EP1226276A2

EP1226276A2 - Diagnostic test for cephalic pain

Info

Publication number: EP1226276A2
Application number: EP00972963A
Authority: EP
Inventors: Ian James Purvis; Linda Catherine Mccarthy
Original assignee: Glaxo Group Ltd
Current assignee: Glaxo Group Ltd
Priority date: 1999-10-19
Filing date: 2000-10-19
Publication date: 2002-07-31
Also published as: WO2001029255A2; WO2001029256A2; WO2001029255A3; JP2003512062A; GB9924717D0; AU1152001A; WO2001029256A3; WO2001029255A9; AU7935600A

Abstract

A method of diagnosing susceptibility to cephalic pain in an individual, which method comprises typing in a sample from the individual the insulin receptor gene region or insulin receptor protein of the individual and determining thereby whether the individual is susceptible to cephalic pain.

Description

DIAGNOSTIC TEST FOR CEPHALIC PAIN

Field of the invention

The invention relates to the diagnosis of susceptibility to cephalic pain and agents which can be used in the diagnosis.

Background of the invention

Cephalic pain disorders are generally multifactorial disorders, many of which have an unknown etiology. No biochemical marker has been found for many of these disorders, and therefore diagnosis can only be done by clinical symptoms. Both environmental and genetic factors are thought to contribute to cephalic pain disorders. In the case of susceptibility to migraine familial aggregation is observed, and segregation analysis of the pattern of inheritance of migraine within families indicates a multifactorial inheritance (not a simple Mendelian inheritance). A multifactorial inheritance means that many genes contribute to the genetic predisposition to migraine, making it difficult to identify the individual susceptibility genes in linkage studies.

Summary of the invention

The inventors have shown that the insulin receptor is involved in the etiology of migraine. They have found that polymorphisms in the insulin receptor gene cause susceptibility to cephalic pain, and in particular to migraine.

Accordingly, the invention provides a method of diagnosing susceptibility to cephalic pain in an individual, which method comprises typing in a sample from the individual the insulin receptor gene region or insulin receptor protein of the individual and determining thereby whether the individual is susceptible to cephalic pain.

The invention also provides a method of diagnosing susceptibility to cephalic pain in an individual, which method comprises typing in vivo the insulin receptor gene region or insulin receptor protein of the individual and determining thereby whether the individual is susceptible to cephalic pain.

Description of the Figure

Figure 1 shows the principle of the Taqman (trade mark) allelic discrimination assay, adapted to detect a polymorphism according to the invention. Two allelic specific primers, G and A, differ in their sequence at the polymorphic site (either G or A) and in the fluorescent dye attached to their 5 ' end (either F or H). In the Figure, only the allele corresponding to probe G is present. Probe G can therefore anneal without mismatch to the template and. as Taq DNA polymerase extends from the non- specific primer upstream, the nucleotides containing the fluorescent dye F and quenching agent can be removed from the specific primer by the 5' to 3 ' endonuclease activity of Taq. Released from the quenching agent, the dye then fluoresces and this can be detected to determine that the allele corresponding to probe G is present in the sample.

Description of sequences in Sequence Listing

SEQ ID NO's: 1 to 22 are the sequences of exons 1 to 22 of the insulin receptor gene; SEQ ID NO: 23 is the complete coding sequence of the insulin receptor mRNA; SEQ ID NO: 24 is the sequence of the mRNA for the insulin receptor precursor; and SEQ ID NO: 25 is the complete sequence from exons 14 to 17 of the insulin receptor gene, including introns.

Detailed description of the invention

The present invention is concerned with the diagnosis of cephalic pain. The insulin receptor gene region or insulin receptor protein of an individual is typed. The individual's susceptibility to cephalic pain can thus be determined. The cephalic pain is typically a cluster headache, chronic paroxysmal hemicrania. headache associated with vascular disorders, headache associated with substances or their withdrawal (for example drug withdrawal), tension headache and, in particular, migraine with aura or migraine without aura. The typing of the insulin receptor gene region or insulin receptor protein may comprise the measurement of any suitable characteristic of the gene region or receptor to determine whether the individual is susceptible to cephalic pain. As discussed below such a characteristic includes a phenotype which is affected by the insulin receptor.

