U.S. patent application number 12/752219 was filed with the patent office on 2011-09-15 for interleukin-9 receptor mutants.
Invention is credited to Luigi Grasso, Kenneth J. Holroyd, Roy Clifford Levitt, Nicholas C. Nicolaides.
Application Number | 20110224406 12/752219 |
Document ID | / |
Family ID | 21863773 |
Filed Date | 2011-09-15 |
United States Patent
Application |
20110224406 |
Kind Code |
A1 |
Levitt; Roy Clifford ; et
al. |
September 15, 2011 |
INTERLEUKIN-9 RECEPTOR MUTANTS
Abstract
This invention relates to the diagnosis, treatment and methods
for discovery of new therapeutics for atopic asthma and related
disorders based on variants of Asthma Associated Factor 2. One
embodiment of the invention is a variant of AAF2 wherein codon 173
is deleted resulting in the loss of glutamine 173 from the mature
protein precursor. This single amino acid deletion results in a
non-functional AAF2 protein and therefore the presence of this
phenotype should be associated with less evidence of atopic asthma.
Correspondingly, the lack of susceptibility to an asthmatic, atopic
phenotype is characterized by the loss of glutamine at codon 171
The invention includes isolated DNA molecules which are variants of
the wild type sequence as well as the proteins encoded by such DNA
and the use of such DNA molecules and expressed protein in the
diagnosis and treatment of atopic asthma.
Inventors: |
Levitt; Roy Clifford;
(Ambler, PA) ; Grasso; Luigi; (Philadelphia,
PA) ; Nicolaides; Nicholas C.; (Boothwyn, PA)
; Holroyd; Kenneth J.; (Collegeville, PA) |
Family ID: |
21863773 |
Appl. No.: |
12/752219 |
Filed: |
April 1, 2010 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12116706 |
May 7, 2008 |
7704710 |
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12752219 |
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11700260 |
Jan 31, 2007 |
7384767 |
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12116706 |
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11371157 |
Mar 9, 2006 |
7208292 |
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11700260 |
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10320646 |
Dec 17, 2002 |
7056698 |
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11371157 |
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09596377 |
Jun 16, 2000 |
6602850 |
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10320646 |
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08980872 |
Dec 1, 1997 |
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09596377 |
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60032224 |
Dec 2, 1996 |
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Current U.S.
Class: |
530/350 ;
536/23.5 |
Current CPC
Class: |
C12Q 1/6883 20130101;
A61P 11/06 20180101; A61K 38/00 20130101; C12Q 2600/156 20130101;
C07K 14/7155 20130101 |
Class at
Publication: |
530/350 ;
536/23.5 |
International
Class: |
C07K 14/715 20060101
C07K014/715; C07H 21/04 20060101 C07H021/04; C07H 21/02 20060101
C07H021/02 |
Claims
1. An isolated DNA molecule having a nucleotide sequence encoding
human interleukin-9 receptor selected from the group consisting of
a sequence containing an G to A nucleic acid variant at position
1273, a sequence wherein nucleic acids 759-761 (SEQ ID NO: 3) have
been deleted, a sequence wherein nucleic acids 613-617 (SEQ ID NO:
7) have been deleted, a sequence containing a stop codon at nucleic
acids 435437 (SEQ ID NO: 5), a sequence wherein nucleic acids
613-641 (SEQ ID NO: 6) have been deleted, and fragments
thereof.
2. The isolated DNA molecule of claim 1, wherein the sequence
contains an G to A nucleic acid variant at position 1273 or
fragments thereof.
3. The isolated DNA molecule of claim 1, wherein nucleic acids
759-761 (SEQ ID NO: 3) have been deleted or fragments thereof.
4. (canceled)
5. The isolated DNA molecule of claim 1, wherein nucleic acids
613-617 (SEQ ID NO: 7) have been deleted or fragments thereof.
6. The isolated DNA molecule of claim 1, wherein nucleic acids
613-641 (SEQ ID NO: 6) have been deleted or fragments thereof.
7. The isolated DNA molecule of claim 1, wherein nucleic acids
1067-1151 (SEQ ID NO: 4) have been deleted or fragments
thereof.
8-9. (canceled)
10. The isolated RNA molecule of claim 9, wherein the sequence
contains an A to G nucleic acid variant at position 1273 or
fragments thereof.
11. The isolated RNA molecule of claim 9, wherein nucleic acids
759-761 have been deleted or fragments thereof.
12. (canceled)
13. The isolated RNA molecule of claim 9, wherein nucleic acids
613-617 have been deleted or fragments thereof.
14. The isolated RNA molecule of claim 9, wherein nucleic acids
613-641 have been deleted or fragments thereof.
15. The isolated RNA molecule of claim 9, wherein nucleic acids
1067-1151 have been deleted or fragments thereof.
16. An isolated protein molecule having an amino acid sequence
encoding human interleukin-9 receptor selected from the group
consisting of a sequence containing a Histidine at position 344, a
sequence wherein Glutamine 173 has been deleted, a sequence wherein
the molecule is terminated after amino acid 64, a sequence wherein
the molecule is encoded by the DNA of claim 4, a sequence wherein
the molecule is encoded by the DNA of claim 5 or fragments
thereof.
17. The isolated protein molecule of claim 16, wherein the sequence
contains a histidine at position 344 or fragments thereof.
18. The isolated protein molecule of claim 16, wherein glutamine
173 has been deleted or fragments thereof.
19. The isolated protein molecule of claim 16, wherein the molecule
is terminated after amino acid 64 or fragments thereof.
20. The isolated protein molecule of claim 16, wherein the molecule
is encoded by the DNA of claim 5 or fragments thereof.
21. The isolated protein molecule of claim 16, wherein the molecule
is encoded by the DNA of claim 6 or fragments thereof.
22-55. (canceled)
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This is a divisional application of application Ser. No.
12/116,706 (filed May 7, 2008, now U.S. Pat. No. 7,704,710, issued
Apr. 27, 2010) which is a divisional of application Ser. No.
11/700,260 (filed Jan. 31, 2007, now U.S. Pat. No. 7,384,767,
issued Jun. 10, 2008) which is a divisional of application Ser. No.
11/371,157 (filed Mar. 9, 2006; now U.S. Pat. No. 7,208,292, issued
Apr. 24, 2007) which is divisional of application Ser. No.
10/320,646 (filed Dec. 17, 2002; now U.S. Pat. No. 7,056,698,
issued Jun. 6, 2006) which is a divisional of application Ser. No.
09/596,377 (filed Jun. 16, 2000; now U.S. Pat. No. 6,602,850,
issued Aug. 5, 2003) which is a divisional of application Ser. No.
08/980,872 (filed Dec. 1, 1997; now abandoned) which claims the
benefit of Provisional Application No. 60/032,224 (filed Dec. 2,
1996) all of which are incorporated herein by reference in their
entirety.
FIELD OF THE INVENTION
[0002] This invention describes biologic variability in the IL-9
receptor (Asthma Associated Factor 2) (SEQ ID NO 1) 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. In addition, 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.
BACKGROUND OF THE INVENTION
[0003] 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.
[0004] 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.
[0005] While 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..sup.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..sup.1 Thus, an enormous burden is placed on our health-care
resources in the treatment of these disorders.
[0006] Both the diagnosis and treatment of asthma and related
disorders are problematic..sup.1 In particular, the assessment of
inflamed lung tissue is often difficult, and frequently the cause
of the inflammation cannot be determined. Although atopic asthma is
an ecogenetic disorder, knowledge about the particular variant
genes has only recently been discovered. Methods to detect these
genetic variations and their role in inflammation, diagnosis and
prognosis remain to be determined. What is needed in the art is the
development of technology to expedite the diagnosis of atopic
asthma that specifically relates to variation in genes responsible
for susceptibility/resistance to this atopic disease.
[0007] Current treatments suffer their own set of disadvantages.
