EP3068930A2 - Biomarker for melk activity and methods of using same - Google Patents

Abstract

The methods of the present invention, relate to the surprising determination that the level of phosphorylation of position 406 (e.g., a serine residue.) of human eukaryotic initiation factor 4B (cIF4B), or a corresponding phosphorylatafale amino acid of an ortholog thereof, serves as a bhiraarker for MELK enzymatic (e.g., kinase) and/or oncogenic activity. The methods of the present invention further ceiate to the surprising determination that the level of phosphorylation of position 3 (e.g., a threonine residue) and/or position 10 (e.g., a serine residue) and/or position 11 (e.g., a threonine residue) of human Historic M3, or a corresponding phosphorylatable amino acid of an ortholog thereof, also serves as a biomarker for MELK enzymatic (e.g., kinase) and/or oncogenic activity.

Description

BIOMARKER FOR MELK ACTIVITY AND METHODS OF USING SAME

Cross- Reference to Related Applications

This application claims the benefit of U.S. Provisional Application Nos. 61/954,046, filed on 17 March 2014, and 61/902,877, filed on 12 November 2013; the entire contents of each of said applications is incorporated herein in its entirety by this reference.

Background of the Invention

The protein kinase, maternal embryonic leucine zipper kinase (MELK), is known to be involved in regulating cell cycle progression, cellular proliferation, apoptosis, and mRNA splicing (Badouel el al. (2006) Cell Cycle 5:883-889 and Badouel el al. (2010) Exp. Cell Res. 316:2166-2173). MELK has also been identified using gene expression profile analyses to be associated with a number of cancers, including breast, lung, bladder, lymphoma, and cervical cancer cells and mammary tumor formation in animal models (Komatsu el al. (2013) Int. J. Oncol. 42:478-506; Pickard et al. (2009) Breast Cancer Res. 1 1 :R60; Hebbard et al. (2010) Cancer Res. 70:8863-8873; Lin et al. (2007) Breast Cancer Res. 9:R17; WO 2004/031413; WO 2007/7013665; and WO 2006/085684). Despite this association, however, functional analyses of MELK-mcdiatcd oncogenesis have not been performed to date and the mechanisms of MELK-mediatcd oncogenesis and, by extension, assays for determining agents useful in regulating such oncogenesis, arc not known. This lack of understanding has prevented the identification of biomarkcrs that reliably report MELK enzymatic and/or oncogenic activity. While certain MELK-targeting inhibitors of kinase activity arc known (sec, for example, Chung el al. (2012) Oncolarget 3: 1629-1640), there is a clear need in the art to identify biomarkcrs of MELK-mcdiatcd ontogenesis in order to provide rapid and effective means for evaluating MELK-targeted anti-cancer therapies.

Summary of the Invention

The present invention is based, at least in part, on the discovery that the level of phosphorylation of position 406 (e.g., a serine residue) of human cukaryotic initiation factor 4B (eIF4B) is a reliable biomarkcr for maternal embryonic leucine zipper kinase (MELK) activity suitable for use in measuring MELK enzymatic activity for preclinical and clinical applications. Similarly, the present invention is based, at least in part, on the discovery that the level of phosphorylation of position 3 (e.g., a threonine residue) and/or position 10 (e.g., a serine residue) of human Histonc H3 and/or position 1 1 (e.g., a threonine residue) is also a reliable biomarker for MELK activity suitable for use in measuring MELK enzymatic activity or preclinical and clinical applications.

In one aspect, a method of identifying an agent which inhibits kinase or oncogenic activity of human maternal embryonic leucine zipper kinase (MELK) or an ortholog thereof, comprising a) contacting a sample comprising i) human MELK or an ortholog thereof and ii) human cukaryotic initiation factor 4B (eIF4B) or an ortholog thereof, with the agent; and b) determining the ability of the agent to inhibit Scr-406 phosphorylation of human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B, wherein decreased phosphorylation identifies an agent which inhibits kinase or oncogenic activity of human MELK or the ortholog thereof, is provided. In one embodiment, the inhibition of said Ser-406 phosphorylation of human eIF4B or a corresponding phosphorylatablc amino acid in an ortholog of human eIF4B is determined by comparing the amount of Ser-406 phosphorylated human elF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B, in the sample relative to a control. In another embodiment, the control is the amount of Ser-406 phosphorylated human clF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B in the sample relative to said amount in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent. In still another embodiment, the inhibition of said Scr-406 phosphorylation of human eIF4B or a corresponding

phosphorylatable amino acid in an ortholog of human eIF4B is determined by comparing the ratio of the amount of Scr-406 phosphorylated human eIF4B, or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B, in the sample relative to the total amount of human eIF4B or ortholog thereof, to a control. In yet another embodiment, the control is the ratio of the amount of Scr-406 phosphorylated human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B in the sample relative to said ratio in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent. In another embodiment, the method further comprises determining the amount of a protein translated from an RNA with highly structured 5'UTR, optionally wherein the protein is selected from the group consisting of cellular myclocytomatosis oncogene (c-Myc), X-linkcd inhibitor of apoptosis protein (XIAP), and ornithine decarboxylase (ODC 1 ). In still another embodiment, the method further comprises a step of determining whether the agent directly binds said human eIF4B or said ortholog thereof, or said human MELK or said ortholog thereof. In yet another embodiment, the sample is selected from the group consisting of in vitro, ex vivo, and in vivo samples. In another embodiment, the sample comprises cells (e.g., cancer cells, such as a cancer selected from the group consisting of any cancer in which MELK or eIF4B is amplified or overexpressed, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or eIF4B is activated by other kinases). In still another embodiment, the cells are obtained from a subject. In yet another embodiment, the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow. In another embodiment, the amount of Ser-406

phosphorylatcd human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B is determined by an immunoassay using a reagent which specifically binds with Ser-406 phosphorylated human eIF4B or corresponding

phosphorylated ortholog of human eIF4B (e.g., a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluoresence assay, an enzyme immunoassay, an immunoprccipitation assay, a chemiluminescence assay, an immunohistochemical assay, a dot blot assay, or a slot blot assay). In still another embodiment, the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human eIF4B or corresponding ortholog of human eIF4B and a detection antibody or fragment thereof which specifically binds with Ser-406

phosphorylatcd human eIF4B or a corresponding phosphorylatcd ortholog of human eIF4B. In yet another embodiment, said human eIF4B or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1. In another embodiment, the agent is a small molecule, or an antibody or antigen-binding fragment thereof. In still another embodiment, the agent decreases the amount of Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B by at least 50%.

In another aspect, a method for assessing the efficacy of an agent for inhibiting kinase activity of human MELK or an ortholog thereof in a subject, comprising a) detecting in a subject sample at a first point in time, the amount of Ser-406 phosphorylatcd human eIF4B or the amount of a human eIF4B ortholog phosphorylatcd at a corresponding amino acid of human eIF4B; b) repeating step a) during at one or more subsequent points in time after administration of the agent; and c) comparing the amount of phosphorylated human eIF4B or ortholog thereof detected in step a) with said amount detected in step b), wherein a higher amount of Ser-406 phosphory latcd human eIF4B or the amount of the human eIF4B ortholog phosphorylatcd at a corresponding amino acid of human eIF4B in the first point in time relative to at least one subsequent point in time, indicates that the agent inhibits kinase activity of human MELK or the ortholog thereof, is provided. In one embodiment, the amount of Ser-406 phosphorylated human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B is determined by an immunoassay using a reagent which specifically binds with Ser-406 phosphorylatcd human eIF4B or corresponding phosphorylatcd ortholog of human eIF4B (e.g., a

radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluorcsencc assay, an enzyme immunoassay, an immunoprecipitation assay, a chemi luminescence assay, an immunohistochemical assay, a dot blot assay, or a slot blot assay). In another embodiment, the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human eIF4B or corresponding ortholog of human eIF4B and a detection antibody or fragment thereof which specifically binds with Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylated ortholog of human eIF4B. In still another embodiment, the sample is selected from the group consisting of ex vivo and in vivo samples. In yet another embodiment, the sample comprises cancer cells (e.g., cancer cells selected from the group consisting of any cancer in which MELK or eIF4B is amplified or ovcrcxprcsscd, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or clF4B is activated by other kinases). In another embodiment, the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow. In still another embodiment, the sample in step a) and/or step b) is a portion of a single sample obtained from the subject. In yet another embodiment, the sample in step a) and/or step b) is a portion of pooled samples obtained from the subject. In another embodiment, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer between the first point in time and the subsequent point in time. In still another embodiment, said human eIF4B or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Tabic 1. In yet another embodiment, the agent is a small molecule, or an antibody or antigen-binding fragment thereof. In another embodiment, the agent decreases the amount of Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human clF4B by at least 50%.

In still another aspect, a method of treating a subject afflicted with cancer comprising administering to the subject an agent that inhibits Ser-406 phosphorylation of human eIF4B or a corresponding phosphorylatable amino acid in an ortholog of human eIF4B, thereby treating the subject afflicted with the cancer, is provided. In one embodiment, the agent is administered in a pharmaceutically acceptable formulation. In another embodiment, the agent is a small molecule, or an antibody or antigen-binding fragment thereof. In still another embodiment, the agent directly binds said human eIF4B or the ortholog thereof, or said human MELK or the ortholog thereof. In yet another embodiment, the cancer is selected from the group consisting of any cancer in which MELK or eIF4B is amplified or overexpressed, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or eIF4B is activated by other kinases. In another embodiment, said human eIF4B or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1. In still another embodiment, the agent is a small molecule, or an antibody or antigen-binding fragment thereof. In yet another embodiment, the agent decreases the amount of Scr-406 phosphorylatcd human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B by at least 50%. In another embodiment, the method further comprises administering one or more additional anti-cancer agents.

In yet another aspect, a method of determining the function or activity of human MELK or an ortholog, comprising a) detecting in a sample the amount of Ser-406 phosphorylatcd human clF4B or the amount of a human eIF4B ortholog phosphorylatcd at a corresponding amino acid of human eIF4B; b) repeating step a) in the same sample or a test sample at one or more subsequent points in time after manipulation of the sample and/or manipulation of the same sample or test sample; and c) comparing the amount of phosphorylatcd human eIF4B or ortholog thereof detected in step a) with said amount detected in step b), wherein a modulated of Ser-406 phosphorylatcd human eIF4B or the amount of the human eIF4B ortholog phosphorylatcd at a corresponding amino acid of human eIF4B in the first point in time relative to at least one subsequent point in time and/or at least one subsequent manipulation of the same sample or test sample, indicates that the function or activity of human MEL or an ortholog thereof is modulated, is provided. In one embodiment, the amount of Scr-406 phosphorylatcd human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human clF4B is determined by an immunoassay using a reagent which specifically binds with Scr-406 phosphorylatcd human elF4B or corresponding phosphorylatcd ortholog of human eIF4B (e.g., a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluoresence assay, an enzyme immunoassay, an immunoprecipitation assay, a chemi luminescence assay, an immunohistochemical assay, a dot blot assay, or a slot blot assay). In another embodiment, the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human eIF4B or corresponding ortholog of human eIF4B and a detection antibody or fragment thereof which specifically binds with Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylatcd ortholog of human eIF4B. In still another embodiment, the sample is selected from the group consisting of in vi/ro, ex vivo, and in vivo samples. In yet another embodiment, the sample comprises cells or the method uses a cell-based assay. In another embodiment, the cells are cancer cells selected from the group consisting of any cancer in which MELK or eIF4B is amplified or overexpressed, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or eIF4B is activated by other kinases. In still another embodiment, the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow. In yet another embodiment, the same sample or test sample in step a) and/or step b) is a portion of a single sample obtained from a subject. In another embodiment, the same sample or test sample in step a) and/or step b) is a portion of pooled samples obtained from a subject. In still another embodiment, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer between the first point in time and the subsequent point in time. In yet another embodiment, said human eIF4B or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1. In another embodiment, the manipulation of the sample is selected from the group consisting of contacting the sample with a test agent, contacting the sample with an upstream signal of the MELK signaling pathway, and contacting the sample with a MELK inhibitor. In still another embodiment, the test agent is a small molecule, or an antibody or antigen-binding fragment thereof. In yet another embodiment, the test agent decreases the amount of Scr-406 phosphorylatcd human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B by at least 50%. In another aspect, a method of identifying an agent which inhibits kinase or oncogenic activity of human MELK or an ortholog thereof, comprising: a) contacting a sample comprising i) human MELK or an ortholog thereof and ii) human Histone H3 or an ortholog thereof, with the agent; and b) determining the ability of the agent to inhibit Thr-3 phosphorylation of human Histone H3 or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3; and/or Ser- 10 phosphorylation of human Histone H3 or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3; and/or Thr-11 phosphorylation of human Histone H3 or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, wherein decreased phosphorylation identifies an agent which inhibits kinase or oncogenic activity of human MELK or the ortholog thereof is provided. In one embodiment, the inhibition of said Thr-3 phosphorylation and/or Ser- 10 phosphorylation and/or Thr-11 phosphorylation of human Histone H3, or a corresponding phosphorylatable amino acid in an ortholog of human Histone H3, is determined by comparing the amount of Thr-3 phosphorylated human Histone H3 and/or Ser- 10 phosphorylated human Histone H3 and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, in the sample relative to a control. In another embodiment, the control is the amount of Thr-3 phosphorylated and/or Ser- 10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, in the sample relative to said amount in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent. In still another embodiment, the inhibition of said Thr-3 phosphorylation and/or Ser- 10 phosphorylation and/or Thr-11 phosphorylation of human Histone H3, or a corresponding phosphorylatable amino acid in an ortholog of human Histone H3, is determined by comparing the ratio of the amount of Thr-3 phosphorylated and/or Ser- 10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, in the sample relative to the total amount of human Histone H3 or ortholog thereof, to a control. In yet another embodiment, the control is the ratio of the amount of Thr-3 phosphorylated and/or Ser- 10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3 in the sample relative to said ratio in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent. In another embodiment, the method further comprises determining the amount of a mitosis-specific protein. In still another embodiment, the method further comprises a step of determining whether the agent directly binds said human Histone H3 or said ortholog thereof, or said human MELK or said ortholog thereof. In yet another embodiment, the sample is selected from the group consisting of in vitro, ex vivo, and in vivo samples. In another embodiment, the sample comprises cells, such as cancer cells (e.g., cells from a cancer selected from the group consisting of any cancer in which MELK or Histone H3 is amplified or overexpressed, any cancer having an activating mutation of MELK or Histone H3, and any cancer in which MELK or Histone H3 is activated by other kinases). In still another embodiment, the cells arc obtained from a subject. In yet another embodiment, the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow. In another embodiment, the amount of Thr-3 phosphorylated and/or Ser-10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a

corresponding phosphorylatable amino acid in the ortholog of human Histone H3, is determined by an immunoassay using a reagent which specifically binds with Thr-3 phosphorylated or Ser-10 phosphorylated or Thr-11 phosphorylated human Histone H3, or corresponding phosphorylated ortholog of human Histone H3. In still another embodiment, the immunoassay is a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluorcscncc assay, an enzyme immunoassay, an immunoprccipitation assay, a chcmilumincsccnce assay, an immunohistochemical assay, a dot blot assay, or a slot blot assay. In yet another embodiment, the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human Histone H3 or corresponding ortholog of human Histone H3 and a detection antibody or fragment thereof which specifically binds with Thr-3 phosphorylated or Scr-10 phosphorylated or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylated ortholog of human Histone H3. In another embodiment, the human Histone H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1. In still another embodiment, the agent is a small molecule, or an antibody or antigen-binding fragment thereof. In yet another embodiment, the agent decreases the amount of Thr-3 phosphorylated and/or Ser- 10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, by at least 50%.

