD45+ cells in hematopoietic tissues of blast crisis CML engrafted mice; Figure 9b graphically illustrates data from a FACS quantitation of common myeloid progenitors (CMP), granulocyte- macrophage progenitors (GMP) and megakaryocyte-erythroid progenitors (MEP) populations within each hematopoietic tissue; Figure 9c graphically illustrates data showing a comparison of cell cycle status of human CD45+ blast crisis CML progenitors engrafted mice in the bone marrow and spleen; Figure 9d illustrates representative FACS plots comparing Ki67 and 7AAD in bone marrow engrafted viable human CD45+ cells after 14 days of vehicle or PF-04449913 treatment; Figure 9c graphically illustrates data from a gene set enrichment analysis for the significantly down-regulated pathway "Regulators of Cell Cycle"; Figure 9f graphically illustrates data showing isoform-level transcriptome measurements of cell cycle genes in vehicle-treated and PF-04449913- treated blast crisis CML LSC and in normal CD34+CD38+Lin" FACS-purified
progenitors; and, Figure 9g graphically illustrates data showing the relative expression of the 75 isoforms in PF-0449913 -treated and in normal cells relative to vehicle treated cells; all figures are also further described, below.
Figure 10a graphically illustrates data showing: Left, Differentiation into CFU-
Mix (black), BFU-E (red), CFU-G (orange), CFU-M (yellow), CFU-GM (blue) of normal cord blood HSPC was assessed in hematopoietic progenitor assays (n=3) after PF- 04449913 (1 μΜ) or vehicle treatment for 12 days, Right, illustration of representative photomicrographs of cord blood colonies after 12 days of treatment with vehicle (DMSO) or PF-04449913 (1 μΜ); Figure 10b graphically illustrates FACS analysis data from experiments where human cord blood (n=3), CD34+38+Lin"PI" cells were plated on SL/M2 stroma and treated with vehicle (DMSO) or PF-04449913 (1 μΜ) for 7 days followed by FACS analysis; Figure 10c illustrates representative FACS plots depicting HSPC, myeloid and lymphoid differentiation in human cord blood engrafted mice after 14 days of treatment with vehicle (n=3) or PF-04449913 100 mg/kg (n=4), after staining with murine CD45, CD34, CD 13 and CD4; Figure lOd graphically illustrates data from a FACS analysis used to determine the total human CD45+, HSPC, myeloid and lymphoid cell count in bone marrow after 14 days of treatment with vehicle (n=3, green) or 100 mg/kg of PF-04449913 (n=4, purple); Figure lOe graphically illustrates data summarizing a FACS quantification of GO (green), Gl (light blue) and G2/S (navy) human CD45+ cells in cord blood engrafted marrow after 14 days of treatment with vehicle (n=3) or PF- 04449913 lOOmg/kg (n=4); all figures are also further described, below.
Figure 1 1a schematically illustrates in vivo experiments where RAG2"/"yc "/" pups were transplanted intrahepatically with 50,000 CD34+ cells within 48 hours of birth; and after 8 to 10 weeks, blast crisis CML engrafted mice were treated daily for 14 days by oral gavage with vehicle, PF-04449913 (100 mg/kg), Dasatinib (50 mg/kg) or combination (PF-04449913 100 mg/kg and Dasatinib 50 mg/kg); and then hematopoietic tissues were FACS analyzed for leukemia engraftment and qRT-PCR for BCR-ABL1 transcripts; Figure 1 lb graphically illustrates a myeloid sarcoma count of blast crisis CML engrafted mice in each treatment group vehicle (n=13, green), PF-04449913 (n=7, purple), dasatinib (n=6, red) and combination (n=3, black) after 14 days of treatment; Figure 11c graphically illustrates BCR-ABL1 transcripts in the spleens of blast crisis CML engrafted mice after 14 days of treatment with vehicle (green, n=9), PF-04449913 (purple, n=l 1), dasatinib (n=8, red) or combination (n=5, black); Figure 1 Id graphically illustrates Shh gene expression in FACS purified human progenitor cells from blast crisis LSC engrafted mouse marrow treated with vehicle (n=3, green), PF-04449913 (n=4, purple) dasatinib (n=4, maroon), combination (n=3, dark grey) was analyzed via qPCR array (SA Biosciences); Figure 1 le graphically illustrates FACS analysis of percentage of marrow engrafted blast crisis LSC (n=3 patients) after 14-day treatment with vehicle (n=31, green), PF-04449913 (n=25, purple), dasatinib (n=27, maroon) and combination (n=27, grey); Figure 1 If graphically illustrates myeloid sarcoma counts in mice serially transplanted with vehicle (n=12, green), PF-04449913 (n=12, purple), dasatinib (n=8, maroon) or combination (n=3, grey) treated human progenitors; all figures are also further described, below.
Figure 12a schematically illustrates the chemical structure of PF-04449913, a selective smoothened (SMO) antagonist; Figure 12b graphically illustrates data from a competition-binding assay using a characterized cyclopamine-competitive SMO antagonist. PF-04449913 competes with the radiolabeled SMO antagonist for binding to human SMO (amino acids 181-787) with an IC50 of 4 nM; Figure 12c graphically illustrates data from a study inhibiting Shh-stimulated luciferase expression using mouse embryonic fibroblasts expressing luciferase under control of an 8X Gli-response element (Gli-Luc MEFs); Figure 12d graphically illustrates data from a study showing dose- dependent inhibition by PF-04449913 in the Gli-Luc MEF reporter assay; PF-04449913 inhibits Shh stimulated reporter activity with an IC50 of 6.8 nM (n=5); all figures are also further described, below.
Figure 13a graphically illustrates data from a study showing anti -tumor activity of
PF-04449913 against Ptch+/-p53+/- medulloblastoma; Figure 13b graphically illustrates data from a study showing dose dependent anti-tumor efficacy of PF-04449913 against Ptch+/-p53+/- medulloblastoma allografts; Figure 13c graphically illustrates data from a study showing Hh pathway inhibition in PF-04449913 treated Ptch+/-p53+/- medulloblastoma allografts; Figure 13d graphically illustrates data from a study showing which genes are significantly down-regulated by PF-04449913 treatment in Ptch+/~p53_/~ mice; Figure 13e graphically illustrates data from a study showing gene signatures are enriched for within the top 31 PF-04449913-downregulated genes in Ptch+/-p53 -/- mice; all figures are also further described, below.
Figure 14a graphically illustrates data from a study showing the percentage of weight changes in groups of mice over the course of 14 days of treatment with vehicle, PF-04449913, dasatinib, or a combination thereof; Figure 14b illustrates representative photographs of spleens from no transplant, blast crisis CML engrafted mice treated with vehicle or PF-04449913; Figure 14c graphically illustrates representative FACS plots of blast crisis CML engrafted mice treated with vehicle, PF-04449913, dasatinib, or combination; Figure 14d graphically illustrates total blast LSC count in bone marrow, spleen and liver after 14 days of treatment with vehicle (n=15) or PF-04449913 (n=14); all figures are also further described, below. Figure 15a graphically illustrates heat-map of normalized expression values on log2 scale for 10,573 highly expressed genes in FACS-purified primary blast crisis CML CD34+CD38"Lin" and CD34+CD38+Lin"; RAG2"/"g-c"/" marrow engrafted blast crisis CML CD34+CD38"Lin" and CD34+CD38+Lin"; and normal cord blood CD34+CD38"Lin" and CD34+CD38+Lin" samples; Figure 15b graphically illustrates a gene set enrichment analysis (GSEA) summary table obtained from SOLiD RNAseq data comparing PF- 04449913 treated mice (n=4) to control (n=4) (average 24.7 - 58.0 million mapped reads/sample); Figure 15c graphically illustrates a GSEA enrichment plot for the significantly down-regulated pathway (regulation of Cell Cycle); Figure 15d graphically illustrates a cell cycle analysis of bone marrow from blast crisis CML engrafted mice after 14 days of vehicle (n=8) or PF-04449913 (n=8). *p<0.05 for both G0 and Gi population compared with vehicle treatment; all figures are also further described, below.
Figure 16a schematically illustrates a heatmap from unsupervised agglomerative hierarchical clustering of sonic hedgehog (SHH) pathway genes using RNA Seq data from FACS-purified progenitors (CD34+CD38+lin"PL) from 8 chronic phase (CP) and 9 blast crisis (BC) patients, 3 normal cord blood (CB) and 3 normal peripheral blood (NPB) sample; Figure 16b graphically illustrates a principal components plot derived from RNA Seq data for 41 genes in the SHH pathway, from 8 chronic phase (CP; black triangles) and 9 blast crisis (BC; red circles) subjects, as well as 3 cord blood normal samples (CB; blue diamonds) and 3 normal peripheral blood (NPB; blue circles); Figure 16c graphically illustrates box plots for GLI2 expression of 7 chronic phase (CP) and 6 blast crisis (BC) non-treated subjects, as well as 3 cord blood normal samples (CB) and 3 normal peripheral blood (NPBc); Figure 16d graphically illustrates quantitative RT-PCR data where GLI1 and GLI2 transcripts were compared using quantitative RT-PCR in FACS- purified human cord blood and normal peripheral blood CD34+CD38+Lin"PI" progenitor cells (n=9, black), chronic phase CML (n=7, blue) and in blast crisis CML (n=10, red) patient samples; all figures are also further described, below.
Figure 17a schematically illustrates the chemical structure of PF-04449913, a selective smoothened (SMO) antagonist; Figure 17b graphically illustrates a FACS analysis, which revealed a significant reduction in blast crisis leukemic progenitor survival (n=4 patients) following 7 days of PF-04449913 (1 mM, purple) compared with vehicle (DMSO, blue) treatment in SL/M2 co-cultures; Figure 17c graphically illustrates data from a Colony forming unit (CFU) survival experiment where cord blood (n=3) or AML (n=4 patients) CD34 cells were plated on SL/M2 co-cultures and treated with vehicle (DMSO) or PF-04449913 (luM) for 7 days, and colony forming unit (CFU) survival was determined and compared to vehicle treatment; Figure 17d graphically illustrates spleen weight in blast crisis CML LSC engrafted mice after 14 days of treatment with vehicle (n=16, blue) or PF-04449913 (n=12; 100 mg/kg daily, purple); Figure 17e graphically illustrates nanoproteomic (CB1000) traces of total GLI2 protein after vehicle (blue) and PF-04449913 (green) treatment; Figure 17f graphically illustrates a quantification of GLI2 protein expression in sorted progenitors derived from vehicle (n=3) or PF-04449913 (n=3) treated LSC engrafted mice. GLI2 expression was determined after normalizing the area under the curve (AUC) to a p2-microglobulin (b2M) loading control (Student's t-test *p=0.001); Figure 17g illustrates
photomicrographs of confocal fluorescence microscopic images of an analysis of spleen sections from no transplant or LSC engrafted mice treated with vehicle or PF-04449913; all figures are also further described, below.
Figure 18a graphically illustrates a heatmap from unsupervised agglomerative hierarchical clustering of cell cycle pathway genes using RNA Seq data from FACS- purified progenitors (CD34+CD38+lin~PI~) from 8 chronic phase (CP) and 9 blast crisis (BC) patients sample; Figure 18b schematically illustrates a network analysis performed on differentially expressed genes between BC and CP revealed CDK IA as a key hub for cell cycle difference; Figure 18c graphically illustrates representative FACS plots comparing Ki67 and 7AAD in bone marrow engrafted viable human CD45+ cells after 14 days of vehicle or PF-04449913 treatment; Figure 18c graphically illustrates data from a cell cycle analysis of bone marrow from blast crisis CML engrafted mice after 14 days of vehicle (n=8) or PF-04449913 (n=8); Figure 18e schematically and graphically illustrates a GSEA enrichment plot for the significantly down-regulated pathway; Figure 18f graphically illustrates normalized gene expression values for the 18 genes in the core enrichment subset from the "Regulation of Cell Cycle" pathway; all figures are also further described, below.
Figure 19a summarizes the characteristics of patients enrolled in clinical trial NCT01546038; Figure 19b graphically illustrates the clinical response to PF-04449913 in the bone marrow of AML patient samples; Figure 19c illustrates representative FACS cell cycle plots of Ki67 and 7AAD staining of human CD34+CD38- and CD34+ CD38+ cells derived from primary patient samples after 4 weeks (C1D28) of treatment with PF- 04449913 (40mg) on the Phase 1 clinical trial; Figure 19d graphically illustrates cell cycle analysis (peripheral blood-CD45+PI-) from a secondary AML patient that was treated with PF-04449913 (40mg) for 4 weeks on the Phase 1 clinical trial; Figure 19e summarizes the characteristics of patient samples analyzed for their cell cycle study; all figures are also further described, below.
Figure 20a schematically illustrates in vivo experiments using RAG2"/"yc "/" pups that were transplanted intrahepatically with 50,000 CD34+ cells within 48 hours of birth, as discussed in detail, below; Figure 20b graphically illustrates a myeloid sarcoma count in blast crisis CML engrafted mice in each treatment group vehicle (n=13, blue), PF- 04449913 (n=7, purple), dasatinib (n=6, red) and combination (n=3, black) after 14 days of treatment; Figure 20c graphically illustrates a FACS analysis of percentage of marrow engrafted blast crisis progenitor LSC (n=3 patients) after 14-day treatment with vehicle (n=31, blue), PF-04449913 (n=25, purple), dasatinib (n=27, maroon) and combination (n=27, grey). Graph shows percentage of CD34+CD38+lin- cells in the bone marrow; *p<0.05 by ANOVA and Tukey post-hoc analysis; Figure 20d graphically illustrates data showing the amount of BCR-ABL transcripts in the blast crisis CML engrafted marrow mice after 14 days of treatment with vehicle (blue, n=9), PF-04449913 (purple, n=l 1), dasatinib (n=8, red) or combination (n=5, black); Figure 20e graphically illustrates a qPCR array assay showing Hedgehog pathway gene expression in FACS purified human progenitor cells from blast crisis LSC engrafted mouse marrow treated with vehicle (n=3, blue), PF-04449913 (n=4, purple) dasatinib (n=4, maroon), combination (n=3, dark grey) was analyzed by hedgehog (SHH) (SAbiosciences); Figure 20e graphically illustrates data of myeloid sarcoma count from mice serially transplanted with FACS purified human progenitors from LSC engrafted mice treated with vehicle (n=12, green), PF-04449913 (n=12, purple), dasatinib (n=8, maroon) or combination (n=7, grey); all figures are also further described, below.
Figure 21a graphically illustrates data from a competition-binding assay using a characterized cyclopamine-competitive SMO antagonist; Figure 21b graphically illustrates data showing that the inhibition of Shh stimulated luciferase expression using mouse embryonic fibroblasts expressing luciferase under control of an 8X GLI-response element (GLI-LUC MEFs); Figure 21c graphically illustrates data showing the dose dependent inhibition by PF-04449913 in the GLI-Luc MEF reporter assay; Figure 21d graphically illustrates data showing anti-tumor activity of PF-04449913 against Ptch+A p53+/- medulloblastoma; Figure 2 le graphically illustrates data showing the dose dependent anti-tumor efficacy of PF-04449913 against Ptch+/-p53+/- medulloblastoma allografts; Figure 21 f graphically illustrates data showing genes significantly down- regulated by PF-04449913 treatment in Ptch+/~p53~A mice; Figure 21g graphically illustrates data showing Hh pathway inhibition in PF-04449913 treated Ptch+/-p53+/- medulloblastoma allografts; Figure 2 lg summarizes the gene signatures enriched for within the top 31 PF-04449913-downregulated genes in Ptch+/-p53 -/- mice); all figures are also further described, below.
Figure 22a is a GSEA analysis summary table obtained from RNA sequencing data comparing PF-04449913 treated engrafted mice (n=4) to control (n=4) (average 24.7-58.0 million mapped reads/sample); Figure 22 b summarizes the characteristics of patients enrolled and sequenced using the gene expression profile by Affymetrix
GENECHIP 1.0 ST™ after PF-04449913 treatment for 28 days (C1D28); Figure 21c summarizes a GSEA analysis summary table obtained from patients (n=8) sequenced after PF-04449913 treatment (C1D28); all figures are also further described, below.
Figure 23a graphically illustrates data showing the differentiation into CFU-Mix (purple), BFU-E (red), CFU-G (orange), CFU-M (yellow), CFU-GM (blue) of normal cord blood progenitors, as assessed in hematopoietic progenitor assays (n=3) after PF- 04449913 (ImM) or vehicle treatment for 14 days; Figure 23b graphically illustrates data from a FACS analysis used to determine the total human CD45+, hematopoietic stem and progenitor cell (HSPC), myeloid and lymphoid cell count in bone marrow after 14 days of treatment with vehicle (n=3, green) or 100 mg/kg of PF-04449913 (n=4, purple); Figure 23c graphically illustrates data from a FACS quantification of GO (green), Gl (light blue) and G2/S (navy) human CD45+ cells in cord blood engrafted marrow after 14 days of treatment with vehicle (n=3) or PF-04449913 lOOmg/kg (n=4); Figure 23c illustrates representative FACS plots depicting HSPC, myeloid and lymphoid differentiation (panel B) in human cord blood engrafted mice after 14 days of treatment with vehicle or 100 mg/kg of PF-04449913; all figures are also further described, below.
SPLICED ISOFORM BIOMARKERS TO ASSESS RESPONSES TO CANCER STEM CELL TARGETED THERAPIES
Figure 24 illustrates a mechanism of action analysis using nanoproteonomics
(CB1000) technology to show the nanoproteomics of SAR302503, panels show phospho- JAK2 protein (upper left); total JAK2 protein (upper right); phospho-STAT5A protein (lower right) and 2-microblobulin (lower right) status after vehicle (blue) or selective JAK2 inhibitor (SAR302503; green) treatment; all figures are also further described, below.
Figure 25A graphically illustrates RNA-seq-based expression levels of isoforms involved in the Jak/Stat pathway, in vehicle-treated (blue) and SAR302503 -treated (red) blast crisis CML sorted progenitors; Figure 25B graphically illustrates specific isoform expression after treatment with SAR302503 (JAK2 inhibitor) and dasatinib (BCR-ABL inhibitor), relative to vehicle treatment; all figures are also further described, below.
Like reference symbols in the various drawings indicate like elements.
DETAILED DESCRIPTION
RNA EDITING AS A NOVEL CANCER STEM CELL TARGET
The invention provides compositions and methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, e.g., leukemia or Chronic Myeloid Leukemia (CML). While the invention is not limited by any particular mechanism of action, compositions and methods of the invention can slow or inhibit RNA editing by, e.g., inhibiting or slowing the expression of or the activity of an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide.
Unlike many known treatments for CML, which focus directly on the Bcr-abl protein pathway, this invention targets the RNA editing events that lead to Chronic Myeloid Leukemia (CML) progression. ADARl is an RNA editing enzyme, required for hematopoiesis; and levels of ADARl were assessed in isolated human normal and cancer stem cells (CSC) at various times during the progression of CML. Data described herein demonstrates a crucial role for ADARl in both cell differentiation and self-renewal of hematopoietic stem cells. Hence, in alternative embodiments, the invention provides compositions and methods that target, or inhibit ADARl, and treat or ameliorate diseases and conditions responsive to the inhibition of cell differentiation and/or self-renewal of hematopoietic stem cells, such as cancer, e.g., CML. In alternative embodiments, the invention provides a model for the development of therapeutics for treating CML patients, as well as for diagnosing and monitoring CML patients.
Experiments described herein using cells isolated from normal cord blood, CML chronic phase (noted as "CP" in figures), and CML blast crisis (noted as "BC" in figures) indicate that the expression of ADARl pi 50 is increasing as CML progresses from Chronic to Blast phase. Results include: qRT-PCR data that show that blast crisis leukemia stem cells harbor higher levels of ADARl pl50 isoform, (vs. chronic phase or normal); increased ADARl expression (in vitro transduction of lentiviral ADARl pi 50) changes normal and chronic phase progenitors to a preferred differentiation to a GMP (Granulocyte- macrophage progenitor) population found in the leukemia stem cells in CML; and ADARl knockdown (shRNA) leads to a universal (blast and chronic phase) decrease of self-renewal capacity.
ADARl is significantly upregulated in cancer stem cell population as CML progresses from chronic phase to blast crisis, the final phase of the disease, and because ADARl deletion in CML patient sample reduces cancer stem cell renewal capacity, the compositions and methods of the invention are effective for diagnosing, treating and ameliorate diseases and conditions responsive to the inhibition of cell differentiation and/or self-renewal of hematopoietic stem cells, such as cancer, e.g., CML.
Polypeptides and peptides
In alternative embodiments, the invention provides compositions and methods for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, e.g., leukemia or Chronic Myeloid Leukemia (CML), comprising use of polypeptides, e.g., antibodies, and/or peptides, e.g., aptamers, that inhibit or slow the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl enzyme.
Polypeptides and peptides used to practice the invention (e.g., an ADARl enzyme-inhibiting peptide or polypeptide) can comprise a recombinant protein, a synthetic protein, a peptidomimetic, a non-natural peptide, or a combination thereof. Peptides and proteins used to practice the invention can be recombinantly expressed in vitro or in vivo. The peptides and polypeptides used to practice the invention can be made and isolated using any method known in the art. Polypeptide and peptides used to practice the invention can also be synthesized, whole or in part, using chemical methods well known in the art. See e.g., Caruthers (1980) Nucleic Acids Res. Symp. Ser. 215- 223; Horn (1980) Nucleic Acids Res. Symp. Ser. 225-232; Banga, A.K., Therapeutic Peptides and Proteins, Formulation, Processing and Delivery Systems (1995) Technomic Publishing Co., Lancaster, PA. For example, peptide synthesis can be performed using various solid-phase techniques (see e.g., Roberge (1995) Science 269:202; Merrifield (1997) Methods Enzymol. 289:3-13) including any automated polypeptide synthesis process known in the art. Antibodies
In alternative embodiments, compositions and methods of the invention comprise use of antibodies to inhibit or slow the expression of or the activity of: an ADAR1 gene (adenosine deaminase acting on RNA 1), an ADAR1 gene product, an AD AR1 transcript, and/or an ADAR1 enzyme.
In alternative embodiments, an antibody for practicing the invention can comprise a peptide or polypeptide derived from, modeled after or substantially encoded by an ADAR1 gene (SEQ ID NO: 1) or transcript (SEQ ID NO:2), or a peptide or polypeptide derived from, modeled after a protein as set forth in SEQ ID NO:3, or subsequences thereof, or immunogenic fragments thereof, capable of specifically binding an antigen or epitope, see, e.g. Fundamental Immunology, Third Edition, W.E. Paul, ed., Raven Press, N.Y. (1993); Wilson (1994) J. Immunol. Methods 175:267-273; Yarmush (1992) J. Biochem. Biophys. Methods 25:85-97.
In alternative embodiments, an antibody for practicing the invention includes antigen-binding portions, i.e., "antigen binding sites," (e.g., fragments, subsequences, complementarity determining regions (CDRs)) that retain capacity to bind antigen (e.g., a Bcl-2 family protein, or immunogenic fragments thereof) including (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al, (1989) Nature 341 :544-546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). Single chain antibodies are also included by reference in the term "antibody."
Methods of immunization, producing and isolating antibodies (polyclonal and monoclonal) are known to those of skill in the art and described in the scientific and patent literature, see, e.g., Coligan, CURRENT PROTOCOLS ΓΝ IMMUNOLOGY, Wiley/Greene, NY (1991); Stites (eds.) BASIC AND CLINICAL IMMUNOLOGY (7th ed.) Lange Medical Publications, Los Altos, CA ("Stites"); Goding, MONOCLONAL ANTIBODIES: PRINCIPLES AND PRACTICE (2d ed.) Academic Press, New York, NY (1986); Kohler (1975) Nature 256:495; Harlow (1988) ANTIBODIES, A
LABORATORY MANUAL, Cold Spring Harbor Publications, New York. Antibodies also can be generated in vitro, e.g., using recombinant antibody binding site expressing phage display libraries, in addition to the traditional in vivo methods using animals. See, e.g., Hoogenboom (1997) Trends Biotechnol. 15:62-70; Katz (1997) Annu. Rev. Biophys. Biomol. Struct. 26:27-45.
In alternative embodiments, antibodies used to practice this invention comprise
"affinity matured" antibodies, e.g., antibodies comprising with one or more alterations in one or more hypervariable regions which result in an improvement in the affinity of the antibody for antigen; e.g., an ADAR1 protein, or immunogenic fragments thereof. In alternative embodiments, antibodies used to practice this invention are matured antibodies having nanomolar or even picomolar affinities for the target antigen, e.g., a targeted transcriptional activating factor. Affinity matured antibodies can be produced by procedures known in the art.
