WO2001021794A9 - Smad associating polypeptides - Google Patents

Abstract

The invention describes Smad associating proteins (SAPs) and nucleic acids that encode SAPs, including fragments and biologically functional variants thereof, as well as antibodies that bind thereto. Methods and products for using such nucleic acids and polypeptides also are provided.

Description

SMAD ASSOCIATING POLYPEPTIDES

Field of he Invention

This invention relates to nucleic acids and encoded polypeptides which interact with Smad proteins. The invention also relates to agents which bind the nucleic acids or polypeptides. The invention further relates to methods of using such nucleic acids and polypeptides in the treatment and/or diagnosis of disease.

Background ofthe Invention Members ofthe transforming growth factor-β (TGF-β) family are multifunctional cytokines with elicit a wide range of cellular effects, including growth inhibition, differentiation and apoptosis (Heldin et al., Nature 390:465-471, 1997). The signaling induced by TGF-β family members are initiated through a heteromeric transmembrane kinase complex that consists of type I and type II receptors. The activated type I receptor induces the phosphorylation of receptor-activated Smads (R-Smads) which heteromerize with Smad4. These complexes translocate from the cytoplasm to the nucleus to direct transcriptional regulation of responsive genes (Heldin et al., 1997).

Recently, Smadό and Smad7 were isolated, which form a subfamily among the Smads and function to inhibit the intracellular signaling by R-Smad/Smad4 complexes. Smadό and Smad7 constitutively associate with type I receptor by blocking association and phosphorylation of R-Smads (Hayashi et al., Cell 89:1165-1173, 1997; Imamura et al., Nature 389:622-626, 1997; Nakao et al., Nature 389:631-635, 1997). Smadό and Smad7 are rapidly induced by members ofthe TGF-β family (Afrakhte et al, Biochem. Biophys. Res. Commun. 249:505-511, 1998), suggesting that inhibitory Smads may take part in a negative feedback control mechanism to modulate the signaling induced by members of TGF-β family.

The central role of Smads and TGF-β in cellular processes presents a need for additional factors to modulate Smads and TGF-β interactions with signal transduction pathways.

Summary of the Invention Using the yeast two hybrid system, proteins that specifically bind with Smadό and Smad7 have been isolated. The invention provides these isolated Smad associating proteins (SAPs) and fragments of those molecules, as well as agents which bind such polypeptides, including antibodies. The invention also provides nucleic acid molecules encoding SAPs, unique fragments of those molecules, expression vectors containing the foregoing, and host cells transfected with those molecules. The foregoing can be used in the diagnosis or treatment of conditions characterized by the expression of a Smad associating protein, or in the treatment of conditions characterized by the expression of a SAP, or in the treatment of a condition characterized by the expression of a Smad nucleic acid or polypeptide, or by the inadequate or excessive activity of a Smad polypeptide. The invention also provides methods for identifying pharmacological agents useful in the diagnosis or treatment of such conditions. Here, the identification of several SAPs is presented. The SAPs bind to Smad polypeptides including S adδ and Smad7 and thus are components of TGF-β superfamily signaling pathways. According to one aspect ofthe invention, isolated nucleic acid molecules are provided. The isolated nucleic acid molecules are nucleic acid molecules which hybridize under stringent conditions to a molecule consisting ofthe nucleic acid sequence set forth in SEQ ID NO:3 or SEQ ID NO:5 and which code for a polypeptide which binds Smadό, or nucleic acid molecules that differ from the foregoing nucleic acid molecules in codon sequence due to the degeneracy ofthe genetic code, or complements ofthe foregoing nucleic acid molecules. Preferably the isolated nucleic acid molecule consists of SEQ ID NO:3 or SEQ ID NO:5.

According to another aspect ofthe invention, isolated nucleic acid molecules are provided which are unique fragments of nucleotides 1-2399 of SEQ ID NO:3 between 12 and 2398 nucleotides in length or of nucleotides 1-855 of SEQ ID NO:5 between 12 and 854 nucleotides in length. Also provided are complements ofthe foregoing unique fragments provided that the nucleic acid molecule excludes sequences consisting of GenBank accession numbers AF176069, AF293384, AA305358, AI219112, N33797 and AB030502. In certain embodiments, the isolated nucleic acid molecule consists of at least 22, 25, 30, 40, 50, 75 or 100 contiguous nucleotides. In other embodiments, the isolated nucleic acid molecule consists of between 20 and 32 contiguous nucleotides. According to still another aspect of he invention, expression vectors including any of the foregoing isolated nucleic acid molecules operably linked to a promoter are provided. Also provided are host cells transformed or transfected with the expression vectors, as well as transgenic non-human animals including the expression vectors. According to yet another aspect ofthe invention, methods for producing a polypeptide are provided. The methods include culturing the foregoing host cells under conditions which permit the expression of polypeptide. Preferably the methods include isolating the polypeptide.

In another aspect ofthe invention, isolated polypeptides are provided which are encoded by the foregoing isolated nucleic acid molecules. Preferred isolated polypeptides include molecules comprising the amino acid sequences of SEQ ID NO:4, SEQ ID NO:6, fragments or functional variants of SEQ ID NO:4, and a fragments or functional variants of SEQ ID NO:6.

According to still another aspect ofthe invention, isolated polypeptides are provided which include a fragment or functional variant of SEQ ID NO:2. In certain embodiments the fragment of SEQ ID NO:2 consists of amino acids 1-101+234-424, 106-424 or 234-424.

According to yet another aspect ofthe invention, an isolated complex of polypeptides is provided. The complex includes one ofthe foregoing polypeptide bound to a polypeptide selected from the group consisting of Smadό, Smad7 and fragments thereof. Also included as an aspect ofthe invention are isolated polypeptides which bind selectively a polypeptide encoded by the foregoing isolated nucleic acid molecules, provided that the isolated polypeptide is not a Smad, ST AM or cyclin polypeptide. In certain embodiments, the isolated polypeptide binds to an epitope defined by a polypeptide consisting ofthe sequence of SEQ ID NOs:2, 4 or 6. In other embodiments, the isolated polypeptide is an antibody fragment selected from the group consisting of a Fab fragment, a F(ab)₂ fragment or a fragment including a CDR3 region selective for a SAP polypeptide. In still other embodiments the isolated polypeptide is a monoclonal antibody, a humanized antibody or a chimeric antibody.

According to still another aspect ofthe invention, methods for modulating TGF-β superfamily signal transduction in a mammalian cell are provided. The methods include contacting the mammalian cell with an amount of an agent which increases the amount of a Smad associating protein selected from the group consisting of SAP1/AMSH (SEQ ID NO:2)_s SAP2 (SEQ ID NO:4), SAP3 (SEQ ID NO:6), Hsp40 homolog (U40992; SEQ ID NO:8), Uba80 (X63237; SEQ ID NO: 10), Tax-1 binding protein (U33822; SEQ ID NO: 12), rabaptin-5 (NM 504703; SEQ ID NO: 14), and 26S proteinase S5a (U51007; SEQ ID NO:16) or a fragment thereof in the cell effective to reduce TGF-β superfamily signal transduction in the mammalian cell. In certain embodiments, the agent is a nucleic acid molecule encoding one of he foregoing polypeptides.

According to another aspect ofthe invention, methods for regulating the cell cycle in a mammalian cell are provided. The methods include contacting the mammalian cell with an amount of an agent which increases the amount of SAP2 (SEQ ID NO:4), or a fragment thereof, in the cell effective to bind a cyclin and regulate the cell cycle in the mammalian cell.

In further aspects ofthe invention, methods for identifying lead compounds for a pharmacological agent are provided. In certain embodiments, the methods include forming a mixture comprising a Smadό or Smad7 polypeptide, a SAP polypeptide, and a candidate pharmacological agent, incubating the mixture under conditions which, in the absence ofthe candidate pharmacological agent, permit a first amount of specific binding ofthe SAP polypeptide by the Smadό or Smad7 polypeptide, and detecting a test amount ofthe specific binding ofthe SAP polypeptide by the Smadό or Smad7 polypeptide. A reduction ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which disrupts the Smadό-SAP or Smad7-SAP binding, and an increase ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which enhances the Smadό-SAP or Smad7-SAP binding. Preferably the SAP polypeptide is selected from the group consisting of SAP1/AMSH, SAP2, SAP3 and fragments thereof.

In other embodiments, the methods include forming a mixture comprising an ALK kinase, a Smad polypeptide, a SAP polypeptide, and a candidate pharmacological agent, incubating the mixture under conditions which, in the absence ofthe candidate pharmacological agent, permit a first amount of specific binding ofthe SAP polypeptide by the Smad polypeptide, and detecting a test amount ofthe specific binding ofthe SAP polypeptide by the Smad polypeptide. A reduction ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which disrupts the Smad-SAP binding, and an increase ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which enhances the Smad-SAP binding. In preferred embodiments, the SAP polypeptide is selected from the group consisting of SAPl/AMSH, SAP2, SAP3 and fragments thereof, the Smad polypeptide is selected from the group consisting of Smad2, Smad3, Smad4, Smadό, Smad7 and fragments thereof, and the ALK kinase is selected from the group consisting of ALK5, constitutively activated ALK5, ALKό, constitutively activated ALKό and fragments thereof having kinase activity .

The use ofthe foregoing compositions in the preparation of a medicament is also contemplated.

These and other aspects ofthe invention will be described in further detail in connection with the detailed description ofthe invention.

Brief Description of the Figures Fig. 1 depicts a schematic structures of SmadόS and Smad7 mutants used in the yeast two hybrid assay. The human short form of Smadό and mouse Smad7 were inserted into pEG202. Fig. 2 shows the evaluation of Smadό-associating proteins using yeast two hybrid assay. Smad2, Smad4, SmadόS and Smad7 were used as baits to examine interaction with Smadό-associating proteins in yeast.

Fig. 3 depicts a map of isolated AMSH (SAP1) clones. Fig. 4 shows a map of isolated SAP2 clones. Fig. 5 shows a schematic illustration of SAPl/AMSH mutants. NLS, putative nuclear localization signal; PI and P2, proposed SH3 binding regions; JSH, JAB1 subdomain homologous regions.

Brief Description ofthe Sequences SEQ ID NO: 1 is the nucleotide sequence of human SAPl/AMSH.

SEQ ID NO:2 is the amino acid sequence of human SAPl/AMSH. SEQ ID NO:3 is the nucleotide sequence of human SAP2. SEQ ID NO:4 is the amino acid sequence of human SAP2. SEQ ID NO: 5 is the nucleotide sequence of human SAP3. SEQ ID NO:6 is the amino acid sequence of human SAP3. SEQ ID NOJ is the nucleotide sequence ofthe Hsp40 homolog having GenBank accession number U40992.

SEQ ID NO:8 is the amino acid sequence ofthe Hsp40 homolog having GenBank accession number U40992.

SEQ ID NO:9 is the nucleotide sequence of Uba80, having GenBank accession number X63237.

SEQ ID NO: 10 is the amino acid sequence of Uba80, having GenBank accession number X63237.

SEQ ID NO:ll is the nucleotide sequence of Tax-1 binding protein, having GenBank accession number U33822 SEQ ID NO:12 is the amino acid sequence of Tax-1 binding protein, having GenBank accession number U33822.

SEQ ID NO:13 is the nucleotide sequence of rabaptin-5, having GenBank accession number NM_004703.

