Ion channel arrays

Abstract

The invention relates to ion channel arrays, method of producing such an array, including the primer sets and kits comprising the ion channel array. The invention also relates to a subset of methods for the evaluation of ion channel expression profiles using the ion channel array such as expression profile of a certain biological material, several biological materials and to identify therapeutic, prophylactic and/or toxic agents involved either directly or indirectly in the response of the ion channel expression.

1 . An ion channel array comprising a multiplicity of individual ion channel polynucleotide spots stably associated with a surface of a solid support, wherein an individual ion channel polynucleotide spot comprises an ion channel polynucleotide composition comprising a non-conserved region of an ion channel polynucleotide family member, the spots representing at least two different regions of an ion channel polynucleotide family member.  
     
     
         2 . The array according to  claim 1 , wherein the multiplicity of individual spots represents at least two different ion channel polynucleotide family members and/or at least two different ion channel families.  
     
     
         3 . The array according to any of the preceding claims, wherein the non-conserved regions of the ion channel polynucleotide family member have less than 90% intrafamily identity.  
     
     
         4 . The array according to any of the preceding claims, wherein the non-conserved regions of the ion channel polynucleotide family member have less than 85% intrafamily identity.  
     
     
         5 . The array according to any of the preceding claims, wherein the non-conserved regions of the ion channel polynucleotide family member have less than 80% intrafamily identity.  
     
     
         6 . The array according to any of the preceding claims, wherein the non-conserved regions of the ion channel polynucleotide family member have less than 75% intrafamily identity.  
     
     
         7 . The array according to any of the preceding claims, wherein the non-conserved regions of the ion channel polynucleotide family member have less than 50% intrafamily identity.  
     
     
         8 . The array according to any of the preceding claims, wherein the non-conserved regions of the ion channel polynucleotide family member have at least 50% interspecies identity.  
     
     
         9 . The array according to  claim 8 , wherein the non-conserved regions of the ion channel family member have at least 60% interspecies identity.  
     
     
         10 . The array according to  claim 9 , wherein the non-conserved regions of the ion channel family member have at least 65% interspecies identity.  
     
     
         11 . The array according to  claim 10 , wherein the non-conserved regions of the ion channel family member have at least 70% interspecies identity.  
     
     
         12 . The array according to  claim 11 , wherein the non-conserved regions of the ion channel family member have at least 75% interspecies identity.  
     
     
         13 . The array according to  claim 12 , wherein the non-conserved regions of the ion channel family member have at least 80% interspecies identity.  
     
     
         14 . The array according to any of the preceding claims, wherein the non-conserved regions of the ion channel polynucleotide family member have an average length of from about 3 to about 9,000 nucleotides, from about 3 to about 6,000, from about 3 to about 3,000, from about 200 to 750, from about 200 to 700, from about 200 to 500, from about 250 to 400 or from about 290 to 350.  
     
     
         15 . The array according to any of the preceding claims, wherein said different regions of an ion channel polynucleotide family member are polynucleotide regions from the same polynucleotide strand and the regions are at least non-overlapping polynucleotide regions of the strand.  
     
     
         16 . The array according to any of the preceding claims, wherein an ion channel polynucleotide family is polynucleotides encoding polypeptides involved in transporting the same species of ions across biological membranes.  
     
     
         17 . The array according to any of the preceding claims, wherein the ion channel polynucleotide family is selected from the group consisting of voltage-gated ion channels, Gap-junction ion channels, ligand-gated ion channels, heat-activated ion channels, intracellular ion channels, ion channel gated by intracellular ligands such as cyclic nucleotide-gated channels or calcium-activated ion channels and any other polynucleotides encoding polypeptides capable of transporting ions across biological membranes.  
     
     
         18 . The array according to any of the preceding claims, wherein the polynucleotide composition comprises one or more of the same non-conserved region of an ion channel polynucleotide family member.  
     
     
         19 . The array according to  claim 18 , wherein the polynucleotide composition comprises one or more of the same non-conserved region in the single stranded or double stranded form.  
     
     
         20 . The array according to any of the preceding claims, wherein the non-conserved region of an ion channel polynucleotide family member is of DNA, RNA, cDNA, natural, synthetic, semisynthetic origin or is a chemical analogous such as LNA and PNA.  
     
