U.S. patent application number 09/969528 was filed with the patent office on 2002-10-17 for novel grb2 associating polypeptides and nucleic acids encoding therefor.
This patent application is currently assigned to The Regents of the University of California. Invention is credited to Jefferson, Anne Bennett, Majerus, Philip W., Pot, David A., Williams, Lewis T..
Application Number | 20020150567 09/969528 |
Document ID | / |
Family ID | 24235970 |
Filed Date | 2002-10-17 |
United States Patent
Application |
20020150567 |
Kind Code |
A1 |
Pot, David A. ; et
al. |
October 17, 2002 |
NOVEL GRB2 ASSOCIATING POLYPEPTIDES AND NUCLEIC ACIDS ENCODING
THEREFOR
Abstract
The present invention generally relates to novel GRB2
associating proteins and nucleic acids which encode these protein.
In particular, these novel proteins possess inositol polyphosphate
5-phosphatase and phosphatidylinositol 5-phosphatase activities,
important in growth factor mediated signal transduction. As such,
the proteins, nucleic acids encoding the proteins, cells capable of
expressing these nucleic acids and antibodies specific for these
proteins will find a variety of uses in a variety of screening,
therapeutic and other applications.
Inventors: |
Pot, David A.; (San
Francisco, CA) ; Williams, Lewis T.; (Tiburon,
CA) ; Jefferson, Anne Bennett; (University City,
MO) ; Majerus, Philip W.; (University City,
MO) |
Correspondence
Address: |
TOWNSEND AND TOWNSEND AND CREW, LLP
TWO EMBARCADERO CENTER
EIGHTH FLOOR
SAN FRANCISCO
CA
94111-3834
US
|
Assignee: |
The Regents of the University of
California
300 Lakeside Drive, 22nd Fl.
Oakland
CA
94612
|
Family ID: |
24235970 |
Appl. No.: |
09/969528 |
Filed: |
October 1, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09969528 |
Oct 1, 2001 |
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09418540 |
Oct 14, 1999 |
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6296848 |
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09418540 |
Oct 14, 1999 |
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08560005 |
Nov 17, 1995 |
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6001354 |
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Current U.S.
Class: |
424/94.6 ;
435/196; 435/320.1; 435/325; 435/69.1; 536/23.2 |
Current CPC
Class: |
C12N 9/16 20130101; A61K
38/00 20130101; C07K 16/18 20130101; C07K 14/4702 20130101; A61P
43/00 20180101 |
Class at
Publication: |
424/94.6 ;
435/196; 435/325; 435/69.1; 435/320.1; 536/23.2 |
International
Class: |
A61K 038/51; C07H
021/04; A61K 038/53; C12N 009/16; C12P 021/02; C12N 005/06 |
Goverment Interests
[0001] The present invention was made with government support under
Grant Nos. HL32898 and HL16634, awarded by the National Institutes
of Health. The government has certain rights in this invention.
Claims
What is claimed is:
1. A substantially pure polypeptide, comprising an amino acid
sequence that is substantially homologous to the amino acid
sequence shown in FIG. 10 (SEQ ID NO:2), or biologically active
fragments thereof.
2. The substantially pure polypeptide of claim 1, wherein said
polypeptide comprises the amino acid sequence shown in FIG. 10 (SEQ
ID NO:2) or biologically active fragments thereof.
3. The substantially pure polypeptide of claim 1, wherein said
polypeptide further comprises a heterologous protein fused to said
amino acid sequence that is substantially homologous to the amino
acid sequence shown in FIG. 10 (SEQ ID NO:2), or biologically
active fragments thereof.
4. A pharmaceutical composition, comprising an effective amount of
the polypeptide of claim 1 in combination with a pharmaceutically
acceptable carrier.
5. The substantially pure polypeptide of claim 1, wherein said
polypeptide comprises an inositol polyphosphate 5-phosphatase
activity, whereby said polypeptide is capable of hydrolyzing a
5-phosphate from Ins(1,3,4,5)P.sub.4 and PtdIns(3,4,5)P.sub.3, but
not Ins(1,4,5)P.sub.3 or PtdIns(4,5)P.sub.2.
6. The substantially pure polypeptide of claim 1, wherein said
polypeptide is capable of associating with GRB2.
7. The substantially pure polypeptide of claim 1, wherein said
polypeptide is capable of binding a GRB2--SH3 domain.
8. An isolated nucleic acid segment, said nucleic acid segment
encoding a polypeptide having an amino acid sequence substantially
homologous to the amino acid sequence shown in FIG. 10 (SEQ ID
NO:2), or biologically active fragments thereof.
9. The isolated nucleic acid segment of claim 8, wherein said
nucleic acid segment comprises at least about 15 contiguous
nucleotides from a nucleotide sequence that is substantially
homologous to the nucleotide sequence shown in FIG. 10 (SEQ ID
NO:1).
10. The isolated nucleic acid segment of claim 9, wherein said
nucleic acid segment comprises at least about 15 contiguous
nucleotides from the nucleic acid segment as shown in FIG. 10 (SEQ
ID NO:1).
11. The isolated nucleic acid segment of claim 8, wherein said
nucleic acid segment encodes a polypeptide having an inositol
polyphosphate 5-phosphatase activity, whereby said polypeptide is
capable of hydrolyzing a 5-phosphate from Ins(1,3,4,5)P.sub.4 and
PtdIns(3,4,5)P.sub.3, but not Ins(1,4,5)P.sub.3 or
PtdIns(4,5)P.sub.2.
12. The isolated nucleic acid segment of claim 8, wherein said
nucleic acid further comprises a segment which encodes a
heterologous protein, whereby said nucleic acid is expressed as a
fusion protein.
13. An expression vector, said expression vector comprising a
nucleic acid segment operably linked to a promoter sequence,
wherein said nucleic acid segment is the nucleic acid of claim
8.
14. A recombinant host cell, wherein said host cell has been
transfected with the expression vector of claim 13, whereby said
host cell is capable of expressing said nucleic acid segment.
15. The recombinant host cell of claim 14, wherein said host cell
is selected from the group consisting of bacterial, mammalian,
plant, fungal and insect cells.
16. The recombinant host cell of claim 15, wherein said host cell
is an Sf9 insect cell.
17. An isolated antibody, said antibody being specifically
immunoreactive with a polypeptide having an amino acid sequence
substantially homologous to the amino acid sequence shown in FIG.
10 (SEQ ID NO:2) or its biologically active fragments.
18. The isolated antibody of claim 17, wherein said antibody is
capable of blocking or inhibiting one or more biological activities
of the polypeptide having the amino acid sequence shown in FIG. 10
(SEQ ID NO:2).
19. The isolated antibody of claim 17, wherein said antibody is
specifically immunoreactive with a polypeptide having the amino
acid sequence shown in FIG. 10 (SEQ ID NO:2).
20. The isolated antibody of claim 17, wherein said antibody is a
monoclonal antibody.
21. A pharmaceutical composition, comprising an effective amount of
the isolated antibody of claim 17 in combination with a
pharmaceutically acceptable carrier.
22. A method of preparing a substantially pure polypeptide having
inositol polyphosphate 5-phosphatase activity, comprising:
inserting the nucleic acid segment of claim 8, into an expression
vector; transfecting a host cell capable of expressing said nucleic
acid segment with said expression vector; culturing said host cell
under conditions which result in expression of said nucleic acid
segment; and recovering said protein having inositol polyphosphate
5-phosphatase activity.
23. A method of determining whether a test compound is an agonist
or antagonist of a GRB2/GA5Ptase interaction, the method
comprising: contacting GRB2 with GA5Ptase or a biologically active
fragment thereof, under conditions conducive to forming a
GRB2/GA5Ptase complex, in the presence and absence of the test
compound; and determining the amount of GRB2/GA5Ptase complex
formed in the presence and absence of said test compound, an
increase or decrease in the amount of GRB2/GA5Ptase complex formed
in the presence of said test compound being indicative that the
test compound is an agonist or antagonist of GRB2/GA5Ptase
interaction, respectively.
24. A method for determining whether a test compound is an agonist
or antagonist of an inositol polyphosphate 5-phosphatase activity,
comprising: incubating a mixture of inositol polyphosphate
substrate and GA5Ptase, in the presence and absence of the test
compound; assaying the mixture to determine an amount of a product
of GA5Ptase activity on said inositol polyphosphate substrate in
the presence and absence of the test compound; and comparing the
amount of product of GA5Ptase activity in the presence of the test
compound to the amount of product of GA5Ptase activity in the
absence of the test compound, an increase or decrease in the amount
of product of GA5Ptase activity in the presence of the test
compound being indicative that the test compound is an agonist or
antagonist of an inositol polyphosphate 5-phosphatase activity,
respectively.
25. The method of claim 24, wherein said inositol polyphosphate
substrate is selected from the group consisting of
Ins(1,3,4,5)P.sub.4 and PtdIns(3,4,5)P.sub.3.
26. A method of identifying the presence of GRB2 in a sample,
comprising incubating said sample with the polypeptide of claim 6,
and detecting binding between said polypeptide and a portion of
said sample, said binding being indicative of the presence of GRB2
in said sample.
27. A method of purifying GRB2 from a mixture of different proteins
containing GRB2, comprising: immobilizing the polypeptide of claim
6, on a solid support; contacting said mixture of proteins with
said solid support under conditions in which said polypeptide binds
GRB2; washing said solid support to remove unbound proteins; and
eluting GRB2 from said solid support in substantially pure
form.
28. A kit for determining whether a test compound is an agonist or
antagonist of GA5Ptase activity, comprising: a GA5Ptase
polypeptide, or catalytically active fragment thereof; a GA5Ptase
substrate; and instructions for assaying for the presence of said
substrate and a product of GA5Ptase.
29. The kit of claim 26, wherein said GA5Ptase substrate is
selected from the group consisting of Ins(1,3,4,5)P.sub.4 and
PtdIns(3,4,5)P.sub.3.
30. The kit of claim 26, wherein said GA5Ptase and said substrate
are lyophilized, and further comprising a buffer solution for
reconstituting said GA5Ptase and said substrate.
31. A method of treating a patient suffering from a proliferative
disorder, the method comprising administering to said patient a
therapeutically effective amount of the polypeptide of claim 6.
32. A substantially pure polypeptide, said polypeptide being
immunologically cross-reactive with an antibody to a GA5ptase
protein, or biologically active fragment thereof.
Description
[0002] The present invention generally relates to novel GRB2
associating polypeptides and nucleic acids which encode these
polypeptides. In particular, these novel polypeptides possess
inositol polyphosphate 5-phosphatase activity, important in growth
factor mediated signal transduction. As such, the polypeptides,
nucleic acids encoding the polypeptides, cells capable of
expressing these nucleic acids and antibodies specific for the
polypeptides will find a variety of uses in a wide range of
screening, therapeutic and other applications.
BACKGROUND OF THE INVENTION
[0003] Receptor signaling pathways are the subject of widespread
research efforts. A better understanding of these signaling
pathways will lead to the design of new and more effective drugs in
the treatment of many diseases. Of particular interest are the
growth factor and related receptor signaling pathways and their
role in cell growth and differentiation. Binding of a particular
growth factor to its receptor on the cell plasma membrane can
stimulate a wide variety of biochemical responses, including
changes in ion fluxes, activation of various kinases, alteration of
cell shape, transcription of various genes and modulation of
enzymatic activities in cellular metabolism.
[0004] Growth factors play a role in embryonic development, cancer,
atherosclerosis and the responses of tissues to injury. Growth
factors are involved in several normal developmental processes as
well as in pathological conditions. Many growth factor receptors
are tyrosine kinases whose signalling is dependent upon tyrosine
phosphorylation of both the receptor and other molecules. Specific
phosphorylated tyrosine residues on these receptors recruit soluble
intracellular signaling molecules to the complex upon growth factor
stimulation, thus initiating the growth factor signaling cascade.
