WO1998027997A1 - A method for diagnosis and treatment of inflammatory bowel diseases including crohn's disease and chronic ulcerative colitis - Google Patents

Abstract

The human Asthma Associated Factor 1 (AAF1) has been shown to up regulate the Th2 mediated immune response to antigen and to induce a Th2 mediated response in an animal which normally has a Th1 mediated response. Inflammatory bowel diseases (IBD) are dominated by a Th1 mediated, antigen induced, inflammatory response. Therefore, the invention involves the treatment of IBD by the up regulation of the Th2 mediated immune response induced by AAF1 or fragments thereof or other AAF1 agonists.

Description

A METHOD FOR DIAGNOSIS AND TREATMENT OF INFLAMMATORY BOWEL

DISEASES INCLUDING CROHN'S DISEASE AND

CHRONIC ULCERATIVE COLITIS

CROSS-REFERENCE TO RELATED APPLICATION

This application is related to U.S. Provisional Application Serial No.

60/034,331 which was filed December 20, 1996. It is also related to the subject matter of U.S. Patent Application Serial Nos. 08/697,419, 08/697,360, 08/697,473, 08/697,472, 08/697,471 , 08/702, 105, 08/702, 110, 08/702, 168 and

08/697,440, all of which were filed on August 23, 1996, and 08/874,503 filed on June 13, 1997. All of these applications are herein incorporated by reference.

FIELD OF THE INVENTION This invention relates to a method for diagnosis and treatment of inflammatory bowel diseases (IBD) and other Th1 mediated diseases comprising the up regulation of the response mediated by the interleukin-9 ("IL-9") pathway.

BACKGROUND OF THE INVENTION Inflammation is a complex process in which the body's defense system combats foreign entities. While the battle against foreign entities may be necessary for the body's survival, some defense systems improperly respond to foreign entities, even innocuous ones, as dangerous and thereby damage surrounding tissue in the ensuing battle. Inflammatory bowel diseases (IBD) are a group of diseases characterized by an inappropriate inflammatory response to environmental stimuli. This group includes Crohn's diseases and chronic nonspecific ulcerative colitis. Other related Th1 mediated diseases include multiple sclerosis, diabetes, arthritis and lupus. IBD is generally characterized by intermittent episodes of activation of the immune system leading to acute inflammation in the walls of the colon and/or the small bowel. Inflammatory cells accumulate in the colonic mucosa, resulting in the ultimate destruction of normal epithelium. It is a chronic disabling disorder that can lead to fibrosis and fistula formation and may ultimately require resection of the bowel. In addition, a long-standing colitis has been shown to be associated with a significant risk for development of carcinoma.

The mechanism of susceptibility to IBD remains unknown. Many studies have shown, however, clear genetic predisposition resulting in a mucosal inflammatory response to some environmental stimulus. In addition, studies have shown that CD4 positive helper T-cells are involved in inflammatory bowel disease¹. These cells can be classified into two distinct populations based on their pattern of cytokine production. "Th1" cells produce interleukin(IL)-2, IL-12, interferon(IFN)-γ and tumor-necrosis factor(TNF)-β while "Th2" cells produce IL-4, IL-5, IL-6, IL-9, and IL-13^1,2. In addition, a Th2 response to antigen results in the generation of IgE antibodies. Several studies implicate primarily the Th1 pathway^3,4 in the development of inflammatory bowel diseases. The Th1 immune response has also been implicated in other diseases such as multiple sclerosis and other autoimmune diseases. The relationship between Th2 cells and the cytokine IL-9 implicates another inflammatory response, atopic allergy. Atopic allergy 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 leads to a Th2 mediated allergic inflammation and may occur after 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 to this inflammatory reaction and include T cells and antigen presenting cells, B cells that produce IgE, and mast cells/basophils and eosinophils that bind IgE.

By analyzing the DNA of families that exhibit asthma-related disorders, the inventors, hereon known as applicant, have identified a polymorphism in the IL-9 gene that correlates with the biologic variability of serum total IgE. Specifically, instead of the hydrophilic amino acid threonine, the variant IL-9 contains the hydrophobic amino acid methionine at position 117 of the IL-9 precursor protein

(MetlL-9; SEQ ID NO:1)(Figure 3). Individuals with a threonine at amino acid 117 of IL-9 (ThrlL-9; SEQ ID NO:2) (Figure 2) in either one or both of their alleles (Thr/Thr or Thr/Met) generally exhibit susceptibility to an asthmatic phenotype, and these genotypes are characterized by higher mean serum total IgE levels, indicating a Th2 mediated response. In contrast, those individuals with a methionine (Met) at codon 117 of IL-9 in both alleles (Met/Met) exhibit a lack of asthma, fewer abnormal skin test responses, and a lower serum total IgE. Thus, the Met/Met genotype of IL-9 appears to protect against asthma or atopic allergy. Further evidence defining the role of IL-9 in the Th2 mediated immune response derives directly from the applicant's observation that IL-9 is significant to a number of antigen-induced responses in mice. When the functions of IL-9 are down regulated by antibody pretreatment prior to aerosol challenge with antigen, the animals are significantly protected from the antigen induced IgE response. As noted above, the Th2 response is up regulated by the cytokine IL-9, and applicant has shown that blocking the interaction of IL-9 with its receptor can prevent an antigen induced IgE response. Accordingly, applicant believes that IBD can be treated with compounds that up regulate the activity of IL-9, thus converting the Th1 mediated immune response characteristic of IBD to a Th2 mediated response. For example, it has been shown that a Th2 cytokine (IL-10) can be used to treat an IBD-like disease by converting the Th1 inflammatory response to a Th2 mediated immune response⁵ Therefore, applicant believes that treatment will involve up regulating the Th2 pathway which can be accomplished by the action of IL-9, IL-9 agonists or the like.

SUMMARY OF THE INVENTION

Applicant has satisfied the long felt need for a treatment for IBD by providing methods to identify compounds that are capable of up regulating the activity of IL-9. In developing these methods, applicant has demonstrated IL-9's role in causing Th2 mediated antigen-induced responses in mice leading to elevated serum total IgE.