In still another aspect, a method for assessing the efficacy of an agent for inhibiting kinase activity of human MELK or an ortholog thereof in a subject, comprising: a) detecting in a subject sample at a first point in time, the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histonc H3, or the amount of a human Histonc H3 ortholog phosphorylated at a corresponding amino acid of human Histone H3; b) repeating step a) during at one or more subsequent points in time after administration of the agent; and c) comparing the amount of phosphorylated human Histone H3 or ortholog thereof detected in step a) with said amount detected in step b), wherein a higher amount of Thr-3 phosphorylated and/or Ser-10 phosphorylated and/or Thr-11 phosphorylatcd human Histone H3, or the amount of the human Histone H3 ortholog phosphorylatcd at a corresponding amino acid of human Histonc H3, in the first point in time relative to at least one subsequent point in time, indicates that the agent inhibits kinase activity of human MELK or the ortholog thereof is provided. In one embodiment, the amount of Thr-3 phosphorylated and/or Ser- 10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, is determined by an immunoassay using a reagent which specifically binds with Thr-3 phosphorylated human Histone H3 or Scr- 10 phosphorylated human Histone H3 or Thr-11 phosphorylated human Histone H3, or corresponding phosphorylatcd ortholog of human Histonc H3. In another embodiment, the immunoassay is a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluorcscncc assay, an enzyme immunoassay, an immunoprecipitation assay, a chcmilumincsccncc assay, an immunohistochemical assay, a dot blot assay, or a slot blot assay. In still another embodiment, the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human Histonc H3 or corresponding ortholog of human Histonc H3 and a detection antibody or fragment thereof which specifically binds with Thr-3 phosphorylatcd or Ser-10 phosphorylated or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatcd ortholog of human Histonc H3. In yet another embodiment, the sample is selected from the group consisting of ex vivo and in vivo samples. In another embodiment, the sample comprises cancer cells (e.g. , cancer cells selected from the group consisting of any cancer in which MELK or Histonc H3 is amplified or ovcrexprcsscd, any cancer having an activating mutation of MELK or Histonc H3, and any cancer in which MELK or Histonc H3 is activated by other kinases). In still another embodiment, the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow. In yet another embodiment, the sample in step a) and/or step b) is a portion of a single sample obtained from the subject. In another embodiment, the sample in step a) and/or step b) is a portion of pooled samples obtained from the subject. In still another embodiment, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer between the first point in time and the subsequent point in time. In yet another

embodiment, the human Histone H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1. In another embodiment, the agent is a small molecule, or an antibody or antigen- binding fragment thereof. In still another embodiment, the agent decreases the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histone H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3, by at least 50%.

In yet another aspect, a method of treating a subject afflicted with cancer comprising administering to the subject an agent that inhibits Thr-3 phosphorylation and/or Ser-10 phosphorylation and/or Thr-11 phosphorylation of human Histone H3, or a corresponding phosphorylatablc amino acid in an ortholog of human Histone H3, thereby treating the subject afflicted with the cancer is provided. In one embodiment, the agent is administered in a pharmaceutically acceptable formulation. In another embodiment, the agent is a small molecule, or an antibody or antigen-binding fragment thereof. In still another embodiment, the agent directly binds said human Histone H3 or the ortholog thereof, or said human MELK or the ortholog thereof. In yet another embodiment, the cancer is selected from the group consisting of any cancer in which MELK or Histone H3 is amplified or

ovcrcxprcsscd, any cancer having an activating mutation of MELK or Histone H3, and any cancer in which MELK or Histone H3 is activated by other kinases. In another

embodiment, the human Histone H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1. In still another embodiment, the agent is a small molecule, or an antibody or antigen-binding fragment thereof. In yet another embodiment, the agent decreases the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11

phosphorylatcd human Histone H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3, by at least 50%. In another embodiment, the method further comprises administering one or more additional anti-cancer agents. In another aspect, a method of determining the function or activity of human MELK or an ortholog, comprising: a) detecting in a sample the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human historic H3 or the amount of a human Histone H3 ortholog phosphorylated at a corresponding amino acid of human Histone H3; b) repeating step a) in the same sample or a test sample at one or more subsequent points in time after manipulation of the sample and/or manipulation of the same sample or test sample; and c) comparing the amount of phosphorylated human Histone H3 or ortholog thereof detected in step a) with said amount detected in step b), wherein a modulated amount of Thr-3 phosphorylatcd and/or Scr-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histone H3, or the amount of the human Histone H3 ortholog phosphorylated at a corresponding amino acid of human Histone H3, in the first point in time relative to at least one subsequent point in time and/or at least one subsequent manipulation of the same sample or test sample, indicates that the function or activity of human MELK or an ortholog thereof is modulated is provided. In one embodiment, the amount of Thr-3 phosphorylated and/or Ser-10 phosphorylated and/or Thr-11

phosphorylated human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, is determined by an immunoassay using a reagent which specifically binds with Thr-3 phosphorylatcd or Scr- 10 phosphorylatcd or Thr-11 phosphorylatcd human Histone H3, or corresponding phosphorylated ortholog of human Histone H3. In another embodiment, the immunoassay is a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluoresence assay, an enzyme

immunoassay, an immunoprecipitation assay, a chemiluminescence assay, an

immunohistochemical assay, a dot blot assay, or a slot blot assay. In still another embodiment, the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human Histone H3 or corresponding ortholog of human Histone H3 and a detection antibody or fragment thereof which specifically binds with Thr-3 phosphorylatcd or Scr-10 phosphorylatcd or Thr-11 phosphorylatcd human Histone H3, or a corresponding phosphorylatcd ortholog of human Histone H3. In yet another embodiment, the sample is selected from the group consisting of in vitro, ex vivo, and in vivo samples. In another embodiment, the sample comprises cells or the method uses a cell-based assay. In still another embodiment, the cells arc cancer cells selected from the group consisting of any cancer in which MELK or Histone H3 is amplified or ovcrcxprcsscd, any cancer having an activating mutation of MELK or Histonc H3, and any cancer in which MELK or Histonc H3 is activated by other kinases. In yet another embodiment, the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow. In another embodiment, the same sample or test sample in step a) and/or step b) is a portion of a single sample obtained from a subject. In still another embodiment, the same sample or test sample in step a) and/or step b) is a portion of pooled samples obtained from a subject. In yet another embodiment, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer between the first point in time and the subsequent point in time. In another embodiment, the human Histonc H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table I . In still another embodiment, the manipulation of the sample is selected from the group consisting of contacting the sample with a test agent, contacting the sample with an upstream signal of the MELK signaling pathway, and contacting the sample with a MELK inhibitor. In yet another embodiment, the test agent is a small molecule, or an antibody or antigen-binding fragment thereof. In another embodiment, the test agent decreases the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histonc H3, or a

corresponding phosphorylatablc amino acid in the ortholog of human Histonc H3, by at least 50%.

It will also be understood that certain embodiments of the present invention can be used with more than one method described herein, according to knowledge available to the skilled artisan.

Brief Description of Figures

Figure 1 shows that MELK interacts with eIF4B. Flag-MELK was conditionally expressed in MDA-MB-468 cells. Mitotic lysatcs were subjected to anti-Flag

immunoprccipitation followed by tandem mass spcctromctric analysis. The left panel shows the number of peptides recovered from the immunoprecipitatcs. The right panel shows validation of the interaction between MELK and eIF4B during mitosis. Note that Flag-MELK is doxycycline-induciblc.

Figure 2 shows the results of peptide library screening to identify an optimal substrate motif for MELK. The top panel shows the results of a spatially arrayed peptide library subjected to in vitro phosphorylation using recombinant full-length MELK. Each peptide contains one residue fixed at one of nine positions relative to the centrally fixed phosphoacccptor {i.e., serine or threonine). Reactions were spotted onto the membrane and the spots were exposed to a phosphor storage screen. The bottom panel shows a sequence logo generated using quantified and normalized data from the screen. Note that MELK has a strong selection for arginine at the -3 position relative to the phosphoacceptor site.

Figure 3 shows that MELK phosphorylates eIF4B at S406 in vitro. Recombinant full-length MELK or the kinase domain of MELK was subjected to in vitro kinase assays using immunoprccipitatcd Flag-eIF4B (wild type) or Flag-eIF4B (S406A). Robust phosphorylation of eIF4B at S406 was observed in the presence of MELK. This phosphorylation was abolished when wild type (wt) eIF4B was replaced with a mutant eIF4B (S406A).

Figure 4 shows that MELK does not phosphorylates eIF4B at S422 in vitro.

Recombinant full-length or kinase domain of MELK was subjected to in vitro kinase assay using immunoprecipitated Flag-eIF4B (wild type) or Flag-eIF4B (S422A). Reactions were analyzed by immunoblotting.

Figure 5 shows that MELK regulates phosphorylation of eIF4B at S406 in vivo. Left panels show MELK knockdown impairs the phosphorylation of eIF4B at S406. MDA- MB-468 cells stably expressing tetracycline-inducible (tct-on) small hairpin MELK (shMELK) in the presence or absence of doxycyclinc were harvested through treatment of nocodazolc, and subjected to immunoblotting. Right panels show that a MELK inhibitor impairs the phosphorylation of eIF4B at S406. Mitotic MDA-MB-468 cells were treated for 30 min with vehicle or 200 nM OTSSP167, a MELK inhibitor (Chung et al. (2012) Oncotarget 3: 1629- 1640). Lysatcs were used for immunoblotting.

Figure 6 shows the results of treating mitotic cells for 30 min with mTOR inhibitors (e.g., Rapamycin and Torin 1 ) versus treating such cells with MELK inhibitors (e.g.,

OTSSP67). The results indicate that MELK inhibition, but not mTOR inhibition, suppressed the phosphorylation of eIF4B at S406.

Figure 7 shows that knocking down MELK or eIF4B decreases the protein abundance of XIAP, c-Myc, and ODC1 during mitosis. MDA-MB-468 and MDA-MB-231 cells stably expressing tet-on shMELK or sh-eIF4B were treated with doxycyclinc or vehicle control. Mitotic cells were harvested by nocodazolc-induccd arrest at

prometaphase. Note that the mRNA of XIAP, c-Myc, and ODC 1 have been shown to contain structured 5'UTR and their total levels remain unchanged. Figure 8 shows that knocking down MELK decreases the translation of lucifcrasc driven by the 5' UTR of c-Myc or ODC1 during mitosis. MDA-MB-231 cells stably expressing tet-on shMELK were transfected with the indicated bicistronic vector in the presence or absence of doxycycline. Nocodazole-arrested mitotic cells were harvested two days after transfection and subjected to a luciferase assay. The ratio of Renilla luciferase to firefly luciferase (RLJFL) was normalized to the value of control vector. Note that the left bar corresponds to Dox (-) and the right bar corresponds to Dox (+) for each pair of bars shown in the graph reporting relative RL/FL ratios.

Figure 9 shows that MELK phosphorylatcs Histonc H3 at Thr-3, Scr-10 and Thr-11 in vitro. Recombinant Histonc H3 was incubated with or without recombinant MELK

(kinase domain) for 30 min. at 30 °C in the presence of ATP. Reactions were terminated by adding SDS sample buffer. Samples were then subjected to immunoblotting using the indicated antibodies.

Figure 10 shows that knocking down MELK decreases the mitotic phosphorylation of Histonc H3 at Thr-3, Scr-10 and Thr-11, but not Scr-28. MDA-MB-468 cells stably transduced with tet-on shMELK were untreated or treated with doxycycline (200 ng/ml) in order to induce gene silencing. Cells were then treated with nocodazolc (200 ng/ml) for 20 hours. Mitotic cells were harvested by shake-off and cell lysatcs were subjected to immunoblotting using the indicated antibodies.

Figure 11 shows that knocking down MELK does not affect the phosphorylation of

Aurora kinases, which arc known kinases for Histonc H3 at Scr 10. MDA-MB-468 cells stably transduced with tet-on shMELK were untreated or treated with doxycycline (200 ng/ml) to induce gene silencing. Cells were treated with nocodazolc (200 ng/ml) for 20 hours. Mitotic cells were harvested by shake-off and cell lysatcs were subjected to immunoblotting using the indicated antibodies.

Figure 12 shows that a MELK inhibitor suppresses MELK-induccd

phosphorylation of Histonc H3 at Scr 10 in vitro. Recombinant Histonc H3 was incubated without or with recombinant MELK (kinase domain) for 30 min. at 30 °C in the absence or presence of OTSSP167 (200 ng/ml final). Reactions were terminated by adding SDS sample buffer. Samples were subjected to immunoblotting using the indicated antibodies.

Figure 13 shows that a MELK inhibition suppresses the mitotic phosphorylation of Histonc H3 at Thr-3, Scr-10 and Thr-11, but not Scr-28, in a concentration-dependent manner. Mitotic cells were harvested through nocodazolc-induccd cell cycle arrest at prometaphase (200 ng/ml nocodazolc, 20 hours). Cells were treated with the small chemical inhibitor of MELK, OTSSP167, for 30 min, at the indicated concentrations. Cell lysatcs were then prepared for immunoblotting. Detailed Description of the Invention

The methods of the present invention relate to the surprising detennination that the level of phosphorylation of position 406 (e.g. , a serine residue) of human eukaryotic initiation factor 4B (eIF4B), or a corresponding phosphorylatablc amino acid of an ortholog thereof, serves as a biomarker for MELK enzymatic (e.g., kinase) and/or oncogenic activity. Specifically, decreased phosphorylation of, for example, Ser-406 of human eIF4B (e.g., by directly or indirectly inhibiting MELK-mcdiatcd phosphorylation of Ser-406) corresponds with a reduction in MELK enzymatic activity (e.g., kinase activity) and MELK -mediated oncogenic effects. Such a biomarker is particularly advantageous for preclinical and clinical applications because the phosphorylation state of eIF4B is directly associated with the MELK oncogene itself. Similarly, the methods of the present invention also relate to the surprising determination that the level of phosphorylation of position 10 (e.g., a serine residue) of human Histonc H3, or a corresponding phosphorylatablc amino acid of an ortholog thereof, and/or the level of phosphorylation of position 1 1 (e.g., a threonine residue) of human Histonc H3, or a corresponding phosphorylatablc amino acid of an ortholog thereof, serves as a biomarker for MELK enzymatic (e.g., kinase) and/or oncogenic activity. Specifically, decreased phosphorylation of, for example, Thr-3 of human Histone H3 (e.g., by directly or indirectly inhibiting MELK-mediated

phosphorylation of Thr-3) and/or Scr- 10 of human Histonc H3 (e.g., by directly or indirectly inhibiting MELK-mcdiatcd phosphorylation of Scr-10) and/or Thr-11 of human Histone H3 (e.g., by directly or indirectly inhibiting MELK-mediated phosphorylation of Thr-11 ) corresponds with a reduction in MELK enzymatic activity (e.g., kinase activity) and MELK-mcdiatcd oncogenic effects. Such a biomarkcr is particularly advantageous for preclinical and clinical applications because the phosphorylation state of Histonc H3 is directly associated with the MELK oncogene itself. In some embodiments, Ser-406 of human eIF4B, Thr-3 of human Histonc H3, Ser- 10 of human Histonc H3, and/or Thr-11 of human Histonc H3, as well as any corresponding phosphorylatablc amino acid of an ortholog thereof, including in any combination thereof, arc contemplated for use according to the present invention. In other embodiments, Scr-28 of human eIF4B or a corresponding phosphorylatablc amino acid of an ortholog thereof is not regulated by MELK and is not used according to the present invention.