Typically the characteristic which is measured is one which can be influenced by a cephalic pain susceptibility polymoφhism in the insulin receptor gene region or protein (e.g any such polymoφhism mentioned herein). The individual may or may not have a cephalic pain susceptibility polymoφhism, but the gene region or receptor may have been affected by other factors (environmental or genetic) which have caused an effect which is typically similar to the effect ol the susceptibility polymoφhism Such an effect may be any ot the effects of the polymoφhisms discussed herein

Typically the typing comprises identifying whether the individual has a cephalic pain susceptibility polymoφhism. or a polymoφhism which is in linkage disequilibrium with 5 such a polymoφhism, in (1) the insulin receptor gene region or (n) the insulin receptor protein

Polymorphisms

Polymoφhisms which are in linkage disequilibrium with each other in a population

10 tend to be found together on the same chromosome Typically one is found at least 30% of the times, for example at least 40 %, 50%, 70% or 90%, of the time the other is found on a particular chromosome in individuals in the population Thus polymoφhisms which are not functional susceptibility poiymoφhisms. but are in linkage disequilibrium with the functional polymoφhisms, may act as a marker indicating the presence ot the l-> polymoφhism Poiymoφhisms which are in linkage disequilibrium with anv ot the poiymoφhisms mentioned herein are typically within 500kb, preterablv within 400kb, 200kb, 100 kb, 50kb, lOkb, 5kb or 1 kb ot the polymoφhism Similarly the term 'insulin receptor gene region" generally encompasses any of these distances from 5' to the transcription start site and 3' to the transcription termination site

20 As mentioned above the polymoφhism which is typed may be in the insulin receptor gene region or protein The polvmoφhism is typically an insertion, deletion or substitution with a length of at least 1 , 2, 5 or more base pairs or amino acids

In the case of a gene region polymoφhism, the polymoφhism is typically a substitution of 1 base pair, I e a single polynucleotide polymoφhism (SNP) The

25 polymoφhism may be 5' to the coding region, in the coding region, in an mtron or 3' to the coding region The polymoφhism which is detected is typically the functional mutation which contributes to cephalic pain, but may be a polymoφhism which is in linkage disequilibrium with the functional mutation

Thus generally the polymoφhism will be associated with cephalic pain, for example

30 as can be determined in a case/control study (e g as mentioned below) The polymoφhism will generally cause a change in any of the characteristics of the receptor discussed herein, such as expression, activity, expression variant, cellular localisation or the pattern of expression in different tissues The agent may modulate any of the following activities of the insulin receptor insulin binding. IGF- 1 binding, kinase activity (e g tyrosine. threomne or senne kinase activity), autophosphorylation. internalisation. re-cycling, interactions with regulatory proteins, or interactions with signalling complexes The polymoφhism may modulate the ability of the receptor to cause directly (or indirectly through another component) post-translational modifications, such as seπne/threonine phosphorylation, dephosphorylation (via senne /threomne- or tyrosine phosphatases) or glycosylation The polymoφhism typically has an agonist or antagonist effect on any of these characteristics ot the receptor Generally this will lead to a consequent increase or decrease in the activity of the pathway The polymoφhism may be any of the following polymoφhisms INSBa, INSCa, exon8 pol l , exonl 1 pol l , exonl 7 pol2, exonό pol l , exon7 pol l , exon7 pol2. exonδ pol2, eκon9 pol3. exonl 4 pol l or INSR-c 4479C>T These poiymoφhisms are defined in Table 2 below with reference to the sequence flanking the polymoφhism The form ot the poh moφhisms is allele 2 as defined in Table 2 for each of INSBa, INSCa, exonS pol l , exon l 1 pol l and exonl7 pol2 For each ot exonό pol l , exon7 pol l , exon7 pol2, exon8 pol2, exon9 pol3, exonl 4 poll and INSR-c 4479C>T, the form ot the polymoφhism is allele 1 or 2 as defined in Table2. Each of exonό pol l , exon7 pol l , exon7 pol2, exon8 pol2, exon9 pol3, exonl 4 pol l and INSR-c 4479C>T is in linkage disequilibrium with one of the associated poiymoφhisms. l e with one of INSBa, INSCa, exonδ pol l , exonl 1 pol l and exonl 7 pol2 The polymoφhism may be a polymoφhism at the same location as any of these particular poiymoφhisms (in the case ot a SNP, it will be an A, T, C or G at any of the locations) The polymoφhism may be in linkage disequilibrium with any of these particular poiymoφhisms The polymoφhism will have a sequence which is different from or the same as the corresponding region in any one of SEQ ID NOS 1 to 25 A polymoφhism which can be typed to determine susceptibility to cephalic pain may be identified by a method comprising determining whether a candidate polymoφhism in the insulin receptor gene region or insulin receptor protein is (l) associated with cephalic pain or (n) is in linkage disequilibrium with a polymoφhism which is associated with cephalic pam, and thereby determining whether the polymoφhism can be typed to determine susceptibility to cephalic

Detection of polymorphisms

The polymoφhism is typically detected by directly determining the presence of the polymoφhism sequence in a polynucleotide or protein of the individual. Such a polynucleotide is typically genomic DNA or mRNA, or a polynucleotide derived from these polynucleotides, such as in a library made using polynucleotide from the individual (e.g. a cDNA library). The processing of the polynucleotide or protein before the carrying out of the method is discussed further below.

