Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
  • C07K14/7155—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons for interleukins [IL]
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/156—Polymorphic or mutational markers

Definitions

• Associated Factor 2 (SEQ ID N01) and relates these sequence variants to susceptibility to asthma, atopic allergy, and related disorders.
• This invention also teaches methods that utilize these IL-9 receptor sequence variants for the diagnosis of susceptibility or resistance to asthma and atopic allergy.
• methods are described that use variant IL-9 receptors in the development of pharmaceuticals for asthma which depend on the regulation of IL-9 activity.
• Atopic allergy is a disorder where genetic background dictates the response to environmental stimuli.
• the disorder is generally characterized by an increased ability of lymphocytes to produce IgE antibodies in response to ubiquitous antigens. Activation of the immune system by these antigens also leads to allergic inflammation which may occur after their ingestion, penetration through the skin, or after inhalation. When this immune activation occurs and pulmonary inflammation ensues, this disorder is broadly characterized as asthma.
• Certain cells are important in this inflammatory reaction in the airways and they include T cells and antigen presenting cells, B cells that produce IgE, and mast cells/basophils that store inflammatory mediators and bind IgE, and eosinophils that release additional mediators. These inflammatory cells accumulate at the site of allergic inflammation, and the toxic products they release contribute to the tissue destruction related to the disorder.
• asthma is generally defined as an inflammatory disorder of the airways, clinical symptoms arise from intermittent airflow obstruction. It is a chronic, disabling disorder that appears to be increasing in prevalence and severity. 1 It is estimated that 30-40% of the population suffer with atopic allergy, and 15% of children and 5% of adults in the population suffer from asthma.
• the main therapeutic agents, ⁇ -agonists reduce the symptoms, i.e., transiently improve pulmonary functions, but do not affect the underlying inflammation so that lung tissue remains in jeopardy.
• constant use of ⁇ -agonists results in desensitization which reduces their efficacy and safety.
• the agents that can diminish the underlying inflammation, the anti- inflammatory steroids have their own known list of side effects that range from immunosuppression to bone loss. 2 Because of the problems associated with conventional therapies, alternative treatment strategies have been evaluated. 38 39 Glycophorin A, 37 cyclosporin, 38 and a nona peptide fragment of IL-2, 36 all inhibit interleukin-2 dependent T lymphocyte proliferation. 28 They are, however, known to have many other effects. 2 For example, cyclosporin is used as a immunosuppressant after organ transplantation. While these agents may represent alternatives to steroids in the treatment of asthmatics, 36"39 they inhibit interleukin-2 dependent
• T lymphocyte proliferation and potentially critical immune functions associated with homeostasis are highly critical immune functions associated with homeostasis.
• therapies represent the most likely way to avoid toxicity associated with nonspecific treatment.
• the therapies would selectively target a pathway, which is downstream from immune functions, such as IL-2 mediated T lymphocyte activation, that is necessary for the development of asthma and which would explain the episodic nature of the disorder and its close association with allergy.
• IL-2 mediated T lymphocyte activation that is necessary for the development of asthma and which would explain the episodic nature of the disorder and its close association with allergy.
• Nature demonstrates that a pathway is the appropriate target for asthma therapy when biologic variability normally exists in the pathway and individuals demonstrating the variability are not immunocompromised or ill except for their symptoms of atopic asthma.
• asthma atopic allergies including asthma
• these disorders are heterogeneous and may be difficult to define because they can take many forms
• certain features are found in common among asthmatics. Examples of such features include abnormal skin test response to allergen challenge, eosinophilia in the lung, bronchial hyperresponsiveness (BHR), bronchodilator reversibility, and airflow obstruction. 3 10 These expressions of asthma related traits may be studied by quantitative or qualitative measures.
• IL-9 and the IL-9 receptor now extend well beyond those originally recognized. While the IL-9 pathway serves as a stimulator of T cell growth, this cytokine is also known to mediate the growth of erythroid progenitors, B cells, mast cells, and fetal thymocytes. 22,23 The IL-9 pathway acts synergistically with IL-3 in causing mast cell activation and proliferation. 24 The IL-9 pathway also potentiates the IL-4 induced production of IgE, IgG, and IgM by normal human B lymphocytes, 25 and the IL-4 induced release of IgE and IgG by murine B lymphocytes.
• IL-9 binds to a specific receptor expressed on the surface of target cells. 23,29,30
• the receptor actually consists of two protein chains: one protein chain, known as the IL-9 receptor, binds specifically with IL-9; the other protein chain is shared in common with the IL-2 receptor.
• a cDNA encoding the human IL-9 receptor has been cloned and sequenced 23,29,30 This cDNA codes for a 522 amino acid protein which exhibits significant homology to the murine IL-9 receptor.
• the extracellular region of the receptor is highly conserved, with 67% homology existing between the murine and human proteins.
• the cytoplasmic region of the receptor is less highly conserved.
• the human cytoplasmic domain is much larger than the corresponding region of the murine receptor.
• the IL-9 receptor gene has also been characterized. 30 It is thought to exist as a single copy in the mouse genome and is composed of nine exons and eight introns. 30
• the human genome contains at least four IL-9 receptor pseudogenes.