The biological activity of IL-9 results from its binding to the IL-9 receptor and the consequent propagation of a regulatory signal in specific cells. Therefore, IL-9 functions can be up regulated by the interaction of IL-9 or IL-9 agonists with it's receptor. Thus, one embodiment of this invention is the treatment of IBD and other Th1 mediated diseases by the administration of human IL-9. The IL-9 protein can be obtained through isolation, recombinant production or like methods known in the are. Administering agonists of IL-9 that have enhanced binding to its receptor is one key mechanism and such agonists are within the claimed invention. Examples include administration of polypeptide products encoded by the DNA sequences of IL-9 wherein the DNA sequences contain various mutations. These mutations may be point mutations, insertions, deletions, or spliced variants of IL-9.

The skilled artisan will also readily recognize that all molecules containing the 3-dimensional structural conformation and which contain the residues for receptor binding are within the scope of this invention. Specifically, residues 43-60 and 71-90 of the mature protein appear to be important for receptor binding. Applicant has shown that the peptides KP-20 (residues 71-90; SEQ ID

NO:3) and KP-89 (SEQ ID NO:6) act as a receptor agonist. In addition, these residues in the native IL-9 molecule are predicted to form anti-parallel helical structures. The three dimensional structure of the protein suggests that specifically serine 52 and/or glutamic acid 53 interact with lysine 85, serine 56 interacts with lysine 82, and threonine 59 interacts with valine 78. The three dimensional coordinates of these anti-parallel helices and the related functional groups represent the 3-dimensional conformation important in receptor binding and compounds which simulate these relationships are within the scope of this invention. The invention further includes fragments of the molecules. By fragments, applicant means portions of a 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. Another embodiment of this invention relates to the use of isolated DNA sequences containing various mutations such as point mutations, insertions, deletions, or splice site mutations of IL-9 or the IL-9 receptor in gene therapy. The structure of both IL-9 and the IL-9 receptor have been examined and analyzed in great detail and amino acid residues of IL-9 involved in receptor binding have been identified. Based on structural studies and the binding characteristics of this specific binding pair, this invention further includes small molecules tailored such that their structural conformation provides the residues essential for interacting with the IL-9 receptor. Such interaction results in up regulation of the activity of the receptor and these molecules are, therefore, useful in treating IBD.

Another embodiment of this invention is directed to the up regulation of downstream signaling pathways involved in IL-9 function. IL-9 induces tyrosine phosphorylation of Stat3 which appears to be unique to the IL-9 signaling pathway⁶ and is useful as a target for activators. Specific and nonspecific activators of tyrosine kinase are, therefore, useful in downstream up regulation of the physiological activity of IL-9, and are part of the invention. The products discussed above represent various effective therapeutic agents in treating IBD and other related inflammatory disorders. This invention also includes the use of truncated polypeptides encoded by the DNA molecules described above. These polypeptides are capable of up regulating the activity of the IL-9 receptor. Thus, applicant has provided agonists, and methods of identifying agonists, that are capable of up regulating the activity of IL-9 and its receptor and are useful for the treatment of IBD and related disorders.

Lastly, applicant provides a method for assaying the functions of IL-9 and its receptor to identify compounds or agents that may be administered in an amount sufficient to up regulate either the expression or functions of IL-9 and the IL-9 receptor.

The accompanying figures, which are incorporated in and constitute a part of this specification, illustrate several embodiments of the invention and, together with the description, serve to explain the principle of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 : Histogram of the correlation between human IL-9 gene alleles and serum total IgE titers measured in international units. S/S denotes Thr/Thr individuals, S/R denotes Thr/Met individuals and R/R denotes Met/Met individuals.

Figure 2: cDNA sequence (SEQ ID NO:4) of Thr117 version of IL-9 and

the translated protein sequence (SEQ ID NO:2).

Figure 3: cDNA sequence (SEQ ID NO:5) of Met117 version of IL-9 and the translated protein sequence (SEQ ID NO:1).

Figure 4: Purified recombinant Met117 and Thr117 versions of IL-9.

Figure 5: Amino acid sequence for peptides derived from human IL-9 residues 71-90. Figure 6: Effect of various cytokines on the growth of D2 cells in serum- free medium.

Figure 7: Effect of IL-9 derived peptides on the growth of the cytokine dependent D2 cell line in serum free medium.

Figure 8: Characterization of the role of IL-9 in the elevation of serum IgE levels in response to antigen in vivo.

Figure 9: Effect of IL-9 on the induction of a Th2 mediated immune response in transgenic mice.

Figure 10: Effect of IL-9 on the induction of a Th2 mediated immune response in a natural Th1-like mouse model.

DETAILED DESCRIPTION OF THE INVENTION

Applicant has resolved the needs in the art by providing agents that modify the activity of IL-9 which may be used in the prevention or treatment of IBD including Crohn's disease and chronic nonspecific ulcerative colitis. In addition, applicant has provided methods useful for the discovery of new agents to up regulate the activity of IL-9. All references cited in this application are expressly incorporated by reference herein.

IBD encompasses inflammatory disorders of the gastrointestinal tract with irreversible tissue destruction. The IL-9 gene refers to the genetic locus of interleukin-9, a cytokine exhibiting a variety of functions involving the regulation of human myeloid and lymphoid systems.

Accordingly, the invention provides a method of treating or alleviating IBD comprising administration of a compound that up regulates the IL-9 pathway. As those of skill in the field would recognize, treatment or alleviation encompasses the reduction or elimination of inflammation.

The invention also includes degenerate sequences of the IL-9 DNA as well as sequences that are substantially homologous. The source of the IL-9 of the invention is preferably human. Alternatively, the DNA or fragments thereof may be synthesized using methods known in the art. It is also possible to produce the compounds 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 or to synthesize them by chemical methods well known in the art. See, for example, the methods set forth in Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2d ed.

Cold Spring Harbor Laboratory Press (1985).

Using a model accepted in the art, elevation of serum IgE, applicant has demonstrated the function of the IL-9 pathway in the Th2 mediated response to antigen in some strains of inbred mice (DBA/2)⁷. The presence of a Th2 response to antigen suppresses the Th1 response seen in IBD, and therefore, this assay can be used to identify drugs for the treatment of IBD.

The evidence defining the role of IL-9 in the Th2 mediated response to antigen derives directly from the applicant's observation that IL-9 is important to a number of antigen induced responses in mice. When the functions of IL-9 are down regulated by antibody pretreatment prior to aerosol challenge with antigen, the animals are significantly protected from the antigen induced responses.

