WO2015077725A1 - Diagnostic de sous-groupes liés à idh1 et traitement du cancer - Google Patents

Diagnostic de sous-groupes liés à idh1 et traitement du cancer Download PDF

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WO2015077725A1
WO2015077725A1 PCT/US2014/067168 US2014067168W WO2015077725A1 WO 2015077725 A1 WO2015077725 A1 WO 2015077725A1 US 2014067168 W US2014067168 W US 2014067168W WO 2015077725 A1 WO2015077725 A1 WO 2015077725A1
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regulation
akt
subject
cell
therapeutic
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PCT/US2014/067168
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English (en)
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Anna Joy
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Dignity Health
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Priority to CA2923672A priority Critical patent/CA2923672A1/fr
Publication of WO2015077725A1 publication Critical patent/WO2015077725A1/fr
Priority to US14/826,578 priority patent/US10731221B2/en
Priority to US16/923,803 priority patent/US20200340066A1/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/501—Detection characterised by immobilisation to a surface being an array of oligonucleotides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease

Definitions

  • the invention relates to medicine, for example, methods, compositions and kits for classifying and treating tumors.
  • GBM diagnosed by histopathology is a collection of molecular and clinical subtypes. For example, there are two classes of GBM based on clinical presentation [1], [2]. Primary GBM arise de novo in older patients and are associated with poorer prognosis. Secondary GBM are rare (-5-10% of total GBM), progress from lower grade tumors, occur more frequently in younger patients with better prognosis and have a different molecular profile. Studies using gene expression, DNA copy number, miRNA, and DNA methylation show these molecular characteristics can divide GBM into subclasses, some with different clinical characteristics [3], [4], [5], [6], [7], [8], [9].
  • PN proneural
  • PROLIF Proliferative
  • MES mesenchymal
  • CLAS Classical
  • DNA methylation identifies a subset of PN tumors with glioma CpG island methylator phenotype (GCIMP) that are younger, longer surviving and tightly associated with IDH1 mutations [8].
  • GFR/PI3K/AKT growth factor receptor/phosphatidylinositol 3-kinase/AKT pathway
  • Various embodiments of the present invention provide a method for classifying a cancer in a subject.
  • the method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining an expression pattern of AKT pathway components in the biological sample; and classifying the cancer based on the determined expression pattern of AKT pathway components in the biological sample.
  • Various embodiments of the present invention provide a method for diagnosing whether a subject has a cancer subtype.
  • the method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether an expression pattern of AKT pathway components is present in the biological sample; and diagnosing the subject as having the cancer subtype if the expression pattern of AKT pathway components is determined to be present in the biological sample.
  • the method comprises selecting, choosing or prescribing a therapeutic for the subject after diagnosis.
  • the method comprises instructing or directing the subject to receive a therapeutic after diagnosis.
  • the method comprises administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the diagnosed cancer subtype.
  • the cancer subtype is an AKT subtype including but not limited to CI, PN, MES, CLAS, SL, and PROLIF subtypes.
  • Various embodiments of the present invention provide a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject.
  • the method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether an expression pattern of AKT pathway components is present in the biological sample; providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject if the expression pattern of AKT pathway components is determined to be present in the biological sample, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer subtype.
  • the cancer subtype is an AKT subtype including but not limited to CI , PN, MES, CLAS, SL, and PROLIF subtypes.
  • Various embodiments of the present invention provide a method for treating an AKT cancer subtype in a subject.
  • the method may consist of or may consist essentially of or may comprise: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating the AKT cancer subtype in the subject.
  • kits for classifying a cancer in a subject and/or for diagnosing whether a subject has a cancer subtype may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; instructions for using the one or more detection agents to classify the cancer in the subject, and/or diagnose whether a subject has the cancer subtype.
  • kits for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; instructions for using the one or more detection agents to classify the cancer in the subject, and/or diagnose whether a subject has the cancer subtype.
  • kits for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or
  • the kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; a quantity of a therapeutic; and instructions for using the one or more detection agents and the therapeutic to treat, prevent, reduce the likelihood of having, reduce the severity of and/or slow the progression of the cancer subtype in the subject
  • kits for treating an AKT cancer subtype in a subject may consist of or may consist essentially of or may comprise: a quantity of a therapeutic; and instructions for using the therapeutic to treat the AKT cancer subtype in the subject.
  • compositions, and kits of the present invention find utility in the classification and treatment of various tumors, including but not limited to various forms of brain tumors.
  • FIG. 1 depicts, in accordance with various embodiments of the invention, that AKT pathway gene expression classifies GBM.
  • Figure 2 depicts, in accordance with various embodiments of the invention, validation of AKT subgroups in an independent dataset.
  • AKT pathway genes in discovery (A) and validation (B) datasets have similar patterns of expression in subgroups. Tumors in the discovery and validation set were first grouped by AKT subgroup membership then ordered by correlation coefficient. AKT gene order in the discovery set was determined by one-way hierarchical clustering and retained in the validation set.
  • Discovery (C) and validation (D) datasets have similar DNA CNA. The percentage of patients in the discovery (A) and validation (B) datasets with copy number gains or losses in chr7, 10 and 19q is shown.
  • Figure 3 depicts, in accordance with various embodiments of the invention, Akt classification for 5 glioblastoma subgroups. Previous classification systems distribute non- randomly in AKT subgroups. Distribution of Phillips (A), TCGA (B) and G-CIMP (C) subgroups in AKT subgroups.
  • A Phillips
  • B TCGA
  • C G-CIMP
  • Figure 4 depicts, in accordance with various embodiments of the invention, that AKT subgroups are prognostic.
  • Log rank p value 0.0005 (B; SL vs. rest); 0.0029 (B; PROLIF vs. rest) and 0.003 (D; SL vs rest). Survival differences did not reach significance in (A) and (C).
  • Figure 5 depicts, in accordance with various embodiments of the invention, evidence that SL subtype (AKT subgroup 5) patients are sensitive to alkylating agents BCNU and CCNU.
  • FIG. 6 depicts, in accordance with various embodiments of the invention, that AKT subgroups have distinct genomic alterations.
  • A Copy number alterations in TCGA AKT subgroups. The GISTIC method was applied to TCGA samples in each subgroup with copy number information. Data are presented as a G score which is an integrated score of the prevalence of the copy-number change times the average (log2 -transformed) amplitude. The green line shows significance threshold (FDR q values to account for multiple -hypothesis testing). Regions with subgroup-specific CNA are highlighted in yellow.
  • B Distribution of clinical information and mutations, CNA and mRNA expression for glioma-associated genes in AKT subgroups.
  • Figure 7 depicts, in accordance with various embodiments of the invention, that subgroups have distinct patterns of expression for PI3K/AKT/mTOR pathway components (distinct Akt pathway activation).
  • Tumors x axis
  • A Z transformed mRNA
  • B protein and phospho-protein expression
  • C The Pearson correlation coefficient for AKT pS473 vs. RPS6 pS235/236 (light gray) and AKT pS473 vs. RPS6 pS240/244 (dark gray) for each subgroup is shown (C).
  • This model shows loss of AKT and mTOR inhibitors (PHLPP, TSC and pAMPK) increases output of the AKT/mTOR/S6 axis (pRPS6) in the MES subgroup. Conversely, increased expression of these inhibitors decreases output in the SL subgroup. Red, grey and green represent high, intermediate and low expression/activity, respectively. Dashed line is indirect interaction.
  • FIG 8 depicts, in accordance with various embodiments of the invention, summary of features in AKT subtypes (AKT CI /subgroup 1 ; AKT PN/subgroup 2; AKT MES/subgroup 3; AKT CLAS/subgroup 4; AKT SL/subgroup 5; AKT PROLIF/subgroup 6).
  • FIG. 10 depicts, in accordance with various embodiments of the invention, average expression of AKT pathway genes in subgroups.
  • Hierarchical clustering using AKT pathway genes was used to group GBM patients and genes in the discovery (GBM 195) dataset. Tumors in the validation dataset were grouped by AKT class keeping the same order of genes.
  • the expression of AKT pathway genes in each class was averaged and is shown as a heatmap; red and green respectively represent high/increased and low/decreased average expression relative to the median of all tumors. Black represents minimal expression difference relative to the median of all tumors.
  • Figure 11 depicts, in accordance with various embodiments of the invention, Log2 (tumor/normal) DNA copy number in subgroups. Amplifications (red) and deletions (blue) in subgroups (y axis) were determined by segmentation analysis of normalized signal intensities from TCGA SNP arrays using GISTIC and viewed with IGV by chromosomal location (x axis).
  • Figure 12 depicts, in accordance with various embodiments of the invention, distribution of clinical and molecular information by subgroup in the discovery dataset (GBM195).
  • the table lists the number of tumors with the specified feature in each subgroup in the discovery dataset.
  • Features with statistically significant enrichment in a subgroup after Bonferroni correction (p ⁇ 0.05) are highlighted.
  • Figure 13 depicts, in accordance with various embodiments of the invention, distribution of clinical and molecular information by subgroup in the validation dataset (TCGA).
  • the table lists the number of tumors with the specified feature in each subgroup in the validation dataset.
  • Features with statistically significant enrichment in a subgroup after Bonferroni correction (p ⁇ 0.05) are highlighted in dark grey.
  • Features with statistically significant enrichment in a subgroup before Bonferroni correction are highlighted in light grey.
  • Figure 14 depicts, in accordance with various embodiments of the invention, focal DNA amplifications in subgroups. Copy number alterations in subgroups were evaluated using GISTIC and the q score for statistically significant focal DNA copy number gains (q score ⁇ 0.25) listed. Focal copy number changes common to all subgroups (q ⁇ 0.25 in all subgroups) are not reported.
  • Figure 15 depicts, in accordance with various embodiments of the invention, focal DNA deletions in subgroups. Copy number alterations in subgroups were evaluated using GISTIC and the q score for statistically significant focal DNA copy number losses (q score ⁇ 0.25) are listed. Focal copy number changes common to all subgroups (q ⁇ 0.25 in all subgroups) are not reported.
  • Figure 16 depicts, in accordance with various embodiments of the invention, median expression values of AKT pathway genes in each AKT cancer subgroup in the discovery dataset corresponding to the heatmap in Figure 10.
  • the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are useful to an embodiment, yet open to the inclusion of unspecified elements, whether useful or not. It will be understood by those within the art that, in general, terms used herein are generally intended as “open” terms (e.g., the term “including” should be interpreted as “including but not limited to,” the term “having” should be interpreted as “having at least,” the term “includes” should be interpreted as “includes but is not limited to,” etc.).
  • the terms “treat,” “treatment,” “treating,” or “amelioration” when used in reference to a disease, disorder or medical condition refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent, reverse, alleviate, ameliorate, inhibit, lessen, slow down or stop the progression or severity of a symptom or condition.
  • the term “treating” includes reducing or alleviating at least one adverse effect or symptom of a condition. Treatment is generally “effective” if one or more symptoms or clinical markers are reduced. Alternatively, treatment is “effective” if the progression of a disease, disorder or medical condition is reduced or halted.