• the human IL-9 receptor gene has been mapped to the 320 kb subtelomeric region of the sex chromosomes X and Y. 23 In spite of these studies, no variants of the IL-9 receptor gene have been discovered. There is, therefore, a specific need for genetic information on atopic allergy, asthma, bronchial hyperresponsiveness, and for elucidation of the role of IL-9 receptor in the etiology of these disorders. This information can be used to diagnose atopic allergy and related disorders using methods that identify genetic variants of this gene that are associated with these disorders. Furthermore, there is a need for methods utilizing the IL-9 receptor variants to develop therapeutics to treat these disorders.
• IL-9 receptor also known as Asthma Associated Factor 2 or AAF2
• AAF9 Asthma Associated Factor 2
• Applicants have discovered natural variants of the human IL-9 receptor (also known as Asthma Associated Factor 2 or AAF2) and have linked these variants to the pathogenesis of asthma and related disorders. These discoveries have led to the development of diagnostic methods, and methods to discover pharmaceuticals for the treatment of therapeutics for atopic asthma.
• the IL-9 receptor is critical to a number of antigen-induced responses in mice, including bronchial hyperresponsiveness, eosinophilia and elevated cell counts in bronchial lavage, and elevated serum total IgE.
• a G to A nucleic acid variant occurs at position 1273 of the cDNA (SEQ ID NO 2) which produces the predicted amino acid substitution of a histidine for an arginine at codon 344 of the human IL-9 receptor precursor protein.
• SEQ ID NO 2 the cDNA
• the invention includes purified and isolated DNA molecules having such a sequence as well as the proteins encoded by such DNA.
• IL-9 ( Figure 16); therefore, individuals with this allele would be less susceptible to atopic asthma and related disorders.
• Applicants have further determined that a variant of the IL-9R genomic DNA exists wherein nt-213, a thymine residue in intron 5 (213 nt upstream from exon 6), has been converted to a cytosine nucleotide. It is likely that such a variation can cause an increase in the frequency of the splice variant which removes the glutamine residue at the start of exon 6.
• IL-9 functions can be interrupted by the interaction of IL-9 antagonists with IL-9 or its receptor. Down regulation, i.e., reduction of the functions controlled by IL-9, is achieved in a number of ways. Administering antagonists that can interrupt the binding of IL-9 to its receptor is one key mechanism, and such antagonists are within the claimed invention. Examples include administration of polypeptide products encoded by the DNA sequences of a naturally occurring soluble form of the IL-9 receptor, wherein the DNA sequences code for a polypeptide comprising exons 2 and 3 (SEQ ID NO 5).
• Methods to identify agonists and antagonists of the IL-9 receptor pathway can be identified by assessing receptor-ligand interactions which are well described in the literature. These methods can be adapted to high throughput automated assays that facilitate chemical screenings and potential therapeutic identification. Agonists are recognized by identifying a specific interaction with the IL-9 receptor. Loss of binding for a putative ligand which is labeled when a 100- to 1000-fold excess of unlabeled ligand is used is generally accepted as evidence of specific receptor binding. Many labels and detection schemes can be used during these experiments. A similar loss of binding when increasing concentrations of test compound are added to a known ligand and receptor is also evidence for an antagonist.
• variant receptors provides the means to construct expression vectors that can be used to make soluble receptor for receptor binding assays. Mutagenesis of these soluble receptors can be used to determine which amino acid residues are critical to bind ligand and aid in the structure-based design of antagonists.
• Cells lacking human IL-9 receptor can be transiently or stably transfected with expression vectors containing a variant receptor and used to assay for IL-9 pathway activity. These activities may be cellular proliferation, or prevention of apoptosis which have both been ascribed to the IL-9 pathway. These cells can be used to identify receptor agonists and antagonists as described above.
• the methods discussed above represent various effective methods utilizing the variant forms of IL-9 receptor to develop therapeutics for atopic asthma and other related disorders. A number of techniques have been described that may be used to diagnose atopic asthma that recognize single nucleotide variants in the IL-9 receptor including DNA sequencing, restriction fragment length polymorphisms
• RFLPs allele specific oligonucleotide analyses
• ASO allele specific oligonucleotide analyses
• LCR ligation chain reaction
• SSCP single stranded conformational polymorphism analyses
• polyclonal and monoclonal antibodies which recognize specifically the structure of the various forms of the IL-9 receptor are also within the scope of this invention and are useful diagnostic methods for describing susceptibility or resistance to atopic asthma and related disorders.
• the methods discussed above represent various effective methods for diagnosing atopic asthma and other related disorders.
• applicants have provided methods that use the IL-9 receptor to identify antagonists that are capable of regulating the interaction between IL-9 and its receptor. More specifically, applicants provide a method for assaying the functions of the IL-9 receptor to identify compounds or agents that may be administered in an amount sufficient to down-regulate either the expression or functions of the IL-9 pathway.
• Figure 1 Schematic representation of the human IL receptor cDNA. Boxes depict exon 2 to 9 encompassing the coding region (relative size in scale, except the 3' untranslated part of exon 9, outlined by dashed line). Transmembrane region is encoded by exon 7, intracellular domain by exon 8 and 9, and the extracellular by exon 2 to 6.
• Figure 2 Translated cDNA sequence of the wild type IL-9R precursor protein with Arg allele at codon 344 (nucleotides 1272-1274) and the 8 Ser/4 Asn repeats starting at codon 410 (nucleotides 1470-1472).
• Figure 3 Translated cDNA sequence of the IL-9R precursor protein with the His allele at codon 344 (nucleotides 1272-1274) and the 9 Ser/4 Asn repeats starting at codon 410 (nucleotides 1470-1472).
• Figure 4 Translated cDNA sequence of IL-9R precursor protein with the deletion of exon 8 causing a frame shift in exon 9, the production of 11 non- wild type amino acids and a premature stop codon.
• Figure 5 Translated cDNA sequence of IL-9R precursor protein with the deletion of Glutamine at codon 173.
