US20180008709A1 - Methods and compositions for increasing susceptibility to radiation treatment by inhibiting suppression of numerical chromosomal instability of cancer cells - Google Patents

Methods and compositions for increasing susceptibility to radiation treatment by inhibiting suppression of numerical chromosomal instability of cancer cells Download PDF

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US20180008709A1
US20180008709A1 US15/544,811 US201615544811A US2018008709A1 US 20180008709 A1 US20180008709 A1 US 20180008709A1 US 201615544811 A US201615544811 A US 201615544811A US 2018008709 A1 US2018008709 A1 US 2018008709A1
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cells
chromosome
radiation
tumor
ionizing radiation
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Samuel F. BAKHOUM
Zaki I. BASSEM
Duane A. COMPTON
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Dartmouth College
Memorial Sloan Kettering Cancer Center
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Memorial Sloan Kettering Cancer Center
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K41/00—Medicinal preparations obtained by treating materials with wave energy or particle radiation ; Therapies using these preparations
    • A61K41/0038—Radiosensitizing, i.e. administration of pharmaceutical agents that enhance the effect of radiotherapy
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/5375—1,4-Oxazines, e.g. morpholine
    • A61K31/5377—1,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/1703—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • A61K38/1709—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/45—Transferases (2)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61N—ELECTROTHERAPY; MAGNETOTHERAPY; RADIATION THERAPY; ULTRASOUND THERAPY
    • A61N5/00—Radiation therapy
    • A61N5/10—X-ray therapy; Gamma-ray therapy; Particle-irradiation therapy
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61N—ELECTROTHERAPY; MAGNETOTHERAPY; RADIATION THERAPY; ULTRASOUND THERAPY
    • A61N5/00—Radiation therapy
    • A61N5/10—X-ray therapy; Gamma-ray therapy; Particle-irradiation therapy
    • A61N2005/1092—Details
    • A61N2005/1098—Enhancing the effect of the particle by an injected agent or implanted device

Definitions

  • the present disclosure relates to the field of cancer therapy using agents that promote whole-chromosomal instability, as irradiation sensitization agents, and thus to make patients more sensitive to radiation therapy, thereby increasing the effect of radiation therapy.
  • IR ionizing radiation
  • DSBs DNA double-strand breaks
  • HR homologous recombination
  • NHEJ non-homologous end joining
  • HR repair is less error-prone than NHEJ, as the latter can join DSB ends of genomic DNA, which can lead to chromosomal translocations, acentric chromatin fragments as well as dicentric chromosomes which have two centromeres.
  • Acentric chromatin fragments exhibit a high likelihood of missegregation during the subsequent mitosis, as they are incapable of establishing canonical attachment to spindle microtubules at the kinetochores.
  • dicentric chromatin often leads to the formation of chromatin bridges where each centromere is attached to microtubules emanating from opposite spindle poles. Forces exerted by the mitotic spindle break chromatin bridges in a process termed the breakage-fusion-bridge cycle.
  • telomere dysfunction can also be initiated by telomere dysfunction and replication stress. It is thus clear that DNA breaks generated by IR in dividing cells can directly lead to structural chromosomal instability (s-CIN), whose hallmarks are chromatin bridges and acentric chromatin fragments.
  • s-CIN structural chromosomal instability
  • w-CIN Another form of genome instability, present in the majority of solid tumors, is numerical (or whole) chromosomal instability (w-CIN).
  • w-CIN primarily arises from errors in whole chromosome segregation during mitosis and it generates widespread aneuploidy in tumor cells.
  • a phenotypic hallmark of w-CIN, both in cell culture and human tumor samples, is the presence of chromosomes that lag in the middle of the mitotic spindle during anaphase. These lagging chromosomes can directly lead to chromosome missegregation and aneuploidy.
  • w-CIN does not exist separately from s-CIN, as it was recently shown that lagging chromosomes can also undergo severe structural damage by generating whole-chromosome containing micronuclei. These micronuclei are defective in DNA replication and repair and possess a faulty nuclear envelope leading to the pulverization of their enclosed chromosomes. Thus w-CIN can in turn lead to s-CIN.
  • IR IR-associated cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic cytoplasmic
  • w-CIN can be used to increase or decrease the sensitivity of a dividing cell to ionizing radiation.
  • the present disclosure provides new experimental evidence elucidating one of the mechanisms—previously unreported—by which cell-cycle dependent vulnerability of cancer cells undergoing mitosis to ionizing radiation occurs.
  • the inventors have shown that treatment with ionizing radiation leads to mitotic chromosome segregation errors in vivo and to long-lasting aneuploidy in tumor-derived cell lines. These mitotic errors generate an abundance of micronuclei that predispose chromosomes to subsequent catastrophic pulverization by IR thereby independently amplifying radiation-induced genome damage.
  • Experimentally suppressing whole chromosome missegregation reduces downstream chromosomal defects and significantly increases the viability of irradiated mitotic cells, giving rise to tumor cell resistance to further radiation.
  • orthotopically transplanted human glioblastoma tumors in which chromosome missegregation rates have been reduced through overexpression of kinesins are rendered markedly more resistant to ionizing radiation, exhibiting diminished markers of cell death in response to radiation treatment.
  • This disclosure thus identifies a novel mitotic pathway for radiation-induced genome damage, which occurs outside the primary nucleus and augments chromosomal breaks. This relationship between radiation treatment and whole chromosome missegregation can be exploited to enhance efficacy of radiation treatments of solid malignant tumors susceptible to radiation treatment and thus to reduce the likelihood of resistance. It can also be used to spare noncancerous tissues or organs from deleterious effects of radiation.
  • the present disclosure provides a method for increasing susceptibility of cancer cells to ionizing radiation to a radiosensitizing agent that has one of the following properties: (a) it perturbs the process of chromosome segregation thereby increasing chromosome missegregation; or (b) it is an inhibitor of an agent that promotes faithful chromosome segregation induces numeric chromosome instability in said cells and this instability is induced substantially simultaneously with or closely prior to or closely after irradiating the cells.
  • the radiosensitizing agent inhibits one or more of the following directly or indirectly: Kif2b, MCAK, MPS1, Eg5/Kinesin-5, Polo-like kinase 4, MCAK, Bub1 and Hec1.
  • Kif2b Kif2b
  • MCAK MCPEG
  • MPS1 Eg5/Kinesin-5
  • Polo-like kinase 4 MCAK
  • Bub1 Hec1.
  • the agent thus specifically targets proteins involved in maintaining or promoting faithful chromosome segregation.
  • the cancer cells are solid tumor cancer cells for which radiation is an indicated therapeutic modality.
  • tumors include head-and-neck cancer, rectal adenocarcinoma, glioblastoma multiform.
  • the radiosensitizing agent is selected from the group consisting of MPS1 inhibitors, Eg5/Kinesin-5 inhibitors, Polo-like kinase 4 inhibitors, MCAK inhibitors, Bub1 inhibitors and Hec1 inhibitors. (Bub1 and Hec1 inhibitors will produce the desired chromosomal instability but so will activators as described below.)
  • the ionizing radiation is administered in one or in multiple (at least two) divided doses.
  • the present disclosure provides a method for increasing cytotoxicity of ionizing radiation in a subject to be treated for a solid malignant tumor susceptible to treatment with ionizing radiation, the method comprising administering systemically to the subject or locally to the tumor an inhibitor of suppression of numerical chromosome instability incident to a first dose of said radiation, thereby enhancing chromosome missegregation during mitosis substantially simultaneously with or closely preceding treatment of the tumor with a subsequent dose of ionizing radiation.
  • This subsequent dose can be delivered either closely before, closely after or up to 1 or even 2 months after increasing chromosomal instability as long as the chromosomal instability induction substantially persists.
  • a method for reducing damage of noncancerous cells or tissue incident to ionizing radiation aimed at cancerous cells or tissue comprising exposing the noncancerous cells or tissue to a radioprotective agent (such as agonists of Kif2b or MCAK) which is an enhancer of suppression of chromosome missegregation and reduces numeric chromosome instability in said cells simultaneously with or immediately prior to or immediately following irradiating the cancerous cells or tissue with a therapeutically effective dose and regimen of ionizing radiation.
  • a radioprotective agent such as agonists of Kif2b or MCAK
  • the radioprotective agent is or specifically activates a protein involved in faithful chromosome segregation maintenance.