The main therapeutic agents, .beta.-agonists, reduce the symptoms,
i.e., transiently improve pulmonary functions, but do not affect
the underlying inflammation so that lung tissue remains in
jeopardy. In addition, constant use of .beta.-agonists results in
desensitization which reduces their efficacy and safety..sup.2 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..sup.2
[0008] Because of the problems associated with conventional
therapies, alternative treatment strategies have been
evaluated..sup.36-39 Glycophorin A,.sup.37 cyclosporin,.sup.38 and
a nona peptide fragment of IL-2,.sup.38 all inhibit interleukin-2
dependent T lymphocyte proliferation..sup.28 They are, however,
known to have many other effects..sup.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,.sup.36-39 they inhibit interleukin-2
dependent T lymphocyte proliferation and potentially critical
immune functions associated with homeostasis. What is needed in the
art is technology to expedite the development of therapeutics that
are specifically designed to treat the cause, and not the symptoms,
of atopic asthma. These 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. 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 illt except for their symptoms of atopic
asthma.
[0009] Because of the difficulties related to the diagnosis and
treatment of atopic allergies including asthma, the complex
pathophysiology of these disorders is under intensive study. While
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..sup.3-1 These expressions of asthma
related traits may be studied by quantitative or qualitative
measures.
[0010] In many cases, elevated IgE levels are correlated with BHR,
a heightened bronchoconstrictor response to a variety of
stimuli..sup.4, 6, 8, 9 BHR is believed to reflect the presence of
airway inflammation,'' and is considered a risk factor for
asthma..sup.11-12 BHR is accompanied by bronchial inflammation,
including eosinophil infiltration into the lung and an allergic
diathesis in asthmatic individuals..sup.6, 8, 13-18
[0011] A number of studies document a heritable component to atopic
asthma..sup.4, 10 Family studies, however, have been difficult to
interpret since these disorders are significantly influenced by age
and gender, as well as many environmental factors such as
allergens, viral infections, and pollutants..sup.19-21 Moreover,
because there is no known biochemical defect associated with
susceptibility to these disorders, the mutant genes and their
abnormal gene products can only be recognized by the anomalous
phenotypes they produce.
[0012] The functions of IL-9 and the IL-9 receptor (the IL-9
pathway) 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..sup.22, 23
The IL-9 pathway acts synergistically with IL-3 in causing mast
cell activation and proliferation..sup.24 The IL-9 pathway also
potentiates the IL-4 induced production of IgE, IgG, and IgM by
normal human B lymphocytes,.sup.25 and the IL-4 induced release of
IgE and IgG by murine B lymphocytes..sup.26 A role for the IL-9
pathway in the mucosal inflammatory response to parasitic infection
has also been demonstrated..sup.27, 28
[0013] Nevertheless, it is not known how the sequence of the IL-9
receptor specifically correlates with atopic asthma and bronchial
hyperresponsiveness. It is known that IL-9 binds to a specific
receptor expressed on the surface of target cells..sup.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..sup.23 In addition, a cDNA encoding the human IL-9
receptor has been cloned and sequenced.sup.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..sup.23
[0014] The IL-9 receptor gene has also been characterized..sup.30
It is thought to exist as a single copy in the mouse genome and is
composed of nine exons and eight introns..sup.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..sup.23
[0015] 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.
SUMMARY OF THE INVENTION
[0016] 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. In addition,
applicants have determined that 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. These findings
typify atopic asthma and the associated allergic inflammation.
[0017] Furthermore, applicants have determined that 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. When the arginine residue occurs in both alleles
in one individual, it is associated with less evidence of atopic
asthma. Thus, applicants have identified the existence of a
non-asthmatic phenotype characterized by arginine at codon 344 when
it occurs in both IL-9 receptor gene products in one individual. As
an additional significant corollary, applicants have identified the
existence of susceptibility to an asthmatic, atopic phenotype
characterized by a histidine at codon 344. Thus, the invention
includes purified and isolated DNA molecules having such a sequence
as well as the proteins encoded by such DNA.
[0018] Applicants have also determined that a splice variant of the
IL-9R exists wherein the glutamine residue at position 173 of the
IL-9R precursor protein has been deleted (SEQ ID NO 3) (FIG. 5).
Applicants have further shown that this variant is not able to
transcribe a signal through the Jak-Stat pathway (FIG. 15) and is
unable to induce cellular proliferation upon stimulation with IL-9
(FIG. 16); therefore, individuals with this allele would be less
susceptible to atopic asthma and related disorders.
[0019] 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.
[0020] In addition, applicants have discovered a variant of IL-9R
wherein exon 8 has been deleted (SEQ ID NO 4) which results in a
change in reading frame and a premature stop codon in exon 9. Such
a variant would most likely be prevented from transmitting a signal
through the Jak-Stat pathway and, therefore, individuals with this
allele would also be less susceptible to atopic asthma and related
disorders.
[0021] 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
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): Two other
variations can produce soluble forms of the IL-9R receptor which
comprise exons 2, 3 and 4 and In one case four amino acids from a
different reading frame in exon 5 (SEQ ID NO 6) (FIG. 6) and in the
other case there are 27 amino acids from a different reading frame
in exon 5 (SEQ ID NO 7) (FIG. 7).
[0022] 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.
[0023] Knowledge of the 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.
[0024] 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.
[0025] 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.
[0026] 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), ligation chain reaction (LCR), chemical cleavage,
and single stranded conformational polymorphism analyses (SSCP). A
skilled artisan will recognize that the use of one or more of these
techniques, as well as others in the literature, may be used to
detect one or more variations in the IL-9 receptor gene or mRNA
transcript and are within the scope of the present invention.
[0027] Still other techniques may be used to detect amino acid
variants in the IL-9 receptor including ELISAs,
immunoprecipitations, Westerns, and immunoblotting. Thus,
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.
[0028] The methods discussed above represent various effective
methods for diagnosing atopic asthma and other related
disorders.
[0029] Thus, 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.
[0030] Having identified the role of the IL-9 pathway in atopic
allergy, bronchial hyperresponsiveness and asthma, applicants also
provide a method for the diagnosis of susceptibility and resistance
to atopic allergy, asthma, and related disorders.
[0031] 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
[0032] FIG. 1: Schematic representation of the human IL receptor
cDNA. Boxes depict axon 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. Arrows indicate polymorphisms or aberrant splices
affecting partial sequence of the exon; a) deletion of the first 5
or 29 nucleotides in axon 5; b) deletion of the first 3 nucleotides
in exon 6 (codon 173); c) arg/gly polymorphism at codon 310; d)
arg/his polymorphism at codon 344; e) polymorphism at codon 410+n
consisting of either 8 or 9 serines;*) complete deletion of exon 3,
4 or 8.
[0033] FIG. 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). The corresponding peptide (SEQ ID NO: 27)
is also shown.
[0034] FIG. 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). The corresponding peptide (SEQ ID NO: 28) is also
shown.
[0035] FIG. 4: Translated cDNA sequence of IL-9R precursor protein
with the deletion of exon 8 causing the frame shift in exon 9, the
production of 11 non-wild type amino acids and a premature stop
codon. The corresponding peptide (SEQ ID NO: 30) is also shown.
[0036] FIG. 5: Translated cDNA sequence of IL-9R precursor protein
with the deletion of Glutamine at codon 173. The corresponding
peptide (SEQ ID NO: 29) is also shown.
[0037] FIG. 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. The
corresponding peptide (SEQ ID NO: 32) is also shown.
[0038] FIG. 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. The
corresponding peptide (SEQ ID NO: 33) is also shown.
[0039] FIG. 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. The corresponding peptide (SEQ ID NO: 31) is also
shown.
[0040] FIG. 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
Ser/4 Asn repeats, 9 Ser/3 Asn repeats, and 10 Ser/2 Asn repeats in
exon 9. The Arg/Arg individuals are protected from atopic allergy.
The Arg/His and His/His individuals are susceptible to atopic
allergy (P=0.002).
[0041] FIG. 10: Map of the expression construct of the IL-9
receptor.
[0042] FIG. 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.
[0043] FIG. 12: Expression of human IL-9 receptor variants in TS1
cells showing differential mobility between the Arg 344 variant
with B Ser/4 Asn repeats (GM) and His 344 variant with 9 ser/4 Asn
repeats (GH9). A mobility shift is seen demonstrating differential
post-translational modification of these two variant form of the
IL-9 receptor.