• Figure 6 Translated cDNA sequence of IL-9R precursor protein with an alternate splice in exon 5 resulting in a premature stop codon and the production of 27 non-wild type amino acids.
• Figure 7 Translated cDNA sequence of IL-9R precursor protein with an alternate splice in exon 5 resulting in a premature stop codon and the production of 4 non-wild type amino acids.
• Figure 8 Translated cDNA sequence of IL-9R precursor protein with the deletion of exon 4 producing a stop codon as the first codon of exon 5.
• Figure 9 Table showing the association between the IL-9 receptor genotype and atopic allergy.
• the Arg/Arg individuals are homozygous for the Arg allele with the 8 Ser/4 Asn repeats.
• the Arg/His individuals are heterozygous for the Arg allele with the 8 Ser/4 Asn repeats and the His allele with the 9 Ser/4 Asn repeats, 9 Ser/3 Asn repeats, and 10 Ser/2 Asn repeats in exon 9.
• the His/His individuals are homozygous for the His allele with the 9
• FIG. 10 Map of the expression construct of the IL-9 receptor.
• Figure 11 Western blot of recombinant IL-9 receptor proteins (left: Arg allele with the 8 Ser/4 Asn repeats; right: His allele with the 9 Ser/4 Asn repeats) using C terminal antibody probe in TK " transfected cell line.
• Figure 12 Expression of human IL-9 receptor variants in TS1 cells showing differential mobility between the Arg 344 variant with 8 Ser/4 Asn repeats
• Figure 14 Immunoreactivity of an anti-human IL-9 receptor neutralizing antibody with wild type and Delta-Q receptors.
• Figure 15 Activation of members of Jak, Stat, and Irs families via different variants of the human IL-9 receptor.
• TS1 cells expressing either GH9, ⁇ QGR8, or ⁇ QGH9 were starved for 6 hours and then treated for 5 minutes without cytokine (-), with murine IL-9 (m), or with human IL-9 (h).
• Cell extracts were immunoprecipitated with various antibodies specific for different members of Jak, Stat and Irs families.
• IL-9R is the His 344 variant with 9 Ser residues starting at codon 410; ⁇ QGR8 and ⁇ QGH9 are the ⁇ Q173 variants on the wild type and the His 344 + 9 - Ser background, respectively.
• Figure 17 Genomic DNA sequence of intron 5 of the IL-9R with a variation at nucleic acid 213 nt upstream from exon 6 where a T residue is changed to a
• Applicants have resolved the needs in the art by elucidating an IL-9 pathway, and compositions that affect that pathway, which may be used in the treatment, diagnosis, and development of methods to identify agents to prevent or treat atopic asthma and related disorders.
• Asthma encompasses inflammatory disorders of the airways with reversible airflow obstruction.
• Atopic allergy refers to atopy, and related disorders including asthma, bronchial hyperresponsiveness (BHR), rhinitis, urticaria, allergic inflammatory disorders of the bowel, and various forms of eczema.
• Atopy is a hypersensitivity to environmental allergens expressed as the elevation of serum total IgE or abnormal skin test responses to allergens as compared to controls.
• BHR refers to bronchial hyperresponsiveness, a heightened bronchoconstrictor response to a variety of stimuli.
• IL-9R IL-9 receptor
• the IL-9 receptor gene also known as Asthma Associated Factor 2 or AAF2 refers to the genetic locus of interleukin-9 receptor, a cytokine receptor associated with a variety of functions involving the regulation of human myeloid and lymphoid systems.
• the human IL-9 receptor gene of the present invention is found in the subtelomeric region of the XY chromosomes.
• polymorphism applicants mean a change in a specific DNA sequence, termed a "locus," from the prevailing sequence.
• locus is defined as polymorphic when artisans have identified two or more alleles encompassing that locus and the least common allele exists at a frequency of 1 % or more.
• Exon 3, 4, 5, 6 and 8 were affected by aberrant splicing events in samples where full-length cDNAs could also be cloned. Some transcripts showed complete deletion of exon 3, which causes a frameshift creating a stop codon after a stretch of 79 unrelated residues. In the case of deletion of exon 4, a frameshift is also generated and the first codon in exon 5 is converted to a stop codon. In some other cDNAs, exon 5 presented partial deletion of the first 5 or 29 nucleotides, both deletions leading to frameshifts resulting in early stop codons within exon 5.
• the putative truncated protein would lack most of the extracellular domain as well as all the transmembrane and cytoplasmic domains. If secreted, these forms might function as soluble receptors.
• the first three nucleotides of exon 6, corresponding to codon 173, were frequently found spliced out, resulting in deletion of the glutamine at this codon with no other changes in the remaining protein sequence.
• This splice variant is possibly related to a variant found in intron 5 of the genomic DNA (SEQ ID NO 24) which would increase the frequency of the splice variant ( Figure 17 and Example 12).
• Applicants have also found allelic variations limited to the coding sequence of exon 9.
• Codon 310 encodes for either arginine or glycine, depending on whether the first nucleotide at that codon is an adenine or a guanidine, respectively.
• codon 410 (from hereon termed "410+n") begins a stretch of either 8 or 9 AGC trinucleotides repeats which would be translated in 8 or 9 serines, respectively.
• codon 344 the second nucleotide is either adenine or guanidine, the two possible residues encoded by this codon being histidine or arginine, respectively.
• codon 344 and 410+n a correspondence between codon 344 and 410+n was observed wherein arginine at codon 344 is consistently found with 8 serines at codon 410+n and histidine at codon 344 is found with 9 serines.
• the human IL-9 receptor cDNA originally cloned from a human megakaryoblastic leukemic cell line, Mo7e, presented 9 serines at codon 410+n and, unlike applicants' clones, an arginine at codon 344. 29
• Another megakaryoblastic leukemic cell line UT-7 has been reported to carry the same arginine/9-serines allele.
• the invention also includes the proteins encoded by these nucleic acid sequences.
• the invention further includes fragments of the molecules.
• fragments applicants mean portions of the nucleic acid sequence that maintain the function of the full sequence. As would be known in the art, fragments result from deletions, additions, substitutions and/or modifications.
