AU2005207886A1

AU2005207886A1 - Novel brain natriuretic peptide variants and methods of use thereof

Info

Publication number: AU2005207886A1
Application number: AU2005207886A
Authority: AU
Inventors: Michal Ayalon-Soffer; Yossi Cohen; Gad S. Cojocaru; Alexander Diber; Zurit Levine; Amit Novik; Sarah Pollock
Original assignee: Compugen USA Inc
Current assignee: Compugen USA Inc
Priority date: 2004-01-27
Filing date: 2005-01-27
Publication date: 2005-08-11
Also published as: CA2554599A1; EP1730181A2; WO2005072055A9; WO2005072055A2

Description

WO 2005/072055 PCT/IB2005/000995 1 Novel Brain Natriuretic Peptide Variants and Methods of use thereof FIELD OF THE INVENTION The present invention is related to novel nucleotide and protein sequences that are 5 variants of BNP, and assays and methods of use thereof BACKGROUND OF THE INVENTION Degradation and remodeling of the ECM are essential processes for normal repair after tissue trauma. The physiological response to tissue trauma is a complex process 10 involving multiple factors including cell migration and replication, turnover of extracellular matrix (ECM) components and changes to the cellular microenvironment. Essentially, such a response involves the repair or replacement of damaged tissues. The precise nature of such repair or replacement depends upon the tissues involved, although all such processes involve certain basic principles. The normal and necessary repair of any tissue after any trauma 15 requires the coordination of a wide array of factors by regulated gene expression. Fibrosis is therefore typically a reaction to tissue trauma. A number of different factors are believed to affect or modulate the biological pathways or mechanisms leading to tissue fibrosis. Such factors may include early inflammatory actions, a local increase in fibroblast cell populations, modulation of the synthetic function of fibroblasts, and altered 20 regulation of the biosynthesis and degradation of collagen. The pathophysiological response to the tissue trauma seen in fibrosis results in the formation of abnormal tissues which do not duplicate the functionality of the original organ tissue, so that the repair of tissue trauma does not lead to a complete restoration of organ capacity and function. One example of a fibrotic process which results from 25 pathophysiological responses to tissue trauma is cardiac fibrosis. Cardiac fibrosis has a number of causes, which lead to the deposition of fibrotic tissue. For example, cardiac fibrosis may result from heart failure, hypertension and other cardiac pathological/disease states. As the deposition of such fibrotb tissue increases, the ability of the heart to function decreases, leading to disability and eventually death of the patient. The formation of fibrotic 30 tissue in the heart is characterized by the deposition of abnormally large amounts of extracellular matrix components, including collagen, as well as other matrix proteins. Therefore, the cardiac fibrotic process needs to be inhibited in order to prevent damage to the cardiac tissue and hence to the ability of the heart to function.

WO 2005/072055 PCT/IB2005/000995 2 Cardiac fibroblasts are important to the cardiac fibrotic process because they produce interstitial proteins and other myocardial components which have been implicated in heart failure (Hess et al, Circ., 63:360-371 (1981); Villari et al, Am J. Cardiol., 69:927-934 (1992); Villari et al, JACC, 22:1477-1484 (1993); Brilla et al, Circ. Res., 69:107-115 (1991); 5 and Sabbab et a], Mol. & Cell Biochem., 147:29-34 (1995)). The pathology of heart failure is clearly associated with fibrosis for a number of cardiac pathological or disease states, including those associated with both volume and pressure overload (Iaron et al, Am. J. Cardiol., 35:725-739 (1975); Schwarz et al, Am. J. Cardiol., 42:661-669 (1978); Fuster et al, Circ., 55:504-508 (1976); Bartosova et al, J. 10 Physiol., 200:285-295 (1969); Weber et al, Circ., 83:1849-1865 (1991); Schaper et al, Basic Res. Cardiol., 87:S1303-S1309 (1992); Boluyt et al, Circ. Res., 75:23-32 (1994); and Bishop et al, J. Mol. Cell Cardiol., 22:1157-1165 (1990)). Cardiac surgery also may cause cardiac fibrosis; such fibrosis may also lead to the requirement for an additional operation, which is often associated with higher morbidity and mortality. 15 Detection and/or quantitation of cardiac fibrosis is therefore very important for preventing or treating such fibrosis. Various imaging techniques may be used to see the effects of cardiac fibrosis, but actually detecting such fibrosis at the molecular level currently requires an invasive procedure to obtain a tissue sample (biopsy), as there are no conunercially available non-invasive tests for detection of cardiac fibrosis at the molecular 20 level. BNP (Brain Natriuretic Peptide) belongs to a family of natriuretic peptides produced by the heart. BNP and its related natriuretic peptide ANP contain a 17-amino acid ring structure and are produced by the cardiac atria in response to volume overload and by ventricles in response to pressure overload, respectively (Broomsma et al., 2001. 25 Cardiovascular Research 51, 442-449.; McCullough et al., 2003. Reviews in cardiovascular medicine 4, suppl. 7, S3-S 12). These hormones have powerful diuretic, natriuretic, vascular smooth muscle relaxing and vasodilation actions, thus lowering blood volume and blood pressure (Azzay et al., 2003. Heart Failure Review 8, 315-320.). With its impressive physiologic actions, BNP was an attractive target for development as a therapeutic agent for 30 heart failure and/or as a diagnostic marker. Both ANP and BNP are formed as pre-pro-polypeptides. Human BNP is derived from the 134-aa precursor preproBNP. Upon stimulation of release, a 26-aa signal peptide sequence is cleaved from the N-terminus of preproBNP. During release into circulation, the WO 2005/072055 PCT/IB2005/000995 3 remaining proBNP 1-108 prohonnone is further cleaved by corin, a membrane -bound serine protease, into an N-terminal pro-BNP1-76 fragment and the active 32-peptide, C -terminal proBNP77-108 honnone termed BNP (Azzay et al., 2003. Heart Failure Review 8, 315-320.). The principal function of ANP and BNP is to protect the cardiovascular system from volume 5 overload. They are secreted in response to the wall stretch, ventricular dilation and/or increased pressures resulting from fluid overload (Azzay et al., 2003. Heart Failure Review 8, 315-320.). Both cause intravascular volume contraction by inducing a shift of fluid from the capillary bed to the interstitium, resulting in a decrease in preload and blood pressure. BNP has the important ability to decrease left ventricular filling pressures without a resultant 10 reflex tachycardia, reflex vasoconstriction, and further activation of vasoconstricting neurohumoral systems. BNP also has lusiotropic effects and has been demonstrated to inhibit cardiac fibrosis. The natriuretic peptides also appear to exhibit an antimitogenic effect in the heart and other organ systems, suggesting a potential role in the modulation of cell growth. Additional evidence suggests a direct vasodilatory effect on the coronary arteries with a 15 reduction in myocardial oxygen consumption. In addition to these cardiac and vascular properties, BNP has a direct effect on renal hemodynamics and function. Increased glomerular filtration is the result of an unbalanced vasodilatation of the afferent arterioles and vasoconstriction of the efferent arterioles. There also appears to be a direct tubular effect on sodium and water handling, resulting in 20 natriuresis and diuresis as well as inhibition of aldosterone and rennin release. The net effect of these properties is balanced vasodilatation of the arterial and venous beds as well as natriuresis and diuresis (Fonarow G.C, 2003. Heart Failure Review 8, 321-325.). Most effects of ANP and BNP are mediated through binding to the A-type natriuretic peptide receptor, which activates guanyl cyclase, leading to the formation of cyclic guanosine 25 monophosphate (cGMP). CGMP ha s potent vasodilatory actions and acts as a second messenger for BNP. The A-type natriuretic peptide receptor is expressed in a variety of tissues, including kidney, blood vessels, adrenal glands, heart, lungs, adipose tissue, eye, pregnant uterus and placenta. Clearance of ANP and BNP from the blood is effected in two ways: through a special clearance receptor, the C-type natriuretic receptor, and through 30 enzymatic degradation by neutral endopeptidases (Broomsma et al., 2001. Cardiovascular Research 51, 442-449). The natriuretic peptides are characterized by a 17 aa central ring structure, which is formed by a disulfide bridge and is suggested to be necessary for the WO 2005/072055 PCT/IB2005/000995 4 binding of these peptides to their respective receptors and for their biological activity (Azzay et al., 2003. Heart Failure Review 8, 315-320.). ANP and BNP are both expressed more in Atria than Ventrcles. BNP has a more favorable expression in ventricles (atria:ventricle expression ration 3:1 compared with 40:1 to 5 ANP). In a situation of a failing heart both BNP and ANP expression is increased 100-fold above normal levels (Trends Endocrinol Metab. 2003 Nov;14(9):411-6). However, BNP rise is often larger and more rapid than ANP, and it emerged as a superior marker for heart failure and left- ventricular dysfunction (Azzay et al., 2003. Heart Failure Review 8, 315 320.). BNP was shown to have a diagnostic benefit for few different clinical purposes: 1. 10 Elevated plasma levels of BNP are found in conditions of increased cardiac wall stress. In congestive heart failure (CHF), circulating concentrations of BNP are clearly elevated and this elevation reflects the severity of the condition. Therefore it can be used to establish prognosis in patients with heart failure. In addition, it provides a tool to monitor changes in the severity of failure without using more sophisticated diagnostic modalities like Echo 15 imaging. 2. Several studies have clearly shown that natriuretic peptides are excellent prognostic indicators for survival in heart failure. 3. Detection of response to treatment : a continued increase in plasma concentration would be indicative of unsuccessful, and a decrease of successful, treatment. 4. In myocardial 20 infarction ANP and BNP concentrations are also elevated, and are of prognosti: value for indicating patients most at risk. 5. BNP measurements help to differentiate between cardiac versus non-cardiac causes of dyspnea (Lancet. 1994 Feb 19;343(8895):440-4). However there is limited evidence that it can be a useful marker for the very early detection of cardiac damage or heart failure when patients are still asymptomatic. 25 The N -terminal proBNP (ntBNP) is more stable and its serum levels rise more then BNP, therefore it is theoretically a better marker for BNP overproduction than BNP itself. Yet, its added value over BNP diagnostic wise is minor. When studying CHF population with left ventricular ejection fraction (LVEF) < 40% BNP and ntBNP showed no difference in the diagnostic properties. For patients with LVEF<50% (less severe patients), ntBNP showed 30 slight improvement over BNP - receiver operating characteristics area under curve of 0.82 for ntBNP and 0.794 for BNP (Eur J Heart Fail. 2004 Mar 15;6(3):295-300).

WO 2005/072055 PCT/IB2005/000995 5 SUMMARY OF THE INVENTION The background art does not teach or suggest variants of BNP. The background art also does not teach or suggest variants of BNP that are useful as diagnostic markers. The background art also does not teach or suggest variants of BNP that are useful as diagnostic 5 markers for cardiac diseases and/or pathology. The present invention overcomes these deficiencies of the background art by providing BNP variants, which may optionally be used as diagnostic markers. Preferably these BNP variants are useful as diagnostic markers for cardiac diseases and/or pathology, including but not limited to for heart failure and left ventricular 10 disfunction. According to preferred embodiments of the present invention, cardiac disease and/or pathology and/or condition and/or disorder may comprise one or more of Myocardial infarct, acute coronary syndrome, angina pectoris (stable and unstable), cardiomyopathy, myocarditis, congestive heart failure or any type of heart failure, the detection of reinfarction, the detection of success of thrombolytic therapy after Myocardial infarct, 15 Myocardial infarct after surgery, assessing the size of infarct in Myocardial infarct, the differential diagnosis of heart related conditions from lung related conditions (as pulmonary embolism), the differential diagnosis of Dyspnea, and cardiac valve related conditions. As used herein the phrase "cardiac disease" includes any type of cardiac pathology and/or disorder and/or damage, including both chronic and acute damage, as well as 20 progression from acute to chronic damage of the heart, and also propagation of one acute event to another acute event. An example of the latter may occur when an infarct is followed by another infarct in a relatively short period of time, such as within 24 hours for example. An infarct may also lead to acute heart failure immediately after the infarct, as another example. These non-limiting examples are intended to demonstrate that cardiac disease may 25 also comprise a plurality of acute events. These variant markers may be described as "BNP variant disease markers". According to one embodiment of the present invention markers are specifically released to the bloodstream under disease conditions according to one of the above differential variant marker conditions. Optionally and preferably, the variant marker is detected in a biological 30 sample which may optionally be taken from a subject (patient). According to preferred embodiments of the present invention, examples of suitable biological samples include but are not limited to blood, serum, plasma, blood cells, urine, sputum, saliva, stool, spinal fluid, lymph fluid, the external secretions of the skin, respiratory, intestinal, and genitourinary WO 2005/072055 PCT/IB2005/000995 6 tracts, tears, milk, neuronal tissue, and any human organ or tissue. In a preferred embodiment, the biological sample comprises cardiac tissue and/or a serum sample and/or a urine sample and/or any other tissue or liquid sample. The sample can optionally be diluted with a suitable eluant before contacting the sample to the antibody, if an antibody is used. 5 Localization was determined according to four different software programs: tmhmm (from Center for Biological Sequence Analysis, Technical University of Denmark DTU, http://www.cbs.dtu.dk/servicesTMHMM/TMHMM2.Ob.guide.php) or tmpred (from EMBnet, maintained by the ISREC Bionformatics group and the LICR Information Technology 10 Office, Ludwig Institute for Cancer Research, Swiss Institute of Bioinformatics, http://www.ch.embnet.org/softwarelTMPRED-form.html) for transmembrane region prediction; signalphmm and signalpnn (both from Center for Biological Sequence Analysis, Teclmical University of Denmark DTU, http://www.cbs.dtu.dk/services/SignaIP/background/prediction.php) for signal peptide prediction. 15 The terms "signalphmm and signalp nn" refer to two modes of operation for the program SignalP: hmm refers to Hidden Markov Model, while nn refers to neural networks. Localization was also determined through manual inspection of known protein localization and/or gene structure, and the use of heuristics by the individual invertor. In some cases for the manual inspection of cellular localization prediction inventors used the ProLoc 20 computational platform [Einat Hazkani-Covo, Erez Levanon, Galit Rotman, Dan Graur and Amit Novik; (2004) Evolution of multicellularity in metazoa: comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila and Caenorhabditis. Cell Biology International 2004;28(3):171-8.], which predicts protein localization based on various parameters including, protein domains (e.g., prediction of trans- membranous regions 25 and localization thereof within the protein), pI, protein length, amino acid composition, homology to pre-annotated proteins, recognition of sequence patterns which direct the protein to a certain organelle (such as, nuclear localization signal, NLS, mitochondria localization signal), signal peptide and anchor modeling and using unique domains from Pfam that are specific to a single compartment. 30 Information is given in the text with regard to SNPs (single nucleotide polymorphisms). A description of the abbreviations is as follows. "T - > C" means that the SNP results in a change at the position given in the table from T to C. Similarly, "M - > Q" WO 2005/072055 PCT/IB2005/000995 means that the SNP has caused a change in the corresponding amino acid sequence, from methionine (M) to glutamine (Q). If, in place of a letter at the right hand side for the nucleotide sequence SNP, there is a space, it indicates that a frameshift has occurred. A frameshift may also be indicated with a hyphen (-). A stop codon is indicated with an 5 asterisk at the right hand side (*). As part of the description of an SNP, a comment may be found in parentheses after the above description of the SNP itself. This comment may include an FTId, which is an identifier to a SwissProt entry that was created with the indicated SNP. An FTId is a unique and stable feature identifier, which allows to construct links directly from position-specific annotation in the feature table to specialized protein 10 related databases. The FTId is always the last component of a feature in the description field, as follows: FTId=XXX number, in which XXX is the 3-letter code for the specific feature key, separated by an underscore from a 6-digit number. In the table of the amino acid mutations of the wild type proteins of the selected splice variants of the invention, the header of the first column is "SNP position(s) on amino acid sequence", representing a position of a 15 known mutation on amino acid sequence. SNPs may optionally be used as diagnostic markers according to the present invention, alone or in combination with one or more other SNPs and/or any other diagnostic marker. Preferred embodiments of the present invention comprise such SNPs, including but not limited to novel SNPs on the known (WT or wild type) protein sequences given below, as well as novel nucleic acid and/or amino acid 20 sequences formed through such SNPs, and/or any SNP on a variant amino acid and/or nucleic acid sequence described herein. The below list relates to abbreviations on the histogram showing EST expression of this cluster (tissues not shown had neglible or no expression). ADP = adipocyte 25 BLD = blood BLDR = bladder BRN = brain BONE = bone BM = bone marrow 30 BRS = mammary gland CAR cartilage CNS = central nervous system COL = colon WO 2005/072055 PCT/IB2005/000995 8 E-ADR = endocrineadrenal gland E-PAN = endocrinepancreas E-PT = endocrineparathyroid thyroid ENDO = endocrine unchar 5 EPID =epididymis GI = gastrointestinal tract GU = genitourinary HN= head and neck HRT =heart 10 KD=kidney LI = liver LUNG = lung LN = lymph node MUS = muscle 15 OV=ovary PNS = peripheral nervous system PRO= prostate SKIN = skin SPL = spleen 20 SYN synovial membrane TCELL = immune T cells THYM thymus TST = testes UTER = cervix-uterus 25 VAS = vascular The Homology to the wild type was determined by Smith-Waterman version 5.1.2 Using Special (non default) parameters as follows: -model=sw.model 30 -GAPEXT=0 -GAPOP=100.0 -MATRIX=blosum100 WO 2005/072055 PCT/IB2005/000995 9 It should be noted that the terms "segment", "seg" and "node" are used interchangeably in reference to nucleic acid sequences of the present invention; they refer to portions of nucleic acid sequences that were shown to have one or more properties as described below. They are also the building blocks that were used to construct complete 5 nucleic acid sequences as described in greater detail below. Optionally and preferably, they are examples of oligonucleotides which are embodiments of the present invention, for example as amplicons, hybridization units and/or from which primers and/or complementary oligonucleotides may optionally be derived, and/or for any other use. As used herein the phrase "cardiac disease" includes any type of cardiac pathology 10 and/or disorder and/or damage, including both chronic and acute damage, as well as progression from acute to chronic damage of the heart, and also propagation of one acute event to another acute event. An example of the latter may occur when an infarct is followed by another infarct in a relatively short period of tirne, such as within 24 hours for example . An infarct may also lead to acute heart failure immediately after the infarct, as another 15 example. These non-limiting examples are intended to demonstrate that cardiac disease may also comprise a plurality of acute events. The term "marker" in the context of the present invention refers to a nucleic acid fragment, a peptide, or a polypeptide, which is differentially present in a sample taken from patients having a cardiac disease, such as acute cardiac damage for example, as compared to 20 a comparable sample taken from subjects who do not have cardiac disease. As used herein the phrase "differentially present" refers to differences in the quantity of a marker present in a sample taken from patients having cardiac disease as compared to a comparable sample taken from patients who do not have cardiac disease. For example, a nucleic acid fragment may optionally be differentially present between the two samples if 25 the amount of the nucleic acid fragment in one sample is significantly different from the amount of the nucleic acid fragment in the other sample, for example as measured by hybridization and/or NAT-based assays. A polypeptide is differentially present between the two samples if the amount of the polypeptide in one sample is significantly different from the amount of the polypeptide in the other sample. It should be noted that if the marker is 30 detectable in one sample and not detectable in the other, then such a marker can be considered to be differentially present. For example, in the case of acute cardiac damage, it is possible that a marker (such as a protein or fragment thereof) could optionally be present in a blood sample from the patient, indicating the presence of damage; lack of presence of such a WO 2005/072055 PCT/IB2005/000995 10 marker (and/or presence at a low level) would therefore optionally and preferably indicate a lack of such damage. Alternatively, chronically damaged heart might cause a low level of the marker to be present in the blood sample, while acute damage would cause a high level to be present. One of ordinary skill in the art could easily detennine such relative levels of 5 the markers; further guidance is provided in the description of each individual marker below. As used herein the phrase "diagnostic" means identifying the presence or nature of a pathologic condition. Diagnostic methods differ in their sensitivity and specificity. The "sensitivity" of a diagnostic assay is the percentage of diseased individuals who test positive 10 (percent of "true positives"). Diseased individuals not detected by the assay are "false negatives." Subjects who are not diseased and who test negative in the assay are termed "true negatives." The "specificity" of a diagnostic assay is 1 minus the false positive rate, where the "false positive" rate is defined as the proportion ofthose without the disease who test positive. While a particular diagnostic method may not provide a definitive diagnosis of a 15 condition, it suffices if the method provides a positive indication that aids in diagnosis. As used herein the phrase "diagnosing" refers to classifying a disease or a symptom, determining a severity of the disease, monitoring disease progression, forecasting an outcome of a disease and/or prospects of recovery. The term "detecting" may also optionally encompass any of the above. 20 Diagnosis of a disease according to the present invention can be effected by determining a level of a polynucleotide or a polypeptide of the present invention in a biological sample obtained from the subject, wherein the level determined can be correlated with predisposition to, or presence or absence of the disease. It should be noted that a "biological sample obtained from the subject" may also optionally comprise a sample that 25 has not been physically removed from the subject, as described in greater detail below. As used herein, the term "level" refers to expression levels of RNA and/or protein or to DNA copy number of a marker of the present invention. Typically the level of the marker in a biological sample obtained from the subject is different (i.e., increased or decreased) from the level of the same variant in a similar sample 30 obtained from a healthy individual (examples of biological samples are described herein). Numerous well known tissue or fluid collection methods can be utilized to collect the biological sample from the subject in order to determine the level of DNA, RNA and/or polypeptide of the variant of interest in the subject.

WO 2005/072055 PCT/IB2005/000995 11 Examples include, but are not limited to, fine needle biopsy, needle biopsy, core needle biopsy and surgical biopsy (e.g., brain biopsy), and lavage. Regardless of the procedure employed, once a biopsy/sample is obtained the level of the variant can be determined and a diagnosis can thus be made. 5 Deternining the level of the same variant in normal tissues of the same origin is preferably effected along-side to detect an elevated expression and/or amplification and/or a decreased expression, of the variant as opposed to the nonnal tissues. A "test amount" of a marker refers to an amount of a marker present in a sample being tested. A test amount can be either in absolute amount (e.g., microgram/ml) or a 10 relative amount (e.g., relative intensity of signals). A "test amount" of a marker refers to an amount of a marker in a subject's sample that is consistent with a diagnosis of cardiac disease. A test amount can be either in absolute amount (e.g., microgram/ml) or a relative amount (e.g., relative intensity of signals). A "control amount" of a marker can be any amount or a range of amounts to be 15 compared against a test amount of a marker. For example, a control amount of a marker can be the amount of a marker in a patient with cardiac disease or a person without cardiac disease. A control amount can be either in absolute amount (e.g., microgram/ml) or a relative amount (e.g., relative intensity of signals). "Detect" refers to identifying the presence, absence or amount of the object to be 20 detected. A "label" includes any moiety or item detectable by spectroscopic, photo chemical, biochemical, immunochemical, or chemicalmeans. For example, useful labels include 32P, 35S, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin-streptavadin, dioxigenin, haptens and proteins for which antisera or 25 monoclonal antibodies are available, or nucleic acid molecules with a sequence complementary to a target. The label often generates a measurable signal, such as a radioactive, chromogenic, or fluorescent signal, that can be used to quantify the amount of bound label in a sample. The label can be incorporated in or attached to a primer or probe either covalently, or through ionic, van der Waals or hydrogen bonds, e.g., incorporation of 30 radioactive nucleotides, or biotinylated nucleotides that are recognized by streptavadin. The label may be directly or indirectly detectable. Indirect detection can involve the binding of a second label to the first label, directly or indirectly. For example, the label can be the ligand of a binding partner, such as biotin, which is a binding partner for streptavadin, or a WO 2005/072055 PCT/IB2005/000995 12 nucleotide sequence, which is the binding partner for a complementary sequence, to which it can specifically hybridize. The binding partner may itself be directly detectable, for example, an antibody may be itself labeled with a fluorescent molecule. The binding partner also may be indirectly detectable, for example, a nucleic acid having a complementary nucleotide 5 sequence can be a part of a branched DNA molecule that is in turn detectable through hybridization with other labeled nucleic acid molecules (see, e.g., P. D. Falirlander and A. Klausner, Bio/Technology 6:1165 (1988)). Quantitation of the signal is achieved by, e.g., scintillation counting, densitometry, or flow cytometry. Exemplary detectable labels, optionally and preferably for use with immunoassays, 10 include but are not limited to magnetic beads, fluorescent dyes, radiolabels, enzymes (e.g., horse radish peroxide, alkaline phosphatase and others commonly used in an ELISA), and calorimetric labels such as colloidal gold or colored glass or plastic beads. Alternatively, the marker in the sample can be detected using an indirect assay, wherein, for example, a second, labeled antibody is used to detect bound marker-specific antibody, and/or in a 15 competition or inhibition assay wherein, for exmple, a monoclonal antibody which binds to a distinct epitope of the marker are incubated simultaneously with the mixture. "Immunoassay" is an assay that uses an antibody to specifically bind an antigen. The immunoassay is characterized by the use of specific binding properties of a particular antibody to isolate, target, and/or quantify the antigen. 20 The phrase "specifically (or selectively) binds" to an antibody or "specifically (or selectively) immunoreactive with," when referring to a protein or peptide (or other epitope), refers to a binding reaction that is determinative of the presence of the protein in a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two 25 times greater than the background (non-specific signal) and do not substantially bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody tbat is selected for its specificity for a particular protein. For example, polyclonal antibodies raised to seminal basic protein from specific species such as rat, mouse, or human can be selected to obtain only those polyclonal 30 antibodies that are specifically immunoreactive with seminal basic protein and not with other proteins, except for polymorphic variants and alleles of seminal basic protein. This selection may be achieved by subtracting out antibodies that cross-react with seminal basic protein molecules from other species. A variety of imrnnoassay formats may be used to select WO 2005/072055 PCT/IB2005/000995 13 antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Antibodies, A Laboratory Manual (1988), for a description of immunoassay formats and conditions that can be used to determine specific 5 immunoreactivity). Typically a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background. According to preferred embodiments of the present invention, preferably any of the above nucleic acid and/or amino acid sequences further comprises any sequence having at least about 70%, preferably at least about 80%, more preferably at least about 90%, most 10 preferably at least about 95% homology thereto. All nucleic acid sequences and/or amino acid sequences shown herein as embodiments of the present invention relate to their isolated form, as isolated polynucleotides (including for all transcripts), oligonucleotides (including for all segments, amplicons and primers), peptides (including for all tails, bridges, insertions or heads, 15 optionally including other antibody epitopes as described herein) and/or polypeptides (including for all proteins). It should be noted that oligonucleotide and polynucleotide, or peptide and polypeptide, may optionally be used interchangeably. Unless otherwise noted, all experimental data relates to variants of the present invention, named according to the segment being tested (as expression was tested through 20 RT-PCR as described). According to preferred embodiments of the present invention, there is provided an isolated polynucleotide comprising a nucleic acid sequence selected from the group consisting of: HUMNATPEPPEA_1_TI, HUMNATPEPPEA_1_T2, HUMNATPEPPEA_1_T3 or HUMNATPEPPEA_1_T4. 25 According to preferred embodiments of the present invention, there is provided an isolated polynucleotide segment comprising a nucleic acid sequence selected from the group consisting of: HUMNATPEPPEA_1_node 0, HUMNATPEPPEA_1_node_1, HUMNATPEPPEA_1_node_2, HUMNATPEPPEAInode_3, HUMNATPEPPEA_1_node_4, HUMNATPEPPEA_1_node_5, or 30 HUMNATPEPPEA_1_node_6. According to preferred embodiments of the present invention, there is provided an isolated polypeptide comprising an amino acid sequence selected from the group consisting of: HUMNATPEPPEA_1 P2, HUMNATPEPPEA_1_P3 or HUMNATPEPPEA_1_P7.