For example, one embodiment, antibodies used to practice this invention are designed to bind to, or affinity matured to bind to, a polypeptide encoded by SEQ ID NO: l, or subsequences thereof:
1 gaccagacca ttgattcccg actgaaggta gagaaggcta cgtggtgggg gagggtgggg 61 ggagggtcgc ggccgcactg gcagcctccg ggtgtccggc cgtgtcccga ggaagtgcaa
121 gacccggtaa gagcctctgt ccttctcggc tacacctgcc tgggctggaa cgcgcggccc
181 atgcggcctc tccagtctct ggcgttgatg ttagaggaag cgtgggggcg ccccggcagg 241 gcactgaggg tggccgcagg gctgggtggg gacgcagctg gtaggggcac agtggccggt
301 ctcggcagcc ttccaggagg cggacgcccg ggccggtgta cttttgtgcg tgtgtgcgcg
361 cccgtgtgtg cgcgagtgtg ggcggcagag gctgcgcacg gatgctccgg cgctcgtgcc
421 agccggagcc cagcagctgg gtaccaaagg cccaacagct gggtaccaaa ggcccttgtt
481 tccctctcgc cggctccccc gcctcggaga gtgactggag agtgagctgc ctgggactcg 541 ccgcggtagg cgcttttgct gcgccttcta ccacaaactg cgttaggacc ggccctttat
601 cccagagata acatcgccgc cctggcgtgc cttccacagg gaaggcgtag gaggccactg
661 tggaaagctc actgcggggt cacggccgcc gcgctcagcc tgtctggcct ggtgcaggag
721 gcctagttgc gtcacctcct cttccttctc tgtttagctt gatttggggg ccccactaga 781 gggtaatccg gccccaggtg tttcgtgttg gtatcagagt ttgggaaact tgccttccaa 841 aaagggatac ctgtcattgg attttgaatg ttgtgtggag gagcccaagt atgcaattag 901 cggagggagc agagtctagg ctgccacggg aggagacttg caaacagagg cctacacagt 961 gtcttgttgc tagagaggga ggcaggattg ctagagcggg tcattggggg cagagaaggc 102 aggggcgtca aactgtcagc agttgtgatg ccaacttctt tctccaccag agaagccttg 108 ttcccatcct tttaaagatc tcttgaaata tcttggtcgt tatttacaaa cagttagtgc 114 ttgctatatg ggaaaaaggg aaatagagtg gaaaggggac atgaactttg gagtcaggtc 120 tgccactttg cagctgtttg acattgaatg agttatttaa cctctccact cctacttggg 126 cttatctaca aaatgaagat aattatatct accttgcccg aggtgtcaga attcgaagtg 132 tctagctatt attagtaagg gcccagtacc caggagcttg gacttgctcc cttgctgaag 138 gtttcctatt ggtacagctg cttgagaagc aggggaactt tttgctattt tagatgtttg 144 ctattctgcc agatatgata tgcagacttg ggggtggtag tggaggggaa atctcaaaat 150 ccataatctc tctgctgtac acttcattaa attctagaac tgcaaagagg tgaagatctc 156 actttaggcc gggtgcagtg gctcatgcct gtaatcccag cactttggga ggccgaggca 162 ggtggatcat gtgaggtcag gagttcgaga ccagcctggc caacatggtg aaaccccgtc 168 tctactaaaa atacaaaaat tagaccagca tgatggtgca catctgtgat cccagctact 174 tgggaggctg aggcaggaca atctctcaaa cccaggtggt ggaggttgca gtgagccaat 180 atccaccatt gcaccccagc ctggacgaca gcgaaactgt atctcaaaaa aaaaaaaact 186 cactttatta attatagctt ctcattttat tttattattt ttcaatttta tcccgagtag 192 ctgggatcac agatgtgcac caccatgcct ggctaatttt tttttttttt tttttttgag 198 acagagtctc actccatcgc gcaggctgga gtgcaatgat gcgatctcag ctcactgcaa 204 actctacctc ccgggttcaa gtgagtctcc ctcctcagcc tcccgagtag ctgggattac 210 aggagcatgc caccatgcct ggctaatttt tgtattttta gtaagacagg gtttcaccat 216 gttggccagg ctggtctcga actcctgacc tcaggtgatc cacctgcctc ggcctcccaa 222 actgctggga ttacaggtat gagccaccgt gcctggccta tgcccggcta atttttgtat 228 ttttagtaga gatggggttt caccatgttg gccaggctgg tctcgaactc ctgacctcaa 234 gtgatctgcg cacttaggcc tcccagagtg atgggattac aggcatgagc caccgcgcca 240 ggcctttcgc ttctctttag cacttgctat gtacctgaca cggtgttgag cactttacat 246 atactaactt atttcatccc tctaacaact gagtgcacta aatattatcc ccattttata 252 gatgcagaag tgaatcttgg ctaaggtcct gacattaatt aacggcaaag ctggaacttg 258 aagccagctg tgtggtttga gtcttgctct ttctcagtgt ctagcaagtc ttgctcttgc 264 ccttgctcat caggctatgt ggtttgagtc ttgctctttc tcagtgacta gtatcccagc 270 aatgtaaacc tggtgcagtg ggggaaagga ggcccagaca gagtttagtg ggccaggatt 276 ggctgcaaga ataacatctc aaattgtcta atgatacatt atcttttatt ttacattttt 282 tactcagcat tgtccagata tgaaccaagg tttggccttt tcacccagag aaaaaggaca 288 ggctcatggg tacactgtgc tgggatgacg ggcacaaagt aggtattcgg aaaatgcttg 294 tggaaaaaag aaatcctgag gcattgttat ttctgccaga aggaggccca gtgcttatta 300 cacacaggct ccttaagcca gctattttta tactataaca cactgtaata tgagcatttt 306 tctgattcat ggatttaaag atttgaagcc ctgtttcaga ccaagattgg tagtattatc 312 tgtgaccaac tgattagagt tctcaaatat gtgaacaaca gaatctgagc ttttgggctt 318 ctgtagtaat ctcttgagat agagcaattt gttttgctat aacatctgtt agacttggac 324 cttaatgggt acaactgctt gagttttctg gagaacactg gatgattgtt tgacatcagg 330 gataaagagt tcaaaatatt aagtttgtct caaaattaaa tatttgggaa agacctgtga 336 ttgatgtgca ttcattgtag gaatagtaca ctagttttaa acagatgata ttcctggtat 342 ttttgatgag ctattctgtg tcttaaagat gtttaaagat gacttgtagt tgtatagtga 348 actattagga acatacaaaa tttatataac ccatccatat agactgtgac ttacaccccc 354 ctcagttcct ccacccaagg aggtctagtt gctgcttcta taccctctgg ttaccttgaa 360 gctacctatt tcaccatctt tatcagactt tatcagactt aataggtgag accctctgac 366 atcagcctcc ctttccttct gtaccacccc ttgccacatg cacacagaat gaagctcttc 372 tccaaaagga ctgtatatta atctacttgc aagtggcaca aacccagtgt aaattaactt 378 aagcaaaaaa aggttttttc ctccctttga ttatttaact agaaagtcca aaggcaagct 384 tcaggcatgg ctggatcctg gggctaaaat gatgtcatga gggctttctt ggcccttcct 390 ttttcggctc cgttttcttt attgacttca ttctctcttg ctgctttctt tttctttttt 396 tttttttgag atggagtctt gctcgtcttg ctctgtcgcc cccaggctgg agtgcagtgg 402 cacgatcttg gctggcggca acctccacct cccaggttca agtgattctc ctgcctcagc 408 ctcccgggta gctaggatta caggagcccg tcactacccc cggctaattt ttgtattttt 414 agtagaaatg gggtttcact atgttggcca ggctggtctt gaactcctga cctcaggtga 420 tccacccgcc tcagcctccc aaagtgctgg gattacaggc atgagctact gtgcccggcc 426 ttcttgctgc tttctctatg catactgaaa aagctccctg tcagcaaccc caagcctatg 432 acctgatggc tgtcttttag cgttgtaaat taaccattgc tgacaaggaa atagggagac 4381 cacaattgga gaggtctaca tcataggctc actcttggga tgaggaagta aactgcccgt
4441 ccataacctt atgggatggg gaagttcaga ggtcctaggc aggcagaaac agcacatgac
4501 tactgcaggg gtgtgtgtat gcacacatgt gtgcttacat gtgtgctctt atctcacttc
4561 tttggggtcc ttctagagcc ttccaactgg aatgaatcca gtgggttgtg tttgtccatc 4621 aaactttgac tcccactgtg gcatccatta tgtgctctcc gtcctttctg tacctttgca
4681 tctgctgttt gggttgccct tccccattgc ttcatctggc tgatccttct agattcaggt
4741 catgcttctc ccagaagcct tccttgacac cttccttaat gagctaggca tcccttctct
4801 ctgctcccat aaacacctga gcacaacccc cttgtagatg ttatttctgt ttgataatta
4861 tctgtttatt ggtcatgtct ccactagacg gagagcccct tgaggacaga gtgtcctttg 4921 ctttgtattc cttatctcct acccttagct agtattattt gtcttcatag cactcataac
4981 tgacattgta tatttatttg tttatttatt gcctgtctct cctcattgac tgtctttcat
5041 tagcttcatg agaacaatgt ggaaaggaat tttctttgat caaagcaaaa caaaactacc
5101 ttgaggccta ggacagtgcc tcatactggc atatagtata tgttcagtaa atgtttatta
5161 aatgaatgaa tggaaatctt cccacaggaa gaaaacactg gcattatgtt gatgaacatt 5221 ccagtctgca tgatagatac acttctcact gtaaagatct gaaacttgag taccatggca
5281 tcccaggaag gtagcacacc tcttcccata tgtgtttgaa cctgcagagg tcaggcccaa
5341 ggagcctcca gctggaaatt ctaccctgtg tgatgtttca ctcctctcaa acttttctga
5401 actttgatag gttgtatatt aaggccttct ccatattttg gggccctttc cttggagtat
5461 ttatttttaa aacatttatt taagcactta caaggtgaca ggcactgttc ttagtccttt 5521 ataaatagca actcactctt ggactggagt ttggggacca agggttgtca actttaaaac
5581 ttttttcttt ttaagtacca aaacactcaa gaacagaaat aagactactc tgcatctagt
5641 ccatcttgcc ctccagaagt agagctatct aacagcctga tacaggtctt gtccctgccc
5701 tttcctcagg tttttacagc catagctagt aaatataaca tactgcatct catcgccttt
5761 gtttggtctt cacccaaacg cagccacgct ctgccgcagg atatgtggca gagccaggtg 5821 gggaatcagt ggctcagagc ccactctgct tttcaggaca taggctgctc aagcatctgt
5881 cttcagccct ctcccaggga gggcctaaac ccacatcctc aggcccctgc agagcacatc
5941 catcttcctg gttacatgtt atgccttatc tgtgggaacc ctagccacgc cacacccaca
6001 cctcaacaca tgaagaaagg gaaaaaatac ccctttcttt cttttgacaa caacaaaaaa
6061 gtacttctcc tacaaataga gacttgaaat gacagggtta ttatttaacc ccgctcttac 6121 tccaaacatc caagcggcag tttcagccta gctgcagtac tctgttgtag tgcttagtcc
6181 tgatttgctt cctaagaagt gaataccagt ttccactgcc atcagcaatg cctgagtact
6241 tactgtgcct ctccctcacc ctaccctcct ctccagaact gagtatttta ctaaaaaagg
6301 aaaatcttag ctaaatttga aatagcatct cattttaatt tgcatttttt attataattg
6361 tttgagccct ttttacccat actgagccat ttttatttct actttttaaa tttttggtta 6421 atgttttgtc tattcactta ttgtgtttaa gtgattttta aaatatacaa atattctgaa
6481 aaacatgagt ttatcctcat ggtaaaaagc aaacaatttt atttgcagtt aattcttttt
6541 agtttattgt ttgccatcta attttggctt tatcattaaa aatacaaatc tatttttcat
6601 tcttttttag acaaatttta ttctttttga tttcttttgc ttgtgagcat aaaaaggttt
6661 ttttccttat tctatattct agtttttttt atggtttgca tttttacata tgacttttaa 6721 aaagctagca ttcagtttta tttcagattt taataagata tttgatgaaa atagtgtaat
6781 attttaaata aaatcagttt taattaaagg tctatgtttt gttttaagga tgtttatatt
6841 actgtactta tattttttct ttttaaataa tttatcagaa tagcgaacag cttgcttgac
6901 aaaactaaga ttcacatata tagataatca taattttagt gttcttagcg tttccataaa
6961 ttgctgcatg aaaagatatt tatgtgtggc tgtctggttt aaagaggcac tcgtgcttgg 7021 caacagcttt tcagcatgta gccaagatga caaattcagc ctcttccagt tcctcttcct
7081 cactatttcc ctaagatttt tttcatggga gcataactat gtgtatctct gtgcacagat
7141 tttatgtgta cctttcaatg tattttaaca aaaatatatc catttaacta tccaaatcaa
7201 gaaataaaac attttcatta cctcagaaag ctcccctgtg gtagtcacca ctacccccaa
7261 aggccaacac tattgatgtc tgatatctat cactatagat tagattagtt ttgcctgttc 7321 taaaatttca tgtcagtatg tgcttttgtt tgtggcttct ttcagtgagg atcaaccatg
7381 ttgcatgtgt cagtatccat tgtgtgaata tgcatcaagt tatttattca ttagttgatt
7441 gacatttggg ttattccagt ttggggctat taagaagaat aaagctctat gaacagtttt
7501 ttttcctgtt ttttattgta gtaaaataca caacataaaa tttaccatct taaaccattg
7561 tttgtttttt tttttgagac ggagccttgc tctgttaccc aggctggagt gcagtggcac 7621 gatcttggct ccctgcaacc tccacctccc aggttcaagc aattctctgc cttagcctcc
7681 caagtagctg ggattacagg cacccaccac catgcccagc taatgtttgt atttttaata
7741 gagacggagt ttcatcacct tggccaggct ggtcttgaac tcctgacctt gtggtccacc
7801 cgccttggcc tcccaaagtg ctgggattac aggcatgagc caccgcgcct ggcccgtaaa
7861 ccatttttaa gtgtatagtt cagtagtgtt aggtatagtc acattgttgt gcaacaaatc 7921 tccagaactt tttcatcttg cagatctaaa actatattca ttaacaactc ctcttttccc 7981 ccatcctcca gcccctggtt ctatggacat tcttgtacaa gtctttttgt ggccattttt 8041 cttgggtaag tacccaggag tataaatgct gggtctagcc ttagaagaaa ctgccttaca 8101 gttttctcga atagttagtc gtaccatttt atgttcccac agtatacaaa aatgctagtt 8161 tgcttcatat cctcaccaac attaggtatt gtgagtcttt ttttatttta gccattctgt 8221 agctgtgaag cggcatccca ttgtggtttt attacatgtt ctagtcagtt atttacatgt 8281 ctgttcccat tactagactg tgaacttcat aagggaaggt tcatgcagta agtagttttg 8341 ttttttttgt tgttgttctt attaaccttc ctcttcttat tttgagggtg atacatgctt 8401 tattattaaa aagaacttaa aaattataga aagctattaa aaagccaata aaatcacagg 8461 ttagcccacc tctcagacat catcaggagt attttggtct ttcaggcagt gctgtgttgg 8521 ttcgtacaga cagaacagtt cccatgatgg ttgattcagc aacccagcat tgttccagcc 8581 cactgccttg ctatcctctg gacatcactt attcccagcg aggagccctt ttctcagaca 8641 gccccagaca gattgttttt gtggtttgct ggccacaaat gtatcacatg tatcactgac 8701 aaaagaagta gaatcctcaa tactggatta aattagatta attaacatcc ttcctctggg 8761 gctggggagg gaacctggcc ttcttaggaa agtggacaga atcagggcac tctcagaaag 8821 ggaggcatag ttctagcgta ggccactaac attatctgcc tctttttttt tgagatggag 8881 tctcactctg ttgcccaggc tggagtgcag tggcacaatc tcagctcact gcaacctctg 8941 cttcccaggt tcaagcgatc ctcctgcctc tgccccacta gtagctggga ttacaagtac 9001 ctgccaccac gcccggctaa tgtttgtatt tttagtagag acggggtttc gccatgttgg 9061 ccaggctggt ctcaaactcg tgacctcagg tgatccacct gcctcggact tccaaagtgc 9121 tgagattaca ggcataagcc accacggccg gcctgcttct tggtgttttt atttaatttt 9181 tttacactta gtctgtcaat acatttgcaa tttgttttgg cttattaata taaggctaga 9241 ctctagactt tttttttttc caaatagcca ttcagttggc ccagctccat ctgttgaata 9301 acgctttttc tcactgctgt ttttggttcc tcatcatgca ttggatttct gcacatacta 9361 ggctctgttt ggagggaggt ggttcttttc tgttagtctg aagctctacc cttgctttat 9421 accagtgctg ccttggttta attagcgtag ctgtcttctt tttaaaaaac tgttttgttt 9481 gttcttgtac ttgaacttta tttattccca tccaatgacc tattaattgc atctgaactt 9541 tagagtaatc attttgtcag gtatccactc cttactgccc caacctcata gtatttgcag 9601 taaatcgtta tttaatttga tattaattag tattcataaa gtattctgcc atcacatttg 9661 agactggtat gtccttctat ttaagacata tattcctcag cagagttttg taattttcca 9721 catgtaagct cttcacattt cttagggtta gtcctagata cttctttttt ttaatttaat 9781 gttttatttg ctattaagaa tatggtattc ttaatagcaa ataaaacatt aaagtatata 9841 aagaatatat acttactata tgaagaaggt atacttatat attactatag taatgtatat 9901 attactatat aaagaatata tactttagat gcatatatac atatgcatat aaagaagcta 9961 ttgtgtttta tatgtttctc ttatattcaa ccatattcct tgactggtat tggttctaag 10021 agtttttcag ttgatcctct tgaatcaact agggttatga tgatatcatc tgcaaataat 10081 ctatttttct ttttaatagt ttatctctta tttttgtttc ataatgtaga atatgtaaga 10141 atttccatag gtagaaaaga tattaaatat atatatttaa catgtgttaa ataccatatt 10201 tgttttaaga ccactgagca taaagacttg ctattgattt aataacagat ttggggggca 10261 ctatattaaa tgtatactta cactgtaatt catattccaa tatcagaaat gttaggatgt 10321 aaaaagcagt gcatcttaga attaaggaaa ataacaatgg taatggtagc cctccttttt 10381 ctcgtttgag tggtagtgtc taactgttcc attctacata tgatattggc tgttgattta 10441 tgatagacag tctttattat taaggggtcc tcacacatct tcctgtttgg aagaggtttt 10501 gtgttggttt aatcagctta ggagggaaag gtgatcatca gggtcacttt cgtgcagaat 10561 cccacctctg cccacaattc ctgccttctt tgaactttct ttgttaaagt aagaatctag 10621 actctggcat caaagattga tatgctaagc agaagtttac tgcccagcag agaaccagtt 10681 gagtgcaaaa gttaggctct gagatctaag ccttgagggt ggcaatgagg gatgaggtag 10741 gtttttaaaa ctcatggtct ccatcccata ttaggaaatc aaagtctcca aatgctactt 10801 attggccagt gttatctgga ctaggcattg tctaagcaac aagcaggaca ggacgcttgc 10861 aggggttttt gataagttat ctctcactat gtctatgagt caggataata gtgccccagt 10921 cattgttttg gtagaagtcc agtccactgg ctaggcagcc atgttgggat tcatcacttt 10981 gtagtttcta actttttact gtattccata ttggaaagtt cagccctcct ctgagatacc 11041 cattgtccac tagaactcca gacagaagtg ctggagaggg cagtgggcca ggtcaggaag 11101 acataagcca gagttgaagt acaacagtgg aaagaacaaa gtctttggag cagtgcctct 11161 taaccttcgt tctgggtaca cagatctatc tgggagtctg aaagctatgg gctgtctctt 11221 gagggaaatg cgcatgttgc gtttttcagt aaatattttt gagcacgctg aaagcaaaac 11281 acttgtatag ccctagcttc ttggaacttg tagtaagaga gacagatatt taccaaaaaa 11341 ccacatgaag aaatgtaaaa ttacaagtgt aaatatgctc caaaagagag gagggggtct 11401 tgaaatcatg cgatgggagg gggtaggggt tagagctcaa gctcttcctc cagaagtgtt 11461 gactaccctg agatctgaag ggcaaatcat aggatagtgg aaaggaggag aaataatcca 11521 gagagagggg caagtatgtg gcaggaggga gcatggcaat ctagagggag gaaaagaagg 11581 ctcagggagg ctgggggaca gagagatggg gcatggtcca acagaaggga gaaggatggc 11641 agggctaggc cacgtaaggc tttggagcca tcgtgtaaag atgtttgcct ttatcttaag 11701 agcattagga agccatcaaa gtattttttg ttaataatgt aaatatttga tatgcataaa 11761 agattcctgc agcatatatg tatcactgaa atacaacaat gaaacgaatg cacgtgaacc 11821 taacaccttc ccctgaatga gaaccttatc tgtattgctg aagcctccct tgtcgcctct 11881 tggatcccat ctgcctgtgt tccccctccc cccttaattg ctaggttaga attttcttga 11941 attccatgca tgacatgatc agattttggt tttcagagat cacacaagct gtgtcgagaa 12001 gactggatag aaaagaggcc aaagtacatg cggggaaacc agtttggagg ttgtaatcac 12061 aaaacacaat cttactaaaa gtttgtctgc attttatttt attgccttgg aaatttattt 12121 ctttcacaga tgatttattt tcatcatttt aaaaatataa attaatggta tcttcctaga 12181 aaaaaataaa atcagataaa actaaaagct ctaattctgt tggacaataa tgagaaggct 12241 gtactgtttg gcttaactaa aaaatgtggt gaggcatggt ggctcacgcc tgtaattcca 12301 gcactcaggg aggccaaggc aggcagattg cttgagccca ggagttcgtg actggcctgg 12361 gcaacatagt gcggccctat ttctacgaaa aaaaattttt ttaattagcc aagcatggtg 12421 gtatgtgcct gtagtcccag ctgcttaaga agctgaggca ggaggattgc ttgagcccag 12481 gagtttgaga ttgcagtgag acatgactgt accactgcac tctggcctgg gtgacagaga 12541 ccttgtcttt taaaaaataa ataaaggaca tcatggctgt gcataagtac atctatgaca 12601 gctagtctgt tttggccttt tccctttgat gtacccaaat gcagaaactc ctatctcgcc 12661 tagcaaagcc tctggcagcc ctggacttgg agctccctgg tttgtattgt ccagcaaaga 12721 tgctgtagta gtttcccgtg gctgtctgct gtaaaaaaat aaccacaaac taggtggctt 12781 aaaacaatgg aaatttatta tctgacagtg ctggaggcca gaaatctgaa atcagtatca 12841 ctgggccatg ttggcagggc tgtgctccct ccagaggctg taggggagaa tccattcctt 12901 gcctctccca acctctggtg ggtgctggca tcgcttgtgt tgcggctgcg tcgctctagt 12961 cttcaaggct agcatcttcg aatcattctc tactctgtct tcacatggcc ttttcctctg 13021 tgtgtgtagg tggaaatttt tttgaacttg ccaacactaa aagaaacact tttaaagacc 13081 agtgttcact tgaaaatggc tctctgtcaa attccaagaa aaccagttca ctgaaagtca 13141 gttctacaaa agcccctcca tcctacccct ttgcctcctc agtttcctcc tcaatcttct 13201 gctctacagc agcagggaga cagcagagca tatttcctct aaattctatt aagaagacag 13261 aataaaaact ggtcaattaa gactagggag atttaagaaa aaagtaaatg caacatattg 13321 gttgtttcgt aaattggtta tccaaggaat tgaccatttg gcaaactgac tttcggcaaa 13381 ttggctgttg gtgaaatcag cctatttccc tgagaaacac tgcagaaggc agggcagtgg 13441 ctgccttgag cctgcccagg acaggactgt gactgtcccc tcctgctttc tacaagccat 13501 ggagataggg gcattgctct tgcatgaggc tggggctgag agcagccccc tacaggctgg 13561 atctggatcc tagggaagaa gaagatggga gatctccccc tttgggtcct gactcaatag 13621 aacccaaatg taggccagta gcggaacctc tgtgctagcc agagtcaggc cagaagtcag 13681 tcaggtgctg catccaagaa caatctagca tcggagaagc ggcttaaggg tgtcagaata 13741 taatgtataa aaccacaagt tgtatagggt caccccgtgg ggtagttatc cgactgaatg 13801 tacatttatt agttatacat acttgcaaaa gattgcacac aggcctgtta gtcattatta 13861 ttagtattat tttacatatg taatattatt gcaaatgtta tatctttatt atataatact 13921 taagcctggc acatatagct agttgataaa taccactttt tttctttgtt actagataac 13981 ttactggagt ggataaatgc acttaatagc ttttggagac ctctttttct tctgggggta 14041 cctgaggcat ttcttgcttt cttttttttt ttttttgaga tggagtttcg ctcttgttgc 14101 tcagggtgga gtgcagtggt gcgatctcgg ctcactgcaa cctccgcctc ccaggttcaa 14161 gtgattctcc tgcctcagcc tccctagtag ctaggattac aggcatgtgc caccacaccc 14221 ggctaatttt gtatttttag taaagacgga gtttctctat gttagtcagg cgggtctcga 14281 actcccgacc tcaggtgatc cacccacctc ggtgtcccaa agtgctggga ttacaggcat 14341 gagccaccgc gcctggccac atttcttgct ttcttgtaac ttcaaaagcc agttttagct 14401 gggagcaatg gttcacgcct gtaatcccag catttttgga ggccgaggca ggcggatcac 14461 ctgagatcag gagtttgcga ccagcctggc caacatggtg agaccccacc tctactaaaa 14521 atataaaaat tagccaggca tgatagcgcg tgcctgtagt cccagctact tgggaggctg 14581 aggcaggaga atcacttgta cctgggaggt ggaggttgca gtgagccgag atcatgccac 14641 tgcactccag cctggataac agagtgagat tctggctcaa aaaaaaaaaa aaaaaaaaag 14701 ccatttgtga tcattaacat caatagaata tatgtcagca taaatactgc cacagagcac 14761 tactcagcca gttgggcaac tcactcttct ctaccaaaag ctttacaggt tatcaaagca 14821 agtgggttta ctgtgggagg ctactgtgaa ttttggaaat taatgttgag ggactagcgc 14881 agtggctcac acctgtaatc ccaacatttt gggaggccga ggcaggcgga tcacgaagtc 14941 aggagattga gaccatcctg gctaacacgg tgaaacgccg tctctactaa aaatacaaaa 15001 aattacccag gcatggtggc atgtgcctgt agtcccagct actcgggagg ctgagacagg 15061 agaatcactt gaacctggga ggtggaggtt gcagtgagct gagatcgcac cactgcactc 15121 caacctgggc aacagagcga gactctatct caaaaaaaga aagaaagaaa gaaaattaat 15181 gttgttagga actgttgtag tggaataaaa actcagtgat aaagaattga ggagaaacaa
15241 cgataacaaa aaaggagggc aataaatttg tgcctagcaa ctctgaattg cttactatac
15301 atttcctaag agttattcta aaatgatgcc ctggtactta aaaataactg agcaggctgg
15361 gcgtggtggc tcacacctgt aatcccagca ctttgggagg ccaagaccgg cagatgacga 15421 ggtcaggaga tcgagaccat cctggctaac acagtgaaac cccgtctcta ataaaaatac
15481 aaaaaaatag ccgggtgtgg tggcaggcac ctgtagtccc agccactcgg gaggctgagg
15541 caggagaatg gcgtgaaccc aggaggcgga gcttgcagtg agccaagatt gcaccactgc
15601 actccagcct gggtgacaga gccagactcc atctcaaaaa aaaaaaaaaa aaaaaaaaaa
15661 aactgagtaa tttattactt tctttgataa tatgttgcaa attgtttaga atacattcac 15721 aggcagtaca tttctgtccc agtatcactg tatgagcaaa tactgaagga gtttgcagac
15781 atctgcttta cagtagacag gagatagatg ttccaattgg atatagccca tgtgtgtagt
15841 aaagtctggt tataggaaat tacagattaa aaaagactgt tgttgtaaac atgtatccct
15901 gcacgcagta aggttaaaca gaagatccac aacaaaccaa attaacaatt actaagtcag
15961 actaacagtt acttatagtt aaaaagcaag aatagcaggg attggaaaac aaaaccaact 16021 caggagccct gataatagca tgtcctttcc tataggtggg gaagtctcac cccctgaatg
16081 cacctataga gctagagctt ggcactgcta tgtggaagcc agacttctga gaatactgag
16141 tttctgagta cttcattttt agacagtaac tcttaatcat ttaggtggtt tttaataagt
16201 agacctaggt ggtatagata catctggggt catttcacag gcccctgggg aggtgagcca
16261 ttctttatag gaagagctcc tcccttgaga ggactgacca cccatgtgtt ggcagtgccg 16321 ttacgcacgg ggaagttacg cacagggaaa atgctcgaag ggtaggcacg gatgaatgat
16381 gaattaacaa tgggtgattt ttattgtgtt tgcttgtctg tattttctga aataaaccta
16441 ttatttttgg ttaatttttt taaagacttt catccaactc gtcaagttcc tacaatagaa
16501 cagttaaaaa aaaaaagaca tcatcacctc acaaccatgg gggagttaaa acaattactg
16561 agggggagga gatgaaacgt ttatgaataa gactgtctgc agttacttga gctgctaaga 16621 ttaaatgaca ataggagttg ttgttctttc aaggcataaa ctgaccttct gttgaggaaa
16681 gttcactgct ttgccactgt gtcctatgtt agattaaaag gggtgggggg agcagcggtg
16741 cagcttccct cgcacagtag ttgtgattaa agcttttctg gatcatttct gaagaagggt
16801 aaaggctttc agattgtctt gcctgaagac aagaaagcag aggtaagata taactcctgt
16861 tacttaaacg gaggaaaaaa aacatgggga agtggactgg aattgcaaca gcaagagttt 16921 gttgtggttc ttgtttgttt ttacctttta aatttgtgaa atacagcata tatatacaga
16981 aacatgaata aaacgtaaat gtataatgaa attattggaa agcaaacata tgtagccact
17041 acccaagtca agagctagaa catcaccggt acccaaaaga tttcttccca gtcaaaactc
17101 ccacctttct ccctagaagt gattaaccac aattttgtct tttttttttt ttttttcttt
17161 tttttttttt ttgagacggt gtcttgctct gtctccaggc tggagtgcaa tggcacaatc 17221 ttggctcact gcaacctccg actccctgct tcaagcgttt ctaccacgtc agcctcccca
17281 gtagctggga ctacaggcac acgccaccat gcccagctaa ttttttgtac ttttagtaga
17341 gatggggttt cactatgttg gccaggatgg tctcgatccc ctgacctcgt gatccgccca
17401 cctcggcctc ccaaagtgct gggattacag gcatgagcca ctgcgcccgg cctcattttg
17461 tcttttatgc agagcatact atagtttggt tttgcctggc ttgggacttt ctgtaagtgg 17521 gatcatatag tatacatatg gcttttccca ctcagtatca tatttagata attagctacc
17581 ttgttgcatg cgtagatctt tcatttttgt tgctgtattg tattccatca tgggcatatg
17641 ccaccattta tccattttac ttttgatgga catttgggtt gtttccagtt tgggggctat
17701 taattacaaa taatgcaacc atgaacttct tggggtttac cattaccttt ctagataatg
17761 gtaaactggt ttcctgtagt gactaagagc tgctctgcat ccttgctgcc acctggtcta 17821 atcagatggc taatgctgtc tgtctggtga atggacagta gctcactgta gctatactgt
17881 gcatttctct gatgtgatgg ggttgagaac cttttcatat gtttgatatt ttttatctcc
17941 tgtgaagttg tctttcgatt gtttttgccc attgttatac ctactgaggg gtctgttatt
18001 ctttcaacta accagccctc tgaaggcgaa tataaggata caaaacatgc ttcctgcccc
18061 cgaggagatg acttgacaat tctagaggca gatatatgaa caagaagtac atgataattg 18121 tgattactga ggcatccatc ttccctagca gactagctaa aggatggcgc tcttatttgt