A. MELK, eIF4B, and Histone H3 Molecules

As used herein, "MELK" refers to the MELK member of the protein kinase superfamily and is alternatively known as "pEG3 kinase," "protein kinase Eg3," "protein kinase," and "serine/threonine-protein kinase MELK." At least nine splice variants encoding nine distinct human MELK isoforms exist. Human MELK transcript variant 1 (NM_014791.3) encodes the long human MELK isoform 1 (NP_55606.1 ). Human MELK transcript variant 2 (NM 001256685.1) lacks an exon in the 3' coding region compared to transcript variant I, but maintains the reading frame and results in an isoform

(NP_001243614.1 ) that is shorter than isoform 1. Human MELK transcript variant 3 (NM_001256687.1) lacks an exon in the 5' coding region compared to transcript variant 1 , but maintains the reading frame and results in an isoform (NP_001243616.1 ) that is shorter than isoform 1. Human MELK transcript variant 4 (NM 001256688.1 ) lacks two consecutive exons in the 5^* coding region compared to transcript variant 1 , but maintains the reading frame and results in an isoform (NP_001243617.1 ) that is shorter than isoform 1. Human MELK transcript variant 5 (NM_001256689.1 ) initiates translation at an alternate start codon and lacks an exon in the 5' coding region compared to transcript variant 1 and thus results in an isoform (NP_001243618.1 ) that is shorter than and has a distinct N-tcrminus from isoform 1. Human MELK transcript variant 6

(NM_001256690.1 ) initiates translation at an alternate start codon and lacks two consecutive exons in the 5^* coding region compared to transcript variant 1 , but maintains the reading frame and results in an isoform (NP_(X⁾ 1243619.1 ) that is shorter than and has a distinct N-terminus from isoform 1. Human MELK transcript variant 7

(NM_001256691.1 ) initiates translation at an alternate start codon and lacks two exons in the 5' coding region compared to transcript variant 1 , but maintains the reading frame and results in an isoform (NP_001243620.1 ) that is shorter than and has a distinct N-tcrminus from isoform 1. Human MELK transcript variant 8 (NM_001256692.1) lacks three exons in the 5' coding region and initiates translation at a downstream, in-frame start codon compared to transcript variant 1 and results in an isoform (NP_001243621.1 ) that has a shorter N-terminus than isoform 1. Finally, human MELK transcript variant 9

(NM_001256693.1 ) lacks two consecutive exons in the 5' coding region and initiates translation at a downstream, in-frame start codon compared to transcript variant 1 and results in an isoform (NP_001243622.1) that has a shorter N-terminus than isoform 1. The protein domains and structural basis for the regulation of MELK autophosphorylation and activation of kinase activities on target proteins is known (see, at least Cao et al. (2013) PLoS One 8:e70031 and Canevari et al. (2013) Biochemistry 52:6380-6387).

Mouse MELK nucleic acid (NM_010790.2) and amino acid (NP_034920.2) sequences are publicly available on the GenBank database maintained by the U.S. National Center for Biotechnology Information. Nucleic acid and polypeptide sequences of MELK orthologs in species other than mice and humans are also well known and include, for example, chimpanzee MELK (XM_001 169038.3, XP_001 169038.1, XM_001 168991.3, XP 001 168991.1 , XM_001 168745.3, XP_001 168745.1, XM_001 168775.3,

XP_001 168775.1 , XM_003951427.1 , XP 003951476.1 , XM_520578.4, XP_520578.3, XM_001 168822.3, XP_001 168822.2, XM_003312085.2, XP_003312133.1 ,

XM_003951428. I , XP 003951477.1 , XM_003312086.2, and XP_003312134.1 ), monkey MELK (XM_001 1 15076.2 and XP_001 1 15076.2), dog MELK (XM_003431578.1 , XP_003431626.1, XM_538730.3, XP_538730.2, XM_003431579.1, and

XP_003431627.1 ), cow MELK (NM_001 1 1 1260.1 and NP_001 104730.1 ), rat MELK (NM_001 108662.1 and NP_001 102132.1 ), chicken MELK (NM_001031509.1 and NP_001026680.1), and zcbrafish MELK (NM_206888.2 and NP_996771.2).

As used herein, "eIF4B" refers to the cukaryotic translation initiation factor 4B member of the cukaryotic translation initiation factor family and is alternatively known as "EIF-4B" and "PR01843." Human eIF4B nucleic acid (NM_00I417.4) and amino acid (NP_001408.2) sequences are publicly available on the GenBank database maintained by the U.S. National Center for Biotechnology Information. Nucleic acid and polypeptide sequences of eIF4B orthologs in species other than humans arc also well known and include, for example, mouse eIF4B (NM_145625.3 and NP_663600.2), chimpanzee eIF4B (XM_003313676.1 , XP 003313724.1 , XM_001 142097.3, and XP_001 142097.3), monkey CIF4B (NM_001 195808.1 and NP_001 182737.1), dog eIF4B (XM_853888.2,

XP 858981.2, XM_853812.2, and XP_858905.2), cow eIF4B (NM_001035028.2 and NP_001030200.1 ), rat eIF4B (NM_001008324.1 and NP_001008325.1 ), and chicken eIF4B (XM_003643408.2 and XP_003643456.2). In addition, "Ser-406" of eIF4B refers to the amino acid numbering of the human eIF4B. Accordingly, a skilled artisan will readily understand that Scr-406 of the human eIF4B polypeptide is conserved across numerous species and that although those specific residues may be referenced herein, the methods of the present invention apply equally well to the corresponding residues {e.g.,

phosphorylatablc amino acids) of isoforms, homologs, and orthologs in other species corresponding to said Ser-406 of human eIF4B.

As used herein, the term "Histone H3" refers to the H3 member of the Histone family, which comprises proteins used to form the structure of nucleosomes in eukaryotic cells. Eukaryotes have chromatin arranged around proteins in the form of nucleosomes, which are the smallest subunits of chromatin and include approximately 146-147 base pairs of DNA wrapped around an octamcr of core histone proteins (two each of H2A, H2B, H3, and H4). Mammalian cells have three known sequence variants of Histone H3 proteins, denoted H3.1 , H3.2 and H3.3, that arc highly conserved differing in sequence by only a few amino acids. Post-translational modification of Histone H3 residues are important in many cellular processes and phosphorylation of serine 10 and/or serine 28 are important for cell division and proliferation regulation. Phosphorylated Histone H3 at serine 10 is a specific biomarker for mitotic cells, similar to other well-known mitosis-specific markers, such as phosphorylated MPM-2, phosphorylated retinoblastoma protein 1 (Rb), phosphorylated cdc2, BubR 1 , cyclin B 1 , cdc25c, cdk 1 , cdc27, and the like. Any serine, threonine, or tyrosine residue can be phosphorylated. In some embodiments, other possible

phosphorylation sites include threonine 3, threonine 6, threonine 1 1 , serine 31 , tyrosine 41, serine 57, threonine 80, and threonine 107.

As used herein, the term "Histone H3" can refer to H3.1 , H3.2, or H3.3 individually or collectively. These amino acid sequences include a methionine as residue number 1 that is cleaved off when the protein is processed. Thus, for example, serine 1 1 in the Histone H3 amino acid sequences shown in Table 1 below corresponds to serine (Scr) 10 of the present invention. These three protein variants arc encoded by at least fifteen different genes/transcripts. Sequences encoding the Histone H3.1 variant are publicly available as HIST1H3A (NM_003529.2; NP_003520.1 ), HIST1 H3B (NM_003537.3; NP_003528.1 ), HIST1H3C (NM_003531.2; NP_003522.1), HIST1 H3D (NM_003530.3; NP_003521.2), HIST1H3E (NM_003532.2; NP_003523.1 ), HIST1H3F (NM_021018.2; NP_066298.1 ), HIST1H3G (NM_003534.2; NP_003525.1 ), HIST1 H3H (NM_003536.2; NP_003527.1 ), HIST1 H3I (NM_003533.2; NP_003524.1), and HIST1 H3J (NM_003535.2; NP_003526.1). Sequences encoding the Histone H3.2 variant arc publicly available as HIST2H3A

(NM_001005464.2; NP_001005464.1 ), HIST2H3C (NM_021059.2; NP_066403.2), and HIST2H3D (NM_001 123375.1 ; NP_001 1 16847.1 ). Sequences encoding the Histone H3.3 variant arc publicly available as H3F3A (NM_002107.3; NP_002098.1) and H3F3B (NM_005324.3; NP_005315.1 ). Sec U.S. Pat. Publ. 2012/0202843 for additional details. Moreover, polypeptide sequences for Histone H3 orthologs, as well as nucleic acid sequences that encode such polypeptides, are well-known in many species, and include, for example, Histone H3.1 orthologs in mice (NM O 13550.4; NP 038578.2), chimpanzee (XM_527253.4; XP_527253.2), monkey (XM_001088298.2; XP_001088298.1 ), dog (XM_003434195.1 ; XP_003434243.1), cow (XM_002697460.1 ; XP_002697506.1 ), rat (XM_001055231.2; XP_001055231.1 ), and zebrafish (NM_001 100173.1 ;

NP_001093643.1 ). Histone H3.2 orthologs in mice (NM_ 178215.1 ; NP_835587.1 ), chimpanzee (XM_524859.4; XP_524859.2), monkey (XM_001084245.2;

XP 001084245.1 ), dog (XM_003640147.1 ; XP 003640195.1 ), cow (XM_002685500.1 ; XP_002685546.1 ), rat <NM_001 107698.1 ; NP_001 101 168.1), chicken (XM_001233027.2; XP_001233028.1), and zebrafish (XM_002662732. 1 ; XP_002662778.1 ). Similarly, Histone H3.3 orthologs in mice (XM_892026.4; XP_8971 19.3), monkey (XM_001085836.2;

XP_001085836.1), cow (NM_001099370.1 ; NP_001092840.1), rat (NM_053985.2;

NP 446437.1 ), chicken (NM_205296.1 ; NP_990627.1 ), and zebrafish (NM_200003.1 ; NP 956297.1 ), arc well-known. Antibodies for the detection of phosphorylated H3 histone, such as phosphorylated Histone H3 at Thr-3, Scr-10, Thr-11, and other

phosphorylatablc residues of Histone H3, as well as methods for making such antibodies are known in the art. In addition, for example, "Ser-10" of Histone H3 refers to the amino acid numbering of the human Histone H3. Accordingly, a skilled artisan will readily understand that Ser- 10 of the human Histone H3 polypeptide is conserved across numerous species and that although those specific residues may be referenced herein, the methods of the present invention apply equally well to the corresponding residues (e.g.,

phosphorylatablc amino acids) of isoforms, homologs, and orthologs in other species corresponding to said Scr-10 of human Histone H3. The same applies to Thr-3 and Thr-11.

Representative MELK,eIF4B, and Histone H3 orthologs arc provided herein (e.g., at least at Table 1 and the Examples) as follows: Table 1

Human MELK. (isoform 1 ) cDNA Sequence (NM_014791.3) conventional amino acids, unnatural amino acids such as alpha,alpha-disubstitutcd amino acids, N-alkyl amino acids, lactic acid, and other unconventional amino acids may also be suitable components for polypeptides described herein. There is a known and definite correspondence between the amino acid sequence of a particular protein and the nucleotide sequences that can code for the protein, as defined by the genetic code (shown below). Likewise, there is a known and definite correspondence between the nucleotide sequence of a particular nucleic acid and the amino acid sequence encoded by that nucleic acid, as defined by the genetic code.

GENETIC CODE

An important and well known feature of the genetic code is its redundancy, whereby, for most of the amino acids used to make proteins, more than one coding nucleotide triplet may be employed (for example, illustrated above). Therefore, a number of different nucleotide sequences may code for a given amino acid sequence. Such nucleotide sequences arc considered functionally equivalent since they result in the production of the same amino acid sequence in all organisms (although certain organisms may translate some sequences more efficiently than they do others). Moreover, occasionally, a methylated variant of a purine or pyrimidine may be found in a given nucleotide sequence. Such methylations do not affect the coding relationship between the trinucleotide codon and the corresponding amino acid. In addition, a skilled artisan will understand how to mutate nucleotides of a specific codon so as to specifically alter an encoded amino acid based on the relevant codon chart. Additional desired nucleic acid and/or amino acid modifications can be engineered using site-directed mutagenesis and PCR-mediated mutagenesis techniques.

The "nucleic acid" can take any of a number of forms {e.g, DNA, mRNA, cDNA) that encode a biomarker described herein. For example, such biomarker nucleic acid molecules include DNA {e.g., genomic DNA and cDNA) comprising the entire or a partial sequence of a desired gene or the complement or hybridizing fragment of such a sequence. The biomarker nucleic acid molecules also include RNA comprising the entire or a partial sequence of a desired gene or the complement of such a sequence, wherein all thymidine residues arc replaced with uridine residues. A "transcribed polynucleotide" is a polynucleotide {e.g., an RNA, a cDNA, or an analog of one of an RNA or cDNA) which is complementary to or homologous with all or a portion of a mature RNA made by transcription of a biomarker of the present invention, at least in part, and normal post- transcriptional processing {e.g., splicing), if any, of the transcript, and reverse transcription of the transcript.

The terms "homology" or "identity," as used interchangeably herein, refer to sequence similarity between two polynucleotide sequences or between two polypeptide sequences, with identity being a more strict comparison. The phrases "percent identity or homology" and "% identity or homology" refer to the percentage of sequence similarity found in a comparison of two or more polynucleotide sequences or two or more polypeptide sequences. Two or more sequences can be anywhere from 0-100% similar, or any integer value there between. Identity or similarity can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules arc identical at that position. A degree of similarity or identity between polynucleotide sequences is a function of the number of identical or matching nucleotides at positions shared by the polynucleotide sequences. A degree of identity of polypeptide sequences is a function of the number of identical amino acids at positions shared by the polypeptide sequences. A degree of homology or similarity of polypeptide sequences is a function of the number of amino acids at positions shared by the polypeptide sequences. The term "substantial homology" refers to homology of at least 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or more (e.g., about 96%, 96.5%, 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or more). In one embodiment, biomarkcr nucleic acid molecules encode a protein or portion thereof which includes an amino acid sequence which is sufficiently homologous to an amino acid sequence described herein such that the protein or portion thereof maintains, for example, the ability to phosphorylatc eIF4B, to phosphorylate Histone H3, and/or the ability to be phosphorylated by MELK.

The comparison of sequences and determination of percent homology between two sequences can be accomplished using a mathematical algorithm. The alignment can be performed using the Clustal Method. Multiple alignment parameters include GAP Penalty =10, Gap Length Penalty = 10. For DNA alignments, the pairwise alignment parameters can be Htuplc=2, Gap pcnalty=5, Window=4, and Diagonal savcd=4. For protein alignments, the pairwise alignment parameters can be Ktuple=l , Gap penalty=3,

Window=5, and Diagonals Saved=5. Similarly, the percent identity between two amino acid sequences is determined using the Necdleman and Wunsch (J. Mot. Biol. (48):444-453 ( 1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available online), using cither a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available online), using a

NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Meyers and W. Miller (CABIOS, 4: 1 1- 17 ( 1989)) which has been incorporated into the ALIGN program (version 2.0) (available online), using a PAM 120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. Methods for the production of nucleic acids (e.g., MELK, eIF4B, and/or mRNAs translated from nucleic acids having structured 5' regions are known in the art and include standard hybridization, PCR, and/or synthetic nucleic acid techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.