WO 2005/072055 PCT/IB2005/000995 14 According to preferred embodiments of the present invention, there is provided an isolated chimeric polypeptide encoding for HUMNATPEPPEA_1_P2, comprising a first arnino acid sequence being at least 90 % homologous to MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLET SGLQEQRNHLQGKLSEL 5 QVEQTSLEPLQESPRPTGVWKSREVATEGIRGHRKMVLYTLRAPRSPKMVQGSGCF GRKMDRISSSSGLGCK corresponding to amino acids I - 129 of ANFBHUMAN, which also corresponds to amino acids I - 129 of HUMNATPEPPEA__P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide 10 having the sequence GKHPLPPRPPSPIPVCDTVRVTLGFVVSGNHTL corresponding to amino acids 130 - 162 of HUMNATPEPPEA_1_P2, wherein said first and second amino acid sequences are contiguous and in a sequential order. According to preferred embodiments of the present invention, there is provided an isolated polypeptide encoding for a tail of HUMNATPEPPEA_1_P2, comprising a 15 polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GKHPLPPRPPSPIPVCDTVRVTLGFVVSGN TL in HUMNATPEPPEA_1_P2. According to preferred embodiments of the present invention, there is provided an 20 isolated chimeric polypeptide encoding for HUMNATPEPPEA_1 P3, comprising a first amino acid sequence being at least 90 % homologous to MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLETSGLQ corresponding to amino acids I - 44 of ANFB_HUMAN, which also corresponds to amino acids 1 - 44 of HUMNATPEPPEA_1_P3, and a second amino acid sequence being at least 70%, 25 optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRAEGSSGGLDSSNERVLTCCPKRPSSFLWN corresponding to amino acids 45 - 75 of HUMNATPEPPEA_1_P3, wherein said first and second amino acid sequences are contiguous and in a sequential order. 30 According to preferred embodiments of the present invention, there is provided an isolated polypeptide encoding for a tail of HUMNATPEPPEA_1_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to WO 2005/072055 PCT/IB2005/000995 15 the sequence VRAEGSSGGLDSSNERVLTCCPKRPSSFLWN in HUMNATPEPPEA1_P3. According to preferred embodiments of the present invention, there is provided an isolated chimeric polypep tide encoding for HUMNATPEPPEA_1_P7, comprising a first 5 amino acid sequence being at least 90 % homologous to MVLYTLRAPRSPKMVQGSGCFGRKMDRISSSSGLGCKVLRRH corresponding to amino acids 93 - 134 of ANFB_HUMAN, which also corresponds to amino acids I - 42 of HUMNATPEPPEA_1_P7. According to preferred embodiments of the present invention, there is provided an 10 antibody capable of specifically binding to an epitope of an amino acid sequence as described herein. Optionally amino acid sequence corresponds to a tail as described herein. Also optionally, the antibody is capable of differentiating between a splice variant having said epitope and a corresponding known protein. 15 According to preferred embodiments of the present invention, there is provided a kit for detecting heart disorders, comprising a kit detecting overexpression of a splice variant as described herein. Optionally, the kit comprises a NAT-based technology. Also optionally, the kit further comprises at least one primer pair capable of selectively hybridizing to a nucleic acid sequence as described herein. 20 Optionally, the kit further comprises at least one oligonucleotide capable of selectively hybridizing to a nucleic acid sequence as described herein. Also optionally, the kit comprises an antibody as described herein. Preferably, the kit further comprises at least one reagent for performing an ELISA or a Western blot. According to preferred embodiments of the present invention, there is provided a 25 method for detecting heart disorders, comprising detecting overexpression of a splice variant according to any of the above claims. Optionally, detecting overexpression is performed with a NAT-based technology. Also optionally, detecting overexpression is performed with an immunoassay. Preferably, the immunoassay comprises an antibody as described herein. According to preferred embodiments of the present invention, there is provided a 30 biomarker capable of detecting a BNP variant-detectable disease, comprising any of the above nucleic acid sequences or a fragment thereof, or any of the above amino acid sequences or a fragment thereof.

WO 2005/072055 PCT/IB2005/000995 16 According to preferred embodiments of the present invention, there is provided a method for screening for variant-detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay as described herein. 5 According to preferred embodiments of the present invention, there is provided a method for diagnosing a BNP variant detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay as described herein. According to preferred embodiments of the present invention, there is provided a 10 method for monitoring disease progression and/or treatment efficacy and/or detection of acute over chronic exacerbation of a BNP variant-detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay as described herein. According to preferred embodiments of the present invention, there is provided a 15 method of selecting a therapy for a BNP variant-detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay as described herein and selecting a therapy according to said detection. Optionally, the BNP variant-detectable disease comprises heart failure and/or left ventricular disfunction. 20 According to preferred embodiments of the present invention, there is provided a nucleic acid construct comprising the isolated polynucleotide as described herein. Optionally, the nucleic acid construct further comprises a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation. Optionally, the nucleic acid construct further comprises a positive and a negative 25 selection marker for selecting for homologous recombination events. According to preferred embodiments of the present invention, there is provided a host cell comprising the nucleic acid construct as described herein. According to preferred embodiments of the present invention, there is provided an isolated polypeptide comprising an amino acid sequence at least 70 % identical to a 30 polypeptide as described herein, as determined using the LALIGN software of EMBnet switzerland (http://www.ch.embnet.org/index.html) using default parameters or an active portion thereof.

WO 2005/072055 PCT/IB2005/000995 17 According to preferred embodiments of the present invention, there is provided an oligonucleotide specifically hybridizable with a nucleic acid sequence encoding a polypeptide as described herein. According to preferred embodiments of the present invention, there is provided a 5 pharmaceutical composition comprising a therapeutically effective amount of a polypeptide as described herein and a phannaceutically acceptable carrier or diluent. According to preferred embodiments of the present invention, there is provided a method of treating BNP-related disease in a subject, the method comprising upregulating in the subject expression of a polypeptide as described herein, thereby treating the BNP-related 10 disease in a subject. Optionally, upregulating expression of said polypeptide is effected by: (i) administering said polypeptide to the subject; and/or (ii) administering an expressible polynucleotide encoding said polypeptide to the subject. According to preferred embodiments of the present invention, there is provided an 15 isolated oligonucleotide, comprising an amplicon selected from the group consisting of SEQ ID NOs: 20, 23 or 26. According to preferred embodiments of the present invention, there is provided a primer pair, comprising a pair of isolated oligonucleotides capable of amplifying an amplicon or segment as described herein. Optionally, the primer pair comprises a pair of 20 isolated oligonucleotides selected from the group consisting of: SEQ NOs 18 and 19; 21 and 22; 24 and 25; or 27 and 28. Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms 25 used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). All of these are hereby incorporated by reference as if fully set forth herein. As used herein, the following terms 30 have the meanings ascribed to them unless specified otherwise. BRIEF DESCRIPTION OF THE DRAWINGS WO 2005/072055 PCT/IB2005/000995 18 The invention is herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only, and are presented in the cause of 5 providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for a fundamental understanding of the invention, the description taken with the drawings making apparent to those skilled in the art how the several forms of the invention may be embodied in practice. 10 In the drawings: Figure 1 shows a schematic summary of quantitative real-time PCR analysis. Figure 2 shows expression of ESTs in each category, as "parts per million". Figure 3A shows a comparison of the genomic structure for the variant transcript HUMNATPEP_PFA_1_TI and the known or "WT" transcript. Figure 3B shows a 15 comparison of the structure of the variant protein HUMNATPEPPEA_1_P2 in comparison to the structure of the known or "WT" protein. Figure 4 shows the expression of ANFB1-UMAN Natriuretic peptide transcripts detectable by HUM\NATPEP seg5 amplicon in heart tissue samples as opposed to other tissues. 20 Figure 5 is a histogram showing specific expression of HUMNATPEP seg2 transcripts in heart tissue samples as opposed to other tissues. Figure 6 is a hisiogram showing relative expression of the above- indicated Homo sapiens natriuretic peptide precursor B (NPPB) known protein transcripts in heart tissue samples as opposed to other tissues. 25 Figure 7: presents RTPCR results of known BNP transcript and the HUMNATPEPPEA_1_Ti splice variant, as described above. The expression of known BNP transcript was found to occur in normal heart tissue, while no expression of HUMNATPEPPEA_1_Ti variant was detected in this tissue panel. Specific expression of the HUMNATPEPPEA_1_T1 variant in focal fibrosis heart tissue was demonstrated. "N" 30 means normal heart tissue; "F" means fibrotic heart tissue; "Neg " means negative control, without reverse transcriptase.

WO 2005/072055 PCT/IB2005/000995 19 DESCRIPTION OF PREFERRED EMBODIMENTS The present invention overcomes these deficiencies of the background art by providing BNP variants, which may optionally be used as diagnostic markers. Preferably these BNP variants are useful as diagnostic markers for cardiac diseases 5 and/or pathology, including but not limited to heart failure and left ventricular disfunction. The variants of the present invention may optionally be used, additionally or alternatively, for therapeutic uses, including but not limited to, diuretic, natriuretic, vascular smooth muscle relaxing and vasodilation actions, and lowering blood volume and blood pressure. These variants may optionally be used for therapeutic treatment of heart failure. 10 The present invention is of novel markers for cardiac disease that are both sensitive and accurate. Biomo lecular sequences (amino acid and/or nucleic acid sequences) uncovered using the methodology of the present invention and described herein can be efficiently utilized as tissue or pathological markers and/or as drugs or drug targets for treating or prevent ing a disease. 15 These markers are specifically released to the bloodstream under conditions of cardiac disease and/or cardiac pathology, including but not limited to cardiac damage, and/or are otherwise expressed at a much higher level and/or specifically expressed in heart. The method of the present invention identifies clusters (genes) which are characterized in that the transcripts are differentially expressed in heart muscle tissue compared with other normal 20 tissues, preferably in comparison to skeletal muscle tissue. In acute conditions under which heart muscle tissue experiences hypoxia (with or without necrosis), intracellular proteins that are not normally secreted can leak through the cell membrane to the extracellular space. Therefore, heart muscle tissue differentially expressed proteins, as through analysis of EST expression, are potential acute heart damage markers. 25 Leakage of intracellular content can also occur in chronic damage to the heart muscle, therefore proteins selected according to this method are potential markers for chronic heart conditions. When a protein that is differentially expressed in heart muscle is secreted, it is even more likely to be useful as a chronic heart damage marker, since secretion implies that the protein has a physiological role exterior to the cell, and therefore may be 30 used by the heart muscle to respond to the chronic damage. This rationale is empirically supported by the non-limiting examples of the proteins BNP (brain natriuretic peptide) and ANF (atrial nairiuretic factor), which are differentially expressed heart muscle proteins that are secreted and which were shown to be markers for congestive heart failure. In addition, WO 2005/072055 PCT/IB2005/000995 20 BNP and ANF are not only differentially expressed in heart tissue, they are also overexpressed dramatically (hundreds of times greater expression) when heart failure occurs. Other heart specific secreted proteins might present similar overexpression in chronic damage. 5 Optionally and preferably, the markers described herein are overexpressed in heart as opposed to muscle, as described in greater detail below. The measurement of these markers, alone or in combination, in patient samples provides information that the diagnostician can correlate with a probable diagnosis of cardiac disease and/or cardiac pathology, including but not limited to cardiac damage. 10 The present invention therefore also relates to diagnostic assays for cardiac disease and/or cardiac pathology, including but not limited to cardiac damage, and methods of use of such maikers for detection of cardiac disease and/or cardiac pathology, including but not limited to cardiac damage (alone or in combination), optionally and preferably in a sample taken from a subject (patient), which is more preferably some type of blood sample. 15 The present invention therefore also relates to diagnostic assays for cardiac disease and/or cardiac pathology, including but not limited to cardiac damage, and methods of use of such markers for detection of cardiac disease and/or cardiac pathology, including but not limited to cardiac damage (alone or in combination), optionally and preferably in a sample taken from a subject (patient), which is more preferably some type of blood sample. 20 In another embodiment, the present invention relates to bridges, tails, heads and/or insertions, and/or analogs, homologs and derivatives of such peptides. Such bridges, tails, heads and/or insertions are described in greater detail below with regard to the Examples. As used herein a "tail" refers to a peptide sequence at the end of an amino acid sequence that is unique to a splice variant according to the present invention. Therefore, a 25 splice variant having such a tail may optionally be considered as a chimera, in that at least a first portion of the splice variant is typically highly homologous (often 100% identical) to a portion of the corresponding known protein, while at least a second portion of the variant comprises the tail. As used herein a "head" refers to a peptide sequence at the beginning of an amino 30 acid sequence that is unique to a splice variant according to the present invention. Therefore, a splice variant having such a head may optionally be considered as a chimera, in that at least a first portion of the splice variant comprises the head, while at least a second WO 2005/072055 PCT/IB2005/000995 21 portion is typically highly homologous (often 100% identical) to a portion of the con-esponding known protein. As used herein "an edge portion" refers to a connection between two portions of a splice variant according to the present invention that were not joined in the wild type or 5 known protein. An edge may optionally arise due to a join between the above "known protein" portion of a variant and the tail, for example, and/or may occur if an internal portion of the wild type sequence is no longer present, such that two portions of the sequence are now contiguous in the splice variant that were not contiguous in the known protein. A "bridge" may optionally be an edge portion as described above, but may also include a join 10 between a head and a "known protein" portion of a variant, or a join between a tail and a "known protein" portion of a variant, or a join between an insertion and a "known protein" portion of a variant. Optionally and preferably, a bridge between a tail or a head or a unique insertion, and a "known protein" portion of a variant, comprises at least about 10 amino acids, more 15 preferably at least about 20 amino acids, most preferably at least about 30 amino acids, and even more preferably at least about 40 amino acids, in which at least one amino acid is from the tail/head/insertion and at least one amino acid is from the "known protein" portion of a variant. Also optionally, the bridge may comprise any number of amino acids from about 10 to about 40 amino acids (for example, 10, 11, 12, 13...37, 38, 39, 40 amino acids in length, 20 or any number in between). It should be noted that a bridge cannot be extended beyond the length of the sequence in either direction, and it should be assumed that every bridge description is to be read in such manner that the bridge length does not extend beyond the sequence itself. Furthermore, bridges are described with regard to a sliding window in certain 25 contexts below. For example, certain descriptions of the bridges feature the following format: a bridge between two edges (in which a portion of the known protein is not present in the variant) may optionally be described as follows: a bridge portion of CONTIG NAMEP1 (representing the name of the protein), comprising a polypeptide having a length "n", wherein n is at least about 10 amino acids in length, optionally at least about 20 amino 30 acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise XX (2 amino acids in the center of the bridge, one from each end of the edge), having a structure as follows (numbering according to the WO 2005/072055 PCT/IB2005/000995 22 sequence of CONTIG-NAME P1): a sequence starting from any of amino acid numbers 49 x to 49 (for example); and ending at any of amino acid numbers 50 + ((n-2) - x) (for example), in which x varies from 0 to n2. In this example, it should also be read as including bridges in which n is any number of amino acids between 10-50 amino acids in 5 length. Furthermore, the bridge polypeptide cannot extend beyond the sequence, so it should be read such that 49-x (for example) is not less than 1, nor 50 + ((n-2) - x) (for example) greater than the total sequence length. In another embodiment, this invention provides antibodies specifically recognizing the splice variants and polypeptide fragments thereof of this invention. Preferably such 10 antibodies differentially recognize splice variants of the present invention but do not recognize a corresponding known protein (such known proteins are discussed with regard to their splice variants in the Examples below). In another embodiment, this invention provides an isolated nucleic acid molecule encoding for a splice variant according to the present invention, having a nucleotide 15 sequence as set forth in any one of the sequences listed herein, or a sequence complementary thereto. In another embodiment, this invention provides an isolated nucleic acid molecule, having a nucleotide sequence as set forth in any one of the sequences listed herein, or a sequence complementary thereto. In another embodiment, this invention provides an oligonucleotide of at least about 12 nucleotides, specifically hybridizable with the nucleic 20 acid molecules of this invention. In another embodiment, this invention provides vectors, cells, liposomes and compositions comprising the isolated nucleic acids of this invention. In another embodiment, this invention provides a method for detecting a splice variant according to the present invention in a biological sample, comprising: contacting a biological sample with an antibody specifically recognizing a splice variant according to the 25 present invention under conditions whereby the antibody specifically interacts with the splice variant in the biological sample but do not recognize known corresponding proteins (wherein the known protein is discussed with regard to its splice variant(s) in the Examples below), and detecting said interaction; wherein the presence of an interaction correlates with the presence of a splice variant in the biological sample. 30 In another embodiment, this invention provides a method for detecting a splice variant nucleic acid sequences in a biological sample, comprising: hybridizing the isolated nucleic acid molecules or oligonucleotide fragments of at least about a minimum length to a nucleic acid material of a biological sample and detecting a hybridization complex; wherein WO 2005/072055 PCT/IB2005/000995 23 the presence of a hybridization complex correlates with the presence of a splice variant nucleic acid sequence in the biological sample. According to the present invention, the splice variants described herein are non limiting examples of markers for diagnosing cardiac disease and/or cardiac pathology, 5 including but not limited to cardiac damage. Each splice variant marker of the present invention can be used alone or in combination, for various uses, including but not limited to, prognosis, prediction, screening, early diagnosis, detennination of progression, therapy selection and treatment monitoring of cardiac disease and/or cardiac pathology, including but not limited to cardiac damage. 10 According to optional but preferred embodiments of the present invention, any marker according to the present invention may optionally be used alone or combination. Such a combination may optionally comprise a plurality of markers described herein, optionally including any subcombination of markers, and/or a combination featuring at least one other marker, for example a known marker. Furthermore, such a combination may 15 optionally and preferably be used as described above with regard to determining a ratio between a quantitative or semi-quantitative measurement of any marker described herein to any other marker described herein, and/or any other known marker, and/or any other marker. With regard to such a ratio between any marker described herein (or a combination thereof) and a known marker, more preferably the known marker comprises the "known protein" as 20 described in greater detail below with regard to each cluster or gene. According to other preferred embodiments of the present invention, a splice variant protein or a fragment thereof, or a splice variant nucleic acid sequence or a fragment thereof, may be featured as a biomarker for detecting cardiac disease and/or cardiac pathology, including but not limited to cardiac damage, such that a biomarker may optionally comprise 25 any of the above. According to still other preferred embodiments, the present invention optionally and preferably encompasses any amino acid sequence or fragment thereof encoded by a nucleic acid sequence corresponding to a splice variant protein as described herein. Any oligopeptide or peptide relating to such an amino acid sequence or fragment thereof may optionally also (additionally or alternatively) be used as a biomarker, including 30 but not limited to the unique amino acid sequences of these proteins that are depicted as tails, heads, insertions, edges or bridges. The present invention also optionally encompasses antibodies capable of recognizing, and/or being elicited by, such oligopeptides or peptides.

WO 2005/072055 PCT/IB2005/000995 24 The present invention also optionally and preferably encompasses any nucleic acid sequence or fragment thereof, or amino acid sequence or fragment thereof, conesponding to a splice variant of the present invention as described above, optionally for any application. Non-limiting examples of methods or assays are described below. 5 The present invention also relates to kits based upon such diagnostic methods or assays. Nucleic acid sequences and Oligonucleotides Various embodiments of the present invention encompass nucleic acid sequences 10 described hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous thereto, sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or artificially induced, either randomly or in a targeted fashion. 15 The present invention encompasses nucleic acid sequences described herein; fragments thereof, sequences hybridizable therewith, sequences homologous thereto [e.g., at least 50 %, at least 55 %, at least 60%, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 95 % or more say 100 % identical to the nucleic acid sequences set forth below], sequences encoding similar polypeptides with different codon usage, altered 20 sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or man induced, either randomly or in a targeted fashion. The present invention also encompasses homologous nucleic acid sequences (i.e., which form a part of a polynucleotide sequence of the present invention) which include sequence regions unique to the polynucleotides of the present invention. 25 In cases where the polynucleotide sequences of the present invention encode previously unidentified polypeptides, the present invention also encompasses novel polypeptides or portions thereof, which are encoded by the isolated polynucleotide and respective nucleic acid fragments thereof described hereinabove. A "nucleic acid fragment" or an "oligonucleotide" or a "polynucleotide" are used 30 herein interchangeably to refer to a polymer of nucleic acids. A polynucleotide sequence of the present invention refers to a single or double stranded nucleic acid sequences which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide WO 2005/072055 PCT/IB2005/000995 25 sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above). As used herein the phrase "complementary polynucleotide sequence" refers to a sequence, which results from reverse transcription of messenger RNA using a reverse 5 transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase. As used herein the phrase "genomic polynucleotide sequence" refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome. 10 As used herein the phrase "composite polynucleotide sequence" refers to a sequence, which is composed of genomic and cDNA sequences. A composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal 15 sequences. Such intronic sequences may further include cis acting expression regulatory elements. Preferred embodiments of the present invention encompass oligonucleotide probes. An example of an oligonucleotide probe which can be utilized by the present invention is a single stranded polynucleotide which includes a sequence complementary to 20 the unique sequence region of any variant according to the present invention, including but not limited to a nucleotide sequence coding for an amino sequence of a bridge, tail, head and/or insertion according to the present invention, and/or the equivalent portions of any nucleotide sequence given herein (including but not limited to a nucleotide sequence of a node, segment or amplicon described herein). 25 Alternatively, an oligonucleotide probe of the present invention can be designed to hybridize with a nucleic acid sequence encompassed by any of the above nucleic acid sequences, particularly the portions specified above, including but not limited to a nucleotide sequence coding for an amino sequence of a bridge, tail, head and/or insertion according to the present invention, and/or the equivalent portions of any nucleotide sequence given herein 30 (including but not limited to a nucleotide sequence of a node, segment or amplicon described herein). Oligonucleotides designed according to the teachings of the present invention can be generated according to any oligonucleotide synthesis method known in the art such as WO 2005/072055 PCT/IB2005/000995 26 enzymatic synthesis or solid phase synthesis. Equipment and reagents for executing solid phase synthesis are commercially available from, for example, Applied Biosystems. Any other means for such synthesis may also be employed; the actual synthesis of the oligonucleotides is well within the capabilities of one skilled in the art and can be 5 accomplished via established methodologies as detailed in, for example, "Molecular Cloning: A laboratory Manual" Sambrook et al., (1989); "Current Protocols in Mlecular Biology" Volumes 1-111 Ausubel, R. M., ed. (1994); Ausubel et al., "Current Protocols in Molecular Biology", John Wiley and Sons, Baltimore, Maryland (1989); Perbal, "A Practical Guide to Molecular Cloning", John Wiley & Sons, New York (1988) and 'Oligonucleotide Synthesis" 10 Gait, M. J., ed. (1984) utilizing solid phase chemistry, e.g. cyanoethyl phosphoramidite followed by deprotection, desalting and purification by for example, an automated trityl-on method or HPLC. Oligonucleotides used according to this aspect of the present invention are those having a length selected from a range of about 10 to about 200 bases preferably about 15 to 15 about 150 bases, more preferably about 20 to about 100 bases, most preferably about 20 to about 50 bases. Preferably, the oligonucleotide of the present invention features at least 17, at least 18, at least 19, at least 20, at least 22, at least 25, at least 30 or at least 40, bases specifically hybridizable with the biomarkers of the present invention. The oligonucleotides of the present invention may comprise heterocylic nucleosides 20 consisting of purines and the pyrimidines bases, bonded in a 3' to 5' phosphodiester linkage. Preferably used oligonucleotides are those modified at one or more of the backbone, internucleoside linkages or bases, as is broadly described hereinunder. Specific examples of preferred oligonucleotides useful according to this aspect of the present invention include oligonucleotides containing modified backbones or non-natural 25 intermucleoside linkages. Oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone, as disclosed in U.S. Pat. NOs: 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466, 677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; and 5,625,050. 30 Preferred modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkyl phosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3T-amino WO 2005/072055 PCT/IB2005/000995 27 phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3'-5? linkages, 2'-5' linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'. Various salts, mixed 5 salts and free acid forns can also be used. Alternatively, modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl intemucleoside linkages, mixed heteroatom and alkyl or cycloalkyl intemucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These 10 include those having morpholino linkags (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having 15 mixed N, 0, S and CH 2 component parts, as disclosed in U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623, 070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439. 20 Other oligonucleotides which can be used according to the present invention, are those modified in both sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for complementation with the appropriate polynucleotide target. An example for such an oligonucleotide mimetic, includes peptide nucleic acid (PNA). United States patents that 25 teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Other backbone modifications, which can be used in the present invention are disclosed in U.S. Pat. No: 6,303,374. Oligonucleotides of the present invention may also include base modifications or 30 substitutions. As used herein, "unmodified" or "natural" bases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified bases include but are not limited to other synthetic and natural bases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2- WO 2005/072055 PCT/IB2005/000995 28 aninoadenine, 6- methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2 thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8 5 hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5 trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7 methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3 deazaguanine and 3-deazaadenine. Further bases particularly useful for increasing the binding affinity of the oligomeric compounds of the invention include 5-substituted 10 pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2 aminopropyladenine, 5 -propynyluracil and 5-propynylcytosine. 5 -methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2 C and are presently preferred base substitutions, even more particularly when combined with 2'-0 methoxyethyl sugar modifications. 15 Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates, which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl 20 residues, a phospholipid, e.g., di- hexadecyl-rac-glycerol or triethylammonium 1,2-di-0 hexadecyl- rac-glycero-3-H-phosphonate, a polyamine or a polyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl oxycholesterol moiety, as disclosed in U.S. Pat. No: 6,303,374. It is not necessary for all positions in a given oligonucleotide molecule to be 25 uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an oligonucleotide. It will be appreciated that oligonucleotides of the present invention may include further modifications for more efficient use as diagnostic agents and/or to increase bioavailability, therapeutic efficacy and reduce cytotoxicity. 30 To enable cellular expression of the polynucleotides of the present invention, a nucleic acid construct according to the present invention may be used, which includes at least a coding region of one of the above nucleic acid sequences, and further includes at least one cis acting regulatory element. As used herein, the phrase "cis acting regulatory element" WO 2005/072055 PCT/IB2005/000995 29 refers to a polynucleotide sequence, preferably a promoter, which binds a trans acting regulator and regulates the transcription of a coding sequence located downstream thereto. Any suitable promoter sequence can be used by the nucleic acid construct of the present invention. 5 Preferably, the promoter utilized by the nucleic acid construct of the present invention is active in the specific cell population transformed. Examples of cell type specific and/or tissue-specific promoters include promoters such as albumin that is liver specific, lymphoid specific promoters [Calame et al., (1988) Adv. Immunol. 43:235-275]; in particular promoters of T-cell receptors [Winoto et al., (1989) EMBO 1. 8:729-733] and 10 immunoglobulins; [Banerji et al. (1983) Cell 33729-740], neuron-specific promoters such as the neurofilament promoter [Byme et al. (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477], pancreas-specific promoters [Edlunch et al. (1985) Science 230:912-916] or mammary gland-specific promoters such as the milk whey promoter (U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). The nucleic acid construct of the present 15 invention can further include an enhancer, which can be adjacent or distant to the promoter sequence and can function in up regulating the transcription therefrom. The nucleic acid construct of the present invention preferably further includes an appropriate selectable marker and/or an origin of replication. Preferably, the nucleic acid construct utilized is a shuttle vector, which can propagate both in E. coli (wherein the 20 construct comprises an appropriate selectable marker and origin of replication) and be compatible for propagation in cells, or integration in a gene and a tissue of choice. The construct according to the present invention can be, for example, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial chromosome. Examples of suitable constructs include, but are not limited to, pcDNA3, pcDNA3.1 25 (+/-), pGL3, PzeoSV2 (+/-), pDisplay, pEF/myc/cyto, pCMV/myc/cyto each of which is commercially available from Invitrogen Co. (www.invitrogen.com). Examples of retroviral vector and packaging systems are those sold by Clontech, San Diego, Calif., includingRetro-X vectors pLNCX and pLXSN, which permit cloning into multiple cloning sites and the trasgene is transcribed from CMV promoter. Vectors derived from Mo-MuLV 30 are also included such as pBabe, where the transgene will be transcribed from the 5'LTR promoter. Currently preferred in vivo nucleic acid transfer techniques include transfection with viral or non-viral constructs, such as adenovirus, lentivirus, Herpes simplex I virus, or WO 2005/072055 PCT/IB2005/000995 30 adeno-associated virus (AAV) and lipid-based systems. Useful lipids for lipid-mediated transfer of the gene are, for example, DOTMA, DOPE, and DC -Chol [Tonkinson et al., Cancer Investigation, 14(1): 54-65 (1996)]. The most preferred constructs for use in gene therapy are viruses, most preferably adenoviruses, AAV, lentiviruses, or retroviruses. A 5 viral construct such as a retroviral construct includes at least one transcriptional promoter/enhancer or locus -defining element(s), or other elements that control gene expression by other means such as alternate splicing, nuclear RNA export, or post translational modification of messenger. Such vector constructs also include a packaging signal, long terminal repeats (LTRs) or portions thereof, and positive and negative strand 10 primer binding sites appropriate to the virus used, unless it is already present in the viral construct. In addition, such a construct typically includes a signal sequence for secretion of the peptide from a host cell in which it is placed. Preferably the signal sequence for this purpose is a mammalian signal sequence or the signal sequence of the polypeptide variants of the present invention. Optionally, the construct may also include a signal that directs 15 polyadenylation, as well as one or more restriction sites and a translation termination sequence. By way of example, such constructs will typically include a 5' LTR, a tRNA binding site, a packaging signal, an origin of second-strand DNA synthesis, and a 3' LTR or a portion thereof. Other vectors can be used that are non-viral, such as cationic lipids, polylysine, and dendrimers. 20 Hybridization assays Detection of a nucleic acid of interest in a biological sample may optionally be effected by hybridization-based assays using an oligonucleotide probe (non-limiting examples of probes according to the present invention were previously described). 25 Traditional hybridization assays include PCR, RT-PCR, Reaktime PCR, RNase protection, in-situ hybridization, primer extension, Southern blots (DNA detection), dot or slot blots (DNA, RNA), and Northern blots (RNA detection) (NAT type assays are described in greater detail below). More recently, PNAs have been described (Nielsen et al. 1999, Current Opin. Biotechnol. 10:71-75). Other detection methods include kits containing probes 30 on a dipstick setup and the like. Hybridization based assays which allow the detection of a variant of interest (i.e., DNA or RNA) in a biological sample rely on the use of oligonucleotides which can be 10, WO 2005/072055 PCT/IB2005/000995 31 15, 20, or 30 to 100 nucleotid es long preferably from 10 to 50, more preferably from 40 to 50 nucleotides long. Thus, the isolated polynucleotides (oligonucleotides) of the present invention are preferably hybridizable with any of the herein described nucleic acid sequences under 5 moderate to stringent hybridization conditions. Moderate to stringent hybridization conditions are characterized by a hybridization solution such as containing 10 % dextrane sulfate, I M NaCl, I % SDS and 5 x 106 cpm 3p labeled probe, at 65 0 C, with a final wash solution of 0.2 x SSC and 0.1 % SDS and final wash at 65 0 C and whereas moderate hybridization is effected using a hybridization solution 10 containing 10 % dextrane sulfate, 1 M NaCl, 1 % SDS and 5 x 106 cpm 32 P labeled probe, at 65 OC, with a final wash solution of 1 x SSC and 0.1 % SDS and final wash at 50 o C. More generally, hybridization of short nucleic acids (below 200 bp in length, e.g. 17 40 bp in length) can be effected using the following exemplary hybridization protocols which can be modified according to the desired stringency; (i) hybridization solution of 6 x SSC and 15 1 % SDS or 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5 % SDS, 100 pg/ml denatured salmon sperm DNA and 0.1 % nonfat dried milk, hybridization temperature of 1 - 1.5 'C below the Tm, final wash solution of 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5 % SDS at I - 1.5 'C below the Tm; (Y) hybridization solution of 6 x SSC and 0.1 % SDS or 3 M TMACI, 0.01 M sodium phosphate 20 (pH 6.8), 1 mM EDTA (pH 7.6), 0.5 % SDS, 100 Rg/ml denatured salmon sperm DNA and 0.1 % nonfat dried milk, hybridization temperature of 2 - 2.5 'C below the Tm, final wash solution of 3 M TMACI, 0.01 M sodium phosphate (pH 6.8), 1 mM EDTA (pH 7.6), 0.5 % SDS at 1 - 1.5 'C below the Tm, final wash solution of 6 x SSC, and final wash at 22 oC; (iii) hybridization solution of 6 x SSC and 1 % SDS or 3 M TMACI, 0.01 M sodium phosphate 25 (pH 6.8), 1 mM EDTA (pH 7.6), 0.5 % SDS, 100 gg/m denatured salmon sperm DNA and 0.1 % nonfat dried milk, hybridization temperature. The detection of hybrid duplexes can be carried out by a mber of methods. Typically, hybridization duplexes are separated from unhybridized nucleic acids and the labels bound to the duplexes are then detected. Such labels refer to radioactive, fluorescent, 30 biological or enzymatic tags or labels of standard use in the art. A label can be conjugated to either the oligonucleotide probes or the nucleic acids derived from the biological sample.