• the source of the IL-9 receptor variants of the invention is human.
• the DNA or fragment thereof may be synthesized using methods known in the art. It is also possible to produce the compound by genetic engineering techniques, by constructing DNA by any accepted technique, cloning the DNA in an expression vehicle and transfecting the vehicle into a cell which will express the compound. See, for example, the methods set forth in Sambrook, et al., Molecular Cloning: A Laboratory Manual. 2d ed., Cold Spring Harbor Laboratory Press (1985).
• variant IL-9 receptor sequences which may be associated with atopic allergy and an asthma-like phenotype, and others which may be associated with the lack of an asthma-like phenotype, provides methods of diagnosing susceptibility to atopic asthma and related disorders.
• Certain variants can produce soluble receptors which can be used for treating these disorders.
• a receptor is a soluble or membrane-bound component that recognizes and binds to molecules
• the IL-9 receptor of the invention is the component that recognizes and binds to IL-9.
• the functions of the IL-9 receptor consist of binding to IL-9 or an IL-9-like molecule and propagating its regulatory signal in specific cells. 29,30,34,35 Human IL-9 has been shown to cause phosphorylation of the IL-9 receptor itself and the activation of proteins of the Jak-Stat pathway,
• one aspect of the invention is therapeutics for the treatment of atopic asthma which inhibit interactions in the Jak-Stat pathway.
• the ⁇ Q173 variant could not activate any proteins in the Jak-Stat pathway ( Figure 15).
• the ⁇ Q173 variant could not support cellular proliferation upon IL-9 stimulation ( Figure 16). Therefore, individuals who express the ⁇ Q173 variant are less likely to be susceptible to atopic asthma and related disorders.
• One aspect of the invention is therapeutics that increase the expression of the ⁇ Q173 splice variant for the treatment of atopic asthma and related disorders.
• One diagnostic embodiment involves the recognition of variations in the DNA sequence of the IL-9 receptor gene or transcript.
• nucleic acid molecule also known as a probe
• the nucleic acid molecule will bind specifically to the codon for Arg344 of the mature IL-9 receptor protein, or to His344, and in another embodiment will bind to both Arg344 and to His344. In yet another embodiment, it will bind to the codon for Gin 173.
• Another method of recognizing DNA sequence variation associated with these disorders is direct DNA sequence analysis by multiple methods well known in the art. 44 Another embodiment involves the detection of DNA sequence variation in the IL-9 receptor gene associated with these disorders.
• IL-9 receptors 40"44 include the polymerase chain reaction, restriction fragment length polymorphism (RFLP) analysis, and single-stranded conformational analysis.
• RFLP restriction fragment length polymorphism
• applicants provide specifically for a method to recognize, on a genetic level, the polymorphism in IL-9 receptor associated with the His344 and Arg344 alleles using an ASO PCR.
• the ligation chain reaction can be used to distinguish these alleles of IL-9 receptor genes.
• the present invention also includes methods for the identification of antagonists of IL-9 and its receptor.
• Antagonists are compounds that are themselves devoid of pharmacological activity, but cause effects by preventing the action of an agonist.
• an antagonist of the invention may test for competitive binding with a known agonist or for down-regulation of IL-9-like functions as described herein and in the cited literature. 2,22 35
• Specific assays may be used to screen for pharmaceuticals useful in treating atopic allergy based on IL-9 receptor's known role on the proliferation of T lymphocytes, IgE synthesis and release from mast cells. 29,30,33"35
• Another assay involves the ability of human IL-9 receptor to specifically induce the rapid and transient tyrosine phosphorylation of multiple proteins in Mo7e cells. 34 Because this response is dependent upon the expression and activation of the IL-9 receptor, it represents a simple method or assay for the characterization of potentially valuable compounds.
• the tyrosine phosphorylation of Stat3 transcriptional factor appears to be specifically related to the functions of the IL-9 receptor, 35 and this response represents a simple method or assay for the characterization of compounds within the invention.
• Still another method to characterize the function of the IL-9 receptor involves the use of the well known murine TS1 clone transfected with a human receptor which can be used to assess human IL-9 function with a cellular proliferation assay. 29 These methods can be used to identify antagonists of the IL-9 receptor.
• the invention includes the down-regulation of IL-9 expression or function by administering soluble IL-9 receptor molecules that bind IL-9.
• soluble IL-9 receptor molecules that bind IL-9.
• Applicants and Renauld, et al. 29 have shown the existence of a soluble form of the IL-9 receptor. This molecule can be used to prevent the binding of IL-9 to cell-bound receptor and act as an antagonist of IL-9.
• Soluble receptors have been used to bind cytokines or other ligands to regulate their function. 45
• a soluble receptor is a form of a membrane-bound receptor that occurs in solution, or outside of the membrane. Soluble receptors may occur because the segment of the molecule which commonly associates with the membrane is absent.
• a soluble receptor may represent a fragment or an analog of a membrane-bound receptor.
• Applicants have identified three splice variants of the human IL-9 receptor that result in the production of proteins that could act as soluble receptors.
• One splice variant resulted in the deletion of exon 4 which introduced a frame- shift resulting in a stop codon as the first codon of exon 5.
• This variant would produce a peptide of about 45 residues that contains an epitope reactive with antibodies that block the IL-9/IL-9R interaction.
• the other two variants contain deletions in exon 5 that will produce premature stop codons early in the exon, but, in these cases, without the deletion of exon 4.
• These variants would produce a protein of about 100 residues also containing the epitope recognized by blocking antibody. Soluble IL-9 receptors may be used to screen for potential therapeutics, including antagonist useful in treating atopic asthma and related disorders.