These responses include elevated serum IgE levels; which is a hallmark of the

Th2 mediated response. The demonstrations of an IL-9 sequence associated with a Th2 like phenotype (Thr/Thr or Thr/Met) and one associated with a Th1 phenotype (Met/Met) suggest that the use of either a Th2 or a Th1 response to antigen is dependent on IL-9, and therefore, regulating the function of IL-9 should determine whether a Th1 or Th2 antigen response is used. Thus, applicant also provides methods for treating IBD based on the relationship between IL-9 and the use of either a Th1 or Th2 based immune response.

In one embodiment, the applicant provides a method of detecting MetlL-9 in an individual as an indication of enhanced susceptibility to Th1 mediated response to antigen as in IBD.

In a further embodiment the compound may resemble the Thr allele of IL-9 in structure and thereby acts to up regulate the IL-9 pathway, to increase either the expression of IL-9 or the functions controlled by IL-9. Alternatively, the compound of the invention may exist as a fragment of IL-9 with a structural composition similar to ThrlL-9. In another embodiment of the invention, the compound may retain functions comparable to ThrlL-9, but may not resemble ThrlL-9 in structure. For example, the composition of the compound may include molecules other than amino acids. This example is merely illustrative and one of ordinary skill in the art would readily recognize that other substitutions and/or deletion analogues of IL-9 resulting in effective agonists are also within the scope of this invention.

Applicant also teaches the regulation of the activity of IL-9 by administering agonists to the IL-9 receptor. The skilled artisan will readily recognize that all molecules containing 3-dimensional structural conformation and residues for receptor binding are within the scope of this invention. As one example, Applicant has shown that the peptide KP-20 (produced using standard peptide automated synthesis techniques, for example, the Applied Biosystems Model 431A Peptide Synthesizer) acts as an IL-9 agonist on the D2 cell line. Specifically, applicant demonstrates that residues 43-60 and 71-90 of the mature protein appear to be important for receptor binding. In addition, these residues include most of exon 4 (amino acids 44-88) and are predicted to form anti-parallel helical structures. The three dimensional structure of the protein suggests that specifically serine 52 and/or glutamic acid 53 interact with lysine 85, serine 56 interacts with lysine 82, and threonine 59 interacts with valine 78. The three dimensional coordinates of these parallel helices and the related functional groups represent the 3-dimensional conformation for receptor binding and compounds that simulate these relationships are within the scope of this invention.

To select the agonists of the invention, one may employ specific assays based on IL-9's known regulation, in part, of the proliferation of T lymphocytes,

IgE synthesis, and release from mast cells.⁶'^8"13 Another assay involves the ability of human IL-9 to specifically induce the rapid and transient tyrosine phosphorylation of multiple proteins in M07e cells.¹¹ Because this response is dependent on 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 actions of IL-9,⁶ and the response further represents a simple method or assay for the characterization of compounds within the invention. Still another method to characterize the function of IL-9 and IL-9-like molecules involves the well known murine TS1 clone and the D10 clone available from ATCC used to assess human IL-9 function with a cellular proliferation assay.¹² The term agonist, according to this invention, includes compounds that mimic at least some of the effects of endogenous compounds by interacting or binding with a receptor. Agonists that interact or bind to the IL-9 receptor on the surface of certain cells initiate a series of biochemical and physiological changes that are characteristic of this cytokine's actions.^2,68"19 To identify other agonists of the invention, one may test for binding to the IL-9 receptor or for IL-9-like functions as described herein and in the cited literature.^2,6,8"20

In a further embodiment, these agonists may be analogues of IL-9. IL-9 analogues may be produced by point mutations in the isolated DNA sequence for the gene, nucleotide substitutions, and/or deletions which can be created by methods that are all well described in the art.²⁴

A specific example of an agonistic peptide derived from IL-9 is KP-20 (SEQ ID NO:3) which is derived from exon 4. Exon 4 encodes 44 amino acids while the peptide mentioned above contains 18 amino acids. This peptide exhibits considerable agonistic activity when assayed on the human D2 cell line. Splice variants of IL-9 can be formed by deletion of any one or more of the IL-9 exons 1 through 5. In addition, other peptides derived from these exons can show agonistic activity and, accordingly, are useful in treating IBD.

In another embodiment, the agonists of the invention are antibodies to the IL-9 receptor. The antibodies to the IL-9 receptor may be either monoclonal or polyclonal made using standard techniques well known in the art (See Harlow & Lane's Antibodies - A Laboratory Manual (Cold Spring Harbor Laboratory, 1988)). They can be used to interact with the IL-9 receptor and up regulate its activity. Antibodies are also produced from peptide sequences of the IL-9 receptor using standard techniques in the art (see Protocols in Immunology, Chap. 9,

Wiley). Peptides can be identified to produce antibodies that will bind to the IL-9 receptor and activate the biological response, thus up regulating the IL-9 activity.

In still another embodiment, the compounds of the invention may be coupled or combined to chemical moieties, including proteins that up regulate the IL-9 pathway for therapeutic benefit in IBD.²¹ These proteins may be coupled or combined with other cytokines and growth factors including²² IL-4, IL-5, IL-3, IL-2, IL-13, and IL-10 that may offer additional therapeutic benefit in IBD. In addition, the IL-9 of the invention may also be conjugated through phosphorylation or conjugated to biotinylate, thioate, acetylate, iodinate, by crosslinking reagents known in the art.

Isolated DNA sequences containing various mutations such as point mutations, insertions, deletions, or spliced mutations of IL-9 are useful in gene therapy to produce highly active forms of IL-9. By isolated, applicants mean that

the DNA is free of at least some of the contaminants associated with the

nucleic acid or polypeptides occurring in a natural environment.

In addition to the direct up regulation of the IL-9 receptor, this invention also encompasses methods of downstream regulation which involve activation of signal transduction. In particular, a further embodiment of this invention is drawn to up regulation of tyrosine phosphorylation. It is known in the art that highly exergonic phosphoryl-transfer reactions are catalyzed by various enzymes known as kinases. In other words, a kinase transfers phosphoryl groups between ATP and a metabolite. IL-9 induces tyrosine phosphorylation of multiple proteins; it is known in the art that, in addition to the activation of JAK1 and JAK3 tyrosine kinases, IL-9 also induces tyrosine phosphorylation of Stat3.⁸ Phosphorylation of

Stat3 is unique to the IL-9 signal transduction pathway and hence is a target for regulation.⁶ This invention includes within its scope the use of compounds which are specific up regulators of protein tyrosine kinases. Thus, activators of these kinases are useful in the modulation of signal transduction and are useful in the treatment of IBD.