A "biomarker protein" is a protein encoded by or corresponding to a biomarker of the present invention. The terms "protein" and "polypeptide" are used interchangeably herein. In one embodiment, the protein is at least 50%, 60%, 70%, 80%, 90%, and 95% or more (e.g., 95.5%, 96%, 96.5%, 97%, 97.5%, 98%, 98.5%, 99%, 99.1 %, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or more) homologous to the entire amino acid sequence of a MELK and/or clF4B and/or Histone H3 protein described herein. In addition, biologically active portions of MELK and/or eIF4B and/or Histone H3 proteins described herein are included which have at least 50%, 60%, 70%, 80%, 90%, and 95% or more (e.g., 95.5%, 96%, 96.5%, 97%, 97.5%, 98%, 98.5%, 99%, 99.1 %, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or more) homology to a fragment of a MELK and/or eIF4B and/or Histone H3 protein described herein, e.g., a domain or motif, and that is capable of phosphorylating eIF4B, phosphorylating Histone H3, or being phosphorylatcd by MELK. Typically, biologically active portions (peptides, e.g., peptides which arc, for example, 5, 10, 15, 20, 30, 35, 36, 37, 38, 39, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, or more amino acids in length) comprise a domain or motif, e.g., a MELK kinase domain, eIF4B domain encompassing an amino acid residue phosphorylatablc by MELK such as a MELK-mediated phosphorylation substrate motif having an arginine at -3 amino acid residue positions relative to serine/threonine (e.g., Scr406 or Scr422 of human eIF4B), or Histone H3 domain encompassing an amino acid residue phosphorylatablc by MELK such as a human Histone H3 region comprising Serl 0. Moreover, other biologically active portions, in which other regions of the protein arc deleted, can be prepared by recombinant techniques and evaluated for one or more of the activities described herein.

Methods for the production of proteins (e.g., MELK and/or eIF4B and/or Histone H3) arc known in the art and include e.g., the expression of the protein in appropriate cells starting from a cDNA or the production by subsequent addition of amino acids to a starting amino acid (sec Current Protocols, John Wiley & Sons, Inc., New York). Furthermore, methods for the production of protein fragments arc known in the art and include the cleavage of the protein with appropriate proteases or the generation of nucleic acid fragments encoding the protein fragments and subsequent expression of the fragments in appropriate cells. Methods for the production of mutated proteins, e.g., by exchanging and/or deleting one or more amino acids, arc known in the art.

B. Diagnostic Methods

Methods are provided for identifying agents, such as small molecules and antibodies, which inhibit oncogenic and/or kinase activity of human MELK or an ortholog thereof, comprising: a) contacting a sample comprising i) human MELK or an ortholog thereof and ii) human cukaryotic initiation factor 4B (eIF4B) or an ortholog thereof, with the agent; and b) determining the ability of the agent to inhibit Ser-406 phosphorylation of human clF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B, wherein decreased phosphorylation identifies an agent which inhibits kinase or oncogenic activity of human MELK or the ortholog thereof. Similarly, methods are provided for identifying agents, such as small molecules and antibodies, which inhibit oncogenic and/or kinase activity of human MELK or an ortholog thereof, comprising: a) contacting a sample comprising i) human MELK or an ortholog thereof and ii) human Histonc H3 or an ortholog thereof, with the agent; and b) determining the ability of the agent to inhibit Thr-3 phosphorylation and/or Scr-10 phosphorylation and/or Thr-11 phosphorylation of human Histonc H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histonc H3, wherein decreased phosphorylation identifies an agent which inhibits kinase or oncogenic activity of human MELK or the ortholog thereof. These methods are also referred to herein as drug screening assays and typically include the step of screening a candidate/test compound or agent for the ability to interact with (e.g., bind to) a MELK and/or eIF4B and/or Histonc H3 protein, to modulate the phosphorylation of eIF4B by MELK, to modulate the interaction of a phosphorylatablc residue of eIF4B with a MELK-mediatcd intracellular signaling target, to modulate the phosphorylation of Histonc H3 by MELK, and/or to modulate the interaction of a phosphorylatablc residue of Histonc H3 with a MELK-mediated intracellular signaling target. Test compounds or agents which have one or more of these abilities can be used as drugs to treat disorders characterized by aberrant, abnormal, and/or unwanted MELK and/or eIF4B and/or Histonc H3 nucleic acid expression and/or protein activity, such as cancer. Candidate/test compounds include, for example, small organic and inorganic molecules (e.g., molecules obtained from

combinatorial and natural product libraries). Similarly, antibody agents that, for example bind to MELK in a manner that modulates phosphorylation of a residue by MELK, modulates eIF4B activity normally driven by MELK-mediated phosphorylation, and/or modulates Histonc H3 activity normally driven by MELK-mediated phosphorylation, can be useful agents. The skilled artisan can also readily make other modulatory agents, such as aptamers, antisense RNA, siRNA, that are capable of interacting with MELK nucleic acids and/or proteins to affect MELK-mediated phosphorylation of eIF4B or Histone H3 (see, at least Chung et al. (2012) 3: 1629-1640; WO 2013/109388; WO 2012/016082; WO 2013/045539; each of which is incorporated herein in its entirety by this reference.

The term "sample," "tissue sample," "subject sample," "subject cell or tissue sample" or "specimen" each refer to a collection of similar cells obtained from a tissue of a subject or subject either as in vitro (e.g., cultured), ex vivo, or in vivo (e.g., isolated primary cells) samples. The source of the tissue sample may be solid tissue as from a fresh, frozen and/or preserved organ, tissue sample, biopsy, or aspirate; blood or any blood constituents; bodily fluids such as whole blood, serum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow, amniotic fluid, peritoneal fluid or interstitial fluid; or cells from any time in gestation or development of the subject. The tissue sample may contain compounds that arc not naturally intermixed with the tissue in nature such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics or the like. The sample may further comprise cancer cells, such as ovarian, lung, breast, and multiple myeloma cancer cells or any cancer in which MELK and/or eIF4B and/or Histonc H3 is amplified or ovcrexpresscd, has an activating mutation, or is activated by other kinases.

The terms "subject" and "patient" are used interchangeably. As used herein, the terms "subject" and "subjects" refer to an animal, e.g., a mammal including a non-primate (e.g., a cow, pig, horse, donkey, goat, camel, cat, dog, guinea pig, rat, mouse, sheep) and a primate (e.g., a monkey, such as a cynomolgous monkey, gorilla, chimpanzee and a human).

The term "inhibit" refers to a statistically significant decrease in a metric of interest, such as the reduction of Thr-3 phosphorylatcd and/or Ser- 10-phosphorylatcd and/or Thr-11- phosphorylatcd Histone H3, Ser-406-phosphorylated eIF4B, MELK enzymatic activity (e.g., kinase activity), cancer progression, and the like. Such statistically significant decrease can be at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more relative to a control, For example, a test compound administered and analyzed according to the methods described herein can comprise a bona fide inhibitor of MELK enzymatic activity (e.g., kinase activity) by decreasing Ser-406-phosphorylated eIF4B amounts, Thr-3 phosphorylatcd Histonc H3 amounts, Scr- 10-phosphorylatcd Histonc H3 amounts, and/or Thr-11 -phosphorylatcd Histonc H3 amounts by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more relative to that of no MELK ligand administration or over a given amount of time. In one embodiment, the term "MELK inhibitor" is a substance, such as a small molecule, antibody, antisense nucleic acid, small interfering nucleic acid, which interferes with the phosphorylation of human eIF4B at Ser-406 or at a corresponding phosphorylation site in an eIF4B ortholog thereof, the phosphorylation of human Histone H3 at Thr-3 or at a corresponding phosphorylation site in a Histonc H3 ortholog thereof, the phosphorylation of human Histonc H3 at Scr- 10 or at a corresponding phosphorylation site in a Histone H3 ortholog thereof, and/or the phosphorylation of human Histone H3 at Thr- I I or at a corresponding phosphorylation site in a Histone H3 ortholog thereof. Exemplary MELK inhibitors are well known in the art, such as OTSSP 167, siomycin A, thiostrepton, and anti-MELK antibodies are disclosed, for example, in Chung el al. (2012) Oncotarget 3:1629-1640; WO 2013/045539; WO 2013/109388; and WO 2012/016082; each of which is incorporated in its entirety herein by this reference.

The term "altered amount" of a biomarker or "altered level" of a biomarker refers to increased or decreased expression, modification, and/or activity of a biomarker of the present invention, at least in part in a sample as compared to that in a control sample.

The amount of a biomarker in a subject is "significantly" higher or lower than the normal amount of a biomarker, if the amount of the biomarker is greater or less, respectively, than the normal level by an amount greater than the standard error of the assay employed to assess amount, or at least two, three, four, five, ten or more times that amount. Alternatively, the amount of the biomarker in the subject can be considered "significantly" higher or lower than the normal amount if the amount is at least about two, at least about three, at least about four, or at least about five times, higher or lower, respectively, than the normal amount of the biomarker (e.g., in a control sample or the average expression level of the biomarkcrs of the present invention in several control samples).

"Likely to," as used herein, refers to an increased probability, that an item, object, thing or person will occur such as at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,

45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 1 10%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, or more (or any range inclusive). Thus, in one embodiment, an agent that is likely to inhibit MELK-mcdiatcd phosphorylation of eIF4B has an increased probability of inhibiting Scr-406 phosphorylation of human eIF4B or a corresponding phosphorylatable amino acid in an ortholog of human eIF4B. In another embodiment, an agent that is likely to inhibit MELK-mediatcd phosphorylation of Histone H3 has an increased probability of inhibiting Thr-3 phosphorylation, Ser-10

phosphorylation, and/or Thr-11 phosphorylation of human Histone H3, or a corresponding phosphorylatable amino acid in an ortholog of human Histone H3.

Test compounds of the present invention, at least in part, can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring dcconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K.S. ( 1997) Anticancer Drug Des. 12: 145).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90:6909; Erb et al.

(1994) Proc. Natl. Acad. Sci. USA 91 : 1 1422; Zuckcrmann et al. ( 1994) J. Med. Chem. 37:2678; Cho et al. ( 1993) Science 261 : 1303; Carrcll et al ( 1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. ( 1994) Angew. Chem. Int. Ed. Engl. 33:2061 ; and in Gallop et al. ( 1994) J. Med. Chem. 37: 1233.

Libraries of compounds may be presented in solution (e.g., Houghtcn ( 1992) Biotechniqiies 13:412-421 ), or on beads (Lam ( 1991 ) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (Ladncr USP 5,223,409), spores (Ladncr USP '409), plasmids (Cull et al. ( 1992) Proc Natl Acad Sci USA 89: 1865- 1869) or on phage (Scott and Smith (1990) Science 249:386-390); (Devlin ( 1990) Science 249:404-406); (Cwirla et al. (1990) Proc. Natl. Acad. Sci. 87:6378-6382); (Felici (1991) J. Mol. Biol. 222:301 -310); (Ladncr supra.).

In one embodiment, the inhibition of Scr-406 phosphorylation of human eIF4B or a corresponding phosphorylatable amino acid in an ortholog of human eIF4B is determined by comparing the amount of Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human clF4B, in the sample relative to a control. The control can be the amount of amount of Scr-406 phosphorylatcd human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B in the sample relative to said amount in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent. The phosphorylation level of eIF4B is generally determined by measuring the amount of phosphorylatcd elF4B protein and, optionally, of unphosphorylated eIF4B, and normalizing the amount of phosphorylated protein to the total protein in the sample being analyzed. The calculated response phosphorylation level in the presence of the test compound and the basal or background phosphorylation levels (e.g., in the absence of the test compound or at a earlier timcpoint after test compound

administration) arc thus not affected by differences in the absolute quantity of the indicator protein at a given time.

The discriminatory time point, or predetermined time after administering the test compound to cells, can be selected to achieve a calibrated statistically significant difference between Ser-406 phosphorylation levels in the sample relative to controls. The difference may be maximal at the predetermined time but that is not required and depends on other parameters of the test. In addition, whereas the calculation of ratios as described herein is beneficial in providing useful comparative numbers, calculation of absolute differences between phosphorylated eIF4B levels upon administration of test compounds relative to controls, and between test subjects and control subjects, could also be employed and would be effective.

In some embodiments, the methods described above can further comprise determining the amount of determining the amount of a protein translated from an mRNA with highly structured 5' untranslated region (5'UTR), optionally wherein the protein is selected from the group consisting of cellular myelocytomatosis oncogene (c-Myc), X- linkcd inhibitor of apoptosis protein (XIAP), and ornithine decarboxylase (ODC 1). It is known that eIF4B stimulates the hclicasc activity of cIF4A for unwinding the secondary structure of 5'UTR of mRNA and that eIF4B is important for the translation of mRNA with structured 5'UTR (Dmitriev et al. (2003) Mol. Cell Biol. 23:8925-8933 and Shahbazian et al. (2010) Mol. Cell Biol. 30 1478- 1485). The skilled artisan is well aware of mRNA with structured 5'UTR encoding oncogenic proteins, such as c-Myc, XIAP (X-linked inhibitor of apoptosis protein), ODC (ornithine decarboxylase), VEGF, HIF-1 alpha, and the like (see, at least Bert et al. (2006) RNA 12: 1074- 1083).

Phosphorylation is a biochemical reaction in which a phosphate group is added to Scr, Thr or Tyr residues of a protein and is catalyzed by protein kinase enzymes.

Phosphorylation normally modifies the functions of target proteins, often causing activation. As part of the cell's homcostatic mechanisms, phosphorylation is only a transient process that is reversed by other enzyme called phosphatases. Therefore, protein phosphorylation levels change over time and can be evaluated in a number of well-known manners, including, for example, by immunological approaches. For example, the amount of Ser-406 phosphorylated human eIF4B or a corresponding phosphorylatable amino acid in an ortholog of human eIF4B is determined by an immunoassay using a reagent which specifically binds with Ser-406 phosphorylated human eIF4B or corresponding

phosphorylated ortholog of human eIF4B. Such an immunoassay comprise a number of well known forms, including, without limitation, a radioimmunoassay, a Western blot assay, an immunofluorescence assay, an enzyme immunoassay, an immunoprccipitation assay, a chemiluminescence assay, an immunohistochemical assay, a dot blot assay, or a slot blot assay. General techniques to be used in performing the various immunoassays noted above and other variations of the techniques, such as in situ proximity ligation assay (PLA), fluorescence polarization immunoassay (FPIA), fluorescence immunoassay (FIA), enzyme immunoassay (EIA), nephelometric inhibition immunoassay (NLA), enzyme linked immunosorbent assay (ELISA), and radioimmunoassay (RIA), ELISA, etc. alone or in combination or alternatively with NMR, MALDI-TOF, LC-MS/MS, are known to those of ordinary skill in the art.

In one embodiment, the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human eIF4B or corresponding ortholog of human eIF4B and a detection antibody or fragment thereof which specifically binds with Ser-406 phosphorylated human eIF4B or a corresponding phosphorylated ortholog of human eIF4B. Such an enzyme immunoassay is particularly advantageous because identifying differences in protein levels between related kinase family members or isoforms given the relatively high homology between kinases among themselves and also among their phosphorylated forms.