SEQ ID NO: 14 is tlie amino acid sequence of rabaptin-5, having GenBank accession number NM_004703.

SEQ ID NO:15 is the nucleotide sequence ofthe 26S proteinase S5a, having GenBank accession number U51007.

SEQ ID NO:16 is the amino acid sequence ofthe 26S proteinase S5a, having GenBank accession number U51007.

Detailed Description ofthe Invention The present invention in one aspect involves the cloning of cDNAs encoding several Smad associating proteins (SAPs). The sequence ofthe human nucleic acids for SAPl, SAP2 and SAP3 are presented as SEQ ID NOs:l, 3 and 5, respectively, and the predicted amino acid sequences ofthe protein products are presented as SEQ ID NOs:2, 4 and 6. Analysis of the sequences by comparison to nucleic acid and protein databases determined that SAPl corresponds to the human AMSH gene (GenBank accession numbers NMJ306463, TJ73522) and that SAP2 is related to aXenopus gene, XDRP1 (Funakoshi et al., EMBOJ. 18:5009- 5018, 1999). To the extent that the SAP polypeptides identified herein are similar to previously identified sequences, it is entirely unexpected that the polypeptides are binding partners for Smad proteins.

The invention thus involves in one aspect SAP polypeptides, genes encoding those polypeptides, functional modifications and variants ofthe foregoing, useful fragments ofthe foregoing, as well as therapeutics relating thereto. The expression of these genes affects TGF-β superfamily signal transduction by binding to Smad polypeptides including Smadό and Smad7. The TGF-β superfamily members are well known to those of ordinary skill in the art and include TGF-βs, activins, bone morphogenetic proteins (BMPs), Vgl, Mullerian inhibitory substance (MIS) and growth/differentiation factors (GDFs).

Homologs and alleles ofthe Smad associating protein-encoding nucleic acids ofthe invention can be identified by conventional techniques. Thus, an aspect ofthe invention is those nucleic acid sequences which code for SAP polypeptides and which hybridize to a nucleic acid molecule consisting ofthe coding region of SEQ ID NO:l, SEQ ID NO:3 or SEQ ID NO:5, under stringent conditions. The term "stringent conditions" as used herein refers to parameters with which the art is familiar. Nucleic acid hybridization parameters may be found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor

Laboratory Press, Cold Spring Harbor, New York, 1989, or Current Protocols in Molecular Biology, F.M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. More specifically, stringent conditions, as used herein, refers, for example, to hybridization at 65°C in hybridization buffer (3.5 x SSC, 0.02% Ficoll, 0.02% polyvinyl pyrrolidone, 0.02% Bovine Serum Albumin, 2.5mM NaH₂P0₄(pH7), 0.5% SDS, 2mM EDTA). SSC is 0.15M sodium chloride/0.15M sodium citrate, pH7; SDS is sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid. After hybridization, the membrane upon which the DNA is transferred is washed at 2 x SSC at room temperature and then at 0.1 - 0.5 X SSC/0.1 x SDS at temperatures up to 68°C. There are other conditions, reagents, and so forth which can be used, which result in a similar degree of stringency. The skilled artisan will be familiar with such conditions, and thus they are not given here. It will be understood, however, that the skilled artisan will be able to manipulate the conditions in a manner to permit the clear identification of homologs and alleles of SAP nucleic acids ofthe invention. The skilled artisan also is familiar with the methodology for screening cells and libraries for expression of such molecules which then are routinely isolated, followed by isolation ofthe pertinent nucleic acid molecule and sequencing.

In general homologs and alleles typically will share at least 75% nucleotide identity and/or at least 90% amino acid identity to SEQ ID NOs:l, 3 or 5 and SEQ ID NOs:2, 4 or 6, respectively, in some instances will share at least 90% nucleotide identity and/or at least 95% amino acid identity and in still other instances will share at least 95% nucleotide identity and/or at least 99% amino acid identity. The homology can be calculated using various, publicly available software tools developed by NCBI (Bethesda, Maryland) that can be obtained through the Internet (ftp:/ncbi.nlm.nih.gov/pub/). Exemplary tools include the BLAST system available at http://www.ncbi.nlm.nih.gov, preferably using default settings. Pairwise and ClustalW alignments (BLOSUM30 matrix setting) as well as Kyle-Doolittle hydropathic analysis can be obtained using the MacVector sequence analysis software (Oxford Molecular Group). Watson-Crick complements ofthe foregoing nucleic acids also are embraced by the invention.

In screening for nucleic acids encoding Smad associating proteins with sequence homology to the SAP nucleic acids described herein, a Southern blot may be performed using the foregoing conditions, together with a radioactive probe. After washing the membrane to which the DNA is finally transferred, the membrane can be placed against X-ray film to detect the radioactive signal.

As used herein with respect to nucleic acids, the term "isolated" means: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) recombinantly produced by cloning; (iii) purified, as by cleavage and gel separation; or (iv) synthesized by, for example, chemical synthesis. An isolated nucleic acid is one which is readily manipulable by recombinant DNA techniques well known in the art. Thus, a nucleotide sequence contained in a vector in which 5' and 3' restriction sites are known or for which polymerase chain reaction (PCR) primer sequences have been disclosed is considered isolated but a nucleic acid sequence existing in its native state in its natural host is not. An isolated nucleic acid may be substantially purified, but need not be. For example, a nucleic acid that is isolated within a cloning or expression vector is not pure in that it may comprise only a tiny percentage ofthe material in the cell in wliich it resides. Such a nucleic acid is isolated, however, as the term is used herein because it is readily manipulable by standard techniques known to those of ordinary skill in the art. An isolated nucleic acid as used herein is not a naturally occurring chromosome.

As used herein with respect to polypeptides, "isolated" means separated from its native environment and present in sufficient quantity to permit its identification or use. Isolated, when referring to a protein or polypeptide, means, for example: (i) selectively produced by expression cloning or (ii) purified as by chromatography or electrophoresis. Isolated proteins or polypeptides may be, but need not be, substantially pure. The term "substantially pure" means that the proteins or polypeptides are essentially free of other substances with which they may be found in nature or in vivo systems to an extent practical and appropriate for their intended use. Substantially pure polypeptides may be produced by techniques well known in the art. Because an isolated protein may be admixed witli a pharmaceutically acceptable carrier in a pharmaceutical preparation, the protein may comprise only a small percentage by weight ofthe preparation. The protein is nonetheless isolated in that it has been separated from the substances with which it may be associated in living systems, i.e. isolated from other proteins. The invention also includes degenerate nucleic acids which include alternative codons to those present in the native materials. For example, serine residues are encoded by the codons TCA, AGT, TCC, TCG, TCT and AGC. Each ofthe six codons is equivalent for the purposes of encoding a serine residue. Thus, it will be apparent to one of ordinary skill in the art that any ofthe serine-encoding nucleotide triplets may be employed to direct the protein synthesis apparatus, in vitro or in vivo, to incorporate a serine residue into an elongating Smad7 polypeptide. Similarly, nucleotide sequence triplets which encode other amino acid residues include, but are not limited to: CCA, CCC, CCG and CCT (proline codons); CGA, CGC, CGG, CGT, AGA and AGG (arginine codons); ACA, ACC, ACG and ACT (threonine codons); AAC and AAT (asparagine codons); and ATA, ATC and ATT (isoleucine codons). Other amino acid residues may be encoded similarly by multiple nucleotide sequences. Thus, the invention embraces degenerate nucleic acids that differ from the biologically isolated nucleic acids in codon sequence due to the degeneracy ofthe genetic code.

The invention also provides modified nucleic acid molecules which include additions, substitutions and deletions of one or more nucleotides. In preferred embodiments, these modified nucleic acid molecules and/or the polypeptides they encode retain at least one activity or function ofthe unmodified nucleic acid molecule and/or the polypeptides, such as Smad binding, antigenicity, enzymatic activity, receptor binding, etc. In certain embodiments, the modified nucleic acid molecules encode modified polypeptides, preferably polypeptides having conservative amino acid substitutions as are described elsewhere herein. The modified nucleic acid molecules are structurally related to the unmodified nucleic acid molecules and in preferred embodiments are sufficiently structurally related to the unmodified nucleic acid molecules so that the modified and unmodified nucleic acid molecules hybridize under stringent conditions known to one of skill in the art.

For example, modified nucleic acid molecules which encode polypeptides having single amino acid changes can be prepared. Each of these nucleic acid molecules can have one, two or three nucleotide substitutions exclusive of nucleotide changes corresponding to the degeneracy ofthe genetic code as described herein. Likewise, modified nucleic acid molecules which encode polypeptides having two amino acid changes can be prepared which have, e.g., 2-6 nucleotide changes. Numerous modified nucleic acid molecules like these will be readily envisioned by one of skill in the art, including for example, substitutions of nucleotides in codons encoding amino acids 2 and 3, 2 and 4, 2 and 5, 2 and 6, and so on. In the foregoing example, each combination of two amino acids is included in the set of modified nucleic acid molecules, as well as all nucleotide substitutions which code for the amino acid substitutions. Additional nucleic acid molecules that encode polypeptides having additional substitutions (i.e., 3 or more), additions or deletions (e.g., by introduction of a stop codon or a splice site(s)) also can be prepared and are embraced by the invention as readily envisioned by one of ordinary skill in the art. Any ofthe foregoing nucleic acids or polypeptides can be tested by routine experimentation for retention of structural relation or activity to the nucleic acids and/or polypeptides disclosed herein.

The invention also provides isolated unique fragments of SEQ ID NOs:l, 3 or 5 or complements of SEQ ID NOs: 1, 3 or 5 of sufficient length to represent a sequence unique within the human genome, and identifying a nucleic acid encoding a Smad associating polypeptide. A unique fragment is one that is a 'signature' for the larger nucleic acid. It, for example, is long enough to assure that its precise sequence is not found in molecules outside ofthe SAP nucleic acids defined above. A unique fragment includes a sequence of contiguous nucleotides which is not identical to any sequence selected from the sequence group consisting of (1) sequences having the GenBank accession numbers AF176069, AF293384, AA305358, AI219112, N33797, AB030502 and other sequences publicly available as ofthe filing date of this application, (2) complements of (1), and (3) fragments of (1) and (2). Thus a unique fragment excludes, by definition, sequences consisting solely of EST and/or gene sequences such as those described by GenBank accession numbers AF176069, AF293384, AA305358, AI219112, N33797 and AB030502.

A fragment which is completely composed ofthe sequence described in the foregoing GenBank deposits is one which does not include any ofthe nucleotides unique to the sequences ofthe invention. Thus, a unique fragment must contain a nucleotide sequence other than the exact sequence of those in GenBank or fragments thereof. The difference may be an addition, deletion or substitution with respect to the GenBank sequence or it may be a sequence wholly separate from the GenBank sequence.

Unique fragments can be used as probes in Southern blot assays to identify such nucleic acids, or can be used in amplification assays such as those employing PCR. As known to those skilled in the art, large probes such as 200 250, 300 or more nucleotides are preferred for certain uses such as Southern blots, while smaller fragments will be preferred for uses such as PCR. Unique fragments also can be used to produce fusion proteins for generating antibodies or determining binding ofthe polypeptide fragments, as demonstrated in the Examples, or for generating immunoassay components. Likewise, unique fragments can be employed to produce nonfused fragments ofthe SAP polypeptides such as the N- terminal and C-terminal fragments disclosed herein, useful, for example, in the preparation of antibodies, in immunoassays, and as a competitive binding partner ofthe SAPs and/or other polypeptides which bind to Smad 6 or Smad7 polypeptides, for example, in therapeutic applications. Unique fragments further can be used as antisense molecules to inhibit the expression of SAP nucleic acids and polypeptides, particularly for therapeutic purposes as described in greater detail below.