  • the radioprotective agent is Kif2b or MCAK or an agonist or activator of Kif2b or MCAK.
  • w-CIN in induced preferentially in cancer cells.
  • Main contributors to cancer cell specificity are the following: 1) induction of w-CIN according to the present disclosure occurs mostly in rapidly dividing cells (such as cancer cells); and 2) the higher chromosomal missegregation before treatment, the more sensitive cells are to interventions aimed at further increasing w-CIN.
  • the tumor includes, but is not limited to tumors of the following organs: the skin, breast, brain, cervix, testis, heart, lung, gastrointestinal tract, genitourinary tract, liver, bone, nervous system, reproductive system, and adrenal glands.
  • adrenal tumors include for example adrenocortical carcinoma, bile duct, bladder, bone (e.g., Ewing's sarcoma, osteosarcoma, malignant fibrous histiocytoma), brain/CNS (e.g., astrocytoma, glioma, glioblastoma, childhood tumors, such as atypical teratoid/rhabdoid tumor, germ cell tumor, embryonal tumor, ependymoma), breast (including without limitation ductal carcinoma in situ, carcinoma, cervical, colon/rectum, endometrial, esophageal, eye (e.g., melanoma, retinoblastoma), gallbladder, gastrointestinal, kidney (e.g., renal cell, Wilms' tumor), heart, head and neck, laryngeal and hypopharyngeal, liver, lung, oral (e.g., lip, mouth, salivary gland) meso
  • the present inventors thus have discovered that increasing chromosome missegregation together with radiation treatment would lead to sensitization of the tumor to radiation therapy. This in turn permits 1) to decrease dose of radiation and achieve the same effect, 2) to maintain dose of radiation and increase tumor sensitization in otherwise resistant tumors, 3) to increase radioprotection of normal organs.
  • FIG. 1 (A-E) is a combination of high-resolution immunofluorescence microscopy images and graphical representation thereof showing that w-CIN is induced by IR in vitro.
  • FIG. 1A are examples of U251 cells fixed 25 min after exposure to 12 Gy and exhibiting lagging chromosomes (LC), chromatin bridges (CB), acentric chromatin (AC) or a combination (LC+AC) obtained through high-resolution fluorescence microscopy. Scale bar, 5 ⁇ m.
  • FIG. 1B is a series of bar graphs showing percentage of chromosome missegregation in anaphase spindles of RPE1, HCT116 and U251 cells as a function of IR dose.
  • FIG. 1 c are images obtained by FISH showing HCT116 nuclei stained for DNA (grey cloud right panel), centromere (white dots right panel) and telomere (white dots on the outer edges of grey cloud right panel) probes for human chromosome 2.
  • White arrow denotes an aneuploid nucleus containing three copies of chromosome 2.
  • 1E is a bar graph showing percentage of chromosome missegregation in anaphase spindles of HCT116 p53 ⁇ / ⁇ cells exposed to 0 Gy (top) or 6 Gy (bottom) as a function of time after irradiation (mo, months)
  • FIG. 2 shows in vivo induction of chromosome segregation errors by IR.
  • FIGS. 2A and 2D are schematic representations of experimental design.
  • FIG. 2B is an image of H&E staining of SC-HCT116 p53 ⁇ / ⁇ xenografts.
  • FIG. 2C is a graph showing percentage of anaphase cells exhibiting lagging chromosome in response to IR.
  • FIG. 2E is a graph of tumor-derived cells karyotype analysis.
  • FIG. 3 shows that IR-induced chromosome segregation errors lead to widespread chromosomal damage.
  • FIGS. 3A and 3D are schematic representations of experimental design.
  • FIG. 3B is an image of cells containing micronucleus.
  • FIG. 3C is a graph depicting percentage of cells containing micronuclei as a function of IR dose.
  • FIG. 3E is an image of mitotic spread containing pulverized chromosomes.
  • FIG. 3F is a graph showing percentage of mitotic spreads.
  • FIG. 3G is an image of cells containing micronuclei.
  • FIG. 3H is a graph of ⁇ -H2AX fluorescence intensity following IR.
  • FIG. 3I is a graph showing a percentage of anaphase spindles containing lagging chromosomes as a function of IR dose.
  • FIG. 4 (A-C) shows that Kif2b overexpression does not alter IR-induced DNA breaks or repair.
  • FIG. 4A is a graph showing fluorescence intensity of ⁇ -H2AX in Kif2b overexpression cells.
  • FIG. 4B is a graph showing the average number of ⁇ -H2AX foci per nucleus as a function of IR dose in Kif2b overexpression cells.
  • FIG. 4C is a series of images of cells stained for DNA and ⁇ -H2AX following IR.
  • FIG. 5 shows that chromosome segregation errors alter the viability of irradiated mitotic cells.
  • FIGS. 5A and 5B are graphs of surviving fraction of cells versus radiation dose.
  • FIG. 6 (A-L) shows that reducing chromosome segregation errors induces radiation resistance in vivo.
  • FIG. 6A is a schematic representation of experimental design.
  • FIG. 6B are bioluminescence images of mice.
  • FIG. 6C is a graph showing normalized bioluminescence over time in xenografts.
  • FIG. 6D is an image showing H&E staining.
  • FIG. 6E is an image showing Ki67 positive cells.
  • FIG. 6F is a graph showing percentage of Ki67 positive cells.
  • FIG. 6G is a graph showing mitotic count in U251 xenografts.
  • FIG. 6H is an image of atypical mitotic cells.
  • FIG. 6I is a graph showing a percent of atypical mitotic cells in xenografts.
  • FIG. 6J is an image showing cleaved caspase 3 (CC3) tumor.
  • FIG. 6K is a graph showing quantification of CC3 positive cells.
  • FIG. 6L is a schematic representation linking IR to chromosome segregation errors and downstream chromosomal structural defects.
  • FIG. 7 illustrates chromosome segregation errors in irradiated mitotic cells.
  • FIGS. 7A and 7B are images of anaphase spindle in U251 cells.
  • FIG. 7C is an autoradiograph of a Western blot of U251 cells stained with GFP and DM1- ⁇ antibodies.
  • FIG. 8 shows that overexpression of Kif2b alters viability of irradiated mitotic cells without altering basal growth rates or ploidy in culture.
  • FIG. 8A is a plot of surviving cellular fraction and radiation dose.
  • FIG. 8B is a plot of number of cells per plate as a function of time.
  • FIG. 8C is a bar graph showing karyotypic distribution of GFP-expressing and GFP-Kif2b expressing U251 cells.
  • FIG. 9 is a plot of absolute bioluminescence signal as a function of time after intracranial injection of U251 cells expressing GFP or GFP-Kif2b. Data derived from a sample experiment. IR treatment (24 Gy total) was administered starting on day 18 with 4Gy fractions every other day. The experiment was performed with three animals in each arm and was replicated three times. The data shows that Kif2b overexpression leads to tumor radiation resistance. Error bars show the standard error of the mean (SEM) of animals within an arm of a representative experiment.
  • SEM standard error of the mean
  • FIG. 10 is an autoradiograph of a Western blot showing Kinesin-13 overexpression in U251 cells.
  • Upper autoradiograph is a Western blot of U251 cells expressing GFP-tagged kinesin-13 proteins Kif2b (lane 1), Kif2b (lane 2), MCAK (lane 3), and GFP (lane 4) stained using anti-GFP antibodies.
  • DM1- ⁇ antibody was used to blot for a-tubulin as a loading control (lower autoradiograph).
  • Molecular weight markers in kDa are depicted on the left side of the immunoblots.
  • FIG. 11 shows computational models of w-CIN in clonally expanding populations.
  • FIG. 11A is a schematic of cancer cells, which frequently missegregate whole chromosomes leading to karyotypic heterogeneity.
  • FIGS. 11B and 11C are distribution curves showing respectively the dependence of clonal fitness (B) and adaptive capacity (C) on chromosome missegregation rates (pmisseg) for diploid and tetraploid-derived clonal populations.
  • Subject means a patient (human or veterinary) or an experimental animal, such as a mouse or other rodent.
  • Time interval of increased susceptibility means the period of time after administration of the CIN promoting agent, or radiosensitizing agent during which the resulting increase in w-CIN or lagging chromosomes is still substantially present.