WO 2005/072055 PCT/IB2005/000995 32 Probes can be labeled according to numerous well known methods. Non-limiting examples of radioactive labels include 3H, 14C, 32P, and 35S. Non-limiting examples of detectable markers include ligands, fluorophores, chemiluminescent agents, enzymes, and antibodies. Other detectable markers for use with probes, which can enable an increase in 5 sensitivity of the method of the invention, include biotin and radio -nucleotides. It will become evident to the person of ordinary skill that the choice of a particular label dictates the manner in which it is bound to the probe. For example, oligonucleotides of the present invention can be labeled subsequent to synthesis, by incorporating biotinylated dNTPs or rNTP, or some similar means (e.g., photo 10 cross- linking a psoralen derivative of biotin to RNAs), followed by addition of labeled streptavidin (e.g., phycoerythrin-conjugated streptavidin) or the equivalent. Alternatively, when fluorescently- labeled oligonucleotide probes are used, fluorescein, lissamine, phycoerythrin, rhodamine (Perkin Elmer Cetus), Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, FluorX (Amersham) and others [e.g., Kricka et al. (1992), Academic Press San Diego, Calif] can be 15 attached to the oligonucleotides. Those skilled in the art will appreciate that wash steps maybe employed to wash away excess target DNA or probe as well as unbound conjugate. Further, standard heterogeneous assay formats are suitable for detecting the hybrids using the labels present on the oligonucleotide primers and probes. 20 It will be appreciated that a variety of controls may be usefully employed to improve accuracy of hybridization assays. For instance, samples may be hybridized to an irrelevant probe and treated with RNAse A prior to hybridization, to assess false hybridization. Although the present invention is not specifically dependent on the use of a label for the detection of a particular nucleic acid sequence, such a label might be beneficial, by 25 increasing the sensitivity of the detection. Furthermore, it enables automation. Probes can be labeled according to numerous well known methods. As commonly known, radioactive nucleotides can be incorporated into probes of the invention by several methods. Non-limiting examples of radioactive labels include 3 H, 14 C, 32 P, and _S. 30 Those skilled in the art will appreciate that wash steps may be employed to wash away excess target DNA or probe as well as unbound conjugate. Further, standard heterogeneous assay formats are suitable for detecting the hybrids using the labels present on the oligonucleotide primers and probes.

WO 2005/072055 PCT/IB2005/000995 33 It will be appreciated that a variety of controls may be usefully employed to improve accuracy of hybridization assays. Probes of the invention can be utilized with naturally occurring sugar-phosphate backbones as well as modified backbones including phosphorothioates, dithionates, alkyl 5 phosphonates and a-nucleotides and the like. Probes of the invention can be constructed of either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and preferably of DNA. NAT Assays Detection of a nucleic acid of interest in a biological sample may also optionally be 10 effected by NAT-based assays, which involve nucleic acid amplification technology, such as PCR for example (or variations thereof such as real-time PCR for example). As used herein, a "primer" defines an oligonucleotide which is capable of annealing to (hybridizing with) a target sequence, thereby creating a double stranded region which can serve as an initiation point for DNA synthesis under suitable conditions. 15 Amplification of a selected, or target, nucleic acid sequence may be carried out by a number of suitable methods. See generally Kwoh et al., 1990, Am. Biotechnol. Lab. 8:14 Numerous amplification techniques have been described and can be readily adapted to suit particular needs of a person of ordinary skill. Non-limiting examples of amplification techniques include polymerase chain reaction (PCR), ligase chain reaction (LCR), strand 20 displacement amplification (SDA), transcription-based amplification, the q3 replic ase system and NASBA (Kwoh et al., 1989, Proc. NatI. Acad. Sci. USA 86, 1173-1177; Lizardi et al., 1988, BioTechnology 6:1197-1202; Malek et al., 1994, Methods Mol. Biol., 28:253-260; and Sambrook et al., 1989, supra). The terminology "amplification pair" (or "primer pair") refers herein to a pair of 25 oligonucleotides (oligos) of the present invention, which are selected to be used together in amplifying a selected nucleic acid sequence by one of a number of types of amplification processes, preferably a polymerase chain reaction. Other types of amplification processes include ligase chain reaction, strand displacement amplification, or nucleic acid sequence based amplification, as explained in greater detail below. As commonly known in the art, the 30 oligos are designed to bind to a complementary sequence under selected conditions. In one particular embodiment, amplification of a nucleic acid sample from a patient is amplified under conditions which favor the amplification of the most abundant differentially expressed nucleic acid. In one preferred embodiment, RT-PCR is carried out WO 2005/072055 PCT/IB2005/000995 34 on an mRNA sample from a patient under conditions which favor the amplification of the most abundant mRNA. In another preferred embodiment, the amplification of the differentially expressed nucleic acids is carried out simultaneously. It will be realized by a person skilled in the art that such methods could be adapted for the detection of differentially 5 expressed proteins instead of differentially expressed nucleic acid sequences. The nucleic acid (i.e. DNA or RNA) for practicing the present invention may be obtained according to well known methods. Oligonucleotide primers of the present invention may be of any suitable length, depending on the particular assay format and the particular needs and targeted genomes 10 employed. Optionally, the oligonucleotide primers are at least 12 nucleotides in length, preferably between 15 and 24 molecules, and they may be adapted to be especially suited to a chosen nucleic acid amplification system As commonly known in the art, the oligonucleotide primers can be designed by taking into consideration the melting point of hybridization thereof with its targeted sequence (Sambrook et al., 1989, Molecular Cloning 15 A Laboratory Manual, 2nd Edition, CSH Laboratories; Ausubel et al., 1989, in Current Protocols in Molecular Biology, John Wiley & Sons Inc., N.Y.). It will be appreciated that antisense oligonucleotides may be employed to quantify expression of a splice isoform of interest. Such detection is effected at the pre-mRNA level. Essentially the ability to quantitate transcription from a splice site of interest can be effected 20 based on splice site accessibility. Oligonucleotides may compete with splicing factors for the splice site sequences. Thus, low activity of the antisense oligonucleotide is indicative of splicing activity. The polymerase chain reaction and other nucleic acid amplification reactions are well known in the art (various non limiting examples of these reactions are described in greater 25 detail below). The pair of oligonucleotides according to this aspect of the present invention are preferably selected to have compatible melting temperatures (Tm), e.g., melting temperatures which differ by less than that 7 *C, preferably less than 5 OC, more preferably less than 4 OC, most preferably less than 3 0 C, ideally between 3 0 C and 0 "C. Polymerase Chain Reaction (PCR): The polymerase chain reaction (PCR), as 30 described in U.S. Pat. Nos. 4,683,195 and 4,683,202 to Mullis and Mullis et al., is a method of increasing the concentration of a segment of target sequence in a mixture of genomic DNA without cloning or purification. This technology provides one approach to the problems of low target sequence concentration. PCR can be used to directly increase the concentration of WO 2005/072055 PCT/IB2005/000995 35 the target to an easily detectable level. This process for amplifying the target sequence involves the introduction of a molar excess of two oligonucleotide primers which are complementary to their respective strands of the double-stranded target sequence to the DNA mixture containing the desired target sequence. The mixture is denatured and then allowed to 5 hybridize. Following hybridization, the primers are extended with polymerase so as to form complementary strands. The steps of denaturation, hybridization (annealing), and polymerase extension (elongation) can be repeated as often as needed, in order to obtain relatively high concentrations of a segment of the desired target sequence. The length of the segment of the desired target sequence is determined by the relative 1 0 positions of the primers with respect to each other, and, therefore, this length is a controllable parameter. Because the desired segments of the target sequence become the dominant sequences (in terms of concentration) in the mixture, they are said to be "PCR-amplified." Ligase Chain Reaction (LCR or LAR): The ligase chain reaction [ LCR; sometimes referred to as "Ligase Amplification Reaction" (LAR)] has developed into a well-recognized 15 alternative method of amplifying nucleic acids. In LCR, four oligonucleotides, two adjacent oligonucleotides which uniquely hybridize to one strand of target DNA, and a complementary set of adjacent oligonucleotides, which hybridize to the opposite strand are mixed and DNA ligase is added to the mixture. Provided that there is complete complementarity at the junction, ligase will covalently link each set of hybridized molecules. 20 Importantly, in LCR, two probes are ligated together only when they base-pair with sequences in the target sample, without gaps or mismatches. Repeated cycles of denaturation, and ligation amplify a short segment of DNA. LCR has also been used in combination with PCR to achieve enhanced detection of single -base changes: see for example Segev, PCT Publication No. W09001069 Al (1990). However, because the four 25 oligonucleotides used in this assay can pair to form two short ligatable fragments, there is the potential for the generation of target-independent background signal. The use of LCR for mutant screening is limited to the examination of specific nucleic acid positions. Self-Sustained Synthetic Reaction (3SR/NASBA): The self-sustained sequence replication reaction (3SR) is a transcription-based in vitro amplification system that can 30 exponentially amplify RNA sequences at a uniform temperature. The amplified RNA can then be utilized for mutation detection. In this method, an oligonucleotide primer is used to add a phage RNA polymerase promoter to the 5' end of the sequence of interest. In a cocktail of enzymes and substrates that includes a second primer, reverse transcriptase, RNase H, WO 2005/072055 PCT/IB2005/000995 36 RNA polymerase and ribo-and deoxyribonucleoside triphosphates, the target sequence undergoes repeated rounds of transcription, cDNA synthesis and second-strand synthesis to amplify the area of interest. The use of 3SR to detect mutations is kinetically limited to screening small segments of DNA (e.g., 200-300 base pairs). 5 Q-Beta (Qp) Replicase: In this method, a probe which recognizes the sequence of interest is attached to the replicatable RNA template for Q P replicase. A previously identified major problem with false positives resulting from the replication of unhybridized probes has been addressed through use of a sequence-specific ligation step. However, available thermostable DNA ligases are not effective on this RNA substrate, so the ligation 10 must be perfonned by T4 DNA ligase at low temperatures (37 degrees C.). This prevents the use of high temperature as a means of achieving specificity as in the LCR, the ligation event can be used to detect a mutation at the junction site, but not elsewhere. A successful diagnostic method must be very specific. A straight-forward method of controlling the specificity of nucleic acid hybridization is by controlling the temperature of 15 the reaction. While the 3SR/NASBA, and Qp systems are all able to generate a large quantity of signal, one or more of the enzymes involved in each cannot be used at high temperature (i.e., > 55 degrees C). Therefore the reaction temperatures cannot be raised to prevent non specific hybridization of the probes. If probes are shortened in order to make them melt more easily at low temperatures, the likelihood of having more than one perfect 20 match in a complex genome increases. For these reasons, PCR and LCR currently dominate the research field in detection technologies. The basis of the amplification procedure in the PCR and LCR is the fact that the products of one cycle become usable templates in all subsequent cycles, consequently doubling the population with each cycle. The final yield of any such doubling system can be 25 expressed as: (1+X) n =y, where "X" is the mean efficiency (percent copied in each cycle), "n" is the number of cycles, and "y" is the overall efficiency, or yield of the reaction. If every copy of a target DNA is utilized as a template in every cycle of a polyinerase chain reaction, then the mean efficiency is 100 %. If 20 cycles of PCR are perfonned, then the yield will be 220, or 1,048,576 copies of the starting material. If the reaction conditions reduce the mean 30 efficiency to 85 %, then the yield in those 20 cycles will be only 1.8520, or 220,513 copies of the starting material. In other words, a PCR running at 85 % efficiency will yield only 21 % as much final product, compared to a reaction running at 100 % efficiency. A reaction that is reduced to 50 % mean efficiency will yield less than 1 % of the possible product.

WO 2005/072055 PCT/IB2005/000995 37 In practice, routine polymerase chain reactions rarely achieve the theoretical maximum yield, and PCRs are usually run for more than 20 cycles to compensate for the lower yield. At 50 % mean efficiency, it would take 34 cycles to achieve the million- fold amplification theoretically possible in 20, and at lower efficiencies, the number of cycles 5 required becomes prohibitive. In addition, any background products that amplify with a better mean efficiency than the intended target will become the dominant products. Also, many variables can influence the mean efficiency of PCR, including target DNA length and secondary structure, primer length and design, primer and dNTP concentrations, and buffer composition, to name but a few. Contamination of the reaction 10 with exogenous DNA (e.g., DNA spilled onto lab surfaces) or cross-contamination is also a major consideration. Reaction conditions must be carefully optimized for each different primer pair and target sequence, and the process can take days, even for an experienced investigator. The laboriousness of this process, including numerous technical considerations and other factors, presents a significant drawback to using PCR in the clinical setting. 15 Indeed, PCR has yet to penetrate the clinical market in a significant way. The same concerns arise with LCR, as LCR must also be optimized to use different oligonucleotide sequences for each target sequence. In addition, both methods require expensive equipment, capable of precise temperature cycling. Many applications of nucleic acid detection technologies, such as in studies of alle lie 20 variation, involve not only detection of a specific sequence in a complex background, but also the discrimination between sequences with few, or single, nucleotide differences. One method of the detection of allele -specific variants by PCR is based upon the fact that it is difficult for Taq polymerase to synthesize a DNA strand when there is a mismatch between the template strand and the 3' end of the primer. An allele -specific variant may be detected 25 by the use of a primer that is perfectly matched with only one of the possible alleles; the mismatch to the other allele acts to prevent the extension of the primer, thereby preventing the amplification of that sequence. This method has a substantial limitation in that the base composition of the mismate h influences the ability to prevent extension across the mismatch, and certain mismatches do not prevent extension or have only a minimal effect. 30 A similar 3'- mismatch strategy is used with greater effect to prevent ligation in the LCR. Any mismatch effectively blocks the action of the thermostable ligase, but LCR still has the drawback of target- independent background ligation products initiating the amplification. Moreover, the combination of PCR with subsequent LCR to identify the WO 2005/072055 PCT/IB2005/000995 38 nucleotides at individual positions is also a clearly cumbersome proposition for the clinical laboratory. The direct detection method according to various preferred embodiments of the present invention may be, for example a cycling probe reaction (CPR) or a branched DNA 5 analysis. When a sufficient amount of a nucleic acid to be detected is available, there are advantages to detecting that sequence directly, instead of making more copies of that target, (e.g., as in PCR and LCR). Most notably, a method that does not amplify the signal exponentially is more amenable to quantitative analysis. Even if the signal is enhanced by 10 attaching multiple dyes to a single oligonucleotide, the correlation between the final signal intensity and amount of target is direct. Such a system has an additional advantage that the products of the reaction will not themselves promote further reaction, so contamination of lab surfaces by the products is not as much of a concern. Recently devised techniques have sought to eliminate the use of radioactivity and/or improve the sensitivity in automatable 15 formats. Two examples are the "Cycling Probe Reaction" (CPR), and "Branched DNA" (bDNA). Cyclingprobe reaction (CPR): The cycling probe reaction (CPR), uses a long chimeric oligonucleotide in whic h a central portion is made of RNA while the two termini are made of DNA. Hybridization of the probe to a target DNA and exposure to a thermostable 20 RNase H causes the RNA portion to be digested. This destabilizes the remaining DNA portions of the duplex, releasing the remainder of the probe from the target DNA and allowing another probe molecule to repeat the process. The signal, in the form of cleaved probe molecules, accumulates at a linear rate. While the repeating process increases the signal, the RNA portion of the oligonucleotide is vulnerable to RNases that may carried 25 through sample preparation. BranchedDNA: Branched DNA (bDNA), involves oligonucleotides with branched structures that allow each individual oligonucleotide to carry 35 to 40 labels (e.g., alkaline phosphatase enzymes). While this enhances the signal from a hybridization event, signal from non- specific binding is similarly increased. 30 The detection of at least one sequence change according to various preferred embodiments of the present invention may be accomplished by, for example restriction fragment length polymorphism (RFLP analysis), allele specific oligonucleotide (ASO) WO 2005/072055 PCT/IB2005/000995 39 analysis, Denaturing/Temperature Gradient Gel Electrophoresis (DGGE/TGGE), Single Strand Confonration Polymorphism (SSCP) analysis or Dideoxy fingerprinting (ddF). The demand for tests which allow the detection of specific nucleic acid sequences and sequence changes is growing rapidly in clinical diagnostics. As nucleic acid sequence data 5 for genes from humarE and pathogenic organisms accumulates, the demand for fast, cost effective, and easy-to-use tests for as yet mutations within specific sequences is rapidly increasing. A handful of methods have been devised to scan nucleic acid segments for mutations. One option is to determine the entire gene sequence of each test sample (e.g., a bacterial 10 isolate). For sequences under approximately 600 nucleotides, this may be accomplished using amplified material (e.g., PCR reaction products). This avoids the time and expense associated with cloning the segment of interest. However, specialized equipment and highly trained personnel are required, and the method is too labor-intense and expensive to be practical and effective in the clinical setting. 15 In view of the difficulties associated with sequencing, a given segment of nucleic acid may be characterized on several other levels. At the lowest resolution, the size of the molecule can be determined by electrophoresis by comparison to a known standard run on the same gel. A more detailed picture of the molecule may be achieved by cleavage with combinations of restriction enzymes prior to electrophoresis, to allow construction of an 20 ordered map. The presence of specific sequences within the fragment can be detected by hybridization of a labeled probe, or the precise nucleotide sequence can be determined by partial chemical degradation or by primer extension in the presence of chain-terminating nucleotide analogs. Restriction fragment length polymorphism (RFLP): For detection of single -base 25 differences between like sequences, the requirements of the analysis are often at the highest level of resolution. For cases in which the position of the nucleotide in question is known in advance, several methods have been developed for examining single base changes without direct sequencing. For example, if a mutation of interest happens to fall within a restriction recognition sequence, a change in the pattern of digestion can be used as a diagnostic tool 30 (e.g., restriction fragment length polymorphism [RFLP] analysis). Single point mutations have been also detected by the creation or destruction of RFLPs. Mutations are detected and localized by the presence and size of the RNA fragments generated by cleavage at the mismatches. Single nucleotide mismatches in DNA WO 2005/072055 PCT/IB2005/000995 40 heteroduplexes are also recognized and cleaved by some chemicals, providing an alternative strategy to detect single base substitutions, generically named the "Mismatch Chemical Cleavage" (MCC). However, this method requires the use of osmium tetroxide and piperidine, two highly noxious chemicals which are not suited for use in a clinical laboratory. 5 RFLP analysis suffers from low sensitivity and requires a large amount of sample. When RFLP analysis is used for the detection of point mutations, it is, by its nature, limited to the detection of only those single base changes which fall within a restriction sequence of a known restriction endonuclease. Moreover, the majority of the available enzymes have 4 to 6 base-pair recognition sequences, and cleave too frequently for many large-scale DNA 10 manipulations. Thus, it is applicable only in a small fraction of cases, as most mutations do not fall within such sites. A handful of rare-cutting restriction enzymes with 8 base-pair specificities have been isolated and these are widely used in genetic mapping, but these enzymes are few in number, are limited to the recognition of G+C-rich sequences, and cleave at sites that tend to be highly 15 clustered. Recently, endonucleases encoded by group I introns have been discovered that might have greater than 12 base-pair specificity, but again, these are few in number. Allele specific oligonucleotide (ASO): If the change is not in a recognition sequence, then allele -specific oligonucleotides (ASOs), can be designed to hybridize in proximity to the mutated nucleotide, such that a primer extension or ligation event can bused as the indicator 20 of a match or a mis- match. Hybridization with radioactively labeled allelic specific oligonucleotides (ASO) also has been applied to the detection of specific point mutations. The method is based on the differences in the melting temperature of short DNA fragments differing by a single nucleotide. Stringent hybridization and washing conditions can differentiate between mutant and wild -type alleles. The ASO approach applied to PCR 25 products also has been extensively utilized by various researchers to detect and characterize point mutations in ras genes and gsp/gip oncogenes. Because of the presence of various nucleotide changes in multiple positions, the ASO method requires the use of many oligonucleotides to cover all possible oncogenic mutations. With either of the techniques described above (i.e., RFLP and ASO), the precise 30 location of the suspected station must be known in advance of the test. That is to say, they are inapplicable when one needs to detect the presence of a mutation within a gene or sequence of interest.