     
         21 . The array according to any of the preceding claims, wherein the non-conserved region of an ion channel polynucleotide family member is obtained from one or more biological materials such as, e.g., an organism, an organ, a tissue, a cell or a biological material produced by a cell culture.  
     
     
         22 . The array according to  claim 21 , wherein the biological material is an organism, such as a microorganism, a plant, a fungus or an animal.  
     
     
         23 . The array according to  claim 22 , wherein the biological material is an animal.  
     
     
         24 . The array according to  claim 23 , wherein the animal is selected from the group consisting of humans, rats, mice, pigs, cows, horses, dogs, guinea pigs, ferrets, rabbits, apes, monkeys, cats and sheep.  
     
     
         25 . The array according to any of the preceding claims, wherein the solid support is made of a flexible or rigid material.  
     
     
         26 . The array according to any of the preceding claims, wherein said array comprises from about 2 to about 100,000 such as, e.g. from about 2 to about 50,000, from about 10 to about 25,000, from about 100 to about 10,000, from about 100 to about 5,000, from about 100 to about 1,000, from about 400 to about 600 or about 500 ion channel polynucleotide spots, or at least 2 such as, e.g. at least 10, at least 25, at least 50, at least 100, at least 300, at least 400, at least 500 or at least 600 spots.  
     
     
         27 . The array according-to-any of the preceding claims, wherein at least one non-conserved polynucleotide region is present in the form of sense single-strands in a spot.  
     
     
         28 . The array according to  claim 27 , wherein said non-conserved polynucleotide region is further present in the form of antisense single-strands in a separate spot.  
     
     
         29 . A method of preparing an array according to any of the preceding claims, said method comprising a) generating said non-conserved regions of ion channel polynucleotide family members, b) preparing a multiplicity of compositions each comprising at least a non-conserved region, and c) stably associating said compositions in individual spots on a surface of a solid support.  
     
     
         30 . The method according to  claim 29 , wherein each said non-conserved region of an ion channel polynucleotide family member is produced by one or more primers specific for said non-conserved region.  
     
     
         31 . A set of primers specific for non-conserved regions of ion channel polynucleotide family members, wherein the set of primers are used in the method according to any of the claims  29 - 30  for the production of an array according to any of the claims  1 - 28 .  
     
     
         32 . A method for the determination of an ion channel polynucleotide expression profile in a biological material, said method comprising a) obtaining a polynucleotide sample from the biological material, b) labelling said sample to obtain a labelled target polynucleotide sample, c) contacting at least one labelled target polynucleotide sample with an array according to any of the claims  1 - 28  under conditions which are sufficient to produce a hybridisation pattern, and d) detecting said hybridisation pattern to obtain the ion channel polynucleotide expression profile of the biological material.  
     
     
         33 . A method for the determination of a difference in ion channel polynucleotide expression profiles from at least a first and a second different biological material, said method comprising obtaining a first ion channel expression profile of the first biological material according to the method of  claim 32 , obtaining a second ion channel expression profile of the second biological material according to the method of  claim 32 , comparing the first and the second ion channel expression profiles to identify any difference in the ion channel expression profiles between the first and the second ion channel expression profiles.  
     
     
         34 . The method according to any of the claims  32 - 33 , wherein the first and the second biological material are of the same kind of biological material.  
     
     
         35 . The method according to the claims  32 - 34 , wherein the first biological material is in a non-stressed state and the second biological material is in a stressed state.  
     
     
         36 . The method according to the  claim 35 , wherein the stress directly or indirectly influence the ion channel expression profile of the first and/or the second biological material.  
     
     
         37 . The method according to any of the claims  32 - 36 , wherein the ion channel polynucleotide family is selected from the group consisting of voltage-gated ion channels, Gap-junction ion channels, ligand-gated ion channels, heat-actvated ion channels, intracellular ion channels, ion channel gated by intracellular ligands such as cyclic nucleotide-gated channels or calcium-activated ion channels and any other polynucleotides encoding polypeptides capable of transporting ions across biological membranes.  
     
     
         38 . The method according to  claim 37 , wherein the ion channel expression profile of the second biological sample is directly or indirectly related to a disease, chemical treatment, biological sample or parts in a biological sample treatment, environmental influences or other physiological or patophysiological changes.  
     
     
         39 . The method according to  claim 38 , wherein the chemical treatment is selected from the group consisting of naturally occurring chemical entities or synthetically derived chemical entities.  
     