  • Effective amount is an amount of a radiosensitizing agent or a radioprotective agent according to the present disclosure sufficient to increase or to decrease w-CIn by at least 5%. This amount varies greatly from agent to agent and may also vary widely (from picograms to milligrams perkilogram of patient weight) according to the tumor and the age and physical condition of the patient as well as other factors. Examples and guidance of effective amounts are provided in the discussion of particular agents.
  • ionizing radiation means any radiation where a nuclear particle has sufficient energy to remove an electron or proton or other particle from an atom or molecule, thus producing an ion and a free electron or radical.
  • ionizing radiation include, but are not limited to, gamma rays, X-rays, protons, electrons, alpha particles, carbon atoms, or particles emitted from a radioactive source including, but not limited to, yttrium and radium. Radiation from implanted material is included. Ionizing radiation is commonly used in medical radiotherapy and the specific techniques for such treatment will be apparent to a person of ordinary skill in the art. Other examples of radiation suitable for use in the present methods are provided elsewhere in the specification.
  • radiosensitizing agent means agents which increase the susceptibility of cells to the damaging effects of ionizing radiation or which become more toxic to a cell after exposure of the cell to ionizing radiation.
  • a radiosensitizing agent may permit lower doses of radiation to be administered and still provide a therapeutically effective dose.
  • agents that increase chromosome missegregation by specifically targeting proteins that are involved in chromosome missegregation (activating such proteins) or in faithful chromosome segregation (inhibiting such proteins) are radiosensitizing agents.
  • chromosome missegregation agents that suppress (or more accurately increase the suppression of) chromosome missegregation.
  • radioprotective agents have the property of enhancing suppression of chromosomal missegregation and reducing numeric chromosomal instability.
  • “Closely” in the context of timing of administration means during an interval of increased radiosensitization of a cancerous cell (while the induced w-CIN substantially persists). This interval can be as short as about 1 hour to about 8 hours, but may extend to about 24 hours, or up to about 1 month or even 2 prior to an irradiation dose depending on the duration of induced w-CIN.
  • substantially in the context of a measurable property means “mostly,” or “a major portion of” (for example 50% or more).
  • a cell substantially retaining induced w-CIN means retaining at least about half of the induced increase in w-CIN perpetrated by a radiosensitizing agent.
  • CIN is considered increased by reference to an untreated cell id it is at least 5% higher than the chromosomal instability of an untreated cell.
  • “Substantially” in the context of “substantially simultaneously” mean at the same time or almost at the same time, e.g., within the same day or 24-hour period.
  • Tumor as used herein means primary or metastatic tumor and includes the list of the tumor in the summary, above.
  • the present disclosure provides for sensitization of tumours to radiation therapy, where radiation therapy can include any radiation used in cancer treatment.
  • the radiation may be curative, adjuvant, or palliative radiotherapy.
  • Such radiation includes, but is not limited to, various forms of ionizing radiation (e.g, as listed supra), external beam radiotherapy (EBRT or XBRT) or teletherapy, brachytherapy or sealed source therapy, radioactive implant therapy, intraoperative radiotherapy, and unsealed source radiotherapy.
  • the radiation is ionizing radiation.
  • Radiation may be electromagnetic or particulate in nature. Electromagnetic radiation includes, but is not limited to, x-rays and gamma rays. Particulate radiation includes, but is not limited to, electron beams, proton beans, neutron beams, alpha particles, and negative pimesons.
  • the unit of absorbed dose is the gray (Gy), which is defined as the absorption of 1 joule per kilogram.
  • the energy of the radiation determines the depth of absorption as well as the nature of the atomic interaction.
  • Radiotherapy can be administered by a conventional radiological treatment apparatus and methods, or by intraoperative and sterotactic methods. Radiation may also be delivered by other methods that include, but are not limited to, targeted delivery, systemic delivery of targeted radioactive conjugates and intracavitary techniques (brachytherapy). Other radiation methods not described above can also be used to practice this invention.
  • ionizing radiation is used to target tissues or cells, such as neoplastic tissues or cells, for selective delivery of an CIN promoting active agent via a delivery vehicle comprising the active agent.
  • target tissues or cells such as neoplastic tissues or cells
  • a delivery vehicle comprising the active CIN promoting agent is administered before, during, or both before and during the exposure to radiation. Radiation immediately preceding delivery of the CIN promoting agent to the tumor is also possible or even 2
  • radiation therapy is delivered using radioactive isotopes (brachytherapy).
  • brachytherapy can be either high-dose rate or low dose rate brachytherapy.
  • High dose rate brachytherapy is usually delivered using Ir-192 (but not exclusively) and can be given in one or more doses and doses.
  • Low dose rate brachytherapy can be delivered using radioactive palladium or iodine and it involves permanent or long-term placement of seeds in and around the target and dose delivery obeys the half-life of the decay of the radioactive substance and can take weeks to months to deliver the majority of the dose.
  • the methods described herein can be used in the treatment of various types of solid tumors.
  • solid tumors have been provided in the Summary of the Disclosure.
  • malignant tumors which can be treated by methods described herein can be used in the treatment of cancer, include without limitation adrenal tumors (e.g., adrenocortical carcinoma), anal, bile duct, bladder, bone tumors (e.g., Ewing's sarcoma, osteosarcoma, malignant fibrous histiocytoma), brain/CNS (tumors e.g., astrocytoma, glioma, glioblastoma, childhood tumors, such as atypical teratoid/rhabdoid tumor, germ cell tumor, embryonal tumor, ependymoma), breast tumors(including without limitation ductal carcinoma in situ, carcinoma, cervical, colon/rectum, endometrial, esophageal, eye (e.g., melanoma, retinoblastoma), gallbladder, gastrointestinal, kidney (e.g., renal cell, Wilms' tumor), heart
  • Radiotherapy can be suitably administered in a dose effective for the particular cancer to be treated, as determined by a person of ordinary skill in the art.
  • the dose of radiation used in conjunction with the agents that specifically promote w-CIN may be similar to the amount administered when radiation is used alone, or, may be reduced.
  • the dosage of radiation may be determined in relation to tumor volume and may depend on the type of tumor being treated. The dosage may also take into account other factors that can be determined by an ordinarily skilled clinician.
  • Radiation treatment may be given as fractionated doses or as a bolus dose.
  • radiation can be administered in a range of 1 to about 50 fractions, with each fraction size being within the range of 0.1 to about 50 Gy.
  • dosage of each fraction is about 2 to about 30 Gy.
  • dosage of each fraction is about 4 to about 25 Gy.
  • dosage of each fraction is about 10 to about 20 Gy.
  • Particular dosage amounts include, but are not limited to, 0.4 (or 40 cGY), 1, 2, 4, 10 and 20 Gy.
  • the source of ionizing radiation comprises an external beam photon irradiation source, which is typically utilized at energy levels ranging from about 10 kV (KeV) to about 18 MV (MeV) per photon beam, or a brachytherapy source directly applied in the tumor cavity.
  • These sources of radiation can include, but are not limited to, yttrium, radium.
  • the source of ionizing radiation comprises an external beam electron irradiation source, which is typically utilized at energy levels ranging from about 10 KeV to about 20 MeV per electron beam.
  • the source of ionizing radiation comprises an external beam proton irradiation source, which is typically utilized at energy levels ranging from about 10 MEV to about 300 MeV per proton beam.
  • a preferred minimum source-axis distance comprises about 80 cm but can range considerably up and down as those skilled in the art appreciate.
  • the subject receives local-regional irradiation via fields that are designed to encompass sites of disease requiring palliation or primary treatment while endeavoring to spare noncancerous tissue as much as possible.
  • a preferred dosage range comprises about 500 to about 1500 cGy, and at times 2400 cGy, with a preferred dosage range comprising about 800 to about 1200 cGy.
  • a preferred dosage range comprises about 1000 to about 3000 cGy, and at times up to 800 cGy, with a preferred dosage range comprising about 1500 to about 2500 cGy, and with a more preferred dosage amount comprising about 200 cGy.
  • a preferred dosage range comprises about 1000 to about 6000 cGy, with a preferred dosage range comprising about 2000 to about 4000 cGy, and with a more preferred dosage amount comprising about 3000 cGy.
  • a preferred dosage range comprises about 1000 to about 7000 cGy, with a preferred dosage range comprising about 2000 to about 5000 cGy, and with a more preferred dosage amount comprising about 3500 CGy.