[0044] FIG. 13: XY specific amplimers for specific amplification of
the IL-9 receptor gene. Pseudogenes on chromosomes 9, 10, 16, or 18
are not amplified by PCR. (M is mouse DNA, His human DNA, and C is
hamster DNA.)
[0045] FIG. 14: Immunoreactivity of an anti-human IL-9 receptor
neutralizing antibody with wild type and .DELTA.-Q receptors. Panel
A): COST cells were transiently transfected with the LXSN vector
alone (A and B), wild type IL-9R(C and D), Wild type IL-9R with 9
Ser residues starting with codon 410 (E and F), .DELTA.-Q 173
variant (G and H) and .DELTA.-Q 173 with 9 Ser residues starting at
codon 410 (I and J) and sequentially incubated with MAB290 and
anti-mouse IgG Texas Red-conjugated antibody (B, D, F, H and J) as
described (Example 8). DAPI staining (A, C, E, G and I) was
included to visualize every cell in the photographed field. Panel
B): as in A) except that cells were first fixed/permabilized and
then incubated with a C-terminal specific antibody (sc698) followed
by incubation with anti-rabbit IgG Texas Red-conjugated antibody.
Bar=10 microns.
[0046] FIG. 15: Activation of members of Jak, Stat, and Irs
families via different variants of the human IL-9 receptor. TS1
cells expressing either GH9, .DELTA.QGR8, or .DELTA.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. Immunoblots were
first reacted with an anti-phosphotyrosine antibody to detect only
tyrosine-phosphorylated proteins and then stripped and reprobed
with the same antibody used to immunoprecipitate each protein. GH9,
.DELTA.QGR8, .DELTA.QGH9 are as indicated in FIG. 16.
[0047] FIG. 16: Proliferation of TS1 cells expressing different
forms of human IL-9 receptor. Cells were seeded in quadruplicate in
96-well plates (1000/well) and treated without cytokine or with
murine or human IL-9 (5 ng/ml). A colorimetric assay was performed
7 days later to determine cell number, and the ratio between
treated/untreated cells (% control) was calculated to assess growth
rate. L.times.SN=cells transfected with the empty vector; GR8 is
wild type IL-9R; GH9 is the His 344 variant with 9 Ser residues
starting at codon 410; .DELTA.QGR8 and A.DELTA.QGH9 are the
.DELTA.Q173 variants on the wild type and the His 344+9-Ser
background, respectively.
[0048] FIG. 17: Genomic DNA sequence of intron 5 of the IL-9R with
a variation at nucleic acid 213 nt upstream from axon 6 where a T
residue is changed to a C residue as indicated by the arrow.
DETAILED DESCRIPTION OF THE INVENTION
[0049] 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.
[0050] 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.
[0051] By analyzing the DNA of individuals that exhibit atopic
allergy and asthma-related disorders, applicants have identified
polymorphisms in the IL-9 receptor (IL-9R) gene that may correlate
with the expression of asthma. 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.
[0052] By polymorphism, applicants mean a change in a specific DNA
sequence, termed a "locus," from the prevailing sequence. In
general, a 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.
[0053] Specific amplification of the authentic IL-9R (gene encoding
for the biologically functional protein located in the XYq
pseudoautosomal region) using standard primer design was not
possible because IL-9R has four highly homologous (>90%
nucleotide identity), non-processed pseudogenes at other loci in
the human genome (chromosome 9, 10, 16, 18). Because of the high
identity of these other genes, genomic PCR amplification using
standard primer design resulted in co-amplification of all genes,
thus making sequence analysis of the authentic gene equivocal. In
order to study authentic IL-9R structure as it may relate to
predisposition to disease such as asthma, discussed in this
application, or other diseases such as cancer (Renauld, et al.,
Oncogene, 9:1327-1332, 1994; Gruss, et al., Cancer Res.,
52:1026-1031, 1992); applicants have designed specific amplimers.
The specific primers were found to be authentic for IL-9R
amplification with no amplification of the 4 pseudogenes. The
primer sequences are shown in Example 2 and their specificity is
demonstrated in FIG. 13.
[0054] Applicants have also amplified, by RT-PCR, the entire coding
region of the IL-9 receptor cDNA using RNA extracted from PBMCs
(peripheral blood mononuclear cells) purified from 50 donors. FIG.
1 illustrates the most frequent variations found in 50 Individuals
analyzed. 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. Hence, in
all instances, 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. Finally, 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. T his 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 (FIG. 17 and Example 12).
[0055] Applicants have also found allelic variations limited to the
coding sequence of exon 9. Polymorphisms involving codon 310 and
410 have been previously disclosed..sup.29, 30 (Kermouni, A., et
al., Genomics, 371-382 (1995)). Codon 310 encodes for either
arginine or glycine, depending on whether the first nucleotide at
that codon is an adenine or a guanidine, respectively. At 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.
[0056] Applicants have found a new polymorphism at codon 344. Here,
the second nucleotide is either adenine or guanidine, the two
possible residues encoded by this codon being histidine or
arginine, respectively. Moreover, 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 megakaryobiastic leukemic cell line,
Mole, presented 9 serines at codon 410+n and, unlike applicants'
clones, an arginine at codon 344..sup.29 Another megakaryoblastic
leukemic cell line UT-7 has been reported to carry the same
arginine/9-serines allele.30 Applicants cloned 18 cDNAs from Mole
cell tine and found that 6 had 8 serines at codon 410+n and
arginine at codon 344. The remaining ten clones presented the
published sequence. Applicants also genotyped the human acute
myelogenous leukemia cell line KG-1 and found that it was
histidine/9-serines homozygous.
[0057] These DNA molecules and corresponding RNA are isolated using
techniques that are standard in the art, such as Sambrook, et al.,
Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring Harbor
Laboratory Press (1985). 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.
[0058] The invention also includes the proteins encoded by these
nucleic acid sequences. The invention further includes fragments of
the molecules. By 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.
[0059] The source of the IL-9 receptor variants of the invention is
human. Alternatively, 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).
[0060] The demonstration of 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.
[0061] A receptor is a soluble or membrane-bound component that
recognizes and binds to molecules, and 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..sup.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, Jak1, Stat1, Stat3,
Stat5, and Irs2, upon binding the human IL-9 receptor (Demoulin,
J-B., et al., Molecular and Cellular Biology, p. 4710-4716,
September 1996). Applicants have examined whether IL-9R or its
variants showed any bias in the activation of these proteins and
extended the analysis to Jak3 and Irs1, It was determined that all
of the proteins of the pathway including Jak3 and Irs1 were
phosphoralated by IL-9R activation. It was also determined that
IL-9R variants with changes at codons 310, 344 and 41 0+n provided
the same up-regulation as wild type IL-91R. Therefore, one aspect
of the invention is therapeutics for the treatment of atopic asthma
which inhibit interactions in the Jak-Stat pathway.
[0062] Unlike the wild type receptor and the other tested variants,
the .DELTA.Q173 variant could not activate any proteins in the
Jak-Stet pathway (FIG. 15). In addition, the .DELTA.Q173 variant
could not support cellular proliferation upon IL-9 stimulation
(FIG. 16). Therefore, individuals who express the .DELTA.Q173
variant are less likely to be susceptible to atopic asthma and
related disorders. One aspect of the Invention, therefore, is
therapeutics that increase the expression of the .DELTA.Q173 splice
variant for the treatment of atopic asthma and related
disorders.
[0063] One diagnostic embodiment involves the recognition of
variations in the DNA sequence of the IL-9 receptor gene or
transcript. One method involves the use of a nucleic acid molecule
(also known as a probe) having a sequence complementary to the IL-9
receptors of the invention under sufficient hybridizing conditions,
as would be understood by those in the art. In one embodiment, 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. These
methods may also be used to recognize other variants of the IL-9
receptor. Another method of recognizing DNA sequence variation
associated with these disorders is direct DNA sequence analysis by
multiple methods well known in the art..sup.44 Another embodiment
involves the detection of DNA sequence variation in the IL-9
receptor gene associated with these disorders.40-44 These include
the polymerase chain reaction, restriction fragment length
polymorphism (RFLP) analysis, and single-stranded conformational
analysis. In a preferred embodiment, 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. In other embodiments, the ligation chain
reaction can be used to distinguish these alleles of IL-9 receptor
genes.
[0064] 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.