     
         40 . The method according to  claim 38 , wherein the disease is selected from the group consisting of asthma, cystic fibrosis, chronic obstructive pulmonary disease and rhinorrhea, convulsions, vascular spasms, coronary artery spasms, renal disorders, polycystic kidney disease, bladder spasms, urinary incontinence, bladder outflow obstruction, irritable bowel syndrome, gastrointestinal dysfunction, secretory diarrhoea, ischaemia, cerebral ischaemia, ischaemic hearth disease, angina pectoris, coronary hearth disease, traumatic brain injury, psychosis, anxiety, depression, dementia, memory and attention deficits, drug addiction and/or abuse, including cocaine or tobacco abuse, Parkinson's disease, Alzheimer's disease, dysmenorrhea, narcolepsy, Reynaud's disease, intermittent claudication, Sjorgren's syndrome, migraine, arrhythmia, hypertension, absence seizures, myotonic muscle dystrophia, xerostomi, diabetes type II, hyperinsulinemia, premature labour, baldness, cancer, schizofrenia or psychosis; a variety of disorders associated with the neural system, for example eating disorders, obsessive compulsive disorders, panic disorders, alcoholism, pain, memory deficits and anxiety including disorders such as pseudodementia or Ganser's syndrome, migraine pain, bulimia, obesity, pre-menstrual syndrome or late luteal phase syndrome, post-traumatic syndrome, memory loss, memory dysfunction, social phobia, attention deficit hyperactivity disorder, chronic fatigue syndrome, premature ejaculation, erectile difficulty, anorexia nervosa, disorders of sleep, autism, mutism, trichotillomania or mood syndrome; auto-immune diseases, e.g. Addison's disease, alopecia areata, Ankylosing spondylitis, haemolytic anemia (anemia haemolytica), pernicious anemia (anemia pemiciosa), aphthae, aphthous stomatitis, arthritis, arteriosclerotic disorders, osteoarthritis, rheumatoid arthritis, aspermiogenese, asthma bronchiale, auto-immune asthma, auto-immune hemolysis, Bechet's disease, Boeck's disease, inflammatory bowel disease, Burkitt's lymphoma, Chron's disease, choriolditis, colitis ulcerosa, Coeliac disease, cryoglo-bulinemia, dermatitis herpetiformis, dermatomyositis, insulin-dependent type I diabetes, juvenile diabetes, idiopathic diabetes insipidus, insulin-dependent diabetes mellisis, auto-immune demyelinating diseases, Dupuytren's contracture, encephalo-myelitis, encephalomyelitis allergica, endophthalmia phacoanaphylactica, enteritis allergica, auto-immune enteropathy syndrome, erythema nodosum leprosum, idiopathic facial paralysis, chronic fatigue syndrome, febris rheumatica, glomerulo nephritis, Goodpasture's syndrome, Graves' disease, Hamman-Rich's disease, Hashimoto's disease, Hashimoto's thyroiditis, sudden hearing loss, sensoneural hearing loss, hepatitis chronica, Hodgkin's disease, haemoglobinuria paroxysmatica, hypogonadism, ileitis regionalis, iritis, leucopenia, leucemia, lupus erythematosus disseminatus, systemic lupus erythematosus, cutaneous lupus erythematosus, lymphogranuloma malignum, mononucleosis infectiosa, myasthenia gravis, traverse myelitis, primary idiopathic myxedema, nephrosis, ophthalmia symphatica, orchitis granulomatosa, pancreatitis, pemphigus, pemphigus vulgaris, pqlyarteritis nodosa, polyarthritis chronica primaria, polymyositis, polyradiculitis acuta, psoreasis, purpura, pyoderma gangrenosum, Quervain's thyreoiditis, Reiter's syndrome, sarcoidosis, ataxic sclerosis, progressive systemic sclerosis, scleritis, sclerodermia, multiple sclerosis, sclerosis disseminata, acquired spenic atrophy, infertility due to antispermatozoan antibodies, thrombocytopenia, idiopathic thrombocytopenia purpura, thymoma, acute anterior uveitis, vitiligo, AIDS, HIV, SCID and Epstein Barr virus associated diseases such as Sjorgren's syndrome, virus (AIDS or EBV) associated B cell lymphoma, parasitic diseases such as Lesihmania, and immunosuppressed disease states such as viral infections following allograft transplantations, graft vs. Host syndrome, transplant rejection, or AIDS, cancers, chronic active hepatitis diabetes, toxic chock syndrome, food poisoning, and transplant rejection.  
     