  • a preferred dosage range comprises about 2000 to about 12000 cGy, with a preferred dosage range comprising about 4000 to about 8000 cGy, and with a more preferred dosage amount comprising about 6000 cGy.
  • radiation is administered 1 to about 50 times. Frequency of radiation treatment can be from 3 times per day to about once per month. In further embodiments, radiation is administered once per 3 weeks, once per 2 weeks, once per week, 2-6 times per week, at least once a day, twice a day or three times a day, or any combination thereof.
  • a suitable administration regimen includes a schedule where fractionations are given 2 times per day for 2 days followed by a month long pause, and this cycle is repeated numerous times.
  • Treatment can be administered for 2-8 consecutive or non-consecutive weeks. Whether given as a bolus or as fractionated doses, total dose of radiation may be, for example, about 2-200 Gy in 2 Gy fractions or an equivalent biological dose using other fractionation schemes. These are just examples of radiation treatment protocols, and the present disclosure encompasses other treatment protocols that may be determined by a clinician of ordinary skill in the art.
  • Actual dosage levels of the agent that promotes CIN and radiation may be varied so as to obtain the desired therapeutic response for a particular subject, composition and mode of administration, without being toxic to the subject.
  • the selected dosage level will depend upon a variety of factors, including the route of administration, the rate of breakdown of the active form of the CIN promoting agent, the duration of treatment, other drugs, compounds, and/or materials used in combination with the particular CIN promoting agent, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and similar relevant factors well known in the art.
  • ionizing radiation When used as disclosed in the present disclosure, ionizing radiation may be used in the same amount and administration regimen. However, it may be possible through the use of radiosensitizing (and conversely radioprotective) agents to lower the dose or the frequency of administration, or both. Conversely, it may be possible to increase the same if used in combination with radioprotective agents. As stated above, methods for fine tuning the radiation intensity and frequency of administration are known in the art.
  • high dose rate brachytherapy is given in one or more doses, where doses can range anywhere from about 0.1 Gy to about 50 Gy.
  • high dose rate brachytherapy is administered intra-operatively.
  • low dose rate brachytherapy is delivered using radioactive palladium or iodine and it involves permanent or long-term placement of seeds in and around the target and dose delivery obeys the half-life of the decay of the radioactive substance and can take weeks to months to deliver the majority of the dose.
  • dose is delivered at a rate of anywhere between 0.001Gy-1Gy/hour in low-dose rate brachytherapy
  • the therapeutic combination of the present disclosure can be combined with other cancer therapies, including, but not limited to, adjunct therapies (such as, but not limited to, surgical tumor resection and chemotherapy).
  • Resection is often a standard procedure for the treatment of tumours.
  • the types of surgery that may be used in combination with the present invention include, but are not limited to, preventative, curative and palliative surgery, and any other method that would be contemplated by those of skill in the art.
  • the agents in the categories described below all alter chromosome missegregation and eventually cause w-CIN by either specifically inhibiting Kif2b, MCAK, MPS1, Eg5/Kinesin-5, Polo-like kinase 4, Mad2, Hec1, Bub1, or BubR1 or by activating Mad2, Hec1, BubR1, or Bub1.
  • the present disclosure provides evidence that over-expression of the microtubule-depolymerizing kinesin-13 proteins, Kif2b or MCAK, which localize to the attachment sites of chromosomes to spindle microtubules at the kinetochores, leads to the suppression of w-CIN in otherwise chromosomally unstable cell This suppression is persistent, lasting more than 30 days both in vitro and in vivo studies. Furthermore, Kif2b overexpressing cells displayed greater than twofold reduction in chromosome segregation errors during anaphase, which led to radiation resistance in vivo ( FIG. 6 ). These findings indicate that the inhibition of proteins that localize to the attachment sites of chromosomes to spindle microtubules at the kinetochores can be used to increase w-CIN in cancer cells and as such promote radiosensitization.
  • Kif2b or MCAK microtubule-depolymerizing kinesin-13 proteins
  • suitable agents that induce numeric chromosomal instability are those that inhibit proteins that localize to the attachment sites of chromosomes to spindle microtubules at the kinetochores during mitosis. Proteins known to localize to the attachment sites of chromosomes to spindle microtubules at the kinetochores during mitosis include, but are not limited to Kif2b and MCAK. Thus, in one embodiment, suitable agents that induce numeric chromosomal instability are those that specifically target and inhibit Kif2b or MCAK.
  • Kif2b belongs to the kinesin-13 family of proteins and localizes to kinetochores during early mitosis (Manning A L et al. Mol. Biol. Cell. 18:2970-2979 (2007)).
  • Kif2b can be inhibited using agents that inhibit Kif2b specifically.
  • One such agent is DHTP ((Z)-2-(4-((5-(4-chlorophenyl)-6-(isopropoxycarbonyl)-7-methyl-3-oxo-3,5-dihydro-2H-thiazolo[3,2-a]pyrimidin-2-ylidene)methyl)phenoxy)acetic acid).
  • DHTP has been shown to be a potent compound that inhibits kinein-13 induced microtubule depolymerization, where the IC 50 of DHTP in inhibiting Kif2b is 1.2 ⁇ M ( FEBS Lett. 27; 588(14):2315-20 (2014)).
  • DHTP possesses inhibitory activity against MCAK, with the IC 50 of DHTP in inhibiting MCAK is 4.6 ⁇ M FEBS Lett. 27; 588(14):2315-20 (2014)).
  • Kif2b can be inhibited using agents that inhibit Kif2b specifically but indirectly (e.g., through specific activation or inhibition of another protein that inhibits or activates Kif2b).
  • agents that inhibit Kif2b specifically but indirectly e.g., through specific activation or inhibition of another protein that inhibits or activates Kif2b.
  • the possibility of such indirect specific effect is not limited to Kif2b but in principle extends to any radiosensitizing or radioprotective agent employed in the present methods.
  • MCAK inhibitors include MCAKsv1. See US Patent Application US20060177828 (Alternatively spliced isoform of mitotic centromere-associated kinesin (MCAK), Armour, Christopher, et al.; Filing Date Sep. 16, 2004; Publication Date Aug. 10, 2006).
  • the core SAC kinases monopolar spindle-1 (Mps1, also known as TTK) is a serine threonine kinase which functions as a core component of the spindle assembly checkpoint (SAC) (Lauze' et al. EMBO J. 14, 1655-1663, (1995)), a key surveillance mechanism that monitors the attachment of spindle microtubules to the kinetochores of the chromosomes during pro-metaphase and halts the transitions to anaphase until all chromosomes are bi-oriented, fully attached, and correctly tensed at the metaphase plate. Mps1 is expressed in the mitosis phase of the cell cycle in proliferating cells.
  • SAC spindle assembly checkpoint
  • Mps1 activity causes cells to prematurely exit mitosis with unattached chromosomes, resulting in severe chromosome missegregation and aneuploidy (Colombo et al. Cancer Res., 70, 10255-10264 (2010); Jemaa et al. Cell Death Differ. 20, 1532-1545 (2013)).
  • Overexpression of Mps1 has been observed in several cancer cell lines and tumor types including lung and breast cancers, where higher Mps1 levels correlate with worse prognosis.
  • Established anti-mitotic drugs such as vinca alkaloids, taxanes, or epothilones activate SAC either by destabilizing or stabilizing spindle microtubules resulting in mitotic arrest. Prolonged arrest in mitosis forces a cell either into a mitotic exit without cytokinesis or into a mitotic catastrophe leading to cell death.
  • Such drugs do not target chromosome missegregation or faithful segregation specifically and are not included within the specifically acting agents of the present disclosure.
  • specific Mps1 inhibitors inactivate the SAC and accelerate progression of cells through mitosis eventually resulting in severe chromosomal missegregation, mitotic catastrophe, and cell death.
  • Mps1 inhibition leads to failure of cells to arrest in mitosis in response to anti-mitotic drugs.
  • the combination of microtubule-interfering agents and Mps1 inhibition strongly increases chromosomal segregation errors and cell death and therefore, constitutes an efficient strategy for selectively eliminating tumor cells.
  • BAY 1161909 has been administered orally, with a starting dose of 0.75 mg twice daily, on a 14-day cycle—D1, D2, D8, D9 and 28 day cycle—D8, D9 D15 and D16 of a 28 day cycle.