The signal can then proceed through a series of steps to the
nucleus and other subcellular locations where the final effects of
activation by the extracellular ligand are produced. Recruitment of
molecules is often carried out by adapter molecules containing only
protein-protein interaction domains with no associated enzymatic
activity. By examining the molecules that interact with these
adapters, important parts of the signaling mechanism can be
discovered, monitored and controlled. One such adapter protein is
GRB2, a 24 kDa cytosolic adapter protein containing two SH3 domains
flanking an SH2 domain, which is known to be involved in linking
many important molecules in signal transduction.
[0005] Because disregulation of the cellular processes involved in
cell growth can have disastrous effects, it is important to
understand and gain control over these processes. This requires
identifying the participants in the signaling events that lead to
mitogenesis and elucidating their mechanism of function. The
identification of these participants is important for a wide range
of diagnostic, therapeutic and screening applications. In
particular, by knowing the structure of a particular participant in
a growth factor activation cascade, one can design compounds which
affect that cascade, to either activate an otherwise inactive
pathway, or inactivate an overly active pathway. Similarly, having
identified a particular participant in a growth factor cascade, one
can also identify situations where that cascade is defective,
resulting in a particular pathological state. The identification of
participants in particular growth factor activation cascades is
thus of critical importance for screening compounds that affect
these cascades and treating a variety of disorders resulting from
anomalies in these cascades, both as therapeutic agents and as
model systems for identification of compounds which affect the
pathway and thus may be useful as therapeutic agents. The present
invention meets these and many other needs.
SUMMARY OF THE INVENTION
[0006] The present invention generally provides substantially pure
polypeptides, comprising an amino acid sequence that is
substantially homologous to the amino acid sequence shown in FIG.
10 (SEQ ID NO:2), or biologically active fragments thereof.
[0007] The present invention also provides isolated nucleic acid
segments, which encode a polypeptide having an amino acid sequence
substantially homologous to the amino acid sequence shown in FIG.
10 (SEQ ID NO:2), or biologically active fragments thereof.
[0008] Also provided are isolated antibodies that are specifically
immunoreactive with a polypeptide having an amino acid sequence
substantially homologous to the amino acid sequence shown in FIG.
10 (SEQ ID NO:2) or its biologically active fragments.
[0009] In a further aspect, the present invention provides methods
of using these polypeptides. In particular, the invention provides
a method of determining whether a test compound is an agonist or
antagonist of a GRB2/GA5Ptase interaction. The method comprises
contacting GRB2 with GA5Ptase (SEQ ID NO:2) under conditions
conducive to forming a GRB2/GA5Ptase complex, in the presence and
absence of the test compound. The amount of GRB2/GA5Ptase complex
formed in the presence and absence of the test compound is then
determined. An increase or decrease in the amount of GRB2/GA5Ptase
complex formed in the presence of the test compound is indicative
that the test compound is an agonist or antagonist of GRB2/GA5Ptase
interaction, respectively.
[0010] In a related aspect, the present invention provides a method
for determining whether a test compound is an agonist or antagonist
of an inositol polyphosphate 5-phosphatase activity. The method
comprises incubating a mixture of inositol polyphosphate substrate
and GA5Ptase, in the presence and absence of the test compound. The
mixture is then assayed to determine the amount of GA5Ptase product
formed in the presence and absence of the test compound. The amount
of product of GA5Ptase activity in the presence of the test
compound is compared to the amount of product of GA5Ptase activity
in the absence of the test compound. An increase or decrease in the
amount of product of GA5Ptase activity in the presence of the test
compound is indicative that the test compound is an agonist or
antagonist of an inositol polyphosphate 5-phosphatase activity,
respectively.
[0011] The present invention also provides a method of identifying
the presence of GRB2 in a sample. The method comprises incubating
the sample with the polypeptide of the invention, and detecting
binding between the polypeptide and a portion of the sample. This
binding is indicative of the presence of GRB2 in the sample.
[0012] Also provided is a method of purifying GRB2 from a mixture
of different proteins containing GRB2. The method comprises
immobilizing the polypeptide of the invention, on a solid support.
The mixture of proteins is then contacted with the solid support
under conditions in which the polypeptide binds GRB2. The solid
support is washed to remove unbound proteins, and GRB2 is eluted
from the solid support.
[0013] The present invention also provides kits for practicing
these methods.
[0014] In a further aspect, the present invention provides a method
of treating a patient suffering from a proliferative disorder. The
method comprises administering to the patient a therapeutically
effective amount of the polypeptide of the invention.
[0015] The present invention also provides substantially pure
polypeptides that are immunologically cross-reactive with
antibodies to the GA5ptase polypeptides and fragments, described
herein.
BRIEF DESCRIPTION OF THE DRAWINGS
[0016] FIG. 1 shows a schematic representation of the probe used to
screen a .lambda.gt11 expression library.
[0017] FIG. 2 shows a ribbon diagram and dendrogram illustrating
relative similarities between inositol polyphosphate
5-phosphatases. Numbers beside the nodes of the dendrogram indicate
the percent identity and (similarity). The black bar above the
ribbon representation of GA5Ptase indicates the region cloned by
interaction with GRB2, whereas the "P" indicates the location of
PXXP motifs.
[0018] FIG. 3 shows a schematic representation of GA5Ptase, GRB2
and GRB3.3 molecules used in Cos7 Immunoprecipitations.
[0019] FIG. 4 shows results of co-immunoprecipitation of GA5Ptase
with wild type GRB2 ("GRB2 wt"), point mutations of GRB2 ("GRB2
P49L", "GRB2 E89K", "GRB2 S90N", "GRB2 G203R") and GRB3.3.
[0020] FIG. 5A shows c-Fos Serum Responsive Element (SRE)
activation when co-expressed with various combinations of GRB2,
c-Ras and GA5Ptase. The error bars indicate standard error of the
mean of triplicate transfections.
[0021] FIG. 5B shows SRE activation when co-expressed as indicated
with GA5Ptase, c-Ras and the various GRB2 point mutations used in
the Cos7 co-immunoprecipitation experiments shown in FIG. 4.
[0022] FIG. 5C shows SRE activation when co-expressed as indicated
with GA5Ptase, v-Ras and GrbRB2 point mutations.
[0023] FIG. 5D shows a comparison of SRE activation when
co-expressed with GA5Ptase versus platelet inositol polyphosphate
5-phosphatase type-II ("5Ptase II").
[0024] FIG. 6 shows the effect of varying concentration of
Ins(1,3,4,5)P.sub.4 on the rate of its hydrolysis by GA5Ptase.
[0025] FIGS. 7A and 7B show the immunoprecipitation of both
GA5Ptase protein and Ins(1,3,4,5)P.sub.4 hydrolyzing activity of
GA5Ptase. HA-tagged GA5Ptase was immunoprecipitated with .alpha.HA
antiserum. Following contact with protein A sepharose, the
supernatant (.cndot.) and protein A sepharose pellet (.degree.)
were Western blotted against .alpha.HA antiserum (FIG. 7B) and
assayed for ability to hydrolyze Ins(1, 3,4,5)P.sub.4 (FIG.
7A).
[0026] FIGS. 8A-C show HPLC analysis of reaction products from
incubation of GA5Ptase with Ins(1,3,4,5)P.sub.4.
[0027] FIG. 8A shows conversion of .sup.3H-Ins(1,3,4,5)P.sub.4 to
.sup.3H-Ins(1,3,4)P.sub.3 (peak) in the presence of GA5Ptase.
[0028] FIG. 8B shows the conversion of .sup.3H-Ins(1,3,4,5)P.sub.4
to .sup.3H-Ins(3,4)P.sub.2 (peak), in the presence of GA5Ptase and
inositol polyphosphate 1-phosphatase.
[0029] FIG. 8C shows the conversion of .sup.3H-Ins(1,3,4,5)P.sub.4
to .sup.3H-Ins(1,3)P.sub.2 (peak) in the presence of GA5Ptase and
inositol polyphosphate 4-phosphatase.
[0030] FIG. 9 shows the hydrolysis of PtdIns(3,4,5)P.sub.3 by
recombinant inositol polyphosphate 5-phosphatases. Specifically
shown is a graph showing hydrolysis with GA5Ptase (open squares)
and human inositol polyphosphate 5-phosphatase II ("5-Ptase II")
(closed squares). Also shown is a TLC autoradiogram indicating
conversion of PtdIns(3,4,5)P.sub.3 to PtdInsP.sub.2 by GA5Ptase and
5-Ptase II (inset).
[0031] FIG. 10 shows the nucleotide sequence (SEQ ID NO:1) and
deduced amino acid sequence (SEQ ID NO:2) of the GRB2 associating
protein GA5Ptase.
[0032] FIG. 11 shows a comparison between the amino acid sequence
of GA5Ptase (SEQ ID NO:2) and that of a number of other inositol
polyphosphate 5-phosphatases. Level of shading indicates similarity
in residue structure. Black boxes indicate a consensus sequence.
The sequences shown are C. elegans inositol polyphosphate
5-phosphatase ("celegptase") (SEQ ID NO:3), S. cereviseae inositol
polyphosphate 5-phosphatase ("ysc5ptase") (SEQ ID NO:4), GA5Ptase
(SEQ ID NO:2), human 51c ("51c") (SEQ ID NO:5), human inositol
polyphosphate 5-phosphatase 75 kDa ("5ptaseii") (SEQ ID NO:6),
human ocr1 protein responsible for human oculocerebrorenal syndrome
("ocr1") (SEQ ID NO:7), Arabidopsis inositol polyphosphate
5-phosphatase ("arab5ptase") (SEQ ID NO:8) and canine inositol
polyphosphate 5-phosphatase 43 kDa ("h5ptase43")(SEQ ID NO:9). The
identified consensus sequence is also provided ("consensus") (SEQ
ID NO:10).
DESCRIPTION OF THE PREFERRED EMBODIMENT
[0033] I. General Description
[0034] The present invention generally provides novel GRB2
associating polypeptides. These polypeptides are generally involved
in signal transduction pathways following growth factor activation.
In particular, the polypeptides of the present invention contribute
to the mediation of inositol polyphosphate based signal
transduction pathways, following growth factor activation.
[0035] Also provided by the present invention are nucleic acids
encoding these novel polypeptides, expression vectors containing
these nucleic acids, cells capable of expressing these expression
vectors, antibodies which specifically recognize and bind these
polypeptides and methods of using these polypeptides and nucleic
acids in screening and therapeutic applications.
[0036] The polypeptides of the present invention have been
identified as possessing unique specificity for inositol
polyphosphates. In particular, the polypeptides of the present
invention have inositol polyphosphate 5-phosphatase activity, and
more particularly, the ability to remove the 5-phosphate from
D-myo-Inositol 1,3,4,5-tetrakisphosphate ("Ins(1,3,4,5)P.sub.4")
and Phosphatidylinositol 3,4,5-trisphosphate
("PtdIns(3,4,5)P.sub.3"), but not D-myo-Inositol
1,4,5-trisphosphate ("Ins(1,4,5)P.sub.3") or Phosphatidylinositol
(4,5)-bisphosphate ("PtdIns(4,5)P.sub.2"). Accordingly, the
polypeptides of the present invention are generally referred to
herein by the abbreviation GA5Ptase, for GRB2 Associating inositol
polyphosphate 5-phosphatase.
[0037] Inositol polyphosphates have been broadly implicated in cell
signalling pathways. For example, stimulation of cell surface
receptors has been found to initiate hydrolysis of membrane-bound
inositol lipid, which produces at least two second messengers:
diacylglycerol (DAG) and inositol(1,4,5)trisphosphate. These
messengers are generated by a membrane transduction process which
comprises three main components: a receptor, a coupling G protein
and phosphoinositidase C. DAG acts by stimulating protein kinase C,
whereas Ins(1,4,5)P.sub.3 releases calcium from internal stores
(see, Berridge and Irvine, Nature (1989) 341:197-205).