Typically the presence of the polymoφhism is determined in a method that comprises contacting a polynucleotide or protein of the individual with a specific binding agent for the polymoφhism and determining whether the agent binds to a polymoφhism in the polynucleotide or protein, the binding of the agent to the polymoφhism indicating that the individual is susceptible to migraine.

Generally the agent will also bind to flanking nucleotides and amino acids on one or both sides of the polymorphism, for example at least 2, 5, 10. 15 or more flanking nucleotide or amino acids in total or on each side. Generally in the method determination of the binding of the agent to the polymoφhism can be done by determining the binding of the agent to the polynucleotide or protein. However in one embodiment the agent is able to bind the corresponding wild-type sequence by binding the nucleotides or amino acids which flank the polymoφhism position, although the manner of binding will be different to the binding of a polynucleotide or protein containing the polymoφhism, and this difference will generally be detectable in the method (for example this may occur in sequence specific PCR as discussed below).

In the case where the presence of the polymoφhism is being determined in a polynucleotide it may be detected in the double stranded form, but is typically detected in the single stranded form.

The agent may be a polynucleotide (single or double stranded) typically with a length of at least 10 nucleotides. for example at least 15. 20, 30 or more polynucleotides. The agent may be molecule which is structurally related to polynucleotides that comprises units (such as purines or pyrimidines) able to participate in Watson-Crick base pairing. The agent may be a protein, typically with a length of at least 10 amino acids, such as at least 20. 30, 50, 100 or more amino acids. The agent may be an antibody (including a fragment of such an antibody which is capable of binding the polymoφhism).

A polynucleotide agent which is used in the method will generally bind to the polymoφhism, and flanking sequence, of the polynucleotide of the individual in a sequence specific manner (e.g. hybridise in accordance with Watson-Crick base pairing) and thus typically has a sequence which is fully or partially complementary to the sequence of the polymoφhism and flanking region. The partially complementary sequence is homologous to the fully complementary sequence.

In one embodiment of the method the agent is as a probe. This may be labelled or may be capable of being labelled indirectly. The detection of the label may be used to detect the presence of the probe on (and hence bound to) the polynucleotide or protein of the individual. The binding of the probe to the polynucleotide or protein may be used to immobilise either the probe or the polynucleotide or protein (and thus to separate it from one composition or solution). In one embodiment the polynucleotide or protein of the individual is immobilised on a solid support and then contacted with the probe. The presence of the probe immobilised to the solid support (via its binding to the polymoφhism) is then detected, either directly by detecting a label on the probe or indirectly by contacting the probe with a moiety that binds the probe. In the case of detecting a polynucleotide polymoφhism the solid support is generally made of nitrocellulose or nylon. In the case of a protein polymoφhism the method may be based on an ELISA system.

The method may be based on an oligonucleotide ligation assay in which two oligonucleotide probes are used. These probes bind to adjacent areas on the polynucleotide which contains the polymoφhism. allowing (after binding) the two probes to be ligated together by an appropriate ligase enzyme. However the two probes will only bind (in a manner which allows ligation) to a polynucleotide that contains the polymoφhism, and therefore the detection of the ligated product may be used to determine the presence of the polymoφhism.

In one embodiment the probe is used in a heteroduplex analysis based system to detect polynucleotide polymoφhisms. In such a system when the probe is bound to polynucleotide sequence containing the polymoφhism it forms a heteroduplex at the site where the polymoφhism occurs (i.e. it does not form a double strand structure). Such a heteroduplex structure can be detected by the use of an enzyme which single or double strand specific. Typically the probe is an RNA probe and the enzyme used is RNAse H which cleaves the heteroduplex region, thus allowing the polymoφhism to be detected by means of the detection of the cleavage products.

The method may be based on fluorescent chemical cleavage mismatch analysis which is described for example in PCR Methods and Applications 3, 268-71 (1994) and Proc. Natl. Acad. Sci. 85, 4397-4401 ( 1998).

In one embodiment the polynucleotide agent is able to act as a primer for a PCR reaction only if it binds a polynucleotide containing the polymoφhism (i.e. a sequence- or allele-specific PCR system). Thus a PCR product will only be produced if the polymoφhism is present in the polynucleotide of the individual. Thus the presence of the polymoφhism may be determined by the detection of the PCR product. Preferably the region of the primer which is complementary to the polymoφhism is at or near the 3' end of the primer. In one embodiment of this system the polynucleotide agent will bind to the wild- type sequence but will not act as a primer for a PCR reaction. The method may be an RFLP based system. This can be used if the presence of the polymoφhism in the polynucleotide creates or destroys a restriction site which is recognised by a restriction enzyme. Thus treatment of a polynucleotide with such a polymoφhism will lead to different products being produced compared to the corresponding wild-type sequence. Thus the detection of the presence of particular restriction digest products can be used to determine the presence of the polymoφhism.

