Patent Application
20070254288
Clinical pain conditions, including inflammatory and neuropathic pain, and pain hypersensitivity syndromes without any clear tissue injury or lesion to the nervous system result from diverse neurobiological mechanisms operating in the peripheral and central nervous systems. Some mechanisms are unique to a particular disease etiology and others are common to multiple pain syndromes. Some mechanisms are transient and some irreversible (Scholz and Woolf, Nat Neurosci 5:1062-1067 (2002)). These include changes in the excitability and threshold of primary sensory neurons, alterations in synaptic processing in the spinal cord, loss of inhibitory interneurons, and modifications in brainstem facilitatory and inhibitory input to the spinal cord. These changes in neuronal activity result from novel gene transcription, posttranslational modifications, alterations in ion channel and receptor trafficking, activation of microglia, neuroimmune interactions, and neuronal apoptosis (Marchand et al., Nat Rev Neurosci 6:521-32 (2005); Woolf et al., Science 288:1765-1769 (2000); Tsuda et al., Trends Neurosci 28:101-107 (2005); Hunt and Mantyh, Nat Rev Neurosci 2:83-91 (2001); Scholz et al., J Neurosci 25:7317-7323 (2005)). Pain hypersensitivity, manifesting as spontaneous pain, pain in response to normally innocuous stimuli (allodynia), and an exaggerated response to noxious stimuli (hyperalgesia) are the dominant features of clinical pain and persist, in some individuals, long after the initial injury is resolved.
Several studies in inbred rodent strains and human twins suggest that the risk of developing chronic pain may be genetically determined (Mogil et al., Pain 80:67-82 (1999); Diatchenko et al., Hum Mol Genet 14:135-43 (2005); Norbury et al., 11th World Congress on Pain, Sydney, Australia Abstract (2005); Fillingim et al., J Pain 6:159-67 (2005); Zondervan et al., Behav Genet 35:177-88 (2005); MacGregor et al., Arthritis Rheum 51:160-7 (2004)). However, prior to the present invention, it was not well understood what perpetuates the maladaptive processes that sustain enhanced pain sensitivity in certain individuals. Neither were reliable predictors of pain response available.
The invention provides methods and kits for predicting pain sensitivity, diagnosing the risk of developing acute or chronic pain based on the identification of pain protective allelic variants in the GCH1 and KCNS1 genes, or the risk of diagnosing an increased risk of developing a tetrahydrobiopterin (BH4)-related disorder in a mammalian subject, based on the identification of allelic variants in the GCH1 gene.
In one particular aspect, the invention features a method for predicting pain sensitivity, diagnosing the risk of developing acute or chronic pain, or diagnosing the risk of developing a BH4-related disorder (e.g., cardiovascular disease or any BH4-related disorder described herein) in a mammalian subject that includes determining the presence or absence of an allelic variant in a GTP cyclohydrolase (GCH1) nucleic acid in a biological sample from the subject, the allelic variant correlating with pain sensitivity, development of acute or chronic pain, or a BH4-related disorder. The GCH1 allelic variant may be present in a haplotype block located within human chromosome 14q22.1-14q22.2 (e.g., an allelic variant including a SNP selected from the group consisting of the SNPs listed in Table 1 or an allelic variant including an A at position C.-9610, a T at position C.343+8900, or both). In certain embodiments, the allelic variant may include an A at position C.-9610, C at position C.-4289, G at position C.343+26, T at position C.343+8900, T at position C.343+10374, G at position C.343+14008, C at position C.343+18373, A at position C.344-11861, C at position C.344-4721, A at position C.454-2181, C at position C.509+1551, G at position C.509+5836, A at position C.627-708, G at position C.*3932, and G at position C.*4279 of the GCH1 sequence (positions relative to the coding exons for the GCH1 gene, as shown in
In another aspect, the invention features a method for predicting pain sensitivity or diagnosing the risk of developing acute or chronic pain in a mammalian subject that includes determining the presence or absence of an allelic variant in a potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1 (KCNS1) nucleic acid in a biological sample from the subject, the allelic variant correlating with pain sensitivity or development of acute or chronic pain. The KCNS1 allelic variant may be present in a haplotype block located within human chromosome 20q12, may cause altered (e.g., increases or decreased) activity, expression, heteromultimerization, or trafficking of the KCNS1 protein. The allelic variant may be present in a regulatory region (e.g., the promotor region a 5′ regulatory region, a 3′ regulatory region, an enhancer element, or a suppressor element), within the coding region (e.g., in an intron or in an exon) of the KCNS1 gene, or any combination thereof. The allelic variant may include a SNP selected from the group consisting of the SNPs listed in Table 2 or may include an A at position 43,157,041 (e.g., include a G at position 43,155,431, A at position 43,157,041, and C at position 43,160,569) of the KCNS1 sequence (positions from SNP browser software and the Panther Classification System public database, November 2005).
In either of the above aspects, the method may include determining whether the nucleic acid sample includes one copy or multiple copies of the allelic variant. The acute pain may be one or more of mechanical pain, heat pain, cold pain, ischemic pain, or chemical-induced pain. The pain may also be peripheral or central neuropathic pain, inflammatory pain, headache pain (e.g., migraine-related pain), irritable bowel syndrome-related pain, fibromyalgia-related pain, arthritic pain, skeletal pain, joint pain, gastrointestinal pain, muscle pain, angina pain, facial pain, pelvic pain, claudication, postoperative pain, post traumatic pain, tension-type headache, obstetric or gynecological pain, or chemotherapy-induced pain. The mammal may be a human.
The presence or absence of the allelic variant may be determined by nucleic acid sequencing or by PCR analysis. In addition, the method may be used to determine the dosing or choice of an analgesic or an anesthetic administered to the subject; whether to include the subject in a clinical trial involving an analgesic; whether to carry out a surgical procedure (e.g., a surgical procedure involving nerve damage or treatment of nerve damage) on the subject; or whether to administer a neurotoxic treatment to the subject. Further, the method may be used to determine the likelihood of pain development in the subject as part of an insurance risk analysis or as criterion for a job assignment. The method may also be used in conjunction with a clinical trial, for example, as a basis for establishing a statistical significant difference between the control group and the experimental group in a clinical trial involving pain or another disorder involving GCH1 such as those described herein.
In either of the above aspects, the allelic variants in Tables 1 and 2 represent exemplary SNPs that may be utilized to predict a subject's pain profile; alternative selection of one or more SNPs may also be used to identify a pain protective phenotype, and these one or more SNPs may be extended beyond the genomic regions described in detail herein. In addition to SNPs, other types of genetic variation (e.g., variable number tandem repeats (VNTRs), or short tandem repeats (STRs)) may be used in the methods of the invention. Such sequences may be derived from public or commercial databases. Novel SNPs may be identified by resequencing of gene regions; such novel SNPs also may be used in the methods of the invention.
The methods of the invention may be performed using any genotyping assay, e.g., those described herein. The methods may further be combined with genotyping for polymorphisms in additional genes known or identified to affect the risk of developing pain (e.g., COMT).
The methods of the invention may employ any genotyping method for identification of human genotypes, haplotypes, or diplotypes. A wide range of methods is known in the art, including chemical assays (e.g., allele specific hybridization, polymerase extension, oligonucleotide ligation, enzymatic cleavage, flap endonuclease discrimination) and detection methods (e.g., fluorescence, colorimetry, chemiluminiscence, and mass spectrometry). Specific methods are described herein. Desirably, a genotyping method is robust, highly sensitive and specific, rapid, amenable to multiplexing and high-throughput analysis, and of reasonable cost.