To identify an antagonist of the invention, one 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..sup.2, 22-35
[0065] 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..sup.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 Mole
cells..sup.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,.sup.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..sup.29 These methods can be used to identify antagonists of
the IL-9, receptor.
[0066] In a further embodiment, the invention includes the
down-regulation of IL-9; expression or function by administering
soluble IL-9 receptor molecules that bind IL-9. Applicants and
Renauld, et al..sup.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..sup.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. This segment is commonly referred to in the art as the
transmembrane domain of the gene, or membrane-binding segment of
the protein. Thus, in one embodiment of the invention, a soluble
receptor may represent a fragment or an analog of a membrane-bound
receptor.
[0067] 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 axon 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 axon, 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.
[0068] Soluble IL-9 receptors may be used to screen for potential
therapeutics, including antagonist useful in treating atopic asthma
and related disorders. 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. In addition, 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.
[0069] In addition, the invention includes pharmaceutical
compositions comprising the compounds of the invention together
with a pharmaceutically acceptable carrier.
[0070] 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 Science, specifically
incorporated herein by reference.
[0071] 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.
[0072] 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. For topical application, these compounds could also be
administered as a powder or spray, particularly in aerosol form. In
a preferred embodiment, the compounds of this invention may 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.
[0073] The active ingredient may be administered in pharmaceutical
compositions adapted for systemic administration. As is known, if a
drug is to be administered systemically, it may be confected as a
powder, pill, tablet or the like, or as a syrup or elixir for oral
administration. For intravenous, intraperitoneal or intralesional
administration, the compound will be prepared as a solution or
suspension capable of being administered by injection. In certain
cases, 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.
[0074] 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.
[0075] 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 e functions expressed by IL-9
receptor are down-regulated using techniques standard in the
art..sup.29, 30, 34, 35 In a specific embodiment, applicants
provide for a method of identifying compounds with functions
comparable to IL-9. In one embodiment, the functions of IL-9
receptor may be assessed in vitro. As is known to lose in the art,
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 elated to the
actions of the IL-9 pathway. Another method to characterize the
unction of IL-9 and IL-9-like molecules depends on the "stable
expression" of the L-9 receptors in murine TS1 clones or TF1
clones, which do not normally express human receptor. These
transfectants can be used to assess human IL-9 receptor function
with a cellular proliferation assay..sup.29
[0076] 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..sup.23.29 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),.sup.30 the
human megakaryoblastic leukemia cell line Mo7e.sup.34, TF1,.sup.29
macrophages, eosinophiles, fetal thymocytes, the human kidney cell
line 293,.sup.3.degree. and murine 320 and embryonic hippocampal
progenitor cell lines..sup.23, 29, 30
[0077] 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 Biology, John Wiley & Sons, Inc.
[0078] 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 identity 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.
[0079] 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.
[0080] A sequential grouping of three nucleotides (a "codon") codes
for one amino acid. Thus, for example, the three nucleotides CAG
code for the amino acid Glutamine. The 20 naturally occurring amino
acids, and their one-letter codes, are as follows:
TABLE-US-00001 Alanine Ala A Arginine Arg R Asparagine Asn N
Aspartic Acid Asp D Asparagine or Asx B Aspartic acid Cysteine Cys
C Glutamine Gin Q Glutamine Acid Glu E Glutamine or Glx Z Glutamic
acid Glycins Gly G Histidine His H Isoleucine Ile I Leucine Leu L
Lysine Lys K Methionine Met M Phenyalanine Phe F Proline Pro P
Serine Ser S Threonin Thr T Tryptopan Trp W Tryosine Tyr Y Valine
Val V
[0081] 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.
[0082] DNA is related to protein as follows:
##STR00001##
[0083] 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.
[0084] 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 axon 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.
[0085] 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 axon modules of the present combinatorial method can comprise
nucleic acid sequences corresponding to naturally occurring axon
sequences or naturally occurring axon sequences which have been
mutated (e.g., point mutations, truncations, fusions).
[0086] 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
[0087] 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).
[0088] 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.
[0089] 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.
[0090] 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, Bacillus, 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
Torulopsis.
[0091] 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 recognize, expression of the polypeptide may be enhanced,
i.e., increased over the standard levels, by careful selection and
placement of these regulatory sequences.
[0092] In other embodiments, 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.
[0093] 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, acetylabons,
phosphorylations, and the like.
[0094] 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. Linkage analysis
methodology has been applied to the mapping of disease genes, for
example, genes relating to susceptibility to asthma, to specific
chromosomes..sup.47, 48
[0095] Applicants wish to incorporate by reference all the
references set forth above and below.
[0096] 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
specification and examples be considered exemplary only with a true
scope of the invention being indicated by the claims.
[0097] Having provided this background information, applicants now
describe preferred aspects of the invention.
Example 1
Identification of IL-9 Receptor Transcript Polymorphisms
[0098] A population of 52 individuals was ascertained randomly with
respect to asthma and atopy from the Philadelphia, Pa., area. Total
serum IgE were assayed by enzyme-linked immunosorbent assay (ELISA,
Genzyme, Cambridge, Mass.).
[0099] To assess the structural forms of the human IL-9 receptor
cDNA, PBMCs from these 52 unrelated donors were isolated and
cultured in the presence of PHA and PMA (described in Example 4).
Previous data from applicants' laboratory demonstrated the kinetics
of expression for IL-9 receptor message in primary cultures peak at
day 6 after mitogen stimulation. Applicants cultured the cells,
therefore, for 6 days at which time the cells were harvested and
their RNA and DNA were isolated as described in Example 5.
[0100] 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.
[0101] Seven major variants were identified from the above screen.
These cDNAs represent a codon 173 deletion, an exon 4 deletion, two
separate deletions in exon 5, an axon 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 FIG. 1.
[0102] Variants were cloned into the eukaryotic expression vector
pCEP4 (Ciontech) 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 3. Function was biologically
assessed as a response to the IL-9 ligand in growth and/or
apoptosis (Examples 7 and 10).
[0103] Experiments in which the full-length 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 B). In situ analysis demonstrated that both
forms of receptor appeared to be expressed in both the hamster and
human lines (FIGS. 11 and 12). Interestingly, while Western blots
of both forms appeared to be expressed at equal levels in both the
human and hamster lines, a differential migration pattern appeared
between the ARG and HIS receptor forms in the TS1 cell line (FIG.
12) which suggests a differential post-translational modification
such as glycosylation, phosphorylation, etc. This biochemical
difference may be the mechanism by which the altered function
results in altered phenotype.
[0104] The frequency of the various substitutions were used as an
unbiased estimate of the prevalence of each variant in the general
population. Genotype was compared to phenotype assessed by
questionnaire. A diagnosis of allergy and asthma was determined by
a physician reviewing the questionnaires. Individuals homozygous
for the Arg344 alleles were significantly less likely to
demonstrate evidence for allergy and asthma when compared to
heterozygotes or homozygous His344 (FIG. 9).
Example 2
Genomic-Analysis of the IL-9 Receptor Genes
[0105] In order to perform genomic analyses of allergic and/or
asthmatic individuals, the following strategy was designed to
create 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. First, 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, N.J.). If the primers only
produce correct sized products from X and Y hybrids, they were then
optimized for robust amplification. In several cases, 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 FIG. 13.
TABLE-US-00002 TABLE 1 X/Y Specific Amplimers of IL-9 Receptor EXON
SENSE PRIMER ANTISENSE PRIMER TEMP SIZE 2 5'-GCA GGT GGG GAC 5'-
AGG CTT GAC ATC GGA CAA 68.degree. 300 bp CCA TG -3' C-3' (SEQ ID
NO 8) (SEQ ID NO 9) 3 5'- CTG GCC TGA AGT 5'- CTG CTT CAA TCC TGG
GGA A- 62.degree. 222 bp ACT TAC C -3' 3' (SEQ ID NO 10) (SEQ ID NO
11) 4 5'- GTG AGT TCC CCA 5'- CAA GGC CCT GCT CCA AA -3' 64.degree.