[0038] PtdIns(3,4,5)P.sub.3 in particular, is the product of
phosphatidyl inositol 3-kinase ("PI3 kinase"), an important agonist
activated signaling protein, stimulated in growth factor mediated
signal transduction. PI3-kinase is known to be involved in the
regulation of cell growth and oncogenic transformation (Cantley et
al., Cell, 64:1657 (1993)). Upon growth factor receptor
stimulation, the wild-type PI3-kinase is activated and can
phosphorylate phosphatidylinositol ("PtdIns") at the 3' position of
the inositol ring. These phosphatidylinositol 3-phosphates are
candidate second messenger molecules. The PI3-kinase enzyme is
found associated with receptor protein tyrosine kinases such as
PDGF-R-.beta., CSF-1 receptor, Insulin receptor and IGF-1 receptor
as well as non-receptor tyrosine kinase oncogenes, e.g., src,
gag-abl and fyn. Studies on mutants of platelet-derived growth
factor (PDGF) receptor have shown that PI3-kinase is a key mediator
of PDGF-mediated mitogenic signaling (Fantl et al., Cell, 69:413
(1992); Valius et al., ibid., 73:321 (1993)). PDGF-R mutants that
are unable to bind PI3-kinase are also unable to induce a mitogenic
response after growth factor stimulation and unable to activate
p21c-Ras (Ras). These data indicate that PI3-kinase acts upstream
of Ras in PDGF-stimulated signaling. Studies also indicate that the
PI3-kinase product, PtdIns(3,4,5)P.sub.3 is not the final product
produced during the initial phases of signaling, indicating further
processing of this signaling molecule. Stephens, et al., Nature
351:33-39 (1991), Hawkins, et al., Nature 358:157-159 (1992).
[0039] The action of the polypeptides of the present invention upon
the specific product of PI3-kinase implicates these polypeptides as
important downstream mediators of growth factor activation
signaling cascades. Furthermore, in addition to inositol
polyphosphate 5-phosphatase activity, the polypeptides of the
invention also associate with GRB2, in cell culture. GRB2 is an
intracellular signalling molecule that is recruited to the cell
membrane/receptor complex upon growth factor stimulation. GRB2 is
specifically recruited to the PDGF, EGF and other tyrosine growth
factor receptors. It is also in the signaling pathway that
activates Ras upon growth factor stimulation. GRB2 is a small
protein (24 kDa) that functions as an adapter molecule using its
two SH3 domains and single SH2 domain to provide a bridge between
other important signaling molecules. Clark, et al., Nature
356:340-344 (1992), Stern, et al., Mol. Biol. Cell 4:1175-1188
(1993). The ability of the polypeptides of the invention to
specifically associate with GRB2 further indicates the importance
of these polypeptides as downstream mediators of growth factor
activation signal transduction, generally.
[0040] The polypeptides of the present invention have also been
shown to activate signaling through the Fos serum response element
(SRE) in fibroblast cells when these polypeptides are co-expressed
with GRB2 and c-Ras. This activation is four to six fold over the
activation seen with GRB2, Ras or GRB2/Ras alone. The Fos SRE is a
gene that is known to be turned on early in growth factor
activation, and has been identified as an upstream event for many
response elements for cell growth. See, e.g., Janknecht et al.,
Carcinogenesis 16(3)443-450 (1995), Piechaczyk et al., Crit. Rev.
Oncol./Hematol. 17(2):93-131 (1994), Maruta et al., Bioessays
16(7):489-496 (1994). The Fos gene is also responsive to a large
number of growth factors. In particular, the Fos SRE is believed to
be the direct target induced by growth factor stimulation through
the Ras oncogene.
[0041] The combination of the activities and specificities of the
polypeptides of the present invention implicates these polypeptides
as key elements in the activation of Ras and as downstream
molecules generally, in agonist activated signal transduction
cascades.
[0042] II. Proteins and Polypeptides of the Invention
[0043] In one aspect, the present invention provides substantially
pure, or isolated polypeptides that are generally characterized by
one or more of the following activities: inositol polyphosphate
5-phosphatase activity; the ability to associate with GRB2; and/or
the ability to enhance activation of the Fos SRE when co-expressed
with c-Ras or c-Ras and GRB2. In particular, the polypeptides of
the present invention will generally possess inositol polyphosphate
5-phosphatase activity, and be capable of removing the 5-phosphate
from D-myo-Inositol 1,3,4,5-tetrakisphosphate
("Ins(1,3,4,5)P.sub.4") and Phosphatidylinositol
3,4,5-trisphosphate ("PtdIns(3,4,5)P.sub.3"), but not
D-myo-Inositol 1,4,5-trisphosphate ("Ins(1,4,5)P.sub.3") or
Phosphatidylinositol (4,5)-bisphosphate ("PtdIns(4,5)P.sub.2").
[0044] The terms "substantially pure" or "isolated", when referring
to proteins and polypeptides, denotes those polypeptides that are
separated from proteins or other contaminants with which they are
naturally associated. A protein or polypeptide is considered
substantially pure when that protein makes up greater than about
50% of the total protein content of the composition containing that
protein, and typically, greater than about 60% of the total protein
content. More typically, a substantially pure protein will make up
from about 75 to about 90% of the total protein. Preferably, the
protein will make up greater than about 90%, and more preferably,
greater than about 95% of the total protein in the composition.
[0045] Particularly preferred polypeptides will have an amino acid
sequence that is substantially homologous to the amino acid
sequence shown in FIG. 10 (SEQ ID NO:2), or biologically active
fragments thereof. Still more preferred polypeptides include the
GA5Ptase protein (SEQ ID NO:2) or biologically active fragments
thereof.
[0046] In describing the polypeptides of the present invention,
conventional amino acid abbreviations will generally be used as
follows: Phenylalanine is Phe or F; Leucine is Leu or L; Isoleucine
is Ile or I; Methionine is Met or M; Valine is Val or V; Serine is
Ser or S; Proline is Pro or P; Threonine is Thr or T; Alanine is
Ala or A; Tyrosine is Tyr or Y; Histidine is His or H; Glutamine is
Gln or Q; Asparagine is Asn or N; Lysine is Lys or K; Aspartic Acid
is Asp or D; Glutamic Acid is Glu or E; Cysteine is Cys or C;
Tryptophan is Trp or W; Arginine is Arg or R; and Glycine is Gly or
G. In the polypeptide notation used herein, the left-hand direction
is the amino terminal direction and the right-hand direction is the
carboxy-terminal direction, in accordance with standard usage and
convention.
[0047] The term "biologically active fragment" as used herein,
refers to portions of the proteins or polypeptides which portions
possess a particular biological activity. For example, such
biological activity may include the ability to bind a particular
protein or substrate, block or otherwise inhibit an interaction
between two proteins or between an enzyme and its substrate, or may
include a particular catalytic activity. With regard to the
polypeptides of the present invention, particularly preferred
polypeptides or biologically active fragments include, e.g.,
polypeptides that possess one or more of the biological activities
described above, such as the ability to associate or bind GRB2 or
affect the binding of GRB2 to its ligand, e.g., GA5Ptase. Also
included are those fragments that bind the GA5Ptase substrates
described above, are capable of affecting the binding of GA5Ptase
to those substrates or that are capable of affecting the hydrolysis
of those substrates. Fragments possessing this catalytic activity
are also termed "catalytically active fragments." Fragments that
are specifically recognized and bound by antibodies raised against
the GA5Ptase polypeptides are also included in the definition of
biologically active fragments. Such fragments are also referred to
herein as "immunologically active fragments." Particularly
preferred polypeptides or biologically active fragments are capable
of enhancing the activation of Fos SRE when co-expressed with Ras
or Ras and GRB2.
[0048] Biologically active fragments of the polypeptides of the
invention will generally be useful where it is desired to analyze a
single particular biological activity of the polypeptide. For
example, where the fragment is used in a model to screen for
agonists or antagonists of GA5Ptase/GRB2 interaction (discussed in
greater detail, below), it may be desirable to utilize only the
GRB2 binding portion of the polypeptides of the invention.
Similarly, therapeutic applications will generally target a single
biological activity of the GA5Ptase signaling operation, e.g. GRB2
binding, substrate binding or substrate catalysis, and as such,
peptides having fewer than all of these activities will be desired,
as discussed in greater detail, below. Alternatively, such
fragments may be useful where use of a full length protein is
unsuitable for the particular application, e.g. therapeutic
treatments where administration of full length proteins is
difficult.
[0049] Generally, biologically active fragments of the above
described proteins will be from about 5 to about 1000 amino acids
in length. Typically, these peptides will be from about 10 to about
500 amino acids in length, more typically about 20 to about 250
amino acids in length, and preferably from about 50 to about 200
amino acids in length. Generally, the length of the fragment may
depend, in part, upon the application for which the particular
peptide is to be used. For example, for raising antibodies, the
peptides may be of a shorter length, e.g., from about 5 to about 50
amino acids in length, whereas for binding applications, the
peptides will generally have a greater length, e.g., from about 50
to about 1000 amino acids in length, preferably, from about 100 to
about 500 amino acids in length, and more preferably, from about
100 to about 200 amino acids in length.
[0050] The terms "substantially homologous" when referring to
polypeptides, refer comparatively to two amino acid sequences
which, when optimally aligned, are at least about 75% homologous,
preferably at least about 85% homologous more preferably at least
about 90% homologous, and still more preferably at least about 95%
homologous. Optimal alignment of sequences for aligning a
comparison window may be conducted by the local homology algorithm
of Smith and Waterman (1981) Adv. Appl. Math. 2:482, by the
homology alignment algorithm of Needleman and Wunsch (1970) J. Mol.
Biol. 48:443, by the search for similarity method of Pearson and
Lipman (1988) Proc. Natl. Acad. Sci. (USA) 85:2444, or by
computerized implementations of these algorithms (GAP, BESTFIT,
FASTA, and TFASTA in the Wisconsin Genetics Software Package
Release 7.0, Genetics Computer Group, 575 Science Dr., Madison,
Wis.).
[0051] The polypeptides of the present invention may also be
characterized by their ability to bind antibodies raised against
proteins having the amino acid sequence shown in FIG. 10 (SEQ ID
NO:2). These antibodies recognize polypeptides that are homologous
to the GA5Ptase polypeptide (SEQ ID NO:2). A variety of immunoassay
formats may be used to select antibodies specifically
immunoreactive with a particular protein or domain. For example,
solid-phase ELISA immunoassays are routinely used to select
monoclonal antibodies specifically immunoreactive with a protein.
See Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold
Spring Harbor Publications, New York, for a description of
immunoassay formats and conditions that can be used to determine
specific immunoreactivity. Antibodies to the polypeptides of the
present invention are discussed in greater detail, below.
[0052] The polypeptides of the present invention may generally be
prepared using recombinant or synthetic methods well known in the
art. Recombinant techniques are generally described in Sambrook, et
al., Molecular Cloning: A Laboratory Manual, (2nd ed.) Vols. 1-3,
Cold Spring Harbor Laboratory, (1989). Techniques for the synthesis
of polypeptides are generally described in Merrifield, J. Amer.
Chem. Soc. 85:2149-2456 (1963), Atherton, et al., Solid Phase
Peptide Synthesis: A Practical Approach, IRL Press (1989), and
Merrifield, Science 232:341-347 (1986). In preferred aspects, the
polypeptides of the present invention may be expressed by a
suitable host cell that has been transfected with a nucleic acid of
the invention, as described in greater detail below.
[0053] Biologically active fragments of the above described
polypeptides may generally be identified and prepared using methods
well known in the art. For example, selective proteolytic
digestion, recombinant deletional methods or de novo peptide
synthesis methods may be employed to identify portions of the above
described peptides that possess the desired biological activity,
e.g., GRB2 binding, substrate binding, catalytic activity and the
like. See, e.g. Sambrook, et al.