As will be recognized by those skilled in the art, the size ofthe unique fragment will depend upon its conservancy in the genetic code. Thus, some regions of SEQ ID NOs : 1 , 3 and/or SEQ ID NO: 5 and its complement will require longer segments to be unique while others will require only short segments, typically between 12 and 32 nucleotides (e.g. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 and 32 bases long). This disclosure intends to embrace each and every fragment of each sequence, beginning at the first nucleotide, the second nucleotide and so on, up to 8 nucleotides short ofthe end, and ending anywhere from nucleotide number 8, 9, 10 and so on for each sequence, up to the very last nucleotide (provided the sequence is unique as described above). Many segments of SEQ ID NO:3 or SEQ ID NO:5, or complements thereof, that are 25 or more nucleotides in length will be unique. Those skilled in the art are well versed in methods for selecting such sequences, typically on the basis ofthe ability ofthe unique fragment to selectively distinguish the sequence of interest from non-SAP nucleic acids. A comparison ofthe sequence ofthe fragment to those on known data bases typically is all that is necessary, although in vitro confirmatory hybridization and sequencing analysis may be performed. A unique fragment can be a functional fragment. A functional fragment of a nucleic acid molecule ofthe invention is a fragment which retains some functional property ofthe larger nucleic acid molecule, such as coding for a functional polypeptide, binding to proteins (e.g., Smads), regulating transcription of operably linked nucleic acids, and the like. One of ordinary skill in the art can readily determine using the assays described herein and those well known in the art to determine whether a fragment is a functional fragment of a nucleic acid molecule using no more than routine experimentation.

As mentioned above, the invention embraces antisense oligonucleotides that selectively bind to a nucleic acid molecule encoding a SAP polypeptide, to modulate TGF-β, activin and/or BMP signaling by reducing the amount of SAPs. This is desirable in virtually any medical condition wherein a reduction of SAP binding to Smad proteins is desirable, e.g., to modulate Smad activity such as in TGF-β signaling.

As used herein, the term "antisense oligonucleotide" or "antisense" describes an oligonucleotide that is an oligoribonucleotide, oligodeoxyribonucleotide, modified oligoribonucleotide, or modified oligodeoxyribonucleotide which hybridizes under physiological conditions to DNA comprising a particular gene or to an mRNA transcript of that gene and, thereby, inhibits the transcription of that gene and/or the translation of that mRNA. The antisense molecules are designed so as to interfere with transcription or translation of a target gene upon hybridization with the target gene or transcript. Those skilled in the art will recognize that the exact length ofthe antisense oligonucleotide and its degree of complementarity with its target will depend upon the specific target selected, including the sequence ofthe target and the particular bases which comprise that sequence. It is preferred that the antisense oligonucleotide be constructed and arranged so as to bind selectively with the target under physiological conditions, i.e., to hybridize substantially more to the target sequence than to any other sequence in the target cell under physiological conditions. Based upon SEQ ID NOs:l, 3 or 5, or upon allelic or homologous genomic and/or cD A sequences, or upon the nucleotide sequences of other Smad associating polypeptides disclosed herein, one of skill in the art can easily choose and synthesize any of a number of appropriate antisense molecules for use in accordance with the present invention. For example, a "gene walk" comprising a series of oligonucleotides of 15-30 nucleotides spanning the length of a SAP nucleic acid can be prepared, followed by testing for inhibition of SAP expression. Optionally, gaps of 5-10 nucleotides can be left between the oligonucleotides to reduce the number of oligonucleotides synthesized and tested.

In order to be sufficiently selective and potent for inhibition, such antisense oligonucleotides should comprise at least 10 and, more preferably, at least 15 consecutive bases which are complementary to the target, although in certain cases modified oligonucleotides as short as 7 bases in length have been used successfully as antisense oligonucleotides (Wagner et al., Nature Biotechnol. 14:840-844, 1996). Most preferably, the antisense oligonucleotides comprise a complementary sequence of 20-30 bases. Although oligonucleotides may be chosen which are antisense to any region ofthe gene or mRNA transcripts, in preferred embodiments the antisense oligonucleotides correspond to N-terminal or 5' upstream sites such as translation initiation, transcription initiation or promoter sites. In addition, 3'-untranslated regions may be targeted. Targeting to mRNA splicing sites has also been used in the art but may be less preferred if alternative mRNA splicing occurs. In addition, the antisense is targeted, preferably, to sites in which mRNA secondary structure is not expected (see, e.g., Sainio et al, Cell Mol. Neurobiol. 14(5) :439-457, 1994) and at which proteins are not expected to bind. Finally, although SEQ ID Nos: 1, 3 or 5 disclose cDNA sequences, one of ordinary skill in the art may easily derive the genomic DNA corresponding to the cDNA of SEQ ID Nos:l, 3 or 5. Thus, the present invention also provides for antisense oligonucleotides which are complementary to the genomic DNA corresponding to SEQ ID Nos:l, 3 or 5. Similarly, antisense to allelic or homologous cDNAs and genomic DNAs are enabled without undue experimentation. In one set of embodiments, the antisense oligonucleotides ofthe invention may be composed of "natural" deoxyribonucleotides, ribonucleotides, or any combination thereof. That is, the 5' end of one native nucleotide and the 3' end of another native nucleotide may be covalently linked, as in natural systems, via a phosphodiester internucleoside linkage. These oligonucleotides may be prepared by art recognized methods which may be carried out manually or by an automated synthesizer. They also may be produced recombinantly by vectors.

In preferred embodiments, however, the antisense oligonucleotides ofthe invention also may include "modified" oligonucleotides. That is, the oligonucleotides may be modified in a number of ways which do not prevent them from hybridizing to their target but which enhance their stability or targeting or which otherwise enhance their therapeutic effectiveness. The term "modified oligonucleotide" as used herein describes an oligonucleotide in which (1) at least two of its nucleotides are covalently linked via a synthetic internucleoside linkage (i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide) and/or (2) a chemical group not normally associated with nucleic acids has been covalently attached to the oligonucleotide. Preferred synthetic internucleoside linkages are phosphorothioates, alkylphosphonates, phosphorodithioates, phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates, carbonates, phosphate triesters, acetamidates, carboxymethyl esters and peptides. The term "modified oligonucleotide" also encompasses oligonucleotides with a covalently modified base and/or sugar. For example, modified oligonucleotides include oligonucleotides having backbone sugars which are covalently attached to low molecular weight organic groups other than a hydroxyl group at the 3' position and other than a phosphate group at the 5' position. Thus modified oligonucleotides may include a 2'-O- al ylated ribose group. In addition, modified oligonucleotides may include sugars such as arabinose instead of ribose. The present invention, thus, contemplates pharmaceutical preparations containing modified antisense molecules that are complementary to and hybridizable with, under physiological conditions, nucleic acids encoding SAP polypeptides, together with pharmaceutically acceptable carriers.

Antisense oligonucleotides may be administered as part of a pharmaceutical composition. Such a pharmaceutical composition may include the antisense oligonucleotides in combination with any standard physiologically and/or pharmaceutically acceptable carriers which are known in the art. The compositions should be sterile and contain a therapeutically effective amount ofthe antisense oligonucleotides in a unit of weight or volume suitable for administration to a patient. The term "pharmaceutically acceptable" means a non-toxic material that does not interfere with the effectiveness ofthe biological activity ofthe active ingredients. The term "physiologically acceptable" refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics ofthe carrier will depend on the route of administration. Physiologically and pharmaceutically acceptable carriers include diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art. As used herein, a "vector" may be any of a number of nucleic acids into which a desired sequence may be inserted by restriction and ligation for transport between different genetic environments or for expression in a host cell. Vectors are typically composed of DNA although RNA vectors are also available. Vectors include, but are not limited to, plasmids, phagemids and virus genomes. A cloning vector is one which is able to replicate in a host cell, and which is further characterized by one or more endonuclease restriction sites at which the vector may be cut in a determinable fashion and into which a desired DNA sequence may be ligated such that the new recombinant vector retains its ability to replicate in the host cell. In the case of plasmids, replication ofthe desired sequence may occur many times as the plasmid increases in copy number within the host bacterium or just a single time per host before the host reproduces by mitosis. In the case of phage, replication may occur actively during a lytic phase or passively during a lysogenic phase. An expression vector is one into which a desired DNA sequence may be inserted by restriction and ligation such that it is operably joined to regulatory sequences and may be expressed as an RNA transcript. Vectors may further contain one or more marker sequences suitable for use in the identification of cells which have or have not been transformed or transfected with the vector. Markers include, for example, genes encoding proteins which increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose activities are detectable by standard assays known in the art (e.g., β-galactosidase, luciferase or alkaline phosphatase), and genes which visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques (e.g., green fluorescent protein). Preferred vectors are those capable of autonomous replication and expression ofthe structural gene products present in the DNA segments to which they are operably joined.

As used herein, a coding sequence and regulatory sequences are said to be "operably" joined when they are covalently linked in such a way as to place the expression or transcription ofthe coding sequence under the influence or control ofthe regulatory sequences. If it is desired that the coding sequences be translated into a functional protein, two DNA sequences are said to be operably j oined if induction of a promoter in the 5 ' regulatory sequences results in the transcription ofthe coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability ofthe promoter region to direct the transcription of tlie coding sequences, or (3) interfere with the ability ofthe corresponding RNA transcript to be translated into a protein. Thus, a promoter region would be operably joined to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript might be translated into the desired protein or polypeptide. The precise nature ofthe regulatory sequences needed for gene expression may vary between species or cell types, but shall in general include, as necessary, 5' non-transcribed and 5' non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like. Especially, such 5' non-transcribed regulatory sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined gene. Regulatory sequences may also include enhancer sequences or upstream activator sequences as desired. The vectors ofthe invention may optionally include 5' leader or signal sequences. The choice and design of an appropriate vector is within the ability and discretion of one of ordinary skill in the art. Expression vectors containing all the necessary elements for expression are commercially available and known to those skilled in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. Cells are genetically engineered by the introduction into the cells of heterologous DNA (RNA) encoding a SAP polypeptide or fragment or variant thereof. That heterologous DNA (RNA) is placed under operable control of transcriptional elements to permit the expression of the heterologous DNA in the host cell.

Preferred systems for mRNA expression in mammalian cells are those such as pRc/CMV (available from Invitrogen, Carlsbad, CA) that contain a selectable marker such as a gene that confers G418 resistance (which facilitates the selection of stably transfected cell lines) and the human cytomegalovirus (CMV) enhancer-promoter sequences. Additionally, suitable for expression in primate or canine cell lines is the pCEP4 vector (Invitrogen), which contains an Epstein Barr virus (EBV) origin of replication, facilitating the maintenance of plasmid as a multicopy extrachromosomal element. Another expression vector is the pEF- BOS plasmid containing the promoter of polypeptide Elongation Factor l , which stimulates efficiently transcription in vitro. The plasmid is described by Mishizuma and Nagata (Nuc. Acids Res. 18:5322, 1990), and its use in transfection experiments is disclosed by, for example, Demoulin (Mol Cell. Biol 16:4710-4716, 1996). Still another preferred expression vector is an adenovirus, described by Stratford-Perricaudet, which is defective for El and E3 proteins (J. Clin. Invest. 90:626-630, 1992). The use ofthe adenovirus as an Adeno.Pl A recombinant is disclosed by Warmer et al., in intradermal injection in mice for immunization against PI A (Int. J. Cancer, 67:303-310, 1996).

