Methods for the diagnosis of oncological disorders using epimetabolic shifters, multidimensional intracellular molecules, or environmental influencers

Abstract

Methods and formulations for diagnosing onocological disorders in humans using epimetabolic shifters, multidimensional intracellular molecules or environmental influencers are described.

1 . A method of assessing whether a subject is afflicted with an oncological disorder, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication that the subject is afflicted with an oncological disorder, thereby assessing whether the subject is afflicted with an oncological disorder.   
     
     
         2 . A method of assessing whether a subject is afflicted with an oncological disorder, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the expression of the marker is modulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication that the subject is afflicted with an oncological disorder, thereby assessing whether the subject is afflicted with an oncological disorder.   
     
     
         3 . A method of prognosing whether a subject is predisposed to developing an oncological disorder, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 5-29; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication that the subject is predisposed to developing an oncological disorder, thereby prognosing whether the subject is predisposed to developing an oncological disorder.   
     
     
         4 . A method of prognosing whether a subject is predisposed to developing an oncological disorder, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the expression of the marker is modulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication that the subject is predisposed to developing an oncological disorder, thereby prognosing whether the subject is predisposed to developing an oncological disorder.   
     
     
         5 . A method of prognosing the recurrence of an oncological disorder in a subject, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication of the recurrence of the oncological disorder, thereby prognosing the recurrence of an oncological disorder in the subject.   
     
     
         6 . A method of prognosing the recurrence of an oncological disorder in a subject, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the expression of the marker is modulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication of the recurrence of the oncological disorder, thereby prognosing the recurrence of an oncological disorder in the subject.   
     
     
         7 . A method of prognosing the survival of a subject with an oncological disorder, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication of survival of the subject, thereby prognosing survival of the subject with an oncological disorder.   
     
     
         8 . A method of prognosing the survival of a subject with an oncological disorder, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the expression of the marker is modulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication of survival of the subject, thereby prognosing survival of the subject with an oncological disorder.   
     
     
         9 . A method of prognosing the aggressiveness on an oncological disorder in a subject, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample indicates that the oncological disorder is aggressive, thereby prognosing the aggressiveness on an oncological disorder in the subject.   
     
     
         10 . A method of prognosing the aggressiveness on an oncological disorder in a subject, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the expression of the marker is modulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample indicates that the oncological disorder is aggressive, thereby prognosing the aggressiveness on an oncological disorder in the subject.   
     
     
         11 . A method of monitoring the progression of an oncological disorder in a subject, the method comprising: comparing the level of expression of a marker present in a first sample obtained from the subject prior to administering at least a portion of a treatment regimen to the subject and the level of expression of the marker present in a second sample obtained from the subject following administration of at least a portion of the treatment regimen, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29, thereby monitoring the progression of an oncological disorder in the subject. 
     
     
         12 . A method of monitoring the progression of an oncological disorder in a subject, the method comprising: comparing the level of expression of a marker present in a first sample obtained from the subject prior to administering at least a portion of a treatment regimen to the subject and the level of expression of the marker present in a second sample obtained from the subject following administration of at least a portion of the treatment regimen, wherein the expression of the marker is modulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions, thereby monitoring the progression of an oncological disorder in the subject. 
     
     
         13 . A method for assessing the efficacy of a therapy for treating an oncological disorder in a subject, the method comprising: comparing the level of expression of a marker present in a first sample obtained from the subject prior to administering at least a portion of the treatment regimen to the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29; and the level of expression of the marker present in a second sample obtained from the subject following administration of at least a portion of the treatment regimen, wherein a modulation in the level of expression of the marker in the second sample as compared to the first sample is an indication that the therapy is efficacious for treating the oncological disorder in the subject. 
     
     
         14 . A method for assessing the efficacy of a therapy for treating an oncological disorder in a subject, the method comprising: comparing the level of expression of a marker present in a first sample obtained from the subject prior to administering at least a portion of the treatment regimen to the subject, wherein the expression of the marker is modulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions; and the level of expression of the marker present in a second sample obtained from the subject following administration of at least a portion of the treatment regimen, wherein a modulation in the level of expression of the marker in the second sample as compared to the first sample is an indication that the therapy is efficacious for treating the oncological disorder in the subject. 
     