  • treatment includes not just the improvement of symptoms or markers, but also a cessation or at least slowing of progress or worsening of symptoms that would be expected in the absence of treatment. Also, “treatment” may mean to pursue or obtain beneficial results, or lower the chances of the individual developing the condition even if the treatment is ultimately unsuccessful. Those in need of treatment include those already with the condition as well as those prone to have the condition or those in whom the condition is to be prevented.
  • “Beneficial results” or “desired results” may include, but are in no way limited to, lessening or alleviating the severity of the disease condition, preventing the disease condition from worsening, curing the disease condition, preventing the disease condition from developing, lowering the chances of a patient developing the disease condition, decreasing morbidity and mortality, and prolonging a patient's life or life expectancy.
  • "beneficial results” or “desired results” may be alleviation of one or more symptom(s), diminishment of extent of the deficit, stabilized (i.e., not worsening) state of a tumor, delay or slowing of a tumor, and amelioration or palliation of symptoms associated with a tumor.
  • disorders may include, but are in no way limited to any form of malignant neoplastic cell proliferative disorders or diseases. Examples of such disorders include but are not limited to cancer and tumor.
  • a “cancer” or “tumor” as used herein refers to an uncontrolled growth of cells which interferes with the normal functioning of the bodily organs and systems, and/or all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.
  • a subject that has a cancer or a tumor is a subject having objectively measurable cancer cells present in the subject's body. Included in this definition are benign and malignant cancers, as well as dormant tumors or micrometastasis. Cancers which migrate from their original location and seed vital organs can eventually lead to the death of the subject through the functional deterioration of the affected organs.
  • the term "invasive” refers to the ability to infiltrate and destroy surrounding tissue.
  • cancer include, but are not limited to, nervous system tumor, nerve sheath tumor, and brain tumor or cancer.
  • brain tumor include, but are not limited to, benign brain tumor, malignant brain tumor, primary brain tumor, secondary brain tumor, metastatic brain tumor, glioma, glioblastoma multiforme (GBM), medulloblastoma, ependymoma, astrocytoma, pilocytic astrocytoma, oligodendroglioma, brainstem glioma, optic nerve glioma, mixed glioma such as oligoastrocytoma, low-grade glioma, high-grade glioma, supratentorial glioma, infratentorial glioma, pontine glioma, meningioma, pituitary adenoma, and nerve sheath
  • Nervous system tumor or nervous system neoplasm refers to any tumor affecting the nervous system.
  • a nervous system tumor can be a tumor in the central nervous system (CNS), in the peripheral nervous system (PNS), or in both CNS and PNS.
  • Examples of nervous system tumor include but are not limited to brain tumor, nerve sheath tumor, and optic nerve glioma.
  • administering refers to the placement an agent as disclosed herein into a subject by a method or route which results in at least partial localization of the agents at a desired site.
  • Route of administration may refer to any administration pathway known in the art, including but not limited to aerosol, nasal, oral, transmucosal, transdermal, parenteral, enteral, topical or local.
  • Parenteral refers to a route of administration that is generally associated with injection, including intracranial, intraventricular, intrathecal, epidural, intradural, intraorbital, infusion, intraarterial, intracapsular, intracardiac, intradermal, intramuscular, intraperitoneal, intrapulmonary, intraspinal, intrasternal, intrathecal, intrauterine, intravenous, subarachnoid, subcapsular, subcutaneous, transmucosal, or transtracheal.
  • the compositions may be in the form of solutions or suspensions for infusion or for injection, or as lyophilized powders.
  • the pharmaceutical compositions can be in the form of tablets, gel capsules, sugar-coated tablets, syrups, suspensions, solutions, powders, granules, emulsions, microspheres or nanospheres or lipid vesicles or polymer vesicles allowing controlled release.
  • the pharmaceutical compositions can be in the form of aerosol, lotion, cream, gel, ointment, suspensions, solutions or emulsions.
  • “administering” can be self-administering. For example, it is considered as “administering” that a subject consumes a composition as disclosed herein.
  • sample or "biological sample” as used herein denotes a sample taken or isolated from a biological organism, e.g., a tumor sample from a subject.
  • exemplary biological samples include, but are not limited to, cheek swab; mucus; whole blood, blood, serum; plasma; urine; saliva; semen; lymph; fecal extract; sputum; other body fluid or biofluid; cell sample; tissue sample; tumor sample; and/or tumor biopsy etc.
  • sample also includes a mixture of the above-mentioned samples.
  • sample also includes untreated or pretreated (or pre- processed) biological samples.
  • a sample can comprise one or more cells from the subject.
  • a sample can be a tumor cell sample, e.g. the sample can comprise cancerous cells, cells from a tumor, and/or a tumor biopsy.
  • a "subject” means a human or animal. Usually the animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, and canine species, e.g., dog, fox, wolf. The terms, "patient”, “individual” and “subject” are used interchangeably herein.
  • the subject is mammal.
  • the mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but are not limited to these examples.
  • the methods described herein can be used to treat domesticated animals and/or pets.
  • "Mammal” as used herein refers to any member of the class Mammalia, including, without limitation, humans and nonhuman primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs, and the like.
  • the term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be included within the scope of this term.
  • a subject can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment (e.g., GBM) or one or more complications related to the condition, and optionally, have already undergone treatment for the condition or the one or more complications related to the condition.
  • a subject can also be one who has not been previously diagnosed as having a condition or one or more complications related to the condition.
  • a subject can be one who exhibits one or more risk factors for a condition or one or more complications related to the condition or a subject who does not exhibit risk factors.
  • a "subject in need" of treatment for a particular condition can be a subject suspected of having that condition, diagnosed as having that condition, already treated or being treated for that condition, not treated for that condition, or at risk of developing that condition.
  • statically significant refers to statistical evidence that there is a difference. It is defined as the probability of making a decision to reject the null hypothesis when the null hypothesis is actually true. The decision is often made using the p- value.
  • variants can include, but are not limited to, those that include conservative amino acid mutations, SNP variants, splicing variants, degenerate variants, and biologically active portions of a gene.
  • a "degenerate variant” as used herein refers to a variant that has a mutated nucleotide sequence, but still encodes the same polypeptide due to the redundancy of the genetic code.
  • alkylating agents refers to compounds and molecules used in cancer treatment that attach an alkyl group (C n H2 n +l) to DNA.
  • alkylating agents include but are not limited to nitrogen mustards such as cyclophosphamide, mechlorethamine or mustine (HN2), uramustine or uracil mustard, melphalan, chlorambucil, ifosfamide, and bendamustine; nitrosoureas such as carmustine (BCNU), lomustine (CCNU), and streptozocinm; alkyl sulfonates such busulfan; and thiotepa and its analogues.
  • nitrogen mustards such as cyclophosphamide, mechlorethamine or mustine (HN2), uramustine or uracil mustard, melphalan, chlorambucil, ifosfamide, and bendamustine
  • nitrosoureas such as carmustine (BCNU),
  • PI3K/AKT/mTOR inhibitor also interchangeably called as PI3K/AKT/mTOR blocker, anti-PI3K/AKT/mTOR reagent, agent, drug or therapeutic, refers to any reagent that inhibits the PI3K/AKT/mTOR signaling, including inhibition of any molecular signaling steps upstream or downstream of PI3K/AKT/mTOR.
  • a PI3K/AKT/mTOR inhibitor can be a small molecule; a nucleic acid such as siRNA, shRNA, and miRNA; a nucleic acid analogue such as PNA, pc-PNA, and LNA; an aptamer; a ribosome; a peptide; a protein; an avimer; an antibody, or variants and fragments thereof.
  • PI3K/AKT/mTOR inhibitor examples include but are not limited to wortmannin, demethoxyviridin, LY294002, perifosine, idelalisib, PX-866, IPI-145, BAY 80-6946, BEZ235, RP6530, TGR 1202, SF1 126, INK1117, GDC-0941 , BKM120, XL147 (also known as SAR245408), XL765 (also known as SAR245409), Palomid, GSK1059615, ZSTK474, PWT33597, IC87114, TG100-115, CAL263, RP6503, PI-103, GNE-477, CUDC-907, and AEZS-136; VQD-002, miltefosine, and AZD5363; rapamycin, temsirolimus, evirolimus, ridaforolimus, epigallocatechin gallate (EGCG), caffeine
  • IDH means isocitrate dehydrogenase.
  • SEQ ID NO: 1 sets forth one non-limiting example of an IDH1 gene sequence.
  • the inventors found the distribution for alterations in glioma-associated genes in subgroups. It was found that subgroup 5 was enriched in tumors with IDH mutations. For example, IDH mutations in glioma may be found at arginine 132 (R132) residue of isocitrate dehydrogenase I (IDH1) or the R172 residue of IDH2.
  • SEQ ID NO:2 sets forth one non-limiting example of an IDH1 sequence, that is, the cDNA sequence of one variant of IDH1.
  • SEQ ID NO:3 sets forth another non-limiting example of an IDH1 sequence, that is, the cDNA sequence of another variant of IDH1.
  • SEQ ID NO:4 sets forth one non-limiting example of an IDH2 gene sequence.
  • PI3K/Akt pathway is one of the 3 core pathways consistently altered in GBM. It often leads to activation of Akt.
  • Akt is an oncogenic serine/threonine kinase that regulates metabolism, survival, autophagy, proliferation, migration, epithelial to mesenchymal (EMT) transition and angiogenesis.
  • EMT epithelial to mesenchymal
  • the pathway is a large and complex with many regulators, activators, effectors and feedback loops.
  • the GFR/PI3K/Akt pathway is an important therapeutic target in glioblastoma (GB), but in the past, response to pathway inhibitors in clinical trials has been lackluster.
  • the inventors examined whether AKT pathway variations contribute to poor response, and classified GBM based on AKT pathway genes. There were at least 5 GBM AKT subgroups. They were concordant with other found subgroups but subdivided them further to give new groups with distinct features. AKT subgroups had different molecular alterations and median survival.
  • IDHl isocitrate dehydrogenase I
  • the present invention provides a method of diagnosing a cancer subtype in a subject comprising obtaining a sample from the subject, assaying the sample to determine an AKT expression profile, and diagnosing the cancer subtype based on the AKT expression profile.
  • the cancer is GBM.
  • the subject is human.
  • the subtype is characterized by a cluster defined by the distribution of alterations in glioma associated genes.
  • the AKT expression profile is defined by a cluster of distribution of alterations in glioma associated genes in the AKT signaling pathway.
  • the cancer subtype is a cancer subtype of GBM.
  • the cancer subtype includes the presence of tumors enriched with one or more IDHl and/or IDH2 mutations.
  • the present invention provides a method of diagnosing a cancer subtype in a subject comprising obtaining a sample from the subject, assaying the sample to determine the presence or absence of IDHl and/or IDH2 mutations, and diagnosing the cancer subtype based on the presence of IDHl and/or IDH2 mutations.
  • the cancer is GBM.
  • the individual is a human.
  • the presence of one or more IDHl and/or IDH2 mutations relative to a normal individual is indicative of the cancer subtype AKT subgroup 5.
  • the present invention provides a method of prognosing GBM disease by diagnosing a GBM disease subtype based on the AKT expression profile, and determining the severity of the disease based on the GBM disease subtype.