In a third aspect, the invention features a method for predicting pain sensitivity, diagnosing the risk of developing acute or chronic pain, or diagnosing the risk of developing a BH4-associated disorder in a mammalian subject. The method includes the steps of (a) contacting a biological sample including a cell (e.g., a smooth muscle cell, an endothelial cell, a vascular cell, a lymphocyte, or a leukocyte) from the subject with a sufficient amount of a composition that (i) increases the level of cyclic AMP in the cell (e.g., a phosphodiesterase inhibitor, an adenyl cyclase activator such as forskolin, or a cAMP, analog such as those described herein), (ii) includes lipopolysaccharide (LPS), or (iii) includes an inflammatory cytokine (e.g., tumor necrosis factor α, interleukin-1β, and interferon-γ); and (b) measuring the expression or activity of GTP cyclohydrolase (GCH1) in the sample, wherein the level of said expression or activity, when compared to a baseline value, is indicative of whether said patient has altered (e.g., increased or decreased) pain sensitivity or is diagnostic of the risk of developing acute or chronic pain or developing a BH4-associated disorder in said subject. A decrease in GCH1 expression or activity relative to a baseline value may be indicative of decreased pain sensitivity or decreased risk of developing acute or chronic pain. GCH1 expression may be measured by determining GCH1 mRNA or GCH1 protein level in the cell. GCH1 activity may be measured by determining neopterin, biopterin, or BH4 levels in the cell.
In a fourth aspect, the invention features a kit for predicting pain sensitivity, diagnosing the risk of developing acute or chronic pain, or diagnosing a propensity to develop a BH4-related disorder in a mammalian subject that includes a set of primers for amplification of a sequence including an allelic variant in a GCH1 gene, and instructions for use. The GCH1 allelic variant may be present in a haplotype block located within human chromosome 14q22.1-14q22.2 (e.g., the GCH1 allelic variant may include a SNP selected from the group consisting of the SNPs listed in Table 1 or the GCH1 allelic variant may include an A at position C.-9610, a T at position C.343+8900, or both). In certain embodiments, the allelic variant may include an A at position C.-9610, C at position C.-4289, G at position C.343+26, T at position C.343+8900, T at position C.343+10374, G at position C.343+14008, C at position C.343+18373, A at position C.344-11861, C at position C.344-4721, A at position C.454-2181, C at position C.509+1551, G at position C.509+5836, A at position C.627-708, G at position C.*3932, and G at position C.*4279 of the GCH1 sequence (positions relative to the exons in the GCH1 gene, as shown in
In a fifth aspect, the invention features a kit for predicting pain sensitivity or diagnosing the risk of developing acute or chronic pain in a mammalian subject that includes a set of primers for amplification of a sequence including an allelic variant in a KCNS1 gene and instructions for use. The KCNS1 allelic variant may be present in a haplotype block located within human chromosome 20q12. The KCNS1 allelic variant may cause altered (e.g., decreased) activity, expression, heteromultimerization, or trafficking of the KCNS1 protein; the allelic variant may include a SNP selected from the group consisting of the SNPs in Table 2 or may include an A at position 43,157,041 (e.g., a G at position 43,155,431, A at position 43,157,041, and C at position 43,160,569) of the KCNS1 sequence (positions from the SNP browser software and the Panther Classification System public database, November 2005).
In a sixth aspect, the invention features a kit for predicting pain sensitivity, diagnosing the risk of developing acute or chronic pain, or diagnosing the risk of developing an BH4-related disorder in a mammalian subject. The kit includes (i) an agent for increasing cyclic AMP levels in a cell, (ii) LPS, or (iii) an inflammatory cytokine (e.g., those described herein); an antibody specific for GTP cyclohydrolase (GCH1); a first primer for hybridization to a GTP cyclohydrolase (GCH1) mRNA sequence; and instructions for use. The kit may further include a second primer, where the first and second primers are capable of being used to amplify at least a portion of the GCH1 mRNA sequence.
In a seventh aspect, the invention features a kit for predicting pain sensitivity, diagnosing the risk of developing acute or chronic pain, or diagnosing the risk of developing an BH4-related disorder in a mammalian subject. The kit includes (i) an agent for increasing cyclic AMP levels in a cell, (ii) LPS, or (iii) an inflammatory cytokine (e.g., those described herein); an antibody specific for GTP cyclohydrolase (GCH1); and instructions for use.
In either the sixth or seventh aspect of the invention, the agent may be an adenyl cyclase activator (e.g., forskolin), a phosphodiesterase inhibitor, or any agent described herein.
As used herein, by “pain sensitivity” is meant the threshold, duration or intensity of a pain sensation including the sensation of pain in response to normally non-painful stimuli and an exaggerated or prolonged response to a painful stimulus.
By “biological sample” is meant a tissue biopsy, cell, bodily fluid (e.g., blood, serum, plasma, semen, urine, saliva, amniotic fluid, or cerebrospinal fluid) or other specimen obtained from a patient or a test subject.
By “increase” is meant a positive change of at least 3% as compared to a control value or baseline level. An increase may be at least 5%, 10%, 20%, 30%, 50%, 75%, 100%, 150%, 200%, 500%, 1,000% as compared to a control value.
By “decrease” is meant a negative change of at least 3% as compared to a control value or baseline level. A decrease may be at least 5%, 10%, 20%, 30%, 50%, 60%, 70%, 80%, 90%, 95%, or 99%, or even 100% as compared to a control value.
By “allelic variant” or “polymorphism” is meant a segment of the genome that is present in some individuals of a species and absent in other individuals of that species. Allelic variants can be found in the exons, introns, or the coding region of the gene or in the sequences that control expression of the gene.
By “baseline value,” is meant value to which an experimental value may be compared. Depending on the assay, the baseline value can be a positive control (e.g., from an individual known to possess a pain protective haplotype). In certain cases, it may be desirable to calculate the baseline value from an average over a population of individuals (e.g., individuals selected at random or individuals selected who possess or lack a particular genetic background, such as zero, one, or two copies of the GCH1 pain protective haplotype). One of skill in the art will know which baseline value is appropriate for the desired comparison and how to calculate such baseline values. Exemplary baseline values and means for determining such values for use in the methods of the invention are described herein.
By “BH4-related disorder” is meant any disease or condition caused by an increase or decrease in BH4 expression, concentration, or activity. Such disorders include any disease related to endothelial cell function such as cardiovascular disease including atherosclerosis, ischemic reperfusion injury, cardiac hypertrophy, vasculitis, hypertension (e.g., systemic or pulmonary), myocardial infarction, and cardiomyopathy. Increased risk of developing a BH4-related disorder is associated with individuals having a sedentary lifestyle, hypertension, hypercholesterolemia, diabetes mellitus, or chronic smoking. BH4 is involved in nitric oxide, 5-HT, dopamine, and nor-epinephrine, production, and any diseases or disorders involving these neurotransmitters, particularly in the cardiovascular and nervous systems, are encompassed by the term BH4-related disorder. For example, a GCH1 haplotype may be a marker for the risk of developing CVS disease (e.g., atherosclerosis, hypertension, myocardial infarction, or cardiomyopathy) as well as nervous system diseases other than pain. BH4-related disorders thus include diabetes, depression, neurodegenerative disorders (e.g., Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, Huntington's disease, multiple sclerosis), schizophrenia, carcinoid heart disease, and autonomic disturbance, or dystonia.
The use of GCH1 and KCNS1 polymorphisms as predictors of the intensity and chronicity or persistence of pain is a powerful tool that can be used to assist treatment decisions, including estimation of the risk-benefit ratio of a medical procedure, for example, surgery involving or treating nerve damage, neurotoxic treatments for cancer or HIV infection. Further, such diagnostic methods may be used to determine the need for aggressive analgesic treatment for patients with increased risk of developing acute or chronic pain or for avoiding damage to nerves in surgery. The methods may be used for determining whether a patient is at an increased risk of developing disorders related to endothelial cell function, including cardiovascular diseases. The methods may also be utilized in clinical trial design, for example, to determine whether to include a subject in a trial involving or testing an analgesic or analgesic procedure. Further, the method may be used, for example, by one in the insurance industry as part of a risk analysis profile for a subject's response to pain or therapy or for a determination of the subject's likelihood (e.g., by a current or potential employer or by an insurance company) of developing an inappropriate pain response.
Other features and advantages of the invention will be apparent from the following Detailed Description, the drawings, and the claims.