18181 gtcatatcct gggtgcttaa cacagtatct gccacataat taggtgctta gtaaagtttt
18241 gttaaatgat cgaatggggc gtttttagcg cagtgtgcaa gtgccctatt aggggtaggc
18301 gcccagtaac tcgagaagca tggagtagga aaccacaaac agcacctgct ccccctcctc
18361 tccccctacc tgctgtgggg aaggcctccc ttgtaaattt gaaaggttga ttcacgggaa 18421 gccgtggagg aggtgcatgc taggccaacg aatagaatgt gcaaaggccc agaaggaaga
18481 cagagcccag cctgcaaggg aatgttaatt tggagtgact aacaccatga aagggcatca
18541 gctggagata ctgctataaa gggactgcct tgtaatttca taagcatggg ggtaaaatta
18601 agattaaaca cagggaaaga acattctcac aggtgaggat ggtgttgaac cctagaataa
18661 tcgtttccca gataccttga acaaaaatcc agcagttaga gaagcctgac catgaagcaa 18721 atttgacttt tgtccctcta gataacaaaa gttatctttt tgaaagtaat ggtgtaattt 18781 gaatgagtgt agagaagcgc tgaagactga gctttactaa agccttcaga cctggatttg 18841 gcagcagcgt ggccttagtc aagcctcggt ttctacacct gcaaagtggg aataatgcct 18901 accttggagg gctgttgtga agattaaggg agataataca tgtaaagtac ttaaccattt 18961 gcctggtggg gtagttttta tgacctagat cctaaattgt tcactgctgc tgttgctact 19021 cttggtactt tttactggct ggcatctgct tgcttaagtt tataacatag taggagcatt 19081 aacaaggtcc cacggtgggg accttggtcg tttgacgaga tctgcgctcc cgcccatccc 19141 ctcccccccc cctccacatt ggagacgcgg ccaccaccgc gctggcgcgg agagagggag 19201 gaccgggcgt catgctgttt ctggcctgag gttttgtgtg cctttgtttt ccttttgctc 19261 tattcgtgta ttcctgccta cggcctgtgc ggggaattag gagctcagta ctgaaacggc 19321 ggttttccta aacagtaccg gacgggcgcg ggggctgacg cctgtaatcc caacactttg 19381 ggaggccgag gtgggcggat ctcttgaagc cgggagttcg agaccaccct ggctaacgtg 19441 gtgaaaccct gttcttacta aaaatacaaa aaaaaaaaaa aaaaaaaagc caggagtgat 19501 ggcgctcgcc tgtaatccca gctactccgt aggctgaggc aggagaatcg cttgaacccg 19561 gggggcagag gttgcagtga gccgagattg cgccattgca ctccagcctg ggcaaaaaga 19621 gcgagactcc gcctcaaaaa aaaaaaaaaa agtaccttcc gtagttctca tgcagcggag 19681 gggttcgact tgtaaccggc ctgaaaccaa gcgtggcgca agatttgctc aagcccctcc 19741 tcttggccaa actttccgga ggggaaggct ttccgaggaa acgaaagcga aattgaaccg 19801 gagccatctt gggcccggcg cgcagacccg cggagtttcc cgtgccgacg ccccggggcc 19861 acttccagtg cggagtagcg gaggcgtggg ggcctcgagg ggctggcgcg gcccagcggt 19921 cgggccaggg tcgtgccgcc ggcgggtcgg gccgggcaat gcctcgcggg cgcaatgaat 19981 ccgcggcagg taagccgggc cggccttgga ccttcgccgc cgtctgggtt cgtttacaac 20041 ctcacaggct ttgtgttgca gtgcgtagcg tgtgcgtctt gtgagtgtta gagtgtgtgt 20101 gtgtgtgtcg tcttgccaag cagcattgct ggtttaggaa tttgtgcgtc ttgtgagtgt 20161 gtgtgtgtgg gtgtgtgtcg tcttgccaag cagcattgct ggtttaggaa tttgtgcgtc 20221 ttgtgagagt gtgtgtgtgt gtgtgtgcgt gtgtgtgtag tcttgccaag cagcattgct 20281 ggtttaggaa tttgtgaatt tgtatcctgc tcattaattc tgcagaatgg agcagtgcgt 20341 gaagagggct tgggggaaaa tgcgcccccg tctgagtagg aaggcctgag cccatgtcaa 20401 ggcagacaca tcgtctccct ttctgctagg gccccttgtg gaacccccta cccccgcttt 20461 agccccactt gaacaacgtt cggactttga gcagcgcaca ctatcctcag ctcaccttat 20521 ccacctcctg aaggccttct gggagttaaa aatggcactt aagctgtagg agaaagcttg 20581 ttaaccactt tatagctaaa aactgggaaa acacaaatgg ccttcagcag gttaacagat 20641 aaactgaaat acatccacat aatgggatac tgcttagtag tgaagaggaa atactgttac 20701 aagtaacaac acgggtgact cgcaagtgcg ttatgctaag cacgagaagc cagactcaaa 20761 aggctgcata ctgtatgagt ccatttatat gacattctgg aaaaaaaaaa ccacagttat 20821 agggatggaa agtggatccg tgggtgccag ggactgggta tcgtggaaga aattgattgt 20881 tgagtggcat gaaaaagctt tttagggaaa tagaaatgtt ctatatcttg attgtggtgg 20941 cgattgtcga aattcataga tttatacact taaaaggata aattttactg tatctaaatt 21001 atatacctca attttgttaa gatatatata tatttttttt tttttaagca ctcctttgaa 21061 aggattaagg acgcctaact tgaaggaaaa gcatttctgc acaggtgtca gtgtattgca 21121 ctgtggaacc tgtgtggtaa aggcaaaggg ggtagtgctt atctcttgat cctaaatatg 21181 tgagaccaga ttaaagtgaa atctgggagg caatgaatgt taaatgagtt gttatgtaat 21241 ttgcatagag gtgatgctga gagatttaga aaggatcact gtgggttgct tgctcacttt 21301 cttgctctcc tattccgtag ctttccaaat ggctgtactc aacggtggct tggtgtttag 21361 gggatttaag gggggcaaaa agaaagatta ataatctcct cctctccctc taaccctact 21421 gccctaagat atccttagca aacttacatc tcctttcttt tctctgtgtt cattccattg 21481 tgcgcacaca tacacattca tggattttct ctttttgttt agggaaaaaa attataatgt 21541 acatactatt ctacaacttt ttgttgtttt attgaacatt atatgattcc taaattatcc 21601 ccaggtgaat acaaatagat atgacacatt ttaaaaaaat aaaataactg gccgggcgtg 21661 gtagctcatg cctgtaatcc cagcactttg ggaggccgag gagggcggat caggagatcg 21721 acaccatcct ggccagcatg gtgaaacccc atctctacta aaaatacaaa aattagctgg 21781 gtgtggtggc gtgcgcctgt aatcccagct actccggagg ctgaggcagg agaatcactt 21841 gaacccggga ggcggagatt gcagtgagct gagatcacac tgcactccag cctgattgca 21901 gtgagccgag atcatgccac tgcactccag cttggcaaca gagcgagact ccgtctcaca 21961 agaaaaaaaa taaccgtgtg agtactattc catagaatga atgtttcata atttaattct 22021 tctatagaca gacattaaaa tattttccag atttgggcca agagtagcag tttaaaaaac 22081 atttagcttt taactgactc tagccacttt gaaacacaat ttttttttcc caaggtcact 22141 caaagagcta ataggagaac ccctaagtcc cataattcag ctctgggagc cagcactcac 22201 tctgtacaca catttgcctc tgtccctagc aatatggtgg gcgtgagggt gcagcaagag 22261 gaacaagaaa gaaatgattg cttgcatagt ggcgtcttgt tcatgcagtc attaattcaa 22321 caaatgtttg ttgagaatca gctttgtgcc aagtgctaga gaggttgaga tgattgaagc 22381 atagtccttg acccccaaga gctcaccatg gaatcaactg aagcccctca tcagtactgt 22441 gttgggaata ttgagagtgg agagttgagt ataacttata ggacacctaa tgttaattac 22501 ctttcagaca ctgcaatgtg tgtgtgccat aaaaaaaaaa aaaatccagt agctctgata 22561 cgagggaaag taaatggttt aacaggtgct gagtaggaga agctcaagga gaggaaaccc 22621 caagggctga agaaggtggg agtcaggagt ctcctgaagc aagtggcatt taaggagctc 22681 tataaggaaa gggtcagagt tgtgataggt ggctgtggag ggagatgtgc cacctggatt 22741 ggcatgtaga gggatagaaa gattataggc ctttgcaatg gcccagtaag aggtaatgag 22801 gggctggaac tggaagaaaa cacatttaag acacagtaca gaggtggcag acaaggtggg 22861 acttggcaac tacctgatga gatccaggag atgaggccag gaggcgggca gcaaagatga 22921 cgcaggtttc tagccttaat aggctaggag gagagtgatg ccattagcaa taagaactac 22981 aggagaagga gctgagtttg agggaactat taatttggtt cagaatatgt gctgtttgag 23041 ttatggcagg atatttaagt ggacagactg tcgacatagt tggaaattca gatcttaagc 23101 tcccacacaa ggtagtggct ggacatagta gatttgagtg ctcttgcttc agagggctag 23161 tttaggttgg ggcagtgatt aaagcaacct aggaaataaa ttataaagga agaagaggtc 23221 cttaaaacct tggagactga ttatataaag ggtggatccg ttaatacagt agctattaaa 23281 aaattataag gggtgggaaa aagggacaaa gaagaaaaaa gaggtgaaag acctttgctg 23341 tgtcaccaaa ccctgggagg agaatttttt aaaagaagag tactcaatcc acagtgaact 23401 aaggcatgtt tgttaaacac aattgaccac cacacagcga agacccaaat gaggttcaag 23461 agaaggaatt tttatggacc ctgttagcac aagtcaaggt ccttctccag taccactggg 23521 aagctttgga gaagaaaagg gggacagtgg gccttgggtg gagaagggaa ctgaccatga 23581 gatccaggtg gggtgaggag gtgtgtgaag tcagagtggg gaagaatcag ggtggcttac 23641 tggcagcttc accggggtca tgcgaggagc aggttccacc agagtaagga gtgaagttgt 23701 agaaacacag ggaagtcacc atcagaaaag agcaggagtc aagaaactat ggcccacagg 23761 tacaaactac ctgtttttat aaataaagct tcatggtaaa tgaattgtaa ataaagtttt 23821 gcatattgtg tgaggctgtt tttgtgctac agtggcagag ctgtctggcc ctttatagaa 23881 aaagtttatc agccactgga aaagagttgc aggatttgag gtcttggtgt gatggcctag 23941 gttagagtca tagtgagatt gaaggagtag ctagacaagc caattgtgtg gcagaaaggt 24001 agggatggag atcactgggt taaggatcct tgtagccagg acaccatgag agtgattgac 24061 aagaatgctg aaatccccta agtgtgtcag gatgtggaag agtagaaggc tagagttatg 24121 gaagaaaggg tcccacctct acctgtgcag cctccaggag agtctgagga gggggcggtg 24181 agtgtgagta aatgttgtca gaatccctcc tcccagtcta caagccccag ggaaaggaag 24241 caaggtgttt actgacaccc ccaggcttat aagtacttcc tggctccatc accctccagt 24301 gaacagccct ggggagaaga cagtactggt ttgcaggtgg gtgggtgggg aaaggggtca 24361 caggtgcttg gtgttctggt aaatgtgcat atgagaacat ggggttgctt gtgccctgtc 24421 cgtcagggtt cagaagaacg tgcagtggaa gcagctatgg ggaagtagct agggaaggta 24481 ggactggtct gaggtggtga ggagcagatg ctgccagctc cacacatcca ggagagcctg 24541 ggtggtttgg gcaaaagtct ctggcatccc ttctgagcct gggtaccaca ctgaagagtg 24601 aggacagtgt gccattttta tcaggaaacc ctccagctcc ctgaagacca aattctgatc 24661 ctcctgggat ggcagtgaag agccacagag atgactctga ggtcccgtgg ccttttccca 24721 cctggagatt gttttcgtta ctgcgctgtt acagccttgg aggactgggg ttcagtttca 24781 tccaatcaca tttcttcttt tgtcatagtc atctaaacga tagatcttag agacaggtgg 24841 gcaaggggtg cactggtgag cctgacttaa ggagaggtca tctcgtccct tccctagtcc 24901 catctccctt ggttattgtt atttcatgtg attgttctgg ttatttcagg ttattctgtt 24961 tttgttttca aaacaataac atatatttgt tgttctgatt ttaaaggggt aattgttttg 25021 gtaactagaa aattaccttc tcaactccct taaattctgt caaagggaaa agtaagttag 25081 gttgctggag aggctatgct gaggcctcag aacctctgta ttcctggaag ttctgcgtgc 25141 tttgcctcct gctcccctct ctgtgttcct gttggcaggc ccctaggcag gatttaggag 25201 gtaggcaagt caccctagcc aagtcataag cccatggctc aattgccttc tcagcccttc 25261 aagggctgtt ccacaggcag caaagggagg ggcctccaca ggttcaccac tgcagcccta 25321 attcattttc tttttccact gtcttattct gcaggggtat tccctcagcg gatactacac 25381 ccatccattt caaggctatg agcacagaca gctcaggtac cagcagcctg ggccaggatc 25441 ttcccccagt agtttcctgc ttaagcaaat agaatttctc aaggggcagc tcccagaagc 25501 accggtgatt ggaaagcaga caccgtcact gccaccttcc ctcccaggac tccggccaag 25561 gtttccagta ctacttgcct ccagtaccag aggcaggcaa gtggacatca ggggtgtccc 25621 caggggcgtg catctcggaa gtcaggggct ccagagaggg ttccagcatc cttcaccacg 25681 tggcaggagt ctgccacaga gaggtgttga ttgcctttcc tcacatttcc aggaactgag 25741 tatctaccaa gatcaggaac aaaggatctt aaagttcctg gaagagcttg gggaagggaa 25801 ggccaccaca gcacatgatc tgtctgggaa acttgggact ccgaagaaag aaatcaatcg 25861 agttttatac tccctggcaa agaagggcaa gctacagaaa gaggcaggaa cacccccttt 25921 gtggaaaatc gcggtctcca ctcaggcttg gaaccagcac agcggagtgg taagaccaga 25981 cggtcatagc caaggagccc caaactcaga cccgagtttg gaaccggaag acagaaactc 26041 cacatctgtc tcagaagatc ttcttgagcc ttttattgca gtctcagctc aggcttggaa 26101 ccagcacagc ggagtggtaa gaccagacag tcatagccaa ggatccccaa actcagaccc 26161 aggtttggaa cctgaagaca gcaactccac atctgccttg gaagatcctc ttgagttttt 26221 agacatggcc gagatcaagg agaaaatctg cgactatctc ttcaatgtgt ctgactcctc 26281 tgccctgaat ttggctaaaa atattggcct taccaaggcc cgagatataa atgctgtgct 26341 aattgacatg gaaaggcagg gggatgtcta tagacaaggg acaacccctc ccatatggca 26401 tttgacagac aagaagcgag agaggatgca aatcaagaga aatacgaaca gtgttcctga 26461 aaccgctcca gctgcaatcc ctgagaccaa aagaaacgca gagttcctca cctgtaatat 26521 acccacatca aatgcctcaa ataacatggt aaccacagaa aaagtggaga atgggcagga 26581 acctgtcata aagttagaaa acaggcaaga ggccagacca gaaccagcaa gactgaaacc 26641 acctgttcat tacaatggcc cctcaaaagc agggtatgtt gactttgaaa atggccagtg 26701 ggccacagat gacatcccag atgacttgaa tagtatccgc gcagcaccag gtgagtttcg 26761 agccatcatg gagatgccct ccttctacag tcatggcttg ccacggtgtt caccctacaa 26821 gaaactgaca gagtgccagc tgaagaaccc catcagcggg ctgttagaat atgcccagtt 26881 cgctagtcaa acctgtgagt tcaacatgat agagcagagt ggaccacccc atgaacctcg 26941 gtaagagacc acccaggaac tgtacctagg gttggggtca ggtgcttttg ctcctgacgc 27001 agtcttggct gatttgtgag cagtgctgtt tggtggcgcc tatcttttcc tccttccctt 27061 ctgcctttta gctaaattcc ccttgattgg ccctttctcc agatattgag cagggaatat 27121 agaccttgga ccagccagaa tcttggctga acaaggggga ggttgactct gttggctgta 27181 atgaagcttc tttagaaatg attggttttg gccgtacgcg gtggctcatg cctgtaatcc 27241 cagcactttt tgaggccgag gcaggcatat cacgaggtca ggagtttgag accagcctgg 27301 ccaacatggt gaaaccctgt ctctactaaa aatacaaaaa ttagctgggc gtggtggcgt 27361 gcacctgtag tcccagctac tcaggaagct gagacaggag aatcacttga acccaggagg 27421 cagaggttgc agtgaactga gattgcgcca ctgcactcca gcctgggcca cagagcaaga 27481 ctccatctca aaaaaaaaaa agaaagaaat gattggtctt gggggccggg gcggtggctt 27541 acgactgtaa tcccagcact ttgggaggcc aaggcaggca gatcatgagg tgaggaattc 27601 gagaccagcc tggccaacat ggtgaaaccc catctctact aaaaatacaa aaattagctg 27661 ggggtggtgg tgcttgcctg taatcccagc tactcgggag gctgaggcag gagaatcact 27721 tgaacccagg aggtggaggt tgtagtgagc cgagattggc gccactgcac tccagcctgg 27781 gcgacagagt gagactccat cttggaaaaa gaaagaaaaa agaaaaacat gattgatctc 27841 catgcatcaa tatcatgcct gcctcctaag gcagaggtaa tgaagactta attcccttct 27901 gtaggccttc ccctcctccc taagccgttt tctgagagag gtgcaggagc aggtgggttg 27961 gggcaggctg catacacagt gggggtgggt tgtgctgcta agcagcagca ggtccacaat 28021 cccccctctg catagctcct ggggggaaag gatggaggag cgtgtgcacg gctgcctgcc 28081 tgttgaaggt ggtggttcta attttataaa cctcctctgc acagatgggt aggctagcac 28141 ttgctgccac tcctgagctg tgaagtcagc ctttacctca ctcagatagc tggtcaggcc 28201 ctgcactgta ggtcctaata ggccagtgga cagattgagg aaaacaggag cttctgaagg 28261 gcataacaga gagcaaaacc actgaagctg agtggctgca gctgcagcca gggaaagagc 28321 cagtaggatg ggggagaatt ccactgacct ttatgtttac ctagcctggt ttctaggggt 28381 gtagattcct ggctagggcc cttattcctt gtcttgactg tcttcatgac accaatttgg 28441 catttcagga gagcggttaa gaaaaggagt tgtgtctgtc caaaagctgg caaggccaga 28501 gctggattgt ttggggtaga gactggatgg ccgtcattct cttttgcctc catccctcct 28561 ccccagagtt ggaggaaagc agtggatttt gtggttagtc attctttgga ctcacactaa 28621 aagaaacatt ggtgccatgt tcaaatatat cagaagacct aggaaataag aaatttgacc 28681 tacttttcta aatgaaatcc cagactgagc aaagagctca ccacatttga aagcttgaac 28741 aaagggggcc taggctaagt ccagaggcct agaacaaatg cttttttatt ttctacataa 28801 caaggggaaa ttccttgtta tgtagaaaat agctggagac aaatggtgct atagagtgac 28861 tcataacaaa ctacggtgat ataggtctag ggacaaaagc aggccactga taagtggcag 28921 atgcctgatc cccctaggta gtggggagtg tgagactggg ttataagaag ccttcactat 28981 cttttaggac cctcccttga ggaggccagt ctaccacaat tgctttagaa tgaaggtctt 29041 ttggttgctc acaagactat aatggtaatt tttggctcat catttttgtg tgtgtgggtt 29101 ttatcttaat tcattgttaa agagatagtg ggtttcccct gagctagttt cctatcatct 29161 gtgcctatgt ttgcttcact gagctatggg gaaagagtca ctggctgctt tgtttacaaa 29221 aagaaaggac aggctgagcc ttaaggagta ggaaggagtt ccttggccta cccttcatct 29281 ccacaagtga aaagcccctt agcgtagcag aaaattccag gttgaaggtc tctttggaga 29341 aggcagaagg agtgacctag actcctgttc acacatctaa tcactttccg tcaagattta 29401 aattccaggt tgtcatcaat ggccgagagt ttcccccagc tgaagctgga agcaagaaag 29461 tggccaagca ggatgcagct atgaaagcca tgacaattct gctagaggaa gccaaagcca 29521 aggacagtgg aaaatcagaa gaatcatccc actattccac agagaaagaa tcagagaagg 29581 taggtgtcct cctgccatct gggaggatca gttccctgtc agtgtctgga ttgtaactga 29641 ctcccttgag gcaatcccag cctaaacaac tgacaccatc tcggagtcag cttcccactc 29701 ttccctctac cctatctcgc cagcccacct ttcctcctct catacccagc tcctctgtct 29761 gctcctgtcc caacataatt ggatttacag aatttcggac ttgaaagaga cctgaaagtt 29821 tattgaggcc aatctcctct cttggaagat gcggaatgag agctccagca gcccctttaa 29881 ctttgggaag ccaacccctt gacaggtggt gggaataaag tcccccatcc ccatcccttc 29941 ttctgtgatg gactaaccag tgttttctta gttttgtttt cttcttgtct ctcattttct 30001 ctagactgca gagtcccaga cccccacccc ttcagccaca tccttctttt ctgggaagag 30061 ccccgtcacc acactgcttg agtgtatgca caaattgggg aactcctgcg aattccgtct 30121 cctgtccaaa gaaggccctg cccatgaacc caagtatgtc ctacgtgtcc tctgtccagc 30181 tgaggttttc tcagaaagaa aaagagacac attttcttcc ttgcctcctc agggatggca 30241 gattgaccaa tttctcctgt ttcaaaatgg ggaaaggagg gctctgaggt cctggttgct 30301 gcttgtgagg cagacaatta gggattagga attcaaaggg aattcctggc ccaccctcta 30361 tctcctctat aagcactagg gaggttcacg gcttggaggt cactcactgt tggtgggaca 30421 gaaaggtaca ggacctgaga agctctctgc ctgtgggtct atagactcac atgttcaaga 30481 gaagtgttcc tggaagaggt gaaactaggt tgatgcttaa atgttgaaag gggtcagcca 30541 ggctaagaga cactggctgt tcaaggcaga agtgactgca tgagatgtga ctgcacagag 30601 gtgatgtgtt caaggaaatt accagtagtg gaggatggca gcctggcaga ggctaggtca 30661 ggctcctcag tcaaaaccat tttaatcctt ctacgtgctt catctcctgt caggttccaa 30721 tactgtgttg cagtgggagc ccaaactttc cccagtgtga gtgctcccag caagaaagtg 30781 gcaaagcaga tggccgcaga ggaagccatg aaggccctgc atggggaggc gaccaactcc 30841 atggcttctg ataaccaggt agggcgtttt cctactcaaa agatacaggt catttttagc 30901 aactgagtgg tttaagattg ccagtgactc cctcaacatt tcctgaagtg tttatggctc 30961 ctctgtttga tggattctcc tttagcctga aggtatgatc tcagagtcac ttgataactt 31021 ggaatccatg atgcccaaca aggtcaggaa gattggcgag ctcgtgagat acctgaacac 31081 caaccctgtg ggtggccttt tggagtacgc ccgctcccat ggctttgctg ctgaattcaa 31141 gttggtcgac cagtccggac ctcctcacga gcccaagtga gtgtcctagt cctggctaat 31201 gcatgtgtca ccagttgggg atggtctgta acccagggaa aacaagggtg tgctttagct 31261 gtgtaggaca gaaggggcga gttgagggaa acaagtccag ccctgtctcc acggcctctt 31321 agaagacaat agacctgcca agagtgaatg cgttcactct tccagtaagc atgatccttt 31381 ttaatttttt gactagtttt aatttttaaa gaaatgtata ggtacattaa aaaatcattc 31441 aggccagaca tggtggctca cgcctgtaat cccagcactt tgggaagttg aggcaggtag 31501 attacctgag gtcgggagtt caagaccagc cggaccatat gaggaaaccc tgtctctact 31561 aaaaatacaa aaattagctg ggcgtggcag cgggtgcctg taatcccagc tactcgggag 31621 gcagacagga gaattgattg aagctgggag gcggaggttg cagtgagctg agatcgcacc 31681 actgcactcc agcctgagca acagagcaag actccatctt gaaaaaaatc attcaagctg 31741 attgaaaaag tagtcatttc aatgaaaagt ctcatttccg tctcagactt ctagtttccc 31801 tccctagacc catatattac tatagccctg cattagcaac tgggatgcgg tctgagaagc 31861 atggttttgt tgttgtgaga acatcagtgt gtatttacat aaacctagat ggcatgggct 31921 cctacacacg tacaggctgt atggtatggc cggttgctcc taggctacaa acctgtacag 31981 catgtaactg tagtgaatac tgtgggcagc tgcaacacac tggtaagtat tggtgtctat 32041 ctaaacagca aaaagataca gtaaaaagac agcataaagg attaaaaaaa tactacacct 32101 gtatagggcg cctgccatga atggagcttg caggactaga agttgctgtg ggtgagtcag 32161 ccagtgagtg gagaatgaat atgagggcct aggacatgac tgtacactaa tgtaggcttt 32221 gtaaacactg ttcacttagg ctaactacat ttatttaaaa tatttttctt taataaatta 32281 accttagctt actgtaactt ttttacttta tttttacttt attttttact ttattaactt 32341 ttttattttt tgttcctttt gtaataatac ttagcttaaa acacaaacat gttgtactgc 32401 tatccaaaaa tatttccttt gtttatatcc ttaattctat agtctttttt ctgtttgtaa 32461 atttttttat ttttttaact ttttaaactt ttttgttgaa agctaagatg aaaatacatt 32521 agctgttagc ctaggcctac acagggtcag gatcctcagt atcactgtct tccacctcca 32581 cgtcttgtcc cactgtaagg tgttcagggg caataacatg catgggggcc gtcatctcct 32641 atggtaacag tgctttctgg aatacctgcc tgaggctttt tttagttact tatttttcta 32701 gaagtagaag gagtatacgc tgaaataatg ataaaaatat agtaaacaca taaggagcgt 32761 gtagcctaga tccctcgcat tcacagttca cagtcgagtt cacactccta caagaatctc 32821 atgctgctgc tgatcccaca ggaggcggag ctcggaccag aatgctttct tgctcgccac 32881 tcacctcttc ctgtgtgccc aggttcctaa caggttacag agccctgcac ttggtgataa 32941 gaatttttca gctccatcat aatcttacgg ggcccctgtc atatgtgtga tttatcattg 33001 aacaaaacac tgttatgcag tacatgacta taccagtttc ttgagtcctt ctagaaattg 33061 ctgtgcataa ctagcacatt ttcccttttg tctttttaaa caagtatatc ttctgtttta 33121 tacgttgact cctttactta ccagacttct tgcatagctg catagtattt cattgaatag 33181 aagctgacaa attcagtttc tcagaagtaa acatttaata gggacttagg aacagaaatg 33241 atgtcttggg tggctgcaag atggtggatc cctgcactta ccctccagaa agtatgcttt 33301 ctatagaggc ttttttggtt aaacatgcag ctggtcacac attatacttt cttgtgaaac 33361 ttatgagcac tagctggtgg ggaggcttgg tagacatctt tgtgtggaat tatttatgct 33421 acccaacact ttgggatgcg ggagtcagat attggtggtc atagtggttt tgcatcaaga 33481 tggcatcact cttgccatgc aaccggcatg ttttcttaat ctctaaggtc tatcacaaag 33541 tggaaaagca aggtgtaaag tgaggggaga ggtgaagatt gtctgtatat gtctagaata 33601 ttttcttgaa ggatcgaaaa aactggcaac tgtgtttgct tctggggaag gagggacact 33661 tttattgtac actcttaact gtttgaattt tcacatgttt ggcatccaac ttgtccattt 33721 taaagtcatt aaggaaaaaa gcttataaaa atgctatctt gttactttaa atttgtctct 33781 ccttaataga agtaatgtca gccgggcgca gtggcttacg cctataatcc cagcactttg 33841 ggaggccgag gtgggtggat catttgagct cagtaatttg agaccagcct ggccaacatg 33901 gtaaaacccc atctctacta aaaatacaaa aaatagctga gcatggtggt atgcccctgt 33961 atgccagcta ctccggaggc tgagcaggag aattacttga acccaggagg cggaagttgc 34021 agtgacctga gattgtgcca ctgcactcca gcctgggtga tggagtgaga ctccgtctca 34081 aaaaaaaaaa caaaaaaatc agaagtaatg gcatttcatt tattcatatt tatgtgttat 34141 ttgcatttcc ttttctgtga accacctgtt cttgtccttt tccagttttc tttcagattg 34201 ttactctcat ggatatgtaa gaacttttaa cataattttt aaaagtagcc ctttgcccaa 34261 catgacccaa tttagaacac acatctgccc actgtttaag ccatctggaa aaggagaggc 34321 ccagtctccc tccagctgct cttctactaa ttcatatcct tcatctcaat aagcacctcc 34381 ttatctttaa gcacagtcct tcagatgata ggttcagtgc atttcctctt tctcttctgt 34441 gaaatcttct gtgaaatcct ttctaggact tcaagtcagc cattcattga gaatgtaaga 34501 acttactatg aactagatgg aagatacaaa aaattgctgc ccctgagtgt gtagcagaca 34561 tatagccata gcagtattga aatgtgccat tggaggtgaa tgcagagtgc tgtggggaca 34621 cagaggacac tgctgccact gtctgccagg gagctgagga aggttgcata gagaggggaa 34681 atgctaattg agtaactacg tttattaact atctcgtaca ataatatact ttagttgctt 34741 cttaatgtga attatgctgg gtcttttttt cctttctgtc tactgtggct ggtgacgtta 34801 actaatttta tgacttcttt tctgtttttt tttttttttt tttttggaga tggagtctca 34861 ctctgtcacc caggctggag tgcagtggcg cagtctcagc tcactgcaac ctccgcctcc 34921 tgggttcaaa caattctctt gcctcagctc ctcgagtagc tgggattaca ggcatctgcc 34981 accacatctg actatttttg tatttttagt agagacagag tttcaccatg ttggccaggc 35041 tggtcttcaa ctcctgacct cagatgatcc acccgcctca gcctcccaaa gtgctgggat 35101 tacaggcatg aaccaccgcg acagccatga cctttaatat ctaaatgctg gagaccactc 35161 agagctcccg attcctccat ctagttgctt acttgtcacc tctgtttgga ttaacatccc 35221 taatatgaca tgtccaaagc agaactcttg ggttttgccc ccttcgcttc atttccccca 35281 agtctttccc agcttagtaa gtgataccac tgtctaccca gtggctcaag tcagaaacct 35341 gaggatcatc ttttcctcta tctcctttac ctccttcgtc aactcatcct taagtcctat 35401 tggttatact tagaatttct atcccaaatc ccttcctctt ctttccacct ccagcgtcag 35461 cactctaatc caagccactg tctcatctag actgtcacaa tagcctccta actgatcttt 35521 atactttatt tactcaacac ttatttatgg agtatcttct atttttttta gaacaggaac 35581 caaacattaa ccaatagtca cctaaagaaa tgtaagatct catatttgat aagtattcca 35641 aagggctgga gttgcagcga gaatcaatta tagcacagtt tgacttagga aggagagggg 35701 gaagggcttc cccaagaagt actgcctgag ctgagacttt aaggatgatg aagagagaaa 35761 gactgagggt tctaggcgaa ggacactgtt aaatcctgtg gtgggagaag cgcagagctg 35821 gcaaagaggc tgagaggagg cacttatggc aatagcccca tttggctagt ggctaccata 35881 ttggatagca cagctctaaa ggattctagt tgcataatta acaaacttta tcatatatgt 35941 aaatatatca gtataaaact ttgcacgtaa gagttcatat tcttttcaaa cacatggggc 36001 agtcatgaaa ttctcctgga tccctgaggt aaagatacta cacaatctgt ccctcctgac 36061 cgccttcacc atcttctttt catgccactg tccctctcat tctgaactta agcccactgg 36121 cctgcacggg cctgccagca tggacaaaga aaagagtgaa ggcatttagt tgcttcggat 36181 catcaaggaa cagtgagaaa ctccatgtgg ttgaacataa acgttgattc cttttactgc 36241 ctgagctgct aagtcttgaa actgaagcct ctgttatatg