[0054] Isolation and purification of the polypeptides of the
present invention can be carried out by methods that are generally
well known in the art. For example, the polypeptides may be
purified using readily available chromatographic methods, e.g., ion
exchange, hydrophobic interaction, HPLC or affinity chromatography,
to achieve the desired purity. Affinity chromatography may be
particularly attractive in allowing the investigator to take
advantage of the specific biological activity of the desired
peptide, e.g., ligand binding, presence of antigenic determinants
or the like. For example, the polypeptides of the present invention
may be purified by taking advantage of their ability to associate
with GRB2. Such affinity purification methods are well known in the
art. In particular, GRB2 may be coupled to a suitable solid support
and contacted with a mixture of proteins containing the
polypeptides of the invention under conditions conducive the
association of these polypeptides with GRB2. Once bound to the
immobilized GRB2, the solid support is washed to remove unbound
material and/or nonspecifically bound proteins. The polypeptides of
the invention may then be eluted from the solid support in
substantially pure form by, e.g. a change in salt, pH or buffer
concentration. Suitable solid supports for affinity purifications
are well known in the art and are generally commercially available
from, e.g. Pharmacia, Inc., or Sigma Chemical Co. Examples of such
solid supports include agarose, cellulose, dextran, silica,
polystyrene or similar solid supports.
[0055] In addition to those polypeptides and fragments described
above, the present invention also provides fusion proteins which
contain these polypeptides or fragments. The term "fusion protein"
as used herein, generally refers to a composite protein, i.e., a
single contiguous amino acid sequence, made up of two distinct,
heterologous polypeptides which are not normally fused together in
a single amino acid sequence. Thus, a fusion protein may include a
single amino acid sequence that contains two similar or identical
polypeptide sequences, provided that these sequences are not
normally found together in a single amino acid sequence. Fusion
proteins may generally be prepared using either recombinant nucleic
acid methods, i.e. as a result of transcription and translation of
a gene fusion, which fusion comprises a segment encoding a
polypeptide of the invention and a segment encoding a heterologous
protein, or by chemical synthesis methods well known in the
art.
[0056] These fusion proteins may be prepared to exhibit a
combination of properties or activities of the derivative proteins.
Typical fusion proteins may include a polypeptide of the invention
fused to a reporter polypeptide, e.g., a substrate, cofactor,
inhibitor, affinity ligand, antibody binding epitope tag, or an
enzyme which is capable of being assayed. Because of their ability
to associate with the GRB2 protein, the polypeptides of the
invention, when included as a portion of the fusion protein, may
act as an affinity ligand to direct the activity of the fused
protein directly to the GRB2 protein. In the case of a fusion
protein including a reporter group, this allows the presence and or
location of the GRB2 protein to be determined. More importantly,
such fusions can also be readily used as a marker for determining
the level of fusion protein/GRB2 interaction. Examples of some
useful fusion partners which can also serve as reporter groups
include affinity ligands and antibody binding epitopes, such as the
influenza virus hemagglutinin (IHA) epitope tag, or
glutathione-S-transferase. Other typical fusion partners include
bacterial .beta.-galactosidase, trpE, protein A, .beta.-lactamase,
.alpha.-amylase, alcohol dehydrogenase and yeast .alpha.-mating
factor. See, e.g., Godowski et al., Science 241:812-816 (1988).
[0057] Also included within the present invention are amino acid
variants of the above described polypeptides. These variants may
include insertions, deletions and substitutions with other amino
acids. For example, in some aspects, amino acids may be substituted
with different amino acids having similar structural
characteristics, e.g. net charge, hydrophobicity, or the like. For
example, phenylalanine may be substituted with tyrosine, as a
similarly hydrophobic residue. Glycosylation modifications, either
changed, increased amounts or decreased amounts, as well as other
sequence modifications are also envisioned.
[0058] Systematic substitution of one or more amino acids of a
consensus sequence with a D-amino acid of the same type (e.g.,
D-lysine in place of L-lysine) may also be used to generate more
stable peptides. In addition, constrained peptides comprising a
consensus sequence or a substantially identical consensus sequence
variation may be generated by methods known in the art (Rizo and
Gierasch (1992) Ann. Rev. Biochem. 61: 387; for example, by adding
internal cysteine residues capable of forming intramolecular
disulfide bridges which cyclize the peptide. Similarly,
modification of the amino or carboxy terminals may also be used to
confer stabilizing properties upon the polypeptides of the
invention, e.g., amidation of the carboxy-terminus or acylation of
the amino-terminus. Substitution of amino acids involved in
catalytic activity can be used to generate dominant negative
inhibitors of signaling pathways.
[0059] Furthermore, although primarily described in terms of
"proteins" or "polypeptides" one of skill in the art, upon reading
the instant specification, will appreciate that these terms also
include structural analogs and derivatives of the above-described
polypeptides, e.g., polypeptides having conservative amino acid
insertions, deletions or substitutions, peptidomimetics and the
like. For example, in addition to-the above described polypeptides
which consist only of naturally-occurring amino acids,
peptidomimetics of the polypeptides of the present invention are
also provided. Peptide analogs are commonly used in the
pharmaceutical industry as non-peptide drugs with properties
analogous to those of the template peptide. These types of
non-peptide compounds are termed "peptide mimetics" or
"peptidomimetics" (Fauchere, J. (1986) Adv. Drug Res. 15:29; Veber
and Freidinger (1985) TINS p.392; and Evans et al. (1987) J. Med.
Chem 30:1229, and are usually developed with the aid of
computerized molecular modeling. Peptide mimetics that are
structurally similar to therapeutically useful peptides may be used
to produce an equivalent therapeutic effect. Generally,
peptidomimetics are structurally similar to a paradigm polypeptide
(i.e., a polypeptide that has a biological or pharmacological
activity), such as naturally-occurring receptor-binding
polypeptide, but have one or more peptide linkages optionally
replaced by a linkage selected from the group consisting of:
--CH.sub.2NH--, --CH.sub.2S--, --CH.sub.2--CH.sub.2--,
--CH.dbd.CH-- (cis and trans), --COCH.sub.2--, --CH(OH)CH.sub.2--,
and --CH.sub.2SO--, by methods known in the art and further
described in the following references: Spatola, A. F. in Chemistry
and Biochemistry of Amino Acids, Peptides, and Proteins, B.
Weinstein, eds., Marcel Dekker, New York, p. 267 (1983); Spatola,
A. F., Vega Data (March 1983), Vol. 1, Issue 3, "Peptide Backbone
Modifications" (general review); Morley, J. S., Trends Pharm Sci
(1980) pp. 463-468 (general review); Hudson, D. et al., Int J Pept
Prot Res (1979) 14:177-185 (--CH.sub.2NH--, CH.sub.2CH.sub.2--);
Spatola, A. F. et al., Life Sci (1986) 38:1243-1249
(--CH.sub.2--S); Hann, M. M., J Chem Soc Perkin Trans I (1982)
307-314 (--CH--CH--, cis and trans); Almquist, R. G. et al., J Med
Chem (1980) 23:1392-1398 (--COCH.sub.2--); Jennings-White, C. et
al., Tetrahedron Lett (1982) 23:2533 (--COCH.sub.2--); Szelke, M.
et al., European Appln. EP 45665 (1982) CA: 97:39405 (1982)
(--CH(OH)CH.sub.2--); Holladay, M. W. et al., Tetrahedron Lett
(1983) 24:4401-4404 (--C(OH)CH.sub.2--); and Hruby, V. J., Life Sci
(1982) 31:189-199 (--CH.sub.2--S--).
[0060] Peptide mimetics may have significant advantages over
polypeptide embodiments, including, for example: more economical
production, greater chemical stability, enhanced pharmacological
properties (half-life, absorption, potency, efficacy, etc.),
altered specificity (e.g., a broad-spectrum of biological
activities), reduced antigenicity, and others.
[0061] For many applications, it may be desirable to provide the
polypeptides of the invention as labeled entities, i.e., covalently
attached or linked to a detectable group, to facilitate
identification, detection and quantification of the polypeptide in
a given circumstance. These detectable groups may comprise a
detectable protein group, e.g. an assayable enzyme or antibody
epitope as described above in the discussion of fusion proteins.
Alternatively, the detectable group may be selected from a variety
of other detectable groups or labels, such as radiolabels (e.g.,
.sup.125I, .sup.32P or .sup.35S) or a chemiluminescent or
fluorescent group. Similarly, the detectable group may be a
substrate, cofactor, inhibitor or affinity ligand. Labeling of
peptidomimetics usually involves covalent attachment of one or more
labels, directly or through a spacer (e.g., an amide group), to
non-interfering position(s) on the peptidomimetic that are
predicted by quantitative structure-activity data and/or molecular
modeling. Such non-interfering positions generally are positions
that do not form direct contacts with the molecules to which the
peptidomimetic binds (e.g., GRB2) to produce the therapeutic
effect. Derivitization (e.g., labeling) of peptidomimetics should
not substantially interfere with the desired biological or
pharmacological activity of the peptidomimetic. Generally,
peptidomimetics of peptides of the invention bind to their ligands
(e.g., GRB2) with high affinity and/or possess detectable
biological activity (i.e., are agonistic or antagonistic to one or
more inositol polyphosphate 5-phosphatase mediated phenotypic
changes).
[0062] III. Pharmaceutical Compositions
[0063] For a variety of applications, it may be desirable to
provide the polypeptides or polypeptide fragments of the invention
as part of a pharmaceutical composition, e.g., in combination with
a pharmaceutically acceptable carrier. In such pharmaceutical
compositions, the polypeptide of the present invention is also
referred to as "the active ingredient." Pharmaceutical formulations
suitable for use in the present invention are generally described
in Remington's Pharmaceutical Sciences, Mack Publishing Co., 17th
ed. (1985).
[0064] The pharmaceutical compositions of the present invention are
intended for parenteral, topical, oral, or local administration.
Where the pharmaceutical compositions are administered
parenterally, the invention provides pharmaceutical compositions
that comprise a solution of the agents described above, e.g.,
proteins or polypeptides of the invention, dissolved or suspended
in a pharmaceutically acceptable carrier, preferably an aqueous
carrier. A variety of aqueous carriers may be used, e.g., water,
buffered water, saline, glycine and the like. These compositions
may be sterilized by conventional, well known methods, e.g.,
sterile filtration. The resulting aqueous solutions may be packaged
for use as is, or lyophilized for combination with a sterile
solution prior to administration. The compositions may also contain
pharmaceutically acceptable auxiliary substances as required to
approximate physiological conditions, such as pH adjusting and
buffering agents, tonicity adjusting agents, wetting agents, and
the like, for example sodium acetate, sodium lactate, sodium
chloride, potassium chloride, calcium chloride, sorbitan
monolaurate, triethanolamine oleate, etc.
[0065] For solid compositions, conventional nontoxic solid carriers
may be used which include, for example, pharmaceutical grades of
mannitol, lactose starch, magnesium stearate, sodium saccharin,
talcum, cellulose, glucose, sucrose, magnesium carbonate, and the
like. For oral administration, a pharmaceutically acceptable
nontoxic composition may be formed by incorporating any of the
normally employed excipients, such as the previously listed
carriers, and generally, 10-95% of active ingredient, and more
preferably 25-75% active ingredient. In addition, for oral
administration of peptide based compounds, the pharmaceutical
compositions may include the active ingredient as part of a matrix
to prevent proteolytic degradation of the active ingredient by
digestive process, e.g., by providing the pharmaceutical
composition within a liposomal composition, according to methods
well known in the art. See, e.g., Remington's Pharmaceutical
Sciences, Mack Publishing Co., 17th Ed. (1985).
[0066] For aerosol administration, the polypeptides are generally
supplied in finely divided form along with a surfactant or
propellant. Preferably, the surfactant will be soluble in the
propellant. Representative of such agents are the esters or partial
esters of fatty acids containing from 6 to 22 carbon atoms, such as
caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic,
olesteric and oleic acids, with an aliphatic polyhydric alcohol or
its cyclic anhydride. Mixed esters, such as mixed or natural
glycerides may be employed. A carrier can also be included, as
desired, as with, e.g., lecithin for intranasal delivery.