The presence of the polymoφhism may be determined based on the change which the presence of the polymoφhism makes to the mobility of the polynucleotide or protein during gel electrophoresis. In the case of a polynucleotide single-stranded conformation polymoφhism (SSCP) analysis may be used. This measures the mobility of the single stranded polynucleotide on a denaturing gel compared to the corresponding wild-type polynucleotide, the detection of a difference in mobility indicating the presence of the polymoφhism. Denaturing gradient gel electrophoresis (DDGE) is a similar system where the polynucleotide is electrophoresed through a gel with a denaturing gradient, a difference in mobility compared to the corresponding wild-type polynucleotide indicating the presence of the polymoφhism.

The presence of the polymoφhism may be determined using a fluorescent dye and quenching agent-based PCR assay such as the Taqman PCR detection system. This is illustrated in Figure 1. In brief, this assay uses an allele specific primer comprising the sequence around, and including, the polymoφhism. The specific primer is labelled with a fluorescent dye at its 5' end , a quenching agent at its 3' end and a 3' phosphate group preventing the addition of nucleotides to it. Normally the fluorescence of the dye is quenched by the quenching agent present in the same primer. The allele specific primer is used in conjunction with a second primer capable of hybridising to either allele 5' of the polymoφhism.

In the assay, when the allele comprising the polymoφhism is present Taq DNA polymerase adds nucleotides to the nonspecific primer until it reaches the specific primer It then releases polynucleotides, the fluorescent dye and quenching agent from the specific primer through its endonuclease activity The fluorescent dye is therefore no longer in proximity to the quenching agent and fluoresces In the presence of the allele which does not comprise the polymoφhism the mismatch between the specific primer and template inhibits the endonuclease activity of Taq and the fluorescent dye is not release from the quenching agent Theretore by measuring the fluorescence emitted the presence or absence of the polymoφhism can be determined

In another method of detecting the polymoφhism a polynucleotide comprising the polymorphic region is sequenced across the region which contains the polvmoφhism to determine the presence ot the polymoφhism

Alternatively the presence of the polymoφhism may be determined indirectly, for example by measuring an effect which the polymoφhism causes This ettect may be in the expression or activity ot the insulin receptor Thus the presence of the polymoφhism may be determined by measuring the activity or level of the expression ot the insulin receptor in the individual

The expression of the insulin receptor may be determined by directly measuring the level of the receptor in the cell or indirectly by measuring the level of any other suitable component in the cell, such as measuring mRNA levels (e g using quantitative PCR, such as bv a Taqman based method)

In one embodiment the method is carried out in vivo, however typically it is carried out in vitro on a sample from the individual The sample typically comprises a body fluid of the individual and may for example be obtained using a swab, such as a mouth swab The sample may be a blood, urine, saliva, cheek cell or hair root sample The sample is typically processed before the method is carried out, for example DNA extraction may be earned out The polynucleotide or protein in the sample may be cleaved either physically or chemically (e g using a suitable enzyme) In one embodiment the part of polynucleotide in the sample is copied (or amplified), e g. by cloning or using a PCR based method Polynucleotide produced in such a procedure is understood to be covered by the term "polynucleotide of the individual" herein

As mentioned above the typing may comprise measuring a phenotype affected by the insulin receptor. Such a phenotype may be as a result of a change in the expression or activity of the insulin receptor. The effect which is measured may be a metabolic effect or an effect of receptor signalling activity, such as the level of a substance (e.g. in the blood or urine) which is related to metabolism (such as insulin or glucose), GLUT4 expression at the cell surface, stimulation of glucose or 2-deoxyglucose or 3-O-methyl glucose uptake into cells, increased glycogen synthase posphorylation, activation and glycogen synthesis, decreased lipolysis, increased fatty acid synthesis and incoφoration into triglyceride, inhibition of gluconeogenesis in hepatocytes.

A preferred effect which is measured is insulin sensitivity. Such methods are well known in the art and are described for example in The International Textbook of Diabetes Mellitus ed Alberti, DeFronzo. Keen and Zimmet (Wiley Press). Insulin sensitivity may be measured by determining the level of a characteristic which is part of the insulin response, such as glucose disposal.

Thus insulin sensitivity may be measured by administering glucose (either as a single administration or a constant infusion) to the individual and determining the level of plasma glucose (e.g. the intravenous glucose tolerance test). In particular embodiments the glucose is labelled (e.g. radioactively). The results from the test may be evaluated using a model of the glucose insulin system, such as the "minimum model" or using homeostatic model assessment (HOMA), for example as described in Ferrannini and Mari ( 1998) J. Hypertension 16, 895-906.

Diagnostic kit

The invention also provides a diagnostic kit that comprises a probe, primer, antibody (including an antibody fragment) or agent as defined herein. The kit may additionally comprise one or more other reagents or instruments (such as mentioned herein) which enable any of the embodiments of the method mentioned above to be carried out.