WO 2005/072055 PCT/IB2005/000995 41 Denaturing/Temperature Gradient Gel Electrophoresis (DGGE/TGGE): Two other methods rely on detecting changes in electrophoretic mobility in response to minor sequence changes. One of these methods, termed "Denaturing Gradient Gel Electrophoresis" (DGGE) is based on the observation that slightly different sequences will display different patterns of 5 local melting when electrophoretically resolved on a gradient gel. In this manner, variants can be distinguished, as differences in melting properties of homoduplexes versus heteroduplexes differing in a single nucleotide can detect the presence of mutations in the target sequences because of the corresponding changes in their electrophoretic mobilities. The fragments to be analyzed, usually PCR products, are "clamped" at one end by a long 10 stretch of G-C base pairs (30-80) to allow compete denaturation of the sequence of interest without complete dissociation of the strands. The attachment of a GC "clamp" to the DNA fragments increases the fraction of mutations that can be recognized by DGGE. Attaching a GC clamp to one primer is critical to ensure that the amplified sequence has a low dissociation temperature. Modifications of the technique have been developed, using 15 temperature gradients, and the method can be also applied to RNA:RNA duplexes. Limitations on the utility of DGGE include the requirement that the denaturing conditions must be optimized for each type of DNA to be tested. Furthermore, the method requires specialized equipment to prepare the gels and maintain the needed high temperatures during electrophoresis. The expense associated with the synthesis of the clamping tail on one 20 oligonucleotide for each sequence to be tested is also a major consideration. In addition, long running times are required for DGGE. The long running time of DGGE was shortened in a modification of DGGE called constant denaturant gel electrophoresis (CDGE). CDGE requires that gels be performed under different denaturant conditions in order to reach high efficiency for the detection of mutations. 25 A technique analogous to DGGE, termed temperature gradient gel electrophoresis (TGGE), uses a thermal gradient rather than a chemical denaturant gradient. TGGE requires the use of specialized equipment which can generate a temperature gradient perpendicularly oriented relative to the electrical field. TGGE can detect mutations in relatively small fragments of DNA therefore scanning of large gene segments requires the use of multiple 30 PCR products prior to running the gel. Single-Strand Conformation Polymorphism (SSCP): Another common method, called "Single-Strand Conformation Polymorphism" (SSCP) was developed by Hayashi, Sekya and colleagues and is based on the observation that single strands of nucleic acid can WO 2005/072055 PCT/IB2005/000995 42 take on characteristic conformations in non-denaturing conditions, and these conformations influence electrophoretic mobility. The complementary strands assume sufficiently different structures that one strand may be resolved from the other. Changes in sequences within the fragment will also change the conformation, consequently altering the mobility and allowing 5 this to be used as an assay for sequence variations. The SSCP process involves denaturing a DNA segment (e.g., a PCR product) that is labeled on both strands, followed by slow electrophoretic separation on a non-denaturing polyacrylamide gel, so that intra-molecular interactions can form and not be disturbed during the run. This technique is extremely sensitive to variations in gel composition and 10 temperature. A serious limitation of this method is the relative difficulty encountered in comparing data generated in different laboratories, under apparently similar conditions. Dideoxyfingerprinting (ddF): The dideoxy fingerprinting (ddF) is another technique developed to scan genes for the presence of mutations. The ddF technique combines components of Sanger dideoxy sequencing with SSCP. A dideoxy sequencing reaction is 15 perfonned using one dideoxy terminator and then the reaction products are electrophoresed on nondenaturing polyacrylamide gels to detect alterations in mobility of the termination segments as in SSCP analysis. While ddF is an improvement over SSCP in terms of increased sensitivity, ddF requires the use of expensive dideoxynucleotides and this technique is still limited to the analysis of fragments of the size suitable for SSCP (i.e., 20 fragments of 200-300 bases for optimal detection of mutations). In addition to the above limitations, all of these methods are limited as to the size of the nucleic acid fragment that can be analyzed. For the direct sequencing approach, sequences of greater than 600 base pairs require cloning, with the consequent delays and expense of either deletion sub-cloning or primer walking, in order to cover the entire 25 fragment. SSCP and DGGE have even more severe size limitations. Because of reduced sensitivity to sequence changes, these methods are not considered suitable for larger fragments. Although SSCP is reportedly able to detect 90 % of single-base substitutions within a 200 base-pair fragment, the detection drops to less than 50 % for 400 base pair fragments. Similarly, the sensitivity of DGGE decreases as the length of the fragment reaches 30 500 base-pairs. The ddF teelmique, as a combination of direct sequencing and SSCP, is also limited by the relatively small size of the DNA that can be screened. According to a presently preferred embodiment of the present invention the step of searching for any of the nucleic acid sequences described here, in tumor cells or in cells WO 2005/072055 PCT/IB2005/000995 43 derived from a cancer patient is effected by any suitable technique, including, but not limited to, nucleic acid sequencing, polymerase chain reaction, ligase chain reaction, self-sustained synthetic reaction, Q P-Replicase, cycling probe reaction, branched DNA, restriction fragment length polymorphism analysis, mismatch chemical cleavage, heteroduplex 5 analysis, allele-specific oligonucleotides, denaturing gradient gel electrophoresis, constant denaturant gel electrophoresis, temperature gradient gel electrophoresis and dideoxy fingerprinting. Detection may also optionally be performed with a chip or other such device. The nucleic acid sample which includes the candidate region to be analyzed is preferably isolated, 10 amplified and labeled with a reporter group. This reporter group can be a fluorescent group such as phycoerythrin. The labeled nucleic acid is then incubated with the probes immobilized on the chip using a fluidics station. describe the fabrication of fluidics devices and particularly microcapillary devices, in silicon and glass substrates. Once the reaction is completed, the chip is inserted into a scanner and patterns of 15 hybridization are detected. The hybridization data is collected, as a signal emitted from the reporter groups already incorporated into the nucleic acid, which is now bound to the probes attached to the chip. Since the sequence and position of each probe immobilized on the chip is known, the identity of the nucleic acid hybridized to a given probe can be determined. It will be appreciated that when utilized along with automated equipment, the above 20 described detection methods can be used to screen multiple samples for a disease and/or pathological condition both rapidly and easily. Amino acid sequences and peptides The terms "polypeptide," "peptide" and "protein" are used interchangeably herein to 25 refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an analog or mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. Polypeptides can be modified, e.g., by the addition of carbohydrate residues to form glycoproteins. The terms "polypeptide," "peptide" and "protein" include glycoproteins, as well as non 30 glycoproteins. Polypeptide products can be biochemically synthesized such as by employing standard solid phase techniques. Such methods include but are not limited to exclusive solid phase synthesis, partial solid phase synthesis methods, fragment condensation, classical WO 2005/072055 PCT/IB2005/000995 solution synthesis. These methods are preferably tsed when the peptide is relatively short (i.e., 10 kDa) and/or when it cannot be produced by recombinant techniques (i.e., not encoded by a nucleic acid sequence) and therefore involves different chemistry. Solid phase polypeptide synthesis procedures are well known in the art and further 5 described by John Morrow Stewart and Janis Dillaha Young, Solid Phase Peptide Syntheses (2nd Ed., Pierce Chemical Company, 1984). Synthetic polypeptides can optionally be purified by preparative high performance liquid chromatography [Creighton T. (1983) Proteins, structures and molecular principles. WH Freeman and Co. N.Y.], after which their composition can be confirmed via amino acid 10 sequencing. In cases where large amounts of a polypeptide are desired, it can be generated using recombinant techniques such as described by Bitter et al., (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi < al. (1984) 15 EMBO J. 3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al. (1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463. The present invention also encompasses polypeptides encoded by the polynucleotide sequences of the present invention, as well as polypeptides according to the amino acid 20 sequences described herein. The present invention also encompasses homologues of these polypeptid es, such homologues can be at least 50 %, at least 55 %, at least 60%, at least 65 %, at least 70 %, at least 75 %, at least 80 %, at least 85 %, at least 95 % or more say 100 % homologous to the amino acid sequences set forth below, as can be determined using BlastP software of the National Center of Biotechnology Information (NCBI) using default 25 parameters, optionally and preferably including the following: filtering on (this option filters repetitive or low-complexity sequences from the query using the Seg (protein) program), scoring matrix is BLOSUM62 for proteins, word size is 3, E value is 10, gap costs are 11, 1 (initialization and extension), and number of alignments shown is 50. Optionally and preferably, nucleic acid sequence homology (identity) is determined using BlastN software of 30 the National Center of Biotechnology Information (NCBI) using default parameters, which preferably include using the DUST filter program, and also preferably include having an E value of 10, filtering low complexity sequences and a word size of 11. Finally, the present invention also encompasses fragments of the above described polypeptides and polypeptides WO 2005/072055 PCT/IB2005/000995 45 having mutations, such as deletions, insertions or substitutions of one or more amino acids, either naturally occurring or artificially induced, either randomly or in a targeted fashion. It will be appreciated that peptides identified according the present invention may be degradation products, synthetic peptides or recombinant peptides as well as peptidomimetics, 5 typically, synthetic peptides and peptoids and semipeptoids which are peptide analogs, which may have, for example, modifications rendering the peptides more stable while in a body or more capable of penetrating into cells. Such modifications include, but are not limited to N terminus modification, C tenninus modification, peptide bond modification, including, but not limited to, CH2-NH, CH2-S, CH2-S=O, O==C-NH, CH2-O, CH2-CH2, S=C-NH, 10 CH=CH or CF=CH, backbone modifications, and residue modification. Methods for preparing peptidomimetic compounds are well known in the art and are specified. Further details in this respect are provided hereinunder. Peptide bonds (-CO-NH-) within the peptide may be substituted, for example, by N methylated bonds (-N(CH3)-CO-), ester bonds (-C(R)H-C-O-0-C(R)-N-), ketomethylen 15 bonds (-CO-CH2-), a-aza bonds (-NH-N(R)-CO-), wherein R is any alkyl, e.g., methyl, carba bonds (-CH2-NH-), hydroxyethylene bonds (-CH(OH)-CH2-), thioamide bonds (-CS NH-), olefinic double bonds (-CH=CH-), retro amide bonds (-NH-CO-), peptide derivatives (-N(R)-CH2-CO-), wherein R is the "normal" side chain, naturally presented on the carbon atom. 20 These modifications can occur at any of the bonds along tlie peptide chain and even at several (2-3) at the same time. Natural aromatic amino acids, Trp, Tyr and Phe, may be substituted for synthetic non natural acid such as Phenylglycine, TIC, naphthylelanine (Nol), ring-methylated derivatives of Phe, halogenated derivatives of Phe or o -methyl-Tyr. 25 In addition to the above, the peptides of the present invention may also include one or more modified amino acids or one or more non amino acid monomers (e.g. fatty acids, complex carbohydrates etc). As used herein in the specification and in the claims section below the term "amino acid" or "amino acids" is understood to include the 20 naturally occurring amino acids; those 30 amino acids often modified post-translationally in vivo, including, for example, hydroxyproline, phosphoserine and phosphothreonine; and other unusual amino acids including, but not limited to, 2-aminoadipic acid, hydroxylysine, isodesmosine, nor-valine, WO 2005/072055 PCT/IB2005/000995 46 nor-leucine and ornithine. Furthermore, the term "amino acid" includes both D- and L-amino acids. Table 1 non-conventional or modified amino acids which can be used with the 5 present invention. Table I Non-conventional amino Code Non-conventional amino acid Code acid a-aminobutyric acid Abu L-N-methylalanine Nmala a-amino-a-methylbutyrate Mgabu L-N-methylarginine Nmarg aminocyclopropane- Cpro L-N-methylasparagine Nmasn Carboxylate L-N-methylaspartic acid Nmasp arninoisobutyric acid Aib L-N-methylcysteine Nmcys aminonorbomyl- Norb L-N-methylglutamine Nmgin Carboxylate L-N-methylglutamic acid Nmglu Cyclohexylalanine Chexa L-N-methylhistidine Nmhis Cyclopentylalanine Cpen L-N-methylisolleucine Nmile D-alanine Dal L-N-methylleucine Nmleu D-arginine Darg L-N-methyllysine Nmlys D-aspartic acid Dasp L-N-methyhnethionine Nmmet D-cysteine Deys L-N-methylnorleucine Nmnle D-glutamine Dgln L-N-methylnorvaline Nmnva D-glutamic acid Dglu L-N-methylornithine Nnorn D-histidine Dhis L-N-methylphenylalanine Nmphe D-isoleucine Dile L-N-methylproline Nmpro D-leucine Dleu L-N-methylserine Nmser D-lysine Dlys L-N-methylthreonine Nmthr D-methionine Dmet L-N-methyltryptophan Nntrp D-omithine Dom L-N-methyltyrosine Nmtyr D-phenylalanine Dphe L-N-methylvaline Nmval WO 2005/072055 PCTIIB2005/000995 4-7 D-proline Dpro L-N -methylethyiglycine Nmetg D-seine Dser L-N -rnethyl--butylglycine Nrntbug D-tlueonine Dthr L-norlevicile Nme D-tryptoplian Dtrp L-norvaline Nva D-tyrosine Dtyr ct-methyl-aminoisobutyrate Maib D-valine Dval cc-methyl-y-aminobutyrate Mgabu D-cx-rethylalanine Dinala ax -methiylcyclohexylalanine Mchexa D-cx-methylarginine Dmarg ax -mnethylcyclopentylalanine Mcpen D- c-methylasparagine Drnasn ax-methyl- c-napthylalanine Manap D-cx-methylaspartate Dmnasp a - methylpenicillamine Mpen D-ac-methylcysteine Dmcys N- (4- aminobutyl)glycine Nglu D- cx-methylglutamine Dmghn N- (2- aininoethyl)glycinie Naeg D- cx-methylhistidine Drnhis N- (3-aminopropyl)glycine Nom D-cx-methylisoleucine Dmile N- amino-cx-miethylbutyrate Nmaabu D-cx-methylleucine Dmleu cx-napthylalanine Anap D-ac-methyllysine Dinlys N-benzylglycine Nphe D-ac-mnethylmethionine Dmmiet N-(2-carbamylethlyl)glycine Ngln D-cx-methylomithine Dmom N-(carbarnyhnethylglycine Nasn D-cx-methylphenylalanine Dmphe N- (2- carboxyethyl)glycine Nglu D-cc-methylproline Dmpro N- (carboxymethyl)glycine Nasp D- x- methylserine Dmnser N-cyclobutylglycine Ncbut D-ac-methyltbreonine Dmthr N-cycloheptylglycine Nchep D- c- methyltryptophan Dmtrp N-cyclohexylglycine Nchex D- cx-methyltyrosine Drnty N-cyclodecylglycine Ncdec D-cx-methylvatine Dmval N-cyclododeclglycine Ncdod D-ax-methylalnine Dnmala N-cyclooctylglycine Ncoct D-ac-methylargifine Dnmarg N-cyclopropylglycine Ncpro D-ac-methylasparagine Dnmasn N-cycloundecylglycine Ncund D- c-methlylasparatate Dnmasp N-(2,2-diphonylethyl)glycine Nbhm D- cx-methylcysteine Dncys N-(3,3- Nbhe diphenylpropyl)glycine WO 2005/072055 PCTIIB2005/000995 48 D-N-methylleucine Dnr-nleu N- (3-indolylyethiyl) glycine Nhtrp D- N-methyllysine Dnmlys N-methyl- y-aminobutyrate Nmgabui N- Nmchiexa D-N-methylrnethionine Dnmmet methylcyclohexylalanine D-N-mediyloi-nithine Dumorn N-methylcyclopentylalanine Nmcpen N-methylglycine Nala D-N-rnethylphenylalanine Dinphe N-methylaminoisobutyrate Nmaib D-N-methylproline Dm-npro N- ( l-rethylpropyl)glycine Nile D-N-methylserine Dnmser N- (2-methylpropyl)glycine Nile D-N-methylserine Dnmser N- (2-mrethylpropyl)glycine Nleu D-N-methylthreonine Dnrnthr D-N-methyltryptophan Dnmtrp N-( 1-methylethyl)glycine Nva D-N-methyltyrosine Dnmtyr N-methyla -napthylalanine Nmanap D-N-metbylvaline Dnmval N-methylpenicillamine Nmpen y-amninobutyric acid Gabu N- (p-hydroxyphenyl)glycine Nhtyr L-t-butylglycine Thug N-(tliiomethlyl)glycine Ncys L-ethylglycine Etg Penicillamine Pen L-hornophenylalanine Hphe L-cc-methylalanine Mala L-ct-methylargini-e Marg L-c-methylasparagine Masn L-c(-methylaspartate Masp L-cx-methy1-t-butylglycine Mibug L-cx-methylcysteine Meys L-methylethylglycine Metg L-methylglutamine Mgln L-ac-methylglutamate Mglu L-a-methylhistidine NUiS L-ox-methylhomo Mhphe phenylalanine L-cX-methylisoleucine Mile N- (2-methylthioethyl)glycine Nmet D-N-methylglutam-ine Dngln N-(3- Narg guanidinopropyl)glycine D-N-methylglutamate Dnmglu N-( 1-hydroxyethiyl)glycine Ntbr D-N-methylhistidine Dnn-ilis N-(hydroxyethyl)glycine Nser D-N-methylisoleucine Dnmile N- (imidazolylethyl)glycine Nis D-N-methylleucine Dnmleu N- (3- indolylyethyl)glycine Nhtrp D-N-methyllysine Drnlys N-methyl~y-aminobutyrate Nmgabu N- Nmchexa D-N-methymethionine Dnmmet WO 2005/072055 PCTIIB2005/000995 methylcyc lohexylalanine D- N-rethylomithine Dninorn N- methylcyclopentylalanine Nmcpen N-methylglycine Nala D-N-methylphenytalanine Diumphe N-methylarninoisobutyrate Nmaib D-N-methylproline Dnmpro N- (1-methylpropyl)glycine Nile D-N-mnethylseiine Dnmser N- (2-mrethylpropyl)glycine Nleu D-N-rnethylthreonine Dnr-nthir D-N-methyltryptophan Dnmtrp N- ( 1-methyletbyl)glycine Nval D-N-methyltyrosine Dnmtyr N-methyla -napthylalanine Nmanap D-N-inethylvaline Dnmval N-rnethylpenicillarnine Nmpein ,y-aminobutyric acid Gabu N-(p-hydroxyphenyl)glycine Nhtyr L-t-butylglycine Tbug N-(thiomethyl)glycine Ncys L-ethylglycine Etg Penicillamine Pen L-homophenylalanine Hphec L-oc-methylalanine Mala L-ct-methylarginine Marg L-oa-methylasparagine Masn L-ec-methylaspartate Masp L-cc-methylt-butylglycine Mtbug L-Q-methyleysteine Mcys L-methylethylglycine Metg L-ce-methylglutamine Mghn L-ax-methylglutarnate Mglu L-cc-methylhistidine Mcais L-cc- Mhiphe methyihomophenylalanine L-cc-methylisoleucine Mie N-(2-methylthioethyl)glycine Nmet L-ax-methylleucine Mleu L-u.-methyllysine Mlys L-Qc-methylmnethioiine Mfirnet L-cx-methiylnorleucine Mle L-Qc-methylnorvaline MNva L-ce-methylomithine Morn k-ax-methylphienylalanine Mphe L-ec-methylproline Mpro L-cx-methylserine mser L-u-methylthreonine Mthr L-ac-methylvaline Mtrp L-a-rnethyltyrosine Mtyr L-Ct-methy11eucine Mval L-N - Nmhphe Nnabhm methiyihomophenylalanine N-(N-(2,2-diphenylethyl) N-(N-(3,3-diphenylpropyl) carbamylmethy-glycine Nnbhm carbamylmethyl(1 )glycine Nnbhe I- carboxy- 1- (2,2- diphenyl Nmbc WO 2005/072055 PCT/IB2005/000995 50 ethylamino)cyclopropane Table ] Cont. Since the peptides of the present invention are preferably utilized in diagnostics which require the peptides to be in soluble form, the peptides of the present invention preferably 5 include one or more non- natural or natural polar amino acids, including but not limited to serine and threonine which are capable of increasing peptide solubility due to their hydroxyl containing side chain. The peptides of the present invention are preferably utilized in a linear form, although it will be appreciated that in cases where cyclicization does not severely interfere with 10 peptide characteristics, cyclic forms of the peptide can also be utilized. The peptides of present invention can be biochemically synthesized such as by using standard solid phase techniques. These methods include exclusive solid phase synthesis well known in the art, partial solid phase synthesis methods, fragment condensation, classical solution synthesis. These methods are preferably used when the peptide is relatively short 15 (i.e., 10 kDa) and/or when it cannot be produced by recombinant techniques (i.e., not encoded by a nucleic acid sequence) and therefore involves different chemistry. Synthetic peptides can be purified by preparative high performance liquid chromatography and the composition of which can be confirmed via amino acid sequencing. In cases where large amounts of the peptides of the present invention are desired, the 20 peptides of the present invention can be generated using recombinant techniques such as described by Bitter et al., (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984) EMBO J. 3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al. (1986) Mol. Cell. Biol. 6:559-565 and Weissbach 25 & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463 and also as described above. Antibodies 30 "Antibody" refers to a polypeptide ligand that is preferably substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, which specifically binds and recognizes an epitope (e.g., an antigen). The recognized immunoglobulin genes WO 2005/072055 PCT/IB2005/000995 51 include the kappa and lambda light chain constant region genes, the alpha, gamma, delta, epsilon and mu heavy chain constant region genes, and the myriad- immunoglobulin variable region genes. Antibodies exist, e.g., as intact immunoglobulins or as a number of well characterized fragments produced by digestion with various peptidases. This includes, e.g., 5 Fab' and F(ab)' 2 fragments. The term "antibody," as used herein, also includes antibody fragments either produced by the modification of whole antibodie s or those synthesized de novo using recombinant DNA methodologies. It also includes polyclonal antibodies, monoclonal antibodies, chimeric antibodies, humanized antibodies, or single chain antibodies. "Fc" portion of an antibody refers to that portion of an immunoglobulin heavy 10 chain that comprises one or more heavy chain constant region domains, CHI, CH2 and CH3, but does not include the heavy chain variable region. The functional fragments of antibodies, such as Fab, F(ab')2, and Fv that are capable of binding to macrophages, are described as follows: (1) Fab, the fragment which contains a monovalent antigenbinding fragment of an antibody molecule, can be produced by digestion 15 of whole antibody with the enzyme papain to yield an intact light chain and aportion of one heavy chain; (2) Fab', the fragment of an antibody molecule that can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab' fragments are obtained per antibody molecule; (3) (Fab')2, the fragment of the antibody that can be obtained by treating whole antibody with 20 the enzyme pepsin without subsequent reduction; F(ab')2 is a dimer of two Fab' fragments held together by two disulfide bonds; (4) Fv, de fined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (5) Single chain antibody ("SCA"), a genetically engineered molecule containing the variabb region of the light chain and the variable region of the 25 heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule. Methods of producing polyclonal and monoclonal antibodies as well as fragments thereof are well known in the art (See for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 1988, incorporated herein 30 by reference). Antibody fragments according to the present invention can be prepared by proteolytic hydrolysis of the antibody or by expression in E. coli or mammalian cells (e.g. Chinese hamster ovary cell culture or other protein expression systems) of DNA encoding the WO 2005/072055 PCT/IB2005/000995 S2 fragment. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab')2. This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking 5 group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab' monovalent fragments. Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab' fragments and an Fc fragment directly. These metho ds are described, for example, by Goldenberg, U.S. Pat. Nos. 4,036,945 and 4,331,647, and references contained therein, which patents are hereby incorporated by reference in their 10 entirety. See also Porter, R. R. [Biochem. J. 73: 119-126 (1959)]. Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light- heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical, or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody. 15 Fv fragments comprise an association of VH and VL chains. This association may be noncovalent, as described in Inbar et al. [Proc. Nat'l Acad. Sci. USA 69:2659-62 (19720]. Alternatively, the variable chains can be linked by an intermolecular disulfide bond or cross linked by chemicals such as glutaraldehyde. Preferably, the Fv fragments comprise VH and VL chains connected by a peptide linker. These single-chain antigen binding proteins (sFv) 20 are prepared by constructing a structural gene comprising DNA sequences encoding the VH and VL domains connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing sFvs are described, for example, by [Whitlow 25 and Filpula, Methods 2: 97-105 (1991); Bird et al., Science 242:423-426 (1988); Pack et al., Bio/Technology 11:1271-77 (1993); and U.S. Pat. No. 4,946,778, which is hereby incorporated by reference in its entirety. Another form of an antibody fragment is a peptide coding for a single complementarity-determining region (CDR). CDR peptides ("minimal recognition units") 30 can be obtained by constructing genes encoding the CDR of an antibody of interest. Such genes are prepared, for example, by using the polymerase chain reaction to synthesize the variable region from RNA of antibody-producing cells. See, for example, Larrick and Fry [Methods, 2: 106-10 (1991)].

WO 2005/072055 PCT/IB2005/000995 53 Humanized forms of non-human (e.g., murine) antibodies are chimeric molecules of immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab') or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human 5 immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise 10 residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a nonhuman immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized 15 antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struot. Biol., 2:593-596 (1992)]. Methods for humanizing non human antibodies are well known in the art. Generally, 20 a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as import residues, which are typically taken from an import variable domain. Humanization can be essentially performed following the method of Winter and co-workers [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al., 25 Science, 239:1534-1536 (1988)], by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such humanized antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non human species. In practice, humanized antibodies are typically human antibodies in which 30 some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies. Human antibodies can also be produced using various techniques known in the art, including phage display libraries [Hoogenboom and Winter, J. Mot. Biol., 227:381 (1991); WO 2005/072055 PCT/IB2005/000995 54 Marks et al., J. Mol. Biol., 222:581 (1991)]. The techniques of Cole et al. and Boerner et al. are also available for the preparation of human monoclonal antibodies (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al., J. Immunol., 147(1):86-95 (1991)]. Similarly, human antibodies can be made by introduction 5 of human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 10 5,633,425; 5,661,016, and in the following scientific publications: Marks et al., Bio/Technology 10,: 779-783 (1992); Lonberg et al., Nature 368: 856-859 (1994); Morrison, Nature 368 812-13 (1994); Fishwild et al., Nature Biotechnology 14, 845-51 (1996); Neuberger, Nature Biotechnology 14: 826 (1996); and Lonberg and Huszar, Intern. Rev. Immunol. 13, 65-93 (1995). 15 Preferably, the antibody of this aspect of the present invention specifically binds at least one epitope of the polypeptide variants of the present invention. As used herein, the term "epitope" refers to any antigenic determinant on an antigen to which the paratope of an antibody binds. Epitopic determinants usually consist of chemically active surface groupings of 20 molecules such as amino acids or carbohydrate side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics. Optionally, a unique epitope may be created in a variant due to a change in one or more post-translational modifications, including but not limited to glycosylation and/or phosphorylation, as described below. Such a change may also cause a new epitope to be 25 created, for example through removal of glycosylation at a particular site. An epitope according to the present invention may also optionally comprise part or all of a unique sequence portion of a variant according to the present invention in combination with at least one other portion of the variant which is not contiguous to the unique sequence portion in the linear polypeptide itself, yet which are able to form an 30 epitope in combination. One or more unique sequence portions may optionally combine with one or more other non- contiguous portions of the variant (including a portion whbh may have high homology to a portion of the known protein) to form an epitope.

WO 2005/072055 PCT/IB2005/000995 55 Immunoassays In another embodiment of the present invention, an immunoassay can be used to qualitatively or quantitatively detect and analyze markers in a sample. This method comprises: providing an antibody that specifically binds to a marker; contacting a sample 5 with the antibody; and detecting the presence of a complex of the antibody bound to the marker in the sample. To prepare an antibody that specifically binds to a mrker, purified protein markers can be used. Antibodies that specifically bind to a protein marker can be prepared using any suitable methods known in the art. 10 After the antibody is provided, a marker can be detected and/or quantified using any of a number of well recognized immunological binding assays. Useful assays include, for example, an enzyme immune assay (EIA) such as enzyme-linked immunosorbent assay (ELISA), a radioimmune assay (RIA), a Western blot assay, or a slot blot assay see, e.g., U.S. Pat Nos. 4,366,241; 4,376,110; 4,517,288; and 4,837,168). Generally, a sample 15 obtained from a subject can be contacted with the antibody that specifically binds the marker. Optionally, the antibody can be fixed to a solid support to facilitate washing and subsequent isolation of the complex, prior to contacting the antibody with a sample. Examples of solid supports include but are not limited to glass or plastic in the form of, e.g., 20 a microtiter plate, a stick, a bead, or a microbead. Antibodies can also be attached to a solid support. After incubating the sample with antibodies, the mixture is washed and the antibody marker complex formed can be detected. This can be accomplished by incubating the washed mixture with a detection reagent. Alternatively, the marker in the sample can be 25 detected using an indirect assay, wherein, for example, a second, labeled antibody is used to detect bound marker-specific antibody, and/or in a competition or inhibition assay wherein, for example, a monoclonal antibody which binds to a distinct epitope of the marker are incubated simultaneously with the mixture. Throughout the assays, incubation and/or washing steps may be required after each 30 combination of reagents. Incubation steps can vary from about 5 seconds to several hours, preferably from about 5 minutes to about 24 hours. However, the incubation time will depend upon the assay format, marker, volume of solution, concentrations and the like.