  • Mps1 inhibitors include N-(4- ⁇ 2-[(2-cyanophenyl)amino][1,2,4]triazolo[1,5-a]pyridin-6-yl ⁇ phenyl)-2-phenylacetamide (Mps-BAY1) (a triazolopyridine), N-cyclopropyl-4- ⁇ 8-[(2-methylpropyl)amino]-6-(quinolin-5-yl)imidazo[1,2-a]pyrazin-3-yl ⁇ benzamide (Mps-BAY2a), and N-cyclopropyl-4- ⁇ 8-(isobutylamino)imidazo[1,2-a]pyrazin-3-yl ⁇ benzamide (Mps-BAY2b).
  • Eg5 a member of the kinesin superfamily, plays a key role in mitosis, as it is required for the formation of a bipolar spindle. Eg5 controls mitosis through bipolar spindle formation and thus chromosome separation (Blangy et al. Cell, 83, 1159-1169 (1995)). Eg5 is overexpressed in many proliferative tissues including leukemia as well as solid tumors such as breast, lung, ovarian, bladder and pancreatic cancers (Hedge et al. Proc. Am. Soc. Clin. Oncol., 22 (2003), Ding et al. Int. J. Urol., 18, 432-438 (2011), Liu et al. J. Pathol., 221, 221-228 (2010)). Given the role that Eg5 plays in promoting faithful chromosomal segregation, the findings of the present disclosure indicate that specifically targeting and inhibiting Eg5 in cancer cells leads to radiosensitization of such cells.
  • Eg5 inhibitors include, but are not limited to 4SC-205, currently in Phase I Clinical Trial (ClinicalTrials.gov ID: NCT01065025, Open Label, Dose Escalation Trial of Oral Eg5 Kinesin-spindle Inhibitor 4SC-205 in Patients With Advanced Malignancies (AEGIS); and AZD4877, which was part of a Phase I trial in patients with solid and lymphoid malignancies (Gerecitano et al. Invest New Drugs . (2):355-62 (2013)). 4SC-205 was administered once or twice weekly at doses of 25 mg-200 mg.
  • AZD4877 In case of AZD4877, a standard 3+3 dose-escalation design was used, where AZD4877 was given as an intravenous infusion on days 1, 4, 8 and 11 of each 21-day cycle (Gerecitano et al. Invest New Drugs. (2):355-62 (2013)).
  • Eg5 inhibitors please refer to El-Nassan H B, Eur J Med Chem. 62:614-31 (2013).
  • Eg5 inhibitors have been shown to be effective against taxol-resistant cancer cells (Marcus et al. J. Biol. Chem., 280 (2005)). Therefore, given the findings of the present disclosure, combining inhibition of proteins that promote faithful segregation of chromosomes with radiation therapy can offer new treatment solutions for tumors resistant to other therapies.
  • PLK4 is a conserved key regulator of centriole duplication (Bettencourt-Dias et al. Curr. Biol. 15, 2199-2207 (2005)). Dysregulation of PLK4 expression causes loss of centrosome numeral integrity, which promotes genomic instability (Ganem et al. Nature 460, 278-282 (2009).
  • the present disclosure comprises the use of PLK4 inhibitors in cancer cells in order to generate cancer cells more susceptible to radiation therapy compared to cancer cells that not treated with PLK4 inhibitor prior to radiation therapy.
  • the PLK4 inhibitor R1530 downregulates the expression of mitotic checkpoint kinase BubR1, which in leads to polyploidy (Tovar et al. Cell Cycle. 9(16):3364-75 (2010)).
  • BubR1 and Bub1 are paralogous serine/threonine kinases that perform different functions in the spindle assembly checkpoint (SAC).
  • SAC spindle assembly checkpoint
  • BubR1 associates with unattached kinetochores, contributes to stabilizing kinetochore-MT attachments and aligning chromosomes, and forms part of the mitotic checkpoint complex (MCC).
  • MCC mitotic checkpoint complex
  • Bub1 binds kinetochores and plays a key role in establishing the mitotic spindle checkpoint and aligning chromosomes in addition to its central role in ensuring fidelity during chromosomal segregation into daughter cells (Yu et al. 4:262-265 (2005)).
  • Bub1 transgenic mice develop aneuploid tumors (Ricke, et al. J. Cell Biol. 193, 1049-1064 (2011)).
  • BubR1 Down-regulation of BubR1 by oncogenic protein breast cancer-specific gene 1 (BCSG1)-mediated inhibition has been observed in advanced stage breast cancer and is believe to promote chromosomal instability (CIN).
  • BCSG1 oncogenic protein breast cancer-specific gene 1
  • CIN chromosomal instability
  • BubR1 overexpression leads to high incidence of aneuploidy coupled with malignant progression (Ando et al. Cancer Sci. 101:639-645 (2010)).
  • BubR1 at basal level functions to prevent missegregation of sister chromatids during mitosis, but either gain or loss of BubR1 expression promote CIN-driven tumorigenesis and cancer progression.
  • the inventors anticipate that either inhibition of activation of BubR1, as well as Bub1 can be manipulated in order to achieve proper radiosensitization.
  • a small molecule agonist could be developed through a chemical screen.
  • Mad2 is a central component of the spindle assembly checkpoint, which is a feedback control that prevents cells with incompletely assembled spindles from leaving mitosis. Partial loss of checkpoint control, via deletion of one MAD2 allele results in a defective mitotic checkpoint in human cancer cells, leading to an increased rate of chromosome missegregation events and an increased frequency of aneuploid metaphases compared to cells control cancer cells (Michel et al. Nature 409, 355-359 (2001)).
  • use of specific Mad2 inhibitors in conjunction with radiation therapy is anticipated to lead to enhanced tumor treatment response.
  • M2I-1 MAD2 inhibitor-1
  • PPI essential protein-protein interaction
  • Hec1 (Highly Expressed in Cancer 1) is one of four proteins of the outer kinetochore Ndc80 complex involved in the dynamic interface between centromeres and spindle microtubules Inhibition of Hec1 phosphorylation abrogates microtubule attachment to the kinetochore and induces chromosome missegregation, underscoring the importance of Hec1 phosphorylation in faithful chromosome segregation and the maintenance of genomic stability in mitosis (Du et al. Oncogene. 27(29):4107-14 (2008)). Thus, inhibition of Hec1 is another method by which w-CIN can be induced, leading to radiosensitization of cancer cells and tumors.
  • Hec1 inhibitors include, but are not limited to TAI-95 and TAI-1 (Huang et al. Mol Cancer Ther. 13(6):1419-30 (2014), Huang et al. J Exp Clin Cancer Res. 33:6, (2014)).
  • TAI-95 is highly potent in breast cancer cell lines, with GI 50 between 14.29 and 73.65 nmol/L.
  • TAI-95 showed excellent oral efficacy in an in vivo breast cancer model, where mice were treated with TAI-95 twice a day for 28 days, using TAI-95 orally at 10, 25, 50 mg/kg (mpk) or intravenously at 10, 25, 50 mpk (Huang et al. Mol Cancer Ther. 13(6):1419-30 (2014).
  • TAI-1 TAI-1 was shown to be effective orally in in vivo animal models of triple negative breast cancer, colon cancer and liver cancer. Furthermore, a 7-day toxicology studies of TAI-1 in mice showed no significant change in body weight, organ weight, and plasma indices when animals were treated with 7.5, 22.5, and 75.0 mg/kg twice a day by oral administration (Huang et al. J Exp Clin Cancer Res. 33:6, (2014).
  • mitotic checkpoint genes known to be implicated in tumors such as Mad2 and Hec1
  • both partial inactivation and overactivation of the mitotic checkpoint promote chromosomal instability.
  • Hec1 overexpression hyperactivates the mitotic checkpoint and induces tumor formation in vivo (Diaz-Rodriguez et al. Proc Natl Acad Sci USA. 105(43):16719-24 (2008)).
  • overexpression of Hec1 resulted in lagging chromosomes and aneuploidy (Diaz-Rodriguez et al. Proc Natl Acad Sci USA. 105(43):16719-24 (2008)).
  • activation or upregulation of Hec1 can also be used to promote CIN, resulting in radiosensitization.