The present invention features methods for diagnosing patients with an altered sensitivity to pain, an altered susceptibility to developing acute or chronic pain, based on the identification of haplotypes in two genes, GCH1 and KCNS1, or a propensity to develop a BH4-related disorder, based on haplotypes in GCH1. These haplotypes can be diagnostic of pain sensitivity, acute or persistent pain development, or abnormal pain amplification. GCH1, a gene encoding a key enzyme in BH4 synthesis, was identified from a group of three genes whose transcripts are upregulated in response to peripheral nerve injury. The presence of a GCH1 haplotype was found to be protective against persistent radicular pain after surgical diskectomy and associated with reduced sensitivity to experimental pain. In addition, we observed that white blood cells from individuals with the pain protective GCH1 haplotype exhibited decreased GCH1 expression and activity upon forskolin challenge, thus demonstrating that the haplotype is functionally significant. Constitutive levels of GCH1 were normal in individuals with the pain protective GCH1 haplotype but the induction of GCH1 mRNA, protein and activity in response to a challenge, was reduced. On this basis, we believe this haplotype may be associated with an altered (e.g., increased or decreased) risk of developing a BH4-related disorder, for example, a disease involving endothelial cell function or a cardiovascular system disease (e.g., ischemic reperfusion injury, cardiac hypertrophy, vasculitis, and systemic and pulmonary hypertension) or a nervous system disease.
A second gene KCNS1 was likewise identified as possessing haplotype markers that correlate with pain sensitivity and chronic pain and that can therefore also be used as diagnostic markers according to the invention. These genes were identified by searching, using microarrays, both for genes regulated over time (3 to 40 days) in the rat DRG in three models of peripheral neuropathic pain: the spared nerve injury (SNI), chronic constriction injury (CCI), and spinal nerve ligation model (SNL) and for those that belong to common metabolic, signaling, or biosynthetic pathways. Transcripts for two of the three enzymes in the BH4 synthetic pathway, GCH1 and SR, were found to be upregulated in these models as was the BH4 recycling enzyme QDPR. Another gene identified with this screen was the potassium channel KCNS1, which was down-regulated in DRG all three models of peripheral neuropathic pain.
Involvement of BH4 Synthesis in Pain
Enzymes that synthesize or recycle the enzyme cofactor BH4, as described below, are upregulated in sensory neurons in response to peripheral nerve injury, and this pathway is also activated by peripheral inflammation. Blocking BH4 synthesis by independently inhibiting two of its synthesizing enzymes reduces acute and established neuropathic pain and prevents or diminishes inflammatory pain. Conversely, BH4 administration produces pain in naïve animals and enhances pain sensitivity in animals with either nerve injury or inflammation. Thus, BH4 synthesizing enzymes may be major regulators of pain sensitivity and BH4 may be an intrinsic pain-producing factor.
BH4 is an essential cofactor for several major enzymes; no reaction occurs in its absence even in the presence of substrate. BH4 levels therefore need to be tightly regulated. The absence or substantial reduction of BH4 production due to a loss-of-function mutation in the coding region of GTP cyclohydrolase or sepiapterin reductase genes results in severe neurological problems from a decrease or absence of amine transmitters (Segawa et al., Ann Neurol 54(Suppl 6):S32-45 (2003); Neville et al., Brain 128:2291-2296 (2005)). Elevation of BH4 levels, by increasing amine and nitric oxide synthesis may also be deleterious, particularly if downstream enzymes are also upregulated. Three days following nerve injury, an upregulation of neuronal tryptophan hydroxylase and neuronal nitric oxide synthase in ipsilateral DRGs occurs, supporting results of previous studies (
Elevated BH4 levels may cause BH4-dependent enzymes expressed in DRG neurons to be activated, may cause BH4 to be released from the neurons (Choi et al., Mol Pharmacol 58:633-40 (2000)) which may then act on neighboring cells (e.g., neuronal or non-neuronal cells) to regulate their enzymatic activity, or may exert a cofactor-independent action (Koshimura et al., J Neurochem 63:649-654 (1994); Mataga et al., Brain Res 551:64-71 (1991); Ohue et al., Brain Res 607:255-260 (1993)). A direct effect of BH4 on the excitability or synaptic efficacy of dorsal horn neurons was not observed. Because BH4 produces pain rapidly (<30 min), the pain-related effects likely do not involve long latency changes such as altered transcription, activation of microglia (Tsuda et al., Trends Neurosci 28:101-107 (2005)), or induction of neuronal cell death (Scholz et al., J Neurosci 25:7317-7323 (2005)). Similarly, as the GTP-cyclohydrolase inhibitor DAHP has a rapid onset of analgesic action and continues to be effective upon repeated administration (see below), a continued excess presence of BH4 may be required for its role in chronic pain. The efficacy of DAHP in the formalin test, peripheral inflammation, and multiple models of neuropathic pain, as described below, indicates a mechanism common to these diverse models. One possibility is the use-dependent central sensitization of dorsal horn neurons (Woolf, C. J., Nature 306:686-688 (1983)), which is common to the formalin, inflammatory, and neuropathic pain models. The effect of the “pain protective” GCH1 haplotype described below on pain arising from repeated heat pain stimulation, supports this idea, as this experimental pain model in humans appears to be contributed to by central changes in excitability (Price et al., Pain 59:165-174 (1994); Eide, P. K., Eur J Pain 4:5-15 (2000); Maixner et al., Pain 76:71-81 (1998); Vierck et al., J Neurophysiol 78:992-1002 (1997)). Nevertheless, DAHP also acts in phase one of the formalin test, and the GCH1 haplotype alters the immediate response to a noxious stimulus in humans. Thus, BH4 appears to contribute to the sensitivity to acute nociceptive stimuli.
Seven days after SNI, nitric oxide levels increase in the DRG, suggesting that NO overproduction contributes to the pain evoked by BH4. Pain producing effects of NO probably involve direct nitrosylation of target proteins (Hara et al., Nat Cell Biol 7:665-674 (2005)), modulation of NMDA receptor activity (Lipton et al., Nature 364:626-632 (1993)), and/or activation of the guanylyl cyclase-cGMP-PKG pathway (Tegeder et al., Proc Natl Acad Sci USA 101:3253-3257 (2004); Lewin et al., Nat Neurosci 2:18-23 (1999)) resulting in increased glutamatergic transmission (Huang et al., Mol Pharmacol 64:521-532 (2003)). Supporting this, inhibition of GTP cyclohydrolase prevents increases in both BH4 and NO, and NOS inhibition reduces mechanical and cold allodynia after SNI. BH4 may act in a paracrine as well as an autocrine fashion, as it is released from neurons (Choi et al., Mol Pharmacol 58:633-640 (2000)) and may both increase enzyme activity and produce cofactor-independent effects (Koshimura et al., J Neurochem 63:649-654 (1994); Shiraki et al., Biochem Biophys Res Commun 221:181-185 (1996)). Considering the latter, we found that BH4 produces a short latency calcium influx in cultured adult DRG neurons partly mediated through nitric oxide synthesis. Although neuronal tryptophan hydroxylase mRNA was upregulated in DRG neurons after SNI serotonin levels remained below detection limits in this tissue. In the spinal cord serotonin is expressed in descending inhibitory and excitatory fibers. DAHP treatment did not, however, significantly reduce serotonin concentrations in the spinal cord and brain stem (data not shown) or alter the forced water swim test (see
To evaluate the potential role of BH4 in human pain, we analyzed whether polymorphisms in GCH1, the rate-limiting BH4 synthesizing enzyme, are associated with specific pain phenotypes. If BH4 is absent or substantially reduced in humans due to rare missense, nonsense, deletion, or insertion mutations in the coding regions of GTP cyclohydrolase (Hagenah et al., Neurology 64:908-911 (2005)) or sepiapterin reductase genes, dopa-responsive dystonia and other severe neurological problems occur due to absence of amine transmitters (Ichinose et al., Nat Genet 8:236-242 (1994); Bonafe et al., Am J Hum Genet 69:269-277 (2001)). It is not known whether pain perception is affected by these rare mutations. Our homozygotes for the pain protective haplotype did not have any neurological diseases. We therefore speculated that the pain protective haplotype embodies a variation in a regulatory site that causes a modest impairment in GTP cyclohydrolase production or function. In support of this, constitutive expression of GTP cyclohydrolase and BH4 production was found to be equivalent in cells of carriers and non-carriers of the pain protective haplotype. However, forskolin-evoked upregulation was significantly reduced in carriers of the pain protective haplotype. Thus, we believe that the locations mediating GCH1 transcription involve elements in the region 5′ to exon-1 and within the large 20 kb intron-1 because the SNPs exclusively found in the pain protective haplotype are located in the putative promoter region of GCH1 (C.-9610G>A) and in intron-1 (C.343+8900A>T), respectively. These SNPs may modify transcription efficiency to signals mediated by cAMP-dependent transcription factors. Although hundreds of transcripts are regulated in DRGs by nerve injury or sustained nociceptor stimulation, and although many chemical agents and biologic molecules affect pain behavior in experimental settings, only few genes have been identified so far that modulate pain sensitivity in humans (Zubieta et al., Science 299:1240-1243 (2003); Mogil et al., Proc Natl Acad Sci USA 100:4867-4872 (2003)). The current finding for GCH1 is one of the first to be replicated across human populations.