Immunological reagents for identifying eIF4B in both phosphorylated and non- phosphorylatcd forms, as well as for detecting MELK, are well known in the art and can be generated using standard techniques, such as by inoculating host animals with appropriate eIF4B phosphor-peptides. Such anti-MELK, anti-eIF4B, and/or anti-phospho-eIF4B antibody reagents {e.g., monoclonal antibody) can be used to isolate and/or determine the amount of the respective proteins such as in a cellular lysatc. Such reagents can also be used to monitor protein levels in a cell or tissue, e.g., white blood cells or lymphocytes, as part of a clinical testing procedure, e.g., in order to monitor an optimal dosage of an inhibitory agent. Detection can be facilitated by coupling {e.g., physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbclliferonc, fluorescein, fluorescein isothiocyanatc, rhodaminc, dichlorotriazinylaminc fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include lucifcrasc, luciferin, and aequorin, and examples of suitable radioactive material include

The screening assays described above can further be adapted to identify candidate/test compounds which modulate {e.g., stimulate or inhibit) the interaction (and most likely MELK and eIF4B oncogenic activity as well) between an eIF4B protein and a target eIF4B protein with which the eIF4B protein normally interacts or modulates to verify that MELK-mcdiatcd enzymatic activity has been reduced in accordance with the reduced amounts of phosphorylated eIF4B levels. Examples of such target molecules or substrates include certain protein encoded by mRNA with structured 5'UTR, such as those described further herein.

As described above for the identification of eIF4B phosphorylation, Thr-3 phosphorylation, Ser-10 phosphorylation, and/or Thr-11 phosphorylation of human Histone H3, or a corresponding phosphorylatable amino acid in an ortholog of human Histone H3, and modulation {e.g., inhibition) thereof, can similarly be determined.

In another embodiment, the invention provides assays for screening candidate/test compounds which interact with {e.g. , bind to) MELK and/or eIF4B and/or Histone H3 protein. "Binding compound" shall refer to a binding composition, such as a small molecule, an antibody, a peptide, a peptide or non-peptide ligand, a protein, an

oligonucleotide, an oligonucleotide analog, such as a peptide nucleic acid, a lectin, or any other molecular entity that is capable of specifically binding to a target protein or molecule or stable complex formation with an analytc of interest, such as a complex of proteins. "Binding moiety" means any molecule to which molecular tags can be directly or indirectly attached that is capable of specifically binding to an analytc. Binding moieties include, but arc not limited to, antibodies, antibody binding compositions, peptides, proteins, nucleic acids and organic molecules having a molecular weight of up to about 1000 daltons and containing atoms selected from the group consisting of hydrogen, fluoride, carbon, oxygen, nitrogen, sulfur and phosphorus. Typically, the assays are cell-based assays. The cell, for example, can be of mammalian origin expressing MELK and/or eIF4B and/or Histone H3, e.g., a cancer cell.

In other embodiments, the assays are cell-free assays which include the steps of combining a MELK and/or eIF4B and/or Histone H3 protein or a biologically active portion thereof, and a candidate/test compound, e.g. , under conditions which allow for interaction of (e.g., binding of) the candidate/test compound to the MELK and/or eIF4B and/or Histone H3 protein or biologically active portion thereof to form a complex, and detecting the formation of a complex, in which the ability of the candidate compound to interact with (e.g., bind to) the MELK and/or eIF4B and/or Histone H3 polypeptide or biologically active fragment thereof is indicated by the presence of the candidate compound in the complex. Formation of complexes between the MELK and/or eIF4B and/or Histone H3 protein and the candidate compound can be quantitated, for example, using standard immunoassays. Such analyses would identify test compounds as MELK and/or eIF4B and/or Histone H3 ligands.

To perform the above drug screening assays, it can be desirable to immobilize cither MELK and/or eIF4B and/or Histone H3 or its target molecule to facilitate separation of complexes from uncomplcxcd forms of one or both of the proteins, as well as to accommodate automation of the assay. Interaction (e.g., binding of) of MELK and/or eIF4B and/or Histone H3 to a target molecule, in the presence and absence of a candidate compound, can be accomplished in any vessel suitable for containing the rcactants.

Examples of such vessels include microtitre plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion polypeptide can be provided which adds a domain that allows the polypeptide to be bound to a matrix. For example, glutathione-S-transfcrase-MELK, - Histone H3, and/or -eIF4B fusion polypeptides can be adsorbed onto glutathione scpharosc beads (Sigma Chemical, St. Louis, Mo.) or glutathione derivatized microtitre plates, which are then combined with the cell lysates (e.g., ³⁵ S-labeled) and the candidate compound, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads arc washed to remove any unbound label, and the matrix immobilized and radiolabcl determined directly, or in the supernatant after the complexes arc dissociated. Alternatively, the complexes can be dissociated from the matrix, separated by SDS-PAGE, and the level of MELK-, Histonc H3-, and/or eIF4B-binding polypeptide found in the bead fraction quantitated from the gel using standard electrophoretic techniques.

Other techniques for immobilizing polypeptides on matrices can also be used in the exemplary drug screening assays of the invention. For example, MELK and/or eIF4B and/or Histone H3 or its target molecule can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylatcd MELK and/or eIF4B and/or Histonc H3 molecules can be prepared from biotin-NHS (N-hydroxy-succinimidc) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, III.), and immobilized in the wells of strcptavidin-coatcd 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with MELK and/or eIF4B and/or Histone H3, but which do not interfere with binding of the polypeptide to its target molecule can be derivatized to the wells of the plate, and MELK and/or eIF4B and/or Histone H3 trapped in the wells by antibody conjugation. As described above, preparations of a MELK- and/or elF4B-binding polypeptide and a candidate compound are incubated in the MELK- and/or eIF4B- and/or Histone H3- prcscnting wells of the plate, and the amount of complex trapped in the well can be quantitated. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the MELK and/or eIF4B and/or Histonc H3 target molecule, or which arc reactive with MELK and/or clF4B and/or Histonc H3 polypeptide and compete with the target molecule; as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the target molecule.

In another aspect, a method for assessing the efficacy of an agent for inhibiting kinase activity of human MELK or an ortholog thereof in a subject, comprising: a) detecting in a subject sample at a first point in time, the amount of Scr-406 phosphorylatcd human eIF4B or the amount of a human eIF4B ortholog phosphorylatcd at a corresponding amino acid of human eIF4B; b) repeating step a) during at one or more subsequent points in time after administration of the agent; and c) comparing the amount of phosphorylatcd human eIF4B or ortholog thereof detected in step a) with said amount detected in step b), wherein a higher amount of Scr-406 phosphorylatcd human eIF4B or the amount of the human clF4B ortholog phosphorylatcd at a corresponding amino acid of human eIF4B in the first point in time relative to at least one subsequent point in time, indicates that the agent inhibits kinase activity of MELK or the ortholog thereof, is provided. Simnilarly, a method for assessing the efficacy of an agent for inhibiting kinase activity of human MELK or an ortholog thereof in a subject, comprising: a) detecting in a subject sample at a first point in time, the amount of Thr-3 phosphorylated, Ser-10 phosphorylated, and/or Thr-11 phosphorylated human Histone H3, or the amount of a human Histone H3 ortholog phosphorylated at a corresponding amino acid of human Histone H3; b) repeating step a) during at one or more subsequent points in time after administration of the agent; and c) comparing the amount of phosphorylated human Histone H3 or ortholog thereof detected in step a) with said amount detected in step b), wherein a higher amount of Thr-3

phosphorylated, Ser-10 phosphorylated, and/or Thr-11 phosphorylated human Histone H3, or the amount of the human Histone H3 ortholog phosphorylated at a corresponding amino acid of human Histone H3 in the first point in time relative to at least one subsequent point in time, indicates that the agent inhibits kinase activity of MELK or the ortholog thereof, is provided.

As used herein, "time course" shall refer to the amount of time between an initial event and a subsequent event. For example, with respect to a subject's cancer progression, time course may relate to a subject's disease and may be measured by gauging significant events in the course of the disease, wherein the first event may be diagnosis and the subsequent event may be proliferation, metastasis, etc.

Once binding is confirmed, additional assays, such as kinase assays to determine inhibition of phosphorylation effects, can be performed according to well-known methods in the art. For example, assays for determining MELK kinase activity are well known in the art (sec, for example, the publications described herein and incorporated by reference in their entirety). Briefly, MELK can be incubated with a suitable substrate in a buffer allowing phosphorylation of eIF4B or Histone H3. Phosphorylation of the substrate can be detected using a labeled phosphate group, such as the use of the radioactive label ³²P present as the ATP source in the buffer. Alternatively, antibodies specific for the phosphorylated products of eIF4B catalytic activity can be used to detect activity. As will be apparent to those of ordinary skill in the art, the assays arc easily amenable to high through-put technologies using robotics and automated processes. Alternatively, the MELK kinase activity can be assayed using a synthetic substrate, such as a peptide library. MELK activity can also be assayed by detecting downstream targets of the kinase such as those described herein. Scr-406-phosphorylatcd eIF4B can be analyzed according to any of the methods and using any of the samples described herein (e.g., single subject samples or pooled subject samples). Candidate compounds which produce a statistically significant change in phosphorylated-eIF4B-dependent responses (e.g., inhibition of human eIF4B

phosphorylation at Ser-406 or a corresponding phosphorylatable amino acid residue in an eIF4B ortholog thereof) can be identified. Such statistically significant changes can be measured according to a number of criteria and/or relative to a number of controls. For example, significant modulation of phosphorylation of Ser-406 can be assessed if the output under analysis is inhibited by 1.1-, 1.2-, 1 .3-, 1.4-, 1.5-, 1.6-, 1.7-, 1.8-, 1.9-, 2.0-, 2.1 -, 2.2-, 2.3-, 2.4-, 2.5-, 2.6-, 2.7-, 2.8-, 2.9-, 3.0-, 3.1-, 3.2-, 3.3-, 3.4-, 3.5-, 3.6-, 3.7-, 3.8-, 3.9-,

4.0-, 4.1-, 4.2-, 4.3-, 4.4-, 4.5-, 4.6-, 4.7-, 4.8-, 4.9-, 5.0-, 5.5-, 6.0, 6.5-, 7.0-, 7.5-, 8.0-, 8.5- , 9.0- 9.5-, 10-, 1 1-, 12-, 13-, 14-, 15-, 16-, 17-, 18-, 19-, 20-fold or more different

(including any range inclusive), relative to a control. In one embodiment, between the first point in time and the subsequent point in time, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer.

As described above for the identification and/or analysis of eIF4B phosphorylation, Thr-3 phosphorylatcd, Ser-10 phosphorylatcd, and/or Thr-11 phosphorylatcd Histone H3, or a corresponding phosphorylatable amino acid in an ortholog of human Histone H3, and modulation (e.g., inhibition) thereof, can similarly be identified and/or analyzed.

The term "cancer" refers to the presence of cells possessing characteristics typical of cancer-causing cells, such as uncontrolled proliferation, immortality, metastatic potential, and certain characteristic morphological features. Cancer cells are often in the form of a tumor, but such cells may exist alone within an animal, or may be a non-tumorigenic cancer cell, such as a leukemia cell. As used herein, the term "cancer" includes prcmalignant as well as malignant cancers. Cancers include, but are not limited to, B cell cancer, e.g..

multiple myeloma, Waldenstrom's macroglobulincmia, the heavy chain diseases, such as, for example, alpha chain disease, gamma chain disease, and mu chain disease, benign monoclonal gammopathy, and immunocytic amyloidosis, melanomas, breast cancer, lung cancer, bronchus cancer, colorectal cancer, prostate cancer, pancreatic cancer, stomach cancer, ovarian cancer, urinary bladder cancer, brain or central nervous system cancer, peripheral nervous system cancer, esophageal cancer, cervical cancer, uterine or endometrial cancer, cancer of the oral cavity or pharynx, liver cancer, kidney cancer, testicular cancer, biliary tract cancer, small bowel or appendix cancer, salivary gland cancer, thyroid gland cancer, adrenal gland cancer, osteosarcoma, chondrosarcoma, cancer of hematological tissues, and the like. Also included arc any cancers in which the gene encoding MELK and/or eIF4B and/or Histone H3 is amplified or overexpressed, or has an activating mutation, or the MELK and/or eIF4B and/or Histone H3 is hyper-activated by other kinases. In some embodiments, ovarian cancers, including serous

cystadenocarcinoma, head and neck cancers, including non-small cell lung cancer

(NSCLC), squamous cell carcinoma, pancreatic cancer, colon cancer, prostate cancer, and/or gliomas can be preferred.

'Treat," "treatment," and other forms of this word refer to the administration of an agent that inhibits the ability of 1) MELK to phosphorylatc eIF4B and/or Histone H3 and/or 2) the ability of eIF4B or Histone H3 to be phosphorylatcd by MELK, to cause a cancer to be ameliorated, to extend the expected survival time of the subject and/or time to progression of a cancer or the like.

"Responsiveness," to "respond" to treatment, and other forms of this verb, as used herein, refer to the reaction of a subject to treatment with an agent capable of inhibiting the ability of 1 ) MELK to phosphorylate eIF4B or Histone H3 and/or 2) the ability of eIF4B or Histone H3 to be phosphorylatcd by MELK. As an example, a subject responds to treatment of the subject or cell thereof with an agent if the assayed condition is modulated by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more relative to that of no administration of the agent or over a given amount of time.

C. Treatment Methods

MELK and/or eIF4B and/or Histone H3 inhibitors described herein can be used to treat cancer. In one embodiment, a method of treating a subject afflicted with cancer comprising administering to the subject an agent that inhibits Ser-406 phosphorylation of human clF4B or a corresponding phosphorylatablc amino acid in an ortholog of human eIF4B, for example an agent that specifically modulates Scr-406 phosphorylation, thereby treating the subject afflicted with the cancer. In another embodiment, such MELK and/or eIF4B and/or Histone H3 inhibitors can also be used to determine the efficacy, toxicity, or side effects of treatment with such an agent. These methods of treatment generally include the steps of administering modulators in a pharmaceutical composition, as described further below, to a subject in need of such treatment, e.g., a subject with cancer or at risk for developing cancer. The term "administering" is intended to include routes of administration which allow the agent to perform its intended function of inhibiting the ability of M ELK to phosphorylatc eIF4B, the ability of eIF4B to be phosphorylated by MELK, the ability of MELK to phosphorylate Histone H3, and/or the ability of Histone H3 to be phosphorylated by MELK. Examples of routes of administration which can be used include injection (subcutaneous, intravenous, parenterally, intraperitoneally, intrathecal, etc.), oral, inhalation, and transdermal. The injection can be bolus injections or can be continuous infusion. Depending on the route of administration, the agent can be coated with or disposed in a selected material to protect it from natural conditions which may

detrimentally affect its ability to perform its intended function. The agent may be administered alone, or in conjunction with a pharmaceutically acceptable carrier. The agent also may be administered as a prodrug, which is converted to its active form in vivo.

The term "effective amount" of an agent inhibiting the ability of MELK to phosphorylate eIF4B and/or the ability of eIF4B to be phosphorylated by MELK is that amount necessary or sufficient to inhibit the ability of MELK to phosphorylate elF4B and/or the ability of eIF4B to be phosphorylated by MELK in the subject or population of subjects as measured, for example, by the levels of Ser-406-phosphorylated human eIF4B or a corresponding phosphorylatablc residue in an eIF4B ortholog thereof according to the methods described above. The same analysis applies to inhibiting the ability of MELK to phosphorylatc Histone H3 and/or the ability of Histone H3 to be phosphorylated by MELK. The effective amount can vary depending on such factors as the type of therapeutic agcnt(s) employed, the size of the subject, or the severity of the disorder.