The invention also embraces so-called expression kits, which allow the artisan to prepare a desired expression vector or vectors. Such expression kits include at least separate portions of each ofthe previously discussed coding sequences. Other components may be added, as desired, as long as the previously mentioned sequences, which are required, are included.

The invention also permits the construction of SAP gene "knock-outs" in cells and in animals, providing materials for studying certain aspects of TGF-β, activin and/or BMP signal transduction.

The invention also provides isolated polypeptides, which include the polypeptides of SEQ ID NOs:2, 4 and 6 and unique fragments of SEQ ID NOs:2, 4 and 6 including fragments shown in Fig. 5 (amino acids 1-226/232-424, 1-194/234-424, 1-233, 1-322/370-424, 1- 111/128-424, 1-101/234-424, 106-424 and 234-424 of SEQ ID NO:2). Such polypeptides are useful, for example, alone or as fusion proteins to test Smad binding, to test phosphorylation, to generate antibodies, and as a components of an immunoassay.

A unique fragment of a SAP polypeptide, in general, has the features and characteristics of unique fragments as discussed above in connection with nucleic acids. As will be recognized by those skilled in the art, the size ofthe unique fragment will depend upon factors such as whether the fragment constitutes a portion of a conserved protein domain. Thus, some regions of SEQ ID NOs:2, 4 and/or 6 will require longer segments to be unique while others will require only short segments, typically between 5 and 12 amino acids (e.g. 5, 6, 7, 8, 9, 10, 11 and 12 amino acids long). Virtually any segment of SEQ ID NOs:4 and 6 that is 10 or more amino acids in length will be unique.

Unique fragments of a polypeptide preferably are those fragments which retain a distinct functional capability ofthe polypeptide. Functional capabilities which can be retained in a unique fragment of a polypeptide include binding of Smadό and/or Smad7, interaction with antibodies, interaction with other polypeptides (such as TβR-I) or fragments thereof, selective binding of nucleic acids or proteins, and enzymatic activity. For example, as exemplified herein, N-terminal and C-terminal SAPl/AMSH fragments such as those depicted in Fig. 5 can be used as a functional equivalent of full length SAPl/AMSH in the methods ofthe invention, including e.g., binding of Smads for modulation of TGF-β signal transduction. Other SAP polypeptide fragments, e.g., other N-terminal or C-terminal fragments, can be selected according to their functional properties. For example, one of ordinary skill in the art can prepare SAP fragments recombinantly and test those fragments according to the methods exemplified below, such as binding to a Smad polypeptide. Those skilled in the art also are well versed in methods for selecting unique amino acid sequences, typically on the basis ofthe ability ofthe unique fragment to selectively distinguish the sequence of interest from non-family members. A comparison ofthe sequence ofthe fragment to those on known data bases typically is all that is necessary.

The invention embraces variants ofthe SAP polypeptides described above. As used herein, a "variant" of a SAP polypeptide is a polypeptide which contains one or more modifications to the primary amino acid sequence of a SAP polypeptide. Modifications which create a SAP variant can be made to a SAP polypeptide 1) to reduce or eliminate an activity of a SAP polypeptide, such as binding to a Smad polypeptide; 2) to enhance a property of a SAP polypeptide, such as protein stability in an expression system or the stability of protein-protein binding; or 3) to provide a novel activity or property to a SAP polypeptide, such as addition of an antigenic epitope or addition of a detectable moiety. Modifications to a SAP polypeptide are typically made to the nucleic acid which encodes the SAP polypeptide, and can include deletions, point mutations, truncations, amino acid substitutions and additions of amino acids or non-amino acid moieties. Alternatively, modifications can be made directly to the polypeptide, such as by cleavage, addition of a linker molecule, addition of a detectable moiety, such as biotin, addition of a fatty acid, and the like. Modifications also embrace fusion proteins comprising all or part ofthe SAP amino acid sequence.

In general, variants include SAP polypeptides which are modified specifically to alter a feature ofthe polypeptide unrelated to its physiological activity. For example, cysteine residues can be substituted or deleted to prevent unwanted disulfide linkages. Similarly, certain amino acids can be changed to enhance expression of a SAP polypeptide by eliminating proteolysis by proteases in an expression system (e.g., dibasic amino acid residues in yeast expression systems in which KEX2 protease activity is present).

Mutations of a nucleic acid which encode a Smad7 polypeptide preferably preserve the amino acid reading frame ofthe coding sequence, and preferably do not create regions in the nucleic acid which are likely to hybridize to form secondary structures, such a hairpins or loops, which can be deleterious to expression ofthe variant polypeptide.

Mutations can be made by selecting an amino acid substitution, or by random mutagenesis of a selected site in a nucleic acid which encodes the polypeptide. Variant polypeptides are then expressed and tested for one or more activities to determine which mutation provides a variant polypeptide with the desired properties. Further mutations can be made to variants (or to non-variant SAP polypeptides) which are silent as to the amino acid sequence ofthe polypeptide, but which provide preferred codons for translation in a particular host. The preferred codons for translation of a nucleic acid in, e.g., E. coli, are well known to those of ordinary skill in the art. Still other mutations can be made to the noncoding sequences of a SAP gene or cDNA clone to enhance expression ofthe polypeptide. The activity of variants of SAP polypeptides can be tested by cloning the gene encoding the variant SAP polypeptide into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the variant SAP polypeptide, and testing for a functional capability ofthe SAP polypeptides as disclosed herein. For example, the variant Smad7 polypeptide can be tested for Smad binding as disclosed in the Examples. Preparation of other variant polypeptides may favor testing of other activities, as will be Icnown to one of ordinary skill in the art.

The skilled artisan will also realize that conservative amino acid substitutions may be made in SAP polypeptides to provide functionally equivalent variants ofthe foregoing polypeptides, i.e, the variants retain the functional capabilities ofthe SAP polypeptides. As used herein, a "conservative amino acid substitution" refers to an amino acid substitution which does not alter the relative charge or size characteristics ofthe protein in which the amino acid substitution is made. Variants can be prepared according to methods for altering polypeptide sequence known to one of ordinary skill in the art such as are found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989, or Current Protocols in Molecular Biology, F.M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. Exemplary functionally equivalent variants ofthe SAP polypeptides include conservative amino acid substitutions of SEQ ID NOs:2, 4 or 6. Conservative substitutions of amino acids include substitutions made amongst amino acids within the following groups: (a) M, I, L, V; (b) F, Y, W; (c) K, R, H; (d) A, G; (e) S, T; (f) Q, N; and (g) E, D.

Conservative amino-acid substitutions in the amino acid sequence of SAP polypeptides to produce functionally equivalent variants of SAP polypeptides typically are made by alteration of a nucleic acid encoding a SAP polypeptide (SEQ ID NOs:l, 3 and 5). Such substitutions can be made by a variety of methods known to one of ordinary skill in the art. For example, amino acid substitutions may be made by PCR-directed mutation, site- directed mutagenesis according to the method of Kunkel (Kunkel, Proc. Nat. Acad. Sci. U.S.A. 82: 488-492, 1985), or by chemical synthesis of a gene encoding a SAP polypeptide. Where amino acid substitutions are made to a small unique fragment of a SAP polypeptide, such as a Smad or SH3 binding site peptide, the substitutions can be made by directly synthesizing the peptide. The activity of functionally equivalent fragments of SAP polypeptides can be tested by cloning the gene encoding the altered SAP polypeptide into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the altered SAP polypeptide, and testing for a functional capability ofthe SAP polypeptides as disclosed herein. Peptides which are chemically synthesized can be tested directly for function, e.g., for binding to Smadό and or Smad7.

The invention as described herein has a number of uses, some ofwhich are described elsewhere herein. First, the invention permits isolation ofthe SAP protein molecules (SEQ ID NOs:2, 4 and 6). A variety of methodologies well-known to the skilled practitioner can be utilized to obtain isolated SAP molecules. The polypeptide may be purified from cells which naturally produce the polypeptide by chromatographic means or immunological recognition. Alternatively, an expression vector may be introduced into cells to cause production ofthe polypeptide. In another method, mRNA transcripts may be microinjected or otherwise introduced into cells to cause production ofthe encoded polypeptide. Translation of mRNA in cell-free extracts such as the reticulocyte lysate system also may be used to produce polypeptide. Those skilled in the art also can readily follow known methods for isolating SAP polypeptides. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography and immune-affinity chromatography.

The isolation ofthe SAP gene also makes it possible for the artisan to diagnose a disorder characterized by expression of SAP. These methods involve determining expression ofthe SAP gene, and/or SAP polypeptides derived therefrom. In the former situation, such determinations can be carried out via any standard nucleic acid determination assay, including the polymerase chain reaction as exemplified in the examples below, or assaying with labeled hybridization probes. The invention also makes it possible isolate proteins such as Smadό and Smad7 by the binding of such proteins to SAP as disclosed herein. The identification of this binding by SAPl , for example, also permits one of skill in the art to block the binding of Smad7 or Smad7 to other Smad-binding proteins, such as other SAPs, such as SAP2 or SAP3. Other SAPs can likewise by used to modulate protein binding to Smads. Binding ofthe proteins can be effected by introducing into a biological system in which the proteins bind (e.g., a cell) a SAP polypeptide including a Smadό or Smad7 binding site in an amount sufficient to block the binding. The identification of Smad binding sites in SAPs also enables one of skill in the art to prepare modified proteins, using standard recombinant DNA techniques, which can bind to proteins such as Smadό and Smad7. For example, when one desires to target a certain protein to a Smadό or Smad7 protein complex, one can prepare a fusion polypeptide ofthe protein and a SAP protein or a fragment thereof having a Smad binding site. Additional uses are described herein.

The invention further provides methods for reducing or increasing TGF-β family signal transduction in a cell. Such methods are useful in vitro for altering the TGF-β signal transduction, for example, in testing compounds for potential to block aberrant TGF-β signal transduction or increase deficient TGF-β signal transduction. In vivo, such methods are useful for modulating growth, e.g., to treat cancer and fibrosis. Such methods also are useful in the treatment of conditions which result from excessive or deficient TGF-β signal transduction. TGF-β signal transduction can be measured by a variety of ways known to one of ordinary skill in the art, such as the reporter systems described in the references cited in the Examples. Various modulators of SAP protein activity can be screened for effects on TGF-β signal transduction using the methods disclosed herein. The skilled artisan can first determine the modulation of a SAP activity, such as Smad binding or TGF-β signaling activity, and then apply such a modulator to a target cell or subject and assess the effect on the target cell or subject. For example, in screening for modulators of SAPs useful in the treatment of cancer, cells in culture can be contacted with SAP modulators and the increase or decrease of growth or focus formation ofthe cells can be determined according to standard procedures. SAP activity modulators can be assessed for their effects on other TGF-β signal transduction downstream effects by similar methods in many cell types. The foregoing also applies to signaling via activin and BMP complexes. The invention also provides, in certain embodiments, "dominant negative" polypeptides derived from SEQ ID NOs:2, 4 and/or 6. A dominant negative polypeptide is an inactive variant of a protein, which, by interacting with the cellular machinery, displaces an active protein from its interaction with the cellular machinery or competes with the active protein, thereby reducing the effect ofthe active protein. For example, a dominant negative receptor which binds a ligand but does not transmit a signal in response to binding of the ligand can reduce the biological effect of expression ofthe ligand. Likewise, a dominant negative catalytically-inactive kinase which interacts normally with target proteins but does not phosphorylate the target proteins can reduce phosphorylation ofthe target proteins in response to a cellular signal. Similarly, a dominant negative transcription factor which binds to a promoter site in the control region of a gene but does not increase gene transcription can reduce the effect of a normal transcription factor by occupying promoter binding sites without increasing transcription.