Here, alterations in the level of the essential enzyme cofactor BH4 modify the sensitivity of the pain system, and single nucleotide polymorphisms in the gene for the rate-limiting BH4-producing enzyme GTP cyclohydrolase alter both responses in healthy humans to noxious stimuli and the susceptibility of patients for developing persistent neuropathic pain. Because the pain protective haplotype in GCH1 is associated with a reduction in the risk of developing persistent pain without signs of dystonia, a treatment strategy that could reduce excess de novo BH4 synthesis in the DRG, but not constitutive BH4 by targeting only induction of GTP cyclohydrolase or by leaving the recycling pathway intact, may provide a means for preventing the establishment or maintenance of chronic pain. Further, identification of a predictor of the intensity and chronicity of pain is a useful tool to assess an individual patient's risk for developing chronic pain. The effect of the pain protective haplotype on both experimental and persistent pain, and the involvement of BH4 in both inflammatory and neuropathic pain, may explain why sensitivity to acute experimental pain is a predictor of postsurgical and eventually chronic pain (Bisgaard et al., Pain 90:261-269 (2001); Bisgaard et al., Scand J Gastroenterol 40:1358-1364 (2005)).
Identification of the Link Between BH4 Synthesis and Chronic Pain
The link between BH4 synthesis and chronic pain was identified by searching the several hundred genes regulated in the dorsal root ganglion (DRG) following sciatic nerve injury for genes belonging to common metabolic, signaling, or biosynthetic pathways (Costigan et al., BMC Neurosci 3:16 (2002)). These genes are involved in producing chronic neuropathic pain. The regulated enzymes are GTP cyclohydrolase, which catalyzes the first, rate-limiting step, and sepiapterin reductase, which performs the final conversion of 6-pyrovoyl-tetrahydropterin to tetrahydrobiopterin (
BH4 is an essential cofactor for phenylalanine, tyrosine, and tryptophan hydroxylase and for nitric oxide synthases. Its availability, along with enzyme and substrate levels, is critical for catecholamine, serotonin, and nitric oxide synthesis and phenylalanine metabolism (Kobayashi et al., J Pharmacol Exp Ther 256:773-9 (1991); Khoo et al., Circulation (2005); Cho et al., J Neurosci 19:878-89 (1999); Thony et al., Biochem J 347(Pt 1):1-16 (2000)). Mutations in GTP cyclohydrolase or sepiapterin reductase that cause a congenital BH4 deficiency in the brain are characterized by symptoms related to monoamine neurotransmitter deficiency, resulting in dopa-responsive motor, psychiatric, and cognitive disorders (Segawa et al., Ann Neurol 54(Suppl 6):S32-45 (2003); Neville et al., Brain 28(Pt 10):2291-2296 (2005)). The production of BH4 is tightly regulated by GTP cyclohydrolase transcription and activity (Frank et al., J Invest Dermatol 111: 1058-1064 (1998); Bauer et al., J Neurochem 82:1300-1310 (2002)). Phosphorylation (Hesslinger et al., J Biol Chem 273:21616-21622 (1998)), feed-forward activation through phenylalanine (Maita et al., Proc Natl Acad Sci USA 99:1212-1217 (2002)), and feedback inhibition through BH4, both acting in concert with a GTP cyclohydrolase feedback regulatory protein (GFRP) (Maita et al., J Biol Chem 279:51534-51540 (2004)), all regulate GTP cyclohydrolase activity. Mutations in GTP cyclohydrolase or sepiapterin reductase that cause monoamine neurotransmitter deficiency, result in dopa-responsive motor, psychiatric and cognitive disorders (Ichinose et al., Nat Genet 8:236-242 (1994); Bonafe et al., Am J Hum Genet 69:269-277 (2001)). Given the absolute requirement for this cofactor for monoamine and nitric oxide synthesis, and the vital roles of these neurotransmitters in the nervous system, increasing BH4 levels may have a profound impact on neuronal signaling. As described herein, BH4 levels are critical for neuropathic and inflammatory pain, and a genetic polymorphism of GTP cyclohydrolase is associated with reduced pain sensitivity and chronicity in humans due to reduced BH4 production.
Upregulation of Tetrahydrobiopterin Synthesizing Enzymes
The expression of GTP cyclohydrolase and sepiapterin reductase over time in L4/5 DRGs was studied in three models of peripheral neuropathic pain: (i) the spared nerve injury (SNI) (Decosterd and Woolf, Pain 87:149-58 (2000)), (ii) chronic constriction injury (CCI) (Bennett and Xie, Pain 33:87-107 (1988)), and (iii) spinal nerve ligation model (SNL) (Kim and Chung, Pain 50:355-63 (1992)). In addition, expression in the intraplantar complete Freund's adjuvant (CFA) paw inflammation model was studied. These models produce long lasting heightened pain sensitivity including mechanical and cold allodynia as well as mechanical and heat hyperalgesia. GTP cyclohydrolase and sepiapterin reductase transcripts were upregulated in lumbar (L4/5) DRGs in all three nerve injury models (SNI
Inhibition of Neuropathic and Inflammatory Pain by Blocking BH4 Synthesis
To test if the observed increase in BH4 synthesis contributes to neuropathic and inflammatory pain, the effects of inhibitors of BH4-synthesizing enzymes in three models of peripheral neuropathic pain and in CFA-induced paw inflammation were analyzed. 2,4-diamino-6-hydroxypyrimidine (DAHP), the prototypic GTP cyclohydrolase inhibitor, was used to block GTP cyclohydrolase activity (Kolinsky and Gross, J Biol Chem 279:40677-40682 (2004); Yoneyama et al., Arch Biochem Biophys 388:67-73 (2001); Xie et al., J Biol Chem 273:21091-21098 (1998)). DAHP, like BH4, specifically binds at the interface of GTP cyclohydrolase and its feedback regulatory protein GFRP to form an inhibitory complex that blocks GTP cyclohydrolase activity (Maita et al., J Biol Chem 279:51534-51540 (2004)). DHAP is a low potency but specific inhibitor. Minor modifications of DAHP cause it to lose this inhibitory activity (Yoneyama et al., Arch Biochem Biophys 388:67-73 (2001)) and prevent DAHP from directly interacting with any of the BH4-dependent enzymes.