Applicant also provides for a method to screen for the compounds that up regulate the expression of IL-9 or the functions controlled by IL-9. One may determine whether the functions expressed by IL-9 are altered using techniques standard in the art.^6,11"13 In one embodiment, serum total IgE may be measured using techniques well known in the art²³ to assess the efficacy of a compound in up regulating the functions of IL-9 in vivo.

In yet another embodiment, the functions of IL-9 may be assessed in vitro. As is known to those in the art, human IL-9 specifically induces the rapid and transient tyrosine phosphorylation of multiple proteins in M07e cells. The tyrosine phosphorylation of Stat3 transcriptional factor appears to be specifically related to the actions of IL-9.

Another method to characterize the function of IL-9 and IL-9-like molecules that depends on the "stable expression" of the human IL-9 receptor uses the well known murine TS1 clones to assess human IL-9 function with a cellular proliferation assay.¹²

The invention also includes a simple screening assay for saturable and specific ligand binding based on cell lines that express the IL-9 receptor.^2,12 The IL-9 receptor is expressed in on a wide variety of cell types, including K562,

C8166-45, B cells, T cells, mast cells, neutrophils, megakaryocytes (UT-7 cells),¹³ the human megakaryoblastic leukemia cell lines M07e,¹¹ TF1,¹² macrophages, fetal thymocytes, the human kidney cell line 293, ³ and murine embryonic hippocampal progenitor cell lines.²'^12,13 In another embodiment, soluble IL-9 receptor may be used to evaluate ligand binding and potential receptor agonists.

In addition, 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 injectable 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 familiar to the skilled person such 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 formulation 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. For topical application, these compounds could also be administered as a powder or spray, particularly in aerosol form. The active ingredient may be administered in pharmaceutical compositions adapted for systemic administration. As is known, if a drug is to be a administered systemically, it may be confected as a powder, pill, tablets or the like, or as a syrup or elixir for oral administration. For intravenous, intraperitoneal or intra-lesional administration, the compound will be prepared as a solution or suspension capable of being administered by injection. In a preferred embodiment, these compounds will be formulated in suppository form. They can also be in an extended release formulation for deposit under the skin or intermuscular injection. The compounds of this invention can also be administered by inhalation. For inhalation therapy, the compound may be in a solution useful for administration by metered dose inhalers, or in a form suitable for a dry powder inhaler.

An effective amount is that amount which will regulate either the expression of IL-9 or the functions controlled by IL-9. 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. However, it is anticipated that in the treatment of IBD 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 effect a therapeutic result in most instances.

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 [1985], or Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY. John Wiley & Sons, Inc. [1994].

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). In addition, 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, consists of two complementary strands of nucleotides, which include the four different base compounds, adenine [A], thymine [T], cytosine [C], and guanine [G]. A of one strand bonds with T of the other strand while C of one strand bonds to G of the other to form complementary "base pairs," each pair having one base in each strand.

A sequential grouping of three nucleotides [a "codon"] codes for one amino acid. Thus, for example, the three nucleotides CAG codes for the amino acid Glutamine. The 20 naturally occurring amino acids, and their one letter codes, are as follows: Alanine Ala A

Arginine Arg R

Asparagine Asn N

Aspartic Acid Asp D

Asparagine or

Aspartic acid Asx B

Cysteine Cys C

Glutamine Gin Q

Glutamine Acid Glu E

Glutamine or

Glutamic acid Glx Z

Glycine Gly G

Histidine His H

Isoleucine He 1

Leucine Leu L Lysine Lys K

Methionine Met M

Phenylalanine Phe F

Proline Pro P

Serine Ser S

Threonine Thr T

Tryptophan Trp w

Tyrosine Tyr Y

Valine Val V 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. Thus, 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. In general, 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

I cDNA

Genomic DNA comprises all the DNA sequences found in an organism's cell. It is "transcribed" into messenger RNA ["mRNA"]. Complementary DNA ["cDNA"] is a complementary copy of mRNA made by reverse transcription of mRNA. Unlike genomic DNA, both mRNA and cDNA contain only the protein-encoding or polypeptide-encoding regions of the DNA, the so-called "exons." Genomic DNA may also include "introns," which do not encode proteins.

In fact, 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. In fact, structural features of introns and the underlying splicing mechanisms form the basis for classification of different kinds of introns.

As to the 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).

Returning now to the manipulation of DNA, DNA can be cut, spliced, and otherwise manipulated using "restriction enzymes" that cut DNA at certain known sites and DNA ligases that join DNA. 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. In particularly preferred embodiments, the host cells include E. coli, Pseudomonas, Bacilles, Streptomyces, Yeast, CHO, R1-1 , B-W, LH, COS-J, COS-7, BSC1 , BSC40, BMT10, and S69 cells. Yeast cells especially include Saccharomyces, Pichia, Candida, Hansenula, and Torulopis.

As those skilled in the art recognize, the expression of the DNA segment by the host cell requires the appropriate regulatory sequences or elements. 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. As those in the art well recognized, expression of the polypeptide may be enhanced, i.e., increased over the standard levels, by careful selection and placement of these regulatory sequences.

In other embodiments, promoters that may be used include the human cytomegalovirus (CMV) promoter, tetracycline inducible promoter, simian virus (SV40) promoter, moloney murine leukemia long terminal repeat (LTR) promoter, glucocorticoid inducible murine mammary tumor virus (MMTV) promoter, Herpes thymidine kinase promoter, murine and human β-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 scaffold attachment region (SAR) enhancer elements. 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. Other embodiments of the invention will be apparent to those skilled in the art from consideration of the specification and practice of the invention disclosed. It is intended that the specifications and examples be considered exemplary only with the true scope of the invention being indicated by the appended claims.

METHODS In conducting the experiments described in the Examples below, applicant used the following methods:

Oligonucleotide Primers.