The end result ofthe expression of a dominant negative polypeptide in a cell is a reduction in function of active proteins. One of ordinary skill in the art can assess the potential for a dominant negative variant of a protein, and using standard mutagenesis techniques to create one or more dominant negative variant polypeptides. For example, given the teachings contained herein of a SAP polypeptides, one of ordinary skill in the art can modify the sequence ofthe SAP polypeptides by site-specific mutagenesis, scanning mutagenesis, partial gene deletion or truncation, and the like. See, e.g., U.S. Patent No. 5,580,723 and Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. The skilled artisan then can test the population of mutagenized polypeptides for diminution in a selected activity (e.g., Smadό binding, modulation of TGF-β signaling activity) and/or for retention of such an activity. Other similar methods for creating and testing dominant negative variants of a protein will be apparent to one of ordinary skill in the art. Dominant negative SAP proteins can include variants in which a portion ofthe Smad binding site has been mutated or deleted to reduce or eliminate SAP interaction with Smadό or Smad7. Other examples include SAP variants in which the ability to accept phosphorylation by MAP kinases is reduced. One of ordinary skill in the art can readily prepare and test SAP variants bearing mutations or deletions in various portions ofthe polypeptide.

The invention also involves agents such as polypeptides which bind to SAP polypeptides and to complexes of SAP polypeptides and binding partners such as Smadό and Smad7. Such binding agents can be used, for example, in screening assays to detect the presence or absence of SAP polypeptides and complexes of SAP polypeptides and their binding partners and in purification protocols to isolate SAP polypeptides and complexes of SAP polypeptides and their binding partners. Such agents also can be used to inhibit the native activity ofthe SAP polypeptides or their binding partners, for example, by binding to such polypeptides, or their binding partners or both.

The invention, therefore, embraces peptide binding agents which, for example, can be antibodies or fragments of antibodies having the ability to selectively bind to SAP polypeptides. Antibodies include polyclonal and monoclonal antibodies, prepared according to conventional methodology.

Significantly, as is well-known in the art, only a small portion of an antibody molecule, the paratope, is involved in the binding ofthe antibody to its epitope (see, in general, Clark, W.R. (1986) The Experimental Foundations of Modern Immunology Wiley & Sons, Inc., New York; Roitt, I. (1991) Essential Immunology, 7th Ed., Blackwell Scientific Publications, Oxford). The pFc' and Fc regions, for example, are effectors ofthe complement cascade but are not involved in antigen binding. An antibody from which the pFc' region has been enzymatically cleaved, or which has been produced without the pFc' region, designated an F(ab')₂ fragment, retains both ofthe antigen binding sites of an intact antibody. Similarly, an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region, designated an Fab fragment, retains one ofthe antigen binding sites of an intact antibody molecule. Proceeding further, Fab fragments consist of a covalently bound antibody light chain and a portion ofthe antibody heavy chain denoted Fd. The Fd fragments are the major determinant of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity) and Fd fragments retain epitope-binding ability in isolation.

Within the antigen-binding portion of an antibody, as is well-known in the art, there are complementarity determining regions (CDRs), which directly interact with the epitope of the antigen, and framework regions (FRs), which maintain the tertiary structure of tlie paratope (see, in general, Clark, 1986; Roitt, 1991). In both the heavy chain Fd fragment and the light chain of IgG immunoglobulins, there are four framework regions (FR1 through FR4) separated respectively by three complementarity determining regions (CDR1 through CDR3). The CDRs, and in particular the CDR3 regions, and more particularly the heavy chain CDR3, are largely responsible for antibody specificity. It is now well-established in the art that the non-CDR regions of a mammalian antibody may be replaced with similar regions of conspecific or heterospecific antibodies while retaining the epitopic specificity ofthe original antibody. This is most clearly manifested in the development and use of "humanized" antibodies in which non-human CDRs are covalently joined to human FR and/or Fc/pFc' regions to produce a functional antibody. See, e.g., U.S. patents 4,816,567, 5,225,539, 5,585,089, 5,693,762 and 5,859,205. Thus, for example, PCT International Publication Number WO 92/04381 teaches the production and use of humanized murine RSV antibodies in which at least a portion ofthe murine FR regions have been replaced by FR regions of human origin. Such antibodies, including fragments of intact antibodies with antigen-binding ability, are often referred to as "chimeric" antibodies. Thus, as will be apparent to one of ordinary skill in the art, the present invention also provides for F(ab')₂, Fab, Fv and Fd fragments; chimeric antibodies in which the Fc and/or FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric F(ab')₂ fragment antibodies in which the FR and/or CDR1 and or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric Fab fragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; and chimeric Fd fragment antibodies in wliich the FR and/or CDR1 and or CDR2 regions have been replaced by homologous human or non- human sequences. The present invention also includes so-called single chain antibodies. Thus, the invention involves polypeptides of numerous size and type that bind specifically to SAP polypeptides, and complexes of both SAP polypeptides and their binding partners. These polypeptides may be derived also from sources other than antibody technology. For example, such polypeptide binding agents can be provided by degenerate peptide libraries which can be readily prepared in solution, in immobilized form or as phage display libraries. Combinatorial libraries also can be synthesized of peptides containing one or more amino acids. Libraries further can be synthesized of peptoids and non-peptide synthetic moieties.

Phage display can be particularly effective in identifying binding peptides useful according to the invention. Briefly, one prepares a phage library (using e.g. ml 3, fd, or lambda phage), displaying inserts from 4 to about 80 amino acid residues using conventional procedures. The inserts may represent, for example, a completely degenerate or biased array. One then can select phage-bearing inserts which bind to the SAP polypeptide. This process can be repeated through several cycles of reselection of phage that bind to the SAP polypeptide. Repeated rounds lead to enrichment of phage bearing particular sequences. DNA sequence analysis can be conducted to identify die sequences ofthe expressed polypeptides. The minimal linear portion of die sequence that binds to the SAP polypeptide can be determined. One can repeat the procedure using a biased library containing inserts containing part or all ofthe minimal linear portion plus one or more additional degenerate residues upstream or downstream thereof. Yeast two-hybrid screening methods also may be used to identify polypeptides that bind to the SAP polypeptides. Thus, the SAP polypeptides of the invention, or a fragment thereof, can be used to screen peptide libraries, including phage display libraries, to identify and select peptide binding partners ofthe SAP polypeptides ofthe invention. Such molecules can be used, as described, for screening assays, for purification protocols, for interfering directly with the functioning of SAP and for other purposes that will be apparent to those of ordinary skill in the art. A SAP polypeptide, or a fragment thereof, also can be used to isolate their native binding partners, including, e.g., Smadό, Smad7 and complexes containing those proteins. Isolation of such binding partners may be performed according to well-known methods. For example, isolated SAP polypeptides can be attached to a substrate (e.g., chromatographic media, such as polystyrene beads^ or a filter), and then a solution suspected of containing a Smadό, Smad7 or complex thereof may be applied to the substrate. If a SAP binding partner which can interact with SAP polypeptides is present in the solution, then it will bind to the substrate-bound SAP polypeptide. The SAP binding partner then may be isolated. Other proteins wliich are binding partners for SAP, such as other Smads, cyclin A, etc., may be isolated by similar methods without undue experimentation. It will also be recognized that the invention embraces the use of SAP cDNAs sequences in expression vectors, as well as to transfect host cells and cell lines, be these prokaryotic (e.g., E. coli), or eukaryotic (e.g., CHO cells, COS cells, yeast expression systems and recombinant baculovirus expression in insect cells). Especially useful are mammalian cells such as human, mouse, hamster, pig, goat, primate, etc. They may be of a wide variety of tissue types, and include primary cells and cell lines. Specific examples include keratinocytes, peripheral blood leukocytes, bone marrow stem cells and embryonic stem cells. The expression vectors require that the pertinent sequence, i.e., those nucleic acids described supra, be operably linked to a promoter.

The invention also includes transgenic non-human animals. As used herein, "transgenic non-human animals" includes non-human animals having one or more exogenous nucleic acid molecules incorporated in germ line cells and/or somatic cells. Thus the transgenic animal include "knockout" animals having a homozygous or heterozygous gene disruption by homologous recombination, animals having episomal or chromosomally incorporated expression vectors, etc. Knockout animals can be prepared by homologous recombination using embryonic stem cells as is well known in the art. The recombination can be facilitated by the cre/lox system or other recombinase systems known to one of ordinary skill in the art. In certain embodiments, the recombinase system itself is expressed conditionally, for example, in certain tissues or cell types, at certain embryonic or post- embryonic developmental stages, inducibly by the addition of a compound which increases or decreases expression, and the like. In general, the conditional expression vectors used in such systems use a variety of promoters which confer the desired gene expression pattern (e.g., temporal or spatial). Conditional promoters also can be operably linked to SAP nucleic acid molecules to increase expression of SAP in a regulated or conditional manner. Tr rø-acting negative regulators of SAP activity or expression also can be operably linked to a conditional promoter as described above. Such tr- y-acting regulators include antisense SAP nucleic acids molecules, nucleic acid molecules which encode dominant negative SAP molecules, ribozyme molecules specific for SAP nucleic acids, and the like. The transgenic non-human animals are useful in experiments directed toward testing biochemical or physiological effects of diagnostics or therapeutics for conditions characterized by increased or decreased SAP expression. Other uses will be apparent to one of ordinary skill in the art. The invention also contemplates gene therapy. The procedure for performing ex vivo gene therapy is outlined in U.S. Patent 5,399,346 and in exhibits submitted in the file history of that patent, all ofwhich are publicly available documents. In general, it involves introduction in vitro of a functional copy of a gene into a cell(s) of a subject which contains a defective copy ofthe gene, and returning the genetically engineered cell(s) to the subject. The functional copy ofthe gene is under operable control of regulatory elements which permit expression ofthe gene in the genetically engineered cell(s). Numerous transfection and transduction techniques as well as appropriate expression vectors are well lαiown to those of ordinary skill in the art, some ofwhich are described in PCT application WO95/00654. In vivo gene therapy using vectors such as adenovirus, retroviruses, herpes virus, and targeted liposomes also is contemplated according to the invention. The invention further provides efficient methods of identifying pharmacological agents or lead compounds for agents active at the level of a SAP or SAP fragment modulatable cellular function. In particular, such functions include TGF-β superfamily signal transduction, cyclin regulation and formation of a SAP protein complex. Generally, the screening methods involve assaying for compounds which interfere with a SAP activity such as Smad binding, etc, although compounds which enhance SAP activity also can be assayed using the screening methods. Such methods are adaptable to automated, high throughput screening of compounds. The target therapeutic indications for pharmacological agents detected by the screening methods are limited only in that the target cellular function be subject to modulation by alteration ofthe formation of a complex comprising a SAP polypeptide or fragment thereof and one or more natural SAP intracellular binding targets, such as Smadό. Target indications include cellular processes modulated by TGF-β superfamily signal transduction following receptor-ligand binding.