335 bp GGA TTG A -3' (SEQ ID NO 13) (SEQ ID NO 12) 5 5'- TGG GGC
TTC AGC 5'- TAT GTA GAG TGG 62.degree. 259 bp CTC ACA TG -3- GGA
GTC TA -3' (SEQ ID NO 14) (SEQ ID NO 15) 6 5'- TGT ATT CTC 5'- TGA
GGT GAA CAG GGG AGA 62.degree. 337 bp GAGGGC TGA G -3' A -3' (SEQ
ID NO 16) (SEQ ID NO 17) 7 5'- CCC TGG GCC CTT 5'-'- ACA AGG GCG
GCC TTT GAT 60.degree. 262 bp CAT GT 3' 4 (SEQ ID NO 18) (SEQ ID NO
19) 8 5'- AGG GAC GAG 5'- CCT GCC CCC CAT GTT CTT 3' 58.degree. 376
bp GTG GGC GGA C -3' (SEO ID NO 21) (SEQ ID NO 20) 9 5'- ATG CTA
CCT 5'- GGA CAT GAT GCA TCT GGC 62.degree. 664 bp GAGCCC TTC C -3'
G-3' (SEQ ID No 22) (SEQ ID NO 23)
[0106] These primers represent a novel method for analyzing DNA
sequence variation in these genes which can be used for diagnosis
of susceptibility or resistance to atopic asthma and related
disorders.
[0107] Using this technology, each exon was examined by DNA
sequence analyses for individuals in applicants populations to
detect sequence variation in the IL-9 receptor gene..sup.44
Sequence polymorphisms were distinguished from artifact by repeated
analyses. An association of the receptor variants with the allergic
phenotypes is set forth in FIG. 9. The sequence of the receptor
alleles is set forth in FIGS. 1-8.
Example 3
IL-9 Receptor Expression and Ligand Binding Assay
[0108] Purified recombinant IL-9 and compounds potentially
resembling IL-9 in structure or function are fluorescently labeled
to high specific activity by using commercially available
techniques according to the supplier's recommendations (Pierce).
Human Mo7e and murine 32D cells are grown and. resuspended at
37.degree. C. in 0.8 ml of Dulbecco's modified Eagle's medium
supplemented with 10% (vol/vol) fetal bovine serum, 50 mM
2-mercaptoethanol, 0.55 mM L-arginine, 0.24 mM L-asparagine, and
1.25 mM L-glutamine or RPMI supplemented with 10% (vol/vol) fetal
bovine serum, 50 mM 2-mercaptoethanol, 0.55 mM L-arginine, 0.24 mM
L-asparagine, and 1.25 mM L-glutamine, respectively. TF1.1 (TF1
cells lacking human IL-9 receptors), T98G, TK, and murine 32D
cells, (Examples 7 and 10) were used as is or after transfection
with the human IL-9 receptor constructs as described below. Plasmid
DNA containing one of the full-length or truncated forms of IL-9
receptors were cloned into pCEP4 plasmid (Clontech) and purified by
centrifugation through Qiagen columns (Qiagen). Plasmid DNA (50
micrograms) was added to the cells in 0.4 cm cuvettes just before
electroporation. After a double electric pulse (750V/74 ohms/40
microfarads and 100 V/74 ohms/2100 microfarads), the cells are
immediately diluted in fresh medium supplemented with IL-9.
[0109] Stable transfected cells were generated after 14 days of
selection with hygromycin B (400 .mu.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 described in
Example 8.
[0110] Cellular receptor binding is visualized directly in real
time with fluorescence microscopy. Binding and internalization is
followed over time in control cells (not transfected), and with
cells transfected with each of the known IL-9 receptor variants. An
excess of unlabeled ligand or blocking antibody is used in parallel
experiments to demonstrate specific binding.
[0111] Soluble IL-9 receptor including amino acids 44 to 270 with
or without a HA ditag is also incubated with different forms of
human labeled recombinant IL-9. Varying amounts of FLAG-tagged
(IBI) ligand are incubated in PBS at, room temperature for 30
minutes with 0.5 .mu.g of soluble receptor. EBC buffer (50 mM Tris
pH 7.5; 0.1 M NaCl; 0.5% NP40) is added (300 .mu.l) along with 1
.mu.g of anti-HA antibody or anti-FLAG monoclonal antibody (IBI)
and incubated for 1 hour on ice. Forty microliters of protein A
sepharose solution were added to each sample and mixed for 1 hour
at 40 C. Samples were centrifuged for 1 minute 11,000.times.G and
pellets were washed 4 times with 500 .mu.l of EBC. Pellets were
dissolved in 26 .mu.l of 2.times.SDS buffer, boiled for 4 minutes,
and electrophoresed through an 18% SOS polyacrylamide gel. Western
blots were probed with an anti-IL-9 receptor antibody (Santa Cruz
Inc.) or anti-FLAG monoclonal antibody (IBI) against FLAG-tagged
rh1L-9 Therapeutic candidates are assessed by measuring the
antagonism of ligand binding. Receptor expression is shown in FIGS.
11 and 14.
Example 4
Cell Isolation and Culture
[0112] Human peripheral blood mononuclear cells (PBMC) were
isolated from healthy donors by density gradient centrifugation
using endotoxin tested Ficoll-Paque PLUS according to the
manufacturer (Phermacia Biotech, AB Uppsala Sweden). PBMC
(5.times.10.sup.6), mouse spleen cells (5.times.10.sup.6), or
5.times.10.sup.8 Mole cells were cultured in 7 ml of RPMI-1640
(Bethesda Research Labs (BRL), Bethesda, Md.) supplemented to a
final concentration of 10% with either isogenic human serum or
heat-inactivated FBS. Cells were cultured for 24 hm at 370 C either
unstimulated, or stimulated with either PMA 5 Ng/mV PHA 5 .mu.g/ml,
or PHA 5 .mu.g/ml and rhIL2 50 ng/ml (R&D Systems, Minneapolis,
Minn.).
Example 5
DNA & RNA Isolations, rtPCR, Cloning, and Sequencing of PCR
Products
[0113] Cytoplasmic RNA and genomic DNA were extracted after 6 days
of mitogen stimulation from cultured PBMCs, as described by
Nicolaides and Stoeckert.46 One .mu.g of RNA from each source was
denatured for >10 minutes at 70.degree. C. and then reverse
transcribed (V+) into cDNA using 2.5 units of Superscript II
reverse transcriptase. (GIBCO, BRL), 1 U/I RNAse Inhibitor, 2.5 mM
oligo d(T) 16 primer, 1 mM each of dATP, dCTP, dGTP, dTTP, 50 mM
KCl, 10 mM Tris-HCL, pH 7.0, 25 mM MgCl.sub.2 at 37.degree. C. for
one hour. A mock reverse transcription reaction was used as a
negative control.
[0114] One-twentieth of the rt reaction was used in PCR (50 .mu.l)
containing 6.7 mM MgCl2, 16.6 mM (NH4)2SO4, 67 mM Tris-HCL, pH 8.8,
10 mM 2-mercaptoethanol, 6% DMSO, 1.25 mM of each dNTP, 2.5 U
Amplitaq DNA polymerase, and 300 ng of each of the oligonucleotides
representing human cDNA IL-9 exon 2 (forward 5'-GCT GGA CCT TGG AGA
GTG-3') (SEQ ID NO: 25) and exon 9 (reverse 5'-GTC TCA GAC AAG GGC
TCC AG-3') (SEQ ID NO: 26). The reaction mixture was subjected to
the following PCR conditions: 120 seconds at 95.degree. C., then 35
cycles at: 30 seconds at 94.degree. C.; 90 seconds at 58.degree.
C.; 90 seconds at 72.degree. C. Finally, the reaction mixture was
cycled one time for 15 minutes at 72.degree. C. for extension.
[0115] PCR products representing hIL-9 receptor cDNA were subjected
to gel electrophoresis through 1.5% agarose gels and visualized
using ethidium bromide staining. Products of a mock reverse
transcriptate reaction, in which H.sub.2O was substituted for RNA,
ware used as a negative control amplification in all
experiments.