WO 2005/072055 PCT/IB2005/000995 56 Usually the assays will be carried out at ambient temperature, although they can be conducted over a range of temperatures, such as 10 'C to 40 "C. The immunoassay can be used to determine a test amount of a marker in a sample from a subject. First, a test amount of a marker in a sample can be detected using the 5 immunoassay methods described above. If a marker is present in the sample, it will form an antibody-marker complex with an antibody that specifically binds the marker under suitable incubation conditions described above. The amount of an antibody- marker complex can optionally be determined by comparing to a standard. As noted above, the test amount of marker need not be measured in absolute units, as long as the unit of measurement can be 10 compared to a control amount and/or signal. Preferably used are antibodies which specifically interact with the polypeptides of the present invention and not with wild type proteins or other isoforms thereof, for example. Such antibodies are directed, for example, to the unique sequence portions of the polypeptide variants of the present invention, including but not limited to bridges, heads, tails and 15 insertions described in greater detail below. Preferred embodiments of antibodies according to the present invention are described in greater detail with regard to the section entitled "Antibodies". Radio -iminunoassay (RIA): In one version, this method involves precipitation of the desired substrate and in the methods detailed hereinbelow, with a specific antibody and 20 radiolabelled antibody binding protein (e.g., protein A labeled with I 25) immobilized on a precipitable carrier such as agarose beads. The number of counts in the precipitated pellet is proportional to the amount of substrate. In an alternate version of the RIA, a labeled substrate and an unlabelled antibody binding protein are employed. A sample containing an unknown amount of substrate is 25 added in varying amounts. The decrease in precipitated counts from the labeled substrate is proportional to the amount of substrate in the added sample. Enzyme linked immunosorbent assay (ELISA): This method involves fixation of a sample (e.g., fixed cells or a proteinaceous solution) containing a protein substrate to a surface such as a well of a microtiter plate. A substrate specific antibody coupled to an 30 enzyme is applied and allowed to bind to the substrate. Presence of the antibody is then detected and quantitated by a colorimetric reaction employing the enzyme coupled to the antibody. Enzymes commonly employed in this method include horseradish peroxidase and alkaline phosphatase. If well calibrated and within the linear range of response, the amount WO 2005/072055 PCT/IB2005/000995 of substrate present in the sample is proportional to the amount of color produced. A substrate standard is generally employed to improve quantitative accuracy. Western blot: This method involves separation of a substrate from other protein by means of an acrylamide gel followed by transfer of the substrate to a membrane (e.g., nylon 5 or PVDF). Presence of the substrate is then detected by antibodies specific to the substrate, which are in turn detected by antibody binding reagents. Antibody binding reagents may be, for example, protein A, or other antibodies. Antibody binding reagents may be radiolabelled or enzyme linked as described hereinabove. Detection may be by autoradiography, colorimetric reaction or chemiluminescence. This method allows both quantitation of an 10 amount of substrate and determination of its identity by a relative position on the membrane which is indicative of a migration distance in the acrylamide gel during electrophoresis. Innunohistochenical analysis: This method involves detection of a substrate in situ in fixed cells by substrate specific antibodies. The substrate specific antibodies may be enzyme linked or linked to fluorophores. Detection is by microscopy and subjective 15 evaluation. If enzyme linked antibodies are employed, a colorimetric reaction may be required. Fluorescence activated cell sorting faces) : This method involves detection of a substrate in situ in cells by substrate specific antibodies. The substrate specific antibodies are linked to fluorophores. Detection is by means of a cell sorting machine which reads the 20 wavelength of light emitted from each cell as it passes through a light beam. This method may employ two or more antibodies simultaneously. Radio -imaging Methods These methods include but are not limited to, positron emission tomography (PET) 25 single photon emission computed tomography (SPECT). Both of these techniques are non invasive, and can be used to detect and/or measure a wide variety of tissue events and/or functions, such as detecting cancerous cells for example. Unlike PET, SPECT can optionally be used with two labels simultaneously. SPECT has some other advantages as well, for example with regard to cost and the types of labels that can be used. For example, 30 US Patent No. 6,696,686 describes the use of SPECT for detection of breast cancer, and is hereby incorporated by reference as if fully set forth herein. Display Libraries WO 2005/072055 PCT/IB2005/000995 58 According to still another aspect of the present invention there is provided a display library comprising a plurality of display vehicles (such as phages, viruses or bacteria) each displaying at least 6, at least 7, at least 8, at least 9, at least 10, 10-15, 12-17, 15-20, 15-30 or 20-50 consecutive amino acids derived from the polypeptide sequences of the present 5 invention. Methods of constructing such display libraries are well known in the art. Such methods are described in, for example, Young AC, et al, "The three-dimensional structures of a polysaccharide binding antibody to Cryptococcus neoformans and its complex with a peptide from a phage display library: implications for the identification of peptide 10 mimotopes" J Mol Biol 1997 Dec 12;274(4):622-34; Giebel LB et al. "Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities" Biochemistry 1995 Nov 28;34(47):15430-5; Davies EL et al., "Selection of specific phage display antibodies using libraries derived from chicken immunoglobulin gene s" J Immunol Methods 1995 Oct 12;186(1):125-35; Jones C RT al. "Current trends in molecular 15 recognition and bioseparation" J Chromatogr A 1995 Jul 14;707(1):3-22; Deng SJ et al. "Basis for selection of improved carbohydrate-binding single-chain antibodies from synthetic gene libraries" Proc Natl Acad Sci U S A 1995 May 23;92(11):4992-6; and Deng SJ et al. "Selection of antibody single -chain variable fragments with improved carbohydrate binding by phage display" J Biol Chem 1994 Apr 1;269(13):9533 -8, which are incorporated 20 herein by reference. Treatment As mentioned hereinabove the BNP variants of the present invention and compositions derived therefrom (i.e., peptides, oligonucleotides) can be used to treat a 25 subject having, being diagnosed with or predisposed to a BNP-related disease, such as cardiac disease. The subject according to the present invention is a mammal, preferably a human which is diagnosed with one of the diseases described hereinabove, or alternatively is predisposed to having one of the diseases described hereinabove. 30 As used herein the term "treating" refers to preventing, curing, reversing, attenuating, alleviating, minimizing, suppressing or halting the deleterious effects of the BNP-related disease.

WO 2005/072055 PCT/IB2005/000995 59 Treating according to the present invention is effected by specifically upregulating the expression in the subject of at least one of the polypeptides of the present invention. As used hereinabove the phrase "active portion" refers to an amino acid sequence portion which is capable of displaying one or more functions of the BNP polypeptides of the 5 present invention. Upregulating methods and agents Upregulating expression of the BNP variants of the present invention may be effected via the administration of at least one of the exogenous polynucleotide sequences of the present invention (e.g., SEQ ID NOs: 1-3, 9-10 and/or 12-14) ligated into a nucleic acid 10 expression construct designed for expression of coding sequences in eukaryotic cells (e.g., mammalian cells). Accordingly, the eyogenous polynucleotide sequence may be a DNA or RNA sequence encoding the variants of the present invention or active portions thereof. It will be appreciated that the nucleic acid construct can be administered to the individual employing any suitable mode of administration, described hereinbelow (i.e., in 15 vivo gene therapy). Alternatively, the nucleic acid construct is introduced into a suitable cell via an appropriate gene delivery vehicle/method (transfection, transduction, homologous recombination, etc.) and an expression system as needed and then the modified cells are expanded in culture and returned to the individual (i.e., ex-vivo gene therapy). To enable cellular expression of the polynucleotides of the present invention, the 20 nucleic acid construct of the present invention further includes at least one cis acting regulatory element. As used herein, the phrase "cis acting regulatory element" refers to a polynucleotide sequence, preferably a promoter, which binds a trans acting regulator and regulates the transcription of a coding sequence located downstream thereto. Any suitable promoter sequence can be used by the nucleic acid construct of the 25 present invention. Preferably, the promoter utilized by the nucleic acid construct of the present invention is active in the specific cell population transformed. Examples of cell type specific and/or tissue-specific promoters include promoters such as albumin that is liver specific [Pinkert et al., (1987) Genes Dev. 1:268-277], lymphoid specific promoters [Calame 30 et al., (1988) Adv. Immunol. 43:235-275]; in particular promoters of T-cell receptors [Winoto et al., (1989) EMBO J. 8:729-733] and immunoglobulins [Banerji et al. (1983) Cell 33729-740], neuron-specific promoters such as the neurofilament promoter [Byrne et al. (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477), pancreas-specific promoters [Edlunch et WO 2005/072055 PCT/IB2005/000995 60 al. (1985) Science 230:912-916] or mammary gland-specific promoters such as the milk whey promoter (U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). The nucleic acid construct of the present invention can further include an enhancer, which can be adjacent or distant to the promoter sequence and can function in up 5 regulating the transcription therefrom. The nucleic acid construct of the present invention preferably further includes an appropriate selectable marker and/or an origin of replication. Preferably, the nucleic acid construct utilized is a shuttle vector, which can propagate both in E. coli (wherein the construct comprises an appropriate selectable marker and origin of replication) and be 10 compatible for propagation in cells, or integration in a gene and a tissue of choice. The construct according to the present invention can be, for example, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial chromosome. Examples of suitable constructs include, but are not limited to, pcDNA3, pcDNA3.1 (+/-), pGL3, PzeoSV2 (+/-), pDisplay, pEF/myc/cyto, pCMV/myc/cyto each of which is 15 commercially available from Invitrogen Co. (www.invitrogen.com). Examples of retroviral vector and packaging systems are those sold by Clontech, San Diego, Calif, including Retro-X vectors pLNCX and pLXSN, which permit cloning into multiple cloning sites and the transgene is transcribed from CMV promoter. Vectors derived from Mo-MuLV are also included such as pBabe, where the transgene will be transcribed from the 5'LTR promoter. 20 Currently preferred in vivo nucleic acid transfer techniques include transfection with viral or non-viral constructs, such as adenovirus, lentivirus, Herpes simplex I virus, or adeno -associated virus (AAV) and lipid-based systems. Useful lipids for lipid-mediated transfer of the gene are, for example, DOTMA, DOPE, and DC -Chol [Tonkinson et al., Cancer Investigation, 14(1): 54-65 (1996)]. The most preferred constructs for use in gene 25 therapy are viruses, most preferably adenoviruses, AAV, lentiviruses, or retroviruses. A viral construct such as a retroviral construct includes at least one transcriptional promoter/enhancer or locus -defining element(s), or other elements that control gene expression by other means such as alternate splicing, nuclear RNA export, or post translational modification of messenger. Such vector constructs also include a packaging 30 signal, long terminal repeats (LTRs) or portions thereof, and positive and negative strand primer binding sites appropriate to the virus used, unless it is already present in the viral construct. In addition, such a construct typically includes a signal sequence for secretion of the peptide from a host cell in which it is placed. Preferably the signal sequence for this WO 2005/072055 PCT/IB2005/000995 61 purpose is a mammalian signal sequence or the signal sequence of the polypeptide variants of the present invention. Optionally, the construct may also include a signal that directs polyadenylation, as well as one or more restriction sites and a translation termination sequence. By way of example, such constructs will typically include a 5' LTR, a tRNA 5 binding site, a packaging signal, an origin of second-strand DNA synthesis, and a 3' LTR or a portion thereof. Other vectors can be used that are non-viral, such as cationic lipids, polylysine, and dendrimers. It will be appreciated that the present methodology may also be effected by specifically upregulating the expression of the variants of the present invention t0 endogenously in the subject. Agents for upregulating endogenous expression of specific splice variants of a given gene include antisense oligonucleotides, which are di-ected at splice sites of interest, thereby altering the splicing pattern of the gene. This approach has been successfully used for shifting the balance of expression of the two isoforms of Bcl-x [Taylor (1999) Nat. Biotechnol. 17:1097-1100; and Mercatante (2001) J. Biol. Chem. 15 276:16411-16417]; IL-5R [Karras (2000) Mol. Pharmacol. 58:380-387]; and c-myc [Giles (1999) Antisense Acid Drug Dev. 9:213-220]. For example, interleukin 5 and its receptor play a critical role as regulators of hematopoiesis and as mediators in some inflammatory diseases such as allergy and asthma. Two alternatively spliced isoforms are generated from the IL-5R gene, which include (i.e., 20 long form) or exclude (i.e., short form) exon 9. The long form encodes for the intact membrane-bound receptor, while the shorter form encodes for a secreted soluble non functional receptor. Using 2'-O-MOE-oligonucleotides specific to regions of exon 9, Karras and co-workers (supra) were able to significantly decrease the expression of the wild type receptor and increase the expression of the shorter isoforms. Design and synthesis of 25 oligonucleotides which can be used according to the present invention are described hereinbelow and by Sazani and Kole (2003) Progress in Molecular and Subcellular Biology 31:217-239. Alternatively or additionally, upregulation may be effected by administering to the subject at least one polypeptide agent of the polypeptides of the present invention or an 30 active portion thereof, as described hereinabove. However, since the bioavailability of large polypeptides is relatively small due to high degradation rate and low penetration rate, administration of polypeptides is preferably confined to small peptide fragments (e.g., about 100 amino acids).

WO 2005/072055 PCT/IB2005/000995 62 An agent capable of up regulating a BNP polypeptide may also be any compound which is capable of increasing the transcription and/or translation of an endogenous DNA or mRNA encoding the BNP polypeptide and thus increasing endogenous BNP activity. An agent capable of upregulating a BNP may also be an exogenous polypeptide 5 including at least a functional portion (as described hereinabove) of the BNP. Upregulation of BNP can be also achieved by introducing at least one BNP substrate. Non-limiting examples of such agents include HOXC10 (Gabellini D, et al., 2003; EMBO J. 22: 3715-24), human securin and cyclin B1 (Tang Z, et al., 2001; Mol. Biol. Cell. 12: 3839 51), cyclins A, geminin H, and Cut2p (Bastians H, et al., 1999; Mol. Biol. Cell. 10: 3927 10 3941). It will be appreciated that upregulation of BNP can be also effected by administration of BNP- expressing cells into the individual. BNP- expressing cells can be any suitable cells, such as lung, ovary, bone marrow which are derived from the individual and are transfected ex vivo with an expression vector 15 containing the polynucleotide designed to express BNP as described hereinabove. Administration of the BNP-expressing cells of the present invention can be effected using any suitable route such as intravenous, intra peritoneal, and intra ovary. According to presently preferred embodiments, the BNP-expressing cells of the present invention are introduced to the individual using intravenous and/or intra organ administrations. 20 BNP-expressing cells of the present invention can be derived from either autologous sources such as self bone marrow cells or from allogeneic sources such as bone marrow or other cells derived from non-autologous sources. Since non-autologous cells are likely to induce an immune reaction when administered to the body several approaches have been developed to reduce the likelihood of rejection of non-autologous cells. These include either 25 suppressing the recipient immune system or encapsulating the non-autologous cells or tissues in irnmunoisolating, semipenneable membranes before transplantation. Encapsulation techniques are generally classified as microencapsulation, involving small spherical vehicles and macroencapsulation, involving larger flat-sheet and hollow-fiber membranes (Uludag, H. et al. Technology of manunalian cell encapsulation. Adv Drug Deliv 30 Rev. 2000; 42: 29-64). Methods of preparing microcapsules are known in the arts and include for example those disclosed by Lu MZ, et al., Cell encapsulation with alginate and alpha phenoxycinnamylidene -acetylated poly(allylamine). Biotechnol Bioeng. 2000, 70: 479-83, WO 2005/072055 PCT/IB2005/000995 63 Chang TM and Prakash S. Procedures for microencapsulation of enzymes, cells and genetically engineered microorganisms. Mol Biotechnol. 2001, 17: 249-60, and Lu MZ, et al., A novel cell encapsulation method using photosensitive poly(allylamine alpha cyanocinnamylideneacetate). J Microencapsul. 2000, 17: 245-51. 5 For example, microcapsules are prepared by complexing modified collagen with a ter-polymer shell of 2-hydroxyethyl methylacrylate (HEMA), methacrylic acid (MAA) and methyl methacrylate (MMA), resulting in a capsule thickness of 2-5 jim. Such microcapsules can be further encapsulated with additional 2-5 jIm ter-polymer shells in order to impart a negatively charged smooth surface and to minimize plasma protein absorption 10 (Chia, S.M. et al. Multi-layered microcapsules for cell encapsulation Biomaterials. 2002 23: 849-56). Other microcapsules are based on alginate, a marine polysaccharide (Sambanis, A. Encapsulated islets in diabetes treatment. Diabetes Thechnol. Ther. 2003, 5: 665-8) or its derivatives. For example, microcapsules can be prepared by the polyelectrolyte 15 complexation between the polyanions sodium alginate and sodium cellulose sulphate with the polycation poly(methylene-co-guanidine) hydrochloride in the presence of calcium chloride. It will be appreciated that cell encapsulation is improved when smaller capsules are used. Thus, the quality control, mechanical stability, diffusion properties, and in vitro 20 activities of encapsulated cells improved when the capsule size was reduced from 1 mm to 400 4m (Canaple L. et al., Improving cell encapsulation through size control. J Biomater Sci Polym Ed. 2002;13: 783-96). Moreover, nanoporous biocapsules with well-controlled pore size as small as 7 nm, tailored surface chemistries and precise microarchitectures were found to successfully immunoisolate microenvironments for cells (Williams D. Small is beautiful: 25 microparticle and nanoparticle technology in medical devices. Med Device Technol. 1999, 10: 6-9; Desai, T.A. Microfabrication technology for pancreatic cell encapsulation. Expert Opin Biol Ther. 2002, 2: 633-46). Downregulating methods and agents Downregulation of BNP can be effected on the genomic and/or the transcript level 30 using a variety of molecules which interfere with transcription and/or translation (e.g., antisense, siRNA, Ribozyme, DNAzyme), or on the protein level using e.g., antagonists, enzymes that cleave the polypeptide and the like.

WO 2005/072055 PCT/IB2005/000995 64 Following is a list of agents capable of downregulating expression level and/or activity of BNP. One example, of an agent capable of downregulating a BNP polypeptide is an antibody or antibody fragment capable of specifically binding BNP. Preferably, the antibody 5 specifically binds at least one epitope of a BNP as described hereinabove. An agent capable of downregulating a BNP transcript is a small interfering RNA (siRNA) molecule. RNA interference is a two step process. The first step, which is termed as the initiation step, input dsRNA is digested into 21-23 nucleotide (nt) small interfering RNAs (siRNA), probably by the action of Dicer, a member of the RNase III family of 10 dsRNA-specific ribonucleases, which processes (cleaves) dsRNA (introduced directly or via a transgene or a virus) in an ATP -dependent manner. Successive cleavage events degrade the RNA to 19-21 bp duplexes (siRNA), each with 2 -nucleotide 3' overhangs [Hutvagner and Zamore Curr. Opin. Genetics and Development 12:225-232 (2002); and Bernstein Nature 409:3 63 -3 66 (2001)]. 15 In the effector step, the siRNA duplexes bind to a nuclease complex to from the RNA-induced silencing complex (RISC). An ATP -dependent unwinding of the siRNA duplex is required for activation of the RISC. The active RISC then targets the homologous transcript by base pairing interactions and cleaves the mRNA into 12 nucleotide fragments from the 3' terminus of the siRNA [Hutvagner and Zamore Curr. Opin. Genetics and 20 Development 12:225-232 (2002); Hammond et al. (2001) Nat. Rev. Gen. 2:110-119 (2001); and Sharp Genes. Dev. 15:485 -90 (2001)]. Although the mechanism of cleavage is still to be elucidated, research indicates that each RISC contains a single siRNA and an RNase [Hutvagner and Zamore Curr. Opin. Genetics and Development 12:225-232 (2002)]. Because of the remarkable potency of RNAi, an amplification step within the RNAi 25 pathway has been suggested. Amplification could occur by copying of the input dsRNAs which would generate more siRNAs, or by replication of the siRNAs formed. Alternatively or additionally, amplification could be effected by multiple turnover events of the RISC [Hammond et al. Nat. Rev. Gen. 2:110-119 (2001), Sharp Genes. Dev. 15:485-90 (2001); Hutvagner and Zamore Curr. Opin. Genetics and Development 12:225-232 (2002)]. For 30 more information on RNAi see the following reviews Tuschl ChemBiochem. 2:239-245 (2001); Cullen Nat. Immunol. 3:597-599 (2002); and Brantl Biochem. Biophys. Act. 1575:15-25 (2002).

WO 2005/072055 PCT/IB2005/000995 65 Synthesis of RNAi molecules suitable for use with the present invention can be effected as follows. First, the BNP transcript mRNA sequence is scanned downstream of the AUG start codon for AA dinucleotide sequences. Occurrence of each AA and the 3' adjacent 19 nucleotides is recorded as potential siRNA target sites. Preferably, siRNA target 5 sites are selected from the open reading frame, as untranslated regions (UTRs) are richer in regulatory protein binding sites. UTR-binding proteins and/or translation initiation complexes may interfere with binding of the siRNA endonuclease complex [Tuschl, T. 2001, ChemBiochem. 2:239-245]. It will be appreciated though, that siRNAs directed at untranslated regions may also be effective, as demonstrated for GAPDH wherein siRNA 10 directed at the 5' UTR mediated about 90 % decrease in cellular GAPDH mRNA and completely abolished protein level (www.ambion.com/techlib/tn/91/912.html). Second, potential target sites are compared to an appropriate genomic database (e.g., human, mouse, rat etc.) using any sequence alignment software, such as the BLAST software available from the NCBI server (www.ncbi.nlm.nih.gov/BLAST/). Putative target 15 sites which exhibit significant homology to other coding sequences are filtered out. Qualifying target sequences are selected as template for siRNA synthesis. Preferred sequences are those including low G/C content as these have proven to be more effective in mediating gene silencing as compared to those with G/C content higher than 55 %. Several target sites are preferably selected along the length of the target gene for evaluation. For 20 better evaluation of the selected siRNAs, a negative control is preferably used in conjunction. Negative control siRNA preferably include the same nucleotide composition as the siRNAs but lack significant homologyto the genome. Thus, a scrambled nucleotide sequence of the siRNA is preferably used, provided it does not display any significant homology to any other gene. 25 Another agent capable of downregulating a BNP transcript is a DNAzyme molecule capable of specifically cleaving an mRNA transcript or DNA sequence of the BNP. DNAzymes are single-stranded polynucleotides which are capable of cleaving both single and double stranded target sequences (Breaker, R.R. and Joyce, G. Chemistry and Biology 1995;2:655; Santoro, S.W. & Joyce, G.F. Proc. Natl, Acad. Sci. USA 1997;943:4262). A 30 general model (the "10-23" model) for the DNAzyme has been proposed. "10-23" DNAzymes have a catalytic domain of 15 deoxyribonucleotides, flanked by two substrate recognition domains of seven to nine deoxyribonucleotides each. This type of DNAzyme can effectively cleave its substrate RNA at purine:pyrimidine junctions (Santoro, S.W. & WO 2005/072055 PCT/IB2005/000995 66 Joyce, G.F. Proc. Natl, Acad. Sci. USA 199; for rev of DNAzymes see Khachigian, LM [Curr Opin Mol Ther4:119-21 (2002)]. Examples of construction and amplification of synthetic, engineered DNAzymes recognizing single and double -stranded target cleavage sites have been disclosed in U.S. Pat. 5 No. 6,326,174 to Joyce et aL DNAzymes of similar design directed against the human Urokinase receptor were recently observed to inhibit Urokinase receptor expression, and successfully inhibit colon cancer cell metastasis in vivo (Itoh et al, 20002, Abstract 409, Ann Meeting Am Soc Gen Ther. www.asgt.org). In another application, DNAzymes complementary to bcr-abl oncogenes were successful in inhibiting the oncogenes expression 10 in leukemia cells, and lessening relapse rates in autologous bone marrow transplant in cases of CML and ALL. Downregulation of a BNP transcript can also be effected by using an antisense polynucleotide capable of specifically hybridizing with an mRNA transcript encoding the BNP. 15 Design of antisense molecules which can be used to efficiently downregulate a BNP must be effected while considering two aspects important to the antisense approach. The first aspect is delivery of the oligonucleotide into the cytoplasm of the appropriate cells, while the second aspect is design of an oligonucleotide which specifically binds the designated mRNA within cells in a way which inhibits translation thereof. 20 The prior art teaches of a number of delivery strategies which can be used to efficiently deliver oligonucleotides into a wide variety of cell types [see, for example, Luft J Mol Med 76: 75-6 (1998); Kronenwett et al. Blood 91: 852-62 (1998); Rajur et al. Bioconjug Chem 8: 935-40 (1997); Lavigne et al. Biochem Biophys Res Commun 237: 566 71 (1997) and Aoki et al. (1997) Biochem Biophys Res Commun 231: 540-5 (1997)]. 25 In addition, algorithms for identifying those sequences with the highest predicted binding affinity for their target mRNA based on a thermodynamic cycle that accounts for the energetics of structural alterations in both the target mRNA and the oligonucleotide are also available [see, for example, Walton et al. Biotechnol Bioeng 65: 1-9 (1999)]. Such algorithms have been successfully used to implement an antisense approach in 30 cells. For example, the algorithm developed by Walton et al. enabled scientists to successfully design antisense oligonucleotides for rabbit beta-globin (RBG) and mouse tumor necrosis factor-alpha (TNF alpha) transcripts. The same research group has more recently reported that the antisense activity of rationally selected oligonucleotides against WO 2005/072055 PCT/IB2005/000995 67 three model target mRNAs (human lactate dehydrogenase A and B and rat gpl 30) in cell culture as evaluated by a kinetic PCR technique proved effective in almost all cases, including tests against three different targets in two cell types with phosphodiester and phosphorothioate oligonucleotide chemistries. 5 In addition, several approaches for designing and predicting efficiency of specific oligonucleotides using an in vitro system were also published (Matveeva et al., Nature Biotechnology 16: 1374 - 1375 (1998)]. Several clinical trials have demonstrated safety, feasibility and activity of antisense oligonucleotides. For example, antisense oligonucleotides suitable for the treatment of 10 cancer have been successfully used [Hohnund et al., Curr Opin Mol Ther 1:372-85 (1999)), while treatment of hematological malignancies via antisense oligonucleotides targeting c myb gene, p53 and Bcl-2 had entered clinical trials and had been shown to be tolerated by patients [Gerwitz Curr Opin Mol Ther 1:297-306 (1999)]. More recently, antiense-mediated suppression of human heparanase gene expression 15 has been reported to inhibit pleural dissemination of human cancer cells in a mouse model [Uno et al., Cancer Res 61:7855-60 (2001)]. Thus, the current consensus is that recent developments in the field of antisense technology which, as described above, have led to the generation of highly accurate antisense design algorithms and a wide variety of oligonucleotide delivery systems, enable 20 an ordinarily skilled artisan to design and implement antisense approaches suitable for downregulating expression of known sequences without having to resort to undue trial and error experimentation. Another agent capable of downregulating a BNP transcript is a ribozyme molecule capable of specifically cleaving an mRNA transcript encoding a BNP. Ribozymes are being 25 increasingly used for the sequence-specific inhibition of gene expression by the cleavage of nRNAs encoding proteins of interest [Welch et al., Curr Opin Biotechnol. 9:486-96 (1998)]. The possibility of designing ribozymes to cleave any specific target RNA has rendered them valuable tools in both basic research and therapeutic applications. In the therapeutics area, ribozymes have been exploited to target viral RNAs in infectious diseases, dominant 30 oncogenes in cancers and specific somatic mutations in genetic disorders [Welch et al., Clin Diagn Virol. 10:163 -71 (1998)]. Most notably, several ribozyme gene therapy protocols for HIV patients are already in Phase 1 trials. More recently, ribozymes have been used for transgenic animal research, gene target validation and pathway elucidation. Several WO 2005/072055 PCT/IB2005/000995 68 ribozymes are in various stages of clinical trials. ANGIOZYME was the first chemically synthesized ribozyme to be studied in human clinical trials. ANGIOZYME specifically inhibits formation of the VEGF-r (Vascular Endothelial Growth Factor receptor), a key component in the angiogenesis pathway. Ribozyme Pharmaceuticals, Inc., as well as other 5 firms have demonstrated the importance of anti-angiogenesis therapeutics in animal models. HEPTAZYME, a ribozyme designed to selectively destroy Hepatitis C Virus (HCV) RNA, was found effective in decreasing Hepatitis C viral RNA in cell culture assays (Ribozyme Pharmaceuticals, Incorporated - WEB home page). Another agent capable of downregulating BNP would be any molecule which binds 10 to and/or cleaves BNP. Such molecules can be BNP antagonists, or BNP inhibitory peptide. It will be appreciated that a non-functional analogue of at least a catalytic or binding portion of BNP can be also used as an agent which downregulates BNP. Another agent which can be used along with the present invention to downregulate BNP is a molecule which prevents BNP activation or substrate binding. 15 Each of the upregulating or downregulating agents described hereinabove or the expression vector encoding BNP can be administered to the individual per se or as part of a pharmaceutical composition which also includes a physiologically acceptable carrier. The purpose of a pharmaceutical composition is to facilitate administration of the active ingredient to an organism. 20 As used herein a "pharmaceutical composition" refers to a preparation of one or more of the active ingredients described herein with other chemical components such as physiologically suitable carriers and excipients. The purpose of a pharmaceutical composition is to facilitate administration of a compound to an organism. Herein the term "active ingredient" refers to the preparation accountable for the 25 biological effect. Hereinafter, the phrases "physiologically acceptable carrier" and "pharmaceutically acceptable carrier" which may be interchangeably used refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biobgical activity and properties of the administered compound. An adjuvant is included under these 30 phrases. One of the ingredients included in the pharmaceutically acceptable carrier can be for example polyethylene glycol (PEG), a biocompatible polymer with a wide range of solubility in both organic and aqueous media (Mutter et al. (1979).