  • this can also be achieved by altering the phosphorylation patterns of Hec1, which can make Hec1 more stable, causing it to latch onto microtubules more strongly, and leading to increased stability and increased chromosome missegregation.
  • Mad2 overexpression has also been shown to promote aneuploidy and tumorigenesis in mice (Sotillo et al. Cancer Cell. 11:9-23 (2007)).
  • agents that cause activation of upregulation of Mad2 can also be used to promote radiosensitization.
  • Noncoding RNA Activated by DNA Damage (NORAD)
  • lncRNAs Long noncoding RNAs
  • LINC00657 a poorly characterized human lncRNA
  • NORAD a poorly characterized RNA activated by DNA damage
  • the authors showed that inactivation of NORAD triggers dramatic aneuploidy in previously karyotypically stable cell lines. They further discovered that NORAD maintains genomic stability by sequestering PUMILIO proteins, which repress the stability and translation of mRNAs to which they bind.
  • Kif2b, MCAK, MPS1, Eg5/Kinesin-5, Polo-like kinase 4, Mad2, and Hec1 can be achieved using monoclonal or polyclonal antibodies and related specific binding moieties such as immunoreactive fragments thereof.
  • Table 1 lists nonlimiting examples of commercially available human-specific monoclonal or polyclonal antibodies against each of these proteins.
  • target proteins can be inhibited or activated for the purposes of inducing w-CIN and consequently radiosensitization were described.
  • the inventors provide approximate threshold levels for inhibition or activation of target genes, wherein such threshold levels are expected to provide levels of target genes sufficient for induction of w-CIN and radiosensitization.
  • Table 2 includes approximate threshold levels for inhibition of genes that promote faithful chromosome segregation, while Table 3 provides such threshold levels for activation of genes that promote chromosome missegregation.
  • target genes and proteins can be reduced or inhibited at any level, including the protein, RNA, or DNA level.
  • any techniques known in the art that are used for reducing protein, RNA, or DNA levels can be used to achieve increase in w-CIN and radiosensitization. Such techniques include, but are not limited to gene deletion, gene disruption, shRNA or antisense approaches.
  • gene modification can be achieved using an engineered nuclease such as a zinc finger nuclease (ZFP), TALE-nuclease (TALEN), or CRISPR/Cas nuclease.
  • Activation or overexpression of proteins that promote faithful chromosome segregation can be used as a method of protection of noncancerous cells against radiation. Since overexpression of Kif2b results in decreased CIN, agents that activate or upregulate Kif2b can be used as radioprotectors. Such radioprotectors can serve to protect noncancerous cells preferentially as the radiation intensity is focused on the tumor (e.g., in conformal radiation), making any radioprotector in the tumor cells practically ineffective. Furthermore, radioprotectors can alternatively be used to shield and protect organs or tissues.
  • the digestive tract can be protected by delivering a radio-protector that is not systemically absorbed but it can have a topical or local effect on the tract, which tends to receive the most damage of ionizing radiation.
  • a radio-protector that is not systemically absorbed but it can have a topical or local effect on the tract, which tends to receive the most damage of ionizing radiation.
  • organs include, but are not limited to the pharynx, esophagus, stomach, small and large intestines, and rectum. This approach to tissue protection can also be applied to other mucosal surface such as the vaginal tract and the cervix.
  • any agent that specifically promotes faithful chromosome segregation, and reduction in lagging chromosomes and/or CIN could be used as a radioprotective agent.
  • Fluorescence in situ hybridization is one of the main methods for the assessment of w-CIN status in tumors. Variations in chromosome copy number across the cell population can be quantified using fluorescently labeled DNA probes that bind to the centromeres of specific chromosomes. FISH thus allows the assessment of the chromosomal state of hundreds of cells, and the rate of change can be inferred from the cell-to-cell variability in chromosome number (Speicer et al. Nat Rev Genet 6: 782-792 (2005)).
  • Additional methods for assessing w-CIN status include, but are not limited to flow and DNA image cytometry. These methods have been discussed by Darzynkiewicz et al. Adv Exp Med Biol 676: 137-147 (2010)). Both of these methods measure cellular DNA content through the use of dyes that bind stoichiometrically to DNA, allowing DNA cell cycle distribution and ploidy to be determined.
  • Single-cell, comparative genomic hybridization (CGH) (Fiegler et al., Nucleic Acids Res 35: e15 (2007)) can yield information on both numerical and structural chromosomal aberrations at a single-cell level, and heterogeneity can then be quantified by comparing multiple cells.
  • Karyotypic complexity measures of CIN are commonly performed on a combined population of cells.
  • Conventional array CGH uses DNA from multiple cells, and can be used to define the both structural chromosomal complexity and copy number changes in a tumor sample (Pinkel et al. Nat Genet 37: S11-S17 (2005)).
  • Chromosoaml instability can also be assessed directly by measuring the frequency of lagging chromosomes in dividing cells undergoing anaphase or telophase. This has been shown in Diffuse Large B Cell Lymphoma as well as rectal cancer but is viable in most tumor specimens where surgical or core biopsies or excision exist and the tissue is either stained using standard Hematoxylin and Eosin staining, immunofluorescence or immunohistochemistry. In the following two papers, the method was used as a prognostic and predictive marker. See for example” Clin Cancer Res. 2011 Dec. 15; 17(24): 7704-11. doi: 10.1158/1078-0432. CCR-11-2049.
  • Chromosomal instability substantiates poor prognosis in patients with diffuse large B-cell lymphoma.
  • Bakhoum SF1 Danilova O V, Kaur P, Levy N B, Compton D A. See also, Cancer. 2014 Jun. 1; 120(11):1733-42. doi: 10.1002/cncr.28656. Epub 2014 Mar. 6.
  • Chromosomal instability portends superior response of rectal adenocarcinoma to chemoradiation therapy.
  • Zaki B I1 Suriawinata A A, Eastman A R, Garner K M, Bakhoum S F
  • the present disclosure provides novel insights into genome damage induced by IR, beyond direct DNA breaks, which damage occurs outside of the primary nucleus.
  • the inventors have shown that when IR is delivered to mitotic cells, it can directly lead to errors in whole-chromosome segregation, which subsequently leads to the formation of micronuclei and chromosome pulverization hours to days later ( FIG. 6I ).
  • the type of missegregation errors in irradiated cells are dependent on the time lapsed after IR exposure. This is likely dependent on the phase of the cell cycle during which cells are irradiated.
  • the multilayered genomic damage described herein provides an explanation for the extraordinarily sensitivity of mitotic cells to IR (Gunderson et al. Clinical Radiation Oncology. Churchill Livingstone; 2011, Terasima et al. Biophys J. 1963; 3:11-33, whereby IR exposure during mitosis not only leads to direct DNA breaks but also to additional numerical and downstream structural chromosomal damage. This cell cycle-dependent sensitivity has been exploited in the way radiation treatment is delivered in clinical settings.
  • a fundamental rationale for dividing radiation treatment dose into small daily fractions is to enact lethal damage onto the sensitive subpopulation of tumor cells, including the mitotic subpopulation, while sparing toxicity to the surrounding normal tissue which typically contains fewer mitotic cells and is more adept at DNA repair (Gunderson et al. Clinical Radiation Oncology. Churchill Livingstone; 2011. Therefore, fractionated radiation therapy can maximize damage to mitotic cell population in otherwise non-synchronized tumors.
  • Chromosome pulverization has been postulated to represent a precursor to massive chromosomal rearrangements known as chromothripsis (Stephens et al. Cell. 144:27-40 (2011)).
  • the findings of the present disclosure indicate that pulverization is likely deleterious to cellular viability. In rare instances, however, these punctuated genomic alterations could lead to selective advantage and generate highly aggressive tumors, which represent a rare but devastating late side-effect of radiation therapy.
  • work described in the present disclosure suggests that chromosome pulverization and subsequent chromothripsis would be a defining feature of radiation-induced secondary tumors.
  • DMEM Dulbecco's modified medium
  • McCoy's medium for HCT116
  • fetal bovine serum 50 IU ml ⁇ 1 penicillin
  • 50 mg ml ⁇ 1 streptomycin 50 mg ml ⁇ 1 streptomycin.
  • U251 cells were kindly provided from the laboratory of Mark A. Israel (Geisel School of Medicine at Dartmouth), HCT116 cells (both p53 +/+ and p53 ⁇ / ⁇ were kindly provided by the laboratory of Bert Vogelstein (Johns Hopkins University).