[0116] PCR products were subcloned into the TA Cloning vector
(Invitrogen, San Diego, Calif.). Amplification of the human cDNA
gave a 1614 by product. Plasmids containing hIL-9 receptor cDNA
inserts were isolated by conventional techniques (Sambrook, J., et
al. (1989) Molecular Cloning: A Laboratory Manual Cold Spring
Harbor Laboratory Press, New York). After amplification the DNA
sequence including and surrounding each insert was analyzed by
sequencing (Sanger et al., 1977, Proc. Nati. Acad. Sci. USA
74:5463) using fluorescent dideoxyterminators and on an automated
sequencer (ABI 377, Perkin Elmer) for determination of PCR-induced
or cloning-induced errors hIL-9 receptor cDNA inserts without
cloning and/or polymerase-induced sequence errors were subcloned
into expression vectors.
Example 6
Cloning and Expression of IL-9 Receptor Constructs In Vitro
[0117] hIL-9 receptors were subcloned into the episomal eukaryotic
expression vector pCEP4 nlontech). Inserts were cloned as
BamHl-Xhol fragments into the pCEP4 polylinker in the sense
orientation to the CMV promoter using standard techniques (FIG.
10). Constructs were expressed in cellular hosts as described.
Example 7
Cellular Assays Using (Mo7e, 32D, TF1.1, TK ts13, and T98G
[0118] Cell lines were used to assess the function of variant IL-9
receptors and for the screening of compounds potentially useful in
the treatment of atopic asthma. Compounds were tested for their
ability to antagonize the anti-apoptotic or baseline proliferative
response elicited by IL-9. Once a baseline anti-apoptotic or
proliferative response was established in a given cell line, a
statistically significant loss of response in assays repeated three
times in triplicate was considered evidence for antagonism. A true
antagonistic response was differentiated from cellular toxicity by
direct observation, trypan blue staining (a technique well known to
one of normal skill in the art), or loss of acid phosphatase
activity. Specificity of antagonism is assessed for each compound
by evaluating whether the activity is demonstrated against other
proliferative agents such as interleukin 3 or interleukin 4.
[0119] Recombinant IL-9 and compounds potentially resembling IL-9
in structure or function were purified and prepared for use in the
appropriate media. Putative agonists and antagonists were prepared
in water, saline, or DMSO and water. Cells were used as is or after
transfection with the IL-9 receptor constructs as described in
Example 3. After 24 hrs of deprivation from growth factors, the
cells were incubated without (control) or with variable amounts of
purified IL-9 and compounds potentially resembling IL-9 in
structure or function.
[0120] Cell proliferation was assayed using the Abacus Cell
Proliferation Kit (Clontech, Palo Alto, Calif.) which determines
the amount of intracellular acid phosphatase present as an
indication of cell number. The substrate p-ntrophenyl 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 370 C for one hour. 1 N 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. Briefly, the assays were run
with quadruplicate samples of cells in flat-bottom microtiter
plates (150 or 200 microliter wells) with or without ligand for 72
to 96 hours at 37 degrees C. Acid phosphatase was used as a measure
of the number of cells present. All experiments are repeated at
least-twice.
[0121] Apoptosis was assayed using the Annexin V kit as described
by the supplier (Clontech) which determines dexamethesone-induced
apoptosis by recognizing extracellular phosphatidyiserine, an early
marker for apoptosis. Apoptotic cell number was scored by
fluorescence microscopy as a percentage of Annexin V stained
cells.
[0122] The Mo7e 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, Minn.). The T98G line is a human glioblastoma cell
line grown in RPMI 1640 (GIBCO/BRL). The hamster fibroblast TK-ts13
line was also used as well as the murine 32D cell line, a murine
myeloid precursor line, and both were cultured in RPMI 1640
(GIBCO/BRL) containing 10% fetal bovine serum (Hyclone) in addition
1 ng/ml m IL-3 was used with the 32 D cell lines. TF1.1 is a human
myeloid leukemia line known to express the IL-2 receptor gamma
subunit (confirmed by Western blots and rtPCR), but, in comparison
to its predecessor (TF1), it no longer bears IL-9 receptor by
rtPCR, immunostaining, and Western blot analyses. TF1.1 is cultured
in RPMI 1640 (GIBCO/BRL) and 10% Fetal bovine serum (Hyclone). All
the cell lines respond to multiple cytokines including IL-9. The
cell lines were fed and reseeded at 2.times.10.sup.5 cells/ml every
72 hours.
[0123] 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 were counted using a hemocytometer and
diluted to a concentration of 1.times.10.sup.5 cells/ml and plated
in a 96-well microtiter plate. Each well contained 0.15 or 0.2 ml,
giving a final concentration of 10 to 50 thousand cells per well
depending on the cell. Mole cells were stimulated with 50 ng/ml
Stem Cell Factor (SCF) (R&D Systems, Minneapolis, Minn.) alone,
50 ng/ml SCF plus 50 ng/ml IL-3 (R&D Systems, Minneapolis,
Minn.), or 50 ng/ml SCF plus 50 ng/ml IL-9. A control was included
which contained 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. TF1.1
cells that were not transfected with IL-9 receptors were used as an
independent control for response and nonspecific cytotoxicity.
Cultures were incubated for 72-96 hours at 370 C in 5%
CO.sub.2.
Example 8
In Situ & Western Analysis of Exogenous IL-9 Receptor in
Transfected Cell Lines
[0124] In situ staining of the IL-9 receptor was carried out as
follows. Cells were grown on coverslips for 24 hours and then
coverslips containing the adherent cells were washed twice in
phosphate buffered saline solution containing calcium and magnesium
(PBS) (Gibco/BRL). For Intracellular staining of the IL-9 receptor,
the cells were fixed in 4% paraformaldehyde/PBS plus 0.1% triton-X
for 15 minutes at room temperature before treatment with anti-human
IL-9 receptor antibody; for extracellular staining, cells were
treated with antibody before fixation. The cells were then washed
twice in PBS and blocked with 7.5% BSA in dH.sub.2O for 30 minutes
at room temperature. PBS washed cells were then incubated with a 10
.mu.g/ml solution of anti-human IL-9 receptor (polyclonal antibody
directed against the carboxy terminus of the IL-9 receptor) in 1%
BSA/PBS for 1 hour at room temperature. Cells were washed three
times in PBS and then incubated in 10 .mu.g/ml solution of an
anti-rabbit rhodamine-conjugated antibody in 1% BSA/PBS for 30
minutes at room temperature. Cells were then washed three times in
PBS and counter-stained using 1 .mu.g/ml DAPI for 1 minute at room
temperature. Cells were washed three times in dH.sub.2O and fixed
to a microscope slide and analyzed by fluorescence microscopy. The
results for the transferred COST cells are shown in FIG. 14.
[0125] Western blots were performed on protein lysates obtained
from direct lysis of cell extracts in 0.5% lysis buffer (Tris 50
mM, NaCl 150 mM, NP40), 1 mM DTT and protease inhibitors) and
boiled for 5 minutes, Samples were electrophoresed on 4-20%
tris-glycine SDS gels (Novex) in tris-glycine running buffer.
Proteins were then transferred to nitrocellulose by electroblot
using the Trans Blot II apparatus (Bio Red). After transfer, the
membrane was blocked in TBS-T ((20 mM Tris, 137 mM NaCl, pH 7.6)
plus 0.05% Tween 20) plus 5% blotto for 1 hour room temperature.
Blots were then probed using a polyclonal antibody directed to the
carboxy terminus of the IL-9 receptor (1 .mu.g/ml) in TBS-T for 1
hour. Blots were then washed three times in TBS-T for 10 minutes
and probed using a secondary anti-rabbit-horse radish peroxidase
conjugated antibody (1:10,000) in TBS-T for 30 minutes. Blots were
washed as above and then incubated with Luminol/enhancer solution
(Pierce), a chemiluminescent substrate, for 5 minutes at room
temperature and then exposed to film for 1-60 seconds. See FIGS. 11
and 12.