WO 2005/072055 PCT/IB2005/000995 69 Herein the tenn "excipient" refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient. Examples, without limitation, of excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols. 5 Techniques for fonnulation and administration of drugs may be found in "Remington's Pharmaceutical Sciences," Mack Publishing Co., Easton, PA, latest edition, which is incorporated herein by reference. Suitable routes of administration may, for example, include oral, rectal, transmucosal, especially transnasal, intestinal or parenteral delivery, including intramuscular, 10 subcutaneous and intramedullary injections as well as intrathecal, direct intraventricular, intravenous, inrtaperitoneal, intranasal, or intraocular injections. Alternately, one may administer a preparatio n in a local rather than systemic manner, for example, via injection of the preparation directly into a specific region of a patient's body. Phannaceutical compositions of the present invention may be manufactured by 15 processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes. Phannaceutical compositions for use in accordance with the present invention may be formulated in conventional manner using one or more physiologically acceptable carriers 20 comprising excipients and auxiliaries, which facilitate processing of the active ingredients into preparations which, can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen. For injection, the active ingredients of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's 25 solution, or physiological salt buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such 30 carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for oral ingestion by a patient. Pharmacological preparations for oral use can be made using a solid excipient, optionally grinding the resulting mixture, and processing the mixture of granules, after WO 2005/072055 PCT/IB2005/000995 70 adding suitable auxiliaries if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium 5 carbomethylcellulose; and/or physiologically acceptable polymers such as polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as cross linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used which may optionally contain gum arabic, tale, polyvinyl 10 pyrrolidone, carbopol gel, polyethylene glycol, titanium dioxide, lacquer solutions and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses. Pharmaceutical compositions, which can be used orally, include push-fit capsules 15 made of gelatin as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules may contain the active ingredients in admixture with filler such as lactose, binders such as starches, lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active ingredients may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene 20 glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for the chosen route of administration. For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner. For administration by nasal inhalation, the active ingredients for use according to the 25 present invention are conveniently delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichloro-tetrafluoroethane or carbon dioxide. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for 30 use in a dispenser may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch. The preparations described herein may be formulated for parenteral administration, e.g., by bolus injection or continuous infusion. Fornulations for injection may be presented WO 2005/072055 PCT/IB2005/000995 71 in unit dosage form, e.g., in ampoules or in multidose containers with optionally, an added preservative. The compositions may be suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. 5 Pharmaceutical compositions for parenteral administration include aqueous solutions of the active preparation in water-soluble form. Additionally, suspensions of the active ingredients may be prepared as appropriate oily or water based injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acids esters such as ethyl oleate, triglycerides or liposomes. Aqueous injection 10 suspensions may contain substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the active ingredients to allow for the preparation of highly concentrated solutions. Alternatively, the active ingredient may be in powder form for constitution with a 15 suitable vehicle, e.g., sterile, pyrogen-free water based solution, before use. The preparation of the present invention may also be formulated in rectal compositions such as suppositories or retention enemas, using, e.g., conventional suppositorybases such as cocoa butter or other glycerides. Pharmaceutical compositions suitable for use in context of the present invention 20 include compositions wherein the active ingredients are contained in an amount effective to achieve the intended purpose. More specifically, a therapeutically effective amount means an amount of active ingredients effective to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those 25 skilled in the art. For any preparation used in the rnethods of the invention, the therapeutically effective amount or dose can be estimated initially from in vitro assays. For example, a dose can be formulated in animal models and such information can be used to more accurately determine useful doses in humans. 30 Toxicity and therapeutic efficacy of the active ingredients described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals. The data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage may vary depending WO 2005/072055 PCT/IB2005/000995 72 upon the dosage form employed and the route ofadministration utilized. The exact fonnulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g., Fingl, et al., 1975, in "The Pharmacological Basis of Therapeutics", Ch. 1 p.1). 5 Depending on the severity and responsiveness of the condition to be treated, dosing can be of a single or a plurality of administrations, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved. The amount of a composition to be administered will, of course, be dependent on the 10 subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, etc. Compositions including the preparation of the present invention fonnulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition. 15 Pharmaceutical compositions of the present invention may, if desired, be presented in a pack or dispenser device, such as an FDA approved kit, which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser may also be 20 accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration. Such notice, for example, may be of labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert. 25 It will be appreciated that treatment of BNP related disease according to the present invention may be combined with other treatment methods known in the art (i.e., combination therapy). The principles and operation of the present invention may be better understood with reference to the drawings and accompanying descriptions. 30 Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways. Also, it is to be WO 2005/072055 PCT/IB2005/000995 73 understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting. As used herein the term "about" refers to ± 10 %. 5 Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in tle claims section below finds experimental support in the following examples. 10 EXAMPLES Reference is now made to the following examples, which together with the above descriptions, illustrate the invention in a non limiting fashion. Generally, the nomenclature used herein and the laboratory procedures utilized in the 15 present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, "Molecular Cloning: A laboratory Manual" Sambrook et al., (1989); "Current Protocols in Molecular Biology" Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., "Current Protocols in Molecular Biology", John Wiley and Sons, Baltimore, Maryland (1989); Perbal, 20 "A Practical Guide to Molecular Cloning", John Wiley & Sons, New York (1988); Watson et al., "Recombinant DNA", Scientific American Books, New York; Birren et al. (eds) "Genome Analysis: A Laboratory Manual Series", Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; "Cell Biology: A Laboratory Handbook", Volumes I 25 III Cellis, J. E., ed. (1994); "Current Protocols in Immunology" Volumes I-II ColiganJ. E., ed. (1994); Stites et al. (eds), "Basic and Clinical Immunology" (8th Edition), Appleton & Lange, Norwalk, CT (1994); Mishell and Shiigi (eds), "Selected Methods in Cellular Immunology", W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 30 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; "Oligonucleotide Synthesis" Gait, M. J., ed. (1984); "Nucleic Acid Hybridization" Hames, B. D., and Higgins S. J., eds. (1985); "Transcription and Translation" WO 2005/072055 PCT/IB2005/000995 74 Haines, B. D., and Higgins S. J., Eds. (1984); "Animal Cell Culture" Freshney, R. I., ed. (1986); "Immobilized Cells and Enzymes" IRL Press, (1986); "A Practical Guide to Molecular Cloning" Perbal, B., (1984) and "Methods in Enzymology" Vol. 1-317, Academic Press; "PCR Protocols: A Guide To Methods And Applications", Academic Press, San 5 Diego, CA (1990); Marshak et al., "Strategies for Protein Purification and Characterization A Laboratory Course Manual" CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated 10 herein by reference. The following sections rehte to Candidate Marker Examples (first section). 15 CANDIDATE MARKER EXAMPLES SECTION This Section relates to Examples of sequences according to the present invention. Description of the methodology undertaken to uncover the biomolecular sequences of the present invention 20 Human ESTs and cDNAs were obtained from GenBank versions 136 (June 15, 2003 fty.nebi.nih.gov/genbank/release.notes/gbl36.release.notes); NCBI genome assembly of April 2003; RefSeq sequences from June 2003; Genbank version 139 (December 2003); Human Genome from NCBI (Build 34) (from Oct 2003); and RefSeq sequences from December '003; and from Incyte LifeSeq library (ESTs only; Incyte Corporation 25 (Wilmington, DE, USA)). With regard to GenBank sequences, the human EST sequences from the EST (GBEST) section and the human mRNA sequences from the primate (GIBPRI) section were used; also the human nucleotide RefSeq mRNA sequences were used (see for example www.ncbi.nhn.nih.gov/Genbank/GenbankOverview.html and for a reference to the EST section, see www.ncbi.nhm.nih.gov/dbEST/; a general reference to dbEST, the EST 30 database in GenBank, may be found in Boguski et al, Nat Genet. 1993 Aug;4(4):332-3; all of which are hereby incorporated by reference as if fully set forth herein). Novel splice variants were predicted using the LEADS clustering and assembly system as described in Sorek, R., Ast, G. & Graur, D. Alu-containing exons are alternatively WO 2005/072055 PCT/IB2005/000995 .75 spliced. Genome Res 12, 1060-7 (2002); US patent No: 6,625,545; and U.S. Pat. Apple. No. 10/426,002, published as US20040101876 on May 27 2004; all of which are hereby incorporated by reference as if fully set forth herein. Briefly, the software cleans the expressed sequences from repeats, vectors and immunoglobulins. It then aligns the 5 expressed sequences to the genome taking alternatively splicing into account and clusters overlapping expressed sequences into "clusters" that represent genes or partial genes. These were annotated using the GeneCarta (Compugen, TekAviv, Israel) platform. The GeneCarta platform includes a rich pool of annotations, sequence information (particularly of spliced sequences), chromosomal information, alignments, and additional 10 information such as SNPs, gene ontology terms, expression profiles, functional analyses, detailed domain structures, known and predicted proteins and detailed homology reports. A brief explanation is provided with regard to the method of selecting the candidates. However, it should be noted that this explanation is provided for descriptive purposes only, and is not intended to be limiting in any way. The potential markers were identified by a 15 computational process that was designed to find genes and/or their splice variants that are specifically expressed in cardiac tissue, as opposed to other types of tissues and also particularly as opposed to muscle tissue, by using databases of expressed sequences. Various parameters related to the information in the EST libraries, determined according to classification by library annotation, were used to assist in locating genes and/or splice 20 variants thereof that are specifically and/or differentially expressed in heart tissues. The detailed description of the selection method and of these parameters is presented in Example 1 below. EXAMPLE I 25 Identication ofdifferentiall> expressed gene products - Algorithm In order to distinguish between differentially expressed gene products and constitutively, expressed genes (i.e., house keeping genes), an algorithm based on an analysis of frequencies was configured. A specific algorithm for identification of transcripts specifically expressed in heart tissue is described hereinbelow. 30 EST analysis ESTs were taken from the following main sources: libraries contained in Genbank version 136 (June 15, 2003 ftp.ncbi.nih.gov/genbank/release.notes/gbl36.release.notes) and WO 2005/072055 PCT/IB2005/000995 76 Genbank version 139 (December 2003); and from the EST portion of LifeSeq, from Incyte Corporation (Wilmington, DE, USA). With regard to GenBank sequences, the human EST sequences from the EST (GBEST) section were used. Library annotation - EST libraries were manually classified according to: 5 1. Tissue origin 2. Biological source - Examples of frequently used biological sources for construction of EST libraries include cancer cell- lines; normal tissues; cancer tissues; foetal tissues; and others such as normal cell lines and pools of normal cell-lines, cancer cell-lines and combinations thereof. A 10 specific description of abbreviations used below with regard to these tissues/cell lines etc is given above. 3. Protocol oflibraiy construction - various methods are known in the art for library construction including normalized library construction; non 15 normalized library construction; subtracted libraries; ORESTES and others (described in the annotation available in Genbank). It will be appreciated that at times the protocol of library construction is not indicated in the information available about that library. The following rules were followed: 20 EST libraries originating from identical biological samples were considered as a single library. EST libraries which included above -average levels of contamination, such as DNA contamination for example, were eliminated. The presence of such contamination was determined as follows. For each library, the number of unspliced ESTs that are not fully 25 contained within other spliced sequences was counted. If the percentage of such sequences (as compared to all other sequences) was at least 4 standard deviations above the average for all libraries being analyzed, this library was tagged as being contaminated and was eliminated from further consideration in the below analysis (see also Sorek, R. & Safer, H.M. A novel algorithm for computational identification of contaminated EST libraries. Nucleic Acids Res 30 31, 1067-74 (2003)for further details). Clusters (genes) having'at least five sequences including at least two sequences from the tissue of interest were analyzed. Splice variants were identified by using the LEADS software package as described above.

WO 2005/072055 PCT/IB2005/000995 77 EXAMPLE 2 Identification of heart tissue specific genes 5 For detection of heart tissue specific clusters, heart tissue libraries/sequences were compared to the total number of libraries/sequences in the cluster and in Genebank, and to the relevant numbers for muscle tissue libraries/sequences. Statistical tools were employed to identify clusters that were heart tissue specific, both as compared to all other tissues and also in comparison to muscle tissue. 10 The algorithm - for each tested tissue T and for each tested cluster the following were examined: 1. Each cluster includes at least 2 libraries from the tissue T. At least 3 clones (weighed - as described above) from tissue T in the cluster; 2, The following equation was then used to determine heart tissue -specific 15 expression as compared to expression in all tissue types for a particular cluster: t /n- t -m in which n is the total number of ESTs available for a cluster, while N is the T1 N -- T- M total number of ESTs available in all of the libraries considered in the analysis (effectively all ESTs in Genbank, except for those that were rejected as belonging to contaminated libraries). This ratio was preferably set to be at least about 8, although optionally the ratio could be set to 20 be at least about 5. 3, The following equation was then used to determine heart tissue -specific expression vs. expression in skeletal muscle tissue for a particular cluster: r/l in which t represents the number of heart tissue-specific ESTs for the cluster, while T is the number of all heart tissue-specific ESTs in the analysis; m is the number of skeletal muscle tissue -specific 25 ESTs for the cluster, while M is the number of all skeletal muscle tissue-specific ESTs in the analysis. This ratio was preferably set to be at least about 4, although optionally the ratio could be set to be at least about 2. 4. Fisher exact test P-values were computed for weighted clone counts to check that the counts are statistically significant according to the following function: F(tT,n,N) 30 which is the probability of a cluster actually being overexpressed in heart tissue, as compared WO 2005/072055 PCT/IB2005/000995 78 to its overall level of expression. The P-value was preferably set to be less than about I e-5, although optionally it could be set to be less than about le-3. Example 3 - Experimental and Marker Data 5 This Example relates to examples of sequences according to the present invention, including experiments involving these sequences, and illustrative, non- limiting examples of methods, assays and uses thereof. The materials and experimental procedures are explained first, as all experiments used them as a basis for the work that was performed. The markers of the present invention were tested with regard to their expression in 10 various heart and non-heart tissue samples. Unless otherwise noted, all experimental data relates to variants of the present invention, named according to the segment being tested (as expression was tested through RT-PCR as described). A description of the samples used in the panel is provided in Table 1 below. Tests were then performed as described below. 15 Table 1: Tissue samples in testing panel Lot no. Source Tissue Pathology Sex/Age 1-Am-Colon (C71) 071PIOB Ambion Colon PM F/43 2-B-Colon (C69) A411078 Biochain Colon PM-Pool of 10 M&F 3-Cl-Colon (C70) 1110101 Clontech Colon PM-Pool of 3 M&F 4-Am-Small Intestine 091PO201AAmbion Small Intestine PM M/75 5-B-Small Intestine A501158 Biochain Small Intestine PM M/63 6-B-Rectum A605138 Biochain Rectum PM M/25 7-B-Rectum A610297 Biochain Rectum PM M/24 8-B-Rectum A610298 Biochain Rectum PM M/27 9-Am-Stomach 11 OP04A Ambion Stomach PM M/16 10-B-Stomach A501159 Biochain Stomach PM M/24 11-B-Esophagus A603814 Biochain Esophagus PM M/26 12-B-Esophagus A603813 Biochain Esophagus PM M/41 13-Am-Pancreas 071P25C Ambion Pancreas PM M/25 14-CG-Pancreas CG-255-2 Ichilov Pancreas PM M/75 15-B-Lung A409363 Biochain Lung PM F/26 16-Am-Lung (L93) 111PO103AAmbion Lung PM F/61 WO 2005/072055 PCT/IB2005/000995 79 17-B-Lung (L92) A503204 Biochain Lung PM M/28 18-Am-Ovaiy (047) 061P43A Ambion Ovary PM F/16 19-B-Ovary (048) A504087 Biochain Ovary PM F/51 20-B-Ovary (046) A504086 Biochain Ovary PM F/41 21-Am-Cervix 101P0101AAmbion Cervix PM F/40 22-B-Cervix A408211 Biochain Cervix PM F/36 23-B-Cervix A504089 Biochain Cervix PM-Pool of 5 M&F 24-B-Uterus A411074 Biochain Uterus PM-Pool of 10 M&F 25-B-Uterus A409248 Biochain Uterus PM F/43 26-B-Uterus A504090 Biochain Uterus PM-Pool of 5 M&F 27-B-Bladder A501157 Biochain Bladder PM M/29 28-Am-Bladder 071P02C Ambion Bladder PM M/20 29-B-Bladder A504088 Bioclnin Bladder PM-Pool of 5 M&F 30-Am-Placenta 021P33A Ambion Placenta PB F/33 31-B-Placenta A410165 Biochain Placenta PB F/26 32-B-Placenta A411073 Biochain Placenta PB-Pool of 5 M&F 33-B-Breast (B59) A607155 Biochain Breast PM F/36 34-Am-Breast (B63) 26486 Ambion Breast PM F/43 35-Am-Breast (B64) 23036 Ambion Breast PM F/57 36-Cl-Prostate (P53) 1070317 Clontech Prostate PB-Pool of 47 M&F 37-Am-Prostate (P42) 061P04A Ambion Prostate PM M/47 38-Am-Prostate (P59) 25955 Ambion Prostate PM M/62 39-Am-Testis lllPO104AAmbion Testis PM M/25 40-B-Testis A411147 Biochain Testis PM M/74 41-Cl-Testis 1110320 Clontech Testis PB-Pool of 45 M&F 42-CG-Adrenal CG-184-10 Ichilov Adrenal PM F/81 43-B-Adrenal A610374 Biochain Adrenal PM F/83 44-B-Heart A411077 Biochain Heart PB-Pool of 5 M&F 45-CG-Heart CG-255-9 Ichilov Heart PM M/75 46-CG-Heart CG-227-1 Ichilov Heart PM F/36 47-Am-Liver 081Pl11AAmbion Liver PM M/64 WO 2005/072055 PCT/IB2005/000995 80 48-CG-Liver CG-93-3 lchilov Liver PM F/19 49-CG-Liver CG-124-4 Ichiloy Liver PM F/34 50-Cl-BM 1110932 Clontech Bone Marrow PM-Pool of 8 M&F 51-CGEN-Blood WBC#5 CGEN Blood M 52-CGEN-Blood WBC#4 CGEN Blood M 53-CGEN-Blood WBC#3 CGEN Blood M 54-CG-Spleen CG-267 lchilov Spleen PM F/25 55-CG-Spleen 111P0106BAmbion Spleen PM M/25 56-CG-Spleen A409246 Biochain Spleen PM F/12 56-CG-Thymus CG-98-7 Ichilov Thymus PM F/28 58-Am-Thymus 101P011AAmbion Thymus PM M/14 59-B-Thymus A409278 Biochain Thymus PM M/28 60-B-Thyroid A610287 Biochain Thyroid PM M/27 61 -B-Thyroid A610286 Biochain Thyroid PM M/24 62-CG-Thyroid CG-119-2 Ichilov Thyroid PM F/66 63-Cl-Salivary Gland 1070319 Clontech Salivary Gland PM-Pool of 24 M&F 64-Am-Kidney 11IPO101BAmbion Kidney PM-Pool of 14 M&F 65-Cl-Kidney 1110970 Clontech Kidney PM-Pool of 14 M&F 66-B-Kidney A411080 Biochain Kidney PM-Pool of 5 M&F 67-CG-Cerebellum CG-183-5 Ichilov Cerebellum PM M/74 68-CG-Cerebellum CG-212-5 Ichilov Cerebellum PM M/54 69-B-Brain A411322 Biochain Brain PM M/28 70-Cl-Brain 1120022 Clontech Brain PM-Pool of 2 M&F 71-B-Brain A411079 Biochain Brain PM-Pool of 2 M&F 72-CG-Brain CG-151-1 Ichilov Brain PM F/86 73-Am-SkeletalMuscle 101PO13A Ambion Skeletal Muscle PM F/28 74-Cl-Skeletal Muscle 1061038 Clontech Skeletal Muscle PM-Pool of 2 M&F Materials and Experimental P rocedures RNA preparation - RNA was obtained from Clontech Franklin Lakes, NJ USA 07417, www.clontech.com), BioChain Inst. Inc. (Hayward, CA 94545 USA 5 www.biochain.com), ABS (Wilmington, DE 19801, USA, http://www.absbioreagents.com) or Ambion (Austin, TX 78744 USA, http://www.ambion.com). Alternatively, RNA was WO 2005/072055 PCT/IB2005/000995 81 generated from tissue samples using TRI-Reagent (Molecular Research Center), according to Manufacturer's instructiors. Tissue and RNA sample-s were obtained from patients or from postmortem. Total RNA samples were treated with DNaseI (Ambion) and purified using RNeasy columns (Qiagen). 5 RT PCR - Purified RNA (1 tg) was mixed with 150 ng Random Hexamer primers (Invitrogen) and 500 pM dNTP in a total volume of 15.6 1tl. The mixture was incubated for 5 min at 65 OC and then quickly chilled on ice. Thereafter, 5 pl of 5X Superscriptll first strand buffer (Invitrogen), 2

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4 gl 0.1M DTT and 40 units RNasin (Promega) were added, aid the mixture was incubated for 10 min at 25 OC, followed by further incubation at 42 0 C for 2 10 min. Then, 1 ht 1 (200units) of SuperscriptIl (Invitrogera) was added and the reaction (final volume of 25 p1) was incubated for 50 min at 42 'C and then inactivated at 70 0 C for 15min. The resulting cDNA was diluted 1:20 in TE buffer (10k mM Tris pH=8, 1 mM EDTA pH=8). Real-Time RT-PCR analysis- cDNA (5ptl), prepared as described above, was used as a template in RealTime PCR reactions using the SYBZR Green I assay (PE Applied 15 Biosystem) with specific primers and UNG Enzyme (Eurogentech or ABI or Roche). The amplification was effected as follows: 50 *C for 2 min, 95 *C for 10 min, and then 40 cycles of 95 "C for 15sec, followed by 60 "C for 1 min. Detecmtion was performed by using the PE Applied Biosystem SDS 7000. The cycle in which the reactions achieved a threshold level (Ct) of fluorescence was registered and was used to calculate the relative transcript quantity 20 in the RT reactions. The relative quantity was calculated using the equation Q=efficiency^-. The efficiency of the PCR reaction was calculated from a standard curve, created by using serial dilutions of several reverse transcription (RT) r- actions To minimize inherent differences in the RT reaction, the resulting relative quantities were normalized to the geometric mean of the relative quantities of several housekeeping (HSKP) genes. Schematic 25 summary of quantitative realtime PCR analysis is presented in Figure 1. As shown, the x axis shows the cycle number. The CT= Threshold Cycle point, which is the cycle that the amplification curve crosses the fluorescence threshold that was set in the experiment. This point is a calculated cycle number in which PCR products signal is above the background level (passive dye ROX) and still in the Geometric/Exponential phase (as shown, once the 30 level of fluorescence crosses the measurement threshold, it has a geometrically increasing phase, during which measurements are most accurate, followed by a linear phase and a plateau phase; for quantitative measurements, the latter two phases do not provide accurate WO 2005/072055 PCT/IB2005/000995 82 measurements). The y-axis shows the normalized reporter fluorescence. It should be noted that this type of analysis provides relative quantification. The sequences of the housekeeping genes measured in all the examples on normal 5 tissue samples panel were as follows: RPL19 (GenBank Accession No. NM_000981), RPLI9 Forward primer (SEQ ID NO:30): TGGCAAGAAGAAGGTCTGGTTAG RPL19 Reverse primer (SEQ ID NO:3 1): TGATCAGCCCATCTTTGATGAG 10 RPL19 -amplicon (SEQ ID NO:32): TGGCAAGAAGAAGGTCTGGTTAGACCCCAATGAGACCAATGAAATCGCCAATG CCAACTCCCGTCAGCAGATCCGGAAGCTCATCAAAGATGGGCTGATCA TATA box (GenBank Accession No. NM 003194), TATA box Forward primer (SEQ ID NO:33): CGGTTTGCTGCGGTAATCAT 15 TATA box Reverse primer (SEQ ID NO:34): TTTCTTGCTGCCAGTCTGGAC TATA box -amplicon (SEQ ID NO:35): CGGTTTGCTGCGGTAATCATGAGGATAAGAGAGCCACGAACCACGGCACTGATT TTCAGTTCTGGGAAAATGGTGTGCACAGGAGCCAAGAGTGAAGAACAGTCCAG ACTGGCAGCAAGAAA 20 Ubiquitin (GenBank Accession No. BC000449) Ubiquitin Forward primer (SEQ ID NO:36): ATTTGGGTCGCGGTTCTTG Ubiquitin Reverse primer (SEQ ID NO:37): TGCCTTGACATTCTCGATGGT Ubiquitin -amplicon (SEQ ID NO:3 8): ATTTGGGTCGCGGTTCTTGTTTGTGGATCGCTGTGATCGTCACTTGACAATGCAG 25 ATCTTCGTGAAGACTCTGACTGGTAAGACCATCACCCTCGAGG TTGAGCCCAGTGACACCATCGAGAATGTCAAGGCA SDHA (GenBank Accession No. NM 004168) SDHA Forward primer (SEQ ID NO:39): TGGGAACAAGAGGGCATCTG SDHA Reverse primer (SEQ ID NO:40): CCACCACTGCATCAAATTCATG 30 SDHA-amplicon (SEQ ID NO:41): TGGGAACAAGAGGGCATCTGCTAAAGTTTCAGATTCCATTTCTGCTCAGTATCCA

GTAGTGGATCATGAATTTGATGCAGTGGTGG

WO 2005/072055 PCT/IB2005/000995 83 DESCRIPTION FOR CLUSTER HUMNATPEP Cluster HUMNATPEP features 4 transcript(s) and 7 segment(s) of interest, the names 5 for which are given in Tables I and 2, respectively, the sequences themselves are given at the end of the application. The selected protein variants are given in table 3. Table 1 - Transcripts of interest Transcript Name SEQ ID NOS HUMNATPEPPEAITI I HUMNATPEP PEA_1_T2 2 HUMNATPEP PEA_1 T3 2 HUMNATPEPPEA_ 1T4 4 Table 2 - Segments of interest Segment Name SEQ ID NOS HUMNATPEPPEA 1 node_0 5 HUMNATPEPPEA1_node1 6 HUMNATPEPPEA 1 node 2 7 HUMNATPEPPEA 1 node_3 8 HUMNATPEPPEA 1_node_4 9 HUMNATPEP PEA 1_node_5 10 HUMNATPEP PEA 1_node_6 11 10 Table 3 -Proteins of interest Protein Name SEQ ID NOS HUMNATPEPPEA 1 P2 13 HUMNATPEP PEA_1_P3 14 HUMNATPEP PEA_1_P7 15 These sequences are variants of the known protein Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 32 (BNP-32)] WO 2005/072055 PCT/IB2005/000995 84 (SwissProt accession identifier ANFBHUMAN), referred to herein as the previously known protein. Protein Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 32 (BNP-32)] is known or believed to have the following 5 function(s): Acts as a cardiac hormone with a variety of biological actions including natriuresis, diuresis, vasorelaxation, and inhibition of renin and aldosterone secretion. It is thought to play a key role in cardiovascular homeostasis. He ips restore the body's salt and water balance. Improves heart function. The sequence for protein Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 32 (BNP 10 32)] is given at the end of the application, as "Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 32 (BNP-32)] amino acid sequence" (SEQ ID NO:12). Known polymorphisms for this sequence are as shown in Table 4. Table 4 -Amino acid mutations for Known Protein SNP position(s) on Comment amo acid sequ~ence 25 R -> L (in dbSNP:5227). /FTId=VAR_014580. 47 R-> H (in dbSNP:5229). /FTId=VAR_014581. 93 M -> L (in dbSNP:5230). /FTId=VAR 014582. 15 Protein Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 32 (BNP-32)] localization is believed to be Secreted. 20 The previously known protein also has the following indication(s) and/or potential therapeutic use(s): Hepatic dysfunction, general; Hypertension, general; Heart failure; Asthma; Renal failure. It has been investigated for clinical/therapeutic use in humans, for example as a target for an antibody or small molecule, and/or as a direct therapeutic; available information related to these investigations is as follows. Potential pharmaceutically 25 related or therapeutically related activity or activities of the previously known protein are as follows: Atrial peptide agonist; Diuretic. A therapeutic role for a protein represented by the cluster has been predicted. The cluster was assigned this field because there was information in the drug database or the public databases (e.g., described herein above) that this protein, WO 2005/072055 PCT/IB2005/000995 85 or part thereof, is used or can be used for a potential therapeutic indication: Hepatopiotective; Antihypertensive; Antihypertensive, diuretic; Cardiostimulant; Vasodilator, coronary; Urological; Antiasthma; COPD treatment. The following GO Annotation(s) apply to the previously known protein. The 5 following annotation(s) were found: fluid secretion, cell surface receptor linked signal transduction, diuresis, natriuresis, negative regulation of angiogenesis, negative regulation of cell growth, regulation of blood pressure, regulation of vascular permeability, regulation of vasodilation which are annotation(s) related to Biological Process; diuretic hormone, which are annotation(s) related to Molecular Function; and extracellular space, which are 10 annotation(s) related to Cellular Component. The GO assignment relies on information from one or more of the SwissProt/TremBl Protein knowledgebase, available from <http://www.expasy.ch/sprot/>; or Locuslink, available from <http://www.ncbi.nllinih.gov/projects/LocusLink/>. 15 The heart-selective diagnostic marker prediction engine provided the following results with regard to cluster HUMNATPEP. Predictions were made for selective expression of transcripts of this clusterin heart tissue, according to the previously described methods. The numbers on the yaxis of Figure 2 below refer to weighted expression of ESTs in each 20 category, as "parts per million" (ratio of the expression of ESTs for a particular cluster to the expression of all ESTs in that category, according to parts per million). Overall, the following results were obtained as shown with regard to the histogram in Figure 2, concerning the number of heart-specific clones in libraries/sequences. 25 This cluster was found to be selectively expressed in heart for the following reasons: in a comparison of the ratio of expression of the cluster in heart specific ESTs to the overall expression of the cluster in non-heart ESTs, which was found to be 18.3. Also the expression levels of this gene in muscle was negligible; and fisher exact test P-values were 30 computed both for library and weighted clone counts to check that the counts are statistically significant, and were found to be 3.40Fr 17.