• a soluble receptor For example, screening for peptides and single-chain antibodies using phage display could be facilitated using a soluble receptor. Phage that bind to the soluble receptor can be isolated and the molecule identified by affinity capture of the receptor and bound phage.
• compound screenings for agents useful in treating atopic asthma and related disorders can incorporate a soluble receptor and ligand that bind in the absence of an antagonist. Detection of the ligand and receptor interaction occurs because of the proximity of these molecules. Antagonists are recognized by inhibiting these interactions.
• the invention includes pharmaceutical compositions comprising the compounds of the invention together with a pharmaceutically acceptable carrier.
• Pharmaceutically acceptable carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectionable solutions. Suitable pharmaceutical carriers are described in Martin, E.W., Remington's Pharmaceutical Sciences, specifically incorporated herein by reference.
• the compounds used in the method of treatment of this invention may be administered systemically or topically, depending on such considerations as the condition to be treated, need for site-specific treatment, quantity of drug to be administered, and similar considerations.
• Topical administration may be used. Any common topical formation such as a solution, suspension, gel, ointment, or salve and the like may be employed. Preparation of such topical formulations are well described in the art of pharmaceutical formulations as exemplified, for example, by Remington's Pharmaceutical Science. Edition 17, Mack Publishing Company, Easton, Pa.
• these compounds could also be administered as a powder or spray, particularly in aerosol form.
• the compounds of this invention may be administered by inhalation.
• the compound may be in a solution useful for administration by metered dose inhalers, or in a form suitable for a dry powder inhaler.
• the active ingredient may be administered in pharmaceutical compositions adapted for systemic administration.
• a drug if a drug is to be a administered systemically, it may be confected as a powder, pill, tablet or the like, or as a syrup or elixir for oral administration.
• the compound will be prepared as a solution or suspension capable of being administered by injection.
• it may be useful to formulate these compounds in suppository form or as an extended release formulation for deposit under the skin or intermuscular injection.
• An effective amount is that amount which will down-regulate the functions controlled by IL-9 receptor.
• a given effective amount will vary from condition to condition and in certain instances may vary with the severity of the condition being treated and the patient's susceptibility to treatment. Accordingly, a given effective amount will be best determined at the time and place through routine experimentation. It is anticipated, however, that in the treatment of asthma and related disorders in accordance with the present invention, a formulation containing between 0.001 and 5 percent by weight, preferably about 0.01 to 1%, will usually constitute a therapeutically effective amount. When administered systemically, an amount between 0.01 and 100 mg per kg body weight per day, but preferably about 0.1 to 10 mg/kg, will affect a therapeutic result in most instances.
• Applicants also provide for a method to screen for the compounds that down- regulate the functions controlled by the IL-9 receptor.
• One may determine whether the functions expressed by IL-9 receptor are down-regulated using techniques standard in the art. 29,30,34,35
• applicants provide for a method of identifying compounds with functions comparable to IL-9.
• the functions of IL-9 receptor may be assessed in vitro.
• human IL-9 receptor activation specifically induces the rapid and transient tyrosine phosphorylation of multiple proteins in cells responsive to IL-9.
• the tyrosine phosphorylation of Stat3 transcriptional factor appears to be specifically related to the actions of the IL-9 pathway.
• Another method to characterize the function of IL-9 and IL-9-like molecules depends on the "stable expression" of the IL-9 receptors in murine TS1 clones or TF1 clones, which do not normally express human receptor.
• the invention also includes a simple screening assay for saturable and specific ligand binding based on cell lines that express the IL-9 receptor variants.
• the IL-9 receptor is expressed in a wide variety of cell types, including K562, C8166-45, KG-1 transfected with the human IL-9 receptors, B cells, T cells, mast cells, HL60, HL60-clone 5, TS1 transfected with the human IL-9 receptors, 32D transfected with the human IL-9 receptors, neutrophils, megakaryocytes (UT-7 cells), 30 the human megakaryoblastic leukemia cell line Mo7e 34 , TF1, 29 macrophages, eosinophiles, fetal thymocytes, the human kidney cell line 293, 30 and murine 32D and embryonic hippocampal progenitor cell lines.
• the practice of the present invention will employ the conventional terms and techniques of molecular biology, pharmacology, immunology, and biochemistry that are within the ordinary skill of those in the art. See, for example, Sambrook, et al., Molecular Cloning: A Laboratory Manual. 2d ed.,Cold Spring Harbor Laboratory Press, or Ausubel, et al., Current Protocols in Molecular Biolo ⁇ v. John Wiley & Sons, Inc. Nonetheless, we offer the following basic background information.
• the body's genetic material, or DNA is arranged on 46 chromosomes, which each comprises two arms joined by a centromere. Each chromosome is divided into segments designated p or q.
• the symbol p is used to identify the short arm of a chromosome, as measured from the centromere to the nearest telomere.
• the long arm of a chromosome is designated by the symbol q.
• Location on a chromosome is provided by the chromosome's number (i.e., chromosome 5) as well as the coordinates of the p or q region (i.e., q31-q33).
• the body bears the sex chromosomes, X and Y. During meiosis, the X and Y chromosomes exchange DNA sequence information in areas known as the pseudoautosomal regions.
• DNA deoxyribonucleic acid
• a sequential grouping of three nucleotides codes for one amino acid.
• the three nucleotides CAG code for the amino acid Glutamine.
• the 20 naturally occurring amino acids, and their one-letter codes, are as follows:
• Amino acids comprise proteins.