  • For plasmid selection cells were maintained in 0.5-1.0 mg ml ⁇ 1 of G418 (geneticin).
  • Cells were g-irradiated using a 137 Cs-irradiator at a rate of 2.38Gy/min or using external beam radiation at 6 MeV delivered by a linear accelerator according to safety rules of Dartmouth and UCSF.
  • Tubulin-specific mAb DM1 ⁇ (Sigma-Aldrich), Anti-centromere antibody (CREST, Dartmouth), Anti-cleaved caspase-3 antibody (Cell Signaling), anti-Ki67-antibody (Ventana), anti-g-H2AX-antibody (Novus Biologicals), GFP-specific antibody (William Wickner, Dartmouth). Antibodies were used at dilutions of 1:1000 or 1:10000 (for GFP-specific antibody).
  • TBS-BSA Tris-buffered saline with 5% bovine serum albumin
  • TBS-BSA Tris-buffered saline with 5% bovine serum albumin
  • Antibodies were diluted in TBS-BSA+0.1% Triton X-100 and coverslips incubated for 3 hours at room temperature, then washed with TBS-BSA for 5 minutes.
  • Secondary antibodies were diluted in TBS-BSA+0.1% Triton X-100 and coverslips incubated for 1 hour at room temperature.
  • FIG. 10 Western blots of U251 cells expressing GFP-tagged kinesin-13 proteins Kif2b (lane 1), Kif2b (lane 2), MCAK (lane 3), and GFP (lane 4) stained using anti-GFP antibodies.
  • DM1- ⁇ antibody was used to blot for a-tubulin as a loading control.
  • Molecular weight markers (in kDa) are depicted on the left side of the immunoblots ( FIG. 10 ).
  • HCT116 p53 ⁇ / ⁇ cells were treated with 100 ⁇ M monastrol or DMSO control for 8 h and then ⁇ -irradiated. Immediately following irradiation, cells were washed with PBS twice and then recovered in fresh media for 1 h.
  • FISH analysis cells were collected by trypsinization, briefly resuspended in 75 mM potassium chloride, fixed, washed twice in 3:1 methanol/acetic acid mix, dropped onto wet slides, air dried, and stained with DAPI. FISH was performed using both ⁇ -satellite and subtelomere probes specific for the centromeric and q arm telomeric regions of chromosomes 2 respectively (Cytocell). Cells were hybridized according to the manufacturer's protocol, and chromosome signals in at least 300 nuclei were scored.
  • HCT116 p53 ⁇ / ⁇ cells 43 were implanted subcutaneously into the flanks of CD1-Nude mice (4-6 week-old males supplied by the UCSF Breeding Core or Jackson Labs). Tumors were measured with calipers. Volume was calculated by the following formula: width ⁇ length ⁇ 0.5. Tumors were exposed to gamma irradiation ( 137 Cs) at fractionated doses (5 consecutive days ⁇ 2Gy) when tumors were ⁇ 300 mm 3 or at a single dose (1 day ⁇ 10Gy) when tumors were ⁇ 800 mm 3 . Tumors were isolated and cultured or sectioned for immunohistochemistry.
  • Cells were either trypsinized (for non-synchronized populations) or collected using mitotic shake-off (for mitotic population) serially diluted and irradiated in their native medium. Cells were then plated in 25-cm 2 T-flasks and clones were grown for 18 days. Clones were stained with Crystal violet and colonies were counted when they reached an approximate size of ⁇ 50 cell/clone 29 . Relative viability was determined based on the 0 Gy dose.
  • Cell Profiler 2.0 (Broad Institute) 44 was used to segment nuclei and for automated counting of foci using the examplesspeckles.cp pipeline. Nuclei were segmented based on their shape and signal intensity, foci were identified based on their intensity and their diameter. Intensity threshold spanned 2.5-100%.
  • Antigen retrieval for immunohistochemistry was performed in Tris EDTA pH 8.0 for 30 minutes at 95 degrees Celsius. Slides were treated with blocking reagent (Vector M.O.M. kit BMK-2202) for 32 minutes. Immunohistochemistry was performed using primary antibodies for Ki67 (Ventana RRF 790-4286, undiluted, room temperature for 16 minutes) or cleaved caspase 3 (Cell Signaling #9661, diluted 1:50 in M.O.M. diluent, 37 degrees Celsius for 60 minutes). Antibody detection was performed using the Ventana IView Detection Kit (760-091).
  • High-resolution fluorescence microscopy was used to examine various types of errors during anaphase in three human cell lines derived from normal human retinal epithelium (RPE1), colorectal cancer (HCT116) or glioma (U251). These cells were either near-diploid and chromosomally stable (RPE and HCT116) or aneuploid and chromosomally unstable (U251). RPE1 and HCT116 had an intact p53-signalling pathway (Thompson et al. Cell Biol. 2010; 188:369-381, whereas U251 contain defective p53 signalling (Gomez-Godinez et al. Nucleic Acids Res. 38:e202-e202. (2010).
  • FIG. 1 a displays U251 cells fixed 25 minutes following exposure to 12 Gy and stained for centromeres using anti-centromere antibody (white dots), and DNA using (light grey cloud).
  • FIG. 1 a shows percentages of chromosome missegregation in response to 0 or 12 Gy IR dose in anaphase spindles of RPE1, U251, and HCT116 cells.
  • the legging chromosomes evaluated after IR exposure displayed centromere staining and maintained attachments to microtubules emanating from opposite spindle poles ( FIG. 7 a ).
  • legging chromosomes exhibited similar levels of staining of ⁇ -H2AX, a marker of DNA double stand breaks (DSBs), compared with the remaining chromosomes ( FIG. 7 b ). Additionally, the inventors did not observe significant increase in spindles with chromatin bridges ( FIG. 1 a, b ).
  • IR exposure on chromosome segregation were further evaluated by exposure of HCT116 cells to 6 Gy, followed by fluorescence in situ hybridization (FISH) using centromere and telomere probes for chromosome 2 on irradiated nuclei 1 hour later.
  • FISH fluorescence in situ hybridization
  • FIG. 1 c exposure of non-synchronized cells to IR did not result in significant short-term change in chromosome number.
  • IR exposure resulted in approximately 2 fold increase in aneuploidy as evidenced by balanced changes in both centromere and telomere probes specific to human chromosome 2 ( FIG. 1 d ).
  • HCCT116 cells devoid of tumor suppressor, p53 were used in this experiment, to allow for the proliferation of aneuploidy cells should they emerge (Thompson and Compton, J Cell Biol. 188(3):369-81, 2010).
  • HCT116 p53 ⁇ / ⁇ cells were exposed to 0 or 6 Gy of IR and chromosome segregation errors were evaluated at 25 minutes, 12 h, 25 h, and 1 month following the IR exposure. As shown in FIG.
  • 12 h after irradiation there was a significant increase in chromatin bridges and acentric chromatin fragments but not lagging chromosomes FIG. 1 e .
  • anaphase spindles examined 24 h or up to 1 month after IR exposure revealed a significant increase in both lagging chromosomes and chromatin bridges ( FIG. 1 e ).
  • HCT116 p53 ⁇ / ⁇ cells that normally exhibit low rates of chromosomes missegregation and are thus considered chromosomally stable and near-diploid (Thompson and Compton, J Cell Biol. 188(3):369-81, 2010).
  • HCT116 p53 ⁇ / ⁇ cells were subcutaneously injected into nude mice and after 25 days transplanted tumours were exposed to 0 or 10 Gy of IR. Following formalin-fixation of tumours 25 min later, tumour sections were stained with hematoxylin and eosin and the effects of radiation on mitotic cells were evaluated ( FIG. 2 a, b ).
  • FIG. 2 a, b the effects of radiation on mitotic cells were evaluated.
  • FIG. 2 b shows an example of normal anaphase and anaphase cells containing lagging chromosomes in HCT116 p53 ⁇ / ⁇ xenografts after IR exposure.
  • tumours exposed to 10 Gy of IR exhibited significantly higher rates of chromosome segregation errors during anaphase compared with control, non-irradiated, tumours.
  • haematoxylin-stained chromatin was frequently visible in the central spindle during anaphase ( FIG. 2 b and insets). This chromatin often contained a central constriction reminiscent of centromeric DNA suggesting that this chromatin encompassed whole chromosomes.