[0067] The amount of the above compositions to be administered to
the patient will vary depending upon what is to be administered to
the patient, the state of the patient, and the manner of
administration. Typically, the polypeptides are administered in an
amount sufficient to affect the growth factor activation cascade,
and thereby cure or at least partially arrest the symptoms of the
disease which is sought to be treated, and its associated
complications. An amount adequate to accomplish this is termed "a
therapeutically effective amount" as described below. Amounts
effective for this use will depend many factors, including the
severity of the disorder and the weight and general state of the
patient, but will generally be in the range of from about 1 mg to
about 5 g of active agent per day, preferably from About 50 mg per
day to about 500 mg per day, and more preferably, from about 50 mg
to about 100 mg per day, for a 70 kg patient.
[0068] IV. Nucleic Acids and Expression Vectors
[0069] In addition to the above described polypeptides, the present
invention also provides isolated nucleic acids encoding these
polypeptides, as well as expression vectors which include these
polynucleotides. Generally, the isolated nucleic acids of the
present invention encode a polypeptide which is capable of
associating with GRB2, and/or possesses inositol polyphosphate
5-phosphatase activity. In preferred aspects, the nucleic acids of
the invention encode a polypeptide having an amino acid sequence
that is substantially homologous to the amino acid sequence shown
in FIG. 10. More preferred are those isolated nucleic acid
sequences that are substantially homologous to the nucleotide
sequence shown in FIG. 10, or fragments thereof, and most preferred
are those nucleic acid sequences having the nucleotide sequence
shown in FIG. 10.
[0070] "Nucleic acids" of the present invention include RNA, cDNA,
genomic DNA, synthetic forms and mixed polymers, both sense and
antisense strands. Furthermore, different alleles of each isoform
are also included. The present invention also provides recombinant
nucleic acids which are not otherwise naturally occurring. The
nucleic acids described herein also include self replicating
plasmids and infectious polymers of DNA or RNA. Unless specified
otherwise, conventional notation for nucleic acids is used herein.
For example, as written, the left hand end of a single stranded
polynucleotide sequence is the 5'-end, whereas the right-hand end
is the 3'-end. The left hand direction of double-stranded
polynucleotide sequences is referred to as the 5' direction. The
direction of 5' to 3' addition of nascent RNA transcripts is
referred to as the transcription direction; sequence regions on the
DNA strand having the same sequence as the RNA and which are 5' to
the 5' end of the RNA transcript are referred to as "upstream
sequences"; sequence regions on the DNA strand having the same
sequence as the RNA and which are 3' to the 3' end of the RNA
transcript are referred to as "downstream sequences".
[0071] The nucleic acids of the present invention may be present in
whole cells, cell lysates or in partially pure or substantially
pure or isolated form. When referring to nucleic acids, the terms
"substantially pure" or "isolated" generally refer to the nucleic
acid separated from contaminants with which it is generally
associated, e.g., lipids, proteins and other nucleic acids. The
substantially pure or isolated nucleic acids of the present
invention will be greater than about 50% pure. Typically, these
nucleic acids will be more than about 60% pure, more typically,
from about 75% to about 90% pure, and preferably, from about 95% to
about 98% pure.
[0072] The DNA compositions will generally include a coding region
which encodes a polypeptide possessing inositol polyphosphate
5-phosphatase activity and capable of associating with GRB2.
Preferred nucleic acids will typically encode polypeptides having
an amino acid sequence which is substantially homologous to the
amino acid sequence shown in FIG. 10 (SEQ ID NO:2), or biologically
active fragments thereof. More preferred nucleic acids will
comprise a segment having more than about 20 contiguous nucleotides
from the nucleotide sequence shown in FIG. 10 (SEQ ID NO:1), with
still more preferred nucleic acids having a nucleotide sequence
that is substantially homologous to the nucleotide sequence shown
in FIG. 10 (SEQ ID No:1). Most preferred nucleic acids are those
which include the nucleotide sequence shown in FIG. 10 (SEQ ID
NO:1).
[0073] The phrase "nucleic acid sequence encoding" refers to a
nucleic acid which directs the expression of a specific protein or
peptide. The nucleic acid sequences include both the DNA strand
sequence that is transcribed into RNA and the RNA sequence that is
translated into protein. The nucleic acid sequences include both
the full length nucleic acid sequences as well as non-full length
sequences derived from the full length protein. It being further
understood that the sequence includes the degenerate codons of the
native sequence or sequences which may be introduced to provide
codon preference in a specific host cell.
[0074] Substantial homology in the nucleic acid context means that
the segments, or their complementary strands, when compared, are
the same when properly aligned, with the appropriate nucleotide
insertions or deletions, in at least about 60% of the nucleotides,
typically, at least about 70%, more typically, at least about 80%,
usually, at least about 90%, and more usually, at least about 95%
to 98% of the nucleotides. Alternatively, substantial homology
exists when the segments will hybridize under selective
hybridization conditions to a strand, or its complement, typically
using a sequence of at least about 20 contiguous nucleotides
derived from the nucleotide sequence shown in FIG. 10. However,
larger segments will usually be preferred, e.g., at least about 30
contiguous nucleotides, more usually about 40 contiguous
nucleotides, and preferably more than about 50 contiguous
nucleotides. Selective hybridization exists when hybridization
occurs which is more selective than total lack of specificity. See,
Kanehisa, Nucleic Acid Res. 12:203-213 (1984).
[0075] There are various methods of isolating the nucleic acids
which encode the polypeptides of the present invention. Typically,
the DNA is isolated from a genomic or cDNA library using labeled
oligonucleotide probes specific for sequences in the desired DNA.
Restriction endonuclease digestion of genomic DNA or cDNA
containing the appropriate genes can be used to isolate the DNA
encoding the polypeptides of the invention. From the nucleotide
sequence given in FIG. 10, a panel of restriction endonucleases can
be constructed to give cleavage of the DNA in desired regions,
i.e., to obtain segments which encode biologically active fragments
of the polypeptides of the invention. Following restriction
endonuclease digestion, DNA encoding the polypeptides of the
invention is identified by its ability to hybridize with a nucleic
acid probe in, for example a Southern blot format. These regions
are then isolated using standard methods. See, e.g., Sambrook, et
al., supra.
[0076] The polymerase chain reaction, or "PCR" can also be used to
prepare nucleic acids which encode the polypeptides of the present
invention. PCR technology is used to amplify nucleic acid sequences
of the desired nucleic acid, e.g., the DNA which encodes the
polypeptides of the invention, directly from mRNA, cDNA, or genomic
or cDNA libraries. Alternatively, solid phase oligonucleotide
synthesis methods may also be employed to produce the nucleic acids
described herein. Such methods include the phosphoramidite method
described by, e.g., Beaucage and Carruthers, Tetrahedron Lett.
22:1859-1862 (1981), or the triester method according to Matteucci,
et al., J. Am. Chem. Soc., 103:3185 (1981), both incorporated
herein by reference. A double stranded fragment may then be
obtained, if desired, by annealing the chemically synthesized
single strands together under appropriate conditions or by
synthesizing the complementary strand using DNA polymerase with an
appropriate primer sequence.
[0077] Appropriate primers and probes for amplifying the nucleic
acids described herein, may be generated from analysis of the
nucleic acid sequences described herein, e.g. at FIG. 10. Briefly,
oligonucleotide primers complementary to the two 3' borders of the
DNA region to be amplified are synthesized. The PCR is then carried
out using the two primers. See, e.g., PCR Protocols: A Guide to
Methods and Applications (Innis, M., Gelfand, D., Sninsky, J. and
White, T., eds.) Academic Press (1990). Primers can be selected to
amplify various sized segments from the nucleic acid sequence.
[0078] The present invention also includes fragments of the above
described nucleic acids. Such fragments will generally comprise a
segment of from about 15 to about 150 nucleotides. These fragments
can be useful as oligonucleotide probes in the methods of the
present invention, or alternatively to encode the polypeptides or
biologically active fragments of the present invention, described
herein. Also provided are substantially similar nucleic acid
sequences, allelic variations and natural or induced sequences of
the above described nucleic acids. Also included are chemically
modified and substituted nucleic acids, e.g. those which
incorporate modified nucleotide bases or which incorporate a
labelling group.
[0079] In one aspect, cDNA encoding the polypeptides of the present
invention, or fragments thereof, may be readily employed as nucleic
acid probes useful for obtaining genes which encode the
polypeptides of the present invention. "Nucleic acid probes" may be
DNA or RNA fragments. DNA fragments can be prepared, for example,
by digesting plasmid DNA, or by use of PCR, or synthesized by
either the phosphoramidite method described above. Where a specific
sequence for a nucleic acid probe is given, it is understood that
the complementary strand is also identified and included. The
complementary strand will work equally well in situations where the
target is a double-stranded nucleic acid.
[0080] Typical nucleic acid probes may be readily derived from the
nucleotide sequence shown in FIG. 10 (SEQ ID NO:1), or
alternatively, may be prepared from the amino acid sequence of the
GA5Ptase protein, as shown in FIG. 10 (SEQ ID NO:2). In particular,
probes may be prepared based upon segments of the amino acid
sequence which possess relatively low levels of degeneracy, i.e.,
few or one possible nucleic acid sequences which encode therefor.
Suitable synthetic DNA fragments may then be prepared. Such cDNA
probes may be used in the design of oligonucleotide probes and
primers for screening and cloning genes which encode the
polypeptides of the invention or related polypeptides, e.g., using
well known PCR techniques. These nucleic acids, or fragments may
comprise part or all of the cDNA sequence that encodes the
polypeptides of the present invention. Effective cDNA probes may
comprise as few as 15 consecutive nucleotides in the cDNA sequence,
but will often comprise longer segments. Further, these probes may
further comprise an additional nucleotide sequence, such as a
transcriptional primer sequence for cloning, or a detectable group
for easy identification and location of complementary
sequences.
[0081] cDNA or genomic libraries of various types may be screened
for new alleles or related sequences using the above probes. The
choice of cDNA libraries normally corresponds to tissue sources
which are abundant in mRNA for the desired polypeptides. Phage
libraries are normally preferred, but plasmid libraries may also be
used. Clones of a library are spread onto plates, transferred to a
substrate for screening, denatured, and probed for the presence of
the desired sequences.
[0082] In addition to comprising a segment which encodes one or
more of the above described polypeptides or biologically active
fragments, the nucleic acids of the present invention may also
comprise a segment encoding a heterologous protein, such that the
gene is expressed to produce the two proteins as a fusion protein,
as substantially described above.