cagttagagt atccaaagct 36301 gggttctcag ccagtagatt aggatctggt tgaaagctag gattcttgat gccttgtctg 36361 gtacatttcc aagctgtttt gctccaccat gctcttccct ctgtgtttgg aaattaccag 36421 ccggagcggt agaagccacc tccctgctcc acttgggcac tttattgtca gcgcagctca 36481 tgcgcccaag atccattcct taccccagag ttagcttaag cctgccagga gtcaaaaaaa 36541 caactcccag caaaacctgg gtccctggcc taaggccgac cttgacctaa tgacctctcc 36601 aggtcaagtc cccttgagct aataggaagt aaatgaggga atggagttgg gcgctttaaa 36661 aatcagacag tgtatgaagt aacagtgact tgtggggaga aaggtagtcc cttctgattt 36721 ctgcttaaga agagagtcca agttggtgct agcatttcgt taagccttcc tcatacttca 36781 taatcttcct ttatagtaag gacaggctca gagcctttgc aggtaacagt atctagtcag 36841 aattttataa catgatttta tcatattctg ttttacagcc accttcaata tgtggcaagt 36901 gatactggtt ttccatttac agtagtgaaa caaagtttcc tatttcagtg tgtttacatt 36961 tttatctctt ttttcatacc tagtattacg gatatttaca tttttagagt ctgtttgttt 37021 attttagaga tggggatctt gctgtctcgc gcaggctgga gtgcagtgat atggtcatag 37081 ctcactgcag ccttgacctc cagggctcaa gtgatcctct caccccagcc tcccaagtag 37141 ctgagactat aggcacagac caccgtgccc agctaaattt tttttttttt ttttaagaga 37201 caggggtctc gctatgttgc ctgggggatt actatgttgc ccaggctggt cttgaactcc 37261 tggcctcaag tgatctccca ccttagctcc tcaagttgct gggattacag gtgtgagcca 37321 caatggctgg ctctaagaag tcaatttaga gaaaaatatt aattaatagt ccaagtaata 37381 cctggatgtg gcacaaatca tgtggtgatt catgaatgac caaaatctag gaaatgctgc 37441 cttagaaaca gcttctgttt gacgggtcca tatgtttgca agactggcca catcttcagc 37501 aaaactaacc cttccttgga acaatgtcag ggtctggcac ttgtcttcat tctctgtttc 37561 tcatcccaaa ggttcgttta ccaagcaaaa gttgggggtc gctggttccc agccgtctgc 37621 gcacacagca agaagcaagg caagcaggaa gcagcagatg cggctctccg tgtcttgatt 37681 ggggagaacg agaaggcaga acgcatgggt ttcacagagg taaccccagt gacaggggcc 37741 agtctcagaa gaactatgct cctcctctca aggtccccag aagcacagcc aaagacagtt 37801 aagacgtcta cttttggtgc cttttttggg gcgggggggt cctcctaact cctaagtgga 37861 ggtggctctt gctgtcatgc gagttattcc taggctttac tcttagcctc gagagagcag 37921 taactgggac actagatgta agaaggaaaa gatgactcac acgacaagta gagcttgatc 37981 tccctgccca cggtgaatat ggtggacaca gcctcagctt tgtggtgctg acacagcctc 38041 ttttccccac agctccctct cactggcagc accttccatg accagatagc catgctgagc 38101 caccggtgct tcaacactct gactaacagc ttccagccct ccttgctcgg ccgcaagatt 38161 ctggccgcca tcattatgaa aaaagactct gaggacatgg gtgtcgtcgt cagcttggga 38221 acaggtgagt gaggctctga gacatgccgc ctcccatggc gcctgaaagc gggtgcctct 38281 catcctcccc tggagtccat gcatgtaagt ccaaggcagg gagaagagac ttcattttag 38341 ctacagtcaa ttcagagtga ggaatgagtt cttagttcct agaggagaga atatgggagt 38401 ctaggatctg agaaactgag gctgtttctg ccttgaagct ttcagaacaa atagccttca 38461 tcctgttttc catcggtttc cttccattat tctatttctg ttttaaacac cttcctaggg 38521 aatcgctgtg tgaaaggaga ttctctcagc ctaaaaggag aaactgtcaa tgactgccat 38581 gcagaaataa tctcccggag aggcttcatc aggtgagcga ggtcagagct gtggcccggc 38641 tgcccggctg tggagagctc cagttccctg ccccacatgg ctctgacacg gcctctgaat 38701 ccccctcaga cagacgggtc atgatgtggc agtggcagcc tttgcttttc acccgtccat 38761 ttgaacctgt ctgatggaat ccatcccctc tgtgagctga gctgcctccc actgctcggc 38821 ctgtttttaa atgctgtcct tttttctgct aactctgctg cttcatgttc ttttctaaaa 38881 acacaaaatg accttttagt cctcagggcc ttgaggatga ggcagctttc catttccgtt 38941 tgaggaccta cacaaccttg atgcccctgc cagctttctc ctctagctca ccttttcttt 39001 aatttatgaa gggagagact tagaaaggag caacagcttc ctgtagtcct tgaatcagtt 39061 tgctctgctc tagaatccct gtagccgcca tagcgaggag ccctcagcag aaatgaagga 39121 gacccaaaag gctaactatg ctttatgaaa tgctgaggtc tcccctggag aatttccacc 39181 tgataaactg tgaaacgtct gcaacattga gacttttcct tactttctca tttggaggtc 39241 agattataga aacaactgct tttcccagaa ttgaacctgc cttcctaacc agactttctt 39301 tttgtaggtt tctctacagt gagttaatga aatacaactc ccagactgcg aaggatagta 39361 tatttgaacc tgctaaggga ggagaaaagc tccaaataaa aaagactgtg tcattccatc 39421 tgtatatcag gtctgtacag ttcctgttgc tgccagggtg ggccctgcca ggctgttaga 39481 attgggtatc caaatgctct cctggcctgt aaatcgaacc tgatacaata agccacactc 39541 cactgtgggt ttgaggtcca tattcaggtg tagatgactc acatgtactg ctgtccacct 39601 ccagtctccc atggtaggcc ttagaaaaca tcccttgctt ctgtcacatc tgactgtttt 39661 ggagccccac gaaattgcag atttcccaca ggtgagtttt aacagccacc cctgtttttc 39721 agcactgctc cgtgtggaga tggcgccctc tttgacaagt cctgcagcga ccgtgctatg 39781 gaaagcacag aatcccgcca ctaccctgtc ttcgagaatc ccaaacaagg aaagctccgc 39841 accaaggtgg agaacggtga gtgatacatg cccccgcctc ctttcctcaa aaggctctgc 39901 aaggtccagg gaccccaagt ctctacaagg ctgctaggat tttaccatta gtcactgggc 39961 acagaggtgc tgtttacagg aaagggaaga cctgggtcag ggagctgtgt ggtaagatca 40021 gggttctatt ttgaatgtgt tagtttggga gatctgggag atccccaagt caaataggag 40081 gtgggggttc ccatgtggag ctcagaggag ggagcttggc tggaaataga aatatgggag 40141 tcatccccct atagggtctt catggccatg agaatgcata ggattacctc aagaaagcgg 40201 ggaggaaatg aagagtgcgg cacaaccaag ccctgaggag ttgacagatg aggatgccaa 40261 atgctggggt cccctcctgt ctagctggca gttgactctg ccttgtccac tggctccttc 40321 tctcctatcc tctcctgtct ccttactgtc tcttcgcatc cactccattg cgttcaggcc 40381 acgtcagcag tcatcatggt ggtcctgaaa ccttgctaaa taccctaaag tatagacaca 40441 gttaccatgg agccggtgct ccactcctag gtatatgctg cagagagatg gagatctgtg 40501 tccacacgga aactaatatg tgaatgttca tggcagcatt actcacaaga gccaaaaaag 40561 tggaaacaac ccagacgtcc atcagctgat ggattcataa ataaaacatc aaatatatcc 40621 ataaattgaa tattattttg gccataaaaa gaagtgaagt gctgatacat gcttacaata 40681 tggatgcact tgaaaacttg atgccaaatg aaaaaagcca gtcacaaaag atcacatatt 40741 gtatgattcc atttatatga aatgtccaga atagacaaat ccatagagac agaaagtaga 40801 tgagtggttg ccagggccag gagtgggaga gttggagaga tgaggagtga ctgcgccaat 40861 gggtagaagg tttctttttg gagcgatgaa atgttctaaa attgactgtg gtgacagttg 40921 cagaactctg tgaatatact aaaaatgact gaattgtatg ctttaaatgg gtgaactgta 40981 tggcatatga actatatctc agtaaagcat ttttttttgt ttttttttaa acccgatagt 41041 ggtttcccac tgcactgcat atacaagcaa aacctgctgt gatcacccgg cctcctctca 41101 tgccactttc cccatccctc gcatatgctc tgtccacact ggctctctgt caggcgcctg 41161 aacagccaat ccgctggctg ccttggggcc tttgcttttg tcctgtgtgc ctgaaacact 41221 tactccagct gtcctcctcc atgtctgggc tcccctgctg ctgctgtccc aggaggtgtc 41281 ccctgtggtc ctccgtcata gctgcctcag agccttcaga gcactgtcag catctggaat 41341 tcttccgtat gtactggcta ctggtttagt gtctattctc ttccctttca atctcctcac 41401 caccatagat gttttaagag cacaaagatc ttacttggtt ttgctcaccg ttctttccca 41461 gcaccaagca tagtgcctgg cgcatagcag gggctgtgaa atatgtgaag aatgaatgaa 41521 tgtagcctgt ggcccaagct taaggaggat agaaaccacg ccagggagtg gtttggtcca 41581 ttggcgcctg tgggtctgac ccaagtctct cacacaggag aaggcacaat ccctgtggaa 41641 tccagtgaca ttgtgcctac gtgggatggc attcggctcg gggagagact ccgtaccatg 41701 tcctgtagtg acaaaatcct acgctggaac gtgctgggcc tgcaaggggc actgttgacc 41761 cacttcctgc agcccattta tctcaaatct gtcacattgg gtaaggggcc tgccttggga 41821 tctggaactg gtctgtcctt cttgtgccca gatcccaaac tgcatgcttt attgccaggt 41881 gttttgtctc ccttatcaaa gtgagcatga ttcactcctc agtaattgat tgagtgtcca 41941 gtctgctgtg gtaggaagat cctggtagcc ccagtcagaa ggtgcttcct aacaaggcag 42001 ctgtttctct ttcttgacaa ctatatcttg tacctccaaa atccccacat gcttctgcct 42061 cttaacagca tttggtgcaa acacaggtat atatgtttct cttttttgta ctcaggttac 42121 cttttcagcc aagggcatct gacccgtgct atttgctgtc gtgtgacaag agatgggagt 42181 gcatttgagg atggactacg acatcccttt attgtcaacc accccaaggt gctataaccc 42241 ccttctattt tccctgacat tttcctcctt ttcaagcagt catgtaaaca gaggaaaaat 42301 gtacactgtg ggcaagggga acattgccca cagtggtagc ccacaaggga acattgccca 42361 cagtggccca ccaccaacat tggttggtct cccaagaact taaactttct tccttttgga 42421 tgccaagggc ttttcttctc ttagtctgga attaatctga atcgaggtgg agttagtatg 42481 tctagagggt gctcagtctt agccaaacag aaccctaaat acaggggaaa gatcatgacc 42541 ccacacttcc tctctcctat gagtcttgag tccctgcttc agaatcttat tcctgaaagg 42601 tttccatctt tctcccgttg cttctgggat tcctaggttg gcagagtcag catatatgat 42661 tccaaaaggc aatccgggaa gactaaggag acaagcgtca actggtgtct ggctgatggc 42721 tatgacctgg agatcctgga cggtaccaga ggcactgtgg atgggtaagg agacaggaga 42781 gcgcagtgag gaccaagcct ctgccctgac ttgcaagggt gcatcatacc tctgcagtct 42841 cagggcttga gagccgcctc ccctcccacg gtgtctccac tgtgagctcc ttatcttaca 42901 ggtcccaggt gaataatgag tgcttttgtt tctctaggcc acggaatgaa ttgtcccggg 42961 tctccaaaaa gaacattttt cttctattta agaagctctg ctccttccgt taccgcaggg 43021 atctactgag actctcctat ggtgaggcca agaaagctgc ccgtgactac gagacggcca 43081 agaactactt caaaaaaggc ctgaaggata tgggctatgg gaactggatt agcaaacccc 43141 aggaggaaaa gaacttttat ctctgcccag tatagtatgc tccagtgaca gatggattag 43201 ggtgtgtcat actagggtgt gagagaggta ggtcgtagca ttcctcatca catggtcagg 43261 ggattttttt ttctcctttt tttttctttt taagccataa ttggtgatac tgaaaacttt 43321 gggttcccat ttatcctgct ttctttggga ttgctaggca aggtctggcc aggcccccct 43381 tttttccccc aagtgaagag gcagaaacct aagaagttat cttttctttc tacccaaagc 43441 atacatagtc actgagcacc tgcggtccat ttcctcttaa aagttttgtt ttgatttgtt 43501 tccatttcct ttccctttgt gtttgctaca ctgacctctt gcggtcttga ttaggtttca 43561 gtcaactctg gatcatgtca gggactgata atttcatttg tggattacgc agacccctct 43621 acttcccctc tttcccttct gagattcttt ccttgtgatc tgaatgtctc cttttccccc 43681 tcagagggca aagaggtgaa cataaaggat ttggtgaaac atttgtaagg gtaggagttg 43741 aaaactgcag ttcccagtgc cacggaagtg tgattggagc ctgcagataa tgcccagcca 43801 tcctcccatc ctgcacttta gccagctgca gggcgggcaa ggcaaggaaa gctgcttccc 43861 tggaagtgta tcactttctc cggcagctgg gaagtctaga accagccaga ctgggttaag 43921 ggagctgctc aagcaatagc agaggtttca cccggcagga tgacacagac cacttcccag 43981 ggagcacggg catgccttgg aatattgcca agcttccagc tgcctcttct cctaaagcat 44041 tcctaggaat attttccccg ccaatgctgg gcgtacaccc tagccaacgg gacaaatcct 44101 agagggtata aaatcatctc tgctcagata atcatgactt agcaagaata agggcaaaaa 44161 atcctgttgg cttaacgtca ctgttccacc cggtgtaata tctctcatga cagtgacacc 44221 aagggaagtt gactaagtca catgtaaatt aggagtgttt taaagaatgc catagatgtt 44281 gattcttaac tgctacagat aacctgtaat tgagcagatt taaaattcag gcatactttt 44341 ccatttatcc aagtgctttc atttttccag atggcttcag aagtaggctc gtgggcaggg 44401 cgcagacctg atctttatag ggttgacata gaaagcagta gttgtgggtg aaagggcagg 44461 ttgtcttcaa actctgtgag gtagaatcct ttgtctatac ctccatgaac attgactcgt 44521 gtgttcagag cctttggcct ctctgtggag tctggctctc tggctcctgt gcattctttg 44581 aatagtcact cgtaaaaact gtcagtgctt gaaactgttt cctttactca tgttgaaggg 44641 actttgttgg cttttagagt gttggtcatg actccaagag cagagcaggg aagagcccaa 44701 gcatagactt ggtgccgtgg tgatggctgc agtccagttt tgtgatgctg cttttacgtg 44761 tccctcgata acagtcagct agacacactc aggaggacta ctgaggctct gcgaccttca 44821 ggagctgagc ctgcctctct cctttagatg acagaccttc atctgggaac gtgctgagcc 44881 agcaccctca gatgatttcc ctccaaactg ctgactaggt catcctctgt ctggtagaga 44941 cattcacatc tttgctttta ttctatgctc tctgtacttt tgaccaaaaa ttgaccaaag 45001 taagaaaatg caagttctaa aaatagacta aggatgcctt tgcagaacac caaagcatcc 45061 caaggaactg gtagggaagt ggcgcctgtc tcctggagtg gaagaggcct gctccctggc 45121 tctgggtctg ctgggggcac agtaaatcag tcttggcacc cacatccagg gcagagaggt 45181 ctgtggttct cagcatcaga aggcagcgca gcccctctcc tcttcaggct acagggttgt 45241 cacctgctga gtcctcaggt tgtttggcct ctctggtcca tcttgggcat taggttctcc 45301 agcagagctc tggccagctg cctcttcttt aactgggaac acaggctctc acaagatcag 45361 aacccccact cacccccaag atcttatcta gcaagcctgt agtattcagt ttctgttgta 45421 ggaagagagc gaggcatccc tgaattccac gcatctgctg gaaacgagcc gtgtcagatc 45481 gcacatccct gcgcccccat gcccctctga gtcacacagg acagaggagg cagagcttct 45541 gcccactgtt atcttcactt tctttgtcca gtcttttgtt tttaataagc agtgaccctc 45601 cctactcttc tttttaatga tttttgtagt tgatttgtct gaactgtggc tactgtgcat 45661 tccttgaata atcacttgta aaaattgtca gtgcttgaag ctgtttcctt tactcacatt 45721 gaagggactt cgttggtttt ttggagtctt ggttgtgact ccaagagcag agtgaggaag 45781 acccccaagc atagactcgg gtactgtgat gatggctgca gtccagtttt atgattctgc 45841 ttttatgtgt cccttgataa cagtgactta acaatataca ttcctcataa ataaaaaaaa 45901 aacaagaatc tgaattctta gaaa (SEQ ID NO: 1)
In another embodiment, antibodies used to practice this invention are designed to bind to, or affinity matured to bind to, a polypeptide encoded by SEQ ID NO:2, or subsequences thereof:
1 gaccagacca ttgattcccg actgaaggta gagaaggcta cgtggtgggg gagggtgggg 61 ggagggtcgc ggccgcactg gcagcctccg ggtgtccggc cgtgtcccga ggaagtgcaa 121 gacccggggt attccctcag cggatactac acccatccat ttcaaggcta tgagcacaga 181 cagctcaggt accagcagcc tgggccagga tcttccccca gtagtttcct gcttaagcaa 241 atagaatttc tcaaggggca gctcccagaa gcaccggtga ttggaaagca gacaccgtca 301 ctgccacctt ccctcccagg actccggcca aggtttccag tactacttgc ctccagtacc 361 agaggcaggc aagtggacat caggggtgtc cccaggggcg tgcatctcgg aagtcagggg 421 ctccagagag ggttccagca tccttcacca cgtggcagga gtctgccaca gagaggtgtt 481 gattgccttt cctcacattt ccaggaactg agtatctacc aagatcagga acaaaggatc 541 ttaaagttcc tggaagagct tggggaaggg aaggccacca cagcacatga tctgtctggg 601 aaacttggga ctccgaagaa agaaatcaat cgagttttat actccctggc aaagaagggc 661 aagctacaga aagaggcagg aacaccccct ttgtggaaaa tcgcggtctc cactcaggct 721 tggaaccagc acagcggagt ggtaagacca gacggtcata gccaaggagc cccaaactca 781 gacccgagtt tggaaccgga agacagaaac tccacatctg tctcagaaga tcttcttgag 841 ccttttattg cagtctcagc tcaggcttgg aaccagcaca gcggagtggt aagaccagac 901 agtcatagcc aaggatcccc aaactcagac ccaggtttgg aacctgaaga cagcaactcc 961 acatctgcct tggaagatcc tcttgagttt ttagacatgg ccgagatcaa ggagaaaatc
1021 tgcgactatc tcttcaatgt gtctgactcc tctgccctga atttggctaa aaatattggc
1081 cttaccaagg cccgagatat aaatgctgtg ctaattgaca tggaaaggca gggggatgtc
1141 tatagacaag ggacaacccc tcccatatgg catttgacag acaagaagcg agagaggatg
1201 caaatcaaga gaaatacgaa cagtgttcct gaaaccgctc cagctgcaat ccctgagacc
1261 aaaagaaacg cagagttcct cacctgtaat atacccacat caaatgcctc aaataacatg
1321 gtaaccacag aaaaagtgga gaatgggcag gaacctgtca taaagttaga aaacaggcaa
1381 gaggccagac cagaaccagc aagactgaaa ccacctgttc attacaatgg cccctcaaaa
1441 gcagggtatg ttgactttga aaatggccag tgggccacag atgacatccc agatgacttg
1501 aatagtatcc gcgcagcacc aggtgagttt cgagccatca tggagatgcc ctccttctac
1561 agtcatggct tgccacggtg ttcaccctac aagaaactga cagagtgcca gctgaagaac
1621 cccatcagcg ggctgttaga atatgcccag ttcgctagtc aaacctgtga gttcaacatg
1681 atagagcaga gtggaccacc ccatgaacct cgatttaaat tccaggttgt catcaatggc
1741 cgagagtttc ccccagctga agctggaagc aagaaagtgg ccaagcagga tgcagctatg
1801 aaagccatga caattctgct agaggaagcc aaagccaagg acagtggaaa atcagaagaa
1861 tcatcccact attccacaga gaaagaatca gagaagactg cagagtccca gacccccacc
1921 ccttcagcca catccttctt ttctgggaag agccccgtca ccacactgct tgagtgtatg
1981 cacaaattgg ggaactcctg cgaattccgt ctcctgtcca aagaaggccc tgcccatgaa
2041 cccaagttcc aatactgtgt tgcagtggga gcccaaactt tccccagtgt gagtgctccc
2101 agcaagaaag tggcaaagca gatggccgca gaggaagcca tgaaggccct gcatggggag
2161 gcgaccaact ccatggcttc tgataaccag cctgaaggta tgatctcaga gtcacttgat
2221 aacttggaat ccatgatgcc caacaaggtc aggaagattg gcgagctcgt gagatacctg
2281 aacaccaacc ctgtgggtgg ccttttggag tacgcccgct cccatggctt tgctgctgaa
2341 ttcaagttgg tcgaccagtc cggacctcct cacgagccca agttcgttta ccaagcaaaa
2401 gttgggggtc gctggttccc agccgtctgc gcacacagca agaagcaagg caagcaggaa
2461 gcagcagatg cggctctccg tgtcttgatt ggggagaacg agaaggcaga acgcatgggt
2521 ttcacagagg taaccccagt gacaggggcc agtctcagaa gaactatgct cctcctctca
2581 aggtccccag aagcacagcc aaagacactc cctctcactg gcagcacctt ccatgaccag
2641 atagccatgc tgagccaccg gtgcttcaac actctgacta acagcttcca gccctccttg
2701 ctcggccgca agattctggc cgccatcatt atgaaaaaag actctgagga catgggtgtc
2761 gtcgtcagct tgggaacagg gaatcgctgt gtgaaaggag attctctcag cctaaaagga
2821 gaaactgtca atgactgcca tgcagaaata atctcccgga gaggcttcat caggtttctc
2881 tacagtgagt taatgaaata caactcccag actgcgaagg atagtatatt tgaacctgct
2941 aagggaggag aaaagctcca aataaaaaag actgtgtcat tccatctgta tatcagcact
3001 gctccgtgtg gagatggcgc cctctttgac aagtcctgca gcgaccgtgc tatggaaagc
3061 acagaatccc gccactaccc tgtcttcgag aatcccaaac aaggaaagct ccgcaccaag
3121 gtggagaacg gagaaggcac aatccctgtg gaatccagtg acattgtgcc tacgtgggat
3181 ggcattcggc tcggggagag actccgtacc atgtcctgta gtgacaaaat cctacgctgg
3241 aacgtgctgg gcctgcaagg ggcactgttg acccacttcc tgcagcccat ttatctcaaa
3301 tctgtcacat tgggttacct tttcagccaa gggcatctga cccgtgctat ttgctgtcgt
3361 gtgacaagag atgggagtgc atttgaggat ggactacgac atccctttat tgtcaaccac 3421 cccaaggttg gcagagtcag catatatgat tccaaaaggc aatccgggaa gactaaggag
3481 acaagcgtca actggtgtct ggctgatggc tatgacctgg agatcctgga cggtaccaga
3541 ggcactgtgg atgggccacg gaatgaattg tcccgggtct ccaaaaagaa catttttctt
3601 ctatttaaga agctctgctc cttccgttac cgcagggatc tactgagact ctcctatggt
3661 gaggccaaga aagctgcccg tgactacgag acggccaaga actacttcaa aaaaggcctg
3721 aaggatatgg gctatgggaa ctggattagc aaaccccagg aggaaaagaa cttttatctc
3781 tgcccagtat agtatgctcc agtgacagat ggattagggt gtgtcatact agggtgtgag
3841 agaggtaggt cgtagcattc ctcatcacat ggtcagggga tttttttttc tccttttttt
3901 ttctttttaa gccataattg gtgatactga aaactttggg ttcccattta tcctgctttc
3961 tttgggattg ctaggcaagg tctggccagg cccccctttt ttcccccaag tgaagaggca
4021 gaaacctaag aagttatctt ttctttctac ccaaagcata catagtcact gagcacctgc
4081 ggtccatttc ctcttaaaag ttttgttttg atttgtttcc atttcctttc cctttgtgtt
4141 tgctacactg acctcttgcg gtcttgatta ggtttcagtc aactctggat catgtcaggg
4201 actgataatt tcatttgtgg attacgcaga cccctctact tcccctcttt cccttctgag
4261 attctttcct tgtgatctga atgtctcctt ttccccctca gagggcaaag aggtgaacat
4321 aaaggatttg gtgaaacatt tgtaagggta ggagttgaaa actgcagttc ccagtgccac
4381 ggaagtgtga ttggagcctg cagataatgc ccagccatcc tcccatcctg cactttagcc
4441 agctgcaggg cgggcaaggc aaggaaagct gcttccctgg aagtgtatca ctttctccgg
4501 cagctgggaa gtctagaacc agccagactg ggttaaggga gctgctcaag caatagcaga
4561 ggtttcaccc ggcaggatga cacagaccac ttcccaggga gcacgggcat gccttggaat
4621 attgccaagc ttccagctgc ctcttctcct aaagcattcc taggaatatt ttccccgcca
4681 atgctgggcg tacaccctag ccaacgggac aaatcctaga gggtataaaa tcatctctgc
4741 tcagataatc atgacttagc aagaataagg gcaaaaaatc ctgttggctt aacgtcactg
4801 ttccacccgg tgtaatatct ctcatgacag tgacaccaag ggaagttgac taagtcacat
4861 gtaaattagg agtgttttaa agaatgccat agatgttgat tcttaactgc tacagataac
4921 ctgtaattga gcagatttaa aattcaggca tacttttcca tttatccaag tgctttcatt
4981 tttccagatg gcttcagaag taggctcgtg ggcagggcgc agacctgatc tttatagggt
5041 tgacatagaa agcagtagtt gtgggtgaaa gggcaggttg tcttcaaact ctgtgaggta
5101 gaatcctttg tctatacctc catgaacatt gactcgtgtg ttcagagcct ttggcctctc
5161 tgtggagtct ggctctctgg ctcctgtgca ttctttgaat agtcactcgt aaaaactgtc
5221 agtgcttgaa actgtttcct ttactcatgt tgaagggact ttgttggctt ttagagtgtt
5281 ggtcatgact ccaagagcag agcagggaag agcccaagca tagacttggt gccgtggtga
5341 tggctgcagt ccagttttgt gatgctgctt ttacgtgtcc ctcgataaca gtcagctaga
5401 cacactcagg aggactactg aggctctgcg accttcagga gctgagcctg cctctctcct
5461 ttagatgaca gaccttcatc tgggaacgtg ctgagccagc accctcagat gatttccctc
5521 caaactgctg actaggtcat cctctgtctg gtagagacat tcacatcttt gcttttattc
5581 tatgctctct gtacttttga ccaaaaattg accaaagtaa gaaaatgcaa gttctaaaaa
5641 tagactaagg atgcctttgc agaacaccaa agcatcccaa ggaactggta gggaagtggc
5701 gcctgtctcc tggagtggaa gaggcctgct ccctggctct gggtctgctg ggggcacagt
5761 aaatcagtct tggcacccac atccagggca gagaggtctg tggttctcag catcagaagg
5821 cagcgcagcc cctctcctct tcaggctaca gggttgtcac ctgctgagtc ctcaggttgt
5881 ttggcctctc tggtccatct tgggcattag gttctccagc agagctctgg ccagctgcct
5941 cttctttaac tgggaacaca ggctctcaca agatcagaac ccccactcac ccccaagatc 6001 ttatctagca agcctgtagt attcagtttc tgttgtagga agagagcgag gcatccctga
6061 attccacgca tctgctggaa acgagccgtg tcagatcgca catccctgcg cccccatgcc
6121 cctctgagtc acacaggaca gaggaggcag agcttctgcc cactgttatc ttcactttct
6181 ttgtccagtc ttttgttttt aataagcagt gaccctccct actcttcttt ttaatgattt
6241 ttgtagttga tttgtctgaa ctgtggctac tgtgcattcc ttgaataatc acttgtaaaa
6301 attgtcagtg cttgaagctg tttcctttac tcacattgaa gggacttcgt tggttttttg
6361 gagtcttggt tgtgactcca agagcagagt gaggaagacc cccaagcata gactcgggta
6421 ctgtgatgat ggctgcagtc cagttttatg attctgcttt tatgtgtccc ttgataacag
6481 tgacttaaca atatacattc ctcataaata aaaaaaaaac aagaatctga attcttagaa
6541 aaaaaaaaaa aaaaaaaaaa a (SEQ ID NO: 2)
In another embodiment, antibodies used to practice this invention are designed to bind to, or affinity matured to bind to, a polypeptide SEQ ID NO:3, or subsequences thereof:
1 mnprqgysls gyythpfqgy ehrqlryqqp gpgsspssfl lkqieflkgq lpeapvigkq 61 tpslppslpg lrprfpvlla sstrgrqvdi rgvprgvhlg sqglqrgfqh psprgrslpq 121 rgvdclsshf qelsiyqdqe qrilkfleel gegkattahd lsgklgtpkk einrvlysla 181 kkgklqkeag tpplwkiavs tqawnqhsgv vrpdghsqga pnsdpslepe drnstsvsed 241 llepfiavsa qawnqhsgvv rpdshsqgsp nsdpgleped snstsaledp lefldmaeik 301 ekicdylfnv sdssalnlak nigltkardi navlidmerq gdvyrqgttp piwhltdkkr 361 ermqikrntn svpetapaai petkrnaefl tcniptsnas nnmvttekve ngqepvikle 421 nrqearpepa rlkppvhyng pskagyvdfe ngqwatddip ddlnsiraap gefraimemp 481 sfyshglprc spykkltecq lknpisglle yaqfasqtce fnmieqsgpp heprfkfqvv 541 ingrefppae agskkvakqd aamkamtill eeakakdsgk seesshyste kesektaesq 601 tptpsatsff sgkspvttll ecmhklgnsc efrllskegp ahepkfqycv avgaqtfpsv 661 sapskkvakq maaeeamkal hgeatnsmas dnqpegmise sldnlesmmp nkvrkigelv 721 rylntnpvgg lleyarshgf aaefklvdqs gpphepkfvy qakvggrwfp avcahskkqg 781 kqeaadaalr vligenekae rmgftevtpv tgaslrrtml llsrspeaqp ktlpltgstf 841 hdqiamlshr cfntltnsfq psllgrkila aiimkkdsed mgvvvslgtg nrcvkgdsls 901 lkgetvndch aeiisrrgfi rflyselmky nsqtakdsif epakggeklq ikktvsfhly 961 istapcgdga lfdkscsdra mestesrhyp vfenpkqgkl rtkvengegt ipvessdivp 1021 twdgirlger lrtmscsdki lrwnvlglqg allthflqpi ylksvtlgyl fsqghltrai 1081 ccrvtrdgsa fedglrhpfi vnhpkvgrvs iydskrqsgk tketsvnwcl adgydleild 1141 gtrgtvdgpr nelsrvskkn ifllfkklcs fryrrdllrl sygeakkaar dyetaknyfk 1201 kglkdmgygn wiskpqeekn fylcpv (SEQ ID NO:3)
Generating and Manipulating Nucleic Acids
In alternative embodiments, compositions and methods of the invention use nucleic acids for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal of hematopoietic stem cells or cancer stem cells. In alternative embodiments, compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the ADAR1 gene (e.g., SEQ ID NO: l) or an ADAR1 gene transcript (e.g., SEQ ID NO:2). In alternative embodiments, compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADAR1 gene or ADAR1 gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA), or a ribozyme.
