Systems and methods for analyzing persistent homeostatic perturbations

Abstract

This invention is in the field of homeostasis analysis. More particularly, it relates to systems and methods for analyzing persistent homeostatic perturbations, i.e. chronic stress, by measuring levels of biomarkers that are related to chronic stress. This invention is also directed to systems and methods for analyzing the molecular mechanisms of chronic stress.

1 . A method for detecting a stress response in a subject comprising detecting altered levels of biomarkers in an SR biomarker panel in a sample from a subject, as compared to a corresponding sample from a normal subject, wherein the panel comprises at least two biomarkers, wherein the biomarkers have a variability index above a threshold value indicating sufficiency to classify samples as coming from stressed or normal subjects, thereby detecting a stress response in the subject. 
   
   
       2 . The method of  claim 1 , wherein the subject is an animal, a plant, a bacterium, a protist, and a fungus. 
   
   
       3 . (canceled) 
   
   
       4 . The method of  claim 2 , wherein the animal is selected from the group consisting of a mammal, a fish, an amphibian, a reptile, a bird. 
   
   
       5 . The method of  claim 4 , wherein the mammal is selected from the group consisting of a human, a dolphin, a whale, an elephant, a dog, a cat, a cow, a sheep, a pig, a horse, a donkey, a mule, and a goat. 
   
   
       6 - 9 . (canceled) 
   
   
       10 . The method of  claim 1 , wherein the SR biomarker panel comprises a biomarker from a stress response pathway is selected from the group consisting of redox, xenobiotics, chaperoning, cell growth, cell death, cell adhesion, neuroendocrine signaling, immunity, deoxyribonucleic acid repair, and microbial activation. 
   
   
       11 . (canceled) 
   
   
       12 . The method of  claim 1 , wherein the SR biomarker panel comprises at least one biomarker selected from the group consisting of β-endorphin, caspase 8, cyclin D1, NADPH-cytochrome P450 reductase, cyclooxygenase 2, cytochrome P450, cytochrome c, epidermal growth factor receptor, ferritin, glucocorticoid receptor, glucose regulated protein 58, glucose regulated protein 75, glutathione S-transferase, heat shock protein 25/27, heat shock protein 40, heat shock protein 60, heat shock protein 70, heat shock protein 90, heat shock transcription factor-1, heme oxygenase-1, interleukin 1β, interleukin 6, interleukin 8, interleukin 10, interleukin 12, laminin, leptin receptor, metallothionein, Mekk-1, Mek-1, inducible nitric oxide synthase II, c-Fos, c-Jun, serotonin receptor, serotonin, substance P, superoxide dismutase Mn, superoxide dismutase Cu/Zn, transforming growth factor β, p53, vasoactive intestinal peptide, and substance P. 
   
   
       13 . The method of  claim 1 , wherein the SR biomarker panel comprises at least three biomarkers. 
   
   
       14 . The method of  claim 13 , wherein the SR biomarker panel comprises heat shock factor-1, ferritin, superoxide dismutase Cu/Zn, Mekk-1, and superoxide dismutase Mn. 
   
   
       15 . The method of  claim 1 , wherein the detection of an altered stress response is further correlated with i) the presence, absence, or severity of a particular disease state; or ii) the likelihood that the subject will contract a particular disease state. 
   
   
       16 . The method of  claim 15 , wherein the disease state is selected from the group consisting of toxic chemical poisoning, radiochemical poisoning, inflammation, brain seizures, cancer, T-cell leukemia, heart lesions, stroke, neurodegenerative disease, tissue trauma, immunological deficiency, viral infection, Alzheimer's disease, vascular dementia, autoimmune disease, gastric ulcer, chronic pain, oral diseases associated with decreased salivation, obesity, metabolic syndrome, diabetes, rapid weight loss, intestinal and blood lipid abnormalities, AIDS, HTLV infection, skin disorders, cystic fibrosis, nasal allergy, protozoan infection, fatigue, anemia, alcohol abuse, infectious diseases, cardiovascular disease, multiple sclerosis, amyotrophic lateral sclerosis, irritable bowel syndrome, depression, panic disorders, post-traumatic stress disorder, and reproductive disorders. 
   
   
       17 - 24 . (canceled) 
   
   
       25 . The method of  claim 1 , further comprising characterizing the stress response as a medical condition, a biological stress, a chemical stress, a psycho-social stress, physical stress, or a combination thereof. 
   