     
         15 . A method of assessing the efficacy of an environmental influencer compound for treating an oncological disorder in a subject in need thereof, the method comprising:
 (1) determining the level of expression of one or more markers present in a biological sample obtained from the subject, wherein the biological sample is exposed to the environmental influencer compound, and wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29 with a positive fold change and/or with a negative fold change;   (2) determining the level of expression of the one or more markers present in a second biological sample obtained from the subject, wherein the sample is not exposed to the environmental influencer compound; and   (3) comparing the level of expression of the one of more markers in the biological sample exposed to the environmental influencer compound and the level of expression of the one of more markers in the biological sample not exposed to the environmental influencer compound,   wherein a decrease in the level of expression of the one or more markers with a negative fold change present in the biological sample exposed to the environmental influencer compound relative to the level of expression of the one or more markers present in the second sample is an indication that the environmental influencer compound is efficacious for treating an oncological disorder to in the subject having an oncological disorder, and,   wherein an increase in the level of expression of the one or more markers with a positive fold change present in the biological sample exposed to the environmental influencer compound relative to the level of expression of the one or more markers present in the second sample is an indication that the environmental influencer compound is efficacious for treating an oncological disorder to in the subject having an oncological disorder,   thereby assessing the efficacy of the environmental influencer compound for treating an oncological disorder to in a subject having an oncological disorder.   
     
     
         16 . A method of assessing the efficacy of an environmental influencer compound for treating an oncological disorder in a subject in need thereof, the method comprising:
 (1) determining the level of expression of one or more markers present in a biological sample obtained from the subject, wherein the biological sample is exposed to the environmental influencer compound, and wherein the expression of the marker is up- or down-regulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions;   (2) determining the level of expression of the one or more markers present in a second biological sample obtained from the subject, wherein the sample is not exposed to the environmental influencer compound; and   (3) comparing the level of expression of the one of more markers in the biological sample exposed to the environmental influencer compound and the level of expression of the one of more markers in the biological sample not exposed to the environmental influencer compound,   wherein a decrease, in the biological sample exposed to the environmental influencer compound, in the level of expression of the one or more down-regulated markers relative to the level of expression of the one or more markers present in the second sample is an indication that the environmental influencer compound is efficacious for treating an oncological disorder to in the subject having an oncological disorder, and,   wherein an increase, in the biological sample exposed to the environmental influencer compound, in the level of expression of the one or more up-regulated markers relative to the level of expression of the one or more markers present in the second sample is an indication that the environmental influencer compound is efficacious for treating an oncological disorder to in the subject having an oncological disorder,   thereby assessing the efficacy of the environmental influencer compound for treating an oncological disorder to in a subject having an oncological disorder.   
     
     
         17 . A method of identifying a compound for treating an oncological disorder in a subject, the method comprising:
 (1) obtaining a biological sample from the subject;   (2) contacting the biological sample with a test compound;   (3) determining the level of expression of one or more markers present in the biological sample obtained from the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29 with a positive fold change and/or with a negative fold change;   (4) comparing the level of expression of the one of more markers in the biological sample with a control sample not contacted by the test compound; and   (5) selecting a test compound that decreases the level of expression of the one or more markers with a negative fold change present in the biological sample and/or increases the level of expression of the one or more markers with a positive fold change present in the biological sample,   thereby identifying a compound for treating an oncological disorder in a subject.   
     
     
         18 . A method of identifying a compound for treating an oncological disorder in a subject, the method comprising:
 (1) obtaining a biological sample from the subject;   (2) contacting the biological sample with a test compound;   (3) determining the level of expression of one or more markers present in the biological sample obtained from the subject, wherein the expression of the marker is up- or down-regulated, in a cancerous cell of the oncological disorder induced to undergo a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation towards levels observed in a normal cell of the subject under normal physiological conditions;   (4) comparing the level of expression of the one of more markers in the biological sample with a control sample not contacted by the test compound; and   (5) selecting a test compound that decreases the level of expression, in the biological sample, of the one or more down-regulated markers, and/or increases the level of expression, in the biological sample, of the one or more up-regulated markers,   thereby identifying a compound for treating an oncological disorder in a subject.   
     
     
         19 . The method of any one of  claims 1 - 18 , wherein the oncological disorder is an oncological disorder selected from the group consisting of: a leukemia, a lymphoma, a melanoma, a carcinoma and a sarcoma. 
     
     
         20 . The method of any one of  claims 1 - 19 , wherein said marker(s) selectively elicits, in a cancerous cell of the mammal, a cellular metabolic energy shift from glycolysis to mitochondrial oxidative phosphorylation, towards levels observed in a normal cell of the mammal under normal physiological conditions. 
     