In alternative embodiments, nucleic acids of the invention are made, isolated and/or manipulated by, e.g., cloning and expression of cDNA libraries, amplification of message or genomic DNA by PCR, and the like.
The nucleic acids used to practice this invention, whether RNA, iRNA, antisense nucleic acid, cDNA, genomic DNA, vectors, viruses or hybrids thereof, can be isolated from a variety of sources, genetically engineered, amplified, and/or expressed/ generated recombinantly. Recombinant polypeptides generated from these nucleic acids can be individually isolated or cloned and tested for a desired activity. Any recombinant expression system can be used, including e.g. bacterial, fungal, mammalian, yeast, insect or plant cell expression systems.
Alternatively, nucleic acids used to practice this invention can be synthesized in vitro by well-known chemical synthesis techniques, as described in, e.g., Adams (1983) J. Am. Chem. Soc. 105:661; Belousov (1997) Nucleic Acids Res. 25:3440-3444; Frenkel (1995) Free Radic. Biol. Med. 19:373-380; Blommers (1994) Biochemistry 33 :7886- 7896; Narang (1979) Meth. Enzymol. 68:90; Brown (1979) Meth. Enzymol. 68: 109; Beaucage (1981) Tetra. Lett. 22: 1859; U.S. Patent No. 4,458,066.
Techniques for the manipulation of nucleic acids used to practice this invention, such as, e.g., subcloning, labeling probes (e.g., random-primer labeling using Klenow polymerase, nick translation, amplification), sequencing, hybridization and the like are well described in the scientific and patent literature, see, e.g., Sambrook, ed.,
MOLECULAR CLONING: A LABORATORY MANUAL (2ND ED.), Vols. 1-3, Cold Spring Harbor Laboratory, (1989); CURRENT PROTOCOLS IN MOLECULAR
BIOLOGY, Ausubel, ed. John Wiley & Sons, Inc., New York (1997); LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY: HYBRIDIZATION WITH NUCLEIC ACID PROBES, Part I. Theory and Nucleic Acid Preparation, Tijssen, ed. Elsevier, N.Y. (1993).
Another useful means of obtaining and manipulating nucleic acids used to practice the methods of the invention is to clone from genomic samples, and, if desired, screen and re-clone inserts isolated or amplified from, e.g., genomic clones or cDNA clones.
Sources of nucleic acid used in the methods of the invention include genomic or cDNA libraries contained in, e.g., mammalian artificial chromosomes (MACs), see, e.g., U.S. Patent Nos. 5,721, 118; 6,025,155; human artificial chromosomes, see, e.g., Rosenfeld (1997) Nat. Genet. 15:333-335; yeast artificial chromosomes (YAC); bacterial artificial chromosomes (BAC); P I artificial chromosomes, see, e.g., Woon (1998) Genomics 50:306-316; P l-derived vectors (PACs), see, e.g., Kern (1997) Biotechniques 23 : 120- 124; cosmids, recombinant viruses, phages or plasmids.
Nucleic acids or nucleic acid sequences used to practice this invention can be an oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin. Compounds use to practice this invention include "nucleic acids" or "nucleic acid sequences" including oligonucleotide, nucleotide, polynucleotide, or any fragment of any of these; and include DNA or RNA (e.g., mRNA, rRNA, tRNA, iRNA) of genomic or synthetic origin which may be single-stranded or double-stranded; and can be a sense or antisense strand, or a peptide nucleic acid (PNA), or any DNA-like or RNA-like material, natural or synthetic in origin, including, e.g., iRNA, ribonucleoproteins (e.g., e.g., double stranded iRNAs, e.g., iRNPs). Compounds use to practice this invention include nucleic acids, i.e., oligonucleotides, containing known analogues of natural nucleotides. Compounds use to practice this invention include nucleic-acid-like structures with synthetic backbones, see e.g., Mata (1997) Toxicol. Appl. Pharmacol. 144: 189-197; Strauss-Soukup (1997) Biochemistry 36:8692-8698; Samstag (1996) Antisense Nucleic Acid Drug Dev 6: 153- 156. Compounds use to practice this invention include "oligonucleotides" including a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands that may be chemically synthesized. Compounds use to practice this invention include synthetic oligonucleotides having no 5' phosphate, and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide can ligate to a fragment that has not been dephosphorylated.
In alternative aspects, compounds used to practice this invention include genes or any segment of DNA or RNA involved in producing a polypeptide chain; it can include regions preceding and following the coding region (leader and trailer) as well as, where applicable, intervening sequences (introns) between individual coding segments (exons). "Operably linked" can refer to a functional relationship between two or more nucleic acid (e.g., DNA or RNA) segments. In alternative aspects, it can refer to the functional relationship of transcriptional regulatory sequence to a transcribed sequence. For example, a promoter can be operably linked to a coding sequence, such as a nucleic acid used to practice this invention, if it stimulates or modulates the transcription of the coding sequence in an appropriate host cell or other expression system. In alternative aspects, promoter transcriptional regulatory sequences can be operably linked to a transcribed sequence where they can be physically contiguous to the transcribed sequence, i.e., they can be cz's-acting. In alternative aspects, transcriptional regulatory sequences, such as enhancers, need not be physically contiguous or located in close proximity to the coding sequences whose transcription they enhance.
In alternative aspects, the invention comprises use of "expression cassettes" comprising a nucleotide sequence used to practice this invention, which can be capable of affecting expression of the nucleic acid, e.g., a structural gene or a transcript (e.g., encoding a DRP or antibody) in a host compatible with such sequences. Expression cassettes can include at least a promoter operably linked with the polypeptide coding sequence or inhibitory sequence; and, in one aspect, with other sequences, e.g., transcription termination signals. Additional factors necessary or helpful in effecting expression may also be used, e.g., enhancers.
In alternative aspects, expression cassettes used to practice this invention also include plasmids, expression vectors, recombinant viruses, any form of recombinant "naked DNA" vector, and the like. In alternative aspects, a "vector" used to practice this invention can comprise a nucleic acid that can infect, transfect, transiently or permanently transduce a cell. In alternative aspects, a vector used to practice this invention can be a naked nucleic acid, or a nucleic acid complexed with protein or lipid. In alternative aspects, vectors used to practice this invention can comprise viral or bacterial nucleic acids and/or proteins, and/or membranes (e.g., a cell membrane, a viral lipid envelope, etc.). In alternative aspects, vectors used to practice this invention can include, but are not limited to replicons (e.g., RNA replicons, bacteriophages) to which fragments of DNA may be attached and become replicated. Vectors thus include, but are not limited to RNA, autonomous self-replicating circular or linear DNA or RNA (e.g., plasmids, viruses, and the like, see, e.g., U.S. Patent No. 5,217,879), and can include both the expression and non-expression plasmids. In alternative aspects, the vector used to practice this invention can be stably replicated by the cells during mitosis as an autonomous structure, or can be incorporated within the host's genome.
In alternative aspects, "promoters" used to practice this invention include all sequences capable of driving transcription of a coding sequence in a cell, e.g., a mammalian cell such as a brain cell. Thus, promoters used in the constructs of the invention include cz's-acting transcriptional control elements and regulatory sequences that are involved in regulating or modulating the timing and/or rate of transcription of a gene. For example, a promoter used to practice this invention can be a cz's-acting transcriptional control element, including an enhancer, a promoter, a transcription terminator, an origin of replication, a chromosomal integration sequence, 5' and 3 ' untranslated regions, or an intronic sequence, which are involved in transcriptional regulation. These cis-acting sequences typically interact with proteins or other biomolecules to carry out (turn on/off, regulate, modulate, etc.) transcription.
"Constitutive" promoters used to practice this invention can be those that drive expression continuously under most environmental conditions and states of development or cell differentiation. "Inducible" or "regulatable" promoters used to practice this invention can direct expression of the nucleic acid of the invention under the influence of environmental conditions or developmental conditions.
Antisense inhibitory nucleic acid molecules
In alternative embodiments, compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the ADAR1 gene (e.g., SEQ ID NO: l) or a ADARl gene transcript (e.g., SEQ ID NO:2). In alternative embodiments, compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADAR1 gene or ADAR1 gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA), or a ribozyme.
Naturally occurring or synthetic nucleic acids can be used as antisense oligonucleotides. The antisense oligonucleotides can be of any length; for example, in alternative aspects, the antisense oligonucleotides are between about 5 to 100, about 10 to 80, about 15 to 60, about 18 to 40. The optimal length can be determined by routine screening. The antisense oligonucleotides can be present at any concentration. The optimal concentration can be determined by routine screening. A wide variety of synthetic, non-naturally occurring nucleotide and nucleic acid analogues are known which can address this potential problem. For example, peptide nucleic acids (PNAs) containing non-ionic backbones, such as N-(2-aminoethyl) glycine units can be used. Antisense oligonucleotides having phosphorothioate linkages can also be used, as described in WO 97/03211 ; WO 96/39154; Mata (1997) Toxicol. Appl. Pharmacol. 144: 189-197; Antisense Therapeutics, ed. Agrawal (Humana Press, Totowa, N.J., 1996). Antisense oligonucleotides having synthetic DNA backbone analogues provided by the invention can also include phosphoro-dithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3'-N-carbamate, and morpholino carbamate nucleic acids.
RNA interference (RNAi)
In one aspect, the invention provides RNAi inhibitory nucleic acid molecules capable of decreasing or inhibiting expression of one or a set of ADAR1 transcripts or proteins, e.g., the transcript (mRNA, message) SEQ ID NO:2 or isoform or isoforms thereof. In one aspect, the RNAi molecule comprises a double-stranded RNA (dsRNA) molecule. The RNAi molecule can comprise a double-stranded RNA (dsRNA) molecule, e.g., siRNA, miRNA (microRNA) and/or short hairpin RNA (shRNA) molecules.
In alternative aspects, the RNAi is about 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. While the invention is not limited by any particular mechanism of action, the RNAi can enter a cell and cause the degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to double-stranded RNA (dsRNA), mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi). A possible basic mechanism behind RNAi, e.g., siRNA for inhibiting transcription and/or miRNA to inhibit translation, is the breaking of a double-stranded RNA (dsRNA) matching a specific gene sequence into short pieces called short interfering RNA, which trigger the degradation of mRNA that matches its sequence.
In one aspect, intracellular introduction of the RNAi (e.g., miRNA or siRNA) is by internalization of a target cell specific ligand bonded to an RNA binding protein comprising an RNAi (e.g., microRNA) is adsorbed. The ligand can be specific to a unique target cell surface antigen. The ligand can be spontaneously internalized after binding to the cell surface antigen. If the unique cell surface antigen is not naturally internalized after binding to its ligand, internalization can be promoted by the
incorporation of an arginine-rich peptide, or other membrane permeable peptide, into the structure of the ligand or RNA binding protein or attachment of such a peptide to the ligand or RNA binding protein. See, e.g., U.S. Patent App. Pub. Nos. 20060030003; 20060025361; 20060019286; 20060019258. In one aspect, the invention provides lipid- based formulations for delivering, e.g., introducing nucleic acids of the invention as nucleic acid-lipid particles comprising an RNAi molecule to a cell, see .g., U.S. Patent App. Pub. No. 20060008910.
Methods for making and using RNAi molecules, e.g., siRNA and/or miRNA, for selectively degrade RNA are well known in the art, see, e.g., U.S. Patent No. 6,506,559; 6,51 1,824; 6,515,109; 6,489,127.
Methods for making expression constructs, e.g., vectors or plasmids, from which an inhibitory polynucleotide (e.g., a duplex siRNA of the invention) is transcribed are well known and routine. A regulatory region (e.g., promoter, enhancer, silencer, splice donor, acceptor, etc.) can be used to transcribe an RNA strand or RNA strands of an inhibitory polynucleotide from an expression construct. When making a duplex siRNA inhibitory molecule, the sense and antisense strands of the targeted portion of the targeted IRES can be transcribed as two separate RNA strands that will anneal together, or as a single RNA strand that will form a hairpin loop and anneal with itself. For example, a construct targeting a portion of a gene, e.g., an NADPH oxidase enzyme coding sequence or transcriptional activation sequence, is inserted between two promoters (e.g., mammalian, viral, human, tissue specific, constitutive or other type of promoter) such that transcription occurs bidirectionally and will result in complementary RNA strands that may subsequently anneal to form an inhibitory siRNA of the invention. Alternatively, a targeted portion of a gene, coding sequence, promoter or transcript can be designed as a first and second antisense binding region together on a single expression vector; for example, comprising a first coding region of a targeted gene in sense orientation relative to its controlling promoter, and wherein the second coding region of the gene is in antisense orientation relative to its controlling promoter. If transcription of the sense and antisense coding regions of the targeted portion of the targeted gene occurs from two separate promoters, the result may be two separate RNA strands that may subsequently anneal to form a gene-inhibitory siRNA used to practice this invention.
In another aspect, transcription of the sense and antisense targeted portion of the targeted gene is controlled by a single promoter, and the resulting transcript will be a single hairpin RNA strand that is self-complementary, i.e., forms a duplex by folding back on itself to create a gene- inhibitory siRNA molecule. In this configuration, a spacer, e.g., of nucleotides, between the sense and antisense coding regions of the targeted portion of the targeted gene can improve the ability of the single strand RNA to form a hairpin loop, wherein the hairpin loop comprises the spacer. In one embodiment, the spacer comprises a length of nucleotides of between about 5 to 50 nucleotides. In one aspect, the sense and antisense coding regions of the siRNA can each be on a separate expression vector and under the control of its own promoter.
Inhibitory Ribozymes
The invention provides ribozymes capable of binding and inhibiting, e.g., decreasing or inhibiting, expression of one or a set of ADAR1 transcripts or proteins, e.g., SEQ ID NO: 1 or SEQ ID NO:2, or isoform or isoforms thereof.
These ribozymes can inhibit a gene's activity by, e.g., targeting a genomic DNA or an mRNA (a message, a transcript). Strategies for designing ribozymes and selecting a gene-specific antisense sequence for targeting are well described in the scientific and patent literature, and the skilled artisan can design such ribozymes using the novel reagents of the invention. Ribozymes act by binding to a target RNA through the target RNA binding portion of a ribozyme which is held in close proximity to an enzymatic portion of the RNA that cleaves the target RNA. Thus, the ribozyme recognizes and binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cleave and inactivate the target RNA. Cleavage of a target RNA in such a manner will destroy its ability to direct synthesis of an encoded protein if the cleavage occurs in the coding sequence. After a ribozyme has bound and cleaved its RNA target, it can be released from that RNA to bind and cleave new targets repeatedly.
Kits and Instructions
The invention provides kits comprising compositions and/or instructions for practicing methods of the invention. As such, kits, cells, vectors and the like can also be provided. In alternative embodiments, the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
COMPOSITIONS AND METHODS FOR DORMANT CANCER STEM CELL DETECTION AND ELIMINATION
In alternative embodiments, the invention provides compositions and methods to detect dormant cancer stem cells, e.g., Chronic Myelogenous Leukemia (CML) stem cells. In alternative embodiments, the invention provides compositions and methods for use to, e.g., therapeutically, initiate, stimulate or force a dormant cancer stem cell, e.g., a Chronic Myelogenous Leukemia (CML) stem cell, into cycle so that it can be targeted by a therapeutic agent or procedure, e.g., chemotherapy, radiation therapy or targeted tyrosine kinase inhibitors, or any agent or procedure that targets dividing cells.
In alternative embodiments, the invention provides compositions and methods comprising or comprising use of sonic hedgehog inhibitors, e.g., inhibitors of
Smoothened (SMO), an integral membrane protein mediator of Hedgehog signaling (see e.g., Shi et al. (2011) Development, Epub 201 1 Aug 18; Su, et al. (2011) Sci. Signal. Jul 5;4(180):ra43), which activate, stimulate or initiate in a stem cell, e.g., a cancer stem cell, a transition from GO to Gl of the cell cycle, thereby sensitizing the stem cells to agents that target dividing cells.
Here we investigated the role of Shh signaling in maintenance of dormancy. We show that, compared to chronic phase CML and normal progenitors, human blast crisis LSC harbor enhanced expression of the Shh transcriptional activator, GLI2, and decreased expression of a transcriptional repressor, GLI3. Treatment of human blast crisis LSC engrafted RAG2"/"yc"/" mice with a novel selective Shh inhibitor, designated PF-04449913 (see Supplementary Figure la for structure), reduced leukemic burden in a niche-dependent manner commensurate with GLI downregulation.
Full transcriptome RNA sequencing performed on FACS-purified human progenitors from PF-04449913 treated blast crisis LSC engrafted mice demonstrated greater Shh gene splice isoform concordance with normal progenitors than vehicle treated controls. In addition, RNA sequencing revealed significantly decreased cell cycle regulatory gene expression and splice isoform analysis demonstrated reversion toward a normal splice isoform signature for many cell cycle regulatory genes.
Moreover, cell cycle FACS analysis showed that selective Shh inhibition permitted dormant blast crisis LSC to enter the cell cycle while normal progenitor cell cycle status was unaffected.
Finally, PF-04449913 synergized with BCR-ABL inhibition to reduce blast crisis LSC survival and self-renewal in concert with increased expression of Shh pathway regulators.
Our findings demonstrate that selective Shh antagonism induces cycling of dormant human blast crisis LSC, rendering them susceptible to BCR-ABL inhibition, while sparing normal progenitors.
The invention also provides novel stem cell, e.g., LSC, splice isoform detection platforms, e.g., as kits of the invention, to assess the efficacy of Shh inhibitor-mediated sensitization. In alternative embodiments, stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify "conversion" of a stem cell to a "normal cell", or to determine or define a molecularly targeted therapy for dormant cancer stem cell elimination strategies that ultimately avert relapse. In alternative embodiments, stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify compounds or treatments that can successfully inhibit Shh expression.
In alternative embodiments, compositions and methods of the invention can be used synergistically to sensitize dormant stem cells, e.g., LSC, to therapeutic agents that target dividing cells including e.g., tyrosine kinase inhibitors, chemotherapy. In alternative embodiments, compositions and methods of the invention can be used sensitize, e.g., radiosensitize, a cancer stem cell, e.g., a LSC and other cancer stem cell populations, through cell cycle induction or stimulation. When CML stem cells were treated with a Smoothened (SMO) protein inhibitor (SMO being a key component of the Hedgehog signaling pathway), dormant stem cells entered the cell cycle, as evidenced by the RNA isoform pattern of a leukemic cancer stem cell reverting to the pattern of a normal cell. Hence, in alternative embodiments, this RNA isoform pattern can be used as a biomarker of response to chemotherapy and a target for drug development, e.g., successful or effective inhibition of Shh give a particular, detectable RNA isoform pattern.
Our findings demonstrate that selective Shh antagonism induces cycling of dormant human blast crisis LSC, rendering them susceptible to BCR-ABL inhibition, while sparing normal progenitors. Implementation of novel cancer stem cell, e.g., a LSC, splice isoform detection platforms of this invention can assess the efficacy of Shh inhibitor-mediated sensitization to molecularly targeted therapies. Implementation of novel LSC splice isoform detection platforms of this invention can identify and determine the effectiveness of dormant cancer stem cell elimination strategies that ultimately avert relapse.
In alternative embodiments, the invention provides splice isoform detection kits or arrays for stem cells, e.g., LSC stem cells. In alternative embodiments, the invention provides nanoproteomic detection kits or arrays for stem cells (to determine an altered proteome caused by an altered RNA splicing pattern, or alternatively spliced transcripts) to determine a response to a stem cell therapy, e.g., a LSC targeted therapy.
Kits and Instructions
The invention provides kits comprising compositions and/or instructions for practicing methods of the invention. As such, kits, cells, vectors and the like can also be provided. In alternative embodiments, the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
Antisense inhibitory nucleic acid molecules
In alternative embodiments, compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the Shh or a Shh gene transcript. In alternative embodiments, compositions and methods of the invention comprise use of an inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the Shh gene or Shh gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA), or a ribozyme.
Naturally occurring or synthetic nucleic acids can be used as antisense oligonucleotides. The antisense oligonucleotides can be of any length; for example, in alternative aspects, the antisense oligonucleotides are between about 5 to 100, about 10 to 80, about 15 to 60, about 18 to 40. The optimal length can be determined by routine screening. The antisense oligonucleotides can be present at any concentration. The optimal concentration can be determined by routine screening. A wide variety of synthetic, non-naturally occurring nucleotide and nucleic acid analogues are known which can address this potential problem. For example, peptide nucleic acids (PNAs) containing non-ionic backbones, such as N-(2-aminoethyl) glycine units can be used. Antisense oligonucleotides having phosphorothioate linkages can also be used, as described in WO 97/03211 ; WO 96/39154; Mata (1997) Toxicol. Appl. Pharmacol.