Injection of a single dose of DAHP (180 mg/kg i.p.) four days after sciatic nerve injury (SNI model), a time when pain hypersensitivity is present, reverses mechanical and cold pain hypersensitivity within 60 minutes (
DAHP (180 mg/kg i.p.) did not change the mechanical threshold for paw withdrawal or radiant heat evoked paw withdrawal latency in naïve animals (
Inhibition of Pain by Blocking Sepiapterin Reductase
To substantiate that the analgesic effects of DAHP result from reduced BH4 synthesis, the effect of N-acetyl-serotonin (NAS), an inhibitor of sepiapterin reductase, was also tested (Milstien and Kaufman, Biochem Biophys Res Commun 115:888-893 (1983)). NAS (100 μg/kg/hr) significantly reduces nerve-injury evoked mechanical and cold allodynia (
Induction of Pain Hypersensitivity by Tetrahydrobiopterin
To determine if BH4 enhances pain sensitivity in naïve animals, we injected its active enantiomer, (6R)-5,6,7,8-tetrahydrobiopterin dihydrochloride, intrathecally (1 μg/μl, 10 μl). 6R-BH4 causes a prompt and long lasting increase in response to noxious radiant heat (
Potential Mechanisms
Availability of BH4 regulates activity of NO synthases as well as tyrosine and tryptophan hydroxylases. Therefore, its pain producing effects may be mediated through excess activity of these enzymes. Following SNI, neuronal tryptophan hydroxylase and neuronal nitric oxide synthase (nNOS) in ipsilateral DRGs are upregulated (
To further analyze potential mechanisms, we employed calcium imaging with cultured adult rat DRG neurons. 6R-BH4 (0.3-10 μM) dose-dependently increased intracellular calcium levels in 67% of recorded cells (n=95;
Bath-applied 6R-BH4 to an isolated adult rat spinal cord slice did not change the frequency or amplitude of AMPA receptor mediated miniature excitatory postsynaptic currents or produced direct inward currents in superficial dorsal horn neurons (6R-BH4 10 μM n=6; 20 μM n=2; data not shown) indicating that BH4, in contrast to nitric oxide (Pan et al., Proc Natl Acad Sci USA 93:15423-15428 (1996)), does not increase glutamatergic transmission.
Pain Protective Haplotype of GTP Cyclohydrolase in Humans
We next determined whether polymorphisms in the genes that code for GTP cyclohydrolase (GCH1), sepiapterin reductase (SPR), or dihydropteridine reductase (QDPR) are linked to a distinct pain phenotype in human patients. DNA from 168 Caucasian adults, participants in a prospective observational study of surgical discectomy for persistent lumbar root pain caused by intervertebral disc herniation, was collected (Atlas et al., Spine 21:1777-1786 (1996); Chang et al., J Am Geriatr Soc 53:785-792 (2005)). Prior to the analyses, a single primary endpoint, persistent leg pain over the first postoperative year, was specified as a reflection of neuropathic pain. Secondary endpoints were changes in levels of anxiety and depression over the first year postoperatively, adjusted for the magnitude of pain relief provided by the surgery. From these participants, 15 single nucleotide polymorphisms (SNPs), spaced evenly through GCH1 (
*0 = common allele, 1 = uncommon allele.
NCBI IDs and SNP physical locations are from the National Center for Biotechnology Information database, August 2005 or the Ensemble Database v.38, April 2006. In few patients not all SNPs could be determined.
We next explored whether this “pain protective haplotype” is also associated with reduced heat, ischemic, and pressure pain sensitivity in two independent cohorts of healthy volunteers (see Methods described below and Table 4). Individuals carrying two copies of the “pain protective haplotype” are significantly less sensitive to mechanical pain and tend to be less sensitive to heat pain and ischemic pain (
Table 4, shown below, shows the associations of heat, mechanical, and ischemic pain with the number of copies of the “pain protective haplotype” in two independent cohorts of healthy volunteers. One cohort was examined at the University of North Carolina at Chapel Hill (UNC) and the second cohort was examined at the University of Florida (UF). Each individual pain measure was standardized to unit normal deviates (z-scores) with a mean of zero and standard deviation of one. Subjects who did not carry the “pain protective haplotype” X were grouped as 0/0, subjects carrying one X haplotype were grouped as X/0, and subjects carrying two copies of X haplotype were grouped as X/X. Independent association study analyses for each cohort and the combined cohorts are presented.
Leukocyte Studies
GCH1 mRNA and protein expression and BH4 synthesis were analyzed in EBV-immortalized leukocytes of patients who participated in the lumbar root pain study (Atlas et al., Spine 21:1777-1786 (1996); Chang et al., J Am Geriatr Soc 53:785-792 (2005)). Baseline expression (mRNA and protein) of GCH1 and BH4 levels did not significantly differ between carriers and non-carriers of the haplotype. Since GCH1 transcription increases in response to cAMP, acting through regulatory elements located in the proximal promoter (Hirayama et al., J Neurochem 79:576-587 (2001); Kapatos et al., J Biol Chem 275:5947-5957 (2000)), the cells were stimulated with forskolin (10 μM, 12 h) to increase adenyl cyclase activity. Forskolin increased GCH1 mRNA (
We also found that LPS, like forskolin, induced GCH1 to a lesser extent in cells from individuals with the pain protective haplotype as compared to individuals without the pain protective haplotype. Previous work has shown that stimulation with LPS, IL-1, TNF, and interferon gamma, like cAMP, increases cellular GTPCH levels and activity. Accordingly, we believe that cells from individuals carrying the pain protective haplotype or having reduced pain sensitivity will exhibit reduced levels/activity of GCH1 when contacted with an inflammatory cytokine or an interferon.
Tetrahydrobiopterin synthesis increases in rat sensory neurons in response both to axonal injury and peripheral inflammation. Blocking the increased BH4 synthesis by independently inhibiting two successive enzymes in the synthesis cascade reduces neuropathic and inflammatory pain and in contrast, BH4 administration produces pain in naïve animals and enhances inflammatory and neuropathic pain sensitivity. Furthermore, a haplotype of GCH1 that reduces its upregulation in response to a forskolin challenge is protective against persistent neuropathic pain and associated with reduced sensitivity to experimental pain in humans. We therefore have identified both a novel pathway involved in the production and modulation of pain and a genetic marker of pain sensitivity.
Materials and Methods for GTP Cyclohydrolase Studies
The following materials and methods were used to generate the results presented in Example 1.
Microarray Hybridization, Real Time RT-PCR, Slot Blot
Extraction of RNA, hybridization on the Affymetrix RGU34A chip in triplicate, and analysis of the array data were as described (Costigan et al., BMC Neurosci 3:16 (2002)). For Northern slot blots total RNA was transferred to nylon membranes, hybridized with 32P-labeled cDNA probes, and quantified using cyclophilin for normalization. Quantitative real-time PCR was performed using the Sybr green detection system with primer sets designed on Primer Express. Specific PCR product amplification was confirmed with gel electrophoresis. Transcript regulation was determined using the relative standard curve method per manufacturer's instructions (Applied Biosystems).
In Situ Hybridization
Fresh frozen DRGs were cut at 18 μm, postfixed, and acetylated. Riboprobes were obtained by in vitro transcription of cDNA and labeled with digoxigenin (Dig-labeling kit, Roche). Sections were hybridized with 200 ng/ml of sense or antisense probes in a prehybridization mix (Blackshaw and Snyder, J Neurosci 17:8083-8092 (1997)) and incubated with anti-Dig-AP (1:1000), developed with NBT/BCIP/levamisole, embedded in glycerol/gelatin or subjected to post in situ immunostaining. Primary antibodies: sheep Dig-AP 1:1000 (Roche), mouse NF200 1:4000 (Sigma), rabbit ATF-3 1:300 (SantaCruz). FITC-labeled Griffonia simplicifolia isolectin B4 (Sigma) 1:500. Blocking and antibody incubations in 1% blocking reagent (Roche).
Nerve Injury Models
Adult male Sprague Dawley rats (150-200 g, Charles River Laboratories) were used. For the SNI model two branches of the sciatic nerve, the common peroneal and the tibial nerve, were ligated and sectioned distally. For the CCI model the sciatic nerve was constricted with three Dexon 4/0 ligatures. For the SNL model, the L5 spinal nerve was tightly ligated. All surgical procedures were under isoflurane anesthesia. For the Formalin test 50 μl of 5% formaldehyde solution were injected into a hindpaw and flinches were counted per minute up to 60 min. Paw inflammation was induced with 50 μl complete Freund's adjuvant (CFA) injected into a hindpaw. Nociceptive analysis was done blinded, and animals were fully habituated to the room and test cages. Mechanical allodynia was assessed with graded strength monofilament von Frey hairs (0.0174-20.9 gram, log scaled), cold allodynia with the acetone test and heat hyperalgesia with the Hargreaves test. Drugs (Sigma) were injected intraperitoneally or intrathecally through a spinal catheter, osmotic pumps were used for infusion. Control animals received vehicle. L4/5 DRG and spinal cord tissue was processed for QRT-PCR, Western blotting, in situ hybridization and immunofluorescence studies.