Example 9
Methods for the Authentic IL-9R Genomic Amplification
[0126] Specific amplification of the authentic IL-9R (gene encoding
for the biologically functional protein located in the XYq
pseudoautosomal region) using standard primer design was not
possible because IL-9R has four highly homologous (>90%
nucleotide identity), nonprocessed pseudogenes at other loci in the
human genome (chromosome 9, 10, 16, 18). Because of the high
identity of these other genes, genomic PCR amplification using
standard primer design resulted in co-amplification of all genes,
thus making sequence analysis of the authentic gene equivocal. In
order to study authentic IL-9R structure as it may relate to
predisposition to disease such as asthma, discussed in this
application, or other diseases such as cancer (Renauld, et al.,
Oncogene, 9:1327-1332, 1994; Gruss, et al., Cancer Res.,
52:1026-1031, 1992), specific amplimers were designed as
follows:
[0127] Sequences of the IL-9R pseudogene and authentic genes were
aligned using Mac Vector software. Intronic sequences surrounding
each exon were then inspected for regions of diversity between the
authentic gene and pseudogenes. Primers were then designed against
these regions, and used to PCR amplify human/rodent hybrid DNAs
containing individual human chromosomes. Products were run on 3%
agarose gels and analyzed for authentic IL-9R amplification with no
amplification of the 4 pseudogenes. Specific PCR amplification
conditions were also optimized by varying annealing temperature and
buffer conditions (DMSO content 5-10%). In cases where
amplification of pseudogenes still occurred, nucleotide changes
were entered into primer sequences to cause greater divergence from
the pseudogenes as compared to the authentic gene, Primer sequences
are shown In Example 2 and their specificity is demonstrated in
FIG. 13.
Example 10
Cell Proliferation Assay and Cytokine Stimulation
[0128] To determine growth response of TS1 cells expressing various
forms of human IL-9 receptor, cells were washed with PBS and
resuspended in D-MEM, 10% fetal bovine serum. 10.sup.3 cells per
well were seeded in triplicate in 96-well microplates and, where
appropriate, recombinant human IL-9 or marine IL-9 (R&D
Systems, Minneapolis, Minn.) was added at a final concentration of
5 ng/ml. Cell proliferation was evaluated after 7 days using an
acid phosphatase assay. Briefly, 50 .mu.l of a buffer containing
0.1 M sodium acetate (pH 5.5), 0.1% Triton X-100 and 10 mM
p-nitrophenyl phosphate (Sigma 104 phosphatase substrate) was added
per well, The plate was incubated for 11/2 hours at room
temperature, the reaction stopped with 10 .mu.l/well of 1 N sodium
hydroxide and the absorbance was read on a Dynatech Model MR600 at
410 nm, To analyze tyrosine-phosphorylation of proteins of the
signal transduction cascade upon cytokine stimulation, TS1 cells
expressing various forms of human IL-9 receptor were washed with
PBS, resuspended in D-MEM, 0.5% bovine serum albumin, and incubated
for 6 hours at 37.degree. C. Successively, 20.times.10.sup.6 cells
were treated for 5 minutes with either human IL-9 or murine IL-9
(100 ng/ml) and immediately washed in cold PBS. Cells were lysed in
RIPA buffer as described in Example 11.
Example 11
Immunoprecipitations, Immunoblotting and Antibodies
[0129] Typically, 20-50.times.10.sup.6 cells were lysed in 1 ml of
RIPA buffer (PBS containing 1% NP40, 0.5% sodium deoxycholate, 0.1%
SDS, 1 mM PMSF, 50 mM sodium fluoride, 1 nM sodium orthovanadate,
and 1.times."Complete" protease inhibitors mixture, Cat. No.
1697498 Boehringer Mannheim) and Incubated for 45 minutes on ice.
Lysates were centrifuged for 20 minutes In an Eppendorf
microcentrifuge and the supernatant recovered and transferred to a
fresh tube. For Immunopreeipkations, 1-5 .mu.g of the antibody were
added to the lysate and incubated overnight at 4.degree. C. 20 ml
of Protein A+G agarose-conjugated beads were added for 2 hrs
followed by four washings using RIPA buffer: Beads were resuspended
in Laemmli buffer and boiled for 3 minutes before electrophoresis.
Proteins were transferred onto immobilion-P membrane (Millipore)
and detected using a horseradish peroxidase-conjugated secondary
antibody followed by a chemiluminescence detection assay (Pierce).
Specific antibodies for murine and human IL-9 receptor (sc698),
murine Jak1, lrs1, lrs2, Stat1, Stat2, Stat3, Stat4, Stat5, and
phosphotyrosine (PY) were purchased from Santa Cruz (Santa Cruz,
Calif.). Anti-Jak3 and monoclonal anti-human IL-9 receptor MAB290
were purchased from Upstate Biotechnology and R&D Systems,
respectively. FIG. 15 demonstrates the activation of members of the
Jak family via different variants of the human IL-9 receptor.
Example 12
Identification of IL-9 Receptor Genomic Polymorphisms
[0130] Genomic DNAs were isolated from PBMCs of volunteer donors as
described (Nicolaides and Stoeckert, Biotechniques 8:154-156,
1990). Sequence analysis of intron 5 of the human IL-9R gene was
performed by PCR using primers of sequence ID NO 14 and sequence ID
NO 17 which resulted in a product with the approximated molecular
size of 1243 basepairs, Amplifications were carried out at
94.degree. C. for 30 seconds, 62.degree. C. for 1.5 minutes,
72.degree. C. for 1.5 minutes for 35 cycles in buffers described
previously (Nicholaides et al., Genomics 30:195-206, 1995).
Products were then purified and sequenced using a standard sequence
protocol. Inspection of the sequences from intron 5 in multiple
individuals found a nucleotide change at -213 nt upstream of axon 6
sequences which resulted in a thymidine (published sequence) to a
cytosine nucleotide change. An example of this change is shown in
FIG. 17.
[0131] 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.
REFERENCES
[0132] 1. Gergen P J, and Weiss K B: The increasing problem of
asthma in the United States. Am Rev Respir Dis 146:823-824, 1992.
[0133] 2. Goodman and Gilman's The Pharmacologic Basis of
Therapeutics, Seventh Edition, MacMillan Publishing Company, N.Y.
USA, 1985. [0134] 3. Burrows B, Martinez F D, Halonen M, Barbee R
A, and Cline M G: Association of asthma with serum IgE levels and
skin-test reactivity to allergens, New Eng J Med 320:271-277, 1989.
[0135] 4. Clifford R D, Pugsley A, Radford M, and Holgate S T:
Symptoms, atopy, and bronchial response to methacholine in parents
with asthma and their children. Arch Dis in Childhood 62:66-73,
1987. [0136] 5. Gergen P J: The association of allergen skin test
reactivity and respiratory disease among whites in the U.S.
population. Arch Intern Med 151:487-492, 1991. [0137] 6. Burrows B,
Sears M R, Flannery E M, Herbison G P, and Holdaway M D:
Relationship of bronchial responsiveness assessed by methacholine
to serum IgE, lung function, symptoms, and diagnoses in 11-year-old
New Zealand children. J Allergy Clin Immunol 90:376-385, 1992.
[0138] 7. Johannson S G O, Bennich H H, and Berg T: The clinical
significance of Prog Clin Immunol 1:1-25, 1972. [0139] 8. Sears M
R, Burrows B, Flannery E M, Herbison G P, Hewitt C J, and Holdaway
M D: Relation between airway responsiveness and serum IgE in
children with asthma and in apparently normal children New Engl. J.
Med 325 (15): 1067-71, 1991. [0140] 9. Halonen M, Stern D, Taussig
L M, Wright A, Ray C G, and Martinez F D: The predictive
relationship between serum IgE levels at birth and subsequent
incidences of lower respiratory illnesses and eczema in infants. Am
Rev Respir Dis 146:666-670, 1992. [0141] 10. Marsh D G, Meyers D A,
and Bias W B: The epidemiology and genetics of atopic allergy. New
Eng J Med 305:1551-1559, 1982. [0142] 11. Hopp R J, Bewtra A K,
Biven R, Nair N M, Townley R G. Bronchial reactivity pattern in
nonasthmatic parents of asthmatics. Ann Allergy 1988; 61: 164-186.
[0143] 12. Hopp R J, Townley R G, Biven R E, Bewtra A K, Nair N M.
The presence of airway reactivity before the development of asthma.
Am Rev Respir Dis 1990; 141:2-8. [0144] 13. Ackerman V, Marini M,
Vittori E, et al. Detection of cytokines and their cell sources in
bronchial biopsy specimens from asthmatic patients: relationship to
atopic status, symptoms, and level of airway hyperresponsiveness.