  • the present invention provides for a method of treating a subject for cancer comprising obtaining a sample from the subject, assaying the sample to determine a cancer subtype based on what is the AKT expression profile, and treating the subject.
  • the cancer is GBM.
  • the subject is human.
  • the subtype is characterized by a cluster defined by the distribution of alterations in glioma associated genes.
  • the treatment comprises administering a therapeutically effective dosage of a composition comprising one or more alkylating agents to the individual. In another embodiment, the treatment comprises administering a therapeutically effective dosage of a composition comprising one or more PI3K/Akt/mTOR inhibitors to the individual.
  • the present invention provides for a method of treating GBM in a subject comprising obtaining a sample from the subject, assaying the sample to diagnose a GBM subtype based on the presence of an AKT expression profile, and treating the subject.
  • the AKT subgroup includes the presence of one or more IDH1 and/or IDH2 mutations.
  • the present invention provides a method of treating an individual for cancer by obtaining a sample from the individual, assaying the sample to determine the presence of one or more IDH1 and/or IDH2 mutations, and treating the individual.
  • treating the individual comprises administration of a therapeutically effective dosage of a composition comprising one or more alkylating agents to the individual.
  • the one or more IDH1 mutations include mutation of arginine 132 (R132) residue of isocitrate dehydrogenase I (IDH1).
  • the one or more IDH2 mutations include the mutation of arginine 172 (R172) residue of IDH2.
  • assaying the sample includes determining the presence of a GBM tumor enriched with one or more IDH1 and/or IDH2 mutations.
  • GFR/PI3K/AKT pathway inhibitors Activity of GFR/PI3K/AKT pathway inhibitors in glioblastoma clinical trials has not been robust. While not wishing to be bound by any theory, the inventors believe that variations in the pathway between tumors contribute to poor response. The inventors clustered GBM based on AKT pathway genes and discovered new subtypes then characterized their clinical and molecular features. There are at least 5 GBM AKT subtypes having distinct DNA copy number alterations, enrichment in oncogenes and tumor suppressor genes and patterns of expression for PI3K/AKT/mTOR signaling components. Gene Ontology terms indicate a different cell of origin or dominant phenotype for each subgroup. Evidence suggests one subtype is very sensitive to BCNU or CCNU (median survival 5.8 vs.
  • AKT subtyping advances previous approaches by revealing additional subgroups with unique clinical and molecular features. Evidence indicates it is a predictive marker for response to BCNU or CCNU and PI3K/AKT/mTOR pathway inhibitors. The inventors demonstrate that Akt subtyping helps stratify patients for clinical trials and augments discovery of class-specific therapeutic targets. Classification and Diagnosis Methods
  • the present invention provides a method for classifying a cancer in a subject.
  • the method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining an expression pattern of AKT pathway components in the biological sample; and classifying the cancer based on the determined expression pattern of AKT pathway components in the biological sample.
  • said classifying comprises classifying the cancer into CI , PN, MES, CLAS, SL, or PROLIF subtype if the biological sample's expression pattern of AKT pathway components is determined to be CI , PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components.
  • Non-limiting examples of CI , PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components may be found in Figure 10.
  • the present invention provides a method for diagnosing whether a subject has a cancer subtype.
  • the method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether an expression pattern of AKT pathway components is present in the biological sample; and diagnosing the subject as having the cancer subtype if the expression pattern of AKT pathway components is determined to be present in the biological sample.
  • the method comprises administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer subtype.
  • the cancer subtype is CI, PN, MES, CLAS, SL, or PROLIF subtype.
  • the expression pattern is CI , FN, MES, CLAS, SL, or PROOF subtype's expression pattern of AKT pathway components.
  • the cancer is a brain tumor, glioma, or GBM.
  • the subject is a human.
  • the subject is a mammalian subject including but not limited to human, monkey, ape, dog, cat, cow, horse, goat, pig, rabbit, mouse and rat.
  • the biological sample comprises a cell, neuron, glia, brain cell, spinal cord cell, brain neuron, brain glia, spinal cord neuron, or spinal cord glia, or a combination thereof.
  • the biological sample comprises a tumor cell or tissue.
  • the biological sample comprises a tumor biopsy or sample.
  • the AKT pathway components comprise one classifier listed in
  • the AKT pathway components comprise two classifiers listed in Table 2. In various embodiments, the AKT pathway components comprise three classifiers listed in Table 2. In various embodiments, the AKT pathway components comprise four classifiers listed in Table 2. In various embodiments, the AKT pathway components comprise five or more classifiers listed in Table 2. In various embodiments, the AKT pathway components comprise all classifiers listed in Table 2.
  • the AKT pathway components comprise ACLY, AKT1, ATXN1, BCL10, CCND1, CDC37, CDK IA, CDK IB, CFD, CHEK1, EGFR, EIF3B, EIF3E, EIF3G, EIF3H, EIF4EBP 1 , EPAS1 , EZH2, FGFR2, FGFR3, FOX03, FYN, GAB1, GAB2, GRB10, GSK3B, HIF1A, HSP90AB1 , HSP90B1 , INPP5D, IRS1, IRS2, KDR, KRAS, MAP3K5, MAPK8IP1 , NRAS, PALLD, PDGFA, PDGFC, PDGFD, PDGFRB, PDKl, PHLPPl, PIK3C2B, PIK3CA, PIK3R1, PKD2, PKN2, PPARGC1A, PPP2R1A, PPP2R2B, RAF
  • said determining is performed by: contacting the biological sample with one or more detection agents that specifically bind to one or more AKT pathway components; and detecting the level of binding between the one or more detection agents and the one or more AKT pathway components.
  • the one or more detection agents are oligonucleotide probes, nucleic acids, DNAs, RNAs, peptides, proteins, antibodies, aptamers, or small molecules, or a combination thereof.
  • said detecting is performed by using a microarray.
  • the microarray is an oligonucleotide microarray, DNA microarray, cDNA microarrays, RNA microarray, peptide microarray, protein microarray, or antibody microarray, or a combination thereof.
  • the method further comprises selecting, choosing or prescribing a therapeutic for the subject after diagnosis. In various embodiments, the method further comprises instructing or directing the subject to receive a therapeutic after diagnosis. In various embodiments, the method further comprises administering a therapeutically effective amount of a therapeutic to the subject, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the diagnosed cancer subtype.
  • the present invention provides a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject.
  • the method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether an expression pattern of AKT pathway components is present in the biological sample; providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject if the expression pattern of AKT pathway components is determined to be present in the biological sample, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of the cancer subtype.
  • the cancer subtype is CI, PN, MES, CLAS, SL, or PROLIF subtype.
  • the expression pattern is CI, PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components.
  • Non-limiting examples of CI , PN, MES, CLAS, SL, or PROLIF subtype's expression pattern of AKT pathway components may be found in Figure 10.
  • the present invention provides a method for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of SL cancer subtype in a subject.
  • the method may consist of or may consist essentially of or may comprise: obtaining a biological sample from the subject; determining whether SL subtype's expression pattern of AKT pathway components is present in the biological sample; providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject if SL subtype's expression pattern of AKT pathway components is determined to be present in the biological sample, thereby treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of SL cancer subtype.
  • the present invention provides a method for treating an AKT cancer subtype in a subject.
  • the method may consist of or may consist essentially of or may comprise: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating the AKT cancer subtype in the subject.
  • the cancer subtype is CI, PN, MES, CLAS, SL, or PROLIF subtype.
  • the present invention provides a method for treating SL cancer subtype in a subject.
  • the method may consist of or may consist essentially of or may comprise: providing a therapeutic; and administering a therapeutically effective amount of the therapeutic to the subject, thereby treating SL cancer subtype in the subject.
  • the present invention provides a method for treating an AKT cancer subtype in a subject.
  • the method comprises administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the AKT cancer subtype, thereby treating the AKT cancer subtype in the subject.
  • the cancer subtype is CI, PN, MES, CLAS, SL, or PROLIF subtype.
  • the subject has been diagnosed with the AKT cancer subtype via methods as described in the present invention.
  • the method may further comprise providing the therapeutic.
  • the present invention provides a method for treating SL cancer subtype in a subject.
  • the method comprises administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the SL cancer subtype, thereby treating the SL cancer subtype in the subject.
  • the subject has been diagnosed with the SL cancer subtype via methods as described in the present invention.
  • the method may further comprise providing the therapeutic.
  • the present invention provides a method for treating an AKT cancer subtype in a subject.
  • the method comprises ordering a diagnostic test to determine if the subject has an AKT cancer subtype; and administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the AKT cancer subtype, thereby treating the AKT cancer subtype in the subject.
  • the diagnostic test is performed via methods as described in the present invention.
  • the cancer subtype is CI , PN, MES, CLAS, SL, or PROLIF subtype.
  • the method may further comprise providing the therapeutic.
  • the present invention provides a method for treating SL cancer subtype in a subject.
  • the method comprises ordering a diagnostic test to determine if the subject has SL cancer subtype; and administering a therapeutically effective amount of the therapeutic to the subject who has been diagnosed with the SL cancer subtype, thereby treating the SL cancer subtype in the subject.
  • the diagnostic test is performed via methods as described in the present invention.
  • the method may further comprise providing the therapeutic.
  • the cancer is a brain tumor, glioma, or GBM.
  • the subject is a human.
  • the subject is a mammalian subject including but not limited to human, monkey, ape, dog, cat, cow, horse, goat, pig, rabbit, mouse and rat.
  • the biological sample comprises a cell, neuron, glia, brain cell, spinal cord cell, brain neuron, brain glia, spinal cord neuron, or spinal cord glia, or a combination thereof.
  • the biological sample comprises a tumor cell or tissue.
  • the biological sample comprises a tumor biopsy or sample.
  • the therapeutic is a nucleic acid, DNA, RNA, peptide, protein, antibody, aptamer, or small molecule, or a combination thereof.
  • the therapeutic is an alkylating agent, or a PI3K/AKT/mTOR inhibitor, or a combination thereof.
  • the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof.
  • Typical dosages of an effective amount of the therapeutic can be in the ranges recommended by the manufacturer where known therapeutic molecules or compounds are used, and also as indicated to the skilled artisan by the in vitro responses in cells or in vivo responses in animal models. Such dosages typically can be reduced by up to about an order of magnitude in concentration or amount without losing relevant biological activity.
  • the actual dosage can depend upon the judgment of the physician, the condition of the patient, and the effectiveness of the therapeutic method based, for example, on the in vitro responsiveness of relevant cultured cells or histocultured tissue sample, or the responses observed in the appropriate animal models.
  • the therapeutic may be administered once a day (SID/QD), twice a day (BID), three times a day (TID), four times a day (QID), or more, so as to administer an effective amount of the therapeutic to the subject, where the effective amount is any one or more of the doses described herein.
  • the therapeutic is administered at about 0.001-0.01 , 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600- 700, 700-800, 800-900, or 900-1000 mg/m 2 , or a combination thereof.
  • the therapeutic is administered at about 0.001-0.01, 0.01-0.1, 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/kg, or a combination thereof.