All primers were designed using OLIGO 4.0. Characterization of the IL-9 gene was carried out using primers surrounding each of the 5 exons of the reported sequence. The primer sequences surrounding each exon were: exon 1 [upper] [5' GCT CCA GTC CGC TGT CAA 3'] and [lower] [5' CTC CCC CTG CAG CCT ACC 3'][product size 150 bp]; exon 2 [upper] [5" CGG GGC TGA CTA AAG GTT CT 3'] and [lower] [5' GTT CTT AAA GAG CAT TCA CT 3'][product size 99 bp]; exon 3 [upper] [5' ATT TTC ACA TCT GGA ATC TTC ACT 3'] and [lower][5" AAT CCA AGG TCA ACA TTA TG 3'][product size 113 bp]; exon 4 [upper] [5' TTT CTT TGA ATA AAT CCT TAC 3'] and [lower] [5' GAA ATC ACC AAC AGG AAC ATA 3'][product size 206 bp]; and exon 5 [upper] [5' ATC AAC TTT CAT CCC CAC AGT 3^*] and [lower] [5' GGA TAA ATA ATA TTT CAT CTT CAT 3']. Each exon was examined first by a single strand conformational polymorphism assay (SSCP).^25,26 The primers for exon 5 produced a 160 bp product after polymerase chain reaction (PCR) amplification which was also examined by direct solid phase sequence analysis.²⁵²⁶ The upper primer was synthesized with a 5' biotin label and, following amplification, the PCR product was captured by a streptavidin-linked paramagnetic bead (Dynal) and characterized by Sanger sequencing as described elsewhere.²⁶ Sequence polymorphisms were distinguished from artifact by repeated analyses. SSCP analysis.

SSCP, a method for detection of polymorphisms on the basis of changes in migration of single-stranded DNA exposed to an electric field,²⁵ was carried out as set forth in Schwengel et al., (1993)²⁶ at room temperature with and without 10% glycerol using 6% polyacrylamide gel electrophoresis at a cross-linking monomer concentration of 2.67%. Four μl of PCR product was mixed with 5 μl 2X stop buffer (95% formamide, 20 mM EDTA, 0.05% BPB, 0.05% xylene cyanol), and 1 μl 0.5% SDS and 50 μM EDTA, denatured at 85-90°C for 8 minutes, and then immediately placed on ice. Electrophoresis was carried out at 12 watts for approximately 24 hours for glycerol containing gels and 12 hours for non-glycerol gels. The gels were then dried and exposed to Kodak XAR® film. DNA Sequencing. Direct DNA sequencing of the PCR products was accomplished using solid phase techniques after verifying the presence of the correct size PCR product on a 1% agarose gel stained with ethidium bromide as set forth in Schwengel et al., 1994.²⁶ Twenty μl of PCR product was incubated with 40 μl of Dynabeads® m-280 (Dynal) for 15 minutes. The beads were washed and diluted as suggested by the manufacturer. Each sample was subsequently washed with B&W buffer containing 10 mM tris-HCI pH 7.5, 1 mM EDTA, 2 M NaCI, denatured with 0.1 N NaOH, and then washed with 0.1 N NaOH, B&W buffer, and 10 mM Tris-HCI pH 8 and 1 mM EDTA. The pellet of beads was resuspended with 10 μl of H₂0. Sanger sequencing reactions were carried out using Sequenase (United States Biochemical Co.). ³⁵S-dATP or ³³P-dATP was incorporated into the sequencing reactions, and the products were electrophoresed through either 5% or 6% polyacrylamide gels containing 7 M urea. Gels were dried without fixing and exposed to X-ray film. Alleles were determined by comparing the genotypes of parents and offspring. Infrequent artifacts were easily distinguished from true sequence polymorphisms by repetition.

DNA was available and extracted from peripheral leukocytes. Genomic DNA was diluted to a concentration of 200 μg/ml for amplification.^23,27 Simple sequence repeats (SSR) including DXYS154 were selected from the Genome Data Base (GDB; Welch library, Johns Hopkins University, Baltimore, MD). Genotyping of the sKK-1 marker was carried out using the following primers sKK-1 U [5' CAA ATC TGA AGA GCA AAC TAT 3'] and sKK-1 L [5' TTA AAA AAT TCA TTT CAG TAT TCT 3'] which produce a 90 bp product. Each SSR product was amplified by PCR²⁵ and sized according to methods previously described.^23,27 Sample handling was carried out as described by Weber et al. with minor modifications.^23,27,28 Genotypes were determined from two independent readings of each autoradiograph. Individuals genotyping the families were blinded to the clinical data.

RFLP Analysis.

As a result of the C to T polymorphism at position 3365, a Sty1 restriction fragment length polymorphism (RFLP) was produced at position 52 of the IL-9 exon 5 PCR product. To test for the presence of this DNA sequence variant the lower primer from exon 5 was end-labeled prior to PCR amplification. The PCR product was then digested with Sty1 producing two fragments 108 bp (labeled) and 52 bp (unlabeled) in length. This RFLP was used along with SSCP to confirm the presence of this polymorphism in families and individuals. Having provided this background information, applicant now describes preferred aspects of the invention.

EXAMPLE 1 Identification of an IL-9 Gene Polymorphism Applicant demonstrated conserved linkage between the mouse and humans for BHR. These data suggest that variation in the functions of this gene or DNA sequence may be important in regulating bronchial responsiveness in the mouse. Using the methods described above, a unique product of the correct size was identified by gel electrophoresis for each of the exons of human IL-9 after PCR. A single polymorphism was identified by SSCP in exon 5 of the human IL-9 gene. Direct DNA sequence analysis demonstrated a C to T nucleotide substitution at position 3365 (GenBank accession number M30136) of the human IL-9 gene as the cause of the novel SSCP conformer. This DNA sequence change predicts a nonconservative substitution of a methionine (Figure 3) (hydrophobic) for a threonine (Figure 2)(hydrophilic) at amino acid 117 of the IL-9 protein.

Exon 5 codes for this segment of the protein which is within the most highly conserved interval of human IL-9 as compared to the mouse IL-9 sequence. Individuals were genotyped from various populations to examine the frequency of these alleles by direct analyses of the nucleotide substitution in the coding sequence of human IL-9. Two of 394 individuals from a group of asthmatic families were homozygous (Met/Met) at codon 117 (0.5%). There were 91 (23.1 %) heterozygous, and 301 (76.4%) homozygous (Thr/Thr) individuals.

The true prevalence for this IL-9 variant is likely to be significantly higher because the Italian population of families was ascertained through symptomatic patients with asthma. From a separate ethnically diverse population ascertained randomly with respect to atopy and asthma, there were 1 of 49 individuals homozygous for (Met/Met) at codon 117 (2.0%). There were 11 (22.4%) heterozygous, and 37

(75.5%) homozygous (Thr/Thr) individuals. The prevalence of the Met/Thr heterozygotes was 18.9% in a fourth population ascertained randomly with respect to atopy and asthma. Thus, approximately 20% of the population are likely to represent carriers of the T allele at position 3,365 as compared to the reported sequence (GenBank accession number M30136). Because it is well known in the art that the frequency of any allele in the population is p2 + 2pq + q2, then, approximately 4% of the population is expected to be Met/Met homozygous at codon 117 of IL-9.