A wide variety of assays for pharmacological agents are provided, including, labeled in vitro protein-protein binding assays, electrophoretic mobility shift assays, immunoassays, cell-based assays such as two- or three-hybrid screens, expression assays, etc. For example, three-hybrid screens are used to rapidly examine the effect of transfected nucleic acids on the intracellular binding of SAP or SAP fragments to specific intracellular targets. The transfected nucleic acids can encode, for example, combinatorial peptide libraries or antisense molecules. Convenient reagents for such assays, e.g., GAL4 fusion proteins, are known in the art. An exemplary cell-based assay involves transfecting a cell with a nucleic acid encoding a SAP polypeptide fused to a GAL4 DNA binding domain and a nucleic acid encoding a Smad domain which interacts with SAP fused to a transcription activation domain such as VP16. The cell also contains a reporter gene operably linked to a gene expression regulatory region, such as one or more GAL4 binding sites. Activation of reporter gene transcription occurs when the SAP and Smad fusion polypeptides bind such that the GAL4 DNA binding domain and the VP16 transcriptional activation domain are brought into proximity to enable transcription ofthe reporter gene. Agents which modulate a SAP polypeptide mediated cell function are then detected through a change in the expression of reporter gene. Methods for determining changes in the expression of a reporter gene are known in the art. SAP fragments used in the methods, when not produced by a transfected nucleic acid are added to an assay mixture as an isolated polypeptide. SAP polypeptides preferably are produced recombinantly, although such polypeptides may be isolated from biological extracts. Recombinantly produced SAP polypeptides include chimeric proteins comprising a fusion of a SAP protein with another polypeptide, e.g., a polypeptide capable of providing or enhancing protein-protein binding, sequence specific nucleic acid binding (such as GAL4), enhancing stability ofthe SAP polypeptide under assay conditions, or providing a detectable moiety, such as green fluorescent protein or Flag epitope as provided in the examples below. The assay mixture is comprised of a natural intracellular SAP binding target such as Smadό or a fragment thereof capable of interacting with SAP. While natural SAP binding targets may be used, it is frequently preferred to use portions (e.g., peptides or nucleic acid fragments) or analogs (i.e., agents which mimic the SAP binding properties ofthe natural binding target for purposes ofthe assay) ofthe SAP binding target so long as the portion or analog provides binding affinity and avidity to the SAP fragment measurable in the assay. The assay mixture also comprises a candidate pharmacological agent. Typically, a plurality of assay mixtures are run in parallel with different agent concentrations to obtain a different response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration of agent or at a concentration of agent below the limits of assay detection. Candidate agents encompass numerous chemical classes, although typically they are organic compounds. Preferably, the candidate pharmacological agents are small organic compounds, i.e., those having a molecular weight of more than 50 yet less than about 2500, preferably less than about 1000 and, more preferably, less than about 500. Candidate agents comprise functional chemical groups necessary for structural interactions with polypeptides and/or nucleic acids, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two ofthe functional chemical groups and more preferably at least three ofthe functional chemical groups. The candidate agents can comprise cyclic carbon or heterocyclic structure and/or aromatic or polyaromatic structures substituted with one or more ofthe above-identified functional groups. Candidate agents also can be biomolecules such as peptides, saccharides, fatty acids, sterols, isoprenoids, purines, pyrimidines, derivatives or structural analogs ofthe above, or combinations thereof and the like. Where the agent is a nucleic acid, the agent typically is a DNA or RNA molecule, although modified nucleic acids as defined herein are also contemplated.

Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides, synthetic organic combinatorial libraries, phage display libraries of random peptides, and the like. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural and synthetically produced libraries and compounds can be readily be modified through conventional chemical, physical, and biochemical means. Further, known pharmacological agents may be subjected to directed or random chemical modifications such as acylation, alkylation, esterifϊcation, amidification, etc. to produce structural analogs ofthe agents.

A variety of other reagents also can be included in the mixture. These include reagents such as salts, buffers, neutral proteins (e.g., albumin), detergents, etc. which may be used to facilitate optimal protein-protein and/or protein-nucleic acid binding. Such a reagent may also reduce non-specific or background interactions ofthe reaction components. Other reagents that improve the efficiency ofthe assay such as protease, inhibitors, nuclease inhibitors, antimicrobial agents, and the like may also be used.

The mixture ofthe foregoing assay materials is incubated under conditions whereby, but for the presence ofthe candidate pharmacological agent, the SAP polypeptide specifically binds the cellular binding target, a portion thereof or analog thereof. The order of addition of components, incubation temperature, time of incubation, and other perimeters ofthe assay may be readily determined. Such experimentation merely involves optimization ofthe assay parameters, not the fundamental composition ofthe assay. Incubation temperatures typically are between 4°C and 40°C Incubation times preferably are minimized to facilitate rapid, high throughput screening, and typically are between 0.1 and 10 hours. After incubation, the presence or absence of specific binding between the SAP polypeptide and one or more binding targets is detected by any convenient method available to the user. For cell free binding type assays, a separation step is often used to separate bound from unbound components. The separation step may be accomplished in a variety of ways. Conveniently, at least one ofthe components is immobilized on a solid substrate, from which the unbound components may be easily separated. The solid substrate can be made of a wide variety of materials and in a wide variety of shapes, e.g., microtiter plate, microbead, dipstick, resin particle, etc. The substrate preferably is chosen to maximum signal to noise ratios, primarily to minimize background binding, as well as for ease of separation and cost. Separation may be effected for example, by removing a bead or dipstick from a reservoir, emptying or diluting a reservoir such as a microtiter plate well, rinsing a bead, particle, chromatographic column or filter with a wash solution or solvent. The separation step preferably includes multiple rinses or washes. For example, when the solid substrate is a microtiter plate, the wells may be washed several times with a washing solution, which typically includes those components ofthe incubation mixture that do not participate in specific bindings such as salts, buffer, detergent, non-specific protein, etc. Where the solid substrate is a magnetic bead, the beads may be washed one or more times with a washing solution and isolated using a magnet.

Detection may be effected in any convenient way for cell-based assays such as two- or three-hybrid screens. The transcript resulting from a reporter gene transcription assay of SAP polypeptide interacting with a target molecule typically encodes a directly or indirectly detectable product, e.g., β-galactosidase activity, luciferase activity, and the like. For cell free binding assays, one ofthe components usually comprises, or is coupled to, a detectable label. A wide variety of labels can be used, such as those that provide direct detection (e.g., radioactivity, luminescence, optical or electron density, etc), or indirect detection (e.g., epitope tag such as the FLAG epitope, enzyme tag such as horseradish peroxidase, etc.). The label may be bound to a SAP binding partner, or incorporated into the structure ofthe binding partner.

A variety of methods may be used to detect die label, depending on the nature ofthe label and other assay components. For example, the label may be detected while bound to the solid substrate or subsequent to separation from the solid substrate. Labels may be directly detected through optical or electron density, radioactive emissions, nonradiative energy transfers, etc. or indirectly detected witii antibody conjugates, strepavidin-biotin conjugates, etc. Methods for detecting the labels are well known in the art.

The invention provides SAP-specific binding agents, methods of identifying and making such agents, and their use in diagnosis, therapy and pharmaceutical development. For example, SAP-specific pharmacological agents are useful in a variety of diagnostic and therapeutic applications, especially where disease or disease prognosis is associated with improper utilization of a pathway involving SAP, e.g., TGF-β receptor-Smad complex formation, TGF-β superfamily signaling, cyclin regulation ofthe cell cycle, etc. Novel SAP- specific binding agents include SAP -specific antibodies and other natural intracellular binding agents identified with assays such as two hybrid screens, and non-natural intracellular binding agents identified in screens of chemical libraries and tlie like.

In general, the specificity of SAP binding to a binding agent is shown by binding equilibrium constants. Targets which are capable of selectively binding a SAP polypeptide preferably have binding equilibrium constants of at least about 10⁷ M^"1, more preferably at least about 10^s M^"1, and most preferably at least about 10⁹ M^"1. The wide variety of cell based and cell free assays may be used to demonstrate SAP-specific binding. Cell based assays include one, two and three hybrid screens, assays in which SAP-mediated transcription is inhibited or increased, etc. Cell free assays include SAP-protein binding assays, immunoassays, etc. Other assays useful for screening agents which bind SAP polypeptides include fluorescence resonance energy transfer (FRET), and electrophoretic mobility shift analysis (EMSA).

Various techniques may be employed for introducing nucleic acids ofthe invention into cells, depending on whether the nucleic acids are introduced in vitro or in vivo in a host. Such techniques include transfection of nucleic acid-CaPO₄ precipitates, transfection of nucleic acids associated with DEAE, transfection with a retrovirus including the nucleic acid of interest, liposome mediated transfection, and the like. For certain uses, it is preferred to target the nucleic acid to particular cells. In such instances, a vehicle used for delivering a nucleic acid ofthe invention into a cell (e.g., a retrovirus, or other virus; a liposome) can have a targeting molecule attached tliereto. For example, a molecule such as an antibody specific for a surface membrane protein on the target cell or a ligand for a receptor on the target cell can be bound to or incorporated within the nucleic acid delivery vehicle. For example, where liposomes are employed to deliver the nucleic acids ofthe invention, proteins which bind to a surface membrane protein associated with endocytosis may be incorporated into the liposome formulation for targeting and/or to facilitate uptake. Such proteins include capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, proteins that target intracellular localization and enhance intracellular half life, and the like. Polymeric delivery systems also have been used successfully to deliver nucleic acids into cells, as is known by those skilled in the art. Such systems even permit oral delivery of nucleic acids. When administered, the therapeutic compositions of the present invention are administered in pharmaceutically acceptable preparations. Such preparations may routinely contain pharmaceutically acceptable concentrations of salt, buffering agents, preservatives, compatible carriers, supplementary immune potentiating agents such as adjuvants and cytokines and optionally other therapeutic agents. The therapeutics ofthe invention can be administered by any conventional route, including injection or by gradual infusion over time. The admimstration may, for example, be oral, intravenous, intraperitoneal, intramuscular, intracavity, subcutaneous, or transdermal. When antibodies are used therapeutically, a preferred route of admimstration is by pulmonary aerosol. Techniques for preparing aerosol delivery systems containing antibodies are well known to those of skill in the art. Generally, such systems should utilize components which will not significantly impair the biological properties ofthe antibodies, such as the paratope binding capacity (see, for example, Sciarra and Cutie, "Aerosols," in Remington's Pharmaceutical Sciences, 18th edition, 1990, pp 1694-1712; incorporated by reference). Those of skill in the art can readily determine the various parameters and conditions for producing antibody aerosols without resort to undue experimentation. When using antisense preparations ofthe invention, slow intravenous administration is preferred.