  • the therapeutic is administered once, twice, three or more times. In various embodiments, the therapeutic is administered about 1-3 times per day, 1-7 times per week, 1-9 times per month, or 1-12 times per year. In various embodiments, the therapeutic is administered for about 1-10 days, 10-20 days, 20-30 days, 30-40 days, 40-50 days, 50-60 days, 60-70 days, 70-80 days, 80-90 days, 90-100 days, 1-6 months, 6- 12 months, or 1-5 years.
  • “mg/kg” refers to mg per kg body weight of the subject
  • mg/m2 refers to mg per m2 body surface area of the subject.
  • the therapeutic is administered to a human.
  • the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof.
  • the effective amount of the therapeutic is any one or more of about 0.001-0.01 , 0.01-0.1 , 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300- 400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 ⁇ g/kg/day, or a combination thereof.
  • the effective amount of the therapeutic is any one or more of about 0.001-0.01 , 0.01-0.1 , 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300- 400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 ⁇ g/m 2 /day, or a combination thereof.
  • the effective amount of the therapeutic is any one or more of about 0.001-0.01 , 0.01-0.1 , 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300- 400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/kg/day, or a combination thereof.
  • the effective amount of the therapeutic is any one or more of about 0.001-0.01 , 0.01-0.1 , 0.1-0.5, 0.5-5, 5-10, 10-20, 20-50, 50-100, 100-200, 200-300, 300- 400, 400-500, 500-600, 600-700, 700-800, 800-900, or 900-1000 mg/m 2 /day, or a combination thereof.
  • ' g/kg/day" or “mg/kg/day” refers to ⁇ g or mg per kg body weight of the subject per day
  • ' g/m2/day or "mg/m2/day” refers to ⁇ g or mg per m2 body surface area of the subject per day.
  • the therapeutic may be administered at the prevention stage of a condition (i.e., when the subject has not developed the condition but is likely to or in the process to develop the condition).
  • the therapetuic may be administered at the treatment stage of a condition (i.e., when the subject has already developed the condition).
  • the target condition is GBM.
  • the patient may be treated with the methods described herein when the patient has not yet developed GBM, or is likely to develop GBM, or is in the process of developing GBM, or has already developed GBM.
  • the therapeutic may be administered using the appropriate modes of administration, for instance, the modes of administration recommended by the manufacturer for each of the therapeutic.
  • various routes may be utilized to administer the therapeutic of the claimed methods, including but not limited to aerosol, nasal, oral, transmucosal, transdermal, parenteral, enteral, topical, local, implantable pump, continuous infusion, capsules and/or injections.
  • the therapeutic is administered intracranially, intraventricularly, intrathecally, epidurally, intradurally, topically, intravascularly, intravenously, intraarterially, intratumorally, intramuscularly, subcutaneously, intraperitoneally, intranasally, or orally.
  • the therapeutic is provided as a pharmaceutical composition.
  • the composition is formulated for via any route of administration, including but not limited to intracranial, intraventricular, intrathecal, epidural, intradural, topical, intravascular, intravenous, intraarterial, intratumoral, intramuscular, subcutaneous, intraperitoneal, intranasal or oral administration. Methods for these administrations are known to one skilled in the art. Preferred pharmaceutical compositions will also exhibit minimal toxicity when administered to a mammal.
  • the pharmaceutical compositions according to the invention can contain any pharmaceutically acceptable excipient.
  • “Pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and desirable, and includes excipients that are acceptable for veterinary use as well as for human pharmaceutical use. Such excipients may be solid, liquid, semisolid, or, in the case of an aerosol composition, gaseous.
  • excipients include but are not limited to starches, sugars, microcrystalline cellulose, diluents, granulating agents, lubricants, binders, disintegrating agents, wetting agents, emulsifiers, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservatives, antioxidants, plasticizers, gelling agents, thickeners, hardeners, setting agents, suspending agents, surfactants, humectants, carriers, stabilizers, and combinations thereof.
  • the pharmaceutical compositions according to the invention can contain any pharmaceutically acceptable carrier.
  • “Pharmaceutically acceptable carrier” as used herein refers to a pharmaceutically acceptable material, composition, or vehicle that is involved in carrying or transporting a compound of interest from one tissue, organ, or portion of the body to another tissue, organ, or portion of the body.
  • the carrier may be a liquid or solid filler, diluent, excipient, solvent, or encapsulating material, or a combination thereof.
  • Each component of the carrier must be “pharmaceutically acceptable” in that it must be compatible with the other ingredients of the formulation.
  • compositions according to the invention can also be encapsulated, tableted or prepared in an emulsion or syrup for oral administration.
  • Pharmaceutically acceptable solid or liquid carriers may be added to enhance or stabilize the composition, or to facilitate preparation of the composition.
  • Liquid carriers include syrup, peanut oil, olive oil, glycerin, saline, alcohols and water.
  • Solid carriers include starch, lactose, calcium sulfate, dihydrate, terra alba, magnesium stearate or stearic acid, talc, pectin, acacia, agar or gelatin.
  • the carrier may also include a sustained release material such as glyceryl monostearate or glyceryl distearate, alone or with a wax.
  • the pharmaceutical preparations are made following the conventional techniques of pharmacy involving dry milling, mixing, and blending for powder forms; milling, mixing, granulation, and compressing, when necessary, for tablet forms; or milling, mixing and filling for hard gelatin capsule forms.
  • a liquid carrier When a liquid carrier is used, the preparation will be in the form of a syrup, elixir, emulsion or an aqueous or non-aqueous suspension.
  • Such a liquid formulation may be administered directly p.o. or filled into a soft gelatin capsule.
  • the pharmaceutical compositions according to the invention may be delivered in a therapeutically effective amount.
  • the precise therapeutically effective amount is that amount of the composition that will yield the most effective results in terms of efficacy of treatment in a given subject.
  • This amount will vary depending upon a variety of factors, including but not limited to the characteristics of the therapeutic compound (including activity, pharmacokinetics, pharmacodynamics, and bioavailability), the physiological condition of the subject (including age, sex, disease type and stage, general physical condition, responsiveness to a given dosage, and type of medication), the nature of the pharmaceutically acceptable carrier or carriers in the formulation, and the route of administration.
  • One skilled in the clinical and pharmacological arts will be able to determine a therapeutically effective amount through routine experimentation, for instance, by monitoring a subject's response to administration of a compound and adjusting the dosage accordingly. For additional guidance, see Remington: The Science and Practice of Pharmacy (Gennaro ed. 20th edition, Williams & Wilkins PA, USA) (2000).
  • formulants may be added to the composition.
  • a liquid formulation may be preferred.
  • these formulants may include oils, polymers, vitamins, carbohydrates, amino acids, salts, buffers, albumin, surfactants, bulking agents or combinations thereof.
  • Carbohydrate formulants include sugar or sugar alcohols such as monosaccharides, disaccharides, or polysaccharides, or water soluble glucans.
  • the saccharides or glucans can include fructose, dextrose, lactose, glucose, mannose, sorbose, xylose, maltose, sucrose, dextran, pullulan, dextrin, alpha and beta cyclodextrin, soluble starch, hydroxethyl starch and carboxymethylcellulose, or mixtures thereof.
  • “Sugar alcohol” is defined as a C4 to C8 hydrocarbon having an -OH group and includes galactitol, inositol, mannitol, xylitol, sorbitol, glycerol, and arabitol. These sugars or sugar alcohols mentioned above may be used individually or in combination. There is no fixed limit to amount used as long as the sugar or sugar alcohol is soluble in the aqueous preparation. In one embodiment, the sugar or sugar alcohol concentration is between 1.0 w/v % and 7.0 w/v %, more preferable between 2.0 and 6.0 w/v %.
  • Amino acids formulants include levorotary (L) forms of carnitine, arginine, and betaine; however, other amino acids may be added.
  • Polymers formulants include polyvinylpyrrolidone (PVP) with an average molecular weight between 2,000 and 3,000, or polyethylene glycol (PEG) with an average molecular weight between 3,000 and 5,000.
  • a buffer in the composition it is also preferred to use a buffer in the composition to minimize pH changes in the solution before lyophilization or after reconstitution.
  • Most any physiological buffer may be used including but not limited to citrate, phosphate, succinate, and glutamate buffers or mixtures thereof.
  • the concentration is from 0.01 to 0.3 molar.
  • Surfactants that can be added to the formulation are shown in EP Nos. 270,799 and 268,1 10.
  • liposome Another drug delivery system for increasing circulatory half- life is the liposome.
  • Methods of preparing liposome delivery systems are discussed in Gabizon et ah, Cancer Research (1982) 42:4734; Cafiso, Biochem Biophys Acta (1981) 649: 129; and Szoka, Ann Rev Biophys Eng (1980) 9:467.
  • Other drug delivery systems are known in the art and are described in, e.g., Poznansky et al, DRUG DELIVERY SYSTEMS (R. L. Juliano, ed., Oxford, N.Y. 1980), pp. 253-315; M. L. Poznansky, Pharm Revs (1984) 36:277.
  • the liquid pharmaceutical composition may be lyophilized to prevent degradation and to preserve sterility.
  • Methods for lyophilizing liquid compositions are known to those of ordinary skill in the art.
  • the composition may be reconstituted with a sterile diluent (Ringer's solution, distilled water, or sterile saline, for example) which may include additional ingredients.
  • a sterile diluent Finger's solution, distilled water, or sterile saline, for example
  • the composition is administered to subjects using those methods that are known to those skilled in the art.
  • compositions of the invention may be sterilized by conventional, well-known sterilization techniques.
  • the resulting solutions may be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.
  • the compositions may contain pharmaceutically-acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, and stabilizers (e.g., 1-20% maltose, etc.).
  • the pharmaceutical composition according to the invention can also be a bead system for delivering the therapeutic agent to the target cells.
  • pectin/zein hydrogel bead system may be used to deliver Neuregulin-4 or a pharmaceutical equivalent, analog, derivative or a salt thereof, to the target cells in the subject (Yan F. et al., J Clin Invest. 2011 Jun; 121(6):2242-53).
  • the present invention is also directed to a kit that is used to classify, diagnose and/or treat cancers.
  • the kit is an assemblage of materials or components, including at least one of the inventive elements or modules.
  • the kit contains one or more detection agents that specifically bind to one or more AKT pathway components, as described above; and in other embodiments the kit contains a cancer therapeutic, as described above.
  • the kit contains a composition including a drug delivery molecule complexed with a cancer therapeutic, as described above.
  • the present invention provides a kit for classifying a cancer in a subject.
  • the kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; instructions for using the one or more detection agents to classify the cancer in the subject.
  • the present invention provides a kit for diagnosing whether a subject has a cancer subtype.
  • the kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; instructions for using the one or more detection agents to diagnose whether a subject has the cancer subtype.
  • the present invention provides a kit for treating, preventing, reducing the likelihood of having, reducing the severity of and/or slowing the progression of a cancer subtype in a subject.
  • the kit may consist of or may consist essentially of or may comprise: one or more detection agents that specifically bind to one or more AKT pathway components; a quantity of a therapeutic; and instructions for using the one or more detection agents and the therapeutic to treat, prevent, reduce the likelihood of having, reduce the severity of and/or slow the progression of the cancer subtype in the subject
  • the present invention provides a kit for treating an AKT cancer subtype in a subject.