   
       26 . The method of  claim 25 , wherein the medical condition is selected from the group consisting of cancer, neurodegenerative diseases, dementia, stroke, tissue injury, brain trauma, cardiovascular disease, metabolic syndrome, diabetes, periodontal disease, surgery, autoimmune/inflammatory diseases, lupus erythematosus, psoriasis, asthma, allergy, infectious diseases, HIV/AIDS, post-traumatic stress disorder, drug or alcohol addition, chronic fatigue syndrome, hypertension, and chronic psychological stress. 
   
   
       27 . The method of  claim 25 , wherein the biological stress is caused by a stressor selected from the group consisting of a microbial pathogen, injury, surgery, genetic defect, obesity, starvation, dehydration, strenuous exercise, fatigue, sleep deprivation and jet lag. 
   
   
       28 . The method of  claim 25 , wherein the chemical stress is caused by a stressor selected from the group consisting of hypoxia, hyperoxia, hyponatremia, ozone, smoke, allergens, alcohol, drugs, pesticides, herbicides, heavy metals, industrial toxins, biotoxins, chemical weapons, and a micronutrient deficit. 
   
   
       29 . The method of  claim 25 , wherein the psycho-social stress is caused by a stressor selected from the group consisting of psychological trauma, defeat, restraint, isolation, social disorganization, family separation, parental neglect, new and conflicting roles and information overload. 
   
   
       30 . The method of  claim 25 , wherein the physical stress is caused by a stressor selected from the group consisting of heat, cold, altitude, humidity, mechanical pressure, osmotic pressure, noise, radioactive materials, electromagnetic radiation and gravity. 
   
   
       31 . A method of characterizing a stress response of  claim 25 , further comprising conducting a non-biomarker assay. 
   
   
       32 . The method of  claim 31 , wherein the non-biomarker assay is selected from the group consisting of a health or an environmental assay. 
   
   
       33 . The method of  claim 32 , wherein the health and environmental assay is selected from the group consisting of blood pressure, cholesterol levels, glucose tolerance, hormonal levels, liver function, infectious agents, genetic test, cognitive neuropsychological test, psychological stress test, environmental quality test, and a combination thereof. 
   
   
       34 . The method of  claim 25 , further comprising using the characterizing to determine a treatment regimen. 
   
   
       35 - 47 . (canceled) 
   
   
       48 . A method for screening for an agent that alters a stress response comprising:
 (a) contacting a cell with an agent;   (b) detecting the expression level of biomarkers in an SR biomarker panel in the cell, wherein the panel comprises at least two biomarkers, wherein the biomarkers have a variability index above a threshold value indicating sufficiency to classify samples as coming from stressed or normal subjects; and,   (c) comparing the level of expression of the biomarkers in the SR biomarker panel of the cell contacted with the agent to the level of expression of the biomarkers in the SR biomarker panel of a cell that was not contacted with the agent, wherein the difference in the level of expression or activity of the biomarker is indicative that the agent can alter a stress response.   
   
   
       49 - 50 . (canceled) 
   
   
       51 . The method of  claim 48 , wherein the SR biomarker panel comprises a biomarker from a stress response pathway is selected from the group consisting of redox, xenobiotics, chaperoning, cell growth, cell death, cell adhesion, neuroendocrine signaling, immunity, deoxyribonucleic acid repair, and microbial activation. 
   
   
       52 . (canceled) 
   
   
       53 . The method of  claim 48 , wherein the SR biomarker panel comprises at least one biomarker selected from the group consisting of β-endorphin, caspase 8, cyclin D1, NADPH-cytochrome P450 reductase, cyclooxygenase 2, cytochrome P450, cytochrome c, epidermal growth factor receptor, ferritin, glucocorticoid receptor, glucose regulated protein 58, glucose regulated protein 75, glutathione S-transferase, heat shock protein 25/27, heat shock protein 40, heat shock protein 60, heat shock protein 70, heat shock protein 90, heat shock transcription factor-1, heme oxygenase-1, interleukin 1β, interleukin 6, interleukin 8, interleukin 10, interleukin 12, laminin, leptin receptor, metallothionein, Mekk-1, Mek-1, inducible nitric oxide synthase II, c-Fos, c-Jun, serotonin receptor, serotonin, substance P, superoxide dismutase Mn, superoxide dismutase Cu/Zn, transforming growth factor β, p53, vasoactive intestinal peptide, and substance P. 
   
   
       54 . The method of  claim 48 , wherein the SR biomarker panel comprises at least three biomarkers. 
   
   
       55 . The method of  claim 54 , wherein the SR biomarker panel comprises heat shock factor-1, ferritin, superoxide dismutase Cu/Zn, Mekk-1, and superoxide dismutase Mn. 
   