• Amino acids may be hydrophilic, i.e., displaying an affinity for water, or hydrophobic, i.e., having an aversion to water.
• the amino acids designated as G, A, V, L, I, P, F, Y, W, C and M are hydrophobic and the amino acids designated as S, Q, K, R, H, D, E, N and T are hydrophilic.
• the hydrophilic or hydrophobic nature of amino acids affects the folding of a peptide chain and, consequently, the three- dimensional structure of a protein.
• DNA is related to protein as follows: genomic DNA — > mRNA — > protein t
• Genomic DNA comprises all the DNA sequences found in an organism's cell. It is “transcribed” into messenger RNA ("mRNA”).
• mRNA messenger RNA
• cDNA Complementary DNA
• mRNA and cDNA contain only the protein-encoding or polypeptide-encoding regions of the DNA, the so-called
• Genomic DNA may also include “introns,” which do not encode proteins.
• eukaryotic genes are discontinuous with proteins encoded by them, consisting of exons interrupted by introns. After transcription into RNA, the introns are removed by splicing to generate the mature messenger RNA
• mRNA The splice points between exons are typically determined by consensus sequences that act as signals for the splicing process. Splicing consists of a deletion of the intron from the primary RNA transcript and a joining or fusion of the ends of the remaining RNA on either side of the excised intron. Presence or absence of introns, the composition of introns, and number of introns per gene, may vary among strains of the same species, and among species having the same basic functional gene. Although, in most cases, introns are assumed to be nonessential and benign, their categorization is not absolute. For example, an intron of one gene can represent an exon of another. In some cases, alternate or different patterns of splicing can generate different proteins from the same single stretch of DNA.
• introns and the underlying splicing mechanisms form the basis for classification of different kinds of introns.
• exons these can correspond to discrete domains or motifs as, for example, functional domains, folding regions, or structural elements of a protein; or to short polypeptide sequences, such as reverse turns, loops, glycosylation signals and other signal sequences, or unstructured polypeptide linker regions.
• the exon modules of the present combinatorial method can comprise nucleic acid sequences corresponding to naturally occurring exon sequences or naturally occurring exon sequences which have been mutated (e.g., point mutations, truncations, fusions).
• DNA can be cut, spliced, and otherwise manipulated using "restriction enzymes” that cut DNA at certain known sites and DNA ligases that join DNA.
• restriction enzymes Such techniques are well known to those of ordinary skill in the art, as set forth in texts such as Sambrook, et al., Molecular Cloning: A Laboratory Manual. 2d ed., Cold Spring Harbor Laboratory Press (1985) or Ausubel, et al., Current Protocols in Molecular Biology. John Wiley & Sons, Inc. (1994).
• DNA of a specific size and sequence can then be inserted into a "replicon,” which is any genetic element, such as a plasmid, cosmid, or virus, that is capable of replication under its own control.
• a "recombinant vector” or “expression vector” is a replicon into which a DNA segment is inserted so as to allow for expression of the DNA; i.e., production of the protein encoded by the DNA.
• Expression vectors may be constructed in the laboratory, obtained from other laboratories, or purchased from commercial sources.
• the recombinant vector (known by various terms in the art) may be introduced into a host by a process generically known as "transformation.” Transformation means the transfer of an exogenous DNA segment by any of a number of methods, including infection, direct uptake, transduction, F-mating, microinjection, or electroporation into a host cell.
• Unicellular host cells known variously as recombinant host cells, cells, and cell culture, include bacteria, yeast, insect cells, plant cells, mammalian cells and human cells.
• the host cells include E.coli, Pseudomonas, Bacillus, Streptomyces, Yeast, CHO, R1-1 , B-W, LH,
• Yeast cells especially include Saccharomyces, Pichia, Candida, Hansenula, and Torulopsis.
• the regulatory sequences vary according to the host cell employed, but include, for example, in prokaryotes, a promoter, ribosomal binding site, and/or a transcription termination site. In eukaryotes, such regulatory sequences include a promoter and/or a transcription termination site.
• expression of the polypeptide may be enhanced, i.e., increased over the standard levels, by careful selection and placement of these regulatory sequences.
• promoters that may be used include the human cytomegalovirus (CMV) promoter, tetracycline-inducible promoter, simian virus (SV40) promoter, moloney murine leukemia virus long terminal repeat (LTR) promoter, glucocorticoid inducible murine mammary tumor virus (MMTV) promoter, herpes thymidine kinase promoter, murine and human-actin promoters, HTLV1 and HIV IL-9 5' flanking region, human and mouse IL-9 receptor 5' flanking region, bacterial tac promoter and Drosophila heat shock protein scaffold attachment region (SAR) enhancer elements.
• CMV human cytomegalovirus
• SV40 simian virus
• LTR moloney murine leukemia virus long terminal repeat
• MMTV glucocorticoid inducible murine mammary tumor virus
• SAR heat shock protein scaffold attachment region
• the DNA may be expressed as a polypeptide of any length such as peptides, oligopeptides, and proteins. Polypeptides also include translational modifications such as glycosylations, acetylations, phosphorylations, and the like.
• Another molecular biologic technique of interest to the present invention is "linkage analysis.” Linkage analysis is an analytic method used to identify the chromosome or chromosomal region that correlates with a trait or disorder. 47 Chromosomes are the basic units of inheritance on which genes are organized. In addition to genes, artisans have identified "DNA markers" on chromosomes. DNA markers are known sequences of DNA whose identity and sequence can be readily determined.
• RNA and DNA were isolated as described in Example 5.
• RNAs were reverse transcribed and amplified by PCR using primers specific for full-length IL-9 receptor cDNA as described in Example 5. Amplification products from each individual were cloned into the TA PCR cloning vector and ten clones containing the expected inserts (as determined by digestion and gel electrophoresis) were sequenced in their entirety and analyzed for structural or sequence variation.