  • the kit may consist of or may consist essentially of or may comprise: a quantity of a therapeutic; and instructions for using the therapeutic to treat the AKT cancer subtype in the subject.
  • the subject is a human.
  • the cancer is a brain tumor, glioma, or GBM.
  • the cancer subtype is CI, PN, MES, CLAS, SL, or PROOF subtype.
  • the one or more detection agents are applied to contact a biological sample obtained from the subject; and the level of binding between the one or more detection agents and the one or more AKT pathway components is detected to determine expression patterns of AKT pathway components.
  • the one or more detection agents are oligonucleotide probes, nucleic acids, DNAs, RNAs, peptides, proteins, antibodies, aptamers, or small molecules, or a combination thereof.
  • the level of binding is detected using a microarray.
  • the microarray is an oligonucleotide microarray, DNA microarray, cDNA microarrays, R A microarray, peptide microarray, protein microarray, or antibody microarray, or a combination thereof.
  • the therapeutic is a nucleic acid, DNA, RNA, peptide, protein, antibody, aptamer, or small molecule, or a combination thereof.
  • the therapeutic is an alkylating agent, or a PI3K/AKT/mTOR inhibitor, or a combination thereof.
  • the therapeutic is BCNU or CCNU, a functional equivalent, analog, derivative or salt of BCNU or CCNU, or a combination thereof.
  • the kit is configured particularly for the purpose of treating mammalian subjects. In another embodiment, the kit is configured particularly for the purpose of treating human subjects. In further embodiments, the kit is configured for veterinary applications, treating subjects such as, but not limited to, farm animals, domestic animals, and laboratory animals.
  • kits Instructions for use may be included in the kit. "Instructions for use” typically include a tangible expression describing the technique to be employed in using the components of the kit to affect a desired outcome.
  • the kit also contains other useful components, such as, spray bottles or cans, diluents, buffers, pharmaceutically acceptable carriers, syringes, catheters, applicators (for example, applicators of cream, gel or lotion etc.), pipetting or measuring tools, bandaging materials or other useful paraphernalia as will be readily recognized by those of skill in the art.
  • the materials or components assembled in the kit can be provided to the practitioner stored in any convenient and suitable ways that preserve their operability and utility.
  • the detection agents and/or cancer therapeutics can be in dissolved, dehydrated, or lyophilized form; they can be provided at room, refrigerated or frozen temperatures.
  • the components are typically contained in suitable packaging material(s).
  • packaging material refers to one or more physical structures used to house the contents of the kit, such as inventive compositions and the like.
  • the packaging material is constructed by well-known methods, preferably to provide a sterile, contaminant-free environment.
  • the packaging materials employed in the kit are those customarily utilized in assays and therapies.
  • the term "package” refers to a suitable solid matrix or material such as glass, plastic, paper, foil, and the like, capable of holding the individual kit components.
  • a package can be a glass vial used to contain suitable quantities of a composition as described herein.
  • the packaging material generally has an external label which indicates the contents and/or purpose of the kit and/or its components.
  • the present invention is also directed to a composition that is used to classify and/or diagnose cancers and cancer subtyps.
  • the composition comprises one or more detection agents that specifically bind to one or more AKT pathway components, as described herein; and a biological sample from a subject desiring a classification or diagnosis regarding a cancer.
  • the composition comprises one or more detection agents that specifically bind to one or more AKT pathway components; as described herein; and a biological sample from a subject desiring a classification regarding a cancer.
  • the composition one or more detection agents that specifically bind to one or more AKT pathway components; and a biological sample from a subject desiring a subject diagnosis on whether he/she has the cancer subtype.
  • the cancer subtype is CI , PN, MES, CLAS, SL, or PROLIF subtype.
  • the methods of the invention implement a computer program to calculate a copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression levels.
  • a computer program can be used to perform the algorithms described herein.
  • a computer system can also store and manipulate data generated by the methods of the present invention which comprises a plurality of hybridization signal changes/pro files during approach to equilibrium in different hybridization measurements and which can be used by a computer system in implementing the methods of this invention.
  • a computer system receives probe hybridization data; (ii) stores probe hybridization data; and (iii) compares probe hybridization data to determine the state of AKT pathway components and genomic loci in a biological sample from cancerous or pre-cancerous tissue.
  • a computer system (i) compares the determined copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression levels to a threshold value or reference value; and (ii) outputs an indication of whether said copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression levels is above or below a threshold value, or a genetic signature based on said indication.
  • such computer systems are also considered part of the present invention.
  • the software components can comprise both software components that are standard in the art and components that are special to the present invention (e.g. , dCHIP software described in Lin et al. (2004) Bioinformatics 20, 1233-1240; CRLMM software described in Silver et al. (2007) Cell 128, 991-1002; Aroma Affymetrix software described in Richardson et al. (2006) Cancer Cell 9, 121-132.
  • the methods of the invention can also be programmed or modeled in mathematical software packages that allow symbolic entry of equations and high- level specification of processing, including specific algorithms to be used, thereby freeing a user of the need to procedurally program individual equations and algorithms.
  • the computer comprises a database for storage of hybridization signal profiles. Such stored profiles can be accessed and used to calculate a copy number, copy number loss, copy number gain, LOH, mutation, deletion and expression level.
  • hybridization signal profile of a sample derived from the non-cancerous tissue of a subject and/or profiles generated from population-based distributions of AKT pathway components and genomic loci in relevant populations of the same species were stored, it could then be compared to the hybridization signal profile of a sample derived from the cancerous tissue of the subject.
  • other, alternative program structures and computer systems will be readily apparent to the skilled artisan. Such alternative systems, which do not depart from the above described computer system and programs structures either in spirit or in scope, are therefore intended to be comprehended within the accompanying claims.
  • a laboratory technician or laboratory professional or group of laboratory technicians or laboratory professionals determines whether a sample has a copy number, copy number gain, copy number loss, or expression level as described above (e.g., step (1) in many of the methods above)
  • the same or a different laboratory technician or laboratory professional can analyze a plurality of tests of AKT pathway components and genomic loci to determine whether there is a copy number, copy number loss, copy number gain, LOH, mutation, or deletion to determine the expression levels (e.g., step (2) in many of the methods above).
  • the same or a different laboratory technician or laboratory professional can combine copy number, copy number loss, copy number gain, LOH, mutation, or deletion, or expression level data from the test of AKT pathway components and genomic loci to derive a copy number, copy number loss, copy number gain, LOH, mutation, or deletion, or expression level (e.g., step (3) in many of the methods above).
  • the same or a different laboratory technician or laboratory professional can correlate the copy number, copy number loss, LOH, mutation, or deletion, or expression level to an increased or decreased likelihood of response to a particular therapy (e.g., those mentioned above).
  • a computer readable storage medium comprising: a storing data module containing data from a sample comprising a cancer cell obtained from a subject that represents an expression level from an assay for AKT pathway components and genomic loci; a comparison module that compares the data stored on the storing data module with a reference data and/or control data, and to provide a comparison content, and an output module displaying the comparison content for the user, wherein the expression pattern of AKT pathway components and genomic loci indicates that the subject is has a certain AKT cancer subtype and an appropriate therapy that is likely effective to this AKT cancer subtype should be selected or prescribed and administered to the subject as the subject may not adequately respond to other therapies. Also, the subject may be instructed to take the appropriate therapy that is likely effective to his or her AKT cancer subtype.
  • control data comprises data from a population of cancer patients. In various embodiments, the control data comprises data from a population of non- cancerous healthy individuals. In various embodiments, the control data comprises data from a housekeeping gene expression.
  • Embodiments of the invention can be described through functional modules, which are defined by computer executable instructions recorded on computer readable media and which cause a computer to perform method steps when executed.
  • the modules are segregated by function, for the sake of clarity. However, it should be understood that the modules/systems need not correspond to discreet blocks of code and the described functions can be carried out by the execution of various code portions stored on various media and executed at various times. Furthermore, it should be appreciated that the modules may perform other functions, thus the modules are not limited to having any particular functions or set of functions.
  • the computer readable storage media can be any available tangible media that can be accessed by a computer.
  • Computer readable storage media includes volatile and nonvolatile, removable and non-removable tangible media implemented in any method or technology for storage of information such as computer readable instructions, data structures, program modules or other data.
  • Computer readable storage media includes, but is not limited to, RAM (random access memory), ROM (read only memory), EPROM (erasable programmable read only memory), EEPROM (electrically erasable programmable read only memory), flash memory or other memory technology, CD-ROM (compact disc read only memory), DVDs (digital versatile disks), BLU-RAY disc or other optical storage media, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage media, other types of volatile and non-volatile memory, and any other tangible medium which can be used to store the desired information and which can accessed by a computer including and any suitable combination of the foregoing.
  • Computer-readable data embodied on one or more computer-readable media may define instructions, for example, as part of one or more programs that, as a result of being executed by a computer, instruct the computer to perform one or more of the functions described herein, and/or various embodiments, variations and combinations thereof.
  • Such instructions may be written in any of a plurality of programming languages, for example, Java, J#, Visual Basic, C, C#, C++, Fortran, Pascal, Eiffel, Basic, COBOL assembly language, and the like, or any of a variety of combinations thereof.
  • the computer-readable media on which such instructions are embodied may reside on one or more of the components of either of a system, or a computer readable storage medium described herein, may be distributed across one or more of such components.
  • the computer-readable media may be transportable such that the instructions stored thereon can be loaded onto any computer resource to implement the aspects of the present invention discussed herein.
  • the instructions stored on the computer-readable medium, described above are not limited to instructions embodied as part of an application program running on a host computer. Rather, the instructions may be embodied as any type of computer code (e.g., software or microcode) that can be employed to program a computer to implement aspects of the present invention.
  • the computer executable instructions may be written in a suitable computer language or combination of several languages.
  • the functional modules of certain embodiments of the invention include for example, at a measuring module, a storage module, a comparison module, and an output module.
  • the functional modules can be executed on one, or multiple, computers, or by using one, or multiple, computer networks.
  • the measuring module has computer executable instructions to provide e.g., expression information in non-transitory computer readable form.
  • the measuring module can comprise any system for detecting the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions).
  • Such systems can include DNA microarrays, RNA expression arrays, any ELISA detection system and/or any Western blotting detection system.
  • the information determined in the determination system can be read by the storage module.
  • the "storage module” is intended to include any suitable computing or processing apparatus or other device configured or adapted for storing data or information. Examples of electronic apparatus suitable for use with the present invention include stand-alone computing apparatus, data telecommunications networks, including local area networks (LAN), wide area networks (WAN), Internet, Intranet, and Extranet, and local and distributed computer processing systems. Storage modules also include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage media, magnetic tape, optical storage media such as CD-ROM, DVD, electronic storage media such as RAM, ROM, EPROM, EEPROM and the like, general hard disks and hybrids of these categories such as magnetic/optical storage media.
  • the storage module is adapted or configured for having recorded thereon expression level or protein level information.