144: 189-197; Antisense Therapeutics, ed. Agrawal (Humana Press, Totowa, N.J., 1996). Antisense oligonucleotides having synthetic DNA backbone analogues provided by the invention can also include phosphoro-dithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3'-thioacetal, methylene(methylimino), 3 '-N -carbamate, and morpholino carbamate nucleic acids.
RNA interference (RNAi)
In one aspect, the invention provides RNAi inhibitory nucleic acid molecules capable of decreasing or inhibiting expression of one or a set oiShh transcripts or proteins, e.g., the transcript (mRNA, message) or isoform or isoforms thereof. In one aspect, the RNAi molecule comprises a double-stranded RNA (dsRNA) molecule. The RNAi molecule can comprise a double-stranded RNA (dsRNA) molecule, e.g., siRNA, miRNA (microRNA) and/or short hairpin RNA (shRNA) molecules.
In alternative aspects, the RNAi is about 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in length. While the invention is not limited by any particular mechanism of action, the RNAi can enter a cell and cause the degradation of a single-stranded RNA (ssRNA) of similar or identical sequences, including endogenous mRNAs. When a cell is exposed to double-stranded RNA (dsRNA), mRNA from the homologous gene is selectively degraded by a process called RNA interference (RNAi). A possible basic mechanism behind RNAi, e.g., siRNA for inhibiting transcription and/or miRNA to inhibit translation, is the breaking of a double-stranded RNA (dsRNA) matching a specific gene sequence into short pieces called short interfering RNA, which trigger the degradation of mRNA that matches its sequence.
In one aspect, intracellular introduction of the RNAi (e.g., miRNA or siRNA) is by internalization of a target cell specific ligand bonded to an RNA binding protein comprising an RNAi (e.g., microRNA) is adsorbed. The ligand can be specific to a unique target cell surface antigen. The ligand can be spontaneously internalized after binding to the cell surface antigen. If the unique cell surface antigen is not naturally internalized after binding to its ligand, internalization can be promoted by the incorporation of an arginine-rich peptide, or other membrane permeable peptide, into the structure of the ligand or RNA binding protein or attachment of such a peptide to the ligand or RNA binding protein. See, e.g., U.S. Patent App. Pub. Nos. 20060030003; 20060025361; 20060019286; 20060019258. In one aspect, the invention provides lipid- based formulations for delivering, e.g., introducing nucleic acids of the invention as nucleic acid-lipid particles comprising an RNAi molecule to a cell, see .g., U.S. Patent App. Pub. No. 20060008910.
Methods for making and using RNAi molecules, e.g., siRNA and/or miRNA, for selectively degrade RNA are well known in the art, see, e.g., U.S. Patent No. 6,506,559; 6,51 1,824; 6,515,109; 6,489,127.
Methods for making expression constructs, e.g., vectors or plasmids, from which an inhibitory polynucleotide (e.g., a duplex siRNA of the invention) is transcribed are well known and routine. A regulatory region (e.g., promoter, enhancer, silencer, splice donor, acceptor, etc.) can be used to transcribe an RNA strand or RNA strands of an inhibitory polynucleotide from an expression construct. When making a duplex siRNA inhibitory molecule, the sense and antisense strands of the targeted portion of the targeted IRES can be transcribed as two separate RNA strands that will anneal together, or as a single RNA strand that will form a hairpin loop and anneal with itself. For example, a construct targeting a portion of a gene, e.g., a Shh coding sequence or transcriptional activation sequence, is inserted between two promoters (e.g., mammalian, viral, human, tissue specific, constitutive or other type of promoter) such that transcription occurs bidirectionally and will result in complementary RNA strands that may subsequently anneal to form an inhibitory siRNA of the invention.
Alternatively, a targeted portion of a gene, coding sequence, promoter or transcript can be designed as a first and second antisense binding region together on a single expression vector; for example, comprising a first coding region of a targeted gene in sense orientation relative to its controlling promoter, and wherein the second coding region of the gene is in antisense orientation relative to its controlling promoter. If transcription of the sense and antisense coding regions of the targeted portion of the targeted gene occurs from two separate promoters, the result may be two separate RNA strands that may subsequently anneal to form a gene-inhibitory siRNA used to practice this invention.
In another aspect, transcription of the sense and antisense targeted portion of the targeted gene is controlled by a single promoter, and the resulting transcript will be a single hairpin RNA strand that is self-complementary, i.e., forms a duplex by folding back on itself to create a gene- inhibitory siRNA molecule. In this configuration, a spacer, e.g., of nucleotides, between the sense and antisense coding regions of the targeted portion of the targeted gene can improve the ability of the single strand RNA to form a hairpin loop, wherein the hairpin loop comprises the spacer. In one embodiment, the spacer comprises a length of nucleotides of between about 5 to 50 nucleotides. In one aspect, the sense and antisense coding regions of the siRNA can each be on a separate expression vector and under the control of its own promoter.
Inhibitory Ribozymes
In alternative embodiment, compositions and methods of the invention comprise use of ribozymes capable of binding and inhibiting, e.g., decreasing or inhibiting, expression of one or a set oiShh transcripts or proteins, or isoform or isoforms thereof.
These ribozymes can inhibit a gene's activity by, e.g., targeting a genomic DNA or an mRNA (a message, a transcript). Strategies for designing ribozymes and selecting a gene-specific antisense sequence for targeting are well described in the scientific and patent literature, and the skilled artisan can design such ribozymes using the novel reagents of the invention. Ribozymes act by binding to a target RNA through the target RNA binding portion of a ribozyme which is held in close proximity to an enzymatic portion of the RNA that cleaves the target RNA. Thus, the ribozyme recognizes and binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cleave and inactivate the target RNA. Cleavage of a target RNA in such a manner will destroy its ability to direct synthesis of an encoded protein if the cleavage occurs in the coding sequence. After a ribozyme has bound and cleaved its RNA target, it can be released from that RNA to bind and cleave new targets repeatedly.
Bioisosteres of Compounds used to practice the Invention
In alternative embodiments, the invention also provides bioisosteres of compounds used to practice the invention, e.g., compounds having a structure as set forth in Figure 17a, or PF-04449913. In alternative embodiments, the invention provides compositions that inhibit or slow the expression of a Shh gene, a Shh gene product, a Shh transcript, and/or a Shh polypeptide comprising a PF-04449913, or an equivalent thereof, or a bioisostere thereof.
In alternative embodiments, bioisosteres of the invention are compounds of the invention comprising one or more substituent and/or group replacements with a substituent and/or group having substantially similar physical or chemical properties which produce substantially similar biological properties to a compound of the invention, or stereoisomer, racemer or isomer thereof. In one embodiment, the purpose of exchanging one bioisostere for another is to enhance the desired biological or physical properties of a compound without making significant changes in chemical structures.
For example, in one embodiment, bioisosteres of compounds of the invention are made by replacing one or more hydrogen atom(s) with one or more fluorine and/or deuterium atom(s), e.g., at a site of metabolic oxidation; this may prevent metabolism (catabolism) from taking place. Because the fluorine atom or deuterium is similar in size to the hydrogen atom the overall topology of the molecule is not significantly affected, leaving the desired biological activity unaffected. However, with a blocked pathway for metabolism, the molecule may have a longer half-life or be less toxic, and the like.
SONIC HEDHEGOG TARGETS AS BIOMARKERS OF PROGNOSIS AND RESPONSE FOR HUMAN CHRONIC MYELOGENOUS LEUKEMIA
In alternative embodiments, this invention compositions and methods to analyze or measure biomarkers in human leukemia cells to predict the amount of blastic transformation, the severity of the disease, the progress (e.g., regression) of the disease in light of a particular treatment or drug administration. In alternative embodiments, this invention compositions and methods to analyze or measure biomarkers which are predictors of response to selective Sonic Hedgehog (Shh) inhibition.
This invention is the first to analyze Shh gene expression in human leukemic versus normal progenitors and to identify an increase in GLI2 and commensurate decrease in GLI3 as predictor of blastic transformation. In alternative embodiments, compositions and methods of the invention measure GLI1 and GLI2 transcript and/or GLI1 and GLI2 protein levels to predict a response to selective Shh inhibition, where GLI1 and GLI2 presence is a positive predictor of a response to selective Shh inhibition. In alternative embodiments, GLI1 and/or GLI2 are used as predictive biomarkers, individually or together, of a response to an inhibitor of the Sonic Hedgehog (shh) pathway, including inhibitors of Smoothened (SMO), an integral membrane protein mediator of Hedgehog signaling (see e.g., Shi et al. (2011) Development, Epub 2011 Aug 18; Su, et al. (2011) Sci. Signal. Jul 5;4(180):ra43). Both qRT-PCR and nanoproteomics confirmed these functional biomarkers.
In alternative embodiments, compositions and methods of the invention measure
(determine) levels of GLI2 (increasing) and/or GLI3 (decreasing) as prognostic biomarkers (individually or together) for chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and tyrosine kinase inhibitor resistance. Both qRT-PCR and nanoproteomics confirmed these functional biomarkers.
In alternative embodiments, the invention provides compositions and methods comprising or comprising use of sonic hedgehog inhibitors, e.g., inhibitors of
Smoothened (SMO), which activate, stimulate or initiate in a stem cell, e.g., a cancer stem cell, a transition from GO to Gl of the cell cycle, thereby sensitizing the stem cells to agents that target dividing cells.
Here we investigated the role of Shh signaling in maintenance of dormancy. We show that, compared to chronic phase CML and normal progenitors, human blast crisis LSC harbor enhanced expression of the Shh transcriptional activator, GLI2, and decreased expression of a transcriptional repressor, GLI3. Treatment of human blast crisis LSC engrafted RAG2"/"yc"/" mice with a novel selective Shh inhibitor, designated PF-04449913 (see Supplementary Figure la for structure), reduced leukemic burden in a niche-dependent manner commensurate with GLI downregulation.
Full transcriptome RNA sequencing performed on FACS-purified human progenitors from PF-04449913 treated blast crisis LSC engrafted mice demonstrated greater Shh gene splice isoform concordance with normal progenitors than vehicle treated controls. In addition, RNA sequencing revealed significantly decreased cell cycle regulatory gene expression and splice isoform analysis demonstrated reversion toward a normal splice isoform signature for many cell cycle regulatory genes.
Moreover, cell cycle FACS analysis showed that selective Shh inhibition permitted dormant blast crisis LSC to enter the cell cycle while normal progenitor cell cycle status was unaffected.
Finally, PF-04449913 synergized with BCR-ABL inhibition to reduce blast crisis LSC survival and self-renewal in concert with increased expression of Shh pathway regulators.
Our findings demonstrate that selective Shh antagonism induces cycling of dormant human blast crisis LSC, rendering them susceptible to BCR-ABL inhibition, while sparing normal progenitors.
The invention also provides novel stem cell, e.g., LSC, splice isoform detection platforms, e.g., as kits of the invention, to assess the efficacy of Shh inhibitor-mediated sensitization. In alternative embodiments, stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify "conversion" of a stem cell to a "normal cell", or to determine or define a molecularly targeted therapy for dormant cancer stem cell elimination strategies that ultimately avert relapse. In alternative embodiments, stem cell splice isoform detection platforms and compositions (e.g., kits) of the invention are used to identify compounds or treatments that can successfully inhibit Shh expression.
In alternative embodiments, compositions and methods of the invention can be used synergistically to sensitize dormant stem cells, e.g., LSC, to therapeutic agents that target dividing cells including e.g., tyrosine kinase inhibitors, chemotherapy. In alternative embodiments, compositions and methods of the invention can be used sensitize, e.g., radiosensitize, a cancer stem cell, e.g., a LSC and other cancer stem cell populations, through cell cycle induction or stimulation.
When CML stem cells were treated with a Smoothened (SMO) protein inhibitor (SMO being a key component of the Hedgehog signaling pathway), dormant stem cells entered the cell cycle, as evidenced by the RNA isoform pattern of a leukemic cancer stem cell reverting to the pattern of a normal cell. Hence, in alternative embodiments, this RNA isoform pattern can be used as a biomarker of response to chemotherapy and a target for drug development, e.g., successful or effective inhibition of Shh give a particular, detectable RNA isoform pattern.
Our findings demonstrate that selective Shh antagonism induces cycling of dormant human blast crisis LSC, rendering them susceptible to BCR-ABL inhibition, while sparing normal progenitors. Implementation of novel cancer stem cell, e.g., a LSC, splice isoform detection platforms of this invention can assess the efficacy of Shh inhibitor-mediated sensitization to molecularly targeted therapies. Implementation of novel LSC splice isoform detection platforms of this invention can identify and determine the effectiveness of dormant cancer stem cell elimination strategies that ultimately avert relapse.
In alternative embodiments, the invention provides splice isoform detection kits or arrays for stem cells, e.g., LSC stem cells. In alternative embodiments, the invention provides nanoproteomic detection kits or arrays for stem cells (to determine an altered proteome caused by an altered RNA splicing pattern, or alternatively spliced transcripts) to determine a response to a stem cell therapy, e.g., a LSC targeted therapy.
In alternative embodiments, biomarkers of the invention can be detected using arrays, microarrays, proteomic arrays and the like, e.g., as described by: Oehler, et al, (2009) Blood, "The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data", Oct 8; 114(15):3292-8. Epub 2009 Aug 4; Fan, et al., Nature Medicine, May 2009, "Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens," Volume 15, Number 5: 566-571; OTSieill, et al, Proc. Natl. Acad. Sci. USA, Oct 2006, "Isoelectric focusing technology quantifies protein signaling in 25 cells", Volume 103, Number 44: 16153-16158.
Kits and Instructions
The invention provides kits comprising compositions and/or instructions for practicing methods of the invention. As such, kits, cells, vectors and the like can also be provided. In alternative embodiments, the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof. SPLICED ISOFORM BIOMARKERS TO ASSESS RESPONSES TO CANCER STEM CELL TARGETED THERAPIES
In alternative embodiments, the invention provides compositions and methods for determining the pattern of alternatively spliced transcripts and their protein products to, e.g., distinguish leukemic progenitors from their normal counterparts, e.g., by
determining the pattern of alternatively spliced Stat5a specific splice isoforms. In alternative embodiments, the pattern of alternatively spliced Stat5a specific splice isoforms is used as a novel leukemic stem cell (LSC) identification marker.
In alternative embodiments, the invention provides compositions and methods to assess LSC specific responses to targeted agents such as JAK2 inhibitors, e.g., Stat5a specific splice isoforms can be used as biomarkers of response to JAK2 inhibition.
In alternative embodiments, one or both phosphoStat5a and phospho-JAK2 are used as biomarker or biomarkers of a response to a selective JAK2 inhibition, e.g., when selective JAK2 inhibition is used as a clinical treatment or when selective JAK2 inhibitors are tested in in vitro, in animals, or in clinical trials. In alternative
embodiments, both signatures of response (biomarker of response in clinical trial) are quantitatively measured; and if the alternative spliced forms do not decrease, the self- renewing LSC are resistant to treatment; and, if STAT5a isoforms are decreased or inhibited, LSC self-renewal capacity is decreased.
We have identified novel isoforms of phosphoStat5a and phospho-JAK2 via
RNA-seq that will provide functional LSC markers and will help to determine if different therapies will target this specific population. Our invention is the first to analyze specific isoform expression of STAT5 as a paradigm for human leukemia stem cell identification and to identify splice isoforms that predict cancer stem cell response. In addition, reductions in phosphoStat5a and/or phosphoJAK2 proteins are positive predictors of response to selective JAK2 inhibition. Both qRT-PCR confirmed decreases in transcripts and nanoproteomics confirmed decreases in these alternatively spliced proteins as functional biomarkers of response.
In alternative embodiments, the invention provides compositions and methods that comprise use of splice isoform specific qPCR, and equivalents, and/or nanoproteomics, to detect isoforms that sustain LSC self-renewal, including Stat5a isoforms and other pathway LSC specific splice isoforms in a prognostic kit for cancer stem cells (CSC). In alternative embodiments, the invention provides compositions and methods that comprise use of splice isoforms such as Stat5a isoforms as predictors of LSC response to selective JAK2 inhibition.
In alternative embodiments, the invention provides compositions and methods that comprise use of splice isoform patterns by qPCR and nanoproteomics to predict response to CSC targeted therapy.
In alternative embodiments, the invention provides compositions and methods to detect cancer stem cell specific JAK/STAT signaling pathway splice isoforms by R A sequencing, qRT-PCR and nanoproteomics, validated in CML, but applicable to cancer stem cells in the primary and metastatic niches, particularly in the setting of inflammatory cytokines and interleukins elaborated in cancer.
In alternative embodiments, biomarkers, or alternatively spliced forms, used to practice the invention can be detected using e.g., arrays, microarrays, proteomic arrays and the like, e.g., as described by: Oehler, et al, (2009) Blood, "The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data", Oct 8; 1 14(15):3292-8. Epub 2009 Aug 4; Fan, et al, Nature Medicine, May 2009,
"Nanofluidic proteomic assay for serial analysis of oncoprotein activation in clinical specimens," Volume 15, Number 5: 566-571; O'Neill, et al, Proc. Natl. Acad. Sci. USA, Oct 2006, "Isoelectric focusing technology quantifies protein signaling in 25 cells", Volume 103, Number 44: 16153-16158.
Figure 24: Nanoproteomic SAR302503 mechanism of action analysis. Sorted progenitors from mice spleen that where treated where analyzed using nanoproteonomics (CB 1000) technology. Panels shows phospho-JAK2 protein (upper left); total JAK2 protein (upper right); phospho-STAT5A protein (lower right) and p2-microblobulin (lower right) status after vehicle (blue) or selective JAK2 inhibitor (SAR302503; green) treatment.
Figure 25: Identification and quantification of transcript isoforms in LSC treated with vehicle or a selective JAK2 inhibitor. A) RNA-seq-based expression levels of isoforms involved in the Jak/Stat pathway, in vehicle-treated (blue) and SAR302503- treated (red) blast crisis CML sorted progenitors. B) Specific isoform expression after treatment with SAR302503 (JAK2 inhibitor) and dasatinib (BCR-ABL inhibitor), relative to vehicle treatment demonstrating synergistic inhibition of self-renewal gene isoforms such as phosphoSTAT5a and increases in interferon response genes. Kits and Instructions
The invention provides kits comprising compositions and/or instructions for practicing methods of the invention. As such, kits, cells, vectors and the like can also be provided. In alternative embodiments, the invention provides kits comprising: a composition used to practice a method of any of the invention, or a composition, a pharmaceutical composition or a formulation of the invention, and optionally comprising instructions for use thereof.
The invention will be further described with reference to the following examples; however, it is to be understood that the invention is not limited to such examples.
EXAMPLES
Example 1 : Inhibiting ADAR Enzyme to Decrease in Self-Renewal Capacity or Stem
Cells
RNA EDITING AS A NO VEL CANCER STEM CELL TARGET
This example provides data demonstrating that the methods and compositions of the invention are effective for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells.
Our research focused on dissecting the role of RNA editing in both normal HSC development and the progression of human chronic myeloid leukemia (CML) from chronic phase (CP) to blast crisis (BC). The qRT-PCR data shown here demonstrates that blast crisis LSCs harbor higher levels of IFN responsive ADAR1 pi 50 isoform than chronic phase progenitors and normal cord blood progenitors (p=0.014). An in vitro study of lentiviral ADAR1 pi 50 transduced progenitors from normal cord blood and chronic phase showed a significant change for preferred differentiation to GMP
(Granulocyte-macrophage progenitor) population, which has been shown to be the leukemia stem cells in CML. A similar inclination was observed in lentiviral shRNA ADAR1 transducer progenitors from blast crisis phase and chronic phase. ADAR1 may also play a role in self-renewal, as a significant of decrease in self-renewal capacity was observed in shRNA transducer chronic phase progenitors. The data shown herein illustrates a crucial role for ADAR1 in both cell differentiation and self-renewal of hematopoietic stem cells.
Example 2; Inhibiting Shh and Breaking the Dormancy of Cancer Stem Cells /
Biomarkers for Assessing Cancer Stem Cell Populations
COMPOSITIONS AND METHODS FOR DORMANT CANCER STEM CELL DETECTION AND ELIMINATION
This example provides data demonstrating that the methods and compositions of the invention are effective for: inducing in a stem cell susceptibility to BCR-ABL inhibition; activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle; or initiating cell cycling in a cancer stem cell; or breaking dormancy in a cancer stem cell; or radiosensitizing of a cancer stem cell; or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells; or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor. SONIC HEDHEGOG TARGETS AS BIOMARKERS OF PROGNOSIS AND RESPONSE FOR HUMAN CHRONIC MYELOGENOUS LEUKEMIA
This example provides data demonstrating that the methods and compositions of the invention are effective for measuring or determining, or predicting, chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance, and for measuring or determining, or predicting, a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted
Shh inhibition, or a selective Shh inhibition, comprising measuring or determining, individually or together, levels or amounts of GLIl and/or GLI2 transcript and/or protein. Here we investigated the role of Shh signaling in maintenance of dormancy. We show that, compared to chronic phase CML and normal progenitors, human blast crisis LSC harbor enhanced expression of the Shh transcriptional activator, GLI2, and decreased expression of a transcriptional repressor, GLI3. Treatment of human blast crisis LSC engrafted RAG2"/"yc"/" mice with a novel selective Shh inhibitor, PF-04449913 (see Figure 17a, Supplementary Figure la), reduced leukemic burden in a niche- dependent manner commensurate with GLI downregulation. Full transcriptome R A sequencing performed on FACS-purified human progenitors from PF-04449913 treated blast crisis LSC engrafted mice demonstrated greater Shh gene splice isoform concordance with normal progenitors than vehicle treated controls.
In addition, RNA sequencing after the Shh inhibition revealed significantly decreased cell cycle regulatory gene expression and splice isoform analysis demonstrated reversion toward a normal splice isoform signature for many cell cycle regulatory genes. Moreover, cell cycle FACS analysis showed that selective Shh inhibition permitted dormant blast crisis LSC to enter the cell cycle while normal progenitor cell cycle status was unaffected.
Finally, PF-04449913 synergized with BCR-ABL inhibition to reduce blast crisis LSC survival and self-renewal in concert with increased expression of Shh pathway regulators.
Our findings demonstrate that selective Shh antagonism induces cycling of dormant human blast crisis LSC, rendering them susceptible to BCR-ABL inhibition, while sparing normal progenitors. Implementation of novel LSC splice isoform detection platforms to assess efficacy of Shh inhibitor-mediated sensitization to molecularly targeted therapy may inform dormant cancer stem cell elimination strategies that ultimately avert relapse.
In this study, we investigated whether Shh signaling links human blast crisis LSC quiescence and self-renewal and whether these traits can be uncoupled with a therapeutic Shh antagonist, as a strategy to enhance sensitivity to BCR-ABL1 tyrosine kinase inhibitors (TKI).
First, to determine if Shh pathway activation fuels blastic transformation and LSC generation, chronic phase (n=7), blast crisis CML (n=21) and normal progenitor (n=15) samples (Supplementary Table 1, below) were analyzed by full transcriptome RNA sequencing (Supplementary Table 2, below), qRT-PCR and nanoproteomics.
Supplementary Table 1 : shows CML patient and normal sample characteristics.
Supplementary Table 2: shows Sample Characteristics for Full Transcriptome RNA Sequencing. PATENT
00015-195WO1/SD2012-037-2PCT
Supplementary Table 1
Figure imgf000067_0001
PATENT
00015-195WO1/SD2012-037-2PCT
Figure imgf000068_0001
00015-195WO1/SD2012-037-2PCT
Supplementary Table 2
Cytogenetics on primary patient samples used for RNAseq
Figure imgf000069_0001
Supplementary Table 3
Figure imgf000070_0001
Compared with normal progenitors, both chronic phase and blast crisis CML progenitors were typified by diminished expression of GLI3, a transcriptional repressor. Progression of chronic phase to blast crisis was marked by elevated GLI2, a critical Shh pathway activator (Fig. la). While seminal studies have linked Shh activation to cancer stem cell generation 4"6, others have shown that Shh signaling modulates the malignant niche7.
However, the role of Shh signaling in niche dependent human LSC maintenance had not been established. To recapitulate extrinsic growth regulatory cues provided by the LSC niche, blast crisis LSC were co-cultured on human SCF, IL-3 and G-CSF (SL/M2) stromal layers. Then, a novel small molecule smoothened (SMO) antagonist, PF-04449913, shown to compete for binding to human SMO (amino acids 181-787) with an IC50 of 4 nM (Supplementary Fig. la,); to inhibit Shh stimulated luciferase expression in mouse embryonic fibroblasts with an IC50 of 6.8 nM (n=5) (Supplementary Fig. lb, c); and to significantly reduce medulloblastoma growth in a Ptchl+/~p53+/~ allograft model (Supplementary Fig. 2a, b) at doses that decreased Shh target gene expression
(Supplementary Fig. 2c-e) was utilized to selectively inhibit Shh signaling in human LSC co-culture experiments. In these studies, LSC survival was significantly reduced by targeted SMO inhibition with PF-04449913 (p=0.047) (Fig. lb).
To delineate whether these LSC inhibitory effects could be recapitulated in vivo and if Shh driven LSC survival was niche dependent, human LSC engrafted immune deficient RAG2~/~yc ~/~ mice were treated for 14 days with PF-0444913 (100 mg/kg) by oral gavage. Human LSC engrafted mice were able to sustain treatment with no evidence of weight loss (Supplementary Fig. 3a). Progenitors purified by FACS from PF-04449913 treated LSC engrafted mice displayed reductions in GLI1 (p=0.056) and GLI2 transcript levels (p=0.08) (Fig. lc) in the splenic niche and a corresponding significant decrease (p=0.006) in spleen weight (Fig. Id) and size (Supplementary Fig. 3b). Molecular mechanisms of response were investigated with full transcriptome RNA sequencing analysis which revealed marked differences in gene expression between primary and bone marrow engrafted CML indicative of niche specific effects on gene expression
(Supplementary Fig. 4a). Following PF-044499913 treatment of mice engrafted with human leukemic progenitors, there was a reversion to a normal progenitor splice isoform pattern for 37 of 50 sonic hedgehog pathway genes in PF-04449913 (Fisher exact test, p=0.0048) (Fig. If, g). Of particular interest, Shh pathway gene isoforms that adopted a pattern similar to normal progenitors after Shh inhibitor treatment included pathway regulators such as SUFU, ARRB1, BTRC, CSKN1G1, FBXW1 1, and PRKACB.
Moreover, PF-04449913 treatment of human blast crisis LSC engrafted RAG2~/~ c _/~ mice reduced human GLI protein expression compared with vehicle treated controls as demonstrated by both immunofluorescence (Fig. le) and nanoproteomics (p=0.001) analyses (Fig. lh, i). However, FACS analysis revealed that Shh inhibitor responses were more robust in extramedullary than medullary niches (Supplementary Fig. 3 c, d) suggesting that resistant LSC were more prominent in the marrow perhaps as a consequence of quiescence induction.
Because previous mouse model studies linked Shh signaling to modulation of stem cell cycle control 8, we investigated whether Shh signaling induced dormancy by employing cell cycle FACS and full transcriptome RNA sequencing analysis of blast crisis LSC engrafted in RAG2~/~yc ~/~ mice. While human CD45+ leukemic cells homed to liver, spleen, myeloid sarcomas (tumor) and marrow (Fig. 2a), FACS analysis revealed that blast crisis GMP (LSC) were more prevalent in the marrow than other niches (Fig. 2b). In addition, cell cycle FACS analysis demonstrated that a significantly (p=0.045) greater proportion of marrow resident human leukemic cells were dormant compared with those in the splenic niche (Fig. 2c). Full transcriptome RNA sequencing analysis of engrafted leukemic progenitors revealed repression of cell cycle regulators (family wise p-value 0.02) in response to PF-04449913 compared with vehicle treatment (Fig. 2e and Supplementary Fig. 4b, c) and a shift toward a normal progenitor cell cycle gene splice isoform expression pattern for 75 of 1 10 isoforms (Fisher exact test, p=0.0006) (Fig. 2f, g). Moreover, cell cycle FACS analysis demonstrated that PF-04449913 treatment of LSC engrafted mice reduced the fraction of leukemic progenitors in GO commensurate with an increase in the Gl fraction (Fig. 2d and Supplementary Fig. 4d) suggesting that the dormant LSC population had been induced to enter the cell cycle through selective Shh inhibition potentially rendering them sensitive to agents that target dividing cells.
For Shh inhibition to be effective in LSC eradication, normal hematopoietic stem cells must be spared. While some mouse model studies suggest that Shh signaling is dispensable for adult hematopoiesis 9, others demonstrate that Glil regulates
hematopoietic stem cell fate decisions 10.