• cDNAs represent a codon 173 deletion, an exon 4 deletion, two separate deletions in exon 5, an exon 8 deletion, and a full-length cDNA containing an ARG-to-HIS change at codon 344 of the mature protein . Additional variants exist on each of these genetic backgrounds.
• the Arg allele is associated with 8 Ser/4 Asn repeats and 7 Ser/4 Asn repeats; the His allele is associated with 9 Ser/4 Asn repeats, 9 Ser/3 Asn repeats, and 10 Ser/2 Asn. All of these variants are depicted in Figure 1.
• Variants were cloned into the eukaryotic expression vector pCEP4 (Clontech) which contains a CMV promoter that drives the expression of the cloned cDNA followed by an SV40 polyadenylation signal.
• the vector also contains a hygromycin B resistance gene which is used for selection of eukaryotic cells containing the vector and presumably expressing the cloned cDNA under control of the CMV promoter.
• Recombinant plasmids were analyzed by sequence and those plasmids containing the correct cDNA inserts were transfected into eukaryotic recipient cells such as the Syrian hamster fibroblast TK-ts13, the human glioblastoma T98G, the human myeloid leukemia line TF-1 , and the murine myeloid precursor cell line 32D as described in Example
• IL-9 receptor cDNAs containing the ARG or HIS variants were performed are the TK-ts13 hamster fibroblasts or the human T98G glioblastoma cells.
• Cells were transfected and analyzed 48 hours later by Western blot and in situ staining using human specific carboxy terminal antibodies (Santa Cruz) (Example 8).
• In situ analysis demonstrated that both forms of receptor appeared to be expressed in both the hamster and human lines ( Figures 11 and 12).
• PCR-specific primers for the authentic IL-9 receptor genes located on the X/Y pseudoautosomal regions and exclude the highly conserved IL-9 receptor pseudogenes located on chromosomes 9, 10, 16, and 18.
• sequence alignments were preformed between the two published pseudogenes and the genomic sequence of the IL-9 receptor genes. Primers were then initially designed in divergent regions between the authentic genes and the pseudogenes, and then analyzed by PCR using single chromosome-specific hybrids derived from Coreill DNA Repository (Camden, NJ). If the primers only produce correct sized products from X and Y hybrids, they were then optimized for robust amplification.
• primers directed to the divergent regions were not XY specific; therefore, applicants introduced additional base changes in the particular primer to increase the number of mismatches higher against the pseudogenes as compared to the IL-9 receptor gene sequence.
• Table 1 contains the sequence of the primers and optimal annealing temperatures for XY-specific amplification. The specificity of these primers for XY amplification are demonstrated in Figure 13.
• Table 1 X/Y Specific Amplimers of IL-9 Receptor
• TF1.1 TF1 cells
• IL-9 receptors were cloned into pCEP4 plasmid (Clontech) and
• Plasmid DNA 50
• micrograms was added to the cells in 0.4 cm cuvettes just before electroporation.
• the cells are immediately diluted in fresh medium
• Stable transfected cells were generated after 14 days of selection with
• Hygromycin B 400 ⁇ g/ml to 1.6 mg/ml. Hygromycin-resistant clones were analyzed for IL-9 receptor expression by Western blots and in situ staining as
• Soluble IL-9 receptor including amino acids 44 to 270 with or without a HA ditag
• EBC buffer 50 mM Tris pH 7.5;
• PBMC peripheral blood mononuclear cells
• PBMC peripheral blood mononuclear cells
• mouse spleen cells (5 x 10 6 )
• 5 x 10 6 Mo7e cells were cultured
• RNA from each source was denatured for >10 minutes at 70°C and
• RNA transcriptase (GIBCO, BRL), 1 U/I RNAse Inhibitor, 2.5 mM oligo d(T)16 primer,
• reaction mixture was cycled one time for 15 minutes at 72°C for extension.
• hlL-9 receptors were subcloned into the episomal eukaryotic expression vector
• antagonism is assessed for each compound by evaluating whether the activity is demonstrated against other proliferative agents such as interleukin 3 or
• agonists and antagonists were prepared in water, saline, or DMSO and water.
• the substrate p-nitrophenyl phosphate
• the Mo7e line is a human megakaryoblastic cell line, cultured in RPMI 1640
• the T98G line is a human
• glioblastoma cell line grown in RPMI 1640 (GIBCO/BRL).
• TK-ts13 line was also used as well as the murine 32D cell line, a murine myeloid
• TF1.1 is a human myeloid leukemia line known to express the IL-2
• TF1.1 is cultured in RPMI 1640
• the cell lines were fed and reseeded at 2 X
• the cells were centrifuged for 10 minutes at 2000 rpm and resuspended in
• RPMI 1640 with 0.5% Bovine Serum Albumin (GIBCO/BRL, Gaithersburg, MD) and insulin-transferrin-selenium (ITS) cofactors (GIBCO/BRL, Gaithersburg, MD).
• IL-9 receptor cells were washed with PBS and resuspended in D-MEM, 10% fetal
• bovine serum 10 3 cells per well were seeded in triplicate in 96-well microplates
• nitrophenyl phosphate (Sigma 104 phosphatase substrate) was added per well.
• the plate was incubated for 1-1/2 hours at room temperature, the reaction
• human IL-9 or murine IL-9 (100 ng/ml) and immediately washed in cold PBS.
• human IL-9 receptor (sc698), murine Jak1 , Irs1 , Irs2, Statl , Stat2, Stat3, Stat4, Stat ⁇ , and phosphotyrosine (PY) were purchased from Santa Cruz (Santa Cruz,
• Genomic DNAs were isolated from PBMCs of volunteer donors as described
• intron 5 of the human IL-9R gene was performed by PCR using primers of
• Products were then purified and sequenced using a standard sequence protocol.
• nucleotide change at -213 nt upstream of exon 6 sequences which resulted in a
• Gergen PJ The association of allergen skin test reactivity and respiratory
• bronchoalveolar lavage cells expressing messenger ribonucleic acid for
• lnterleukin-9 and its receptor involvement in mast cell differentiation and T cell
• IgG, IgM and IgE interleukin-4-induced immunoglobulin production by normal
• polygyrus (Nematospiroides dubius): downregulation of specific cytokine
• mice Immunobiologv 1993:189:419-435. 29. Renauld J-C, Pruez C, Kermouni A, et al. Expression cloning of the
• interleukin-9 induces protein tyrosine phosphorylation and synergizes with steel
• Cotton RG Petection of single base changes in nucleic acids.