It will be appreciated that individual dosages may be varied depending upon the requirements of the subject in the judgment of the attending clinician, the severity of the condition being treated and the particular compound being employed. In determining the therapeutically effective amount or dose, a number of additional factors may be considered by the attending clinician, including, but not limited to: the pharmacodynamic

characteristics of the particular agent and its mode and route of administration; the desired time course of treatment; the species of mammal; its size, age, and general health; the specific disease involved; the degree of or involvement or the severity of the disease; the response of the individual subject; the particular compound administered; the mode of administration; the bioavailability characteristics of the preparation administered; the dose regimen selected; the kind of concurrent treatment; and other relevant circumstances. Treatment can be initiated with smaller dosages that arc less than the effective dose of the compound. Thereafter, in one embodiment, the dosage should be increased by small increments until the optimum effect under the circumstances is reached. For convenience, the total daily dosage may be divided and administered in portions during the day if desired.

The effectiveness of any particular agent to treat cancers can be monitored by comparing two or more samples obtained from subjects undergoing cancer treatment. In general, a first sample is obtained from the subject prior to beginning therapy and one or more samples during treatment. In such a use, a baseline of expression of cells from subjects with cancer prior to therapy is determined and then changes in the baseline state of expression of cells from subjects with cancer is monitored during the course of therapy. Alternatively, two or more successive samples obtained during treatment can be used without the need of a prc-trcatmcnt baseline sample. In such a use, the first sample obtained from the subject is used as a baseline for determining whether the expression of cells from subjects with metabolic disorders is increasing or decreasing.

MELK and/or elF4B and/or Histone H3 inhibitors can be administered in pharmaceutically acceptable compositions which comprise a therapeutically-effective amount of the inhibitor formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents. For example, formulations can be adapted for ( 1 ) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, boluses, powders, granules, pastes; (2) parenteral administration, for example, by subcutaneous, intramuscular or intravenous injection as, for example, a sterile solution or suspension; (3) topical application, for example, as a cream, ointment or spray applied to the skin, buccal, or sublingual surfaces; (4) intravaginally or intrarcctally, for example, as a pessary, cream or foam; or (5) nasal/aerosol, for example, as an aqueous aerosol, liposomal preparation or solid particles containing the compound, based on well-known methods in the pharmaceutical arts.

The phrase "pharmaceutically acceptable" is employed herein to refer to those agents, materials, compositions, and/or dosage forms which arc, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

The phrase "pharmaccutically-acccptablc carrier" as used herein means a pharmaccutically-acccptablc material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting the subject chemical from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be "acceptable" in the sense of being compatible with the other ingredients of the formulation and not injurious to the subject. Some examples of materials which can serve as pharmaceutical ly-acceptable carriers include: ( 1 ) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymcthyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipicnts, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, com oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and

polyethylene glycol; ( 12) esters, such as ethyl oleate and ethyl lauratc; ( 13) agar; ( 14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; ( 15) alginic acid; (16) pyrogen- free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other non-toxic compatible substances employed in pharmaceutical formulations.

The term "pharmaccutically-acccptablc salts" refers to the relatively non-toxic, inorganic and organic acid addition salts of the agents that reduce the phosphorylation levels of PKC-iota and/or activity encompassed by the invention. These salts can be prepared in situ during the final isolation and purification of the agents, or by separately reacting a purified agents agent in its free base form with a suitable organic or inorganic acid, and isolating the salt thus formed. Representative salts include the hydrobromide, hydrochloride, sulfate, bisulfatc, phosphate, nitrate, acetate, valerate, oleate, palmitatc, stcaratc, lauratc, benzoate, lactate, phosphate, tosylatc, citrate, malcatc, fumaratc, succinate, tartrate, nap thy late, mesylate, glucoheptonate, lactobionate, and laurylsulphonatc salts and the like (Sec, for example, Bcrge et al. ( 1977) "Pharmaceutical Salts", J. Pharm. Sci. 66: 1 - 19).

In addition, the methods described herein can further comprise treating subjects with MELK and/or eIF4B and/or Histonc H3 inhibitors in addition to administering one or more additional anti-cancer agents and/or use samples from subjects exposed to such anti-cancer agents. Anti -cancer agents arc well known to the skilled artisan and include, without limitation, chemotherapy and radiation, as well as immunotherapy, hormone therapy, and gene therapy using nucleic acid molecules and/or proteins that arc linked to the initiation, progression, and/or pathology of a tumor or cancer.

Chemotherapy includes the administration of a chemotherapeutic agent. Such a chemotherapeutic agent may be, but is not limited to, those selected from among the following groups of compounds: platinum compounds, cytotoxic antibiotics,

antimetabolities, anti-mitotic agents, alkylating agents, arsenic compounds, DNA topoisomerase inhibitors, taxanes, nucleoside analogues, plant alkaloids, and toxins; and synthetic derivatives thereof. Exemplary compounds include, but are not limited to, alkylating agents: cisplatin, trcosulfan, and trofosfamidc; plant alkaloids: vinblastine, paclitaxcl, docctaxol; DNA topoisomerase inhibitors: tcniposidc, crisnatol, and mitomycin; anti-folates: methotrexate, mycophenolic acid, and hydroxyurea; pyrimidine analogs: 5- fluorouracil, doxifluridine, and cytosine arabinoside; purine analogs: mercaptopurine and thioguanine; DNA antimetabolites: 2'-deoxy-5-fluorouridine, aphidicolin glycinate, and pyrazoloimidazole; and antimitotic agents: halichondrin, colchicine, and rhizoxin.

Compositions comprising one or more chemotherapeutic agents (e.g., FLAG, CHOP) may also be used. FLAG comprises fludarabine, cytosine arabinoside (Ara-C) and G-CSF. CHOP comprises cyclophosphamide, vincristine, doxorubicin, and prednisone. In another embodiment, PARP (e.g., PARP-1 and/or PARP-2) inhibitors arc used and such inhibitors are well known in the art (e.g., Olaparib, ABT-888, BSI-201 , BGP-15 (N-Gcne Research Laboratories, Inc.); INO-1001 (Inotck Pharmaceuticals Inc.); PJ34 (Soriano el a/., 2001 ; Pachcr el a/., 2002b); 3-aminobcnzamide (Trcvigcn); 4-amino-l ,8-naphthalimidc;

(Trevigen); 6(5H)-phenanthridinone (Trevigen); benzamide (U.S. Pat. Re. 36,397); and NU 1025 (Bowman et al.). In still another embodiment, the chemotherapeutic agents arc platinum compounds, such as cisplatin, carboplatin, oxaliplatin, ncdaplatin, and iproplatin. Other antineoplastic platinum coordination compounds are well known in the art, can be modified according to well-known methods in the art, and include the compounds disclosed in U.S. Pat. Nos. 4,996,337, 4,946,954, 5,091 ,521, 5,434,256, 5,527,905, and 5,633,243, all of which arc incorporated herein by reference. The foregoing examples of

chemotherapeutic agents arc illustrative, and arc not intended to be limiting.

Radiation therapy can also comprise an additional anti-cancer agent. The radiation used in radiation therapy can be ionizing radiation. Radiation therapy can also be gamma rays, X-rays, or proton beams. Examples of radiation therapy include, but arc not limited to, external-beam radiation therapy, interstitial implantation of radioisotopes (1-125, Pd- 103, Ir- 192), intravenous administration of radioisotopes such as strontium-89, thoracic radiation therapy, intraperitoneal ⁱ²P radiation therapy, and/or total abdominal and pelvic radiation therapy. For a general overview of radiation therapy, sec Hcllman, Chapter 16: Principles of Cancer Management: Radiation Therapy, 6th edition, 2001 , DeVita el al., eds., J. B. Lippencott Company, Philadelphia. The radiation therapy can be administered as external beam radiation or teletherapy wherein the radiation is directed from a remote source. The radiation treatment can also be administered as internal therapy or

brachytherapy wherein a radioactive source is placed inside the body close to cancer cells or a tumor mass. Also encompassed is the use of photodynamic therapy comprising the administration of photosensitizers, such as hematoporphyrin and its derivatives, Vertoporfin (BPD-MA), phthalocyanine, photosensitizer Pc4, dcmcthoxy-hypocrcllin A; and 2BA-2- DMHA.

Additional anti-cancer agents include immunotherapy, hormone therapy, and gene therapy. Such therapies include, but are not limited to, the use of antisense polynucleotides, ribozymes, RNA interference molecules, triple helix polynucleotides and the like, where the nucleotide sequence of such compounds are related to the nucleotide sequences of DNA and/or RNA of genes that are linked to the initiation, progression, and/or pathology of a tumor or cancer. For example, oncogenes, growth factor genes, growth factor receptor genes, cell cycle genes, DNA repair genes, and others, may be targeted in such therapies.

Immunotherapy may comprise, for example, use of cancer vaccines and/or sensitized antigen presenting cells. Immunotherapy can also involve derepression of immunoinhibitory pathways, such as by targeting PD-Ll , PD-L2, PD-1, CTLA-4, and the like. The immunotherapy can involve passive immunity for short-term protection of a host, achieved by the administration of an antibody directed against a cancer antigen or disease antigen {e.g., administration of a monoclonal antibody, optionally linked to a

chcmothcrapcutic agent or toxin, to a tumor antigen). Immunotherapy can also focus on using the cytotoxic lymphocyte-recognized epitopes of cancer cell lines.

Hormonal therapeutic treatments can comprise, for example, hormonal agonists, hormonal antagonists {e.g., flutamidc, bicalutamidc, tamoxifen, raloxifene, lcuprolidc acetate (LUPRON), LH-RH antagonists), inhibitors of hormone biosynthesis and processing, and steroids {e.g., dcxamcthasonc, retinoids, deltoids, betamethasone, Cortisol, cortisone, prednisone, dehydrotcstostcronc, glucocorticoids, mincralocorticoids, estrogen, testosterone, progestins), vitamin A derivatives {e.g., all-trans rctinoic acid (ATRA)); vitamin D3 analogs; anti gestagens (e.g., mifepristone, onapristone), or antiandrogens (e.g., cyprotcronc acetate).

In one embodiment, anti-cancer therapy used for cancers whose phenotype is determined by the methods of the invention can comprise one or more types of therapies described herein including, but not limited to, chemotherapeutic agents,

immunotherapeutics, anti-angiogenic agents, cytokines, hormones, antibodies,

polynucleotides, radiation and photodynamic therapeutic agents. For example, combination therapies can comprise one or more chemotherapeutic agents and radiation, one or more chemotherapeutic agents and immunotherapy, or one or more chemotherapeutic agents, radiation and chemotherapy.

Exemplification

This invention is further illustrated by the following examples, which should not be construed as limiting.

Example 1 : Materials and Methods For Examples 2-3

a. Plasmids

Human eIF4B was cloned from the reverse transcription products of total RNA extracted from human mammary epithelial cells (HMECs), using the primers (forward: ATGGCGGCCTCAGCAAAAAAG; reverse: CTATTCGGCATAATCTTCTC). The 1.8 kb PCR product was then used as template for amplifying Flag-tagged or HA-taggcd eIF4B with restriction sites. The constructs (pWzl-Flag-eIF4B, pTrcx-eIF4B-HA) were verified by sequencing. Site-directed mutagenesis of eIF4B was performed using QuickChangc XL (Stratagenc), and all mutant constructs were confirmed by sequencing.

To generate pLKO-tet-on shRNA targeting human eIF4B, synthesized

oligonucleotides were annealed and ligatcd with digested pLKO vector. The sequences for scramble, sh-eIF4B- l , sh-eIF4B-2 arc GTGGACTCTTGAAAGTACTAT,

GGACCAGGAAGGAAAGATGAA, and GCGG AG A A AC ACCTTG ATC TT, respectively. b. Retroviral and lcntiviral gene delivery

Retroviruses were generated by transacting HEK293T cells with retroviral plasmids and packaging DNA. Generally, 1.6 μg pWzl DNA, 1.2 μg pCG-VSVG and 1.2 μg pCG-gap/pol, 12 ul lipid of Mctafcctcnc Pro (Biontcx) were used. DNA and lipid were diluted in 300 μΐ PBS respectively and mixed. After 15 minutes (min.) of incubation, they were added to one 6-cm dish that was seeded with 3 million HEK293T cells one day earlier. Viral supernatant was collected 48 hours (h) and 72 hours post-transfection. The supernatant was filtered through 0.45 μπ\ membrane, and was added to target cells in the presence of 8 μ^ηιΙ polybrene (Millipore). Lentiviruses were generated with a similar approach with the exception of HEK.293T cells that were transfected with 2 μg pLKO DNA, 1.5 Mg pCMV-dR8.91, and 0.5 Mg pMD2-VSVG. Cells were selected with antibiotics starting 72 h after initial infection. Puromycin and blasticidin were used at the final concentration s of 1.5 Mg/ml and 4 Mg/ml respectively. c. Immunoblotting

For treatment with nocodazolc, cells were refreshed with medium containing nocodazolc (200 ng/ml). Twenty hours after treatment, floating mitotic cells were harvested by gental shake-off. For drug treatment, cells were seeded in multi-well plate, in the presence of OTSSP167 (ChemExpress, HY 15512; 10 mM stock made in DMSO).

Cells were harvested and lysed with RIPA buffer (25 mM Tris, pH 7.4, 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate, and 0.1% sodium dodecyl sulfate) supplemented with protease inhibitors cocktail (Roche) and phosphatase inhibitors cocktail (Thermo Scientific). Cleared lysates were analyzed for protein concentration using a BCA kit (Thermo Scientific). Equal amount of protein ( 10-20 μg) was resolved on SDS-PAGE, and was subsequently transferred onto a nitrocellulose or polyvinylidcnc difluoridc membrane (Amcrsham). The membrane was blocked with 5% non-fat milk and was then incubated with primary antibodies overnight at 4°C. After washing, the membrane was incubated with fluorophorc-conjugatcd secondary antibodies for 1 h at room temperature. The membrane was then washed and scanned with an Odyssey® Infrared scanner (Li-Cor Biosciences).