However, the role of Shh signaling in normal human hematopoietic stem and progenitor cell (HSPC) maintenance had not been examined extensively in vitro or in primary sample xenograft (primagraft) models that permit robust engraftment. Thus, we examined the effects of PF-04449913 treatment on normal HSPC phenotype and function. Following, PF-04449913 treatment the differentiation capacity of normal human HSPC in hematopoietic progenitor assays (Fig. 3 a) was unimpaired and the percentage of HSPC remained constant after 7 days of SL/M2 stromal co-culture period with PF-04449913 (Fig. 3b). When CD34+ cord blood engrafted NSG mice were treated with PF-04449913 (100 mg kg for 14 days), the frequency of HSPC as well as myeloid and lymphoid cell fate commitment remained comparable to vehicle treated controls (Fig. 3c, d). Moreover, human hematopoietic cell cycle status was unaltered (Fig. 3e). These data suggest that, unlike LSC, normal human HSPC survival, cell fate decisions and cell cycle regulation are Shh independent thus, explaining their resistance to Shh inhibition and providing a therapeutic window between normal HSC and LSC.
The reduced dormancy of blast crisis progenitors following Shh inhibition compared with their normal progenitor counterparts provided the impetus for determining if LSC were rendered sensitive to dasatinib, a potent TKI (Fig. 4a). Combination therapy with dasatinib and PF-04449913 reduced myeloid sarcoma (Fig. 4b) formation
(pO.0001) and BCR-ABL expression (p=0.0331) (Fig. 4c) in LSC engrafted marrow. Furthermore, Hedgehog PCR array analysis revealed that dasatinib synergized with PF- 04449913 by significantly increasing expression of negative regulators of the Shh pathway (p<0.05), including NUMB, PRKACB, FKBP8, CSNK1A1 and CSNK1D (Fig. 4d). Combination therapy led to a marked reduction in marrow LSC (p=0.0016) (Fig. 4e) and LSC serial myeloid sarcoma transplantation potential (p=0.02) (Fig. 4f) providing the impetus for developing combination BCR-ABL and Shh inhibitor clinical trials for imatinib resistant and advanced phase CML patients.
While Ptc-1+/" mouse model experiments have linked Shh modulation of cell cycle regulators to hematopoietic stem cell regeneration8, the role of Shh signaling in human normal progenitor and LSC dormancy had not been established. In robust primagaft assays, we show, for the first time, that marrow resident GLI expressing human blast crisis LSC become dormant thereby enabling them to evade therapy. Following treatment with a clinical Shh antagonist, PF-04449913, dormant LSC were activated to enter the cell cycle thereby rendering them susceptible to agents that target proliferating cells, such as dasatinib, and reducing LSC self-renewal potential. In contrast, normal hematopoietic progenitor cell cycle status and cell fate were unaffected. Together these data support clinical implementation of RNA sequencing derived predictive biomarkers of CSC response and selective Shh pathway inhibition as a strategy to invoke cycling of dormant LSC thereby sensitizing them to BCR-ABL inhibitors and obviating therapeutic resistance. This approach may also provide a viable strategy for CSC eradication in other refractory malignancies.
Methods
Patient sample preparation
Normal cord blood and adult peripheral blood samples were purchased from All Cells or obtained from the Cord Blood/Reproductive Sciences Core at UCLA. CML samples were obtained from consenting patients at the UC San Diego, Stanford
University, and the University of Toronto Health Network according to Institutional Review Board approved protocols.
Transcriptome Analysis
The SOLiD™ Total RNA-Seq kit (Applied Biosystems part # 4445374) was used to prepare libraries from normal and blast crisis CML samples, which were sequenced on Solid v.3 plus instruments. Gene isoform models were developed by first combining the isoform models from June 2011 versions of REFSEQ™ n, UCSC Known Genes12, and ENSEMBL™ 13 and then creating a nonredundant set of models using the
"CUFFCOMPARE™" program from version 0.9.3 of the CUFFLINKS™ software package14. Then, we mapped RNA-seq reads to the nucleotide sequences of the isoform models using BWA 15 with default parameters and then translated the alignment coordinates in hgl9/GRCh37 human genome reference sequence coordinates using a custom script.
Stromal co-culture and in vitro drug treatment
Normal or blast crisis CML CD34+ cells were plated on confluent mitomycin-C treated SL/M2 cells with different doses of PF-04449913, dasatinib, a combination of PF- 04449913 and dasatinib, or vehicle for 14 days. After 1 week of culture, FACS was used to quantify human progenitors and progenitors were FACS sorted into hematopoietic progenitor assays. Colonies were scored after 2 weeks in culture.
Human Progenitor Primagrafts and Treatment
Equal numbers of primary normal or blast crisis CML CD34+ cells were transplanted intrahepatically into neonatal RAG2"/"yc"/" mice to form primagrafts, according to established methods l' 3. At 8-12 weeks post-transplant, mice were treated with PF-04449913, Dasatinib, a combination of PF-04449913 and Dasatinib, or drug vehicle for 14 days followed by FACS analysis of human hematopoietic engraftment in hematopoietic tissues.
Quantitative RT-PCR Analysis of GLI family gene Expression
Normal or BC CML cells from patient samples at the University of California San Diego, Stanford University, MD Anderson Cancer Center and the University of Toronto Health Network according to Institutional Review Board approved protocols, were CD34+ selected and FACS-sorted for analyses using a FACS Aria and FLOWJO™ software as described previously19'20. Quantitative PCR (qRT-PCR) was performed in duplicate on an ICYCLER™ using SYBR Greener Super Mix (Invitrogen, Carlsbad, California), GLI primers were purchased from ABSciences-Catalog number 4331 182: GLI
l(HS00171790_ml), GLI 2 (HS00257977_ml) and GLI 3 (HS00609233_ml). The following primers were used in reactions run with SYBR: BCR-ABL Forward:
ctccagactgtccacagcat (SEQ ID NO:4), BCR-ABL Reverse: ccctgaggctcaaagtcaga (SEQ ID NO:5), HPRT Forward: cgtcttgctcgagatgtgatg (SEQ ID NO:6), HPRT Reverse:
tttatagccccccttgagcac (SEQ ID NO:7). Relative levels of mRNA were determined according to standard curves. All values were then normalized to HPRT or RPL27 values from the same sample.
TAQMAN™ primer/probe sets (ABI) for FoxMl (Mm00514924_ml), Glil (Mm00494645_ml), Gli2 (Mm01293117_ml), Mycn (Mm00476449_ml), Ptchl (Mm00436026_ml), Ptch2 (Mm00436047_ml), Sfrpl (Mm00489161_ml), Smo (MmOl 162710_ml) and mouse GAPDH (4352339E), on the ABI 7900HT instrument. Target gene expression levels were normalized to mouse GAPDH and calibrated to vehicle treated mice to yield the relative quantitation (RQ) value.
Confocal Fluorescence Microscopic Analyses
Spleens of xenografted mice that were subjected to 2 weeks of treatment were embedded in OCT freezing media (Sakura, Torrance, CA), frozen and sent off to histology core (UCSD Moores Cancer Center). For immunostaining, antibodies were used with MOM kit (Vector, Burlingame, CA). Primary antibodies used were anti-GLI2 (Abeam) and Alexa 647-conjugated anti-human CD45 (1 :25, Serotec). Stained sections were mounted using PROLONG® Gold antifade with DAPI (Invitrogen). Confocal fluorescence images were acquired using Zeiss LSM510™ or Olympus FLUOVIEW FVlOi™ microscopes and ADOBE PHOTOSHOP CS5™ software.
Nanoproteomic immunoassay
Nanofluidic phospho-proteomic immunoassay (NPI) experiments were performed with the NANOPRO 1000™ instrument (Cell Biosciences) and all samples were run in triplicate at least. The FIREFLY™ system first performed a charge-based separation (isoelectric focusing). Predicted pis were calculated with SCANSITE™. Each sample was run on a panel of different pH gradients (pH 5-8) to optimize the resolution of different peak patterns. After separation and photo-activated in-capillary immobilization, GLI-2 was detected using GLI2-specific antibody (Abeam). A 2-microglubulin-specific antibody 2Μ; Upstate) was used to normalize the amount of loaded protein. The peaks were quantified by calculating the area under the curve (AUC).
Primagrafts, in vivo drug treatment, and engraftment analysis
Immunocompromised RAG2~/~yc~/~ mice were bred and maintained in the UC San Diego Moores Cancer Center vivarium. Neonatal mice were transplanted intrahepatically with normal progenitors or LSC from primary patient samples according to our previously published methods19. Upon detection of tumor or peripheral blood
engraftment, mice were treated daily by oral gavage with vehicle (50% 1,2 Propandiol , 50% HBSS or methylcellulose), PF-04449913 (100 mg/kg dissolved in vehicle), Dasatinib (50 mg/kg dissolved in vehicle), combination of PF-04449913 (100 mg/kg) and dasatinib (50mg/kg). After treatment, mice were euthanized and single cell suspensions of hematopoietic tissues were analyzed for human engraftment by FACS as described previously19'20. Similarly, NOD. Cg-PrkdcAscid I12rgAtmlWjl/SzJ female mice at 7-10 weeks were irradiated sublethally and transplanted with 100K CD34+ human cord blood cells via retro-orbital injection. Eight weeks after transplantation of cord blood cells, the mice were treated for 14 days with either vehicle, or PF-04449913 via oral gavage.
Stromal co-culture and in vitro drug treatment
The mouse bone marrow stromal cell lines M2-10B4 (M2) and SL/SL (SL) were provided by StemCell Technologies on behalf of Dr. Donna Hogge in the Terry Fox Laboratory (Vancouver, British Colombia). One day prior to co-culture, the cell lines were treated with mitomycin-C (1 mg/ml) and plated in a 1 : 1 mixture in total concentration of 100,000/ml. 10,000-20,000 CD34+ blast crisis CML or normal cells were then plated on adherent SL/M2 stromal cells, cultured for 7 days, and analyzed by FACS as described previously19. To assess expansion of normal human HS/PCs. irradiated OP9 (M2 clone) stromal cells (20 Gray on a Saxon-Markl irradiator) were co-cultured with 50,000 human CD34+ cord blood. OP9M2 stroma was grown in AlphaMem from Gibco with 20% Hyclone FBS, 1% pen strep glutamine and supplemented with cytokines: 50ug/ml SCF, lOug/ml thrombopoietin, and lOug/ml Flt3.
Transcriptome Splice isoform analysis
Four vehicle-treated and four PF-04449913 -treated samples constituting two sets of four technical replicates. The reads from the four RNA sequencing experiments under each treatment regimen were then combined for analysis of effects of vehicle and PF- 04449913 -treatment containing a total of 65M and 64M reads, respectively and compared with normal FACS purified cord blood CD34+CD38+Lin" progenitors.
Cell cycle FACS analysis
Single cell suspensions of bone marrow cells from mice treated with PF-0449913 or vehicle were immunostained with Alexa647-conjugated anti-human CD45
(BioLegend) in 2% fetal bovine serum/PBS followed by live cell staining using the LIVE/DEAD® Fixable Near-IR Dead Cell Stain Kit (Invitrogen). Surface stained cells were then fixed in 70% ethanol overnight. Fixed, surface stained cells were
immunostained with FITC-conjugated anti-Ki-67 (Abeam, 1 : 100) in 0.15% saponin/2% fetal bovine serum/PBS, washed twice in saponin-containing staining media and incubated with 7- AAD (^g/mL in 0.1M sodium citrate/ 5mM EDTA pH8.0/ 0.15M NaCl/ 0.5% BSA/ 0.02% saponin). Stained samples were analyzed using a FACSARIA™ and FLOWJO™21. SMO Radioligand Competition Binding Assay
Membranes were prepared from a stable cell line created in HEK293FlpIn-TetR cells (Invitrogen) using Flp recombinase-mediated insertion of the pSecTag-FRT/V5-His vector containing a cDNA encoding amino acids 181-787 of human Smo fused to the murine Igk leader sequence to produce a cell surface expressed Smo 181-781 protein. LacZ-negative cells were analyzed for binding a well characterized cyclopamine- competitive tritiated Smo antagonist22. The tritiated ligand was prepared using Crabtree's catalyst and tritium gas. The labeled material was purified by RP HPLC (53.1 Ci/mmol specific activity at 99% purity). For the binding competition assay, ΙΟΟμΙ of assay buffer was added to all the wells of a 96 well GF/B filter plate (Millipore MULTISCREEN- HTS-FB™ cat# MSFBN6B50) . The plates were counted in a TOPCOU T™
scintillation counter (Perkin Elmer). Data analysis uses EXCEL™ for % Inhibition and GRAPHPAD PRISM™ for IC50 calculation.
Mouse Embryonic Fibroblast Gli-Luciferase Assay
Mouse Embryonic Fibroblasts expressing luciferase under control of an 8X Gli- response element (Gli-Luc MEFs)23 were obtained from the Pfizer transgenic core facility. Luciferase activity was quantified with an ENVISION™ plate reader (Perkin Elmer). Graphpad Prism was used for data analysis and IC50 calculation.
Selective Shh Inhibition in a mouse medulloblastoma allograft model
Primary medulloblastoma tumors were harvested from Ptch+/"p53+/" or Ptch+/~p53_/~ mice and propagated as allografts in SCID-bg mice 6-8 weeks of age (20 grams). Freshly isolated tumor fragments of approximately 50 mm3 were surgically implanted
subcutaneously into the hind flank region. Body weights and tumor size (length and width) were measured at regular intervals using a caliper and tumor volume was calculated using the formula: length (mm) x width (mm) x width (mm) x 0.4. For the tumor growth inhibition studies, cohorts of Ptch+/"p53+/" medulloblastoma allograft bearing mice with tumors ranging from 200 mm3 to 1000 mm3 were dosed daily by oral gavage with vehicle (30% PEG 400/70% PBS) or with PF-04449913 formulated in vehicle.
Assessment of Target Gene Expression in Mouse Model: Microarray Processing
Microarray data were RMA normalized using BIOCONDUCTOR AFFY™ package. Differentially expressed genes were identified based on joint thresholds oft- test pvalue <0.01 and fold change >2. Their human orthologs were mapped using HOMOLOGENE BUILD 62™. They were compared with curated gene sets from a variety of pathway/signature databases and enrichment P-value was determined using hypergeometric statistics calculated with MATLAB™. More specifically, the probability of observing at least (k) genes from a gene set is given by
Figure imgf000078_0001
where (f) is size of the gene set, (n) is the # of differentially expressed genes, (g) is the total number of unique human ortholog genes of mouse probes on the microarray.
The obs/exp ratio was calculated as k/(f*n/g).
Statistical analysis
Statistical analyses were performed with Microsoft Excel and Graphpad Prism software. Continuous variables for each comparison group were assessed for distribution through univariate statistics. If the assumption of normal distribution could be supported, then the Student's t test was performed for comparison of two samples with assessment of equality of variance with an F statistic. If the assumption of normal distribution was not supported, nonparametric testing was performed with the two samples Wilcoxon test using the t approximation for samples with N of less than 20.
FIGURE LEGENDS
Figure 8. Blast Crisis LSC Activate Sonic Hedgehog in Selective Niches: Fig. 8a. GLll and GLI2 transcripts were compared by TaqMan RT-PCR in FACS-purified human cord blood and peripheral blood CD34+CD38+Lin"PI" progenitor cells (n=9, black), chronic phase CML (n=7, blue) and in blast crisis CML (n=10, red) patient samples.
Comparative qRT-PCR analysis of GLI3 transcript levels was performed on normal (n=7, black), chronic phase (n=6, blue) and blast crisis CML (n=7, red) cells. Values were normalized to RPL27 or HPRT housekeeping genes, and set to 1 for the normal progenitors, b. FACS analysis revealed a reduction in leukemic progenitor survival following 7 days of PF-04449913 (1 μΜ, purple) compared with vehicle (DMSO, blue) treatment in SL/M2 co-cultures, c. Down regulation of GLI expression analyzed by TaqMan RT-PCR in human LSC engrafted bone marrow derived from PF-04449913 and vehicle treated mice. d. Spleen size in blast crisis CML LSC engrafted mice after 14 days of treatment with vehicle (n=16, blue) or PF-04449913 (n=6; 100 mg/kg daily, purple), e. Immunofluorescence analysis of splenic sections from no transplant or LSC engrafted mice treated with vehicle or PF-04449913. Photomicrographs of sections stained with DAPI (upper panel) and antibodies specific for human CD45 (upper middle panel), human GLI (lower middle panel) and the merged image (lower panel), f. Isoform-level transcriptome measurements of Shh pathway genes in vehicle-treated (blue) and PF- 04449913 -treated (purple) CML BC LSC and in normal CD34+CD38+Lin" FACS-purified progenitors (black). Of the 87/249 genes/isoforms in the Shh pathway, 50 isoforms of 18 genes were significantly differentially expressed in either PF-04449913 -treated or normal cells when compared to vehicle-treated cells. In 37 of 50 instances (bold), the expression level of treated and normal isoforms followed the same directional change (concordant) when compared to vehicle-treated cells, g. A significant concordance was observed in the relative expression of the 50 isoforms in PF-0449913 -treated and in normal cells relative to vehicle treated cells, h. Nanoproteomic (CB 1000) traces of total GLI protein after vehicle (blue) and PF-04449913 (green) treatment, i. Quantification of GLI protein expression in splenic CD34+ cells derived from vehicle (n=3) or PF-04449913 (n=3) treated LSC engrafted mice. GLI expression was determined after normalizing the area under the curve (AUC) to a p2-microglobulin 2Μ) loading control.
Figure 9. Induction of Blast Crisis LSC Cycling with Sonic Hedgehog Inhibition: Fig. 9a. Frequency of CD45+ cells in hematopoietic tissues (liver n=4, spleen n=3, bone marrow n=6, tumor n=3) of blast crisis CML engrafted mice. b. FACS quantitation of common myeloid progenitors (CMP), granulocyte-macrophage progenitors (GMP) and megakaryocyte-erythroid progenitors (MEP) populations within each hematopoietic tissue, c. Comparison of cell cycle status (GO, green; Gl, light blue; G2/S, navy) of human CD45+ blast crisis CML progenitors engrafted mice in the bone marrow and spleen. More human CD45+ blast crisis cells in the marrow were in GO than those in the splenic niche (n=8) d. Representative FACS plots comparing Ki67 and 7AAD in bone marrow engrafted viable human CD45+ cells after 14 days of vehicle or PF-04449913 treatment, e. Gene set enrichment analysis for the significantly down-regulated pathway "Regulators of Cell Cycle" (please see methods for details). The core enrichment subset shows the 18 most down regulated genes among the 41 genes in the pathway, f. Isoform- level transcriptome measurements of cell cycle genes in vehicle-treated (blue) and PF- 04449913 -treated (purple) blast crisis CML LSC and in normal CD34+CD38+Lin" FACS- purified progenitors (black). Of the 84/454 genes/isoforms in the cell cycle, 110 isoforms of 51 genes were significantly differentially expressed in either PF-04449913 -treated or normal cells when compared to vehicle-treated cells. In 75 of 1 10 instances (bold), the expression level of treated and normal isoforms followed the same directional change (concordant) when compared to vehicle-treated cells, g. A significant concordance was observed in the relative expression of the 75 isoforms in PF-0449913-treated and in normal cells relative to vehicle treated cells.
Figure 10. Shh Inhibition Spares Normal Human Hematopoietic Stem and Progenitor cells: Fig. 10a. Left, Differentiation into CFU-Mix (black), BFU-E (red), CFU-G (orange), CFU-M (yellow), CFU-GM (blue) of normal cord blood HSPC was assessed in hematopoietic progenitor assays (n=3) after PF-04449913 (1 M) or vehicle treatment for 12 days. Right, Representative photomicrographs of cord blood colonies after 12 days of treatment with vehicle (DMSO) or PF-04449913 (1 M). b. Human cord blood (n=3), CD34+38+Lin"PI" cells, plated on SL/M2 stroma and treated with vehicle (DMSO) or PF-04449913 (1 μΜ) for 7 days followed by FACS analysis, c.
Representative FACS plots depicting HSPC, myeloid and lymphoid differentiation in human cord blood engrafted mice after 14 days of treatment with vehicle (n=3) or PF- 04449913 100 mg/kg (n=4). d. FACS analysis was used to determine the total human CD45+, HSPC, myeloid and lymphoid cell count in bone marrow after 14 days of treatment with vehicle (n=3, green) or 100 mg/kg of PF-04449913 (n=4, purple), e. FACS quantification of GO (green), Gl (light blue) and G2/S (navy) human CD45+ cells in cord blood engrafted marrow after 14 days of treatment with vehicle (n=3) or PF- 04449913 lOOmg/kg (n=4).
Figure 1 1. Combined BCR-ABL and Shh Inhibition Reduces LSC Survival in the Niche: Fig. 1 1a. Schematic of in vivo experiments. RAG2"/"yc "/" pups were transplanted intrahepatically with 50,000 CD34+ cells within 48 hours of birth. After 8 to 10 weeks, blast crisis CML engrafted mice were treated daily for 14 days by oral gavage with vehicle, PF-04449913 (100 mg/kg), Dasatinib (50 mg/kg) or combination (PF-04449913 100 mg/kg and Dasatinib 50 mg/kg). Hematopoietic tissues were FACS analyzed for leukemia engraftment and qRT-PCR for BCR-ABLl transcripts, b. Myeloid sarcoma count of blast crisis CML engrafted mice in each treatment group vehicle (n=13, green), PF-04449913 (n=7, purple), dasatinib (n=6, red) and combination (n=3, black) after 14 days of treatment, c. BCR-ABLl transcripts in the spleens of blast crisis CML engrafted mice after 14 days of treatment with vehicle (green, n=9), PF-04449913 (purple, n=l 1), dasatinib (n=8, red) or combination (n=5, black) d. Shh gene expression in FACS purified human progenitor cells from blast crisis LSC engrafted mouse marrow treated with vehicle (n=3, green), PF-04449913 (n=4, purple) dasatinib (n=4, maroon), combination (n=3, dark grey) was analyzed via qPCR array (SA Biosciences). Expression levels of 5 Shh regulatory genes (NUMB, PRKABC, CTNNB 1, FKBP8, CSNK1A1, CSNK1D and STK36) were significantly upregulated by the synergistic effects of PF-04449913 and dasatinib treatment after performing limma test. e. FACS analysis of percentage of marrow engrafted blast crisis LSC (n=3 patients) after 14-day treatment with vehicle (n=31, green), PF-04449913 (n=25, purple), dasatinib (n=27, maroon) and combination (n=27, grey), f. Myeloid sarcoma counts in mice serially transplanted with vehicle (n=12, green), PF-04449913 (n=12, purple), dasatinib (n=8, maroon) or combination (n=3, grey) treated human progenitors.
Figure 12 (Supplementary Figure 1): PF-04449913 structure and chemical properties: Fig. 12a. Chemical structure of PF-04449913, a selective smoothened (SMO) antagonist, b. Competition-binding assay using a characterized cyclopamine-competitive SMO antagonist. PF-04449913 competes with the radiolabeled SMO antagonist for binding to human SMO (amino acids 181-787) with an IC50 of 4 nM (4.3 nM +/- 5.2 nM, N= 5). c. Inhibition of Shh stimulated luciferase expression using mouse embryonic fibroblasts expressing luciferase under control of an 8X Gli-response element (Gli-Luc MEFs). d. Dose dependent inhibition by PF-04449913 in the Gli-Luc MEF reporter assay; PF-04449913 inhibits Shh stimulated reporter activity with an IC50 of 6.8 nM (n=5).
Figure 13 (Supplementary Figure 2): PF-04449913 Inhibits Shh Signaling in Ptch+/"p53+/" Tumor model: Fig. 13a. Anti-tumor activity of PF-04449913 against Ptch+/- p53+/- medulloblastoma. Allograft (-700 mm3) bearing SCID-bg female mice were dosed orally once a day for six days with 100 mg/kg of PF-04449913 or vehicle. Tumor size (length and width) was measured using a caliper at regular intervals and tumor volume was calculated by standard procedure. Results are mean +/- standard error of the mean (n = 3 animals per group), b. Dose dependent anti-tumor efficacy of PF-04449913 against Ptch+/-p53+/- medulloblastoma allografts. Cohorts of allograft (-200 mm3 to 1000 mm3) bearing SCID-bg female mice were dosed orally once a day for six days with different dose levels of PF-04449913. Tumor size (length and width) was measured using a caliper at regular intervals and tumor volume was calculated by standard procedure. The percent change of an individual tumor volume was calculated from the tumor volume on the first day of dosing to the sixth day. Results are expressed as mean +/- standard deviation (n = 3 to 12 animals per group; p< 0.01 for 1 mg/kg group and p< 0.001 for all other groups), c. Hh pathway inhibition in PF-04449913 treated Ptch+/-p53+/- medulloblastoma allografts. Ptch+/-p53+/- allograft bearing SCID-bg female mice were dosed orally once a day for six days with 100 mg/kg of PF-04449913 or vehicle.
Expression levels of FoxMl, Glil, GH2, Mycn, Ptchl, Ptch2, Sfrpl and Smo were determined by real time PCR. The vehicle-treated levels for each gene were normalized to 100%. d. Genes significantly down-regulated by PF-04449913 treatment in Ptch+/~p53_/~ mice. Hierarchical clustering was performed on Z-score transformed data using correlation similarity metric and centroid linkage method, e. Gene signatures enriched for within the top 31 PF-04449913-downregulated genes in Ptch+/-p53 -/- mice. Statistical significance of over-representation and observed/expected ratio were calculated as described in supplementary methods.
Figure 14 (Supplementary Figure 3): LSC Responses to Shh Inhibition are Niche Dependent: Fig. 14a. Percentage of weight changes in each treatment group of mice over the course of 14 days of treatment, b. Representative photographs of spleens from no transplant, blast crisis CML engrafted mice treated with vehicle or PF-04449913. c.
Representative FACS plots of blast crisis CML engrafted mice treated with vehicle, PF- 04449913, dasatinib, or combination, d. Total blast LSC count in bone marrow, spleen and liver after 14 days of treatment with vehicle (n=15) or PF-04449913 (n=14).
Figure 15 (Supplementary Figure 4): Decreased Cell Cycle Regulator Expression
Enhances LSC Cycling: Fig. 15a. Heat-map of normalized expression values on log2 scale for 10,573 highly expressed genes in FACS-purified primary blast crisis CML CD34+CD38"Lin" and CD34+CD38+Lin" (SOLiD RNAseq gene count per million reads >1 in all the 6 samples); RAG2"/"g-c"/" marrow engrafted blast crisis CML CD34+CD38" Lin" and CD34+CD38+Lin"; and normal cord blood CD34+CD38"Lin" and
CD34+CD38+Lin" samples. Hierarchical cluster analysis based on Euclidean distance measure was performed to check the similarities between the samples, b. Gene set enrichment analysis (GSEA) summary table obtained from SOLiD RNAseq data comparing PF-04449913 treated mice (n=4) to control (n=4) (average 24.7 - 58.0 million mapped reads/sample). In this analysis, 13,850 protein-coding genes with >10 reads in at least one sample were included. Read counts were normalized16 and genes ranked by Significance Analysis of Microarrays (SAM) 11. Eight a priori cell cycle pathways were considered in the GSEA analysis 18, with significance assessed by gene-wise permutation. The "Regulation of Cell Cycle" pathway was significantly down-regulated in human progenitors from PF-04449913 treated mice; 7 of 8 investigated pathways decreased. Table columns are pathway name, number of genes (pathway size), nominal p-value; FDR adjusted q- value and adjusted p-value controlling for the family -wise error rate. c. GSEA enrichment plot for the significantly down-regulated pathway (Regulation of Cell Cycle). The horizontal heatmap shows SAM score in descending order for all 13,850 genes. The GSEA enrichment score for the pathway (genes indicated as vertical bars) is indicated as the maximal excursion of the green line. Because the pathway is down regulated, the core enrichment subset consists of the right-most 18 among the 41 genes in the pathway, d. Cell cycle analysis of bone marrow from blast crisis CML engrafted mice after 14 days of vehicle (n=8) or PF-04449913 (n=8). *p<0.05 for both G0 and Gi population compared with vehicle treatment.