Overall, serum total IgE averaged 44.5 I.U. for homozygous individuals (Met/Met), which was significantly different from those who were homozygous wild type (Thr/Thr) (351.7I.U.), or heterozygous (Met/Thr) (320.9 I.U.). See Figure 1. The homozygous protected individuals (Met/Met) failed to demonstrate evidence of atopic allergy except for a single positive skin test in one individual. These data indicate that this novel DNA polymorphism, when inherited in the homozygous state, is associated with protection from atopic allergy, including lower serum total IgE.

EXAMPLE 2 Cloning, expression and purification of recombinant MetlL-9 and ThrlL-9

General Cloning Methods for Constructs hlL-9 was subcloned into procaryotic expression vectors. The TA2AAF1

MET and THR vectors were digested by EcoRI and the 0.420 Kb fragment

(containing an Xho1 site at the 5' end of the hlL-9 cDNA) was cloned into the EcoRI site contained with the polylinker of pBluescript (PBS) (Stratagene).

Clones in the sense orientation to the T3 promoter were then digested with Xho1

(the fragment contained a 5' Xho1 site from the IL-9 cDNA insert from TA vectors and a 3' Xho1 site from the PBS polylinker) and inserts were subcloned into the

Xho1 sites of the pFLAG expression vector. Cloning and expression of IL-9 constructs in the pFLAG-1™ Expression

Vector

For the expression, purification and detection of human IL-9 protein, IL-9 cDNA inserts were subcloned into the Xho2 site of the multiple cloning site (Xho1) of the 5.37 Kb FLAG vector. FLAG technology is centered on the fusion of a low molecular weight (1kD), hydrophilic, FLAG marker peptide to the N-Terminus of a recombinant protein expressed by the pFLAG-1™ Expression Vector(1) (obtained from IBI Kodak). The FLAG-IL-9 fusion cDNA was then subcloned from the pFLAG vector via PCR using primers directed to the 5' ATG sequence located in the OMPA leader sequence and 3' terminator sequence located in the poly linker

3' to the cDNA. Products were then cloned into the PCR-BAC Baculovirus expression plasmid and recombinant viruses were identified and isolated as suggested by the manufacture (Invitrogen). The cells were harvested by centrifugation, and the cell pellet was boiled in 50 μl of Laemmli buffer (Laemmli, 1970) for 10 min and electrophoresed on 10% polyacrylamide gels. The Anti-FLAG™ M1 monoclonal antibody was used for specific and efficient detection of the FLAG fusion protein on Western, slot or dot blots throughout its expression, affinity purification, and FLAG marker removal. The FLAG fusion protein was rapidly purified under mild, non-denaturing conditions in a single step by passing the cell supernate through a column containing the murine Anti-FLAG™ IgG M2 monoclonal antibody covalently attached to agarose (Figure 4). Following affinity purification the fusion protein may be used after removal from the affinity column or the authentic protein may be recovered in biologically active form by specific and efficient proteolytic removal of the FLAG peptide with enterokinase. Final purification was achieved by chromatography on Sephadex G-100 column (100x1.5 cm), packed and equilibrated with 0.05 M ammonium bicarbonate buffer.

SDS-PAGE and Immunoblot Analysis

SDS-PAGE was performed by the method of Laemmli (Laemmli U.K. (1970) Nature 227, 680-685)(incorporated herein by reference in its entirety) by using a 12.5% polyacrylamide gel in a mini-gel system (SE 280 vertical gel unit, Hoefer). For immunoblot analysis, the proteins separated by SDS-PAGE were transferred to nitrocellulose membranes by using the TE 22 Mighty small transfer unit (Hoefer) in 25 mM Tris-glycine buffer, pH 8.3, containing 15% methanol (Towbin H., et al., (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 4350-4354). The unoccupied binding sites on the membrane were blocked by incubating for 1 h with 20 mM Tris-HCI buffer, pH 8.0, containing 2% bovine serum albumin. The membranes were then incubated with 1 :200 dilution of antibodies overnight at 4°C. The membranes were washed and treated with 1:2000 diluted goat anti-rabbit IgG conjugated with either peroxidase or alkaline phosphatase for 1 h. After washing, the bound antibodies were visualized by addition of the super- substrate chemiluminescent reagent (Pierce) or the 4-chloro-1-naphthol color developing reagent. The reaction was stopped by immersing the membranes in distilled water.

Analytical Methods

The molecular mass of the purified proteins was confirmed by matrix assisted laser desorption mass spectrometry using Perceptive Biosystems Voyager Biospectrometry workstation. Amino acid analyses were performed after hydrolysis of the sample in 6N HCl at 110-C for 24h in evacuated sealed glass bulbs. Automated Edman Degradation

The partial amino acid sequence of the purified proteins is determined by automated step-wise sequencing on an Applied Biosystems model 477A gas-phase sequencer with an on-line model 20A PTH analyzer.

EXAMPLE 3

Cell lines and cellular proliferation assays of IL-9 or IL-9 agonists Cell lines were used to assess the function of peptides, as well as all other compounds that stimulate IL-9 function. A proliferative or antiapoptosis response was measured and compared to each of the other cytokines, variant or mutant forms of 11-9, or IL-9 agonists. In addition, compounds were tested for their ability to induce the baseline proliferative response.

The M07e line is a human megakaryoblastic cell line, cultured in RPMI 1640 (GIBCO/BRL, Gaithersburg, MD), 20% Fetal Bovine Serum (Hyclone) and 10 ng/ml IL-3 (R&D Systems, Minneapolis, MN). D2 is a cytokine dependant murine pre mast cell line which responds to IL-9.

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). Cells were counted using a hemocytometer and diluted to a concentration of 1 X

10⁵ cells/ml and plated in a 96-well microtiter plate. Each well contained 0.15 or 0.2 ml, giving a final concentration of 2 x 10⁴ cells per well.