The compositions ofthe invention are administered in effective amounts. An "effective amount" is that amount of a composition that alone, or together with further doses, produces the desired response, e.g. alters favorably the signal transduction resulting from binding of a TGF-β superfamily ligand to specific receptors. In the case of treating a particular disease, such as cancer, the desired response is inhibiting the progression ofthe disease. This may involve only slowing the progression ofthe disease temporarily, although more preferably, it involves halting the progression ofthe disease permanently. This can be monitored by routine methods or can be monitored according to diagnostic methods ofthe invention discussed herein. Such amounts will depend, of course, on the particular condition being treated, the severity ofthe condition, the individual patient parameters including age, physical condition, size and weight, the duration of he treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise ofthe health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose ofthe individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons. The pharmaceutical compositions used in the foregoing methods preferably are sterile and contain an effective amount of SAP or nucleic acid encoding SAP for producing the desired response in a unit of weight or volume suitable for administration to a patient. The response can, for example, be measured by determining the signal transduction enhanced or inhibited by the SAP composition via a reporter system as described herein, by measuring downstream effects such as gene expression, or by measuring the physiological effects ofthe SAP composition, such as regression of a tumor or decrease of disease symptoms. Likewise, the effects of antisense SAP molecules can be readily determined by measuring expression of die individual genes in cells to which an antisense composition is added. Other assays will be known to one of ordinary skill in the art and can be employed for measuring the level ofthe response.

The doses of SAP polypeptide or nucleic acid administered to a subject can be chosen in accordance with different parameters, in particular in accordance with the mode of administration used and the state ofthe subject. Other factors include the desired period of treatment. In the event that a response in a subject is insufficient at the initial doses applied, higher doses (or effectively higher doses by a different, more localized delivery route) may be employed to the extent that patient tolerance permits. In general, doses of SAP are formulated and administered in doses between 1 ng and 1 mg, and preferably between 10 ng and 100 μg, according to any standard procedure in the art. Where nucleic acids encoding SAP of variants thereof are employed, doses of between 1 ng and 0.1 mg generally will be formulated and administered according to standard procedures. Other protocols for the administration of SAP compositions will be known to one of ordinary skill in the art, in which the dose amount, schedule of injections, sites of injections, mode of administration (e.g., intra-tumoral) and the like vary from the foregoing. Administration of SAP compositions to mammals other than humans, e.g. for testing purposes or veterinary therapeutic purposes, is carried out under substantially the same conditions as described above.

When administered, the pharmaceutical preparations ofthe invention are applied in pharmaceutically-acceptable amounts and in pharmaceutically-acceptable compositions. The term "pharmaceutically acceptable" means a non-toxic material that does not interfere with the effectiveness ofthe biological activity ofthe active ingredients. Such preparations may routinely contain salts, buffering agents, preservatives, compatible carriers, and optionally other therapeutic agents. When used in medicine, the salts should be pharmaceutically acceptable, but non-pharmaceutically acceptable salts may conveniently be used to prepare pharmaceutically-acceptable salts thereof and are not excluded from the scope ofthe invention. Such pharmacologically and pharmaceutically-acceptable salts include, but are not limited to, those prepared from the following acids: hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, maleic, acetic, salicylic, citric, formic, malonic, succinic, and the like. Also, pharmaceutically-acceptable salts can be prepared as alkaline metal or alkaline earth salts, such as sodium, potassium or calcium salts.

SAPs may be combined, if desired, with a pharmaceutically-acceptable carrier. The term "pharmaceutically-acceptable carrier" as used herein means one or more compatible solid or liquid fillers, diluents or encapsulating substances which are suitable for administration into a human. The term "carrier" denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application. The components ofthe pharmaceutical compositions also are capable of being co-mingled with the molecules of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy. The pharmaceutical compositions may contain suitable buffering agents, including: acetic acid in a salt; citric acid in a salt; boric acid in a salt; and phosphoric acid in a salt.

The pharmaceutical compositions also may contain, optionally, suitable preservatives, such as: benzalkonium chloride; chlorobutanol; parabens and thimerosal. The pharmaceutical compositions may conveniently be presented in unit dosage form and may be prepared by any ofthe methods well-known in the art of pharmacy. All methods include the step of bringing the active agent into association with a carrier which constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing the active compound into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product.

Compositions suitable for oral administration may be presented as discrete units, such as capsules, tablets, lozenges, each containing a predetermined amount ofthe active compound. Other compositions include suspensions in aqueous liquids or non-aqueous liquids such as a syrup, elixir or an emulsion. Compositions suitable for parenteral administration conveniently comprise a sterile aqueous or non-aqueous preparation of SAP polypeptides or nucleic acids, which is preferably isotonic with the blood ofthe recipient. This preparation may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butane diol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil may be employed including synthetic mono-or di-glycerides. In addition, fatty acids such as oleic acid may be used in the preparation of injectables. Carrier formulation suitable for oral, subcutaneous, intravenous, intramuscular, etc. administrations can be found in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA. In another aspect ofthe invention, SAP polypeptides or nucleic acid are used in the manufacture of a medicament for modulating a TGF-β superfamily ligand response. The medicament can be placed in a vial and be incorporated into a kit to be used for increasing a subject's response to one or more TGF-β family members. In certain embodiments, other medicaments which modulate the same responses or which favorably affect the SAP compositions can also be included in the same kit. The kits can include instructions or other printed material on how to administer the SAP compositions and any other components ofthe kit.

Examples Materials and Methods

DNA constructs pEG-Smad6S, pEG-SmadόSN, pEG-Smad6SC, pEG-Smad7, pEG-Smad7N and pEG- Smad7C were made by PCR and inserted into pEG202 (Golemis et al., Analysis of protein interactions, p. 20.1.1-20.1.40 In F. M. Ausubel, R Brent, RE. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith and K. Struhl (eds.), Current Protocols in Molecular Biology, vol. 3, John Wiley & Sons, Inc., 1999). pEG-Smad2 and pEG-Smad4 was obtained from Dr. R. Derynk (Wu et al., ?/. Cell Biol. 17:2521-2528., 1997). όxMyc-Smadl, 6xMyc-Smad2 and 6xMyc-Smad3 were provided by Dr. K. Miyazono (Nishihara et al., Genes. Cells. 3:613- 623, 1998). 6xMyc-Smad4, 6xMyc-Smad6S, όxMyc-SmadόL and 6xMyc-Smad7 were constructed using 6xMyc-pCDNA3 (Nishihara et al., 1998). Flag-AMSH, Flag- AMSH(DBS2), Flag-AMSH(DBS3), Flag-AMSH(DC2), Flag-AMSH(DJS), Flag- AMSH(DNL) were described previously (Tanaka et al., J. Biol. Chem. 274:19129-19135, 1999). Flag-AMSH(Δ102-233), Flag-AMSH( 106-424) and Flag- AMSH(234-424) were generated by PCR and subcloned into pCMV2-Flag vector (Sigma).

Yeast two-hybrid screening

Several constructs of LexA-Smad fusions in the pEG202 vector and human fetal brain library in the pJG4-5 vector were used. Library screens were carried out using Leu2 and β-galactosidase reporters (pSH18-34) within the yeast strain, EGY48. In brief, EGY48 cells were transformed with pEG-SmadόSN, pSH18-34 and library and plated in galactose- containing medium without histidine. Positive colonies were picked 3-5 days after plating (Golemis et al., 1999). Subsequently, positive colonies were tested again and confirmed as real positive clones. DNA sequence analysis

The nucleotide sequences were determined for both strands witii an ABI310 DNA sequencer.

Immunoprecipitation and Western blotting

Combinations of Smads and AMSH or its mutants in the presence or absence of ALK5ca or ALKόca were transfected in COS7 cells at 1.2 x 10⁶ cells/10 cm-dish using Fugene 6 (Boehringer Mannheim). Forty hours after transfection, the cells were lysed in 1 ml of lysis buffer (20 mM Tris [pH7.4], 150 mM NaCl, 10% glycerol, 1% Triton X-100, 1 mM PMSF and 100 units/ml Trasylol). The cell lysates were precleared with protein G-Sepharose beads (Pharmacia) and incubated with Flag M5 antibody (Sigma) for 2 h at 4°C. Subsequently, protein G-Sepharose beads were added to the reaction mixture and samples were incubated for 30 min at 4°C. After washing the immunoprecipitates with lysis buffer three times, immunoprecipitates and aliquots of cell lysates before immunoprecipitation were separated by SDS-polyacrylamide gel electrophoresis and transferred to a Hybond-C extra membrane (Amersham). The membrane was then probed with Flag M5 or Myc (9E10 monoclonal antibody; Santa Cruz) antibody. Primary antibodies were detected with a horseradish peroxidase-conjugated goat anti-mouse antibody (Amersham) and a chemiluminescent substrate.

[32pjθrthophosphate labeling of cells, tryptic phosphopeptide mapping and two- dimensional phosphoamino acid analysis

COS7 cells were labeled in phosphate-free medium for 3 h. Subsequently, 1 mCi/ml [³²P]orthophosphate was added in the culture medium. After 40 min, the cells were lysed, immunoprecipitated with anti-FlagM5 antibody, separated by SDS-polyacrylamide gel electrophoresis and transferred to a Hybond-C extra membrane. For tryptic phosphopeptide mapping, AMSH bands were localized by exposure on a FujiX Bio-Imager (Fuji), excised from the filter and digested in situ with trypsin (modified sequencing grade; Promega). Two- dimensional phosphopeptide mapping was done using the Hunter thin-layer electrophoresis apparatus (HTLE-7000; CBS Scientific), essentially as described by Boyle et al. (Methods Enzymol 201:110-149, 1991). First dimension electrophoresis was performed in pH 1.9 buffer (formic ackkglacial acetic acid:water; 44:156:1800) for 23 min at 2000 V, and second dimension ascending thin-layer chromatography in isobutyric acid buffer (isobutyric acid:n- butanol:pyridine:glacial acetic acid:water; 1250:38:96:58:558). After exposure, phosphopeptides were eluted from the plates in the pH 1.9 buffer and lyophilized. The fractions were then subjected to two-dimensional phosphoamino acid analysis.

Example 1: Isolation of Smad Associating Proteins

To explore further the mode of actions of Smadό and Smad7, proteins that interact with Smadό and Smad7 have been isolated using the yeast two hybrid system. Using the N-terminal half of Smadό MH2 domain (pEG-SmadόSN) (Fig. 1) as a bait to screen a human fetal brain library (4 x 10⁶ colonies), 12 kinds of distinct positive cDNA clones encoding 7 known and 5 unknown proteins were obtained; the latter molecules were termed Smadό associating proteins (SAPs) 1 through 5 (Fig. 2). Subsequently, the interaction of identified molecules with Smad2, Smad4, Smadό or Smad7 was investigated using the yeast two hybrid system. As seen in Fig. 2, all clones except for dodecenoyl-CoA could bind to either SmadόS or Smad7. However, no or very weak interactions between Smad2 or Smad4 and the identified molecules were seen. Among the novel cDNAs, SAPs 1-3 were further analyzed, ofwhich multiple positive clones were isolated (Fig. 2). The entire coding sequences for SAPl (Fig. 3 and SEQ ID NO:l) and SAP2 (Fig. 4 and SEQ ID NO:3) were obtained as expressed sequence tags (ESTs), but no ESTs encoding SAP3 (SEQ ID NO: 5) could be found.

SAPl was previously isolated and termed "associated molecule with the SH3 domain of STAM" (AMSH) (Tanaka et al., 1999). Thus, SAPl is called AMSH in the following. AMSH was originally found to interact with the signal transducing adaptor molecule (STAM). AMSH has three unique motifs in its structure, i.e., a nuclear translocational signal, an SH3 binding site (SXXP; SEQ ID NOJ) and a JABl subdomain homologous region (JSH) (Fig. 5).