WO 2005/072055 PCT/IB2005/000995 86 One particularly important measure of specificity of expression of a cluster in heart tissue is the previously described comparison of the ratio of expression of the cluster in heart as opposed to muscle. This cluster was found to be specifically expressed in heart as opposed to non-heart ESTs as described above. However, many proteins have been shown to be 5 generally expressed at a higher level in both heart and muscle, which is less desirable. For this cluster, as described above, the expression levels of this gene in muscle was negligible, which clearly supports specific expression in heart tissue. 10 As noted above, cluster HUMNATPEP features 4 transcript(s), which were listed in Table I above. These transcript(s) encode for protein(s) which are variant(s) of protein Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 32 (BNP-32)]. A description of each variant protein according to the present invention is now provided. 15 Variant protein HUMNATPEPPEA_1_P2 according to the present invention has an amino acid sequence as given at the end of the application; it is encoded by transcript(s) HUMNATPEPPEA_1_TI. BNP splice variant HUMNATPEPPEA_1_Ti results from alternative splicing of the BNP gene, thus leading to the extension of exon 2 into the intron 20 and to the generation of an extended 162 amino acid long protein, compared to the 134 amino acid long wild type protein. The protein encoded by this transcript contains the signal P (signal peptide) and the complete natriuretic peptide domain plus a unique sequence of 33 amino acids in its C-terminus. An alignment is given to the known protein (Natriuretic peptides B precursor 25 [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 32 (BNP-32)]) at the end of the application. One or more alignments to one or more previously published protein sequences are given at the end of the application. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows: 30 Comparison report between HUMNATPEPPEA_1_P2 and ANFBHUMAN: 1.An isolated chimeric polypeptide encoding for HUMNATPEPPEA_1_P2, comprising a first amino acid sequence being at least 90 % homologous to WO 2005/072055 PCT/IB2005/000995 8~7 MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLETSGLQEQRNHLQGKLSEL QVEQTSLEPLQESPRPTGVWKSREVATEGIRGHRKMVLYTLRAPRSPKMVQGSGCF GRKMDRISSSSGLGCK corresponding to amino acids 1 - 129 of ANFBHUMAN, which also corresponds to amino acids 1 - 129 of HUMNATPEPPEA_1_P2, and a second amino 5 acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GKHPLPPRPPSPIPVCDTVRVTLGFVVSGNHTL corresponding to amino acids 130 - 162 of JUMNATPEPPEA 1 P2, wherein said first and second amino acid sequences are contiguous and in a sequential order. 10 2.An isolated polypeptide encoding for a tail of HUMNATPEPPEA 1_P2, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GK.HPLPPRPPSPIPVCDTVRVTLGFVVSGNHTL in HUMNATPEPPEA_1_P2. 15 According to another aspect of the present invention there is provided a bridge fragment of HUMNATPEPPEA_1_P2 between 10 and 50 amino acids in length that spans the first and second amino acid sequences described above. There is provided a bridge portion of HUMNATPEPPEA_1_P2, comprising a polypeptide having a length "n", wherein n is at least about 10 amino acids in length, 20 optionally at least about 20 amino acids in length, preferably at least about 30 amino acids in length, more preferably at least about 40 amino acids in length and most preferably at least about 50 amino acids in length, wherein at least two amino acids comprise KG, having a structure as follows (numbering according to SEQ ID NO: 1): a sequence starting from any of amino acid numbers 129-x to 129; ending at any of amino acid numbers 130 + ((n-2) - x), 25 in which x varies from 0 to n-2, such that the value ((n-2) - x) is not allowed to be larger than 32. For example, for peptides of 10 amino acids (such that n=10), the starting position could be as "early" in the sequence as amino acid number 121 if x = n-2 = 8 (ie 121 = 129 8), such that the peptide would end at amino acid number 130 (130 + (8-8=0)). On the other 30 hand, the peptide could start at amino acid number 129 if x = 0 (ie 129 = 129-0), and could end at amino acid 138 (130 + (8 - 0 = 8)). The bridge portion above may also optionally comprise a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least WO 2005/072055 PCT/IB2005/000995 88 about 90% and most preferably at least about 95% homologous to at least one sequence described above. Similarly, the bridge portion may optionally be relatively short, such as from about 4 to about 9 amino acids in length. For four amino acids, the first bridge portion would 5 comprise the following peptides: GCKG, CKGK, KGKH. All peptides feature KG as a portion thereof Peptides of from about five to about nine amino acids could optionally be similarly constructed. The location of the variant protein was determined according to results from a number 10 of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to the cell: secreted. The protein localization is believed to be secreted because both signal peptide prediction programs predict that this protein has a signal peptide, and neither trans membrane region prediction program predicts that this protein has a trans-membrane region.. 15 The variant protein has the following domains, as determined by using InterPro. The domains are described in Table 6: Table 6 -InterPro domain(s) InterPro ID Doman description Analysis type Position(s) on protein IPR000663 Natriuretic peptide FPrintScan 109-118, 118-127 IPR002408 Natriuretic peptide, brain FPrintScan 11-27, 110-120, 120-133, type 28-38, 43-61 IPR000663 Natriuretic peptide HMMPfam 46-128 IPR000663 Natriuretic peptide HMMSmart 105-128 IPR000663 Natriuretic peptide ScanRegExp 112-128 IPR000663 Natriuretic peptide BlastProDom 27-129 Figure 3A shows a comparison of the genomic structure for the variant transcript 20 HUMNATPEPPEA_1_Tl and the known or "WT" transcript. Figure 3B shows a comparison of the structure of the variant protein HUMNATPEPPEA_1_P2 in comparison to the structure of the known or "WT" protein. Variant protein HUMNATPEPPEA _1P2 also has the following non-silent SNPs 25 (Single Nucleotide Polymorphisms) as listed in Table 7, (given according to their position(s) WO 2005/072055 PCT/IB2005/000995 89 on the amino acid sequence, with the alternative amino acid(s) listed; the last colunn indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMNATPEP_ PEA 1 P2 sequence provides support for the deduced sequence of this variant protein according to the present invention). 5 Table 7 -Amino acid mutations SNP positions) on amino Alternative amino acid(s) Previously known SNP? acid sequence 25 R-> L Yes 47 R->H Yes 93 M->L Yes Variant protein HUMNATPEP PEA_1_P2 is encoded by the following transcript(s): HUMNATPEPPEA_1_TI, for which the sequence(s) is/are given at the end of the application. The coding portion of transcript HUMNATPEPPEA 1 TI is shown in bold; 10 this coding portion starts at position 249 and ends at position 734. The transcript also has the following SNPs as listed in Table 8 (given according to their position on the nucleotide sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMNATPEP PEA_1_P2 sequence provides support for the deduced sequence of this variant protein according to the 15 present invention). Table 8 -Nucleic acid SNPs SNP position on nuleeotide Alternative nucleic acid Previously known SNP? 198 A->T Yes 322 G -> T Yes 388 G->A Yes 525 A ->T Yes 888 C -> T Yes 1279 ->T No WO 2005/072055 PCT/IB2005/000995 90 Variant protein HUMNATPEPPEA_1_P3 according to the present invention has an amino acid sequence as given at the end of the application; it is encoded by transcript(s) HUMNATPEPPEA__T2 and HUMNATPEPPEA_1_T3. An alignment is given to the known protein (Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; 5 Brain natriuretic peptide 32 (BNP-32)]) at the end of the application. One or more alignments to one or more previously published protein sequences are given at the end of the application. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows: 10 Comparison report between HUMNATPEP-PEA_1_P3 and ANFBHUMAN: 1.An isolated chimeric polypeptide encoding for HUMNATPEP_PEA_1_P3, comprising a first amino acid sequence being at least 90 % homologous to MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLETSGLQ corresponding to amino acids 1 - 44 of ANFBHUMAN, which also corresponds to amino acids I - 44 of 15 HUMNATPEPPEA_1_P3, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRAEGSSGGLDSSNERVLTCCPKRPSSFLWN corresponding to amino acids 45 - 75 of HUMNATPEPPEA_1_P3, wherein said first and second amino acid sequences are 20 contiguous and in a sequential order. 2.An isolated polypeptide encoding for a tail of HUMNATPEP PEA 1 P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VRAEGSSGGLDSSNERVLTCCPKRPSSFLWN in 25 HUMNATPEP PEA 1 P3. The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to 30 the cell: secreted. The protein localization is believed to be secreted because both signal peptide prediction programs predict that this protein has a signal peptide, and neither trans membrane region prediction program predicts that this protein has a trans-membrane region..

WO 2005/072055 PCT/IB2005/000995 91 Variant protein HUMNATPEPPEA_ 1P3 also has the following nonsilent SNPs (Single Nucleotide Polymorphisms) as listed in Table 9, (given according to their position(s) on the amino acid sequence, with the alternative amino acid(s) listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein 5 HUMNATPEPPEA_1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention). Table 9 -A in ino acid mutations SNP position(s) on amino Alternative amino acid(s) Previously known SNP? acid sequence 25 R->L Yes Variant protein HUINATPEP _PEA_1_P3 is encoded by the following transcript(s): 10 HUMNATPEPPEA_1_T2 and HUMNATPEPPEAIT3, for which the sequence(s) is/are given at the end of the application. The coding portion of transcript HUMNATPEPPEA_1_T2 and HUMNATPEP PEA_1 T3 are shown in bold; this coding portio n starts at position 249 and ends at position 473. The transcript also has the following SNPs as listed in Table 10 (given according to their position on the nucleotide sequence, 15 with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMNATPEPPEA 1_P3 sequence provides support for the deduced sequence of this variant protein according to the present invention). Table 10 - Nucleic acid SNPs SNP position on nucleotide Alternative nucleic acid Previously known SNP? sequence. 198 A -> T Yes 322 G->T Yes 598 C -> G Yes 620 G -> A Yes 757 A -> T Yes 969 -> T No 20 WO 2005/072055 PCT/IB2005/000995 92 Variant protein HUMNATPEPPEA_1_P7 according to the present invention has an amino acid sequence as given at the end of the application; it is encoded by transcript(s) HUMNATPEPPEA_1_T4. An alignment is given to the known protein (Natriuretic peptides B precursor [Contains: Gamma-brain natriuretic peptide; Brain natriuretic peptide 5 32 (BNP-32)]) at the end of the application. One or more alignments to one or more previously published protein sequences are given at the end of the application. A brief description of the relationship of the variant protein according to the present invention to each such aligned protein is as follows: 10 Comparison report between HUMNATPEPPEA_1_P7 and ANFBHUMAN: 1.An isolated chimeric polypeptide encoding for HUMNATPEPPEA__P7, comprising a first amino acid sequence being at least 90 % homologous to MVLYTLRAPRSPKMVQGSGCFGRKMDRISSSSGLGCKVLRRH corresponding to amino acids 93 - 134 of ANFBHUMAN, which also corresponds to amino acids 1 - 42 of 15 HUMNATPEPPEA_1_P7. The location of the variant protein was determined according to results from a number of different software programs and analyses, including analyses from SignalP and other specialized programs. The variant protein is believed to be located as follows with regard to 20 the cell: intracellularly. The protein localization is believed to be intracellular because neither of the trans-membrane region prediction programs predicted a trans -membrane region for this protein. In addition both signalpeptide prediction programs predict that this protein is a non-secreted protein.. 25 Variant protein HUMNATPEPPEA_1_P7 is encoded by the fo allowing transcript(s): HUMNATPEPPEA_1_T4, for which the sequence(s) is/are given at the end of the application. The coding portion of transcript HUMNATPEPPEA_1_T4 is shown in bold; this coding portion starts at position 257 and ends at position 382. The transcript also has the following SNPs as listed in Table I1 (given according to their position on the nucleotide 30 sequence, with the alternative nucleic acid listed; the last column indicates whether the SNP is known or not; the presence of known SNPs in variant protein HUMNATPEPPEA__P7 sequence provides support for the deduced sequence of this variant protein according to the present invention).

WO 2005/072055 PCT/IB2005/000995 93 Table I ] - Nucleic acid SNPs SNP position on nucleotide Alternative nucleic acid Previously known SNP? sequence 198 A ->T Yes 257 A->T Yes 469 -> T No 5 As noted above, cluster HUIMNATPEP features 7 segment(s), which were listed in Table 2 above and for which the sequence(s) are given at the end of the application. These segment(s) are portions of nucleic acid sequence(s) which are described herein separately because they are of particular interest. A description of each segment according to the present invention is now provided. 10 Segment cluster HUMNATPEPPEA_1_node_0 according to the present invention is supported by 21 libraries. The number of libraries was determined as previously described. This segment can be found in the following transcript(s): HUMNATPEPPEA_1_TI, HUMNATPEPPEA_1_T2, HUMNATPEPPEA_ 1T3 and HUMNATPEP PEA IT4. 15 Table 12 below describes the starting and ending position of this segment on each transcript. Table 12 - Segment location on transcripts Transept name Segment starting position Segment 1Tding1position HUMNATPEPPEA_1_TI 1 240 HUMNATPEPPEA_1_T2 1 240 HUMNATPEPPEA_1 T3 1 240 HUMNATPEPPEA 1_T4 1 240 Segment cluster HUMNATPEP PEA 1 node1 according to the present invention is 20 supported by 24 libraries. The number of libraries was determined as previously described. This segment can be found in the following transcript(s): HUMNATPEPPEA_1_T1, WO 2005/072055 PCT/IB2005/000995 94 HUMVNATPEPPEA_1_T2 and HUMNATPEPPEAIT3. Table 13 below describes the starting and ending position of this segment on each transcript. Table 13 - Segment location on transcripts Transcript name Segment starting position Segment ending position HUMNATPEPPEA_1_Ti 241 380 HUMNATPEPPEA 1T2 241 380 HUMNATPEPPEA_1_T3 241 380 5 Segment cluster HUMNATPEPPEA_1_node_2 according to the present invention is supported by 6 libraries. The number of libraries was determined as previously described. This segment can be found in the following transcript(s): HUvNATPEPPEA_1T2 and HUMNATPEPPEA_1_T3. Table 14 below describes the starting and ending position of 10 this segment on each transcript. Table 14 - Segment location on transcripts Transcript name Segment starting position Segment ending position HUMNATPEP PEA 1_T2 381 612 HUMNATPEPPEA_1_T3 381 612 Segment cluster HUMNATPEPPEA_1 node_3 according to the present invention is 15 supported by 25 libraries. The number of libraries was determined as previously described. This segment can be found in the following transcript(s): HUMNATPEPPEA_1_TI, HUMNATPEPPEA_1_T2 and HUMNATPEPPEA_1T3. Table 15 below describes the starting and ending position of this segment on each transcript. Table 15 - Segment location on transcripts Transcript name Segment starting position Segment ending position HUMNATPEPPEA_1_T1 381 508 HUMNATPEP PEA_1 T2 613 740 HUMNATPEPPEA 1 T3 613 740 20 WO 2005/072055 PCT/IB2005/000995 95 Segment cluster HUMNATPEPPEA_1node_4 according to the present invention is supported by 24 libraries. The number of libraries was determined as previously described. This segment can be found in the following transcript(s): HUMNATPEPPEA_1_Ti, 5 HUMNATPEPPEAIT2, HUMNATPEPPEA_1_T3 and HUMNATPEPPEAIT4. Table 16 below describes the starting and ending position of this segment on each transcript. Table 16 - Segment location on transcripts Transcript name Segment starting position Segment ending position HUMNATPEP PEA_1_TI 509 636 HUMNATPEPPEA_1_T2 741 868 HUMNATPEP PEA 1_T3 741 868 HUMNATPEP PEA_1_T4 241 368 10 Segment cluster HUMNATPEPPEA_1_node_5 according to the present invention is supported by 4 libraries. The number of libraries was determined as previously described. This segment can be found in the following transcript(s): HUMNATPEPPEA_1_Ti and HJMNATPEPPEA_1_T3. Table 17 below describes the starting and ending position of this segrnent on each transcript. 15 Table 1 7 - Segment location on transcripts Transcript name Segment starting position Segment ending position I-IJNATPEPPEA_1_Ti 637 1178 HUMNATPEPPEA_1_T3 869 1410 Segment cluster HUMNATPEPPEAInode_6 according to the present invention is supported by 20 libraries. The number of libraries was determined as previously described. 20 This segment can be found in the following transcript(s): HUMNATPEPPEA_1_Ti, HUMNATPEPPEA_1_T2, HUMNATPEPPEA_1_T3 and HUMNATPEPPEAlT4. Table 18 below describes the starting and ending position of this segment on each transcript. Table 18 - Segment location on transcripts WO 2005/072055 PCT/IB2005/000995 96 Transcript name Segment starting position Segment ending position HUMNATPEPPEA I T1 1179 1396 HUMNATPEPPEA 1 T2 869 1086 HUMNATPEPPEA_1_T3 1411 1628 HUMNATPEP PEA IT4 369 586 5 Variant protein alignment to the previously known protein: Sequence name: /tmp/DbNfNQqorT/fgacU726zu:ANFB HUMAN 10 Sequence documentation: Alignment of: HUMNATPEP_PEA_1_P2 x ANFBHUMAN 15 Alignment segment 1/1: Quality: 1257.00 Escore: 0 Matching length: 129 Total length: 129 Matching Percent Similarity: 100.00 Matching Percent Identity: 100.00 20 Total Percent Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0 Alignment: 25 1 MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLETSGLQEQRNHL 50 111111111 1111111i | lii 11 ( i11i || l i i i i I 11ii 1ii1 1 MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLETSGLQEQRNHL 50 51 QGKLSELQVEQTSLEPLQESPRPTGVWKSREVATEGIRGHRKMVLYTLRA 100 30 1 1 1 51 QGKLSELQVEQTSLEPLQESPRPTGVWKSREVATEGIRGHRKMVLYTLRA 100 101 PRSPKMVQGSGCFGRKMDRISSSSGLGCK 129 li l lil0 Iii l 11111 I li Li 1i2 35 101 PRSPKMVQGSGCFGRKMDRISSSSGLGCK 129 WO 2005/072055 PCT/IB2005/000995 97 5 Sequence name: /tmp/IeoAjUOIUc/7tSYchNtfd:ANFBRU4AN Sequence documentation: 10 Alignment of: HUMNATPEPPEA_1_P3 x ANFB HUMAN Alignment segment 1/l: 15 Quality: 417.00 Escore: 0 Matching length: 44 Total length: 44 Matching Percent Similarity: 100.00 Matching Percent Identity: 100.00 Total Percent Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0 20 Alignment: 1 MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLETSGLQ 44 1111 11 111 I III F I II 11I 1 11I 1 11111 1 1 1 I II1 25 1 MDPQTAPSRALIZLLFLHLAFLGGRSHPLGSPGSASDLETSGLQ 44 30 Sequence name: /tmp/moJ5LwI4XU/plTgdoImXI:ANFB HUMAN Sequence documentation: 35 Alignment of: HUMNATPEPPEA_1_P7 x ANFBHUMAN Alignment segment 1/1: 40 Quality: 415.00 Escore: 0 Matching length: 42 Total length: 42 Matching Percent Similarity: 100.00 Matching Percent Identity: 100.00 Total Percent Similarity: 100.00 Total Percent Identity: 100.00 Gaps: 0 45 WO 2005/072055 PCT/IB2005/000995 98 Alignment: 1 IVLYTLRAPRSPKMVQGSGCFGRKMDRISSSSGLGCKVLRRH 42 i I II I i I I I i i i I I I I I I III I i I I i i i I I i I 1 1 5 93 MVLYTLRAPRSPKMVQGSGCFGRKMDRISSSSGLGCKVLRRH 134 10 SEQ ID NO:17 >HUMNATPEPPEAlP2_peptide SPKMVQGSGCFGRKMDRISSSSGLGCKGKHPLPPRPPSPIPVCDTVRVTLGFVVSGN HTL 15 SEQ ID NO:18 >HUMNATPEPPEAlP7_peptide SPKMVQGSGCFGRKMDRISSSSGLGCKVLRRH 20 Expression of ANFB_HUMAN Natriuretic peptides HUMNATPEP transcripts which are detectable by amplicon as depicted in sequence name HUMNATPEPseg5 specifically in heart tissue Expression of ANFBHUMAN Natriuretic peptides transcripts detectable by or according to seg5 node(s), HUMNATPEPseg5 amplicon(s) and HUMNATPEPseg5, 25 HUMNATPEPseg5 primers was measured by real time PCR. In parallel the expression of four housekeeping genes - RPL19 (GenBank Accession No. NM_000981; RPL19 amplicon), TATA box (GenBank Accession No. NM_003194; TATA amplicon), Ubiquitin (GenBank Accession No. BC000449; amplicon - Ubiquitin-amplicon) and SDHA (GenBank Accession No. NM_004168; amplicon - SDHA-amplicon), was measured similarly. For 30 each RT sample, the expression of the above amplicons was normalized to the geometric mean of the quantities of the housekeeping genes. The normalized quantity of each RT sample was then divided by the median of the quantities of the heart tissue samples (Sample Nos. 44-46, Table 1 above, Tissue samples in testing panel), to obtain a value of expression for each sample relative to median of the heart tissue.