Such reagents or instruments include one or more of the following: a means to detect the binding of the agent to the polymoφhism, a detectable label (such as a fluorescent label), an enzyme able to act on a polynucleotide (typically a polymerase, restriction enzyme, ligase, RNAse H or an enzyme which can attach a label to a polynucleotide), suitable buffer(s) (aqueous solutions) for enzyme reagents, PCR primers which bind to regions flanking the polymoφhism, a positive and/or negative control, a gel electrophoresis apparatus, a means to isolate DNA from sample, a means to obtain a sample from the individual (such as swab or an instrument comprising a needle) or a support comprising wells on which detection reactions can be done.

Polynucleotides, proteins and antibodies The invention further provides an isolated polynucleotide or protein that comprises

(i) a polymoφhism that causes susceptibility to cephalic pain or (ii) a naturally occurring polymoφhism that is in linkage disequilibrium with (i). Such polymoφhisms may be any of the polymoφhisms mentioned herein. The polymoφhism that causes susceptibility may be one which is or which is not found in nature. The polynucleotide or protein may comprise human or animal sequence (or be homologous to such sequence). Such an animal is typically a mammal, such as a rodent (e.g a mouse, rat or hamster) or a primate. Such a polynucleotide or protein may comprise any of the human polymoφhisms mentioned herein at the equivalent positions in the animal polynucleotide or protein sequence. The polynucleotide or protein typically comprises the insulin receptor gene region sequence or the insulin receptor protein sequence, or is homologous to such sequences; or is part of (a fragment ot) such sequences. Such sequences may be of a human or animal. In particular the part of the sequence may correspond to any of the sequences given herein in or parts of such sequences. The polynucleotide is typically at least 5, 10, 15, 20, 30, 50, 100, 200, 500, bases long, such as at least Ikb, lOkb, lOOkb, 1000 kb or more in length. The polynucleotide is generally capable of hybridising selectively with a polynucleotide comprising all or part of the insulin receptor gene region sequence, including sequence 5' to the coding sequence, coding sequence, intron sequence or sequence 3' to the coding sequence. Thus it may be capable of selectively hybridising with all or part of the sequence shown in any one of SEQ ID NOS: l to 25 (including sequence complementary to that sequence).

Selective hybridisation means that generally the polynucleotide can hybridize to the gene region sequence at a level significantly above background. The signal level generated by the interaction between a polynucleotide of the invention and the gene region sequence is typically at least 10 fold, preferably at least 100 fold, as intense as interactions between other polynucleotides and the gene region sequence. The intensity of interaction may be measured, for example, by radiolabelling the polynucleotide, e.g. with ^j2P. Selective hybridisation is typically achieved using conditions of medium to high stringency (for example 0.03M sodium chloride and either 0.003M or 0.03M sodium citrate at from about 50°C to about 60°C).

Polynucleotides of the invention may comprise DNA or RNA. The polynucleotides may be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to polynucleotides are known in the art. These include methylphosphonate and phosphorothioate backbones, addition of acridine or polylysine chains at the 3' and/or 5' ends of the molecule. For the puφoses of the present invention, it is to be understood that the polynucleotides described herein may be modified by any method available in the art. The protein of the invention can be encoded by a polynucleotide of the invention.

The protein may comprise all or part of a polypeptide sequence encoded by any of the polynucleotides represented by SEQ ID NOS: l to 25, or be a homologue of all or part of such a sequence. The protein may have one or more of the activities of the insulin receptor, such as being able to bind insulin and/or signalling activity. The protein is typically at least 10 amino acids long, such as at least 20, 50, 100, 300 or 500 amino acids long.

The protein may be used to produce antibodies specific to the polymoφhism, such as those mentioned herein. This may be done for example by using the protein as an immunogen which is administered to a mammal (such as any of those mentioned herein), extracting B cells from the animal, selecting a B cell from the extracted cells based on the ability of the B cell to produce the antibody mentioned above, optionally immortalising the B cell and then obtaining the antibody from the selected B cell.

Polynucleotides or proteins of the invention may cany a revealing label. Labels are also mentioned above in relation to the method of the invention. Suitable labels include radioisotopes such as ²P or ^JDS, fluorescent labels, enzyme labels or other protein labels such as biotin.

Polynucleotides of the invention can be incorporated into a vector. Typically such a vector is a polynucleotide in which the sequence of the polynucleotide of the invention is present. The vector may be recombinant replicable vector, which may be used to replicate the nucleic acid in a compatible host cell. Thus in a further embodiment, the invention provides a method of making polynucleotides of the invention by introducing a polynucleotide of the invention into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector. The vector may be recovered from the host cell. Suitable host cells are described below in connection with expression vectors.

The vector may be an expression vector. In such a vector the polynucleotide of the invention in the vector is typically operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell. The term "operably linked" refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A control sequence "operably linked" to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. Such vectors may be transformed into a suitable host cell as described above to provide for expression of the protein of the invention. Thus, in a further aspect the invention provides a process for preparing the protein of the invention, which process comprises cultivating a host cell transformed or transfected with an expression vector as described above under conditions to provide for expression of the protein, and optionally recovering the expressed protein.