The following antibodies were used for immunoblotting or immunoprccipitation. MELK (Epitomics, 2916), p-eIF4B (S406) (Cell Signaling, 8151), p-eIF4B (S422) (Cell Signaling, 3591), eIF4B (Cell Signaling, 3592), c-Myc (Cell Signaling, 5605), XIAP (Cell Signaling, 2045), p-Akt (S473) (Cell Signaling, 4060), p-MAPK (T202/Y204) (Cell Signaling, 4370), cleaved PARP (Asp214) (Cell Signaling, 9541 ), Aurora A (Cell

Signaling, 4718), Aurora B (Cell Signaling, 3094), p- Aurora A (T288)/Aurora B

(T232)/Aurora C(T198) (Cell Signaling, 2914), p-Histone H3 (T3) (Cell Signaling, 13576), p-Histone H3 (S10) (Cell Signaling, 3377), p-Histone H3 (Tl 1 ) (Cell Signaling, 9767), p- Histone H3 (S28) (Cell Signaling, 9713), ODC (Sigma, Ol 136), Vinculin (Sigma, V9131 , alpha-tubulin (Sigma, T9016), anti-HA magnetic beads (Pierce, 88836), anti-Flag magnetic beads (Sigma, M8823). Secondary antibodies used were Alexa Fluor 680 goat anti-rabbit IgG (Invitrogen, A-21 109) and IRDye800-conjugated anti-mouse IgG (Rockland). d. In vitro kinase assay

Flag-tagged eIF4B or Flag-eIF4B (S406A) was transfected into HEK293T cells (4 μg DNA for cells in one 60 mm dish). Thirty-six hours after transfection, cells were lysed with IP buffer ( 100 mM NaCl, 50 mM Tris, pH 7.5, 0.5% NP-40, 0.5% Sodium dcoxycholatc, supplemented with protcasc/phosphatasc inhibitor cocktail). Ly sates were cleared via incubating with anti-mouse IgG conjugated to magnetic beads (4°C, 30 min), and then immunoprccipitatcd with anti-Flag M2 magnetic beads (Sigma) (4°C, 120 min). The beads with bound antigens were washed 5 times with IP buffer. Beads during the last wash were aliquoted into 1.5 ml microcentrifuge tubes. After removal of IP buffer, the beads were washed once with Ix kinase buffer without ATP (5 mM Tris, pH 7.5, 5 mM - β glycerophosphate, 2 mM dithiothreitol, 0. 1 mM Na3V04, 10 mM MgC12; Cell Signaling). After the wash, 40 μΐ l x kinase buffer with 200 mM ATP was added to each tube, followed by 5 ul buffer without or with 500 ng recombinant MELK. The reaction was incubated at 30°C for 30 min, and terminated by adding 40 ul 2x SDS sample buffer. The samples were then boiled and subjected to immunoblotting. In vitro kinase assays with Histone H3 were performed as above, except that recombinant Histon H3.1 (New England BioLabs, M2503S) was used (50 ng per reaction). e. Positional scanning peptide library screen

Active full-length human MELK was purified from insect cells. The positional scanning peptide library screen was performed as described in Turk et a/. (2006) Nat. Protocol. 1 :375. Briefly, a set of 180 (or 198) biotin-conjugated peptides with the following sequence, Y-A-X-X-X-X-X-S/T-X-X-X-X-A-G-K-K-biotin, was used. In the sequence, S/T means an cquimolar mixture of Scr and Thr. For each peptide, one of the nine X positions represents one of the twenty total amino acids. Peptides were arrayed in a 384-wcll plates in buffer containing 50 mM HEPES, pH 7.5, 20 mM MgCl₂, 0.02 mg/ml BSA, 0.01% Brij 35, 5 mM DTT, 0.5 mM EGTA, and active MELK and γ-[³²P]-ΑΤΡ was added to wells (final [peptide] = 50 μΜ, and [ATP] = 100 μΜ, 0.025 μC/μl in each well). After incubating for 2 h at 30°C, aliquots of the reactions were spotted onto a strcptavidin membrane. The membrane was quenched, washed extensively, dried, and exposed to a phosphor storage screen.

Example 2: Phosphorylation Status of eIF4B is a Biomarker of MELK Enzymatic and Oncogenic Activity

To seek a potential molecular mechanism underlying the importance of MELK for cancer (such as basal-like breast cancer (BBC)), multiple experimental approaches, including immunoprecipitation-tandem mass spectrometry, and phospho-peptide mapping, were explored. When Flag-tagged MELK was immunoprecipitated in mitotic cell lysates and subsequently subject to mass spectrometry analysis, it was found that a translation initiation factor, eIF4B, had a strong association with MELK during mitosis (Figure 1). Using positional phospho-peptide mapping, an optimal substrate motif for MELK was identified having a strong selection for argininc at the -3 position relative to

serine/threonine (Figure 2).

There are two regions flanking the residues of human eIF4B (i.e., at Ser406 and

Ser422), which contain the MELK phosphorylation motif (Figures 3 and 4). To test whether MELK is capable of phosphorylating human eIF4B at these two sites, in vitro kinase assays were performed using purified recombinant MELK with immunoprecipitated eIF4B. It was found that Ser406, but not Ser422, of human eIF4B was readily

phosphorylatcd by full-length MELK or the kinase domain of MELK, and that the observed phosphorylation was abolished when the serine at 406 of human eIF4B was mutated to alanine or other manipulations of MELK (Figures 3-5). These results arc specifically dependent upon MELK, as inhibition of mitotic cells with mTOR inhibitors, such as rapamycin and torins, do not produce the same results (Figure 6; van Gorp el al. (2009) Oncogene 28:95-106). These data indicate that MELK is a kinase that phosphorylates human clF4B at S406 and that eIF4B orthologs in other species arc similarly

phosphorylatcd due to the highly conserved sequence and structural composition of the eIF4B polypeptide region harboring the phosphorylation site (Table 2). Table 2

It is known that eIF4B stimulates the hclicasc activity of cIF4A for unwinding the secondary structure of 5'UTR of mRNA (Dmitriev et al. (2003) Mo/. Cell Biol. 23:8925- 8933 and Shahbazian el al. (2010) Mol. Cell Biol. 30 1478- 1485). Many of these mRNAs encode oncogenic proteins, such as c-Myc, XIAP (X-linked inhibitor of apoptosis protein) and ODC (ornithine decarboxylase). It was determined herein that down-regulation of MELK reduced phosphorylation of eIF4B (p-eIF4B) at S406 in MDA-MB-468 cells during mitosis, which also resulted in markedly reduced levels of c-Myc, XIAP and ODC 1 (Figures 7 and 8). Thus, MELK-mediated S406 phosphorylation of eIF4B during mitosis, is functionally important for the optimal translation of mRNAs with highly structured 5 'UTR, many of which are known to be oncogenic, such as c-Myc, XIAP, and ODC 1. Together, these data indicate that MELK is a novel kinase that regulates eIF4B during mitosis and thereby mediates the translation of mRNAs that harbor structured 5'-UTR and are important for the survival and proliferation of cancer cells. Thus, the level of eIF4B phosphorylation mediated by MELK is a target engagement biomarker for MELK oncogenic activity useful for preclinical and clinical applications.

Example 3: Phosphorylation Status of Histone H3 is a Biomarker of MELK Enzymatic and Oncogenic Activity

Since MELK protein abudancc is highest during mitotis, a cell cycle phase when Histon H3 is heavily phosphorylatcd, a link between MELK and Histone H3

phosphorylation was suggested. In fact, the region flanking the residues of human Histone H3 at Thr-11 contains the optimal MELK phosphorylation motif described in Example 2 above. To test whether MELK is capable of phosphorylating human Histonc H3 at threonine 3 (Thr3), serine 10 (SerlO) and threonine 1 1 (Thrl 1 ), in viiro kinase assays were performed using a purified recombinant kinase domain of human MELK and human Histone H3. It was found that Thr3, Serl O, and Thrl 1 of human Histone H3 were readily phosphorylated by the kinase domain of MELK (Figure 9).

Down-regulation of MELK reduced phosphorylation of Histone H3 at Thr3, SerlO and Thrl 1 in MDA-MB-468 cells during mitosis, but did not affect the phosphorylation of Aurora kinases A, B, or C, which are known kinases that phosphorylate Histonc H3 at SerlO (Figures 10 and 1 1 ). Similarly, inhibition of MELK using the small chemical MELK inhibitor, OTSSP167, in MDA-MB-468 cells reduced phosphorylation of Histone H3 at Thr3/Serl0/Thrl 1 (Figure 12). An OTSSP167 concentration-dependent reduction in phosphorylation of Histone H3 at Thr3, Serl O and Thrl 1 , but not Ser28, was also observed (Figure 13).

These data indicate that MELK is a kinase that phosphorylates human Histone H3 at least at Thr3, Scr 10 and Thrl 1 , but not Scr28, and that Histonc H3 orthologs in other species arc similarly phosphorylated due to the highly conserved sequence and structural composition of the Histonc H3 polypeptide region harboring the phosphorylation site (Table 3).

Histone H3

Human T3/S10/T11 MARTKQTAI ■CSTGGKA

Chimpanzee T3/S10/T11 MARTKQTAI ■CSTGGKA

Monkey T3/S10/T11 MARTKQTAI ■CSTGGKA

Cattle T3/S10/T11 MARTKQTAI ■CSTGGKA

Dog T3/S10/T11 MARTKQTAI ■CSTGGKA

Mouse T3/S10/T11 MARTKQTAI ■CSTGGKA

Rat T3/S10/T11 MARTKQTAI ■CSTGGKA

Zebrafish T3/S10/T11 MARTKQTAI ■CSTGGKA Fission yeast T3/S10/T11 MARTKQTAI ■CSTGGKA

Together, these data indicate that MELK is a novel kinase that regulates Histonc H3 phosphorylation during mitosis and is therefore potentially important for the proliferation of cells (e.g., cancer cells). Thus, the level of Histonc H3 phosphorylation mediated by MELK is a target engagement biomarker for MELK oncogenic activity useful for preclinical and clinical applications. Incorporation by Reference

The contents of all references, patent applications, patents, and published patent applications, as well as the Figures and the Sequence Listing, cited throughout this application are hereby incorporated by reference.

Equivalents

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents arc intended to be encompassed by the following claims.

Claims

What is claimed:

1. A method of identifying an agent which inhibits kinase or oncogenic activity of human maternal embryonic leucine zipper kinase (MELK) or an ortholog thereof, comprising:

a) contacting a sample comprising i) human MELK or an ortholog thereof and ii) human eukaryotic initiation factor 4B (eIF4B) or an ortholog thereof, with the agent; and b) determining the ability of the agent to inhibit Ser-406 phosphorylation of human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human elF4B, wherein decreased phosphorylation identifies an agent which inhibits kinase or oncogenic activity of human MELK or the ortholog thereof.

2. The method of claim 1, wherein the inhibition of said Scr-406 phosphorylation of human clF4B or a corresponding phosphorylatablc amino acid in an ortholog of human eIF4B is determined by comparing the amount of Ser-406 phosphorylated human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B, in the sample relative to a control.

3. The method of claim 2, wherein the control is the amount of Ser-406

phosphorylated human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B in the sample relative to said amount in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent.

4. The method of claim 1 , wherein the inhibition of said Ser-406 phosphorylation of human clF4B or a corresponding phosphorylatablc amino acid in an ortholog of human eIF4B is determined by comparing the ratio of the amount of Ser-406 phosphorylated human eIF4B, or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B, in the sample relative to the total amount of human EIF4B or ortholog thereof, to a control.

5. The method of claim 4, wherein the control is the ratio of the amount of Scr-406 phosphorylated human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B in the sample relative to said ratio in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent.

6. The method of any one of claims 1-5, further comprising determining the amount of a protein translated from an RNA with highly structured 5'UTR, optionally wherein the protein is selected from the group consisting of cellular myclocytomatosis oncogene (c- Myc), X-linked inhibitor of apoptosis protein (XIAP), and ornithine decarboxylase (ODC 1 ).

7. The method of claim 1 , further comprising a step of determining whether the agent directly binds said human eIF4B or said ortholog thereof, or said human MELK or said ortholog thereof.

8. The method of claim 1 , wherein the sample is selected from the group consisting of in vitro, ex vivo, and in vivo samples.

9. The method of claim 1 , wherein the sample comprises cells.

10. The method of claim 9, wherein the cells are cancer cells.

1 1. The method of claim 10, wherein the cancer is selected from the group consisting of any cancer in which MELK or eIF4B is amplified or overexpressed, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or eIF4B is activated by other kinases.

12. The method of claim 9, wherein the cells are obtained from a subject.

13. The method of claim 1 , wherein the sample is selected from the group consisting of tissue, whole blood, serum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow.

14. The method of any one of claims 1 -5, wherein the amount of Ser-406

phosphorylated human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B is determined by an immunoassay using a reagent which specifically binds to Scr-406 phosphorylated human eIF4B or corresponding

phosphorylated ortholog of human eIF4B.

15. The method of claim 14, wherein the immunoassay is a radioimmunoassay, a

Western blot assay, a proximity ligation assay, an immunofluorcscncc assay, an enzyme immunoassay, an immunoprccipitation assay, a chcmi luminescence assay, an

immunohistochemical assay, a dot blot assay, or a slot blot assay.

16. The method of claim 15, wherein the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human eIF4B or corresponding ortholog of human elF4B and a detection antibody or fragment thereof which specifically binds with Ser-406 phosphorylated human eIF4B or a corresponding phosphorylated ortholog of human eIF4B.

17. The method of any one of claims 1-5, wherein said human eIF4B or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1.

18. The method of any one of claims 1 -5, wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

19. The method of any one of claims 1-5, wherein the agent decreases the amount of Ser-406 phosphorylated human elF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B by at least 50%.

20. A method for assessing the efficacy of an agent for inhibiting kinase activity of human MELK or an ortholog thereof in a subject, comprising:

a) detecting in a subject sample at a first point in time, the amount of Ser-406 phosphorylated human eIF4B or the amount of a human eIF4B ortholog phosphorylated at a corresponding amino acid of human clF4B;

b) repeating step a) during at one or more subsequent points in time after administration of the agent; and

c) comparing the amount of phosphorylated human eIF4B or ortholog thereof detected in step a) with said amount detected in step b),

wherein a higher amount of Ser-406 phosphorylated human eIF4B or the amount of the human eIF4B ortholog phosphorylated at a corresponding amino acid of human clF4B in the first point in time relative to at least one subsequent point in time, indicates that the agent inhibits kinase activity of human MELK or the ortholog thereof.

21. The method of claim 20, wherein the amount of Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B is determined by an immunoassay using a reagent which specifically binds with Ser-406 phosphorylated human eIF4B or corresponding phosphorylated ortholog of human eIF4B.

22. The method of claim 21 , wherein the immunoassay is a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluoresence assay, an enzyme immunoassay, an immunoprecipitation assay, a chemi luminescence assay, an

immunohistochemical assay, a dot blot assay, or a slot blot assay.

23. The method of claim 22, wherein the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human elF4B or corresponding ortholog of human elF4B and a detection antibody or fragment thereof which specifically binds with Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylated ortholog of human eIF4B.

24. The method of claim 20, wherein the sample is selected from the group consisting of ex vivo and in vivo samples.

25. The method of claim 20, wherein the sample comprises cancer cells.

26. The method of claim 25, wherein the cancer cells arc cells selected from the group consisting of any cancer in which MELK or eIF4B is amplified or ovcrcxprcsscd, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or eIF4B is activated by other kinases.

27. The method of claim 20, wherein the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow.

28. The method of claim 20, wherein the sample in step a) and/or step b) is a portion of a single sample obtained from the subject.

29. The method of claim 20, wherein the sample in step a) and/or step b) is a portion of pooled samples obtained from the subject.

30. The method of claim 20, wherein between the first point in time and the subsequent point in time, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer.

31. The method of claim 20, wherein said human elF4B or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1.

32. The method of claim 20, wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

33. The method of claim 20, wherein the agent decreases the amount of Ser-406 phosphorylatcd human eIF4B or a corresponding phosphorylatablc amino acid in the ortholog of human eIF4B by at least 50%.

34. A method of treating a subject afflicted with cancer comprising administering to the subject an agent that inhibits Ser-406 phosphorylation of human eIF4B or a corresponding phosphorylatable amino acid in an ortholog of human eIF4B, thereby treating the subject afflicted with the cancer.

35. The method of claim 34, wherein the agent is administered in a pharmaceutically acceptable formulation.

36. The method of claim 34, wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

37. The method of claim 34, wherein the agent directly binds said human elF4B or the ortholog thereof, or said human MELK or the ortholog thereof.