[0083] Typically, the nucleic acids of the present invention will
be used in expression vectors for the preparation of the
polypeptides of the present invention, namely those polypeptides
which possess inositol polyphosphate 5-phosphatase activity and
that are capable of associating with GRB2. The phrase "expression
vector" generally refers to nucleotide sequences that are capable
of affecting expression of a structural gene in hosts compatible
with such sequences. These expression vectors typically include at
least suitable promoter sequences and optionally, transcription
termination signals. Additional factors necessary or helpful in
effecting expression may also be used as described herein. DNA
encoding the polypeptides of the present invention will typically
be incorporated into DNA constructs capable of introduction into
and expression in an in vitro cell culture. Often, the nucleic
acids of the present invention may be used to produce a suitable
recombinant host cell. Specifically, DNA constructs will be
suitable for replication in a prokaryotic host, such as bacteria,
e.g., E. coli, or may be introduced into a cultured mammalian,
plant, insect, yeast, fungi or other eukaryotic cell line. DNA
constructs prepared for introduction into a particular host, e.g.,
bacteria or yeast, will typically include a replication system
recognized by the host, the intended DNA segment encoding the
desired polypeptide, and transcriptional and translational
initiation and termination regulatory sequences operably linked to
the polypeptide encoding segment. A DNA segment is operably linked
when it is placed into a functional relationship with another DNA
segment. For example, a promoter or enhancer is operably linked to
a coding sequence if it stimulates the transcription of the
sequence. DNA for a signal sequence is operably linked to DNA
encoding a polypeptide if it is expressed as a preprotein that
participates in the secretion of the polypeptide. Generally, DNA
sequences that are operably linked are contiguous, and in the case
of a signal sequence both contiguous and in reading phase. However,
enhancers need not be contiguous with the coding sequences whose
transcription they control. Linking is accomplished by ligation at
convenient restriction sites or at adapters or linkers inserted in
lieu thereof. The selection of an appropriate promoter sequence
will generally depend upon the host cell selected for the
expression of the DNA segment. Examples of suitable promoter
sequences include prokaryotic, and eukaryotic promoters well known
in the art. See, e.g., Sambrook et al., Molecular Cloning: A
Laboratory Manual (2d ed.), vols. 1-3 Cold Spring Harbor Laboratory
(1989). The transcriptional regulatory sequences will typically
include a heterologous enhancer or promoter which is recognized by
the host. The selection of an appropriate promoter will depend upon
the host, but promoters such as the trp, lac and phage promoters,
tRNA promoters and glycolytic enzyme promoters are known and
available. See Sambrook et al., (1989).
[0084] Conveniently available expression vectors which include the
replication system and transcriptional and translational regulatory
sequences together with the insertion site for the polypeptide
encoding segment may be employed. Examples of workable combinations
of cell lines and expression vectors are described in Sambrook et
al., and in Metzger et al., Nature 334:31-36 (1988). For example,
where an insect host cell is selected as-the host cell of choice to
express the polypeptide, the cDNA encoding the polypeptides of the
invention may be cloned into a baculovirus expression vector (e.g.
pV-IKS). The recombinant baculovirus may then be used to transfect
a suitable insect host cell, e.g., Sf9 cells, which may then
express the polypeptide. See, e.g., D. K. Morrison et al., Cell
58:649-657 (1989), M. D. Summers and G. E. Smith, A Manual of
Methods for Baculovirus Vectors and Insect Cell Culture Procedures,
Texas Agricultural Station, College Station, Tex. (1987).
[0085] V. Cell Lines
[0086] The vectors containing the DNA segments of interest, e.g.,
those encoding polypeptides of the invention as described above,
can be transferred into the host cell by well known methods which
may vary depending upon the type of host cell used. For example,
calcium chloride transfection is commonly used for prokaryotic
cells, whereas calcium phosphate treatment may be used for other
hosts. See, Sambrook et al. The term "transformed cell" as used
herein, includes the progeny of originally transformed cells, which
progeny express the nucleic acids of the invention.
[0087] Techniques for manipulation of nucleic acids which encode
the polypeptides of the present invention, i.e., subcloning the
nucleic acids into expression vectors, labeling probes, DNA
hybridization and the like, are generally described in Sambrook, et
al., supra.
[0088] In recombinant methods, generally the nucleic acid encoding
a peptide of the present invention is first cloned or isolated in a
form suitable for ligation into an expression vector. After
ligation, the vectors containing the nucleic acid fragments or
inserts are introduced into a suitable host cell, for the
expression of the polypeptide of the invention. The polypeptides
may then be purified or isolated from the host cells. Methods for
the synthetic preparation of oligonucleotides are generally
described in Gait, Oligonucleotide Synthesis: A Practical Approach,
IRL Press (1990).
[0089] VI. Antibodies
[0090] The nucleic acids and polypeptides of the present invention
or fragments thereof, are also useful in producing antibodies,
either polyclonal or monoclonal, which are specifically
immunoreactive with the polypeptides of the present invention.
[0091] The phrase "specifically immunoreactive," when referring to
the interaction between an antibody of the invention and a
particular protein, refers to an antibody that specifically
recognizes and binds with relatively high affinity to the
particular protein, such that this binding is determinative of the
presence of the protein in a heterogeneous population of proteins
and other biologics. Thus, under designated immunoassay conditions,
the specified antibodies bind to a particular protein and do not
bind in a significant amount to other proteins present in the
sample. A variety of immunoassay formats may be used to select
antibodies specifically immunoreactive with a particular protein.
For example, solid-phase ELISA immunoassays are routinely used to
select monoclonal antibodies specifically immunoreactive with a
protein. See Harlow and Lane (1988) Antibodies, A Laboratory
Manual, Cold Spring Harbor Publications, New York, for a
description of immunoassay formats and conditions that can be used
to determine specific immunoreactivity.
[0092] For production of polyclonal antibodies, an appropriate
target immune system is selected, typically a mouse or rabbit, but
also including goats, sheep, cows, guinea pigs, monkeys and rats.
The substantially purified antigen or plasmid is presented to the
immune system in a fashion determined by methods appropriate for
the animal. These and other parameters are well known to
immunologists. Typically, injections are given in the footpads,
intramuscularly, intradermally or intraperitoneally. The
immunoglobulins produced by the host can be precipitated, isolated
and purified by routine methods, including affinity
purification.
[0093] For monoclonal antibodies, appropriate animals will be
selected and the desired immunization protocol followed. After the
appropriate period of time, the spleens of these animals are
excised and individual spleen cells are fused, typically, to
immortalized myeloma cells under appropriate selection conditions.
Thereafter, the cells are clonally separated and the supernatants
of each clone are tested for the production of an appropriate
antibody specific for the desired region of the antigen. Techniques
for producing antibodies are well known in the art. See, e.g.,
Goding et al., Monoclonal Antibodies: Principles and Practice (2d
ed.) Acad. Press, N.Y., and Harlow and Lane, Antibodies: A
Laboratory Manual, Cold Spring Harbor Laboratory, New York (1988).
Other suitable techniques involve the in vitro exposure of
lymphocytes to the antigenic polypeptides or alternatively, to
selection of libraries of antibodies in phage or similar vectors.
Huse et al., Generation of Large Combinatorial Library of the
Immunoglobulin Repertoire in Phage Lambda, Science 246:1275-1281
(1989). Monoclonal antibodies with affinities of 10.sup.8
liters/mole, preferably 10.sup.9 to 10.sup.10 or stronger, will be
produced by these methods.
[0094] The antibodies generated can be used for a number of
purposes, e.g., as probes in immunoassays, for inhibiting
GRB2/GA5Ptase interaction, or interaction with other ligands,
thereby inhibiting or reducing the growth factor signaling cascade,
in diagnostics or therapeutics, or in research to further elucidate
the mechanism of growth factor activation pathways, and
particularly, the growth factor activation of Ras. Where the
antibodies are used to block the interaction between two signaling
molecules, e.g. GRB2 and GA5Ptase, the antibody will generally be
referred to as a "blocking antibody."
[0095] The antibodies of the present invention can be used with or
without modification. Frequently, the antibodies will be labeled by
joining, either covalently or non-covalently, a substance which
provides for a detectable signal. Such labels include those that
are well known in the art, such as the labels described previously
for the polypeptides of the invention. Additionally, the antibodies
of the invention may be chimeric, human-like or humanized, in order
to reduce their potential antigenicity, without reducing their
affinity for their target. Chimeric, human-like and humanized
antibodies have generally been described in the art. Generally,
such chimeric, human-like or humanized antibodies comprise
hypervariable regions, e.g., complementarity determining regions
(CDRs) from a mammalian animal, i.e., a mouse, and a human
framework region. See, e.g., Queen, et al., Proc. Nat'l Acad. Sci.
USA 86:10029 (1989), Verhoeyan, et al., Science 239:1534-1536
(1988). By incorporating as little foreign sequence as possible in
the hybrid antibody, the antigenicity is reduced. Preparation of
these hybrid antibodies may be carried out by methods well known in
the art.
[0096] Preferred antibodies are those monoclonal or polyclonal
antibodies which specifically recognize and bind the polypeptides
of the invention. Accordingly, these preferred antibodies will
specifically recognize and bind the polypeptides which have an
amino acid sequence that is substantially homologous to the amino
acid sequence shown in FIG. 10 (SEQ ID NO:2). Still more preferred
are antibodies which are capable of forming an antibody-ligand
complex with the polypeptides of the invention, whereby the ability
of the polypeptide to associate with GRB2, in vitro, is reduced,
e.g. blocking antibodies.
[0097] VII. Methods of Use
[0098] The polypeptides, antibodies and nucleic acids of the
present invention may be used in a variety of important
applications. Such applications include but are not limited to
screening applications for identifying compounds that affect the
growth factor signal transduction pathways, also termed "signaling
cascades," and therapeutic applications for the treatment of
proliferative cell disorders.
[0099] A. Screening Applications
[0100] In a particular aspect, the present invention provides
methods of screening test compounds to determine whether the test
compounds are capable of affecting growth factor activation signal
transduction pathways. More particularly, the methods described
herein are used to screen compounds for there ability to affect the
interaction of the polypeptides of the invention, and their
respective substrates and ligands, as these interactions are
involved in growth factor activation signal transduction pathways,
and particularly, the growth factor activation of Ras.
[0101] In one aspect, the present invention provides methods of
screening whether a test compound is an agonist or antagonist of
GRB2-mediated signal transduction. More specifically, the
polypeptides of the present invention can be used as a model system
of GRB2/GA5Ptase interaction, to screen for compounds which affect
this interaction. An agonist, antagonist or test compound may be a
chemical compound, a mixture of chemical compounds, a biological
macromolecule, or an extract made from biological materials such as
bacteria, plants, fungi, or animal cells or tissues. Typically,
test compounds may include structural analogs or peptidomimetics
which are derived from the polypeptides described herein, and
particularly the biologically active fragments. Test compounds are
evaluated for potential activity as agonists or antagonists of
functions which result in signal transduction, by inclusion in
screening assays described herein. An "agonist" will enhance the
particular observed activity, e.g. GRB2 association or 5-phosphate
cleavage, while an "antagonist" will diminish the particular
observed activity. The terms "agonist" and "antagonist", as used
herein, do not imply a particular mechanism of function.
Particularly targeted test compounds include polypeptide fragments
of the polypeptides of the present invention and structural analogs
or peptidomimetics of these peptides.
[0102] In a first aspect, the screening methods of the present
invention typically involve the incubation of a polypeptide of the
present invention, or a GRB2 associating fragment thereof, in the
presence of GRB2 as well as a particular test compound. The mixture
is then assayed to determine the levels of GRB2/polypeptide
interaction by determining the amount of GRB2/polypeptide complex
formed in the presence and absence of the test compound. Where the
presence of the test compound results in an increase or decrease in
the amount of complex formed, it will be indicative that the test
compound is an agonist or antagonist of GRB2-mediated signal
transduction, respectively.
[0103] For determination of the amount of GRB2/polypeptide complex
formed, one may employ any number of a variety of well known assay
methods. For example, immunoprecipitation of one polypeptide or
protein that participates in the complex, followed by assaying the
immunoprecipitate for the other participant, will generally
indicate the amount of complex formed. For example, following
co-incubation of the polypeptide of the invention with GRB2, in the
presence of the test compound, the polypeptide may be
immunoprecipitated using an antibody that recognizes and
specifically binds an epitope in the polypeptide's sequence. This
epitope may be a sequence that is endogenous to the polypeptide or
may be exogenously introduced as a labeling group, e.g., an
antibody binding epitope tag or assayable enzyme. Following
immunoprecipitation, the precipitate may be assayed for the
presence of the other participant in the complex, e.g., GRB2, which
may also be labelled, albeit in a distinguishing manner, e.g., a
radiolabel, separately assayable enzyme, distinct antibody binding
epitope tag or the like.