  • Such information may be provided in digital form that can be transmitted and read electronically, e.g., via the Internet, on diskette, via USB (universal serial bus) or via any other suitable mode of communication.
  • stored refers to a process for encoding information on the storage module.
  • Those skilled in the art can readily adopt any of the presently known methods for recording information on known media to generate manufactures comprising expression level information.
  • the reference data stored in the storage module to be read by the comparison module is, for example, expression data obtained from a population of non-cancer subjects, a population of cancer subjects, or expression data obtained from the same subject at a prior time point using the measuring module.
  • the "comparison module” can use a variety of available software programs and formats for the comparison operative to compare expression data determined in the measuring module to reference samples and/or stored reference data.
  • the comparison module is configured to use pattern recognition techniques to compare information from one or more entries to one or more reference data patterns.
  • the comparison module may be configured using existing commercially-available or freely-available software for comparing patterns, and may be optimized for particular data comparisons that are conducted.
  • the comparison module provides computer readable information related to the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions) in an individual, efficacy of treatment in an individual, and/or method for treating an individual.
  • AKT pathway components e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions
  • the comparison module may include an operating system (e.g., UNIX) on which runs a relational database management system, a World Wide Web application, and a World Wide Web server.
  • World Wide Web application includes the executable code necessary for generation of database language statements (e.g., Structured Query Language (SQL) statements).
  • SQL Structured Query Language
  • the executables will include embedded SQL statements.
  • the World Wide Web application may include a configuration file which contains pointers and addresses to the various software entities that comprise the server as well as the various external and internal databases which must be accessed to service user requests.
  • the Configuration file also directs requests for server resources to the appropriate hardware—as may be necessary should the server be distributed over two or more separate computers.
  • the World Wide Web server supports a TCP/IP protocol.
  • Local networks such as this are sometimes referred to as "Intranets.
  • An advantage of such Intranets is that they allow easy communication with public domain databases residing on the World Wide Web (e.g., the GenBank or Swiss Pro World Wide Web site).
  • users can directly access data (via Hypertext links for example) residing on Internet databases using a HTML interface provided by Web browsers and Web servers.
  • the comparison module provides a computer readable comparison result that can be processed in computer readable form by predefined criteria, or criteria defined by a user, to provide a content-based in part on the comparison result that may be stored and output as requested by a user using an output module.
  • the content based on the comparison result may be an expression value compared to a reference showing the susceptibility/adequate response or nonsusceptibility/non-adequate response from standard, conventional or certain therapy.
  • the content based on the comparison result is displayed on a computer monitor.
  • the content based on the comparison result is displayed through printable media.
  • the display module can be any suitable device configured to receive from a computer and display computer readable information to a user.
  • Non-limiting examples include, for example, general-purpose computers such as those based on Intel PENTIUM-type processor, Motorola PowerPC, Sun UltraSPARC, Hewlett-Packard PA-RISC processors, any of a variety of processors available from Advanced Micro Devices (AMD) of Sunnyvale, California, or any other type of processor, visual display devices such as flat panel displays, cathode ray tubes and the like, as well as computer printers of various types.
  • general-purpose computers such as those based on Intel PENTIUM-type processor, Motorola PowerPC, Sun UltraSPARC, Hewlett-Packard PA-RISC processors, any of a variety of processors available from Advanced Micro Devices (AMD) of Sunnyvale, California, or any other type of processor, visual display devices such as flat panel displays, cathode ray tubes and the like, as well as computer printers of various types.
  • AMD Advanced Micro Devices
  • a World Wide Web browser is used for providing a user interface for display of the content based on the comparison result.
  • modules of the invention can be adapted to have a web browser interface.
  • a user may construct requests for retrieving data from the comparison module.
  • the user will typically point and click to user interface elements such as buttons, pull down menus, scroll bars and the like conventionally employed in graphical user interfaces.
  • the present invention therefore provides for systems (and computer readable media for causing computer systems) to perform methods for selecting treatment of cancer in an individual.
  • selecting treatment refers to selecting, choosing or prescribing a cancer treatment for the individual, or instructing or directing the individual to receive a cancer treatment.
  • Systems and computer readable media described herein are merely illustrative embodiments of the invention for detecting the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions) in an individual, and are not intended to limit the scope of the invention. Variations of the systems and computer readable media described herein are possible and are intended to fall within the scope of the invention.
  • the modules of the machine, or those used in the computer readable medium may assume numerous configurations. For example, function may be provided on a single machine or distributed over multiple machines.
  • a computing system can include computer-executable instructions or a computer program (e.g., software) containing computer-executable instructions for formatting an output providing an indication the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions) or a likelihood that a cancer patient will respond to a particular cancer treatment regimen (e.g., a regimen as described above), or a combination of these items.
  • a computer program e.g., software
  • genetic loci e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions
  • a particular cancer treatment regimen e.g., a regimen as described above
  • a computing system can include computer- executable instructions or a computer program (e.g., software) containing computer- executable instructions for determining a desired cancer treatment regimen for a particular patient based at least in part on the expression patterns of AKT pathway components and status of genetic loci (e.g., copy number alterations, copy number gain or loss, LOH, mutations, amplifications and deletions).
  • a computer program e.g., software
  • a computing system can include a pre-processing device configured to process a sample (e.g., cancer cells) such that a SNP array-based assay or sequencing-based assay can be performed.
  • a sample e.g., cancer cells
  • pre-processing devices include, without limitation, devices configured to enrich cell populations for cancer cells as opposed to non- cancer cells, devices configured to lyse cells and/or extract genomic nucleic acid, and devices configured to enrich a sample for particular genomic DNA fragments.
  • determining an expression pattern of AKT pathway components in the biological sample comprises assaying mRNA levels.
  • assaying mRNA levels comprises using RNA sequencing, northern blot, in situ hybridization, hybridization array, serial analysis of gene expression (SAGE), reverse transcription PCR, realtime PCR, real-time reverse transcription PCR, quantitative PCR, or microarray, or a combination thereof.
  • assaying mRNA levels comprises contacting the biological sample with polynucleotide probes capable of specifically hybridizing to mRNA of one or more AKT pathway components and thereby forming probe-target hybridization complexes.
  • Hybridization-based RNA assays include, but are not limited to, traditional "direct probe” methods such as, northern blot or in situ hybridization (e.g., Angerer (1987) Meth. Enzymol 152: 649). The methods can be used in a wide variety of formats including, but not limited to, substrate (e.g. membrane or glass) bound methods or array -based approaches.
  • substrate e.g. membrane or glass
  • in situ hybridization assay cells are fixed to a solid support, typically a glass slide. If a nucleic acid is to be probed, the cells are typically denatured with heat or alkali.
  • the cells are then contacted with a hybridization solution at a moderate temperature to permit annealing of labeled probes specific to the nucleic acid sequence encoding the protein.
  • the targets e.g., cells
  • the probes are typically labeled, e.g., with radioisotopes or fluorescent reporters.
  • Preferred probes are sufficiently long so as to specifically hybridize with the target nucleic acid(s) under stringent conditions.
  • the preferred size range is from about 200 bases to about 1000 bases.
  • assaying mRNA levels comprises contacting the biological sample with polynucleotide primers capable of specifically hybridizing to mRNAs of genes listed in Table 2, forming primer-template hybridization complexes, and performing a PCR reaction.
  • the polynucleotide primers comprises about 15-45, 20-40, or 25-35 bp sequences that are identical (for forward primers) or complementary (for reverse primers) to sequences of genes listed in Table 2.
  • the polynucleotide primers for ACLY can comprise sequences that are identical (for forward primers) or complementary (for reverse primers) to ACLY's bp 1-20, 5-25, 10-30, 15-35, 20-40, 25-45, 30-50, so on and so forth, until the end of ACLY, 4410-4430, 4415-4435, 4420-4440, 4425-4445, 4430-4450. While not listed here exhaustively because of the space, all these polynucleotide primers for ACLY and other genes listed in Table 2 can be used in the present invention.
  • the polynucleotide primers are labeled with radioisotopes or fluorescent molecules.
  • the labeled primers emit radio or fluorescent signals
  • the PCR products containing the labeled primers can be detected and analyzed with a variety of imaging equipment.
  • Fluorogenic quantitative PCR may also be used in the methods of the invention. In fluorogenic quantitative PCR, quantitation is based on amount of fluorescence signals, e.g., TaqMan and sybr green.
  • Other suitable amplification methods include, but are not limited to, ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4: 560, Landegren, et al. (1988) Science 241 : 1077, and Barringer et al. (1990) Gene 89: 1 17), transcription amplification (Kwoh, et al. (1989) Proc.
  • determining an expression pattern of AKT pathway components in the biological sample comprises assaying protein levels.
  • assaying a protein level comprises using western blot, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, or mass spectrometry, or a combination thereof.
  • assaying protein levels comprises contacting the biological sample with antibodies capable of specifically binding to proteins encoded by genes listed in Table 2 and thereby forming antigen-antibody complexes.
  • the expression levels of proteins encoded by genes listed in Table 2, or fragments or variants thereof can be determined using antibodies specific for those individual proteins or fragments or variants thereof and detecting immunospecific binding of each antibody to its respective cognate biomarker protein.
  • Antibodies both polyclonal and monoclonal, can be produced by a skilled artisan either by themselves using well known methods or they can be manufactured by service providers who specialize making antibodies based on known protein sequences.
  • the protein sequences of AKT pathway genes are known and thus production of antibodies against them is a matter of routine.
  • production of monoclonal antibodies can be performed using the traditional hybridoma method by first immunizing mice with an antigen which may be an isolated protein of choice or fragment thereof (for example, a protein encode by a gene listed in Table 2, or a fragment thereof or a variant thereof) and making hybridoma cell lines that each produce a specific monoclonal antibody.
  • the antibodies secreted by the different clones are then assayed for their ability to bind to the antigen using, e.g., ELISA or Antigen Microarray Assay, or immuno-dot blot techniques.
  • the antibodies that are most specific for the detection of the protein of interest can be selected using routine methods and using the antigen used for immunization and other antigens as controls.
  • the antibody that most specifically detects the desired antigen and protein and no other antigens or proteins are selected for the processes, assays and methods described herein.
  • the best clones can then be grown indefinitely in a suitable cell culture medium. They can also be injected into mice (in the peritoneal cavity, surrounding the gut) where they produce an antibody-rich ascites fluid from which the antibodies can be isolated and purified.
  • the antibodies can be purified using techniques that are well known to one of ordinary skill in the art.
  • Any suitable immunoassay method may be utilized, including those which are commercially available, to determine the expression level of an AKT pathway protein or a variant thereof assayed according to the invention. Extensive discussion of the known immunoassay techniques is not required here since these are known to those of skill in the art.
  • suitable immunoassay techniques include sandwich enzyme-linked immunoassays (ELISA), radioimmunoassays (RIA), competitive binding assays, homogeneous assays, heterogeneous assays, etc.
  • “sandwich-type” assay formats can be used.
  • An alternative technique is the “competitive -type” assay.
  • the labeled probe is generally conjugated with a molecule that is identical to, or an analog of, the analyte.
  • the labeled probe competes with the analyte of interest for the available receptive material.