     
         21 . The method of any one of  claims 1 - 20 , wherein the sample comprises a fluid obtained from the subject. 
     
     
         22 . The method of  claim 21 , wherein the fluid is selected from the group consisting of blood fluids, vomit, saliva, lymph, cystic fluid, urine, fluids collected by bronchial lavage, fluids collected by peritoneal rinsing, and gynecological fluids. 
     
     
         23 . The method of  claim 22 , wherein the sample is a blood sample or a component thereof. 
     
     
         24 . The method of any one of  claims 1 - 20 , wherein the sample comprises a tissue or component thereof obtained from the subject. 
     
     
         25 . The method of  claim 24 , wherein the tissue is selected from the group consisting of bone, connective tissue, cartilage, lung, liver, kidney, muscle tissue, heart, pancreas, and skin. 
     
     
         26 . The method of any one of  claims 1 - 25 , wherein the subject is a human. 
     
     
         27 . The method of any one of  claims 1 - 26 , wherein the level of expression of the marker in the biological sample is determined by assaying a transcribed polynucleotide or a portion thereof in the sample. 
     
     
         28 . The method of  claim 27 , wherein assaying the transcribed polynucleotide comprises amplifying the transcribed polynucleotide. 
     
     
         29 . The method of any one of  claims 1 - 26 , wherein the level of expression of the marker in the subject sample is determined by assaying a protein or a portion thereof in the sample. 
     
     
         30 . The method of any one of  claims 1 - 29 , wherein the protein is assayed using a reagent which specifically binds with the protein. 
     
     
         31 . The method of  claim 30 , wherein the reagent is labeled. 
     
     
         32 . The method of  claim 30 , wherein the reagent is selected from the group consisting of an antibody and an antigen-binding antibody fragment. 
     
     
         33 . The method of any one of  claims 1 - 32 , wherein the level of expression of the marker in the sample is determined using a technique selected from the group consisting of polymerase chain reaction (PCR) amplification reaction, reverse-transcriptase PCR analysis, single-strand conformation polymorphism analysis (SSCP), mismatch cleavage detection, heteroduplex analysis, Southern blot analysis, Northern blot analysis, Western blot analysis, in situ hybridization, array analysis, deoxyribonucleic acid sequencing, restriction fragment length polymorphism analysis, and combinations or sub-combinations thereof, of said sample. 
     
     
         34 . The method of any one of  claims 1 - 32 , wherein the level of expression of the marker in the sample is determined using a technique selected from the group consisting of immunohistochemistry, immunocytochemistry, flow cytometry, ELISA and mass spectrometry. 
     
     
         35 . The method of any one of  claims 1 - 34 , wherein the marker is a marker selected from the group consisting of HNF4-alpha, Bcl-xl, Bcl-xS, BNIP-2, Bcl-2, Birc6, Bcl-2-L11 (Bim), XIAP, BRAF, Bax, c-Jun, Bmf, PUMA, cMyc, transaldolase 1, COQ1, COQ3, COQ6, prenyltransferase, 4-hydrobenzoate, neutrophil cytosolic factor 2, nitric oxide synthase 2A, superoxide dismutase 2, VDAC, Bax channel, ANT, Cytochrome c, complex 1, complex II, complex III, complex IV, Foxo 3a, DJ-1, IDH-1, Cpt1C and Cam Kinase II. 
     
     
         36 . The method of any one of  claims 1 - 34 , wherein the marker is a marker associated with apoptosis. 
     
     
         37 . The method of any one of  claims 1 - 34 , wherein the marker is a marker associated with oxidative stress. 
     
     
         38 . The method of any one of  claims 1 - 34 , wherein the marker is a marker associated with heat shock. 
     
     
         39 . The method of any one of  claims 1 - 34 , wherein the marker is a marker associated with angiogenesis. 
     
     
         40 . The method of any one of  claims 1 - 34 , wherein the level of expression of a plurality of markers is determined. 
     
     
         41 . The method of any one of  claims 5 - 8 ,  11  and  12 , wherein the subject is being treated with a therapy selected from the group consisting of an environmental influencer compound, surgery, radiation, hormone therapy, antibody therapy, therapy with growth factors, cytokines, and chemotherapy. 
     