[0104] In an alternative method, one of the participants in complex
formation, e.g., a polypeptide of the invention, may be coupled
with an appropriate reporter group, while another participant,
e.g., GRB2, is immobilized upon a solid support. Useful reporter
groups, or labels have been previously described herein, including,
e.g. radiolabels, such as, .sup.125I, .sup.32P or .sup.35S,
fluorescent or chemiluminescent groups, substrates, cofactors,
inhibitors, affinity ligands, antibody binding epitope tags, or
enzymes which are capable of being assayed, e.g. horseradish
peroxidase, luciferase, or other readily assayable enzymes. These
enzyme groups may be attached to the polypeptide of the present
invention by chemical means or expressed as a fusion protein, as
already described.
[0105] Screening is then carried out by contacting the labeled
participant with the immobilized participant in the presence and
absence of the test compound. The amount of reporter group that
binds to the solid support-bound participant is indicative of the
amount of complex formed. The level of polypeptide bound in the
presence of the test compounds may then be compared to the levels
bound in control experiments, e.g., in the absence of the test
compounds.
[0106] A variety of solid supports may be used in these screening
methods. For example, blot formats may be employed where the
protein or polypeptide is spotted on an appropriate substrate,
e.g., nitrocellulose, PVDF and the like. Alternatively, resin or
bead formats may also be used as the solid supports, including
beads of agarose, cellulose, silica, polystyrene, divinylbenzene
and the like.
[0107] Where the test compound results in an increase in the level
of polypeptide which associates with GRB2, it is indicative that
the test compound is an agonist of GRB2/GA5Ptase interaction, and
more particularly, the GRB2-mediated signal transduction pathway.
Similarly, where the presence of the test compound results in a
decrease in the level of polypeptide GRB2 complex formed, it is
indicative that the test compound is an antagonist of that
interaction and signal transduction pathway.
[0108] In another aspect, the polypeptides of the present invention
can be used as a model system for screening test compounds to
identify agonists or antagonists of inositol polyphosphate
5-phosphatase activity generally, and in particular the inositol
polyphosphate 5-phosphatase activity of GA5Ptase. Because the
processing of phosphatidylinositols and particularly, the cleavage
of the 5-phosphate from PtdIns(3,4,5)P.sub.3 has been linked to the
activation of Ras, it will be desirable to provide a model system
for screening compounds which block or otherwise inhibit this
conversion, and thereby block Ras activation.
[0109] The methods for determining whether a test compound is an
agonist or antagonist of the inositol polyphosphate 5-phosphatase
activity of the polypeptides of the invention, are generally
similar to the above described methods. In particular, these
methods comprise incubating a polypeptide having the desired
inositol polyphosphate 5-phosphatase activity, e.g., GA5Ptase or
catalytically active fragments thereof, with its substrate in the
presence and absence of the test compound. This incubation may be
carried out in vitro or in vivo, e.g., using a transgenic animal
model which has been engineered to express the polypeptides of the
invention. For the polypeptides of the present invention, the
appropriate substrate may generally be selected from, e.g.
D-myo-Inositol 1,3,4,5-tetrakisphosphate ("Ins(1,3,4,5)P.sub.4")
and Phosphatidylinositol 3,4,5-trisphosphate
("PtdIns(3,4,5)P.sub.3"). Following a prescribed reaction time the
reaction mixture is assayed for the production of the products of
inositol polyphosphate 5-phosphatase activity on these substrates.
Assaying for production of the various reaction products, e.g.
Ins(1,3,4)P.sub.3 from Ins(1,3,4,5)P.sub.4, or PtdIns(3,4)P.sub.2
from PtdIns(3,4,5)P.sub.3, may be carried out by a variety of
methods known in the art. For example, HPLC analysis can be readily
used to quantitatively identify the above described reaction
products, using, e.g. tritiated substrates, and the like (see
Example 2, below). Similarly, on a more qualitative level, thin
layer chromatography (TLC) can also be used to identify reaction
products. The levels of the above described reaction products
produced in the presence and absence of the test compound are then
compared. Where the presence of the test compound results in an
increase or decrease in the level of the reaction product produced
by the polypeptide, it is indicative that the test compound is an
agonist or antagonist of inositol polyphosphate 5-phosphatase
activity, respectively, and more particularly, the inositol
polyphosphate 5-phosphatase activity described herein.
[0110] In a related embodiment, the present invention also provides
kits for carrying out the above described screening methods. The
kits of the present invention generally include a polypeptide of
the present invention, e.g. the GA5Ptase polypeptide or a
biologically active fragment thereof, as well as a ligand of the
polypeptide where the binding activity is to be screened, e.g.,
GRB2, or a substrate of that polypeptide where the inositol
polyphosphate 5-phosphatase activity is to be screened, e.g.,
Ins(1,3,4,5)P.sub.4, or PtdIns(3,4,5)P.sub.3. One or more of these
components may generally be provided in premeasured aliquots. The
aliquots can be contained in any suitable container such as a vial
or a tube. The polypeptide component can be provided in solution or
in lyophilized form, and may be immobilized. The polypeptide
preparation may also contain preservatives such as sodium azide or
protease inhibitors such as EDTA. A carrier protein such as BSA or
ovalbumin, usually between 0.5-5%, may also be included to
stabilize the polypeptide. The solution form of GA5Ptase may
contain up to 50% glycerol if the enzyme is to be stored frozen,
e.g., at -20.degree. C. to -70.degree. C. If the GA5Ptase is
provided in lyophilized form, the kit can include a reconstitution
buffer to reconstitute the polypeptide, as well as a reaction
buffer. Alternatively, the polypeptide can be added to the reaction
buffer and the solution freeze dried. This form can be readily
reconstituted in distilled water with the necessary salt components
already present for the particular reaction to be screened, so that
no additional reaction buffer need be supplied. Thus, depending on
the form and composition of the polypeptide preparation, different
buffers may be included in the kit and they may be provided in more
than one aliquot. Although described in substantial detail herein,
these buffers are generally optional. The appropriate substrate or
ligand, depending upon the particular screening method used, may be
provided in a similar fashion to that of the polypeptide component.
The kits will also typically include additional reagents for
carrying out the particular method, e.g. stains for detection,
antibodies, solid supports, and the like, as well as detailed
operating specifications for their use. For example, where binding
interactions are being screened, the ligand component may generally
be supplied within the kit, already coupled to an appropriate
support.
[0111] Once identified, particular agonists or antagonists may then
be used to enhance or block the activity of the polypeptides of the
present invention. This may be particularly useful in therapeutic
applications (see discussion, below).
[0112] B. Therapeutic Applications
[0113] In addition to the above described uses, the polypeptides
and nucleic acids of the present invention may also be used in
therapeutic applications for the treatment of human or non-human
mammalian patients. The term "treatment" refers to the full
spectrum of treatment for a given disorder from which the patient
is suffering, including alleviation of some, most or all symptoms
resulting from that disorder, to an outright cure for the
particular disorder to prevention of the onset of the disorder.
[0114] As described previously herein, the polypeptides of the
present invention have been implicated as providing a critical step
in the growth factor activation cascade, and particularly the
activation of Ras. Activation of Ras has been associated with a
variety of proliferative disorders including atherosclerosis,
inflammatory joint diseases, psoriasis, restenosis following
angioplasty, and cancer.
[0115] Accordingly, treatment of the above described disorders can
generally be carried out by blocking or inhibiting activation of
Ras. This may generally be accomplished by blocking or inhibiting
one or more of the activities of the GA5Ptase polypeptide which are
involved in the signal transduction pathway which activates Ras,
e.g., the polypeptide's ability to bind GRB2, or the polypeptide's
ability to bind to or catalyze the dephosphorylation of its
substrate.
[0116] Generally, inhibition of the particular activity may be
carried out by providing a polypeptide of the invention which will
compete with the endogenous GA5Ptase protein. For example, by
administering to a patient an effective amount of a GRB2
associating fragment of the polypeptides, as described herein, one
can out compete the endogenous GRB2 associating activity of the
endogenous GA5Ptase protein, and thereby reduce the level of Ras
activation. Similarly, by administering to the patient an effective
amount of a substrate binding, although non-catalytic, fragment of
the GA5Ptase peptide, as described herein, one can effectively out
compete the naturally occurring GA5Ptase protein, and thus block
cleavage of the substrate, and the ensuing activation cascade
reactions.
[0117] The quantities of reagents necessary for effective therapy,
also referred to herein as an "effective amount," or
"therapeutically effective amount," will depend upon many different
factors, including means of administration, target site,
physiological state of the patient and other medicants
administered. Thus, treatment doses will need to be titrated to
optimize safety and efficacy. Typically, dosages used in vitro may
provide useful guidance in the amounts useful for in situ
administration of these reagents. Animal testing of effective doses
for treatment of particular disorders will provide further
predictive indication of human dosage. Generally, therapeutically
effective amounts of the GA5Ptase containing polypeptides of the
present invention will be from about 0.0001 to about 10 mg/kg, and
more usually, from about 0.001 to about 0.1 mg/kg of the host's
body weight. Various considerations are described, e.g., in Gilman
et al., (Eds.), Goodman and Gilman's: The Pharmacological Basis of
Therapeutics, (8th ed. 1990), Pergamon Press, and Remington's
Pharmaceutical Sciences (7th ed. 1985) Mack Publishing Co., Easton,
Penn. Methods of administration, also discussed in the above
references, include, e.g., oral, intravenous, intraperitoneal or
intramuscular administration, and local administration, including
topical, transdermal diffusion and aerosol administration, for
therapeutic, and/or prophylactic treatment. The active agent, i.e.,
the polypeptide component, will generally be administered in a
composition additionally comprising a pharmaceutically acceptable
carrier. Suitable pharmaceutically acceptable carriers include
water, saline, buffers and other compounds described in, e.g., the
Merck Index, Merck and Co., Rahway, N.J.
[0118] Constituents of pharmaceutical compositions, in addition to
the active agents, include those generally known in the art for the
various administration methods used. For example, oral forms
generally include powders, tablets, pills, capsules, lozenges and
liquids. Similarly, intravenous, intraperitoneal or intramuscular
formulations will generally be dissolved or suspended in a
pharmaceutically acceptable carrier, e.g., water, buffered water,
saline and the like. Additionally, these compositions may include
additional constituents which may be required to approximate
physiological conditions, such as pH adjusting and buffering
agents, tonicity adjusting agents, wetting agents and the like. For
solid compositions, conventional nontoxic solid carriers may be
used which include, e.g., pharmaceutical grades of mannitol,
lactose, starch, magnesium stearate, sodium saccharin, talcum,
cellulose, glucose, sucrose, magnesium carbonate and the like.
[0119] Administration may also be carried out by way of a
controlled release composition or device, whereby a slow release of
the active ingredient allows continuous administration over a
longer period of time.
[0120] Additionally, inositol polyphosphates play important roles
in cell signaling pathways, the present invention can provide an
exogenous regulatory mechanism in the treatment of disorders where
these regulatory mechanisms are disfunctional. In particular, the
treatment of a particular disorder may comprise gene therapy
techniques involving the mutation, dysregulation or augmentation of
levels of GA5ptase. For example, gene therapy techniques may
involve the introduction into afflicted cells, of genes which
encode a protein or polypeptide which possesses the activity of
GA5ptase. This exogenously introduced protein may then augment
existing levels of this activity in cells that may be otherwise
deficient.
[0121] Strategies for gene therapy are reviewed in Friedmann,
Science 244:1275 (9189). Genetic constructs encoding the PTB domain
or functional derivative of that domain, can be used in these gene
therapy techniques. Delivery of the genetic construct of interest,
i.e., the nucleic acid encoding a GA5ptase protein or fragment, may
be accomplished in vivo by administering the therapy vector to an
individual patient, typically by systemic administration (e.g.,
intravenous, intraperitoneal, intramuscular, subdermal, or
intracranial administration). Alternatively, the vector may be used
to deliver nucleic acids to cells ex vivo, such as cells explanted
from an individual patient or universal donor hematopoietic stem
cells, neurons, etc, e.g., by transfection of the cells with
nucleic acids of interest cloned into retroviruses. Following
transfection, the cells are reimplanted into the patient, usually
after selection for cells which have incorporated the nucleic acid.