The vectors may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide and optionally a regulator of the promoter. The vectors may contain one or more selectable marker genes. Promoters and other expression regulation signals may be selected to be compatible with the host cell for which the expression vector is designed.

The proteins and polynucleotides of the invention may be present in a substantially isolated form. They may be mixed with carriers or diluents which will not interfere with their intended use and still be regarded as substantially isolated. They may also be in a substantially purified form, in which case it will generally comprise at least 90%, e.g. at least 95%, 98% or 99%, of the dry mass of the preparation.

Homologues

Homologues of polynucleotide or protein sequences are referred to herein. Such homologues typically have at least 70% homology, preferably at least 80, 90%, 95%, 97% or 99% homology, for example over a region of at least 15, 20, 30, 100 more contiguous nucleotides or amino acids. The homology may calculated on the basis of amino acid identity (sometimes referred to as "hard homology").

For example the UWGCG Package provides the BESTFIT program which can be used to calculate homology (for example used on its default settings) (Devereux et al (1984) Nucleic Acids Research 12. p387-395). The PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (such as identifying equivalent or corresponding sequences (typically on their default settings), for example as descnbed in Altschul S. F (1993) J Mol Evol 36.290-300, Altschul. S, F et al (1990) J Mol Biol 215.403-10

Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information [http://www.ncbi nlm.mh.gov/). This algorithm involves first identifying high scoring sequence pair (HSPs) by identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence T is referred to as the neighbourhood word score threshold (Altschul et al, supra). These initial neighbourhood word hits act as seeds for initiating searches to find HSPs containing them The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extensions for the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The BLAST program uses as defaults a word length ( W) of 1 1 , the BLOSUM62 scoπng matrix (see Henikoff and Henikoff ( 1992) Proc Natl Λcad Sci USA 89 10915-10919) alignments (B) of 50, expectation (E) of 10, M=5. N=4, and a comparison of both strands

The BLAST algorithm performs a statistical analysis of the similarity between two sequences; see e.g., Karhn and Altschul (1993) Proc Natl Acad Sci USA 90" 5873-5787 One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a sequence is considered similar to another sequence if the smallest sum probability in comparison of the first sequence to the second sequence is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001

The homologous sequence typically differ by at least 1, 2, 5, 10, 20 or more mutations (which may be substitutions, deletions or insertions of nucleotide or amino acids) These mutation may be measured across any of the regions mentioned above in relation to calculating homology. In the case of proteins the substitutions are preferably conservative substitutions. These are defined according to the following Table. Amino acids in the same block in the second column and preferably in the same line in the third column may be substituted for each other:

Trcmsgenic animals

The invention also provides a non-human animal transgenic for a polymoφhism as mentioned above. The animal may be any suitable mammal such as a rodent (e.g. a mouse, rat or hamster) or primate. Typically the genome of all or some of the cells of the animal comprises a polynucleotide of the invention. Generally the animal expresses a protein of the invention. Typically the animal suffers from cephalic pain and can be therefore used in a method to assess the efficacy of agents in relieving anti-cephalic pain. The trangenic model can further be used to assess the ability of agents to modulate insulin receptor signalling activity.

Treatment of patients

The invention provides a method for treating a patient who has been diagnosed as being susceptible to cephalic pain by a method of the invention, comprising administering an effective amount of an anti-cephalic pain agent to the patient. The anti-cephalic pain agent may therefore be administered to a patient to prevent the onset of such pain or to combat an episode of cephalic pain. The invention also provides: use of an anti-cephalic pain agent in the manufacture of a medicament for use in treating a patient who has been diagnosed as being susceptible to cephalic pain by a method of the invention; and a pharmaceutical pack comprising an anti-cephalic pain agent and instructions for administering of the agent to humans diagnosed by the method of the invention. The anti-cephalic pain agent is typically an anti-migraine agent. Suitable anti- migraine agents are a steroid (e.g. hydrocortisone or dexamethasone, a NSAIDs (non- steroidal anti-inflammatory drug)(e.g. ibuprofen), a 5HT1D agonist, lidocaine (e.g. in the form of a nasal spray), an opioid (e.g. codeine or moφhine), an Ergot preparation (e.g. ergotamine or dihydroergotamine), a triptan (e.g. sumatriptan, rizotriptan. naratriptan, zolmitriptan. eletriptan, frovatriptan or almotriptan), alniditan. metoclopramide, chloφromazine. prochloφerazine. a beta-adrenergic antagonist (e.g. propranolol), a tricyclic antidepressant (e.g. amitriptyline), a calcium channel antagonists (e.g. verapamil or diltiazem), cyproheptadine. ALX-0646 (a trytamine analogue), LY334370. U 109291 , IS 159 or PNU- 142633.