M07e cells were stimulated with 50 ng/ml Stem Cell Factor (SCF) (R&D Systems, Minneapolis, MN) alone, 50 ng/ml SCF plus 50 ng/ml IL-3 (R&D Systems, Minneapolis, MN), or 50 ng/ml SCF plus 50 ng/ml IL-9. A control was included which contains cells and basal media only. Serial dilutions of test compounds (i.e, recombinant IL-9 proteins, peptides, small molecules) were added to each test condition in triplicate. Cultures were incubated for 72-96 hours at 37°C in 5% C0₂. Cell proliferation or antiapoptosis was assayed using the Abacus Cell

Proliferation Kit (Clontech, Palo Alto, CA) which determines the amount of intracellular acid phosphatase present as an indication of cell number. The substrate p-nitrophenyl phosphate (pNPP) was converted by acid phosphatase to p-nitrophenol which was measured as an indicator of enzyme concentration. pNPP was added to each well and incubated at 37°C for one hour. 1N sodium hydroxide was then added to stop the enzymatic reaction, and the amount of p-nitrophenol was quantified using a Dynatech 2000 plate reader (Dynatech Laboratories, Chantilly, VA) at 410 nm wavelength. Standard curves that compare cell number with optical absorbance were used to determine the linear range of the assay. Assay results were only used when absorbance measurements are within the linear range of the assay.

D2 cells were treated with increasing amounts of IL-9 and found to survive in serum free media supplemented with IL-9 as compared to serum free medium only (Figure 6). Peptides derived from the IL-9 protein were tested for their ability to stimulate antiapoptotic activity in a similar experiment. Two peptides, (KP-20 and KP-89) (Figure 5) were found to have a stimulatory activity on D2 cells which appeared to be sequence specific because similar peptides containing single residue changes (see Figure 6) were found to have decreased or no activity on the cells (Figure 7). These data demonstrate the ability to create small peptides to act as agonists for IL-9 stimulatory activity on IL-9 responsive cells.

EXAMPLE 4

The role of IL-9 in murine models on serum IgE levels: The response of unsensitized animals

Animals

Certified virus-free male mice ranging in age from 5 to 6 weeks were obtained from the Jackson Laboratory (Bar Harbor, ME). Animals were housed in high-efficiency particulate filtered air (HEPA) laminar flow hoods in a virus and antigen free facility and allowed free access to pelleted rodent chow and water for 3 to 7 days prior to experimental manipulation. The animal facilities were maintained at 22°C and the ligh dark cycle was automatically controlled (10:14 h lightidark). Male and female DBA/2 (D2), C57BL/6 (B6), and (B6D2)F1 (Fi) mice 5 to 6 weeks of age were purchased from the Jackson Laboratory, Bar Harbor, ME, or the National Cancer Institute, Frederick, MD. BXD mice were purchased from the Jackson Laboratory, Bar Harbor, ME. Food and water were present ad libitum.

Serum IgE and lgG3 Analysis

Whole blood was collected for serum IgE measurements by needle puncture of the inferior vena cava in completely anesthetized animals. The samples were spun to separate cells and serum was collected and used to measure total IgE levels. Samples not measured immediately were frozen at -20°C. Bronchoalveolar lavage and cellular analyses was performed as described elsewhere (Kleeberger et al., 1990). All IgE and lgG3 serum samples were measured using an ELISA antibody-sandwich assay. Microtiter plates (Corning #2585096, Corning, NY) were coated, 50 μl per well, with rat anti-mouse antibody (Southern Biotechnology #1130-01 , Birmingham, AL) at a concentration of 2.5 μg/ml in coating buffer of sodium carbonate-sodium bicarbonate with sodium azide (Sigma #S-7795, #S-6014 and #S-8032, St Louis, MO). Plates were covered with plastic wrap and incubated at 4°C for 16 hours. The plates were washed three times with a wash buffer of 0.05% Tween-20 (Sigma #P-7949) in phosphate-buffered saline (BioFluids #313, Rockville, MD), incubating for five minutes for each wash. Blocking of nonspecific binding sites was accomplished by adding 200 μl per well 5% bovine serum albumin (Sigma #A-7888) in PBS, covering with plastic wrap and incubating for 2 hours at 37°C. After washing three times with wash buffer, duplicate 50 μl test samples were added to the wells. Test samples were assayed after being diluted 1:10, 1:50, and 1:100 with 5% BSA in wash buffer. In addition to the test samples a set of IgE and lgG3 standards (PharMingen, San

Diego, CA) at concentrations from 0.8 ng/ml to 200 ng/ml in 5% BSA in wash buffer were assayed to generate a standard curve. A blank of no sample or standard was used to zero the plate reader (background). After adding samples and standards, the plate was covered with plastic wrap and incubated for 2 hours at room temperature. After washing three times with wash buffer, 50 μl of a rat anti-mouse IgE-horseradish peroxidase conjugate (PharMingen #02137E) or a rat anti-mouse lgG3-biotin conjugate (PharMingen #020621) was added at a concentration of 250 ng/ml in 5% BSA in wash buffer. The plate was covered with plastic wrap and incubated 2 hours at room temperature. For IgE analysis, after washing three times with wash buffer, 100 μl of the substrate 0.5 mg/ml

O-phenylenediamine (Sigma #P-1526) in 0.1 M citrate buffer (Sigma #C-8532) was added to every well. After 5-10 minutes the reaction was stopped with 50 μl of 12.5% H₂S0₄ (VWR #3370-4, Bridgeport, NJ) and absorbance was measured at 490 nm on a Dynatech MR-5000 plate reader (Chantilly, VA). For lgG3 analysis, wells were washed and treated with PBS plus avidin-peroxidase according to manufacturers' recommendations (PharMingen). Standard curves were constructed from the standard IgE or lgG3 concentrations with antigen concentration on the x-axis (log scale) and absorbance on the y-axis (linear scale). The concentration of IgE or lgG3 in the samples was interpolated from the standard curve.

EXAMPLE 5 The role of IL-9 in murine models of serum

IgE levels: The serum lαE levels of sensitized animals

Animals, phenotyping, and optimization of antigen sensitization Animals and handling were essentially as described in Example 6.

Sensitization with turkey egg albumin (OVA) and aerosol challenge was carried out to assess the effect on BHR, BAL, and serum IgE. OVA was injected I. P. (25 μg) day 0 prior to OVA or saline aerosolization. Mice were challenged with OVA or saline aerosolization which was given once daily for 5 to 7 days starting on either day 13 or 14. Phenotypic measurements of serum IgE was carried out on day 21. The effect of a 7 day OVA aerosol exposure on serum total IgE. The effect of antibody (Ab) or saline pretreatment on saline aerosol or OVA aerosol was examined by measuring serum IgE. Ab were administered I. P. 2-3 days prior to aerosolization of saline or OVA. Polyclonal neutralizing antibodies for murine IL-9 were purchased from R &

D systems, Minneapolis, MN. After Ab pretreatment the effect on baseline serum IgE levels relative to controls was determined. In additional experiments, recombinant human and murine IL-9 were administered I. P. 1 day before and daily during antigen sensitization (days 13-18). The animals were then phenotyped as described. The phenotypic response of a representative animal treated with saline I. P. on day zero and challenged on days 14-20 with saline (as described in Example 6) is shown in Figure 8-lane 1. Baseline (control) serum total IgE was 9.2 ng/ml.