Figure 16: SHH Pathway Gene Expression Pattern Portends BC Transformation. Using the SHH pathway allowed us to distinguish CML CP from BC and normal counterparts, demonstrating that this pathway is activated with disease progression.
a. Heatmap from unsupervised agglomerative hierarchical clustering of sonic hedgehog (SHH) pathway genes using RNA Seq data from FACS-purified progenitors (CD34+CD38+lin~PI~) from 8 chronic phase (CP) and 9 blast crisis (BC) patients, 3 normal cord blood (CB) and 3 normal peripheral blood (NPB) sample. Red indicates over- and green, under-expression relative to the median RPKM (log2 scale). Grey represent not expressed (RPKM=0). b. Principal components plots derived from RNA Seq data for 41 genes in the SHH pathway, from 8 chronic phase (CP; black triangles) and 9 blast crisis (BC; red circles) subjects, as well as 3 cord blood normal samples (CB; blue diamonds) and 3 normal peripheral blood (NPB; blue circles), c. Box plots for GLI2 expression of 7 chronic phase (CP) and 6 blast crisis (BC) non-treated subjects, as well as 3 cord blood normal samples (CB) and 3 normal peripheral blood (NPB). Two-sided Jonck!ieere- Terpstra trend test: p=0.014. d. GLI1 and GLI2 transcripts were compared using quantitative RT-PCR in FACS-purified human cord blood and normal peripheral blood CD34+CD38+Lin"PT progenitor cells (n=9, black), chronic phase CML (n=7, blue) and in blast crisis CML (n=10, red) patient samples. Values were normalized to RPL27 or HPRT housekeeping genes, and set to 1 for the normal progenitors. (Student's t-test *p<0.05).
Figure 17: Figure 2. Selective SHH Inhibition Reduces BC LSC Burden in Selective Niches. In our preclinical model that utilized human samples, we tested a SHH pathway inhibitor on AML and CML samples and observed a decrease in survival after treatment. We also identified GLI2 as a biomarker of response.
a. Chemical structure of PF-04449913, a selective smoothened (SMO) antagonist, b. FACS analysis revealed a significant (Student's t-test, *p=0.047) reduction in blast crisis leukemic progenitor survival (n=4 patients) following 7 days of PF-04449913 (1 mM, purple) compared with vehicle (DMSO, blue) treatment in SL/M2 co-cultures, c. Cord blood (n=3) or AML (n=4 patients) CD34+ cells were plated on SL/M2 co-cultures and treated with vehicle (DMSO) or PF-04449913 (luM) for 7 days. Colony forming unit (CFU) survival was determined and compared to vehicle treatment. (Student's t-test, **p=0.001). d. Spleen weight in blast crisis CML LSC engrafted mice after 14 days of treatment with vehicle (n=16, blue) or PF-04449913 (n=12; 100 mg/kg daily, purple). A significant (Student t-test, *p=0.006) reduction is observed after PF-044449913 treatment, e. Nanoproteomic (CB 1000) traces of total GLI2 protein after vehicle (blue) and PF- 04449913 (green) treatment, f. Quantification of GLI2 protein expression in sorted progenitors derived from vehicle (n=3) or PF-04449913 (n=3) treated LSC engrafted mice. GLI2 expression was determined after normalizing the area under the curve (AUC) to a b2-microglobulin 2Μ) loading control (Student's t-test *p=0.001) g. Confocal fluorescence microscopic analysis of spleen sections from no transplant or LSC engrafted mice treated with vehicle or PF-04449913. Photomicrographs of sections stained with DAPI and antibodies specific for human CD45, human GLI2 and the merged image.
Figure 18: SHH PATHWAY Inhibition Induces Cycling of Dormant BC LSC. a. Heatmap from unsupervised agglomerative hierarchical clustering of cell cycle pathway genes using RNA Seq data from FACS-purified progenitors (CD34+CD38+lin~PT ) from 8 chronic phase (CP) and 9 blast crisis (BC) patients sample. Red indicates over- and green, under-expression relative to the median RPKM (log2 scale). Grey represent not expressed (RPKM=0). b. Network analysis performed on differentially expressed genes between BC and CP revealed CDKN1A as a key hub for cell cycle difference, c. Representative FACS plots comparing Ki67 and 7AAD in bone marrow engrafted viable human CD45+ cells after 14 days of vehicle or PF-04449913 treatment, d. Cell cycle analysis of bone marrow from blast crisis CML engrafted mice after 14 days of vehicle (n=8) or PF-04449913 (n=8). Student's t-test *p<0.05 for both G0 and Gi population compared with vehicle treatment, e. GSEA enrichment plot for the significantly down- regulated pathway (Regulation of Cell Cycle). The horizontal heatmap shows SAM score in descending order for all 13,850 genes (SHH pathway genes indicated as vertical black bars). The GSEA enrichment score for the pathway (0-45) is indicated as the maximal excursion of the green line. f. Normalized gene expression values for the 18 genes in the core enrichment subset from the "Regulation of Cell Cycle" pathway. All the genes had a negative SAM score and are sorted in order of descending SAM score along the x-axis. This order agrees with the order in the GSEA enrichment plot, where expression levels for these genes are significantly reduced in the PF-04449913 treated mice.
Figure 19: SHH Inhibition in clinical samples. We tested the effects of SHH pathway inhibition in a clinical study and observed similar results to what we observed in our preclinical model.
a. Characteristics of patients enrolled in clinical trial NCT01546038. b. Clinical response to PF-04449913 in the bone marrow of AML patient samples, c. Representative FACS cell cycle plots of Ki67 and 7AAD staining of human CD34+CD38- and CD34+ CD38+ cells derived from primary patient samples after 4 weeks (C1D28) of treatment with PF-04449913 (40mg) on the Phase 1 clinical trial, d. Cell cycle analysis (peripheral blood-CD45+PI-) from a secondary AML patient (AML-4, Supplementary table 1) that was treated with PF-04449913 (40mg) for 4 weeks on the Phase 1 clinical trial. Student's t-test *p<0.05 for both Go and Gi population compared with pre-treatment. e.
Characteristics of patient samples analyzed for their cell cycle study. Patients in red represent clinical responders.
Figure 20: SHH Inhibitor Induced cell cycle activation Enhances BC LSC TKI Sensitivity. Using our preclinical model, we demonstrated that using SHH pathway inhibitor in combination with current therapy is the best possible route for curative treatment.
a. Schematic of in vivo experiments. RAG2"/"yc "/" pups were transplanted intrahepatically with 50,000 CD34+ cells within 48 hours of birth. After 8 to 10 weeks, blast crisis CML engrafted mice were treated daily for 14 days by oral gavage with vehicle, PF-04449913 (100 mg/kg), Dasatinib (50 mg/kg) or combination (PF-04449913 100 mg/kg and Dasatinib 50 mg/kg). Hematopoietic tissues were FACS analyzed for human leukemic engraftment and qRT-PCR for BCR-ABL1 transcripts, b. Myeloid sarcoma count in blast crisis CML engrafted mice in each treatment group vehicle (n=13, blue), PF-04449913 (n=7, purple), dasatinib (n=6, red) and combination (n=3, black) after 14 days of treatment. Graph shows mean +/- SEM; *p<0.05 and *p<0.01 by ANOVA and Tukey post-hoc analysis c. FACS analysis of percentage of marrow engrafted blast crisis progenitor LSC (n=3 patients) after 14-day treatment with vehicle (n=31, blue), PF- 04449913 (n=25, purple), dasatinib (n=27, maroon) and combination (n=27, grey). Graph shows percentage of CD34+CD38+lin- cells in the bone marrow; *p<0.05 by ANOVA and Tukey post-hoc analysis d. BCR-ABL transcripts in the blast crisis CML engrafted marrow mice after 14 days of treatment with vehicle (blue, n=9), PF-04449913 (purple, n=l 1), dasatinib (n=8, red) or combination (n=5, black). Graph shows normalized BCR- ABL expression (HPRT) +/- SEM; *p<0.05 by ANOVA and Tukey post-hoc analysis e. Hedgehog pathway gene expression in FACS purified human progenitor cells from blast crisis LSC engrafted mouse marrow treated with vehicle (n=3, blue), PF-04449913 (n=4, purple) dasatinib (n=4, maroon), combination (n=3, dark grey) was analyzed by hedgehog (SHH) qPCR array (SAbiosciences). The limma method was used to test for main effects of PF-04449913 and Dasatinib, and their synergistic interaction among 41 genes. Null hypotheses were rejected at p=0.05 significance level without adjusting for multiple comparisons. Expression levels of seven genes were significantly altered by synergistic effect of PF-04449913 and Dasatinib (NUMB, PRKACB, CTNNB l, FKBP8, CSNKlAl, CSNK1D and STK36), where five represent SHH regulatory genes (graphed), f. Mice serially transplanted with FACS purified human progenitors from LSC engrafted mice treated with vehicle (n=12, green), PF-04449913 (n=12, purple), dasatinib (n=8, maroon) or combination (n=7, grey) were examined for myeloid sarcomas. Graph shows mean myeloid sarcoma count +/- SEM; *p<0.05 and *p<0.01 by ANOVA and Tukey post-hoc analysis.
Figure 21 (supplementary Figure 1): PF-04449913 chemical properties and Inhibition of Shh Signaling in a Ptch+/"p53+/" Tumor model. This figure summarizes the effect of inhibiting the SHH pathway in a different preclinical mouse model.
a. Competition-binding assay using a characterized cyclopamine-competitive SMO antagonist. PF-04449913 competes with the radiolabeled SMO antagonist for binding to human SMO (amino acids 181-787) with an IC50 of 4 nM (4.3 nM +/- 5.2 nM, N= 5). b. Inhibition of Shh stimulated luciferase expression using mouse embryonic fibroblasts expressing luciferase under control of an 8X GLI-response element (GLI-LUC MEFs). c. Dose dependent inhibition by PF-04449913 in the GLI-Luc MEF reporter assay; PF-04449913 inhibits Shh stimulated reporter activity with an IC50 of 6.8 nM (n=5). d. Anti-tumor activity of PF-04449913 against Ptch+/-p53+/- medulloblastoma. Allograft (-700 mm3) bearing SCID-bg female mice were dosed orally once a day for six days with 100 mg/kg of PF-04449913 or vehicle. Tumor size (length and width) was measured using a caliper at regular intervals and tumor volume was calculated by standard procedure. Results are mean +/- standard error of the mean (n = 3 animals per group), e. Dose dependent anti-tumor efficacy of PF-04449913 against Ptch+/-p53+/- medulloblastoma allografts. Cohorts of allograft (-200 mm3 to 1000 mm3) bearing SCID- bg female mice were dosed orally once a day for six days with different dose levels of PF-04449913. Tumor size (length and width) was measured using a caliper at regular intervals and tumor volume was calculated by standard procedure. The percent change of an individual tumor volume was calculated from the tumor volume on the first day of dosing to the sixth day. Results are expressed as mean +/- standard deviation (n = 3 to 12 animals per group; p< 0.01 for 1 mg/kg group and p< 0.001 for all other groups), f. Genes significantly down-regulated by PF-04449913 treatment in Ptch+/~p53~A mice.
Hierarchical clustering was performed on Z-score transformed data using correlation similarity metric and centroid linkage method, g. Hh pathway inhibition in PF-04449913 treated Ptch+/-p53+/- medulloblastoma allografts. Ptch+/-p53+/- allograft bearing SCID-bg female mice were dosed orally once a day for six days with 100 mg/kg of PF- 04449913 or vehicle. Expression levels of FoxMl, GUI, GH2, Mycn, Ptchl, Ptch2, Sfrpl and Smo were determined by qRT-PCR. The vehicle-treated levels for each gene were normalized to 100%. h. Gene signatures enriched for within the top 31 PF-04449913- downregulated genes in Ptch+/-p53 -/- mice. Statistical significance of over- representation and observed/expected ratio were calculated as described in supplementary methods.
Figure 22 (supplementary Figure 2): Cell cycle analysis in clinical samples - this data supports the effect of these clinical study.
a. GSEA analysis summary table obtained from RNA sequencing data comparing PF-04449913 treated engrafted mice (n=4) to control (n=4) (average 24.7-58.0 million mapped reads/sample). In total, 13,850 protein-coding genes with >10 reads in at least one sample were included. Read counts were normalized— and genes ranked by
Significance Analysis of Microarrays (SAM).— Eight cell cycle pathways were considered in the GSEA analysis-", with significance assessed by gene-wise permutation. The "Regulation of Cell Cycle" pathway was significantly down-regulated in PF- 04449913 purified human progenitors derived from treated mice (family- wise p value =0.02). Table columns show pathway name, number of genes (pathway size), nominal p- value, FDR adjusted q-value. b. Characteristics of patients enrolled and sequenced using the gene expression profile by Affymetrix GeneChip 1.0 ST after PF-04449913 treatment for 28 days (C1D28), Clinical trial Gov.NTC00953758. c. GSEA analysis summary table obtained from patients (n=8) sequenced after PF-04449913 treatment (C 1 D28). GSEA was performed at FDR=5% and data compared pre-treatment (screening) v/s. PF- 04449913 treated. Table columns show pathway name, number of genes (ES), nominal p- value and FDR adjusted q-value.
Figure 23 (supplementary Figure 3): SHH Inhibition Spares Normal Human Hematopoietic Progenitors. We did not observe a toxic effect on the normal counterparts analyzed; thus, a clear therapeutic index for the use of SHH inhibition was demonstrated. a. Differentiation into CFU-Mix (purple), BFU-E (red), CFU-G (orange), CFU-M (yellow), CFU-GM (blue) of normal cord blood progenitors was assessed in
hematopoietic progenitor assays (n=3) after PF-04449913 (ImM) or vehicle treatment for 14 days. b. FACS analysis was used to determine the total human CD45+, hematopoietic stem and progenitor cell (HSPC), myeloid and lymphoid cell count in bone marrow after 14 days of treatment with vehicle (n=3, green) or 100 mg/kg of PF-04449913 (n=4, purple), c. FACS quantification of GO (green), Gl (light blue) and G2/S (navy) human CD45+ cells in cord blood engrafted marrow after 14 days of treatment with vehicle (n=3) or PF-04449913 lOOmg/kg (n=4). d. Representative FACS plots depicting HSPC, myeloid and lymphoid differentiation (panel B) in human cord blood engrafted mice after 14 days of treatment with vehicle or 100 mg/kg of PF-04449913.
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A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.

Claims

WHAT IS CLAIMED IS:
1. A method for treating, ameliorating or preventing diseases and conditions responsive to the inhibition or slowing of cell differentiation and/or self-renewal (or self- renewal capacity) of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells, comprising,
(a) providing a composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide; and
(b) administering a sufficient amount of the composition to an individual in need thereof, wherein a sufficient amount comprises the inhibition or slowing of cell differentiation and/or self-renewal of dysfunctional cells, cancer cells, leukemia cells, hematopoietic stem cells or cancer stem cells.
2. The method of claim 1, wherein the hematopoietic stem cell or cancer stem cell comprises a cancer stem cell, or a leukemia cell, or a Chronic Myeloid
Leukemia (CML) cell, a leukemia stem cell, or a Chronic Myeloid Leukemia (CML) stem cell.
3. The method of claim 1 or claim 2, wherein the composition that inhibits or slows the expression of an ADARl gene, an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide comprises:
(a) an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript;
(b) a polypeptide, peptide or an antibody inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme;
(c) the method of (a), wherein the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA); or
(d) the method of (a) or (c), wherein inhibitory nucleic acid molecule comprises a ribozyme.
4. The method of claim 3, wherein the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the ADARl gene or ADARl gene transcript comprises a single or doublestranded and/or sense or antisense sequence or subsequence comprising SEQ ID NO: l, SEQ ID NO:2 or SEQ ID NO:3.
5. The method of claim 3, wherein the antibody inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme comprises an antibody or antigen-binding fragment thereof that specifically binds to a protein as set forth in SEQ ID NO:3.
6. The method of claim 3, wherein the polypeptide or peptide inhibitory to the expression of the ADARl gene or ADARl gene transcript, or activity or expression of the ADARl enzyme comprises a peptide aptamer or an ADARl -binding polypeptide or peptide.
7. The method of any of claims 1 to 5, wherein composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide is administered in vitro, ex vivo or in vivo.
8. A composition, a pharmaceutical composition or a formulation comprising a composition that inhibits or slows the expression of or the activity of: an ADARl gene (adenosine deaminase acting on RNA 1), an ADARl gene product, an ADARl transcript, and/or an ADARl polypeptide,
wherein optionally the composition, pharmaceutical composition or formulation is formulated for administration in vitro, ex vivo or in vivo,
and optionally the composition, pharmaceutical composition or formulation comprises a composition used to practice a method of any of claims 1 to 7.
9. A kit comprising: a composition used to practice a method of any of claims 1 to 7, or a composition, a pharmaceutical composition or a formulation of claim 8, and optionally comprising instructions for use thereof.
10. A method for activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle, or initiating cell cycling in a cancer stem cell, or breaking dormancy in a cancer stem cell, or inducing in a stem cell susceptibility to BCR-ABL inhibition, comprising,
(a) providing a composition that inhibits a Sonic Hedgehog (Shh), or providing a
Smoothened (SMO) protein inhibitor; and
(b) administering an effective amount of the Sonic Hedgehog (Shh) inhibitor or the Smoothened (SMO) protein inhibitor to the cancer stem cell, thereby activating, stimulating or initiating in the cancer stem cell a transition from GO to Gl of the cell cycle, or initiating cell cycling in the cancer stem cell, inducing in the stem cell susceptibility to BCR-ABL inhibition, or breaking dormancy in the stem cell.
11. A method for radiosensitization of a cancer stem cell, or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells, or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor, comprising,
(a) providing a composition that inhibits a Sonic Hedgehog (Shh), or providing a Smoothened (SMO) protein inhibitor; and
(b) administering an effective amount of the Sonic Hedgehog (Shh) or
Smoothened (SMO) protein inhibitor to the cancer stem cell, thereby radiosensitizing the cancer stem cell, or sensitizing the cancer stem cell to a treatment or protocol that targets dividing cells, or sensitizing the cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor.
12. The method of claim 10 or claim 1 1, wherein the cancer stem cell is a hematopoietic cancer stem cell, or the cancer stem cell is a leukemia stem cell, or a Chronic Myeloid Leukemia (CML) stem cell or a Chronic Myeloid Leukemia (CML) stem cell.
13. The method of any of claims 10 to 12, wherein the composition that inhibits or slows the expression of an Shh gene, an Shh gene product, an Shh transcript, and/or an Shh polypeptide comprises: (a) an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of a Shh gene or Shh gene transcript;
(b) a polypeptide, peptide or an antibody inhibitory to the expression of the Shh gene or Shh gene transcript, or activity or expression of the Shh polypeptide;
(c) the method of (a), wherein the inhibitory nucleic acid molecule or antisense oligonucleotide inhibitory to expression of the Shh gene or Shh gene transcript comprises: an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA); or
(d) the method of (a) or (c), wherein inhibitory nucleic acid molecule comprises a ribozyme.
14. The method of any of claims 10 to 13, wherein the composition that inhibits or slows the expression of a Shh gene, a Shh gene product, a Shh transcript, and/or a Shh polypeptide comprises PF-04449913, or an equivalent thereof, or a bioisostere thereof.
15. The method of claim 13, wherein the antibody inhibitory to the expression of a Shh gene, a Shh gene product or a Shh transcript, or activity or expression of the Shh polypeptide, comprises an antibody or antigen-binding fragment thereof that specifically binds to a Shh protein.
16. The method of claim 13, wherein the polypeptide or peptide inhibitory to the expression of a Shh gene, a Shh gene product or a Shh transcript, or activity or expression of the Shh protein comprises a peptide aptamer or a Shh protein-binding polypeptide or peptide.
17. The method of any of claims 10 to 16, wherein composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide is administered in vitro, ex vivo or in vivo.
18. A composition, a pharmaceutical composition or a formulation comprising a composition that inhibits or slows the expression of or the activity of: a Shh gene, a Shh gene product or a Shh transcript, and/or an Shh polypeptide,
wherein optionally the composition or formulation is formulated for
administration in vitro, ex vivo or in vivo.
wherein optionally the composition that inhibits or slows the expression of the Shh gene, Shh gene product, Shh transcript, and/or Shh polypeptide comprises:
a composition used to practice a method of any of claims 10 to 17,
an inhibitory nucleic acid molecule or an antisense oligonucleotide inhibitory to expression of a Shh gene or Shh gene transcript;
a polypeptide, peptide or an antibody inhibitory to the expression of the Shh gene or Shh gene transcript, or activity or expression of the Shh polypeptide;
an RNAi inhibitory nucleic acid molecule, a double-stranded RNA (dsRNA) molecule, a small interfering RNA (siRNA), a microRNA (miRNA) and/or a short hairpin RNA (shRNA); or a ribozyme, or
any combination thereof.
19. An array or a kit, comprising a cancer stem cell splice isoform and/or proteome detection platform, wherein the array or kit comprises a sufficient plurality of nucleic acids and/or proteins to detect a dormant cancer stem cell from a non-dormant stem cell or a cancer stem cell transitioning from GO to Gl of the cell cycle.
20. A method for determining the effectiveness of a test compound for:
activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle; or initiating cell cycling in a cancer stem cell; or breaking dormancy in a cancer stem cell; or radiosensitizing of a cancer stem cell; or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells; inducing in a stem cell susceptibility to BCR-ABL inhibition; or sensitizing a cancer stem cell to a
chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor, comprising analyzing the cancer stem cell transcript (RNA) splice isoform pattern and/or the proteome before and after contacting the test compound to the stem cell, wherein a change of the cancer stem cell to a non-dormant transcript (RNA) splice isoform pattern and/or the proteome pattern indicates that the test compound is effective for: activating, stimulating or initiating in a cancer stem cell a transition from GO to Gl of the cell cycle; or initiating cell cycling in a cancer stem cell; or breaking dormancy in a cancer stem cell; or radiosensitizing of a cancer stem cell; or sensitizing a cancer stem cell to a treatment or protocol that targets dividing cells; inducing in a stem cell susceptibility to BCR-ABL inhibition; or sensitizing a cancer stem cell to a chemotherapy, a radiation therapy or a targeted tyrosine kinase inhibitor,
wherein optionally the analyzing uses the array or a kit of claim 19.
21. A kit comprising: a composition used to practice a method of any of claims 10 to 17 or claim 20, or a composition, a pharmaceutical composition or a formulation of claim 18, and optionally comprising instructions for use thereof.
22. A method for measuring or determining, or predicting, chronic
myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance, comprising:
measuring or determining, individually or together, levels or amounts of GLI2 transcript and/or protein (increasing) and/or GLI3 transcript and/or protein (decreasing) as prognostic biomarkers of chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance,
wherein increased or increasing levels of GLI2 transcript and/or protein and/or decreasing levels of GLI3 transcript and/or protein indicate and/or predict chronic myelogenous leukemia (CML) progression, Leukemic Stem Cell (LSC) generation and/or tyrosine kinase inhibitor resistance.
23. A method for measuring or determining, or predicting, a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, comprising:
measuring or determining, individually or together, levels or amounts of GLI1 and/or GLI2 transcript and/or protein,
wherein the presence of one or both GLI1 and/or GLI2 transcript and/or protein, and/or increased or increasing levels of one or both GLI1 and/or GLI2 transcript and/or protein indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition.
24. A method for measuring or determining, or predicting, whether a cancer stem cell has or will transition from GO to Gl of the cell cycle, or has or will initiate cell cycling, or has or will break dormancy, or has been induced to have a susceptibility to BCR-ABL inhibition, comprising:
measuring or determining, individually or together, levels or amounts of GLI1 and/or GLI2 transcript and/or protein,
wherein the presence of one or both GLI1 and/or GLI2 transcript and/or protein, and/or increased or increasing levels of one or both GLI1 and/or GLI2 transcript and/or protein, indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, thereby also indicating or predicting whether a cancer stem cell has or will transition from GO to Gl of the cell cycle, or has or will initiate cell cycling, or has or will break dormancy, or has been induced to have a susceptibility to BCR-ABL inhibition.
25. The method of any of claims 22 to 24, wherein the presence, absence and/or amount of a GLI1, GLI2 and/or GLI3 transcript and/or protein is measured using an array, an immunoassay, an immunoprecipitation, a kit, a polymerase chain reaction (PCR), a qRT-PCR, a nanofluidic assay or device, a nanofluidic proteome assay, a chromatography, a nanoproteomics quantification, an isoelectric focusing assay, or a combination thereof.
26. A method for assessing the eradication of self-renewing cancer stem cells, or Leukemic Stem Cells (LSCs), comprising:
measuring or determining, individually or together, levels or amounts of GLI1 and/or GLI2 transcript and/or protein,
wherein the absence of one or both GLI1 and/or GLI2 transcript and/or protein, and/or decreasing levels of one or both GLI1 and/or GLI2 transcript and/or protein, indicates a response to an inhibitor or inhibitors of a Sonic Hedgehog (Shh) pathway, or a targeted Shh inhibition, or a selective Shh inhibition, thereby also indicating or predicting an eradication or diminishment of self-renewing cancer stem cells, or Leukemic Stem
Cells (LSCs).
27. An array, an immunoassay, or a kit comprising nucleic acids, proteins or antibodies capable of determining or measuring the presence, absence and/or amount of a GLI1, GLI2 and/or GLI3 transcript and/or protein.
28. The array or kit comprising: a composition used to practice a method of any of claims 22 to 26, or a composition, and optionally comprising instructions for use thereof.
29. A method for determining or measuring the effectiveness of a treatment, a drug, a therapy or a diet for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells, comprising:
(a) determining or measuring the amount of an alternatively spliced
phosphoStat5a and/or a phospho-JAK2;
(b) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(c) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the treatment, drug, therapy or diet will be effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
30. A method for selecting a diet, a treatment, a drug or a therapy: to treat or ameliorate a leukemic stem cell (LSC), or, for eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells, comprising:
(a) applying, contacting or administering a diet, a treatment, a drug or a therapy to a LSC cell or a cell population or subpopulation, and
(b) (i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2;
(ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or (iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the treatment, drug, therapy or diet will be effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
31. A method for determining or predicting a positive response or monitoring a response (predicting a negative or positive response) to a selective JAK2 inhibition therapy, drug or treatment, comprising
(a) applying, contacting or administering a diet, a treatment, a drug or a therapy to a LSC cell or a cell population or subpopulation, and
(b) (i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2;
(ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein a decrease in the amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the selective JAK2 inhibition therapy, drug or treatment will be (or is) effective for the treatment, prevention or amelioration of a leukemic stem cell (LSC) or cells, or eliminating, killing or reducing the amounts of a leukemic stem cell (LSC) or cells.
32. A method for assessing the resistance, or relative resistance, of a self- renewing leukemic stem cell (LSC) or cells to a selective JAK2 inhibition therapy, drug or treatment, comprising:
(i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2; (ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein an increased amount of, or the presence of, the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the self-renewing leukemic stem cell (LSC) or cells will be resistant, or relatively resistant, to a selective JAK2 inhibition therapy, drug or treatment, or
a decreased amount of, or lack of, the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, determines or predicts that the self-renewing leukemic stem cell (LSC) or cells will be sensitive or responsive to a selective JAK2 inhibition therapy, drug or treatment.
33. A method for distinguishing leukemic progenitors from their normal counterparts, comprising:
(i) determining or measuring the amount of an alternatively spliced phosphoStat5a and/or a phospho-JAK2;
(ii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2; or
(iii) determining or measuring the amount of an alternatively spliced Stat5a and/or a JAK2 transcript or message;
wherein the presence of the alternatively spliced phosphoStat5a and/or a phospho-
JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or
alternatively spliced Stat5a and/or a JAK2 transcript or message, distinguishes the leukemic progenitors from their normal counterparts.
34. The method of any of claims 29 to 33, wherein the method detects a cancer stem cell specific JAK/STAT signaling pathway splice isoforms by RNA sequencing, qRT-PCR and/or nanoproteomics.
35. The method of any of claims 29 to 34, wherein the LSC is a chronic myelogenous or myeloid leukemia (CML) stem cell, or a cancer stem cell in a primary or metastatic niche, or a cancer stem cell in a setting of inflammatory cytokines and interleukins as elaborated in a cancer.
36. The method of any of claims 29 to 25, wherein the presence, absence and/or amount of the alternatively spliced phosphoStat5a and/or a phospho-JAK2, or alternatively spliced Stat5a and/or a JAK2 transcript or message, or alternatively spliced Stat5a and/or a JAK2 transcript or message, is measured by a procedure or device comprising (or comprising use of): a fluorescent activated cell sorter (FACS), an array, an immunoassay, an immunoprecipitation, a kit, a polymerase chain reaction (PCR), a qRT- PCR, a nanofluidic assay or device, a nanofluidic proteome assay, a chromatography, a nanoproteomics quantification, or an isoelectric focusing assay, or any combination thereof.
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