An effective amount of such an agent may be given to a human patient in need thereof. The dose of agent may be determined according to various parameters, especially according to the substance used; the age, weight and condition of the patient to be treated; the route of administration; and the required regimen. A suitable dose may however be from 0.1 to 100 mg/kg body weight such as 1 to 40 mg/kg body weight. Again, a physician will be able to determine the required route of administration and dosage for any particular patient.

The formulation of the agent will depend upon factors such as the nature of the substance and the condition to be treated. Typically the agent is formulated for use with a pharmaceutically acceptable carrier or diluent. For example it may be formulated for oral, parenteral, intravenous, intramuscular or subcutaneous administration. A physician will be able to determine the required route of administration for each particular patient. The pharmaceutical carrier or diluent may be, for example, an isotonic solution.

The effectiveness of particular anti-cephalic agents may be affected by or dependent on whether the individual has particular polymoφhisms in the insulin receptor gene region or insulin receptor. Thus the invention can allow the determination of whether an individual will respond to a particular anti-cephalic pain agent by determining whether the individual has a polymoφhism which affects the effectiveness of that agent. The invention includes a method of treating a patient who has been identified as being able to respond to the agent comprising administering the agent to the patient.

Similarly certain anti-cephalic agents may produce side effects in individuals with particular polymoφhisms in the insulin gene region or protein. Thus the invention can also allow the identification of a patient who is at increased risk of suffering side effects due to such an anti-cephalic agent by identifying whether an individual has such a polymoφhism.

Individuals who carry a particular polymoφhism in the insulin receptor gene may exhibit differences in their ability to regulate metabolic pathways under different physiological conditions and will display altered reactions to different diseases. In addition. differences in metabolic regulation arising as a result of the polymoφhism may have a direct effect on the response of an individual to gene therapy. The polymoφhism may therefore have the greatest effect on the efficacy of drugs designed to modulate the activity of the insulin receptor or other components in its signalling pathway. However, the polymoφhisms may also affect the response to agents acting on other biochemical pathways regulated by the insulin receptor. The invention may therefore be useful both to predict the clinical response to such agents and to determine therapeutic dose.

In a further aspect, the invention can be used to assess the predisposition and /or susceptibility of an individual to diseases mediated by the insulin receptor. Polymoφhisms may be particularly relevant to the development of such diseases. The present invention may be used to recognise individuals who are particularly at risk from developing these conditions.

In a further aspect, the invention may further be used in the development of new drug therapies which selectively target one or more allelic variants of the insulin receptor gene (i.e. which have different polymoφhisms). Identification of a link between a particular allelic variant and predisposition to disease development or response to drug therapy may have a significant impact on the design of new drugs. Drugs may be designed to regulate the biological activity of the variants implicated in the disease process while minimising effects on other variants.

The following Example illustrates the invention:

Example

Clinical criteria for identifying individuals with migraine The following criteria were used to identify individuals with specific types of migraine:

Migraine without aura:

HA (head ache) lasting 4-72 hrs if unsuccessfully treated; HA with at least 2 of the following: unilateral pain; pulsating quality; moderate to severe intensity; aggravation by physical activity;

HA with nausea, or vomiting, or photophobia, or phonophobia (at least 1).

Migraine with aura:

Aura lasting 4-60 minutes;

HA defined as above, with onset accompanying or following aura within 60 minutes.

Familial hemiplegic migraine:

HA fulfills migraine with aura characteristics; aura includes hemiparesis that may be prolonged (> 60 minutes): at least 1 first-degree relative with similar HAs.

Genotyping of individuals for SNPs

Samples were obtained from the study group and genomic DNA extracted using a standard kit and a slating out technique (Cambridge Molecular). The genotypes of the migraineurs with aura and control individuals for individual SNPs within the insulin receptor gene were then determined from the DNA samples obtained using the Taqman allelic discrimination assay.

For each polymoφhic site the allelic discrimination assay used two allele specific primers labeled with a different fluorescent dye at their 5' ends but with a common quenching agent at their 3' ends. Both primers had a 3' phosphate group so that Taq polymerase could not add nucleotides to them. The allele specific primers comprised the sequence encompassing the polymoφhic site and differed only in the sequence at this site. The allele specific primers were only capable of hybridizing without mismatches to the appropriate allele.

The allele specific primers were used in typing PCRs in conjunction with a third primer, which hybridized to the template 5' of the two specific primers. If the allele corresponding to one of the specific primers was present the specific primer would hybridize perfectly to the template. The Taq polymerase, extending the 5' primer, would then remove the nucleotides from the specific probe releasing both the fluorescent dye and the quenching agent. This resulted in an increase in the fluorescence from the dye no longer in close proximity to the quenching agent.