Inflammatory Models
For the Formalin test 50 μl of 5% formaldehyde solution were injected into one hindpaw and flinches were counted per minute up to 60 min. Two hours after formalin injection animals were perfused with 4% PFA in 1×PBS, the spinal cord was dissected and subjected to cFos immunostaining (rabbit pAb Santa Cruz 1:500). For paw inflammation 50 μl complete Freund's Adjuvant (CFA) was injected into the paw.
Nociceptive Behavior
Animals were fully habituated and experiments performed blinded. Threshold for eliciting a withdrawal reflex to graded strength monofilament von Frey hairs (0.0174-20.9 g) was measured to assess mechanical allodynia. To measure cold allodynia, a drop of acetone was applied to the plantar hindpaw, and the time the animal spent licking, shaking or lifting the paw was measured (Tegeder et al., J Neurosci 24:1637-1645 (2004)). Paw withdrawal latency to radiant heat (lamp with 8 V, 50 W) assessed heat evoked pain (Ugo Basile).
Drug Treatment
DAHP was dissolved in 1:1 polyethylene glycol (PEG400) and 1×PBS, pH 7.4 (15 mg/ml) and administered i.p. or intrathecally (250 μg/kg/h; 5 μl/h). For all i.t. injections/infusions a spinal catheter (Recathco) was used and implanted as described (Kunz et al., Pain 110:409-418 (2004)). Infusions with an osmotic pump (Alzet). 6R-BH4 in ACSF was injected i.t. (10 μg, single 10 μl injection). N-acetyl-serotonin in 1×PBS pH 7.4 containing 3% ethanol was delivered by i.t. infusion (100 μg/kg/h; 5 μl/h). Control animals received the appropriate vehicle. All drugs from Sigma-Aldrich.
Plasma and CSF Concentrations of DAHP
Concentrations of DAHP were determined LC/MS-MS on a tandem quadrupole mass spectrometer (PE Sciex API 3000; Applied Biosystems). Extraction was by acetonitrile precipitation; chromatographic separation was performed on a Nucleosil C18 Nautilus column (125×4 mm I.D., 5 μm particle size, 100 Å pore size). Mobile phase was acetonitrile:water (80:20%, v/v), and formic acid (0.1%, v/v). Flow rate was 0.2 ml/min, and injection volume was 5 μl. DAHP eluted at 4.7 min. Mass spectrometer in positive ion mode, 5200 V, 400° C., auxiliary gas flow 6 l/min. The mass transition for the MRM was m/z 127→60. Quantification with Analyst software V1.1 (Applied Biosystems). Coefficient of variation over the calibration range of 10-4000 ng/ml <5%.
Immortalization of Leukocytes and Forskolin Stimulation
Peripheral blood lymphocytes were immortalized with EBV transfection. WBCs were stimulated with PHA in RPMI media, EBV was then added and cells were incubated at 37° C., 4.5% CO2, 90% relative humidity. Immortalized cells were stimulated with 10 μM forskolin for 12 h.
Tissue Concentrations of Neopterin and Biopterin
Homogenized tissue was oxidized with iodine, and pteridines were extracted on Oasis MCX cartridges. Concentrations of total biopterin, neopterin, and the internal standard rhamnopterin were determined by LC/MS-MS. LC analysis under gradient conditions on a Nucleosil C8 column; MS-MS analyses on an API 4000 Q TRAP triple quadrupole mass spectrometer. Precursor-to-product ion transitions of m/z 236→192 for biopterin, m/z 252→192 for neopterin, m/z 265→192 for rhamnopterin were used for the MRM. Linearity from 0.1-50 ng/ml. The coefficient of correlation for all measured sequences was at least 0.99. The intra-day and inter-day variability was <10%.
Electrophysiology
Miniature EPSCs were recorded at −70 mV by whole cell patch clamp in adult rat transverse spinal cord slices (Baba et al., Mol Cell Neurosci 24:818-830 (2003)). Intracellular [Ca]I was measured fluorometrically (ΔF 340/380) in cultured adult DRG neurons loaded with fura-2. 6R-BH4 (0.3-10 μM), DEA-NONOate (50 μM), and L-NAME (10-100 μM) were applied using a multibarrel fast drug delivery system.
Data Analysis
Data are means ±SEM. The number of animals per group was 9-12. Areas under the “effect versus time” curves (AUC) were calculated using the linear trapezoidal rule and compared with Student's t-test or univariate analysis of variance (ANOVA) with subsequent t-tests employing a Bonferroni alpha-correction for multiple comparisons. All other data were analyzed with univariate ANOVA or ANOVA for repeated measurements. P at 0.05 for all tests.
Human Genetic Studies
We genotyped 15 single nucleotide polymorphisms (SNPs), spaced evenly through GCH1, using the 5′ exonuclease method (Primer sets and probes in Table 6A). GCH1 haplotypes were identified in-silico using PHASE software, which implements a modified Expectation/Maximization (EM) algorithm to reconstruct haplotypes from population genotype data. Linkage disequilibrium (D′) between SNPs was used to describe the non-independence of alleles (
Chronic Lumbar Root Pain: Pain Outcome
We collected DNA from 168 Caucasian adults who participated in a prospective observational study of surgical diskectomy for persistent lumbar root pain (demographic data in Table 5 below). Between 1990 and 1992, approximately half of the active spine surgeons in Maine enrolled patients requiring diskectomy for lumbar root pain in a prospective observational study (Atlas et al., Spine 21:1777-1786 (1996)). Patients completed questionnaires pre-operatively, and at 3, 6, and 12 months postoperatively, and then annually through year 10. Pain outcome: leg pain was assessed by four items: Frequencies in the past week of “leg pain”, and of “leg pain after walking”, were rated as “never (0 points),” “very rarely (1),” “a few times (2),” “about ½ the time (3),” “usually (4),” “almost always (5),” and “always (6).” “Percent improvement in pain frequency” scores were calculated by subtracting frequency scores from the baseline score and dividing by the baseline score. Improvements in “leg pain” or in “leg pain after walking” since surgery were rated as “pain completely gone (6),” “much better (5),” “better (4),” “a little better (3),” “about the same (2),” “a little worse (1),” and “much worse (O).” For each variable in each patient, we calculated an area-under-the-curve score for the first year, and converted this score to a z-score by comparing the patient to the rest of the cohort. The z-score expresses the divergence of the experimental result x from the most probable result p as a number of standard deviations, calculated as z=(x−μ)/σ. The primary pain outcome variable was the mean of these four z-scores. Genotype-phenotype associations for each polymorphism were sought using the equation: leg pain over first year=a+b (number of copies of uncommon allele: 0, 1, or 2)+c (sex)+d (age)+e (workman's compensation status)+f (delay in surgery after initial enrollment)+g (Short-Form 36 (SF-36) general health scale)+error.
Experimental Pain Sensitivity in Healthy Subjects
In two separate cohorts of healthy volunteers we analyzed the association of heat, ischemic and mechanical pain with GCH1 diplotypes. One cohort was examined at the University of North Carolina at Chapel Hill (UNC) and the second cohort was examined at the University of Florida (UF). For the association studies, 384 subjects who did not carry the “pain protective haplotype” X as defined by the lumbar root pain study were grouped as 0/0, 153 subjects carrying one X haplotype were grouped as X/0, and 10 subjects carrying two copies of the X haplotype were grouped as X/X.