  • experimental limitations preclude us from resolving lagging chromosomes from acentric chromatin fragments with absolute certainty in fixed tumour tissues.
  • HCT116 p53 ⁇ / ⁇ xenografts were exposed to varying doses of radiation (0 Gy, 10 Gy and five daily fractions of 2 Gy over 5 consecutive days ( FIG. 2 d )).
  • the latter fractionated regimen (2 Gy ⁇ 5 days) aims at targeting an overall larger number of mitotic cells over consecutive days.
  • Cells were subsequently derived from irradiated tumours and passaged in culture for an additional 15 days to obtain sufficient numbers of cells for karyotype analysis ( FIG. 2 d ).
  • lagging chromosomes can lead to downstream defects that culminate in structural chromosomal damage (Hatch et al. Cell. 154:47-60, 2013), such as the exclusion of lagging chromosomes from the primary nucleus in the subsequent G1 phase of the cell cycle, resulting in the formation of micronuclei.
  • RPE1 and U251 cells examined 12 h after IR exposure showed increased frequencies of whole-chromosome-containing micronuclei that positively stained for both DNA and centromeres ( FIG. 3 a -3 c ).
  • mitotic U251 cells obtained by mitotic shake-off were irradiated with 12 Gy and chromosome spreads examined 24 h after irradiation in order to assay for chromosome pulverization in the subsequent mitosis as previously described by Crasta et al. ( Nature. 482:53-58, 2012) ( FIG. 3 d ).
  • the appearance of many small chromosome fragments and decondensed chromatin indicate the consequences of chromosome pulverization ( FIG. 3 e ).
  • 12 Gy of IR to mitotic U251 cells led to a significant increase in the fraction of chromosome spreads displaying pulverized chromosomes.
  • micronuclei are not only defective in DNA repair but can actively generate additional DNA damage. This additional damage is likely the consequence of faulty attempts at DNA repair and defective micronuclei nuclear envelope structures. Therefore, by inducing mitotic errors, IR leads to amplifications of structural chromosomal defects that predominantly occur outside of the primary nucleus (extra-nuclear). Unlike DNA damage caused directly by IR, these defects are precipitated many hours after IR exposure.
  • Kif2b is a microtubule-depolymerizing kinesin-13 protein that specifically corrects erroneous microtubule attachments to chromosomes (Bakhoum et al. Nat Cell Biol. 2009; 11:27-35; Manning et al. Mol Biol Cell. 2007; 18:2970-2979).
  • U251 cells overexpressing GFP-Kif2b displayed greater than twofold reduction in chromosome segregation errors during anaphase compared with control U251 cells, as well as fewer chromosome segregation errors during anaphase after IR exposure.
  • FIG. 3 i In similar experiments, we found that GFP-Kif2b overexpression reduced the frequency of IR-induced lagging chromosomes in otherwise chromosomally stable RPE1 cells (Bakhoum Cancer Discov. 2014; 4:1281-1289). Accordingly, GFP-Kif2b overexpression also led to significant reductions in the frequency of cells containing micronuclei in both RPE1 and U251 cells ( FIG. 3 c ). We then examined mitotic spreads, 24 h after exposure of mitotic cells to IR, for downstream chromosomal breaks known to result from micronuclei.
  • the inventors measured relative ⁇ -H2AX fluorescence intensity in irradiated mitotic U251 cells. As shown in FIG. 4 a , there was no difference between control and GFP-Kif2b-overexpressing U251 cells. Furthermore, when the average number of ⁇ -H2AX foci in the primary nuclei 20 min after IR exposure was compared to that of 12 h after IR exposure, there was no significant difference between control and GFP-Kif2b-overexpressing cells ( FIG. 4 b, c ).
  • Mitosis has long been recognized, for unclear reasons, as the most radiation sensitive phase of the cell cycle (Terasima et al. Biophys J. 1963; 3:11-33; Sinclair et al. Radiat Res. 1966; 29:450-474).
  • the inventors have accomplished to selectively reduce chromosome segregation errors without influencing the canonical IR-induced DNA damage and repair within the primary nucleus. This allows for testing whether whole-chromosome segregation errors might independently contribute towards the sensitivity of mitotic cells to IR.
  • cells were enriched for mitotic cells using mitotic shake-off before irradiation and plating for colony growth ( FIG. 5 a ).
  • FIG. 5 a GFP-Kif2b overexpression led to significant increase in the viability after irradiation, whereby at 12 Gy of IR, these cells were ⁇ 20-fold more resistant compared with control cells.
  • GFP-Kif2b overexpression led to increased viability in RPE1 cells as well ( FIG. 8 a ).
  • GFP-Kif2b overexpression did not alter the growth rate of U251 cells in culture or did it significantly influence their karyotypic distribution or modal chromosome numbers ( FIG. 8 b , 8 c ).
  • GFP-MCAK a second kinesin-13 protein also known to suppress w-CIN
  • GFP-MCAK a second kinesin-13 protein also known to suppress w-CIN
  • overexpression of either GFP alone or the third microtubule-depolymerizing kinesin-13 paralogue, GFP-Kif2a did not alter the clonogenic potential of irradiated cells compared with control ( FIG. 5 a , and FIG. 7 c ).
  • FIG. 6 c shows normalized bioluminescence of intracranial U251 xenografts overexpressing GFP or GFP-Kif2b after initiation of IR treatment.
  • GFP- and GFP-Kif2b-expressing tumours also exhibited similar frequencies of multipolar mitoses known to occur after radiation exposure (Sato et al. Oncogene 19, 5281-5290 (2000)), FIG. 6 h and 6 i .
  • GFP-Kif2b-expressing tumours displayed decreased apoptosis as indicated by lower cleaved caspase 3 staining ( FIGS. 6 j and 6 k ). Therefore, suppression of numerical chromosomal instability by altering kinetochore-microtubule attachment stability leads to significant radiation resistance likely by suppressing cell death resultant from excessive chromosomal damage.
  • TNBC triple negative breast cancer
  • mice Under this genetic background, ⁇ 58% of 60 mice developed spontaneous intraductal carcinomas characterized with high-grade pleomorphic nuclei, significant chromosome copy number alterations (CNAs) and numerous mitoses, highly resembling human TNBC.
  • CNAs chromosome copy number alterations
  • patient-derived xenograft model will be used as well. Briefly, 10 5 cells will be transplanted in the mammary fat pads of immuno-competent BL6 hosts. Once tumors reach 5-mm in diameter, 2Gy daily fractions to a total dose of 24Gy or a biologically equivalent single-dose of 13Gy will be delivered using the JLShepherd @ Associates irradiator (model: MK1-68).
  • breast cancer cell lines are highly dependent on Plk4 function and loss of tumor suppressor phosphatase and tensin homolog (PTEN), a frequent occurrence in TNBC, is synthetically lethal with loss of Plk4 activity Brough, R. et al. Cancer Discovery 1, 260-273 (2011)), making the latter an attractive target to further explore in combination with established therapies in TNBC.
  • Plk4 tumor suppressor phosphatase and tensin homolog
  • CFI-400945 will be administered at a concentration of 9.4 mg/kg daily for 2 weeks as previously described (Mason et al. Cancer Cell 26, 163-176 (2014)). Tumor response will be measured using calipers and bioluminescence imaging. Additionally, measures of the time-to-relapse will be taken and direct comparison will be made between BRCA-proficient and BRCA-deficient tumors. For statistical methods please see Vertebrate Animals section. Targeted sequencing and FISH will be to used assess the PTEN status of these tumors given the known synthetic lethality with the loss of PTEN and plk4.
  • CIN may represent a predictive marker of response to therapies that are known to induce chromosome missegregation (Jamal-Hanjani, M. et al. Annals of Oncology 26, 1340-1346 (2015), Zaki, et al. Cancer 120, 1733-1742 (2014)); these therapies likely drive a tumor from an optimal fitness state to a state so chromosomally unstable that it is no longer compatible with viability.
  • the present inventors have discovered that increasing chromosome missegregation together with radiation treatment would lead to sensitization of the tumor to radiation therapy. This in turn permits 1) to decrease dose of radiation and achieve the same effect, 2) to maintain dose of radiation and increase tumor sensitization in otherwise resistant tumors, 3) to increase radioprotection of normal organs.

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