WO 2005/072055 PCT/IB2005/000995 99 Figure 4 is a histogram showing relative expression of the above- indicated ANFBHUMAN Natriuretic peptides transcripts in heart tissue samples as opposed to other tissues. As is evident from Figure 4, the expression of ANFBHUMAN Natriuretic peptides 5 transcripts detectable by the above amplicon in heart tissue samples was significantly higher than in most other samples (Sample Nos. 1-9, 11-22, 24-26 ,28-43 , 47-74 Table 1, "Tissue samples in testing panel" above). Note that the expression of the above amplicon in one of the heart samples, sample no. 45, was higher compared to its expression in the other two heart samples (sample 44 and 46). Sample no. 45 is from fibrotic heart, and samples 44 and 10 46 are samples from normal hearts. Primer pairs are also optionally and preferably encompassed within the present invention; for example, for the above experiment, the following primer pair was used as a non- limiting illustrative example only of a suitable primer pair: HUiMNATPEPseg5 forward primer; and HUMNATPEPseg5 reverse primer. 15 The present invention also preferably encompasses any amplicon obtained through the use of any suitable primer pair; for example, for the above experiment, the following amplicon was obtained as a non limiting illustrative example only of a suitable amplicon: HUMNATPEPseg5. HUMNATPEPseg5 Forward primer (SEQ ID NO: 18): 20 CTTCCCCCATTCCAGTGTGT HUMNATPEPseg5 Reverse primer (SEQ ID NO: 19): GAGGAAGCGATGTCCAGGTG HUMNATPEPseg5 Amplicon (SEQ ID NO:20): CTTCCCCCATTCCAGTGTGTGACACTGTTAGAGTCACTTTGGGGTTTGTTGTCTCT 25 GGGAACCACACTCTTTGAGAAAAGGTCACCTGGACATCGCTTCCTC Expression of ANFB_HUMAN Natriuretic peptide HUMNATPEP transcripts which are detectable by amplicon as depicted in sequence name HIUMNATPEP seg2 specifically in heart tissue 30 Expression of ANFBHUMAN Natriuretic peptide transcripts detectable by or according to seg2 node(s), HUMNATPEPseg2 amplicon(s) and HUMNATPEPseg2F2, HUMNATPEPseg2R2 primers was measured by real time PCR. In parallel the expression of four housekeeping genes - RPL19 (GenBank Accession No. NM_000981; RPL19 amplicon), WO 2005/072055 PCT/IB2005/000995 100 TATA box (GenBank Accession No. NM _003194; TATA amplicon), Ubiquitin (GenBank Accession No. BC000449; amplicon - Ubiquitin-arnplicon) and SDHA (GenBank Accession No. NM_004168; amplicon - SDHA-amplicon) was measured similarly. For each RT sample, the expression of the above amplicons was nomalized to the geometric mean of the 5 quantities of the housekeeping genes. The nornalized quantity of each RT sample was then divided by the median of the quantities of the heart samples (Sample Nos. 44-46, Table 1, "Tissue samples in testing panel" above), to obtain a value of expression for each sample relative to median of the heart. Figure 5 is a histogram showing relative expression of the above- indicated 10 ANFBHUMAN Natriuretic peptides transcripts in heart tissue samples as opposed to other tissues. As is evident from Figure 5, the expression of ANFB HUMAN Natriuretic peptide transcripts detectable by the above amplicon in heart tissue samples was higher than in most of the other samples (Sample Nos. 1-26, 28-43 , 47-74 Table 1). Note that the expression of 15 the above amplicon in one of the heart samples, sample no. 45, was higher compared to its expression in the other two heart samples (sample 44 and 46). Sample no. 45 is from fibrotic heart, and samples 44 and 46 are samples from nonral hearts. Primer pairs are also optionally and preferably encompassed within the present invention; for example, for the above experiment, the following primer pair was used as a 20 non-limiting illustrative example only of a suitable primer pair: HUMNATPEPseg2F2 forward primer; and HUMNATPEPseg2R2 reverse primer. The present invention also preferably encompasses any amplicon obtained through the use of any suitable primer pair; for example, for the above experiment, the following amplicon was obtained as a non -limiting illustrative example only of a suitable amplicon: 25 HUMNATPEPseg2. Forward primer HUMNATPEPseg2F2 (SEQ ID NO:2 1): GCAGCAATGAAAGGGTCCTC Reverse primer HUMNATPEPseg2R2 (SEQ ID NO:22): CATGGCACCCAAGTGAACC 30 Amplicon HUMNATPEPseg2 (SEQ ID NO:23): GCAGCAATGAAAGGGTCCTCACCTGCTGTCCCAAGAGGCCCTCATCTTTCCTTTG GAATTAGTGATAAAGGAATCAGAAAA.TGGAGAGACTGGGTGCCCTGACCCTGT

ACCCAAGGCAGTCGGTTCACTTGGGTGCCATG

WO 2005/072055 PCT/IB2005/000995 101 Expression of Homo sapiens natriuretic peptide precursor B (NPPB) HUMNATPEP transcripts which are detectable by amplicon as depicted in sequence name HUMNATPEP seg3 -4WT specifically in heart tissue 5 Expression of Homo sapiens natriuretic peptide precursor B (NPPB) transcripts detectable by or according to seg3-4 node(s), HUMNATPEP seg3 -4WT amplicon(s) and primers HUMNATPEP seg3-4WT-F and HUMNATPEP seg3 -4WT-R was measured by real time PCR (this transcript relates to the known protein, or "WT" protein). In parallel the expression of four housekeeping genes - RPL19 (GenBank Accession No. NM_000981; 10 RPL19 amplicon), TATA box (GenBank Accession No. NM_003194; TATA amplicon), Ubiquitin (GenBank Accession No. BC000449; amplicon - Ubiquitin-amplicon) and SDHA (GenBank Accession No. NM_004168; amplicon - SDHA-amplicon) was measured similarly. For each RT sample, the expression of the above amplicons was normalized to the geometric mean of the quantities of the housekeeping genes. The normalized quantity of 15 each RT sample was then divided by the median of the quantities of the heart samples (Sample Nos. 44-46, Table 1, "Tissue samples in testing panel" above), to obtain a value of expression for each sample relative to median of the heart samples. Figure 6 is a histogram showing relative expression of the above- indicated Homo sapiens natriuretic peptide precursor B (NPPB) known protein transcripts in heart tissue 20 samples as opposed to other tissues. As is evident from Figure 6, the expression of Homo sapiens natriuretic peptide precursor B (NPPB) transcripts detectable by the above amplicon(s) in heart tissue samples was higher than in the other samples (Sample Nos. 44-46 Table 1, as above). Note that the expression of the above amplicon in one of the heart samples, sample no. 45, was higher 25 compared to its expression in the other two heart samples (sample 44 and 46). Sample no. 45 is from fibrotic heart, and samples 44 and 46 are samples from normal hearts. Primer pairs are also optionally and preferably encompassed within the present invention; for example, for the above experiment, the following primer pair was used as a non-limiting illustrative example only of a suiable primer pair: HUMNATPEP seg3 -4WT-F 30 forward primer; and HUMNATPEP seg3 -4WT-R reverse primer. The present invention also preferably encompasses any amplicon obtained through the use of any suitable primer pair; for example, for the above experiment, the following WO 2005/072055 PCT/IB2005/000995 102 amplicon was obtained as a non-limiting illustrative example only of a suitable amplicon: HUMNATPEP seg3 -4WT. Forward primer HUMNATPEP seg3 -4WT-F (SEQ ID NO:24): 5 GTCCGGGTTACAGGAGCAGC Reverse primer HUMNATPEP seg3 -4WT-R (SEQ ID NO:25): CCGCCTCAGCACTTTGCAG Amplicon HUMNATPEP seg3-4WT (SEQ ID NO:26): GTCCGGGTTACAGGAGCAGCGCAACCATTTGCAGGGCAAACTGTCGGAGCTGCA 10 GGTGGAGCAGACATCCCTGGAGCCCCTCCAGGAGAGCCCCCGTCCCACAGGTGT CTGGAAGTCCCGGGAGGTAGCCACCGAGGGCATCCGTGGGCACCGCAAAATGG TCCTCTACACCCTGCGGGCACCACGAAGCCCCAAGA-TGGTGCAAGGGTCTGGCT GCTTTGGGAGGAAGATGGACCGGATCAGCTCCTCCAGTGGCCTGGGCTGCAAAG TGCTGAGGCGG 15 Validation of expression of the transcript encoding for HUMMA TPEP PEA I P2: The validation of the above BNP splice variant transcript expression was done by performing RT-PCR amplification of 6 different RNA samples. Two postmortem pancreas 20 tissues, three normal postmortem heart tissues and one heart tissue exhibiting focal fibrosis pathology were used (Table 9 below). Table 9 Lot no. Source Tissue Patholog Sex y /Ag e 44-B-Heart A411077 Biochai PB-Pool nHeart of 5M&F 45-CG-Heart CG-255-9 Ichilov Heart PM M/7 5 46-CG-Heart CG-227-1 Ichilov Heart PM F/3 6 13-Arn- 071P25C Ambion Pancreas PM M/2 Pancreas 5 WO 2005/072055 PCT/IB2005/000995 103 14-CG- CG-255-2 Ichilov Pancreas PM M/7 Pancreas 5 Heart CG-255- Ichilov heart Focal M/7 9 fibrosis 5 RT reaction using random hexamers (Invitrogen, Cat. No. 48190-011) was performed using the standard manufacturer specifications. The primers used for RTPCR were as follows: (a) Forward primer:GTTCAGCCTCGGACTTGGAA ("Primer A"; SEQ ID 5 NO:27) (b) Reverse primer:GTGACTCTAACAGTGTCACACACTGG ("Primer B"; SEQ ID NO:28) (c) Reverse primer (control): CCTTGTGGAATCAGAAGCAGG ("Primer C"; SEQ ID NO:29) 10 Primers A and B were used to identify the BNP variant and should produce an amplicon of length 355bp.Primers A and C were used as a control and should produce two amplicons - the first of the wild type, with a length of 352bp and the second of the splice variant, with a length of 893 bp. The annealing temperature of the primers was as follows (calculated byAT/GC 15 content): Forward-A: 62 deg Reverse-B 1:78 deg Reverse 2-C: 64 deg The RT-PCR conditions included 35 cycles of Denaturation: 94'C-30 see; followed 20 by Annealing: 60'C-30 see; and Elongation: 72'c-60 see, using Taqara Hot start enzyme cat#RO06A, lot#N1401. The results shown in Figure 7 demonstrate that although the BNP wild type product was detected by the RT-PCR in pancreas and in normal heart, expression of the BNP_T2 splice variant was detected only in the heart sample exhibiting focal fibrosis. 25 As can be seen from Figure 7, BNP known transcript gene product was detected by RT-PCR in pancreas, normal heart and in heart focal fibrosis samples . The product size was as expected, about 352bp (primers A+C). The RTPCR reactions designed to detect the transcript for HUMNATPEPPEA_1_P2 splice variant were performed using primers A and B. The product of expected size (355 bp) was detected in heart focal fibrosis sample only.

WO 2005/072055 PCT/IB2005/000995 104 Thus, without wishing to be limited by a single hypothesis, the new BNP splice variant appears to be differentially expressed in heart fibrotic tissue, and thus can be used for detection and/or quantitation of heart failure diseases and specifically cardiac fibrosis. 5 Example 4 - Therapeutic Uses HUMNATPEP PEAl-P2 splice variant contains almost the complete sequence of known BNP (129 a.a out of 133) with the addition of unique sequence of 33 amino acids in its C-tenninus. Structure-function analysis has identified the central ring structure in BNP as 10 critical for the binding to its receptor and for its biological functions. HUMNATPEPPEA_1_P2 splice variant may preserve the ring structure and therefore retain the biological activity of BNP with an advantage of increased half life due to its longer size. The variants of the present invention may optionally be used, additionally or 15 alternatively, for therapeutic uses, including but not limited to, diuretic, natriuretic, vascular smooth muscle relaxing and vasodilation actions, and lowering blood volume and blood pressure. These variants may optionally be used for therapeutic treatment of heart failure. Preferably, the variant comprises HUMNATPEPPEA_1_P2 or a fragment thereof as described herein. 20 Coding regions on the below transcripts are shown in boldface type: SEQ ID NO:1 >HUMNATPEPPEA_1_TI AGGCGCGGAGGGGCTCATTCCCGGGCCCTGATCTCAGAGGCCCGGAATGTGGCT 25 GATAAATCAGAGATAACCCTGCATGGCAGGGCAGGCCCGACACTCAGCTCCAG GATAAAAGGCCACGGTGTCCCGAGGAGCCAGGAGGAGCACCCCGCAGGCTGAG GGCAGGTGGGAAGCAAACCCGGACGCATCGCAGCAGCAGCAGCAGCAGCAGAA GCAGCAGCAGCAGCCTCCGCAGTCCCTCCAGAGACATGGATCCCCAGACAGCA CCTTCCCGGGCGCTCCTGCTCCTGCTCTTCTTGCATCTGGCTTTCCTGGGA 30 GGTCGTTCCCACCCGCTGGGCAGCCCCGGTTCAGCCTCGGACTTGGAAACG TCCGGGTTACAGGAGCAGCGCAACCATTTGCAGGGCAAACTGTCGGAGCTG CAGGTGGAGCAGACATCCCTGGAGCCCCTCCAGGAGAGCCCCCGTCCCAC

AGGTGTCTGGAAGTCCCGGGAGGTAGCCACCGAGGGCATCCGTGGGCACC

WO 2005/072055 PCTIIB2005/000995 105 GCAAAATGGTCCTCTACACCCTGCGGGCACCACGAAGCCCCAAGATGGTGC AAGGGTCTGGCTGCTTTGGGAGGAAGATGGACCGGATCAGCTCCTC CAGTG GCCTGGGCTGCAAAGGTAAGCACCCCCTGCCACCCCGGCCGCCTTC CCCCA TTCCAGTGTGTGACACTGTTAGAGTCACTTTGGGGTTTGTTGTCTCTGGGA 5 ACCACACTCTUGAGAAAAGGTCACCTGGACATCGCTTCCTCTTGTTAACAGCC TTCAGGGCCAAGGGGTGCCTTTGTGGAATTAGTAAATGTGGGCTTATTTCATTAC CATGCCCACAATACCTTCTCCCCACCTCCTACTTCTTATCAAAGGGGCAGpAjjCT CCTTTGGGGGTCTGTTTATCATTTGGCAGCCCCCCAGTGGTGCAGAAAGNkGAAC CAAACATTTCCTCCTGGTTTCCTCTAAACTGTCTATAGTCTCAAAGGCAGAGAGC 10 AGGATCACCAGAGCAATGATAATCCCCAATTTACAGATGAGGAAACTGXG3GCTC AGAGAGTTGCATTAAGCCTCAAACGTCTGATGACTAACAGGGTcIGTGGcyrGGCA CACGATGAciGTAAGCTCAGCCCCTGCCTCCATCTCCCACCCTAACCATCATCACC CTCTCTCTTTCCCTGACAGTGCTGAGGCGGCATTAAGAGGAAGTCCTGGCTGCA GACACCTGCTTCTGATTCCACAAGGGGCTTTTTCCTCAACCCTGTGGCCGCCTTT 15 GAAGTGACTCATTTTTTTAATGTATTTATGTATTTATTTGATTGTTTTATATAAGA TGGTTTCTTACCTTTGAGCACAAAATTTCCACGGTGAAATAAAGTCAACATTATA AGCTTTATCTTTTGAAA SEQ IDNO:2 20 >HTUMNATPEPPEA_1_T2 AGOCGCGGAGGGGCTCATTCCCGGGCCCTGATCTCAGAGGCCCGGAATGTGGCT GATAAATCAGAGATAACCCTGCATGGCAGGGCAGGCCCGACACTCAGCTCCAG GATAAAAGGCCACGGTGTCCCGAGGAGCCAGGAGGAGCACCCCGCAGGCTGAG GGCAGGTGGGAAGCAAACCCGGACGCATCGCAGCAGCAGCAGCAGCAGCAGAA 25 GCAGCAGCAGCAGCCTCCGCAGTCCCTCGAGAGACATGGATCCCCAGACAGCA CCTTCCCGGGCGCTCCTGCTCCTGCTCTTCTTGCATCTGGCTTTCCTGGGA GGTCGTTCCCACCCGCTGGGCAGCCCCGGTTCAGCCTCGGACTTGGAAACG TCCGGGTTACAGGTGAGAGCGGAGGGCAGCTCAGGGGGATTGGACAGCAG CAATGAAAGGGTCCTCACCTGCTGTCCCAAGAGGCCCTCATCTTTCCTfTTG 30 GAATTAGTGATAAAGGAATCAGAAAATGGAGAGACTGGGTGCCCTGACCCTGT ACCCAAGGCAGTCGGTTCACTTGGGTGCCATGAAGGGCTGGTGAGCCCAGGGGT GGGTCCCTGAGGCTTGGACGCCCCCATTCATTGGAGGAGCAGCGCAACCATTTG

CAGGGCAAACTGTCGGAGCTGCAGGTGGAGCAGACATCCCTGGAGCCCCTCCAG

WO 2005/072055 PCTIIB2005/000995 106 GAGAGCCCCCGTCCCACAGGTGTCTGGAAGTCCCGGGAGGTAGCCACCGAGGG CATCCGTGGGCACCGCAAAATGGTCCTCTACACCCTGCGGGCACCACGAAGCCC CAAGATGGTGCAAGGGTCTGGCTGCTTTGGGAGGAAGATGGACCGGATCAGCTC CTCCAGTGGCCTGGGCTGCAAAGTGCTGAGGCGGCATTAAGAGGAAGTCCTGGC 5 TGCAGACACCTGCTTCTGATTCCACAAGGGGCTTTTTCCTCAACCCTCTGGCCGC CTTTGAAGTGACTCATTTTTTTAATGTATTTATGTATTTATTTGATTGTTTTATATA AGATGGTTTCTTACCTTTGAGCACAAAATTTCCACGGTGAAATAAAGTCAACATT ATAAGCTTTATCTTTTGAAA 10 SEQID NO:3 >HUMNATPEP PEA I B3 AGGCGCGGAGGGGCTCATTCCCGGGCCCTGATCTCAGAGGCCCGGAATGTGGCT GATAAATCAGAGATAACCCTGCATGGCAGGGCAGGCCCGACACTCAGCTCCAG GATAAAAGGCCACGGTGTCCCGAGGAGCCAGGAGGAGCACCCCGCAGGCTGAG 15 GGCAGGTGGGAAGCAAACCCGGACGCATCGCAGCAGCAGCAGCAGCAGCAGAA GCAGCAGCAGCAGCCTCCGCAGTCCCTCCAOAGACATGGAT CCCCAGACAGCA CCTTCCCGGGCGCTCCTGCTCCTGCTCTTCTTGCATCTGGCTTTCCTGGGA GGTCGTTCCCACCCGCTGGGCAGCCCCGGTTCAGCCTCGGACTTGGAAACG TCCGGGTTACAGGTGAGAGCGGAGGGCAGCTCAGGGGGATTGGACAGCAG 20 CAATGAAAGGGTCCTCACCTGCTGTCCCAAGAGGCCCTCATCTTTCCTTTG GAATTAGTGATAAAGGAATCAGAAAATGGAGAGACTOGGTCCTGACCCTGT ACCCAAGGCAGTCGGTTCACTTGGGTGCCATGAAGGGCTGGTGAGCCCAGGGGT GGGTCCCTGAGGCTTGGACGCCCCCATTCATTGCAGGAGCAGCGCAACCATTTG CAGGGCAAACTGTCGGAGCTGCAGGTGGAGCAGACATCCCTGGAGCCCCTCCAG 25 GAGAGCCCCCGTCCCACAGGTGTCTGGAAQTCCCGGGAGGTAGCCACCGAGGG CATCCGTGGGCACCGCAAAATGGTCCTCTACACCCTGCGGGCACCACGAGCCC CAAGATGGTGCAAGGGTCTGGCTGCTTTGGGAGGJ&AGATGGACCGGATCAGCTC CTCCAGTGGCCTGGGCTGCAAAGGTAAGCACCCCCTGCCACCCCGGCCGCCTTC CCCCATTCCAGTGTGTGACACTGTTAGAGTCACTTTGGGGTTTGTTGTCTCT4GG 30 AACCACACTCTTTGAGAAAAGGTCACCTGGACATCGCTTCCTCTTGTTACAGCC TTCAGGGCCAAGGGGTGCCTTTGTGGAATTAGTAAATGTGGGCTATTTCATTAC CATGCCCACAATACCTTCTCCCCACCTCCTACTTCTTATCAAGGGGCAGAATCT

CCTTTGGGGGTCTGTTTATCATTTGGCAGCCCCCCAGTGGTGCAGAAGAG-C

WO 2005/072055 PCT/IB2005/000995 107 CAAACATTTCCTCCTGGTTTCCTCTAAACTGTCTATAGTCTCAAAGGCAGAGAGC AGGATCACCAGAGCAATGATAATCCCCAATTTACAGATGAGGAAACTGAGGCTC AGAGAGTTGCATTAAGCCTCAAACGTCTGATGACTAACAGGGTGGTGGGTGGCA CACGATGAGGTAAGCTCAGCCCCTGCCTCCATCTCCCACCCTAACCATCATCACC 5 CTCTCTCTTTCCCTGACAGTGCTGAGGCGGCATTAAGAGGAAGTCCTGGCTGCA GACACCTGCTTCTGATTCCACAAGGGGCTTTTTCCTCAACCCTGTGGCCGCCTTT GAAGTGACTCATTTTTTTAATGTATTTATGTATTTATTTGATTGTTTTATATAAGA TGGTTTCTTACCTTTGAGCACAAAATTTCCACGGTGAAATAAAGTCAACATTATA AGCTTTATCTTTTGAAA 10 SEQ ID NO:4 >HUMNATPEPPEA_1_T4 AGGCGCGGAGGGGCTCATTCCCGGGCCCTGATCTCAGAGGCCCGGAATGTGGCT GATAAATCAGAGATAACCCTGCATGGCAGGGCAGGCCCGACACTCAGCTCCAG 15 GATAAAAGGCCACGGTGTCCCGAGGAGCCAGGAGGAGCACCCCGCAGGCTGAG GGCAGGTGGGAAGCAAACCCGGACGCATCGCAGCAGCAGCAGCAGCAGCAGAA GCAGCAGCAGCAGCCTCCGCAGTCCCTCCGTGGGCACCGCAAAATGGTCCTCT ACACCCTGCGGGCACCACGAAGCCCCAAGATGGTGCAAGGGTCTGGCTGC TTTGGGAGGAAGATGGACCGGATCAGCTCCTCCAGTGGCCTGGGCTGCAAA 20 GTGCTGAGGCGGCATTAAGAGGAAGTCCTGGCTGCAGACACCTGCTTCTGATT CCACAAGGGGCTTTTTCCTCAACCCTGTGGCCGCCTTTGAAGTGACTCATTTTTT TAATGTATTTATGTATTTATTTGATTGTTTTATATAAGATGGTTTCTTACCTTTGA GCACAAAATTTCCACGGTGAAATAAAGTCAACATTATAAGCTTTATCTTTTGAA A 25 It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable 30 subcombination. Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to WO 2005/072055 PCT/IB2005/000995 108 those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims. All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as 5 if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. 10

Claims

1. An isolated polynucleotide comprising a nucleic acid sequence selected from the group consisting of: HUMNATPEPPEA_-_TI, HUMNATPEPPEAI_T2, HUMNATPEPPEA_1_T3 or HUMNATPEPPEAIT4.

2. An isolated polynucleotide segment comprising a nucleic acid sequence selected from the group consisting of: HUMN ATPEP PEA_1_node_0, HUMNATPEPPEA_1_node_1, HUMNATPEPPEA_1_node 2, HUMNATPEPPEA_1_node_3, HUMNATPEPPEAl_node_4, HUMNATPEPPEA_1_node 5, or HUMNATPEPPEA_1_node_6.

3. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of: HUMNATPEPPEA_1_P2, HUMNATPEPPEA_1_P3 or HUMNATPEPPEA_1_P7.

4. An isolated chimeric polypeptide encoding for HUMNATPEPPEA_1_P2, comprising a first amino acid sequence being at least 90 % homologous to MDPQTAPSRALLLLLFLHLAFLGGRSHPLGSPGSASDLETSGLQEQRNHLQGKLSEL QVEQTSLEPLQESPRPTGVWKSREVATEGIRGHRKMVLYTLRAPRSPKIMVQGSGCF GRKMDRISSSSGLGCK corresponding to amino acids 1 - 129 of ANFBHUMAN, which also corresponds to amino acids 1 - 129 of HUMNATPEPPEA_1 P2, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GKHPLPPRPPSPIPVCDTVRVTLGFVVSGNHTL corresponding to amino acids 130 - 162 of HUMNATPEPPEA 1 P2, wherein said first and second amino acid sequences are contiguous and in a sequential order.

5. An isolated polypeptide encoding for a tail of HUMNATPEPPEA_1_P2, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence GKHPLPPRPPSPIPVCDTVRVTLGFVVSGN TL in HUMNATPEPPEA1_P2. WO 2005/072055 PCT/IB2005/000995 110

6. An isolated chimeric polypeptide encoding for HUM[NATPEPPEA__P3, comprising a first amino acid sequence being at least 90 % homologous to MDPQTAPSRALLLLLFLHLAFLGGRSIPLGSPGSASDLETSGLQ corresponding to amino acids 1 - 44 of ANFBHUMAN, which also corresponds to amino acids 1 - 44 of HUMNATPEPPEA_1_P3, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence VRAEGSSGGLDSSNERVLTCCPKRPSSFLWN corresponding to amino acids 45 - 75 of HUMNATPEPPEA_1_P3, wherein said first and second amino acid sequences are contiguous and in a sequential order.

7. An isolated polypeptide encoding for a tail of HUMNATPEPPEA_1_P3, comprising a polypeptide being at least 70%, optionally at least about 80%, preferably at least about 85%, more preferably at least about 90% and most preferably at least about 95% homologous to the sequence VRAEGSSGGLDSSNERVLTCCPKRPSSFLWN in HUMNATPEPPEA_1_P3.

8. An isolated chimeric polypeptide encoding for HUMNATPEPPEA__P7, comprising a first amino acid sequence being at least 90 % homologous to MVLYTLRAPRSPKMVQGSGCFGRKMDRISSSSGLGCKVLRRH corresponding to amino acids 93 - 134 of ANFBHUMAN, which also corresponds to amino acids 1 - 42 of HUMNATPEPPEA_1_P7.

9. An antibody capable of specifically binding to an epitope of an amino acid sequence of any of claims 3-8.

10. The antibody of claim 9, wherein said amino acid sequence corresponds to a tail in claims 5 or 7.

11. The antibody of claim 9 or 10, wherein said antibody is capable of differentiating between a splice variant having said epitope and a corresponding known protein.

12. A kit for detecting heart disorders, comprising a kit detecting overexpression of a splice variant according to any of the above claims. WO 2005/072055 PCT/IB2005/000995 111

13. The kit of claim 12, wherein said kit comprises a NAT-based technology.

14. The kit of claim 13, wherein said kit further comprises at least one primer pair capable of selectively hybridizing to a nucleic acid sequence according to any of the above claims.

15. The kit of claim 14, wherein said kit further comprises at least one oligonucleotide capable of selectively hybridizing to a nucleic acid sequence according to any of the above claims.

16. The kit of claim 12, wherein said kit comprises an antibody according to any of the above claims.

17. The kit of claim 16, wherein said kit further comprises at least one reagent for performing an ELISA or a Western blot.

18. A method for detecting heart disorders, comprising detecting overexpression of a splice variant according to any of the above claims.

19. The method of claim 18, wherein said detecting overexpression is performed with a NAT-based technology.

20. The method of claim 18, wherein said detecting overexpression is performed with an immunoassay.

21. The method of claim 20, wherein said immunoassay comprises an antibody according to any of the above.

22. A biomarker capable of detecting a BNP variant-detectable disease, comprising any of the above nucleic acid sequences or a fragment thereof, or any of the above amino acid sequences or a fragment thereof. WO 2005/072055 PCT/IB2005/000995 112

23. A method for screening for variant-detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay according to any of the above claims.

24. A method for diagnosing a BNP variant detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay according to any of the above claims.

25. A method for monitoring disease progression and/or treatment efficacy and/or detection of acute over chronic exacerbation of a BNP variant-detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay according to any of the above claims.

26. A method of selecting a therapy for a BNP variant-detectable disease, comprising detecting cells affected by a BNP variant-detectable disease with a biomarker or an antibody or a method or assay according to any of the above claims and selecting a therapy according to said detection.

27. Any of the above claims wherein said BNP variant-detectable disease comprises heart failure and/or left ventricular disfunction.

28. An isolated polypeptide encoding for Brain Natriuretic Peptide T2 (SEQ ID NO: 1) comprising a first amino acid sequence being at least 90 % homologous to amino acids 1-129 of wild type BNP corresponding to ANFBHUMAN, and a second amino acid sequence being at least 70%, optionally at least 80%, preferably at least 85%, more preferably at least 90% and most preferably at least 95% homologous to a polypeptide having the sequence GKHPLPPRPPSPIPVCDTVRVTLGFVVSGNHTL, wherein said first and said second amino acid sequences are contiguous and in a sequential order.

29. A nucleic acid construct comprising the isolated polynucleotide of claim 1.

30. The nucleic acid construct of claim 29, further comprising a promoter for regulating transcription of the isolated polynucleotide in sense or antisense orientation. WO 2005/072055 PCT/IB2005/000995 113

31. The nucleic acid construct of claim 30, further comprising a positive and a negative selection marker for selecting for homologous recombination events.

32. A host cell comprising the nucleic acid construct of claim 3 1.

33. An isolated polypeptide comprising an amino acid sequence at least 70 % identical to a polypeptide of claim 3, as determined using the LALIGN software of EMBnet switzerland (http://www.ch.embnet.org/index.html) using default parameters or an active portion thereof.

34. An oligonucleotide specifically hybrid izable with a nucleic acid sequence encoding a polypeptide as in claim 33.

35. A phannaceutical composition comprising a therapeutically effective amount of a polypeptide as in claim 33 and a pharmaceutically acceptable carrier or diluent.

36. A method of treating BNP-related disease in a subject, the method comprising upregulating in the subject expression of a polypeptide as in claim 33, thereby treating the BNP-related disease in a subject.

37. The method of claim 36, wherein said upregulating expression of said polypeptide is effected by: (i) administering said polypeptide to the subject; and/or (ii) administering an expressible polynucleotide encoding said polypeptide to the subject.

38. An isolated oligonucleotide, comprising an amplicon selected from the group consisting of SEQ ID NOs: 20, 23 or 26.

39. A primer pair, comprising a pair of isolated oligonucleotides capable of amplifying said amplicon of claim 38 or a segment of claim 2. WO 2005/072055 PCT/IB2005/000995 114

40. The primer pair of claim 39, comprising a pair of isolated oligonucleotides selected from the group consisting of: SEQ NOs 18 and 19; 21 and 22; 24 and 25; or 27 and 28.