UNC Cohort: This sample group consisted of 212 healthy women aged 18 to 34 years of age (mean age 22.8). Experimental procedures used to assess pain perception are described in (Diatchenko et al., Hum Mol Genet 14:135-143 (2005)). Briefly, measures of heat pain threshold and tolerance (° C.) were averaged across three anatomical test sites, i.e. arm, cheek and foot. Pressure pain thresholds (kg) were assessed over the temporalis and masseter muscles, the temporomandibular joint and the ventral surface of the wrists. Temporal summation of heat pain was assessed by applying fifteen 53° C. heat pulses to the thenar region of the right hand. Subjects were instructed to rate their perception of each pulse using a verbal numerical analog scale using values between “0” and “19” to rate the intensity of non-painful warmth, and “20” (pain threshold) to “100” (most intense pain imaginable) to rate the intensity of heat pain. Ischemic pain threshold and tolerance (seconds) were assessed with the submaximal effort tourniquet procedure.
UF Cohort: This sample group consisted of 192 healthy female and 143 healthy male volunteers aged 18 to 52 years of age (mean age 24.0). Experimental procedures are described in Hastie et al. (Pain 116:227-237 (2005)). Briefly, heat pain threshold and tolerance (° C.) were assessed on the volar forearm, and 0 to 100 ratings of repetitive suprathreshold heat pain were assessed at 2 temperatures, 49 and 52° C. Pressure pain threshold (kg) was assessed at three sites, the masseter and trapezius muscle, and dorsal forearm over the ulna. Ischemic pain threshold and tolerance (seconds) were assessed via the submaximal effort tourniquet procedure.
In order to combine the data across the two cohorts, each subject's value for a given pain measure was standardized to unit normal deviates (z-scores) with a mean of zero and standard deviation of one. Differences between the diplotype groups were determined using one way ANOVA. For the UNC cohort, the effect of the diplotype on the differences in curve profiles (
Genotyping Methods
SNP markers: The physical position and frequency of minor alleles (>0.05) from a commercial database (Celera Discovery System, CDS, July, 2005) were used to select SNPs. 5′ nuclease assays could be designed for fifteen GCH1, three SPR, and eleven QDPR SNPs and genotyped in a highly accurate fashion. These panels of approximately equally-spaced markers covered each gene region plus 4-6 kb upstream and 4-6 kb downstream of each gene. Allele frequencies of all markers and their locations in their respective genes are shown in Tables 3A-3C.
Genomic DNA: Genomic DNA was extracted from lymphoblastoid cell lines and diluted to a concentration of 5 ng/μl. Two-μl aliquots were dried in 384-well plates.
Polymerase chain reaction (PCR) amplification: Genotyping was performed by the 5′ nuclease method using fluorogenic allele-specific probes. Oligonucleotide primer and probes sets were designed based on gene sequences from the CDS, July 2005. Primers and detection probes for each locus in each gene are listed in Tables 6A-6C below.
Reactions were performed in a 5 μl volume containing 2.25 μl TE (Assays On Demand) or 2.375 μl TE (Assays By Design), 2.5 μl PCR Master Mix (ABI, Foster City, Calif.), 10 ng genomic DNA, 900 nM of each forward and reverse primer, and 100 nM of each reporter and quencher probe. DNA was incubated at 50° C. for 2 min and at 95° C. for 10 min, and amplified on an ABI 9700 device for 40 cycles at 92° C. (Assays on Demand) or 95° C. (Assays By Design) for 15 s and 60° C. for 1 min. Allele-specific signals were distinguished by measuring endpoint 6-FAM or VIC fluorescence intensities at 508 nm and 560 nm, respectively, and genotypes were generated using Sequence Detection V. 1.7 (ABI).
Genotyping error rate was directly determined by re-genotyping 25% of the samples, randomly chosen, for each locus. The overall error rate was <0.005. Genotype completion rate was 0.99.
Inference of haplotypes: Haplotype phases—i.e., how the directly measured SNP alleles were distributed into two chromosomes in each patient—were inferred by the expectation-maximization (EM) algorithm (SAS/Genetics, Cary, N.C., USA).
KCNS1 Involvement in Chronic Pain
Voltage-gated potassium channels form the largest and most diversified class of ion channels and are present in both excitable and nonexcitable cells. Such channels generally regulate the resting membrane potential and control the shape and frequency of action potentials. The potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1 (KCNS1) or voltage-gated potassium channel 9.1 (KV9.1) gene encodes a potassium channel alpha subunit expressed in a variety of neurons, including those of the inferior colliculus. The protein encoded by KCNS1 is not functional alone; it can form heteromultimers with member 1 and with member 2 (and possibly other members) of the Shab-related subfamily of potassium voltage-gated channel proteins. This gene belongs to the S subfamily of the potassium channel family. KCNS1 is very highly expressed in the brain but is not detectable in other tissues. Within the brain, highest expression levels were found in the main olfactory bulb, cerebral cortex, hippocampal formation, habenula, basolateral amygdaloid nuclei, and cerebellum.
The opening of some K(+) channels plays an important role in the antinociception induced by agonists of many G-protein-coupled receptors (e.g., alpha(2)-adrenoceptors, opioid, GABA(B), muscarinic M(2), adenosine A(1), serotonin 5-HT(1A) and cannabinoid receptors). Several specific types of K(+) channels are involved in antinociception. The most widely studied are the ATP-sensitive K(+) channels. Drugs that open K(+) channels by direct activation (such as openers of neuronal K(v)7 and K(ATP) channels) produce antinociception in models of acute and chronic pain, suggesting that other neuronal K(+) channels (e.g., K(v) 1.4 channels) may represent an interesting target for the development of new K(+) channel openers with antinociceptive effects (Salinas et al., J. Biol. Chem. 272:24371-24379 (1997); Bourinet et al., Curr. Top. Med. Chem. 5:539-46. (2005); Ocana et al., Eur. J. Pharmacol. 500:203-19 (2004)). A reduction in K(+) channels after nerve injury may increase the risk of developing ectopic or spontaneous firing of neurons. Decreased K(+) channel opening may also reduce efficacy of opiate or other analgesic treatment.
In a manner similar to the identification of the genes involved in BH4 synthesis, the KCNS1 gene has been identified as being involved in chronic pain. Downregulation of the KCNS1 transcript in all three models of peripheral neuropathic pain (
KCNS1 is located on chromosome 20q12. Previously, no KCNS1 mutations or sequence variants had been used for association studies. Because of the lack of available putative functional KCNS1 variants, comprehensive haplotype-based analyses were performed in our chronic pain association study using a series of loci chosen for haplotype informativeness including known synonymous and non-synonymous mutations in the coding region (see markers numbers 4 and 5 respectively;
In Kv9.1, the SNP that changed isoleucine to valine was significant at 0.003 in the Maine low back pain post surgical patients. The primer and probe sequences used in this study for the 5′ nuclease genotyping of the seven KCNS1 markers are shown in Table 9.
Methods and Kits for Diagnosing a Propensity toward Pain Sensitivity, Developing Acute or Chronic Pain, or a Propensity to Develop a BH4-related Disorder
The present invention provides methods and kits useful in the diagnosis of pain sensitivity, the diagnosis of a propensity for, or risk of developing, acute or chronic pain in a subject, based on the discovery of allelic variants and haplotypes in the GCH1 and KCNS1 genes, or the risk of developing a BH4-related disorder based on the discovery of allelic variants and haplotypes in the GCH1 gene. Additional methods and kits are based the discovery that the GCH1 haplotype associated with reduced pain sensitive results in a reduced GCH1 expression and activity in leukocytes when challenged with forskolin, an agent which increases cellular cyclic AMP levels.
The results generated from use of such methods and kits can be used, for example, to determine the dosing or choice of an analgesic administered to the subject, whether to include the subject in a clinical trial involving an analgesic, whether to carry out a surgical procedure on the subject or to choose a method for anesthesia, whether to administer a neurotoxic treatment to the subject, or the likelihood of pain development in the subject (e.g., as part of an insurance risk analysis or choice of job assignment).
In addition, results generate from performing these methods can be used in conjunction with clinical trial data. The gold standard for proof of efficacy of a medical treatment is a statistically significant result in a clinical trial. By incorporating the presence or absence of a pain-protective haplotype into analysis of clinical trial data, it can be possible to generate statistically significant differences between the experimental arm and control groups of the trial. In particular, we believe GCH1 and KCNS1 genotypes or haplotypes can explain some of the variance observed within clinical trials. In particular, the genotypes or haplotypes described herein can be included in statistical analysis of pain trials, or other clinical trials for which GCH1 may be relevant, such as studies of vascular disease or mood.