In order to investigate whether AMSH interacts with Smads in vivo, COS7 cells were transfected with Flag-tagged AMSH and different Myc-tagged-Smads (Smadl, Smad4, SmadόS, SmadόL and Smad7) in the absence and presence of constitutively active ALK6 (ALKόca). Samples were then subjected to immunoprecipitation with Flag antibodies and blotting with Myc antibodies. AMSH interacted with Smad4, SmadόS and SmadόL weakly in the absence of constitutively activate ALKό in COS7 cells. Interestingly, upon transfection with constitutively active ALKό the interaction of AMSH with Smad4, SmadόS and SmadόL increased. Smad7 constitutively bound to AMSH. However, Smadl did not associate with AMSH.

In a similar experiment, ALK5-deρendent interaction of AMSH was explored. COS7 cells were transfected with Flag-tagged AMSH and different Myc-tagged Smads (Smad2, Smad3, Smad4, SmadόS, SmadόL and Smad7) in the absence and presence of constitutively activated ALK5. Interestingly, activated ALK5 (ALK5ca) promoted the interaction of AMSH with Smad2 and in particular Smad3, while Smad4, SmadόS, SmadόL and Smad7 interact with AMSH independent of ALK5.

It is known that Smadό inhibits the BMP pathway more efficiently than the TGF-β pathway (Hata et al., Genes Devel. 12:186-197, 1998). Since BMP receptors possess an intrinsic serine/threonine kinase, it was examined whether or not AMSH was phosphorylated, and it was determined that AMSH was phosphorylated by activated ALKό. However, AMSH might not be a direct substrate for the serine/threonine kinase of ALKό because the phosphorylation of AMSH was detected 4 h after the treatment with OP-1 in COS7 cells which were reconstituted with AMSH, ALKό and BMPR-II.

TGF-β family signaling has been known to be mediated in part through MAP kinase pathways (Atfi et al., J. Biol. Chem. 272:1429-1432, 1997; Sano et al., J. Biol. Chem.

274:8949-8957, 1999). Therefore, the effect of MAP kinase inhibitors was investigated on the phosphorylation of AMSH. Cells were incubated with inhibitors 3 h before the addition of [³²P]orthophosphate, SB203580, a p38 inhibitor, inhibited the phosphorylation of AMSH in a dose-dependent manner, whereas PD98059, an ERK inhibitor, had no effect. The effect of the third MAP kinase pathway, JNK, on the phosphorylation of AMSH was not investigated because no commercial inhibitor is available. The MAP kinases that mainly contribute to the phosphorylation of AMSH are confirmed using dominant negative JNK and p38 in phosphorylation experiments as described above.

Often, the phosphorylation status of a protein correlates within biological activity. Thus, tryptic phosphopeptide mapping of AMSH stimulated with ALKόca we preformed was performed. Four major phosphopeptides were induced by ALKόca. Phosphoamino acid analysis revealed that only serine residues were phosphorylated. The exact position ofthe phosphorylated serine residues in the phosphopeptides is identified by, e.g., amino acid sequencing ofthe phosphopeptides.

Deletion mutants of AMSH were made to find important regions for biological activity (Fig. 5). The in vivo interaction with SmadόL was investigated for two ofthe mutants which were found to associate with SmadόL in the presence of active ALKό. In particular, AMSH(DC2) which lacks the C-terminal half of AMSH interacted with SmadόL interacted more efficiently with SmadόL in the presence of ALKόca. Repetition ofthe same experiment using all mutants depicted in Fig. 5 is performed to identify portions of AMSH which interact with Smadό and Smad7.

The phosphorylation of AMSH mutants by ALKόca was tested as well. AMSH(DBS2) was highly phosphorylated. On the other hand, the phosphorylation of AMSH(DC2) was very weak. These observations suggest that the N-terminal part of AMSH is involved in the interaction with SmadόL, whereas phosphorylation sites are localized in the C-terminal part. The phosphorylation of other mutants depicted in Fig. 5 by ALKόca also is performed to confirm results and further localize phosphorylation sites.

The effect of AMSH and mutants thereof are tested in a luciferase assay for TGF-β- family-dependent activity (e.g., Jonk et al., J. Biol. Chem. 273:21145-21152, 1998) as well as for their effect in aXenopus animal cap assay (e.g., Nakao et al., Nature 389:631-635, 1997). A Xenopus homologue of S AP2 was recently identified and termed XDRP 1.

(GenBank accession number AB030502; Funakoshi et al., EMBO J. 18:5009-5018, 1999). It was reported that XDRP1 binds to c clin A and inhibits its degradation. Since cyclin A is involved in the cell cycle, it is possible that SmadόL regulates the cell cycle through the interaction with SAP2. Alternatively, SAP2 may regulate the degradation of SmadόL. Other aspects ofthe invention will be clear to the skilled artisan and need not be repeated here. Each reference cited herein is incorporated by reference in its entirety.

The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents ofthe features shown and described or portions thereof, it being recognized that various modifications are possible within the scope ofthe invention. We claim:

Claims

1. An isolated nucleic acid molecule selected from the group consisting of

(a) nucleic acid molecules which hybridize under stringent conditions to a molecule consisting ofthe nucleic acid sequence set forth in SEQ ID NO:3 or SEQ ID NO:5 and which code for a polypeptide which binds Smadό,

(b) nucleic acid molecules that differ from the nucleic acid molecules of (a) in codon sequence due to the degeneracy ofthe genetic code, and

(c) complements of (a) and (b).

2. The isolated nucleic acid molecule of claim 1, wherein the isolated nucleic acid molecule consists of SEQ ID NO:3.

3. The isolated nucleic acid molecule of claim 1, wherein the isolated nucleic acid molecule consists of SEQ ID NO:5.

4. An isolated nucleic acid molecule selected from the group consisting of (a) a unique fragment of nucleotides 1-2399 of SEQ ID NO:3 between 12 and 2398 nucleotides in length, (b) a unique fragment of nucleotides 1-855 of SEQ ID NO: 5 between 12 and 854 nucleotides in length, (c) complements of "(a)" and (d) complements of "(b)", provided that the nucleic acid molecule excludes sequences consisting of GenBank accession numbers AI219112 and N33797, AB030502.

5. The isolated nucleic acid molecule of claim 4, wherein the isolated nucleic acid molecule consists of at least 22, 25, 30, 40, 50, 75 or 100 contiguous nucleotides.

6. The isolated nucleic acid molecule of claim 4, wherein the isolated nucleic acid molecule consists of between 20 and 32 contiguous nucleotides.

7. An expression vector comprising the isolated nucleic acid molecule of any of claims 1 , 2, 3 or 4 operably linked to a promoter.

8. A host cell transformed or transfected with the expression vector of claim 7.

9. A method for producing a polypeptide comprising culturing the host cell of claim 8 under conditions which permit the expression of polypeptide.

10. The method of claim 9, further comprising isolating the polypeptide.

11. A transgenic non-human animal comprising the expression vector of claim 7.

12. An isolated polypeptide encoded by the isolated nucleic acid molecule of any of claims 1, 2 or 3.

13. The isolated polypeptide of claim 12, wherein the isolated polypeptide is selected from the group consisting of molecules comprising the amino acid sequence of SEQ ID NO:4, SEQ ID NO:6, a fragment or functional variant of SEQ ID NO:4, and a fragment or functional variant of SEQ ID NO:6.

14. An isolated polypeptide comprising a fragment or functional variant of SEQ ID NO:2.

15. The isolated polypeptide of claim 14, wherein the isolated polypeptide consists of a fragment of SEQ ID NO:2 selected from the group consisting of amino acids 1-101+234-424, 106-424 and 234-424.

16. An isolated polypeptide which binds selectively a polypeptide encoded by the isolated nucleic acid molecule of any of claims 1 , 2 or 3, provided that the isolated polypeptide is not a Smad, STAM or cyclin polypeptide.

17. The isolated polypeptide of claim 16, wherein the isolated polypeptide binds to an epitope defined by a polypeptide consisting ofthe sequence of SEQ ID NOs:2, 4 or 6.

18. The isolated polypeptide of claim 16, wherein the isolated polypeptide is an antibody fragment selected from the group consisting of a Fab fragment, a F(ab)₂ fragment or a fragment including a CDR3 region selective for a SAP polypeptide.

19. The isolated polypeptide of claim 16, wherein the isolated polypeptide is a monoclonal antibody, a humanized antibody or a chimeric antibody.

20. An isolated complex of polypeptides comprising: a polypeptide as claimed in claim 12 bound to a polypeptide selected from the group consisting of Smadό, Smad7 and fragments thereof.

21. A method for modulating TGF-β superfamily signal transduction in a mammalian cell, comprising contacting the mammalian cell with an amount of an agent which increases the amount of a Smad associating protein selected from the group consisting of SAPl/AMSH (SEQ ID NO:2), SAP2 (SEQ ID NO:4), SAP3 (SEQ ID NO:6), Hsp40 homolog (U40992), Uba80 (X63237), Tax-1 binding protein (U33822), rabaptin-5 (NM_004703), and 26S proteinase S5a (U51007) or a fragment thereof in the cell effective to reduce TGF-β superfamily signal transduction in the mammalian cell.

22. The method of claim 21 , wherein the agent is a nucleic acid molecule.

23. A method for regulating the cell cycle in a mammalian cell, comprising contacting the mammalian cell with an amount of an agent which increases the amount of SAP2 (SEQ ID NO:4), or a fragment thereof, in the cell effective to bind a cyclin and regulate the cell cycle in the mammalian cell.

24. A method for identifying lead compounds for a pharmacological agent, comprising forming a mixture comprising a Smadό or Smad7 polypeptide, a SAP polypeptide, and a candidate pharmacological agent, incubating the mixture under conditions which, in the absence of the candidate pharmacological agent, permit a first amount of specific binding ofthe SAP polypeptide by the Smadό or Smad7 polypeptide, and detecting a test amount ofthe specific binding ofthe SAP polypeptide by the Smadό or Smad7 polypeptide, wherein reduction ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which disrupts the Smadό-SAP or Smad7-SAP binding, and wherein increase ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which enhances the Smadό-SAP or Smad7-S AP binding.

25. The method of claim 24, wherein the SAP polypeptide is selected from the group consisting of SAPl/AMSH, SAP2, SAP3 and fragments thereof.

26. A method for identifying lead compounds for a pharmacological agent, comprising forming a mixture comprising an ALK kinase, a Smad polypeptide, a SAP polypeptide, and a candidate pharmacological agent, incubating the mixture under conditions which, in the absence ofthe candidate pharmacological agent, permit a first amount of specific binding ofthe SAP polypeptide by the Smad polypeptide, and detecting a test amount ofthe specific binding ofthe SAP polypeptide by the Smad polypeptide, wherein reduction ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which disrupts the Smad-SAP binding, and wherein increase ofthe test amount of specific binding relative to the first amount of specific binding indicates that the candidate pharmacological agent is a lead compound for a pharmacological agent which enhances the Smad-SAP binding.

27. The method of claim 26, wherein the SAP polypeptide is selected from the group consisting of SAPl/AMSH, SAP2, SAP3 and fragments tiiereof.

28. The method of claim 26, wherein the Smad polypeptide is selected from the group consisting of Smad2, Smad3, Smad4, Smadό, Smad7 and fragments thereof.

29. The method of claim 26, wherein the ALK kinase is selected from the group consisting of ALK5, constitutively activated ALK5, ALK6, constitutively activated ALKό and fragments thereof having kinase activity.