  • Competitive assays are typically used for detection of analytes such as haptens, each hapten being monovalent and capable of binding only one antibody molecule.
  • the detection antibody can be labeled.
  • the detection antibody is labeled by covalently linking to an enzyme, label with a fluorescent compound or metal, label with a chemiluminescent compound.
  • the detection antibody can be labeled with catalase and the conversion uses a colorimetric substrate composition comprises potassium iodide, hydrogen peroxide and sodium thiosulphate;
  • the enzyme can be alcohol dehydrogenase and the conversion uses a colorimetric substrate composition comprises an alcohol, a pH indicator and a pH buffer, wherein the pH indicator is neutral red and the pH buffer is glycine-sodium hydroxide;
  • the enzyme can also be hypoxanthine oxidase and the conversion uses a colorimetric substrate composition comprises xanthine, a tetrazolium salt and 4,5-dihydroxy-l,3-benzene disulphonic acid.
  • the detection antibody is labeled by covalently linking to an enzyme, label with a fluorescent compound or metal, or label with a
  • Direct and indirect labels can be used in immunoassays.
  • a direct label can be defined as an entity, which in its natural state, is visible either to the naked eye or with the aid of an optical filter and/or applied stimulation, e.g., ultraviolet light, to promote fluorescence.
  • colored labels which can be used include metallic sol particles, gold sol particles, dye sol particles, dyed latex particles or dyes encapsulated in liposomes.
  • Other direct labels include radionuclides and fluorescent or luminescent moieties.
  • Indirect labels such as enzymes can also be used according to the invention.
  • enzymes are known for use as labels such as, for example, alkaline phosphatase, horseradish peroxidase, lysozyme, glucose-6-phosphate dehydrogenase, lactate dehydrogenase and urease.
  • the antibody can be attached to a surface.
  • useful surfaces on which the antibody can be attached for the purposes of detecting the desired antigen include nitrocellulose, PVDF, polystyrene, and nylon.
  • detecting the level of antibodies reactive to an AKT pathway protein or a variant thereof includes contacting the sample from the cancer patient with an antibody or a fragment thereof that specifically binds an AKT pathway protein or a variant thereof, forming an antibody-protein complex between the antibody and the AKT pathway protein or the variant thereof present in the sample, washing the sample to remove the unbound antibody, adding a detection antibody that is labeled and is reactive to the antibody bound to the AKT pathway protein or a variant thereof in the sample, washing to remove the unbound labeled detection antibody and converting the label to a detectable signal, wherein the detectable signal is indicative of the level of AKT pathway protein or a variant thereof in the sample from the patient.
  • the effector component is a detectable moiety selected from the group consisting of a fluorescent label, a radioactive compound, an enzyme, a substrate, an epitope tag, electron-dense reagent, biotin, digonigenin, hapten and a combination thereof.
  • the detection antibody is labeled by covalently linking to an enzyme, labeled with a fluorescent compound or metal, labeled with a chemiluminescent compound.
  • the level of AKT pathway protein may be obtained by assaying a light scattering intensity resulting from the formation of an antibody- protein complex formed by a reaction of AKT pathway protein in the sample with the antibody, wherein the light scattering intensity of at least 10% above a control light scattering intensity indicates the likelihood of chemotherapy resistance.
  • an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all tumor samples in the discovery dataset.
  • an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all GBM samples in the discovery dataset.
  • an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all tumor samples in the validation dataset.
  • an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from all GBM samples in the validation dataset. In various embodiments, an AKT pathway gene's reference value of expression level is the AKT pathway gene's median or mean expression level from non-cancerous, non-tumorous, or non-neoplastic cells or tissues. In accordance with the present invention, AKT pathway genes include but are not limited to those listed in Table 2.
  • Reference values may be obtained by various methods known in the field.
  • one or more biopsies from one cancer patient' tumor (hereinafter “Tumor- 1”) may be collected, processed and analyzed to obtain the expression level of one AKT pathway gene (hereinafter “Gene-1") in this tumor (hereinafter “Expression-Tumor- 1 -Gene-1").
  • the same step is used to obtain Gene-1 's expression levels in another 10, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more cancer patients' tumors (hereinafter “Tumor-N), that is, “Expression- Tumor-N- Gene-1" (N is 1, 2, 3, 4, 5, 6, 7, ).
  • Gene-1 's median or mean expression level from all tumors may be used as the reference value of Gene-1 (hereinafter "REF-Gene-1”), to which Gene-l 's expression in a subject's biological sample is compared to so as to determine if Gene- l 's expression is high or low in the subject's biological sample.
  • REF-Gene-1 is the median or mean of Expression-Tumor-N-Gene-1.
  • non-limiting AKT pathway genes i.e., Gene-M
  • Table 2 To determine the expression pattern of AKT pathway genes in a subject's biological sample, one may compare one, two, three, four, five, or more AKT pathway genes' expression levels to their respective reference values.
  • expression pattern As used herein, "expression pattern”, “expression profile” and “expression signature” are exchangeable terms referring to the specific combination or setting of one or more genes' high (increased) expressions and/or low (decreased) expressions relative to reference values.
  • AKT cancer subtypes' expression patterns are the specific combinations of AKT pathway genes' high and low expressions.
  • Figure 10 shows the expression patterns of AKT MES, CLAS, PROLIF, SL and SN subtypes in the validation and discovery datasets. Among the 64 exemplar AKT pathway genes shown in Figure 10, those having high expressions relative to reference values are shown as red, and those having low expressions relative to reference values are shown as green.
  • Various statistical methods may be used to measure the differences in expression levels of an AKT pathway gene between the subject's sample and a reference value of expression level generate by computer algorithm pooling many tumor samples, as described herein, for example, all the GBM samples in the discovery dataset and/or validation dataset.
  • Various statistical methods for example, a two-tailed student t-test with unequal variation, may be used to measure the differences in expression levels of an AKT pathway gene between the subject's sample and a control sample from a normal healthy individual.
  • Various statistical methods for example, a two-tailed student t-test with unequal variation, may be used to measure the differences in expression levels of an AKT pathway gene between the subject's sample and a reference value of expression level generate by computer algorithm pooling many control samples, as described herein. A significant difference may be achieved where the p value is equal to or less than 0.05.
  • the expression level of an AKT pathway gene or a variant thereof in the subject as compared to the reference value is higher by at least or about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%. In various embodiments, the expression level of an AKT pathway gene or a variant thereof in the subject as compared to the reference value is lower by at least or about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100%.
  • the expression level ratio between an AKT pathway gene or a variant thereof in the subject and the reference value is at least or about 1.1 : 1 , 1.2: 1, 1.3: 1 , 1.4: 1, 1.5: 1, 1.6: 1 , 1.7: 1 , 1.8: 1, 1.9: 1, 2: 1 , 2.1 : 1 , 2.2: 1, 2.3: 1, 2.4: 1 , 2.5: 1, 2.6: 1 , 2.7: 1 , 2.8: 1 , 2.9: 1, 3: 1 , 4: 1 , 5: 1 , 6: 1, 7: 1 , 8: 1, 9: 1 or 10: 1 , 15: 1, 20: 1 , 25: 1, 30: 1, 35: 1, 40:1, 45:1, 50:1, 55:1, 60:1, 65:1, 70:1, 75:1, 80:1, 85:1, 90:1, 95:1, or 100:1.
  • the expression level ratio between the reference value and an AKT pathway gene or a variant thereof in the subject is at least or about 1.1:1, 1.2:1, 1.3:1, 1.4:1, 1.5:1, 1.6:1, 1.7:1, 1.8:1, 1.9:1, 2:1, 2.1:1, 2.2:1, 2.3:1, 2.4:1, 2.5:1, 2.6:1, 2.7:1, 2.8:1, 2.9:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1 or 10:1, 15:1, 20:1, 25:1, 30:1, 35:1, 40:1, 45:1, 50:1, 55:1, 60:1, 65:1, 70:1, 75:1, 80:1, 85:1, 90:1, 95:1, or 100:1.
  • the numbers expressing quantities of ingredients, properties such as concentration, reaction conditions, and so forth, used to describe and claim certain embodiments of the invention are to be understood as being modified in some instances by the term "about.” Accordingly, in some embodiments, the numerical parameters set forth in the written description and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by a particular embodiment. In some embodiments, the numerical parameters should be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of some embodiments of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as practicable. The numerical values presented in some embodiments of the invention may contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements.
  • the discovery dataset consisted of 181 GBM (WHO grade IV astrocytoma;
  • the validation dataset consisted of 583 samples; 573 GBM (16 recurrent and 3 secondary) and 10 non-neoplastic samples from The Cancer Genome Atlas (TCGA). Samples were collected and processed as described ([5] Atlas TCG 2008, which is incorporated herein by reference in its entirety as though fully set forth.). IRB or Committee on Human Research approval was obtained for samples used in the discovery and validation datasets as described [3], [4], [10], [21].
  • Table 1 Clinical information for tumors in GBM 195
  • the PI3K/AKT pathway integrates information on cellular environment, energy status, stress and developmental stage to regulate apoptosis, autophagy, translation, metabolism, stem cell function and cell cycle [20], [22]. This involves multiple sites of crosstalk with other pathways.
  • AKT upstream and downstream gene products that directly or indirectly regulate or are regulated by AKT. This includes: (1) proteins or members of protein complexes that bind to, modify or regulate activity or subcellular localization of AKT (2) proteins or members of protein complexes phosphorylated or regulated by AKT, (3) proteins known to regulate or be regulated directly or indirectly by AKT (e.g. AKT through MDM2 regulates levels of TP53 protein).
  • Table 2 AKT pathway gene classifiers used for the discovery and validation datasets discovery validation
  • CDKN1A CDKN 1A Cyclin-dependent kinase inhibitor 1A (p21, Cipl)
  • CDKN1B CDKN 1B Cyclin-dependent kinase inhibitor IB (p27, Kipl) CFD CFD Complement factor D (adipsin)
  • EIF3B EIF3B Eukaryotic translation initiation factor 3, subunit B
  • EIF3E EIF3E Eukaryotic translation initiation factor 3, subunit E
  • EIF3G EIF3G Eukaryotic translation initiation factor 3, subunit G
  • EIF4EBP1 EIF4EBP1 Eukaryotic translation initiation factor 4E binding protein 1
  • HIF1A HIF1A Hypoxia inducible factor 1, alpha subunit
  • KDR KDR Kinase insert domain receptor (a type III receptor tyrosine kinase)
  • MAP3K5 MAP3K5 Mitogen-activated protein kinase kinase kinase 5
  • PPP2R1A PPP2R1A Protein phosphatase 2, regulatory subunit A, alpha
  • PPP2R2B PPP2R2B Protein phosphatase 2, regulatory subunit B, beta
  • TSC1 TSC1 Tuberous sclerosis 1
  • AKT1S1 AKT1 substrate 1 (proline-rich)
  • IGF2 Insulin-like growth factor 2 (somatomedin A)
  • PPP2R2C Protein phosphatase 2, regulatory subunit B, gamma
  • the inventors isolated patient subgroups in the discovery dataset using RMA normalized and median centered data [24].