These methods and kits are described in greater detail below.
Methods and Kits for Identifying Allelic Variants in a Subject
The methods for identifying an allelic variant in a subject can include the identification of the presence or absence of a polymorphism associated with an altered pain phenotype as well as a determination of the number of polymorphic alleles (e.g., 0, 1, or 2 alleles). Kits of the invention can include primers (e.g., 2, 3, 4, 8, 10, or more primers) which can be used to amplify genomic or mRNA to determine the presence or absence of an allelic variant. While the presence of a single allelic variant can be used for this analysis, the presence of multiple pain-protective alleles (for example, multiple pain-protective SNPs) is preferred for diagnostic purposes. Preferably, at least 4, more preferably, at least 8, 10 or 12, and most preferably at least 15 pain-protective allelic variants (e.g., SNPs) are detected and used for diagnostic or predictive purposes. Moreover, while the presence of a single copy of a pain protective allelic variant or haplotype indicates a reduced propensity for pain sensitivity or development of acute or chronic pain, the presence of two copies is further indicative of decreased pain sensitivity or acute or chronic pain propensity.
Detection of allelic variants can be performed by any method for nucleic acid analysis. For example, diagnosis can be accomplished by sequencing a portion of the genomic locus of the GCH1 or KCNS1 gene known to contain a polymorphism (e.g., a SNP) associated with an altered propensity to develop pain sensitivity or acute or chronic pain from a sample taken from a subject. This sequence analysis, as is known in the art and described herein, indicates the presence or absence of the polymorphism, which in turn elucidates the pain sensitivity and pain response profile of the subject.
In addition to sequencing, allelic variant and haplotype analysis may also be achieved, for example, using any PCR-based genotyping methods known in the art. Any primer capable of amplifying regions of the GCH1 or KCNS1 genes known to contain pain-protective polymorphisms may be utilized. Primers particularly useful for GCH1 and KCNS1 genotyping are listed in Tables 6A and 9, respectively, and allelic variants that correlate with altered pain risk are shown in Tables 1 and 2 and
Other methods of genotyping that may be used in the invention include the TaqMan 5′ exonuclease method, which is fast and sensitive, as well as hybridization to microsphere arrays and fluorescent detection by flow cytometry. Chemical assays, including allele specific hybridization (ASH), single base chain extension (SBCE), allele specific primer extension (ASPE), and oligonucleotide ligation assay (OLA), can be implemented in conjunction with microsphere arrays. Fluorescence classification techniques allow genotyping of up to 50 diallelic markers simultaneously in a single well. Typically, it requires less than one hour to analyze a 96-well plate permitting analysis of tens of thousands of genotypes per day.
Additional methods of genotype analysis that can be used in the invention include the SNPlex genotyping system, which is based on oligonucleotide ligation/PCR assay (OLA/PCR) technology and the ZipChute Mobility Modifier probes for multiplexed SNP genotyping. This method allows for the performance of over 200,000 genotypes per day with high accuracy and reproducibility. In one particular example, this method allows for identification of 48 SNPs simultaneously in a single biological sample with the ability to detect 4,500 SNPs in parallel in 15 minutes. While all of the above represent exemplary genotyping methods, any method known in the art for nucleic acid analysis may be used in the invention.
Methods and Kits for Identifying Altered GCH1 Expression or Activity in a Cell
The invention features methods that can be used to determine whether a subject has an altered sensitivity to pain or an altered risk of developing acute or chronic pain or developing an BH4-related disorder. In particular, the invention features methods and kits for determining if GCH1 expression or activity is altered (e.g., increased or decreased) in cells such as leukocytes following a challenge such as administration of an agent that increases cellular cyclic AMP (cAMP) levels, administration of LPS, administration of an inflammatory cytokine (e.g., IL-1, TNF), or administration of an interferon (e.g., interferon gamma). Any agent that increases cAMP levels may be used in the methods of the invention. For example, agents such as adenyl cyclase activators (e.g., forskolin), dexamethasone, cholera toxin, cAMP analogs (e.g., 8-bromo-cyclic AMP, 8-(4-chlorophenylthio)cyclic AMP, N6, O2′-dibutyryl cylic AMP), cyclic AMP phosphodiesterase inhibitors (e.g., 3-isobutyl-1-methylxanthine, flavinoids described by Beretz et al., Cell Mol Life Sci 34:1054-1055, 1978, or any phosphodiesterase inhibitor known in the art), thyrotropin, thyrotripin releasing hormone, vasoactive intestinal polypeptide, and ethanol can be used to increase cAMP levels in a cell.
GCH1 expression or activity may assayed, for example, by measuring levels of GCH1 mRNA (e.g., using a microarray, QT-PCR, northern blot analysis, or any other method known in the art) or GCH1 protein (e.g., using an antibody based detection method such as a Western blot or ELISA). GCH1 activity can be measured using an intermediate or product of the BH4 pathway such as neopterin, biopterin, or BH4. In general, expression or activity of GCH1 in a cell treated with an agent that increases cAMP levels (e.g., forskolin) is measured and then compared to a baseline value or baseline values. A change in GCH1 expression or activity relative to the baseline value(s) is therefore indicative of the test subject's pain sensitivity, the test subject's risk of developing acute or chronic pain, or the test subject's risk of developing an BH4-related disorder.
A baseline value for use in the diagnostic methods of the invention may be established by several different means. In one example, a positive control is used as the baseline value. Here, GCH1 expression or activity level from an individual with the GCH1 pain-protective haplotype treated with an agent is measured and used as a baseline value. Thus, an increase (e.g., of at least 3%, 5%, 10%, 20%, 30%, 40%, 50%, 75%, 90%, 100%, or 200%) in GCH1 expression or activity in the test subject as compared to the baseline value is indicative of increased pain sensitivity or an increased risk of developing acute or chronic pain or developing an BH4-related disorder as compared to an individual with the GCH1 pain protective haplotype.
A baseline value may also be established by averaging GCH1 expression or activity values over a number of individuals. For example, the GCH1 expression or activity in cells from individuals (e.g., at least 2, 5, 10, 20, 50, 100, 200, or 500 individuals) with the GCH1 pain protective haplotype may be used to establish a baseline value for a positive control. A negative control value may likewise be established from a group of individuals (e.g., at least 2, 5, 10, 20, 50, 100, 200, or 500 individuals), for example, either (a) from individuals selected at random or (b) from individuals known to lack copies of the GCH1 pain protective haplotype.
A sample from a test subject may also be compared to multiple baseline values, e.g., established from two or three groups of individuals. For example, three groups of individuals (e.g., where each group independently consists of at least 2, 5, 10, 20, 50, 100, or 200 individuals) may be used to establish three baseline values. In this approach, subjects are separated into the three groups based on whether they have zero, one, or two copies of the GCH1 pain protective haplotype. The level of GCH1 expression or activity upon treatment of cells from each individual with a composition that increases cAMP levels is measured. The average value of GCH1 expression or activity for each group can thus be calculated from these measurements, thereby establishing three baseline values. The value measured from treated sample of the test subject is then compared to the three baseline values. The test subject's pain sensitivity, risk of developing acute or chronic pain, or risk of developing an BH4-related disorder can accordingly be determined on this basis of this comparison.
All patents, patent applications, and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent, patent application, or publication was specifically and individually indicated to be incorporated by reference.
This application claims benefit of U.S. Provisional Application No. 60/742,820, filed Dec. 6, 2005, which is hereby incorporated by reference.
The United States Government has a paid-up license in this invention and the right in limited circumstances to require the patent owner to license others on reasonable terms as provided for by the terms of NS039518, NS038253, Z01 DE00366, Z01 AA000301, DE16558, DE07509, and NS045685 awarded by the National Institutes of Health.
| Number | Date | Country | |
|---|---|---|---|
| 60742820 | Dec 2005 | US |