38. The method of claim 34, wherein the cancer is selected from the group consisting of any cancer in which MELK or eIF4B is amplified or ovcrcxprcsscd, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or eIF4B is activated by other kinases.

39. The method of claim 34, wherein said human elF4B or ortholog thereof, and/or said human M ELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1.

40. The method of claim 34, wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

41. The method of claim 34, wherein the agent decreases the amount of Scr-406 phosphorylated human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human el F4B by at least 50%.

42. The method of claim 34, further comprising administering one or more additional anti-cancer agents.

43. A method of determining the function or activity of human MELK or an ortholog, comprising:

a) detecting in a sample the amount of Ser-406 phosphorylated human eIF4B or the amount of a human eIF4B ortholog phosphorylated at a corresponding amino acid of human eIF4B;

b) repeating step a) in the same sample or a test sample at one or more subsequent points in time after manipulation of the sample and/or manipulation of the same sample or test sample; and

c) comparing the amount of phosphorylated human eIF4B or ortholog thereof detected in step a) with said amount detected in step b),

wherein a modulated of Scr-406 phosphorylated human eIF4B or the amount of the human eIF4B ortholog phosphorylated at a corresponding amino acid of human eIF4B in the first point in time relative to at least one subsequent point in time and/or at least one subsequent manipulation of the same sample or test sample, indicates that the function or activity of human MEL or an ortholog thereof is modulated.

44. The method of claim 43, wherein the amount of Scr-406 phosphorylated human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B is determined by an immunoassay using a reagent which specifically binds with Scr-406 phosphorylated human eIF4B or corresponding phosphorylated ortholog of human eIF4B.

45. The method of claim 44, wherein the immunoassay is a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluorcscnce assay, an enzyme immunoassay, an immunoprecipitation assay, a chemi luminescence assay, an

immunohistochemical assay, a dot blot assay, or a slot blot assay.

46. The method of claim 45, wherein the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human elF4B or corresponding ortholog of human elF4B and a detection antibody or fragment thereof which specifically binds with Ser-406 phosphorylated human eIF4B or a corresponding phosphorylated ortholog of human eIF4B.

47. The method of claim 43, wherein the sample is selected from the group consisting of in vitro, ex vivo, and in vivo samples.

48. The method of claim 43, wherein the sample comprises cells or the method uses a cell-based assay.

49. The method of claim 48, wherein the cells are cancer cells selected from the group consisting of any cancer in which MELK or eIF4B is amplified or ovcrcxprcsscd, any cancer having an activating mutation of MELK or eIF4B, and any cancer in which MELK or eIF4B is activated by other kinases.

50. The method of claim 43, wherein the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow.

51. The method of claim 43, wherein the same sample or test sample in step a) and/or step b) is a portion of a single sample obtained from a subject.

52. The method of claim 43, wherein the same sample or test sample in step a) and/or step b) is a portion of pooled samples obtained from a subject.

53. The method of claim 43, wherein between the first point in time and the subsequent point in time, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer.

54. The method of claim 43, wherein said human elF4B or ortholog thereof, and/or said human M ELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1.

55. The method of claim 43, wherein the manipulation of the sample is selected from the group consisting of contacting the sample with a test agent, contacting the sample with an upstream signal of the MELK signaling pathway, and contacting the sample with a MELK inhibitor.

56. The method of claim 55, wherein the test agent is a small molecule, or an antibody or antigen-binding fragment thereof.

57. The method of claim 55 or 56, wherein the test agent decreases the amount of Ser- 406 phosphorylated human eIF4B or a corresponding phosphorylatable amino acid in the ortholog of human eIF4B by at least 50%.

58. A method of identifying an agent which inhibits kinase or oncogenic activity of human MELK or an ortholog thereof, comprising:

a) contacting a sample comprising i) human MELK or an ortholog thereof and ii) human Histonc H3 or an ortholog thereof, with the agent; and

b) determining the ability of the agent to inhibit Thr-3 phosphorylation of human Histonc H3 or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3; and/or Scr-10 phosphorylation of human Histonc H3 or a corresponding phosphorylatable amino acid in the ortholog of human Histonc H3; and/or Thr-11 phosphorylation of human Histonc H3 or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, wherein decreased phosphorylation identifies an agent which inhibits kinase or oncogenic activity of human MELK or the ortholog thereof.

59. The method of claim 58, wherein the inhibition of said Thr-3 phosphorylated and/or Scr-10 phosphorylation and/or Thr-11 phosphorylation of human Histonc H3, or a corresponding phosphorylatable amino acid in an ortholog of human Histonc H3, is determined by comparing the amount of Thr-3 phosphorylated human Histonc H3 and/or Scr-10 phosphorylated human Histonc H3 and/or Thr-11 phosphorylated human Histonc H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, in the sample relative to a control.

60. The method of claim 59, wherein the control is the amount of Thr-3 phosphorylated and/or Ser-10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3, in the sample relative to said amount in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent.

61. The method of claim 58, wherein the inhibition of said Thr-3 phosphorylation and/or Ser- 10 phosphorylation and/or Thr-11 phosphorylation of human Histone H3 , or a corresponding phosphorylatablc amino acid in an ortholog of human Histone H3 is determined by comparing the ratio of the amount of Thr-3 phosphorylated and/or Ser- 10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3, in the sample relative to the total amount of human Histone H3 or ortholog thereof, to a control.

62. The method of claim 61, wherein the control is the ratio of the amount of Thr-3 phosphorylated and/or Ser-10 phosphorylated and/or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3 in the sample relative to said ratio in the absence of the agent or at an earlier timcpoint after contact of the sample with the agent.

63. The method of any one of claims 58-62, further comprising determining the amount of a mitosis-specific protein.

64. The method of claim 58, further comprising a step of determining whether the agent directly binds said human Histone H3 or said ortholog thereof, or said human MELK or said ortholog thereof.

65. The method of claim 58, wherein the sample is selected from the group consisting of in vitro, ex vivo, and in vivo samples.

66. The method of claim 58, wherein the sample comprises cells.

67. The method of claim 66, wherein the cells are cancer cells.

68. The method of claim 67, wherein the cancer is selected from the group consisting of any cancer in which MELK or Histonc H3 is amplified or overexpresscd, any cancer having an activating mutation of MELK or Histonc H3, and any cancer in which MELK or Histone H3 is activated by other kinases.

69. The method of claim 66, wherein the cells arc obtained from a subject.

70. The method of claim 58, wherein the sample is selected from the group consisting of tissue, whole blood, serum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow.

71. The method of any one of claims 58-62, wherein the amount of Thr-3

phosphorylated and/or Scr-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histone H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, is determined by an immunoassay using a reagent which specifically binds with Thr-3 phosphorylatcd and/or Scr-10 phosphorylatcd or Thr-11 phosphorylatcd human Histonc H3, or corresponding phosphorylated ortholog of human Histone H3.

72. The method of claim 71, wherein the immunoassay is a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluorcscncc assay, an enzyme immunoassay, an immunoprccipitation assay, a chemi luminescence assay, an

immunohistochemical assay, a dot blot assay, or a slot blot assay.

73. The method of claim 72, wherein the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human Histonc H3 or corresponding ortholog of human Histonc H3 and a detection antibody or fragment thereof which specifically binds with Thr-3 phosphorylated and/or Ser-10 phosphorylated or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylated ortholog of human Histone H3.

74. The method of any one of claims 58-62, wherein said human Histonc H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1.

75. The method of any one of claims 58-62, wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

76. The method of any one of claims 58-62, wherein the agent decreases the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histone H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3, by at least 50%.

77. A method for assessing the efficacy of an agent for inhibiting kinase activity of human MELK or an ortholog thereof in a subject, comprising:

a) detecting in a subject sample at a first point in time, the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histone H3, or the amount of a human Histone H3 ortholog phosphorylatcd at a corresponding amino acid of human Histone H3;

b) repeating step a) during at one or more subsequent points in time after administration of the agent; and

c) comparing the amount of phosphorylatcd human Histone H3 or ortholog thereof detected in step a) with said amount detected in step b),

wherein a higher amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histone H3, or the amount of the human Histone H3 ortholog phosphor/ la ted at a corresponding amino acid of human Histone H3, in the first point in time relative to at least one subsequent point in time, indicates that the agent inhibits kinase activity of human MELK or the ortholog thereof.

78. The method of claim 77, wherein the amount of Thr-3 phosphorylated and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histone H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3, is determined by an immunoassay using a reagent which specifically binds with Thr-3 phosphorylated and/or Ser-10 phosphorylated human Histone H3 or Thr-11 phosphorylatcd human Histone H3, or corresponding phosphorylatcd ortholog of human Histone H3.

79. The method of claim 78, wherein the immunoassay is a radioimmunoassay, a

Western blot assay, a proximity ligation assay, an immunofluorcscnce assay, an enzyme immunoassay, an immunoprccipitation assay, a chemi luminescence assay, an

immunohistochemical assay, a dot blot assay, or a slot blot assay.

80. The method of claim 79, wherein the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human Histone H3 or corresponding ortholog of human Histone H3 and a detection antibody or fragment thereof which specifically binds with Thr-3 phosphorylated and/or Ser-10 phosphorylated or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylated ortholog of human Histone H3.

81. The method of claim 77, wherein the sample is selected from the group consisting of ex vivo and in vivo samples.

82. The method of claim 77, wherein the sample comprises cancer cells.

83. The method of claim 82, wherein the cancer cells are cells selected from the group consisting of any cancer in which MELK or Histone H3 is amplified or overexpressed, any cancer having an activating mutation of MELK or Histone H3, and any cancer in which MELK or Histone H3 is activated by other kinases.

84. The method of claim 77, wherein the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow.

85. The method of claim 77, wherein the sample in step a) and/or step b) is a portion of a single sample obtained from the subject.

86. The method of claim 77, wherein the sample in step a) and/or step b) is a portion of pooled samples obtained from the subject.

87. The method of claim 77, wherein between the first point in time and the subsequent point in time, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer.

88. The method of claim 77, wherein said human Histone H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Tabic 1.

89. The method of claim 77, wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

90. The method of claim 77, wherein the agent decreases the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histonc H3, or a corresponding phosphorylatable amino acid in the ortholog of human Histone H3, by at least 50%.

91. A method of treating a subject afflicted with cancer comprising administering to the subject an agent that inhibits Thr-3 phosphorylation and/or Ser-10 phosphorylation and/or Thr-11 phosphorylation of human Histonc H3, or a corresponding phosphorylatable amino acid in an ortholog of human Histonc H3, thereby treating the subject afflicted with the cancer.

92. The method of claim 91 , wherein the agent is administered in a pharmaceutically acceptable formulation.

93. The method of claim 91 , wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

94. The method of claim 91, wherein the agent directly binds said human Histone H3 or the ortholog thereof, or said human MELK or the ortholog thereof.

95. The method of claim 91, wherein the cancer is selected from the group consisting of any cancer in which MELK or Histonc H3 is amplified or ovcrexprcsscd, any cancer having an activating mutation of MELK or Histonc H3, and any cancer in which MELK or Histonc H3 is activated by other kinases.

96. The method of claim 91 , wherein said human Histonc H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1.

97. The method of claim 91, wherein the agent is a small molecule, or an antibody or antigen-binding fragment thereof.

98. The method of claim 91 , wherein the agent decreases the amount of Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histonc H3, or a corresponding phosphory la table amino acid in the ortholog of human Histone H3, by at least 50%.

99. The method of claim 91 , further comprising administering one or more additional anti-cancer agents.

100. A method of determining the function or activity of human MELK or an ortholog, comprising:

a) detecting in a sample the amount of Thr-3 phosphorylatcd and/or Scr-10 phosphorylatcd and/or Thr-11 phosphorylatcd human histonc H,3 or the amount of a human Histonc H3 ortholog phosphorylatcd at a corresponding amino acid of human Histone H3; b) repeating step a) in the same sample or a test sample at one or more subsequent points in time after manipulation of the sample and/or manipulation of the same sample or test sample; and

c) comparing the amount of phosphorylatcd human Histone H3 or ortholog thereof detected in step a) with said amount detected in step b),

wherein a modulated amount of Thr-3 phosphory lated and/or Ser-10 phosphory lated and/or Thr-11 phosphorylated human Histone H3, or the amount of the human Histone H3 ortholog phosphorylatcd at a corresponding amino acid of human Histonc H3, in the first point in time relative to at least one subsequent point in time and/or at least one subsequent manipulation of the same sample or test sample, indicates that the function or activity of human MELK or an ortholog thereof is modulated.

101. The method of claim 100, wherein the amount of Thr-3 phosphorylated and/or Ser- 10 phosphorylatcd and/or Thr-11 phosphorylatcd human Histonc H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histonc H3, is determined by an immunoassay using a reagent which specifically binds with Thr-3 phosphorylatcd and/or Ser-10 phosphorylatcd or Thr-11 phosphorylatcd human Histonc H3, or corresponding phosphorylatcd ortholog of human Histonc H3.

102. The method of claim 101, wherein the immunoassay is a radioimmunoassay, a Western blot assay, a proximity ligation assay, an immunofluoresence assay, an enzyme immunoassay, an immunoprccipitation assay, a chcmi luminescence assay, an

immunohistochemical assay, a dot blot assay, or a slot blot assay.

103. The method of claim 102, wherein the enzyme immunoassay is a sandwich enzyme immunoassay using a capture antibody or fragment thereof which specifically binds with human Histonc H3 or corresponding ortholog of human Histonc H3 and a detection antibody or fragment thereof which specifically binds with Thr-3 phosphorylated and/or Ser-10 phosphorylated or Thr-11 phosphorylated human Histone H3, or a corresponding phosphorylated ortholog of human Histone H3.

104. The method of claim 100, wherein the sample is selected from the group consisting of in vitro, ex vivo, and in vivo samples.

105. The method of claim 100, wherein the sample comprises cells or the method uses a cell-based assay.

106. The method of claim 105, wherein the cells are cancer cells selected from the group consisting of any cancer in which MELK or Histone H3 is amplified or overexpressed, any cancer having an activating mutation of MELK or Histonc H3, and any cancer in which MELK or Histone H3 is activated by other kinases.

107. The method of claim 100, wherein the sample is selected from the group consisting of tissue, whole blood, scrum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow.

108. The method of claim 100, wherein the same sample or test sample in step a) and/or step b) is a portion of a single sample obtained from a subject.

109. The method of claim 100, wherein the same sample or test sample in step a) and/or step b) is a portion of pooled samples obtained from a subject.

1 10. The method of claim 100, wherein between the first point in time and the subsequent point in time, the subject has undergone treatment for cancer, has completed treatment for cancer, and/or is in remission from cancer.

1 1 1. The method of claim 100, wherein said human Histonc H3 or ortholog thereof, and/or said human MELK or ortholog thereof, comprises a nucleic acid sequence or amino acid sequence set forth in Table 1.

1 12. The method of claim 100, wherein the manipulation of the sample is selected from the group consisting of contacting the sample with a test agent, contacting the sample with an upstream signal of the MELK signaling pathway, and contacting the sample with a MELK inhibitor.

1 13. The method of claim 1 12, wherein the test agent is a small molecule, or an antibody or antigen-binding fragment thereof.

1 14. The method of claim 1 12 or 1 13, wherein the test agent decreases the amount of Thr-3 phosphorylated and/or Ser-10 phosphorylated and/or Thr-11 phosphorylated human Histonc H3, or a corresponding phosphorylatablc amino acid in the ortholog of human Histone H3, by at least 50%.