Landscapes

• Chemical & Material Sciences (AREA)
• Life Sciences & Earth Sciences (AREA)
• Health & Medical Sciences (AREA)
• Organic Chemistry (AREA)
• Proteomics, Peptides & Aminoacids (AREA)
• Genetics & Genomics (AREA)
• Zoology (AREA)
• Analytical Chemistry (AREA)
• Engineering & Computer Science (AREA)
• Wood Science & Technology (AREA)
• Biochemistry (AREA)
• General Health & Medical Sciences (AREA)
• Biophysics (AREA)
• Molecular Biology (AREA)
• Immunology (AREA)
• Bioinformatics & Cheminformatics (AREA)
• Microbiology (AREA)
• Physics & Mathematics (AREA)
• General Engineering & Computer Science (AREA)
• Pathology (AREA)
• Biotechnology (AREA)
• Toxicology (AREA)
• Cell Biology (AREA)
• Gastroenterology & Hepatology (AREA)
• Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
• Medicinal Chemistry (AREA)
• Peptides Or Proteins (AREA)
• Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
• Medicines Containing Material From Animals Or Micro-Organisms (AREA)
• Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Priority Applications (1)

Applications Claiming Priority (5)

Related Child Applications (1)

Publications (1)

Family

ID=26708147

Family Applications (1)

Country Status (8)

Family Cites Families (1)

• 1997
  • 1997-12-02 AU AU56891/98A patent/AU746595B2/en not_active Ceased
  • 1997-12-02 ES ES04013403T patent/ES2347962T3/es not_active Expired - Lifetime
  • 1997-12-02 CA CA2271952A patent/CA2271952C/fr not_active Expired - Fee Related
  • 1997-12-02 DE DE69739920T patent/DE69739920D1/de not_active Expired - Lifetime
  • 1997-12-02 JP JP52573798A patent/JP4552076B2/ja not_active Expired - Fee Related
  • 1997-12-02 AT AT04013403T patent/ATE471982T1/de not_active IP Right Cessation
  • 1997-12-02 EP EP97953072A patent/EP0942979A2/fr not_active Withdrawn
  • 1997-12-02 PT PT04013403T patent/PT1471144E/pt unknown
• 2009
  • 2009-03-02 JP JP2009048597A patent/JP2009159976A/ja active Pending

Non-Patent Citations (1)

Also Published As

Similar Documents

Legal Events