If the allele specific primer hybridized to the other allele the mismatch at the polymoφhic site would inhibit the 5^' to 3' endonuclease activity of Taq and hence prevent release of the fluorescent dye. The AB 17700 sequence detection system was used to measure the increase in fluorescence from each specific dye during the thermal cycling PCR directly in PCR reaction tubes. The information from the reactions was then analyzed. If an individual was homozygous for a particular allele only fluorescence corresponding to the dye from that specific primer would be released, if the individual was heterozygous both dyes would fluoresce.

Table 1 shows the P values for the co-inheritance of the associated SNPs with migraine. Table 2 shows the SNPs typed in the sample group to determine association of the SNP with migraine. The polymoφhic site typed is given together with the flanking sequence 5' and 3'. Table 1

Claims

1 A method of diagnosing susceptibility to cephalic pain in an individual, which method composes typing in a sample from the individual the insulin receptor gene region or insulin receptor protein ot the individual and determining thereby whether the individual is susceptible to cephalic pain.

2 A method according to claim 1 wherein the typing comprises identifying whether the individual has a cephalic pain susceptibility polymoφhism, or a polymoφhism which is in linkage diseqiuhbnum with such a polymoφhism, m (I) the insulin receptor gene region or (u) the insulin receptor protein. 3 A method according to claim 2 wherein the said polymoφhism is selected trom INSBa, INSCα, exonδ po l 1 , exonl 1 po l 1 , exon 17 po l2, exonό po l 1 , exon7 po l 1 , exon7 po l 2, exonS po l 2, exon9 po l 3, exon 14 po l I and INSR-c 4479C.T, or is in linkage disequilibrium therewith.

4 A method according to any one of the preceding claims which compnses contacting a polynucleotide or protein of the individual with a specific binding agent for a said polymoφhism and determining whether the agent binds to a said polymoφhism in the polynucleotide or protein, the binding of the agent to the polymoφhism indicating that the individual is susceptible to migraine.

5 A method according to claim 4 wherein the agent is a polynucleotide which is able to bind a polynucleotide containing the said polymoφhism but which does not bind α polynucleotide with the corresponding wild-type sequence

6 A method according to claim 2 or 3 wherein the polymoφhism is detected by measunng the change caused by the polymoφhism in the mobility of a polynucleotide or protein of the individual or protein during gel electrophoresis. 7 A method according to claim 1 w herein the typing compnses measunng the expression or activity of the insulin receptor

8 A method according to claim 1 which compnses measunng a phenotype which is affected by the insulin receptor

9 A method according to claim 8 which compnses measunng insulin sensitivity.

10 A method of diagnosing susceptibility to cephalic pam in an individual, which method compnses typing in vivo the insulin receptor gene region or insulin receptor protein of the individual and determining thereby whether the individual is susceptible to cephalic 1 1 A method according to claim 10 wherein the typing is performed as defined in any one of claims 2 to 5 and 7 to 9

12 A method according to any one of the preceding claims wherein the cephalic pain is migraine

13 Method for treating a patient who has been diagnosed as being susceptible to cephalic pain by a method as defined in anv one of the preceding claims, compnsing αdministenng a therapeutically effective amount of an anti-cephalic pain agent to the patient

14 Use of an anti-cephalic pain agent in the manufacture of a medicament for use in treating a patient who has been diagnosed as being susceptible to cephalic pain by a method as defined in any one ot claims 1 to 12

15 Λ probe, pnmer or antibody which is capable ot detecting a polymoφhism as defined in claim 2 or 3

16 A probe or primer according to claim 15 which is a polynucleotide that has a length of at least 15 nucleotides

17 A kit for diagnosing susceptibility to cephalic pain, compnsing an agent, probe, pnmer or antibody as defined in any one of claims 4, 5, 15 or 16

18 An isolated polynucleotide or protein that compnses (l) a polymoφhism that causes susceptibility to cephalic pain or (u) a naturally occurnng polymoφhism that is in linkage disequihbnum with (l)

19 A polynucleotide or protein according to claim 18 wherein the polymoφhism is as defined in claim 3

20 A polynucleotide or protein according to claim 18 or 19 which has a length of at least 15 nucleotides or at least 15 amino acids 21 A vector incoφorating a polynucleotide as defined in any one of claims 18 to

20

22 A process for the preparation ot a protein as defined in any one of claims 18 to 20, which process comprises

{ι) cultunng a host cell transformed or transfected with a vector according to claim 21 under conditions to provide for expression of the protein, and optionally (u) recovenng the expressed protein

23 A non-human animal which is transgemc for a polymoφhism as defined m claim 2 or 3 24 A method of identifying a polymoφhism which can be typed to determine susceptibility to cephalic pain, comprising determining whether a candidate polymoφhism in the sulin receptor gene region or insulin receptor protein is (I) associated with cephalic pam or (u) is in linkage disequihbnum with a polymoφhism which is associated with cephalic pain, and thereby determining whether the polymoφhism can be typed to determine susceptibility to cephalic pain.