The infusion into the patient of transfected cells can replace
cells which are dysfunctional for the particular regulatory scheme
which results in the disorder being treated.
[0122] C. Affinity Probes
[0123] Because the polypeptides of the present invention associate
with GRB2 proteins, and specifically, via the SH3 domains, these
proteins or their biologically active fragments may be particularly
useful as affinity probes or ligands. In particular, the proteins
can be used to identify or capture GRB2 proteins from a mixture of
different proteins.
[0124] Typically, use of the polypeptides of the present invention
in identifying GRB2 proteins in a mixture of proteins may be
carried out using a Western blotting format. In particular, the
mixture of proteins may be immobilized on a solid support, as
described above. Immobilization may include simple spotting,
electroblotting of SDS-PAGE gels and the like. The blot is then
blocked using a nonspecific protein, i.e., BSA. Labeled
polypeptides of the present invention may then be used to
interrogate the blot, binding to the immobilized GRB2.
[0125] The polypeptides of the present invention may also be used
as affinity ligands to purify Grb2 proteins from a mixture of
proteins. In particular, the polypeptide of the invention is
coupled to a solid support. The support bound polypeptide is then
contacted with the mixture of proteins containing the GRB2 protein
under conditions that are conducive to GA5Ptase/GRB2 binding. The
support is then washed to remove unbound and nonspecifically bound
proteins. Substantially pure GRB2 may then be readily eluted from
the support by, e.g. a change in salt, pH or buffer
concentrations.
[0126] The present invention is further illustrated by the
following examples. These examples are merely to illustrate aspects
of the present invention and are not intended as limitations of
this invention.
VIII. EXAMPLES
Example-1
Cloning and Sequence Analysis of GA5Ptase
[0127] A bacterially expressed GST-GRB2 fusion protein containing a
5 amino acid RRASV heart muscle kinase site was purified and
radioactively labeled with [.sup.32P]ATP. The purified protein was
used to screen a human placental .lambda.gt11 oligo dT primed cDNA
library (Clonetech) using the guanidine-HCl
denaturation/renaturation screening technique initially described
by Blanar and Rutter, Science 256:1014-1018 (1992). A schematic of
this protein is shown in FIG. 1. Because all GRB2, interacting
clones obtained in the first round of screening encoded catalytic
regions of protein tyrosine kinases, duplicate filters were probed
with antiphosphotyrosine antibody to screen against SH2 domain
interactions. One clone was identified that specifically interacted
with GRB2 and was not tyrosine phosphorylated. Sequencing of this
clone indicated that it was a partial cDNA clone with no similarity
to any other protein or cDNA. Multiple PXXP motifs were present,
indicating the likely contact region with the SH3 domains of GRB2.
Northern blot analysis indicated a 4.3 kb long transcript with
broad tissue distribution, the highest being in placenta. Purified
GST-GA5Ptase fragment was produced by cloning the original
.lambda.gt11 cDNA fragment (nucleotides 2687-4146) into pGex1.
Smith, et al., Gene 67:31-40 (1988).
[0128] Binding specificity of this protein fragment for GRB2 was
evaluated by Far-Western blots of the protein with roughly equal
amounts of radioactively labeled GRB2, Vav SH3-SH2--SH3 domains
(amino acids 648-844, Katzav, et al., Embo J. 8:2283-2290 (1989)),
Nck SH3--SH3--SH3 domains (amino acids 1-249, Hu, et al., Mol.
Cell. Biol. 15:1169-1174 (1995)) and p85 SH3 domain (amino acids
1-81, Klippel, et al., Mol. Cell. Biol. 12:1451-1459 (1992)). Only
GRB2 bound specifically to the GST fused fragment of the newly
cloned protein and no proteins bound GST itself. A full length cDNA
clone was obtained by screening a .lambda.gt10 human placental cDNA
library. This 4146 bp clone contained an open reading frame
encoding a 976 amino acid protein. The predicted 110 kDa protein
showed that it has significant homology to a family of proteins
known as inositol polyphosphate 5-phosphatases. FIG. 2 shows a
ribbon diagram and dendrogram indicating relative homology of
GA5Ptase to a number of inositol polyphosphate 5-phosphatases. FIG.
11 also shows a direct sequence comparison of GA5Ptase to these
other phosphatase sequences. Included in the comparison are the C.
elegans inositol polyphosphate 5-phosphatase ("celegptase") (SEQ ID
NO:3), S. cereviseae inositol polyphosphate 5-phosphatase
("ysc5ptase") (SEQ ID NO:4), GA5Ptase (SEQ ID NO:2), human 51c
("51c") (SEQ ID NO:5), the 75 kDa human platelet inositol
polyphosphate 5-phosphatase type-II ("5ptaseii") (SEQ ID NO:6), the
human ocr1 protein responsible for human oculocerebrorenal syndrome
("ocr1") (SEQ ID NO:7), Arabidopsis inositol polyphosphate
5-phosphatase ("arab5ptase") (SEQ ID NO:8) and canine inositol
polyphosphate 5-phosphatase 43 kDa ("h5ptase43") (SEQ ID NO:9). The
identified consensus sequence is also provided ("consensus") (SEQ
ID NO:10).
Example-2
Characterization of Enzymatic activity of GA5Ptase
[0129] The next step was to characterize the nature of the activity
of the GA5ptase protein. FIG. 6 illustrates the effect of varying
concentration of Ins(1,3,4,5)P.sub.4 on the rate of its hydrolysis
by GA5Ptase. FIG. 7 illustrates the coprecipitation of GA5ptase and
IP.sub.4 hydrolyzing activity.
[0130] To ensure that GA5Ptase was in fact an inositol
polyphosphate 5-phosphatase, .sup.3H-Ins(1,3,4,5)P.sub.4 (200
pmoles) was incubated with GA5Ptase (1 .mu.g) for 1 hour at
37.degree. C. An aliquot of the reaction mix was quenched with 500
.mu.l cold water, mixed with 300 cpm .sup.32P-Ins(1,4,5)P.sub.3 as
an internal standard, and analyzed by Absorbosphere.TM. Sax HPLC
using a NaPO.sub.4 gradient. FIG. 8A shows the resulting
chromatogram showing conversion of the Ins(1,3,4,5)P.sub.4 to
Ins(1,3,4)P.sub.3 by GA5Ptase.
[0131] An aliquot of the reaction mix was then incubated with a
purified recombinant inositol polyphosphate 1phosphatase (York, et
al., Proc. Nat'l Acad. Sci. USA 87:9548-9552 (1990)), quenched with
500 .mu.l cold water, mixed with 300 cpm .sup.32P-Ins(1,4)P.sub.2
as an internal standard, and analyzed using Partisil.TM. 10 Sax
HPLC using an NH.sub.4COOH gradient. FIG. 8B shows that the product
of GA5Ptase was converted by the inositol polyphosphate 1
phosphatase to Ins(3,4)P.sub.2.
[0132] A further aliquot of the original reaction mix was incubated
with a purified recombinant inositol polyphosphate 4-phosphatase,
quenched with 500 .mu.l cold water, mixed with
.sup.32P-Ins(3,4)P.sub.2 as an internal standard and again analyzed
using Partisil 10 Sax HPLC using an NH.sub.4COOH gradient. FIG. 8C
shows that the product of GA5Ptase action on Ins(1,3,4,5)P.sub.4
was converted by inositol polyphosphate 4-phosphatase to
Ins(1,3)P.sub.2. These assays confirm that GA5Ptase has inositol
polyphosphate 5-phosphatase activity.
[0133] GA5Ptase (20 ng) and 5ptase II (31 ng) were separately
incubated with 1400 cpm .sup.32P-PtdIns(3,4,5)P.sub.3 in
phosphatidylserine vesicles for 1, 3 or 10 minutes at 37.degree. C.
The reaction was stopped by addition of 30 .mu.l
chloroform/methanol (1:1). The chloroform layer was spotted on an
oxalate-dipped silica gel TLC plate and developed using a solvent
mixture of chloroform/acetone/methanol/acetic acid/water from the
TLC plate and quantified by Cerenkov radiation. Production of
PtdInsP.sub.2 from PtdIns(3,4,5)P.sub.3 is shown in FIG. 9, plotted
as a function of time. Each point shown is the average of
quadruplicate assays. The inset shows an autoradiogram of a TLC
plate indicating conversion of PtdIns(3,4,5)P.sub.3 to
PtdInsP.sub.2 by both GA5Ptase and 5ptase II.
Example-3
Co-Immunoprecipitation of GA5Ptase
[0134] Lysates from Balb 3T3 cells were immunoprecipitated with
GRB2 antibody (Transduction Laboratories) and blotted with
preimmune (P) and immune (I) GA5Ptase polyclonal antibodies.
Co-immunoprecipitation of endogenous GA5Ptase with endogenous GRB2
was detected in unstimulated Balb 3T3 cells using antibodies raised
against two different regions of GA5Ptase (amino acids 47-231 and
891-983). To define the interaction of GA5Ptase with GRB2, both
molecules were co-expressed in Cos cells and co-immunoprecipitated
(FIG. 4).
[0135] Cos7 cells were transiently transfected with GA5Ptase and
either wild type or single point mutations of GRB2 or GRB3.3.
Schematic illustrations of the sequence structure of each of these
proteins is shown in FIG. 3. Point mutations were the human
counterparts of natural C. elegans Sem-5 point mutations. After 2
days of growth, cell lysates were immunoprecipitated with either
myc antibody 9E10 (FIG. 4, odd numbered lanes) or HA antibody 12CA5
(even numbered lanes) and blotted with the same HA and myc
antibodies. Wild type GRB2 or molecules having 2 intact SH3 domains
(E89K, S9ON, GRB3.3) did bind to full length GA5Ptase (closed
circles) but not shorter GA5Ptase proteins. Mutations that disrupt
binding of either SH3 domain (P49L, G203R) markedly reduced (shaded
triangle) or eliminated (open triangle) full length GA5Ptase
binding. This illustrates that GRB2 associates with GA5Ptase
through both of its SH3 domains.
Example-4
Activation of Serum Response Element Upon co-Expression With Ras
and GRB2
[0136] NIH 3T3 cells were transiently transfected with constructs
encoding GRB2, GA5Ptase, c-Ras, GRB2/c-Ras, GA5Ptase/c-Ras,
GA5Ptase/GRB2 and GA5Ptase/c-Ras/GRB2, as listed in FIGS. 5A-D, and
the luciferase indicator plasmid p2FTL. This plasmid contains two
copies of the c-fos serum response element (SRE) (-357 to -276) and
the herpes simplex virus (HSV) thymidine kinase (TK) gene promoter
(-200 to +70) driving the firefly luciferase gene. After growth for
two days in serum depleted media, the cells were harvested and
endogenous luciferase activity was measured in relative light
units. Each value is the average of triplicate transfections, error
bars represent standard error of the mean. Point mutations in GRB2
are the same as those indicated above.
[0137] Substantial synergistic activation of the Fos promoter
occurred when all three cDNAs were expressed. GRB2 mutants that
reduce or eliminate the binding to GA5Ptase did not activate the
Fos SRE as well as wild type (FIGS. 5B and 5C), indicating the
importance of the interaction between GA5Ptase and GRB2. Platelet
inositol polyphosphate 5-phosphatase type II ("5Ptase II"), a
5ptase family member also possessing Ins(1,3,4,5)P.sub.4 and
PtdIns(3,4,5)P.sub.3 hydrolyzing activity can substitute for
GA5Ptase in its activation of cFos transcription (FIG. 5D). These
results indicate the importance of GA5Ptase activity in Fos SRE
activation.
[0138] While the foregoing invention has been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the invention. All publications and patent
documents cited in this application are incorporated by reference
in their entirety for all purposes to the same extent as if each
individual publication or patent document were so individually
denoted.
Sequence CWU 1
1
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