Figure 8-lane 2 shows a representative animal from a group presensitized with OVA I.P on day zero and challenged with saline on days 14-20. These animals did not differ in their serum IgE levels from the unsensitized mice (Figure 8-lane 2).

Figure 8-lane 3 shows a representative animal from those presensitized with OVA I.P on day zero and challenged with antigen (OVA) on days 14-20. These animals developed elevated serum IgE nearly one thousand-fold over controls (Figure 8-lane 1 and 2).

Figure 8-lane 4 shows a representative animal from those presensitized with OVA I.P on day zero, pretreated with polyclonal neutralizing antibodies for murine IL-9 (approximately 200 μg/mouse I.P. in 0.5 ml of PBS), and challenged with antigen (OVA) on days 14-20. These animals were protected from the response to antigen. They did not differ significantly in their serum IgE levels from controls (Figure 8-lanes 1 and 2). These data demonstrate the link between IL-9 and Th2 mediated production of IgE.

EXAMPLE 6 Transgenic IL-9 mice express elevated IgE levels To address the direct role of the ability of IL-9 to induce IgE levels in vivo, which is an indicator of a Th2 immunological response, we analyzed the IgE expression of non-antigen sensitized IL-9 transgenic mice (TG5). These mice have been shown to express IL-9 at constitutively high levels (>1 μg/ml in serum) as compared to the parental strain (FVB/NJ)(Renauld et al., Oncogene 9:1327- 1332, 1994). Serum of TG5 and FVB/NJ mice were prepared as described in Example 5. Analysis of serum total IgE levels were found to be elevated in mice constitutively expressing IL-9 as compared to the parental FVB/NJ strain (Figure 9). These data suggest that increasing IL-9 levels in vivo elicit an immune response that is characteristic of the Th2 humeral response.

EXAMPLE 7

Administration of IL-9 to an animal exhibiting a Th1 phenotype results in a switch to the Th2 phenotype as measured by an increase of total serum IgE levels

To determine if the administration of IL-9 to an murine animal model (C57 black 6) of Th1 phenotype was capable of eliciting a Th2 response, we administered recombinant IL-9 and measured total serum IgE levels. Animals were given saline solution containing 0.5% bovine serum albumin with or without recombinant IL-9. They were then treated with a saline vehicle or vehicle plus 5 μg of IL-9 per day for 10 days. On day 11 they were sacrificed and serum was collected and prepared as described in example 5. Analysis of total serum demonstrated that animals treated with vehicle plus IL-9 had elevated IgE levels as compared to vehicle only treated mice (Figure 10). These data demonstrate the feasibility of using recombinant IL-9 to alter an immunological response from a

Th1 to a Th2-like response and suggests that IL-9 or IL-9 agonists may be useful therapeutics for the treatment of Th1 associated diseases such as IBD or autoimmune diseases. While the invention has been described and illustrated herein by references to various specific materials, procedures and examples, it is understood that the invention is not restricted to the particular material combinations of material, and procedures selected for that purpose. Numerous variations of such details can be implied as will be appreciated by those skilled in the art.

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Other embodiments of the invention described above will be apparent to those skilled in the art from consideration of the specification and practice of the invention disclosed within. It is intended that the specification and examples be considered as exemplary only, with the true scope and spirit of the invention being indicated by the following claims:

Claims

WHAT IS CLAIMED IS:

1. A method of alleviating IBD or related disorders by administering to patients in need a compound that will up regulate the function of IL-9 or the IL-9 receptor.

2. The method of claim 1 , wherein the function of IL-9 or the IL-9 receptor is up regulated by human IL-9, a fragment thereof or an IL-9 agonist.

3. The method of claim 2, wherein the function of IL-9 or the IL-9 receptor is up regulated by human IL-9.

4. The method of claim 2, wherein the function of IL-9 or the IL-9 receptor is up regulated by an IL-9 agonist.

5. The method of claim 4, wherein the function of IL-9 or the IL-9 receptor is up regulated by SEQ ID NO:3.

6. The method of claim 4, wherein the function of IL-9 or the IL-9 receptor is up regulated by SEQ ID NO:6.

7. A method of alleviating IBD by up regulating the activity of interleukin-9 by

administering to patients in need of such treatment an effective amount of

an isolated protein molecule having an amino acid sequence encoding

human IL-9 containing at least 1 exon.

8. A method of alleviating IBD by up regulating the activity of interleukin-9

comprising administering to patients in need of such treatment an effective

amount of an antibody that up regulates the activity of the interleukin-9 receptor.

9. A method of alleviating IBD by up regulating the activity of interleukin-9 by administering to patients in need of such treatment an effective amount of an isolated molecule selected from a group of DNA and RNA having a nucleotide sequence encoding human IL-9.

10. A method of claim 9, wherein the molecule is a DNA molecule having a nucleotide sequence encoding human IL-9.

11. An in vitro method for monitoring a treatment of IBD in a mammalian subject comprising evaluating the levels of an interleukin-9 in a series of biologic samples obtained at different time points from a human subject undergoing therapeutic treatment with polypeptides having the sequence of human interleukin-9 or fragments thereof.

12. The method of claim 1 , wherein said compound is an activator of the signal transduction of protein tyrosine kinase.

13. The method of claim 1 , wherein the compound is a substitution or deletion analogue of human IL-9.

14. The method of claim 1 , wherein the compound has a configuration substantially similar to the 3-D structure corresponding to amino acids 44- 88 of human IL-9 or a fragment thereof.

15. A method of alleviating TH1-mediated diseases by administering IL- 9, fragments thereof, or an IL-9 agonist to thereby convert a TH1- mediated imune response to a TH2 mediated immune response.

16. The method of claim 15, wherein the TH1 -mediated diseases comprise IBD or autoimmune diseases.

17. A method of screening a cell expressing the IL-9 receptor comprising the detection of a specific ligand binding.