     
         41 . A method for identifying a therapeutic, prophylactic and/or toxic agent involved in a direct or indirect action on the ion channel expression profile in a biological material, said method comprises obtaining a first ion channel expression profile of a first biological material according to the method of  claim 32 , obtaining a second ion channel expression profile of a-second biological material according to the method of  claim 32 , applying a test compound to the second biological material and obtaining a third ion channel expression profile thereof according to the method of  claim 32 , comparing the first, second and third ion channel expression profiles, and identifying any differences in the ion channel expression profiles so as to identify any biological response of the test compound on the ion channel expression profile.  
     
     
         42 . The method according to  claim 41  further comprising applying a test compound to the first biological material and obtaining a fourth ion channel expression profile thereof according to the method of  claim 32 , comparing the first, second, third and fourth ion channel expression profiles, and identifying any differences in the ion channel expression profiles so as to identify any biological response of the test compound on the ion channel expression profile.  
     
     
         43 . The method according to claims  41  or  42 , wherein the first and the second biological material are of the same kind of biological material.  
     
     
         44 . The method according to the claims  40 - 43 , wherein the first biological material is in a non-stressed state and the second biological material is in a stressed state.  
     
     
         45 . The method according to the  claim 44 , wherein the stress directly or indirectly influences the ion channel expression profile of the first and/or the second biological material.  
     
     
         46 . The method according to any of the claims  41 - 45 , wherein the ion channel polynucleotide family is selected from the group consisting of voltage-gated ion channels, Gap-junction ion channels, ligand-gated ion channels, heat-activated ion channels, intracellular ion channels, ion channel gated by intracellular ligands such as cyclic nucleotide-gated channels or calcium-activated ion channels and any other polynucleotides encoding polypeptides capable of transporting ions across biological membranes.  
     
     
         47 . The method according to  claim 46 , wherein the ion channel expression profile of the second biological material is direct or indirect measure of a diseased state, a chemical pretreatment, or environmental influences or other physiological or pathophysiological changes.  
     
     
         48 . The method according to  claim 47 , wherein the disease is selected from the same group as defined in  claim 40 .  
     
     
         49 . The method according to any of the claims  41 - 48 , wherein the test compound is a chemical or biological derived compound such as compounds selected from the group consisting of therapeutic, prophylactic and/or toxic chemical entities, physiologically chemical entities, hormones, vitamins, nutrients, pesticides, fungicides, bateriocides and any other organic chemical entity.  
     
     
         50 . The method according to any of the claims  32 - 49 , wherein about 100 μg or less of total RNA of the biological material is used for hybridisation on each individual ion channel polynucleotide spot.  
     
     
         51 . A diagnostic method to determine the differences of ion channel expression profiles between two biological materials; said method comprises obtaining a first ion channel expression profile of a first biological material according to the method of  claim 32 , obtaining a second ion channel expression profile of a second biological material according to the method of  claim 32 , comparing the first and second ion channel expression profile, and identifying any difference in the ion channel expression profiles.  
     
     
         52 . The diagnostic method according to  claim 51 , wherein the difference between the ion channel expression profile of the first and the second ion channel expression profile is directly or indirectly influenced by a patophysiological state or a disease such as diseases claimed in  claim 40 .  
     
     
         53 . The diagnostic method according to  claim 52 , wherein the ion channel expression profile from more than two different biological materials are compared, such as biological materials, which are in different stages of a disease.  
     
     
         54 . The method according to any of the claims  32 - 53 , wherein the biological material is an organism, such as a microorganism, a plant, a fungus or an animal.  
     
     
         55 . The method according to  claim 54 , wherein the animal is selected from the group consisting of humans, rats, mice, pigs, cows, horses, dogs, guinea pigs, ferrets, rabbits, apes, monkeys, cats and sheep.  
     
     
         56 . An ion channel kit for use in a hybridisation assay, said kit comprising an ion channel array according to any of claims  1 - 28 .  
     
     
         57 . The ion channel kit according to  claim 56 , wherein said kit further comprises reagents for generating a labelled target polynucleotide sample.  
     
     
         58 . The ion channel kit according to the claims  56 - 57 , wherein said kit further comprises a hybridisation buffer.