  • the inventors applied consensus k-means clustering with the Pearson's correlation coefficient as the similarity (1 -distance) and complete linkage with 10,000 iterations using a sub-sampling ratio of 0.8.
  • the inventors then plotted the consensus distribution function (CDF) to find the optimal number of AKT subgroups [25].
  • Silhouette width values were computed for each sample [26] and only samples with a positive silhouette width were used in further analyses.
  • the inventors isolated AKT subgroups in the TCGA validation dataset using raw data preprocessed as described for the discovery dataset.
  • TCGA samples were mapped onto AKT subgroups in the discovery dataset by adapting the k means clustering algorithm.
  • the inventors found boundaries for each AKT subgroup in the discovery set by calculating the pairwise correlation coefficients between all samples within a subgroup. The minimum pairwise correlation coefficient was used as the lower boundary for each subgroup.
  • TCGA samples were classified by computing the correlation coefficient between each TCGA and GBM195 sample.
  • TCGA samples were assigned to an AKT subgroup if the average pairwise correlation coefficient with members of the group was greater than the lower boundary of that group. Ties were resolved by selecting the closest cluster.
  • the GISTIC algorithm [27] was applied to the 456 TCGA samples with copy number information and results visualized using the Integrated Genomic Viewer (IGV) [28] to find copy number alterations (CNA) in the validation set.
  • CNA copy number alterations
  • Broad copy number alterations in the discovery dataset were found as described previously [29] using a customized version of the Sanger CNV database [http://www.sanger.ac.uk/research/areas/humangenetics/cnv/].
  • the inventors identified broad copy number alterations in the validation dataset as follows. Briefly, the inventors found the average q value (generated from the GISTIC algorithm) for 15 genes spaced evenly across the region of interest. If > 50% of genes had a q value less than expected by chance after correcting for multiple testing (q ⁇ 0.25), that region was called as a copy number alteration.
  • RPPA reverse phase protein array
  • Example 2 AKT Pathway Genes Define 5 Prognostic Subgroups in Glioblastoma
  • AKT pathway gene expression divides GBM into at least six subgroups
  • the inventors evaluated cluster stability using the consensus cumulative distribution function (CDF) plot of the consensus index ( Figure 1C) [25]. Cluster stability increased for k 2 to 6 but not appreciably for k > 6 ( Figure 1C); suggesting six is the optimum number of GBM AKT subgroups.
  • Silhouette width values were computed for each sample [26] ( Figure IB) and samples with a positive silhouette width were selected for further analyses. The inventors aim to have a classification system where clinical differences are maximized.
  • AKT cluster 1 (AKT CI ; AKT subgroup 1), AKT proneural (AKT PN; AKT subgroup 2), AKT mesenchymal (AKT MES; AKT subgroup 3), AKT classical (AKT CLAS; AKT subgroup 4), AKT secondarylike (AKT SL; AKT subgroup 5) and AKT proliferative (AKT PROLIF; AKT subgroup 6) based on their molecular and clinical features and prior naming [4], [32].
  • FIG. 2 compares AKT pathway gene expression in the discovery ( Figure 2A) and validation ( Figure 2B) sets. It shows the pattern of expression of AKT pathway genes within subgroups is similar in both datasets. Interestingly, the PN subgroup in both datasets contained all nonneoplastic samples (not shown). The inventors examined expression of AKT pathway genes in subgroups ( Figure 10). These data show AKT classes arise from complex patterns of gene expression in subgroups. It did not point to a role for a specific part of the AKT pathway within any subgroup.
  • CNA copy number alterations
  • Figure 2C AKT subgroups from discovery
  • Figure 2D validation datasets
  • the PN subgroup was omitted since it had no CNA information in the discovery dataset.
  • CNA within subgroups were similar in the discovery and validation datasets: a high percentage of tumors with 7gain/10 loss occurred in every subgroup except SL, the SL subgroup had greater frequency of 19q loss and the CLAS subgroup had increased gain of chrl9q relative to the rest. Therefore all subgroup-associated trends in CNA within the discovery dataset were recapitulated in the validation dataset.
  • TCGA, Phillips and G-CIMP subgroups distribute non-randomly in AKT subgroups
  • Phillips, TCGA and G-CIMP subgroups distributed non-randomly in AKT subgroups ( Figure 3A, B and C; Figures 12 and 13).
  • AKT subtyping was a tendency for AKT subtyping to split each Phillips subgroup in two.
  • the AKT PN and SL subtypes were significantly enriched in the Phillips PN subtype ( Figure 3A, Figure 12; p ⁇ 0.5 Bonferroni corrected).
  • the AKT MES and CLAS subtypes were significantly enriched in Phillips MES subtype ( Figure 3 A, Figure 12, p ⁇ 0.5; Bonferroni corrected).
  • the AKT PROLIF subtype was significantly enriched in the Phillips PROLIF subtype ( Figure 3A, Figure 12; p ⁇ 0.5; Bonferroni corrected).
  • AKT SL and PROLIF subtypes were significantly enriched in TCGA PN subtype; while AKT MES and CL subgroups were enriched in the TCGA MES and CL subtype, respectively ( Figure 3B, Figure 13; p ⁇ 0.5; Bonferroni corrected).
  • the AKT PN subtype was a mixture of all the TCGA subgroups.
  • the AKT SL and PROLIF subgroups contained the majority of G-CIMP tumors ( Figure 3C). Taken together these data show AKT classification divides existing subgroups further.
  • AKT subgroups have different clinical characteristics (Figure 4B and D; Figures 12 and 13).
  • the PROLIF subgroup had statistically significant shorter survival than the rest (0.75 vs.
  • AKT subtyping is a predictive marker for sensitivity to BCNU/CCNU
  • AKT CLAS subgroup was significantly enriched in alterations in EGFR and CDKN2A similar to TCGA CLAS subgroup [10].
  • the AKT MES subtype was characterized by mutations in NF1 and RBI and increased mR A for the mesenchymal marker, MET, similar to the TCGA MES subgroup [10], although these did not reach statistical significance.
  • the SL subtype was enriched in IDHl mutations (42% vs 3% SL vs. rest) and GCIMP (47% vs. 4%; SL vs.
  • the PROLIF subtype was also slightly enriched in IDHl mutations (1 1%) in this dataset containing 218 validated samples. However that dropped to 7% when considering all TCGA tumors with IDHl mutation information (not shown). Both the SL and PROLIF subgroups were also enriched in alterations found more frequently in secondary tumors including TP53 mutations and increased mRNA and CN gains for PDGFRA.
  • the PROLIF was distinguished from SL subtype by an increase in mutations and copy number alterations in EGFR and CDKN2A ( Figure 6B) and enrichment in recurrent tumors (18% vs 8%; PROLIF vs rest; Figure 13).
  • Genomic alterations in other RTK/RAS/PI3K/AKT pathway members were either not significantly enriched in any subgroup (PTEN, PIK3R1, MET, SPRY2; Figure 6B) or the frequency was too low to evaluate (ERBB2, KRAS, NRAS, HRAS, PIK3CA, FOXOl, FOX03, AKT1, AKT2, AKT3; not shown); although MET mRNA was enriched and SPRY2 mRNA was low in the MES and CLAS subtypes, respectively (Figure 6B). Taken together these data suggest involvement of oncogenic and tumor suppressor pathways can differ between subgroups.
  • Subgroups have distinct patterns of expression for PISK/AKT/mTOR components
  • the inventors find subgroups have distinct patterns of expression of mRNA (Figure 7A), protein and phospho-proteins (Figure 7B) for PI3K/AKT/mTOR pathway components. The most notable patterns were in the MES and SL subgroups.
  • the MES subtype had decreased expression for inhibitors of mTOR, AKT and PI3K (TSC2 and p-AMPK protein; TSC1 , TSC2, PHLPP1, PHLPP2 and PI3KR1 message). Consistent with increased activity of the AKT/mTOR S6 axis, this subgroup also had elevated p-S6 (Figure 7B) and a high positive correlation between p-AKT and p-S6 ( Figure 7C).
  • the long surviving SL subgroup had the opposite pattern of expression; high expression of AKT and mTOR inhibitors ( Figure 7A and B), decreased expression of pS6 (Figure 7B) and lower correlation between pAKT and pS6 ( Figure 7C).
  • the inventors' proposed pathway map for the MES and SL subgroups (7D) based on this data posits how expression of pathway inhibitors affects output of the AKT/mTOR/S6 axis. This data indicates subgroups will have different sensitivities to pathway inhibitors. GO terms suggest subgroups have a different dominant biological process and cell of origin
  • the inventors used Gene Ontology (GO) to investigate the biological role of genes expressed in tumors and how terms partition in subgroups.
  • Each subgroup, except CLAS had a high percentage of tumors with functionally related terms that suggested a different dominate biological process (Table 3).
  • the CLAS subgroup had a mixture of terms.
  • Each subgroup also had GO terms associated with neurodevelopment (Table 3; highlighted with bolded text; summarized in Figure 8B).
  • the PN and CLAS subgroups had only terms associated with neurogenesis suggesting a committed neural precursor cell of origin.
  • the MES, SL and PROLIF subgroups had terms associated with both neuro- and glio-genesis suggesting a stem cell or early uncommitted progenitor cell of origin.

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Abstract

Cette invention concerne la classification, le diagnostic et le traitement de cancers. Dans un mode de réalisation, cette invention concerne des méthodes et des kits permettant de classifier les cancers en divers sous-types sur la base des profils d'expression des composants de la voie AKT. Dans un autre mode de réalisation, cette invention concerne des méthodes et des kits permettant de diagnostiquer des sous-types de cancers par évaluation des profils d'expression des composants de la voie AKT. Dans un autre mode de réalisation encore, cette invention concerne des méthodes et des kits permettant de traiter un sous-type de cancer par administration d'un agent d'alkylation ou d'un inhibiteur de PI3K/AKT/mTOR à un patient. Les cancers se prêtant aux divers modes de réalisation selon l'invention comprennent, entre autres, les tumeurs du cerveau, les gliomes et GBM.
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Cited By (6)

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Publication number Priority date Publication date Assignee Title
US10731221B2 (en) 2009-12-11 2020-08-04 Dignity Health Diagnosing IDH1 related subgroups and treatment of cancer
WO2020081549A1 (fr) * 2018-10-15 2020-04-23 The Regents Of The University Of California Procédés et matériels pour évaluer et traiter le cancer
US11367508B2 (en) 2019-08-16 2022-06-21 Tempus Labs, Inc. Systems and methods for detecting cellular pathway dysregulation in cancer specimens
WO2021119641A1 (fr) * 2019-12-12 2021-06-17 Tempus Labs, Inc. Preuve du monde réel de tests de diagnostic et de schémas de traitement chez des patientes américaines atteintes d'un cancer du sein
US11367004B2 (en) 2019-12-12 2022-06-21 Tempus Labs, Inc. Real-world evidence of diagnostic testing and treatment patterns in U.S. breast cancer patients with implications for treatment biomarkers from RNA-sequencing data
CN114752677A (zh) * 2022-06-13 2022-07-15 北京思诺普斯生物科技有限公司 一种快速检测idh1突变的引物组、试剂盒及扩增方法和应用

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