   
       56 . A method for constructing a biomarker panel for a stress response in a subject comprising:
 (a) obtaining sample material from a stressed subject;   (b) detecting the expression of two or more biomarkers in the stressed subject,   (c) comparing the level of expression of the biomarkers from the stressed subject to the expression of the biomarker from a normal subject, wherein biomarkers having a difference in the expression in the stressed subject as compared to the normal subject are included in an SR biomarker panel for a stress response.   
   
   
       57 - 62 . (canceled) 
   
   
       63 . A kit for detecting or characterizing a stress response in a subject comprising a sample collection device and two or more biomarker-binding molecules that each selectively bind to one of two or more biomarkers, or to a nucleic acid or protein expression product or a metabolic product of a biomarker, wherein the biomarkers have a variability index above a threshold value indicating sufficiency to classify samples as coming from stressed or normal subjects. 
   
   
       64 . The kit of  claim 63 , wherein the biomarkers are from a stress response pathway. 
   
   
       65 . The kit of  claim 64 , wherein biomarkers are from a stress response pathway is selected from the group consisting of redox, xenobiotics, chaperoning, cell growth, cell death, cell adhesion, neuroendocrine signaling, immunity, deoxyribonucleic acid repair, microbial activation and a combination thereof. 
   
   
       66 . The kit of  claim 63 , comprising three or more biomarker-binding molecules that each selectively bind to one of three or more biomarkers. 
   
   
       67 . The kit of  claim 66 , wherein at least one of the biomarkers is selected from the group consisting of β-endorphin, caspase 8, cyclin D1, NADPH-cytochrome P450 reductase, cyclooxygenase 2, cytochrome P450, cytochrome C, epidermal growth factor receptor, ferritin, glucocorticoid receptor, glucose regulated protein 58, glucose regulated protein 75, glutathione S-transferase, heat shock protein 25/27, heat shock protein 40, heat shock protein 60, heat shock protein 70, heat shock protein 90, heat shock transcription factor-1, heme oxygenase-1, interleukin 1β, interleukin 6, interleukin 8, interleukin 10, interleukin 12, laminin, leptin receptor, metallothionein, Mekk-1, Mek-1, inducible nitric oxide synthase II, c-Fos, c-Jun, serotonin receptor, serotonin, substance P, superoxide dismutase Mn, superoxide dismutase Cu/Zn, transforming growth factor β, p53, vasoactive intestinal peptide, and substance P. 
   
   
       68 . The method of  claim 1 , wherein the expression levels of the biomarkers are measured together using pooled antibodies against the biomarkers to produce a combined SR biomarker score. 
   
   
       69 . The method of  claim 68 , further comprising measuring the expression levels of each of the biomarkers individually. 
   
   
       70 . The method of  claim 56 , wherein step (c) comprises determining a variability index for each biomarker, wherein the biomarkers having the highest variability index are included in the SR biomarker panel. 
   
   
       71 . The method of  claim 70 , wherein the biomarkers having a variability index above a threshold value are included in the SR biomarker panel. 
   
   
       72 . A database comprising a multiplicity of SR biomarker profiles, wherein an SR biomarker profile comprises an expression level of biomarkers in an SR biomarker panel in a sample from a subject, wherein the panel comprises at least two biomarkers, wherein the biomarkers have a variability index above a threshold value indicating sufficiency to classify samples as coming from stressed or normal subjects. 
   
   
       73 . The database of  claim 72 , wherein the SR biomarker panel comprises at least one biomarker selected from the group consisting of β-endorphin, caspase 8, cyclin D1, NADPH-cytochrome P450 reductase, cyclooxygenase 2, cytochrome P450, cytochrome c, epidermal growth factor receptor, ferritin, glucocorticoid receptor, glucose regulated protein 58, glucose regulated protein 75, glutathione S-transferase, heat shock protein 25/27, heat shock protein 40, heat shock protein 60, heat shock protein 70, heat shock protein 90, heat shock transcription factor-1, heme oxygenase-1, interleukin 1β, interleukin 6, interleukin 8, interleukin 10, interleukin 12, laminin, leptin receptor, metallothionein, Mekk-1, Mek-1, inducible nitric oxide synthase II, c-Fos, c-Jun, serotonin receptor, serotonin, substance P, superoxide dismutase Mn, superoxide dismutase Cu/Zn, transforming growth factor β, p53, vasoactive intestinal peptide, and substance P. 
   
   
       74 . The database of  claim 72 , wherein the multiplicity of SR biomarker profiles comprise profiles from stressed subjects and normal subjects. 
   
   
       75 . The database of  claim 74 , wherein the database is used in the identification of a stress response.