     
         42 . The method of any one of  claim 13 - 14  or  41 , wherein the therapy comprises an environmental influencer compound. 
     
     
         43 . The method of  claim 42 , wherein the therapy further comprises a treatment regimen selected from the group consisting of surgery, radiation, hormone therapy, antibody therapy, therapy with growth factors, cytokines, and chemotherapy. 
     
     
         44 . The method of  claim 41  or  42 , wherein the environmental influencer compound is a multidimensional intracellular molecule (MIM) or epimetabolic shifter (epi-shifter). 
     
     
         45 . The method of  claim 41  or  42 , wherein the environmental influencer compound is CoQ-10. 
     
     
         46 . The method of  claim 41  or  42 , wherein the environmental influencer compound is vitamin D3. 
     
     
         47 . The method of  claim 41  or  42 , wherein the environmental influencer compound is a compound selected from the group consisting of acetyl Co-A, palmityl, L-carnitine, tyrosine, phenylalanine, cysteine and a small molecule. 
     
     
         48 . The method of  claim 41  or  42 , wherein the environmental influencer compound is a compound selected from the group consisting of fibronectin, TNF-alpha, IL-5, IL-12, IL-23, an angiogenic factor and an apoptotic factor. 
     
     
         49 . A kit for assessing whether a subject is afflicted with an oncological disorder, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to assess whether the subject is afflicted with the oncological disorder. 
     
     
         50 . A kit for prognosing whether a subject is predisposed to developing an oncological disorder, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to prognose whether the subject is predisposed to developing the oncological disorder. 
     
     
         51 . A kit for prognising the recurrence of an oncological disorder in a subject, the kit comprising reagents for assessing the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to prognose the recurrence of the oncological disorder. 
     
     
         52 . A kit for prognising the recurrence of an oncological disorder, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to prognose the recurrence of the oncological disorder. 
     
     
         53 . A kit for prognising the survival of a subject with an oncological disorder, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to prognose the survival of the subject with the oncological disorder. 
     
     
         54 . A kit for prognosing the aggressiveness on an oncological disorder in a subject, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to prognose the aggressiveness on the oncological disorder in the subject. 
     
     
         55 . A kit for monitoring the progression of an oncological disorder in a subject, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to prognose the progression of the oncological disorder in a subject. 
     
     
         56 . A kit for assessing the efficacy of a therapy for treating an oncological disorder, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to assess the efficacy of the therapy for treating the oncological disorder. 
     
     
         57 . A kit for assessing the efficacy of an environmental influencer compound for treating an oncological disorder to in a subject having an oncological disorder, the kit comprising reagents for determining the level of expression of at least one marker selected from the group consisting of the markers listed in Tables 2-4 & 6-29 and instructions for use of the kit to assess the efficacy of the environmental influencer compound for treating the oncological disorder to in the subject having the oncological disorder. 
     
     
         58 . The kit of any one of  claims 49 - 57 , further comprising means for obtaining a biological sample from a subject. 
     
     
         59 . The kit of any one of  claims 49 - 58 , further comprising a control sample. 
     
     
         60 . The kit of any one of  claims 49 - 59 , wherein the means for determining the level of expression of at least one marker comprises means for assaying a transcribed polynucleotide or a portion thereof in the sample. 
     
     
         61 . The kit of any one of  claims 49 - 59 , wherein the means for determining the level of expression of at least one marker comprises means for assaying a protein or a portion thereof in the sample. 
     
     
         62 . The kit of any one of  claims 49 - 61 , further comprising an environmental influencer compound. 
     
     
         63 . The kit of any one of  claims 49 - 62 , wherein the kit comprises reagents for determining the level of expression of a plurality of markers. 
     
     
         64 . A method of assessing whether a subject is afflicted with a CoQ10 responsive state, the method comprising:
 (1) determining the level of expression of a marker present in a biological sample obtained from the subject, wherein the marker is selected from the group consisting of the markers listed in Tables 2-4 & 6-29; and   (2) comparing the level of expression of the marker present in the biological sample obtained from the subject with the level of expression of the marker present in a control sample,   wherein a modulation in the level of expression of the marker in the biological sample obtained from the subject relative to the level of expression of the marker in the control sample is an indication that the subject is afflicted with the CoQ10 responsive state, thereby assessing whether the subject is afflicted with the CoQ10 responsive state.   
     
     
         65 . The method of  claim 64 , wherein the CoQ10 responsive state is an oncological disorder.