Chest 1994; 105:687-696. [0145] 14. Hamid G, Azzawl M, Ying S, et
al. Expression of mRNA for interleukin-5 in mucosal bronchial
biopsies from asthma. J Clin Invest 1991; 87:1541-1546. [0146] 15.
Djukanovic R, Roche W R, Wilson J W, et al. Mucosal inflammation in
asthma. Am Rev Respir Dis 1990; 142:434-57. [0147] 16. Robinson D
S, Hamid Q, Ying S, et al. Predominant TH2-like bronchoalveolar T
lymphocyte population in atopic asthma. N Engl J Med 1992;
326:298-304. [0148] 17. Robinson D S, Hamid Q. Ying S, et al.
Prednisolone treatment in asthma is associated with modulation of
bronchoalveolar lavage cell interleukin-4, interleukin-5, and
interferon-cytokine gene expression. Am Rev Respir Dis 1993; 148:
401-406. [0149] 18. Robinson D S, Ying S, Bentley A, et al.
Relationship among numbers of bronchoalveolar lavage cells
expressing messenger ribonucleic acid for cytokines, asthma
symptoms, and airway methacholine responsiveness in atopic asthma.
Allergy Clin Immunol 1993; 92:397403. [0150] 19. O'Connor G T,
Sparrow D, and Weiss S T: The role of allergy and nonspecific BHR
in the pathogenesis of COPD. Am Rev Respir Dis 140:225-252, 1989.
[0151] 20. Cogswell J J, Halliday D F, and Alexander J R:
Respiratory Infections In the first year of life in children at the
risk of developing atopy. Brit Med J 284:1011-1013, 1982. [0152]
21. Boushey H A, Holtzman M J, Sheller J R, And Nadel J A: BHR. Am
Rev Res it Dis 121:389413, 1980. [0153] 22. Renauld, J-C, Houssiau,
F, Druez, C. Interleukin-9. Int Rev Exp Pathology 1993; 34A:
99-109. [0154] 23. Renauld, J-C, Kermouni, A, Vink, A, Louahed, J,
Van Snick, J. Interleukin-9 and its receptor: involvement In mast
cell differentiation and T cell oncogenesis. J Leukoc Biol 1995;
57:353-360. [0155] 24. Hultner, L, Moeller, J, Schmitt, E, Jager,
G, Reisbach, G, Ring, J. Dormer, P. Thiol-sensitive mast cell lines
derived from mouse bone marrow respond to a mast cell
growth-enhancing activity different from both IL-3 and IL-4. J
Immunol 1989; 142:3440-3448. [0156] 25. Dugas, B, Renauld, J-C,
Pene, J, Bonnefoy, J, Peti-Frere, C. Braquet, P, Bousquet, J, Van
Snick, J, Mencia-Huerta, J M. Interleukin-9 potentiates the
interleukin-4-induced immunoglobulin (IgG, IgM and IgE) production
by normal human B lymphocytes. Eur J Immunol 1993: 23:1687-1692.
[0157] 26. Petit-Frere, C, Dugas, B, Braquet, P, Mencia-Huerta, J
M. Interleukin-9 potentiates the interleukin-4-induced IgE and IgG1
release from murine B lymphocytes. Immunology 1993; 79:146-151.
[0158] 27. Behnke, J M, Wahid, F N, Grencis, R K, Else, K J,
Ben-Smith, A W, Goyal, P K. Immunological relationships during
primary infection with Heligmosomoides polygyrus (Nematospiroides
dubius): downregulation of specific cytokine secretion (IL-9 and
IL-10) correlates with poor mastocytosis and chronic survival of
adult worms. Parasite Immunol 1993; 15:415-421. [0159] 28. Gessner,
A, Blum, H, Rollinghoff, M. Differential regulation of IL-9
expression after infection with Leischmania major in susceptible
and resistant mice. Immunobiology 1993; 189:419-435. [0160] 29.
Renauld J-C, Druez C, Kermouni A, et al. Expression cloning of the
murine and human interleukin 9 receptor cDNAs. Proc Natl Aced Sci
89:5690-5694 (1992). [0161] 30. Chang M-S, Engel G, Benedict C et
al, Isolation and characterization of the Human interleukin-9
receptor gene. Blood 83:3199-3205 (1994). [0162] 31. Renauld J-C,
Goethals A, Houssiau F, et al. Human P4011L-9. Expression in
activated C04+ T cells, Genomic Organization, and Comparison with
the Mouse Gene. J Immunol 144:4235-4241 (1990). [0163] 32. Kelleher
K, Bean K, Clark S C, et al. Human interleukin-9: genomic sequence,
chromosomal location, and sequences essential. for its expression
in human T-cell leukemia virus (HTLV-1-transformed human T cells.
Blood 77:1436-1441 (1991). [0164] 33. Houssiau F A, Schandene L,
Stevens M, et al. A cascade of cytokines is responsible for IL-9
expression in human T cells. Involvement of IL-2, IL-4, and IL-10.
J of Immunol. 154:2624-2630 (1995). [0165] 34. Miyazawa K, Hendrie
P C, Kim Y-J, et al. Recombinant human interleukin-9 induces
protein tyrosine phosphorylation and synergizes with steel factor
to stimulate proliferation of the human factor-dependent cell line,
Mo7e, Blood 80: 1685-1692 (19992). [0166] 35. Yin T, Tsang M L-S,
Yang Y-C. JAM kinase forms complexes with interleukin-4 receptor
and 4PS/insulin receptor substrate-1-like protein and is activated
by interleukin-4 and Interleukin-9 in T lymphocytes. J Biol Chem
269:26614-26617 (1994). [0167] 36. Zav'yalov V P, Navolotskaya E V,
Isaev I S, et al. Nonapeptide corresponding to the sequence 27-35
of the mature human IL-2 efficiently competes with rIL-2 for
binding to thymocyte receptors. Immunol Lett 31:285-288 (1992).
[0168] 37. Chu J W, and Sharom F J. Glycophorin A interacts with
interleukin-2 and inhibits interleukin-2-dependent T-lymphocyte
proliferation. Cell Immunol 145:223-239 (1992). [0169] 38.
Alexander A G, Barnes N C, Kay A B. Trial of cyclosporin in
corticosteroid-dependent chronic severe asthma. Lapp 339:324-328
(1992). [0170] 39. Morely J. Cyclosporin A in asthma therapy: a
pharmacological rationale. I Autoimmun 5 Suppl A: 265-269 (1992).
[0171] 40. Sheffield V C, Beck J S, Kwitek A E, Sandstrom D W, and
Stone E M: The sensitivity of single-strand conformation
polymorphism analysis for the detection of single base
substitutions. Genomics 16:325-332, 1993. [0172] 41. Orita M,
Suzuki Y, Sekiya T, and Hayashi K: Rapid and sensitive detection of
point mutations and DNA polymorphisms using the polymerase chain
reaction. Genomics 5:874-9, 1989. [0173] 42. Sarkar G, Yoon H-S,
and Sommer S S: Dideoxy fingerprint (ddF): A rapid and efficient
screen for the presence of mutations. Genomics 13:441-443, 1992.
[0174] 43. Cotton R G: Detection of single base changes in nucleic
acids. Biochemical Journal 263(1):1-10; 1989. [0175] 44. Schwengel
D, Nouri N, Meyers D, and Levitt R C: Linkage mapping of the human
thromboxane A2 receptor (TBXA2R) to chromosome 19p13.3 using
transcribed 3' untranslated DNA sequence polymorphisms. Genomics
18:212-215, 1993. [0176] 45. Cytokine Handbook, Angus. Thomson
(1994). [0177] 46. Nicolaides, N. C. and Stoecker, C. J. A simple,
efficient method for the separate isolation of RNA and DNA from the
same cells, Biotechniques 1996; 8:154-156. [0178] 47. Ott J.
Analysis of Human Genetic Linkage. Baltimore, Md.: The Johns
Hopkins University Press, 1991. [0179] 48. Meyers D A, Postma D S,
Panhuysen C I M, et al. Evidence for a locus regulating total serum
IgE levels mapping to chromosome 5. Genomics 1994; 23:484 470.41.
Sequence CWU 1
1
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