JP2006523191A - Secreted polypeptide species associated with cardiovascular disorders - Google Patents

Abstract

The present invention discloses human secreted polypeptides that circulate at high levels in the plasma of patients with cardiovascular disorders. The present invention also provides polypeptides for diagnosis, prognosis and drug development, polynucleotides encoding them, and antibodies specific for these polypeptides.

Description

Detailed Description of the Invention

The present invention relates to polypeptide species that are preferentially secreted in individuals with cardiovascular disorders, isolated polynucleotides that encode such polypeptides, polymorphic variants thereof, and cardiovascular disorder diagnosis and drug development For the use of said nucleic acids and polypeptides or compositions thereof in detection assays.

BACKGROUND OF THE INVENTION Cardiovascular disorders are a significant health risk in industrialized countries. Coronary artery disease (CAD) is characterized by atherosclerosis or arteriosclerosis. Atherosclerosis is the most common cardiovascular disease, the leading cause of heart attacks, strokes and limb gangrene, and thereby the leading cause of death in the United States. Atherosclerosis is a complex disease involving many cell types and molecular factors such as those described in Ross, Nature 362: 801-809 (1993). In normal circumstances, the protective response to damage to arterial wall endothelial cells and smooth muscle cells (SMC) is preceded by inflammation and consists of the formation of fiber fat and fiber lesions or plaques. The progression of atherosclerotic lesions may occlude the involved arteries and may be the result of an excessive inflammatory-fibroproliferative response to various forms of injury. Vascular endothelial cell injury or dysfunction is a common feature of many conditions that predispose an individual to accelerated development of atherosclerotic cardiovascular disease.

  Atherosclerotic plaques occlude related blood vessels and restrict blood flow, resulting in ischemia. Ischemia is a condition characterized by a lack of oxygen supply in organ tissues due to insufficient perfusion. Such inadequate perfusion can have many natural causes including atherosclerotic or restenotic lesions, anemia or stroke. The most common cause of ischemia in the heart is atherosclerosis of the epicardial coronary artery. Due to the reduction in lumen of these vessels, atherosclerosis causes an absolute decrease in basal myocardial perfusion or limits the increase in proper perfusion when demand for flow increases. Coronary blood flow can also be limited by arterial thrombus, convulsions, and rarely by coronary thrombus and by portal stenosis due to syphilitic aortitis. Congenital abnormalities such as anomalous origin of the left anterior descending coronary artery from the pulmonary artery can cause myocardial ischemia and infarction in infants, but this cause is very rare in adults.

  Myocardial ischemia can also occur when myocardial oxygen demand is abnormally elevated, as seen in severe ventricular hypertrophy due to hypertension or aortic stenosis. The latter may indicate angina that is indistinguishable from that caused by coronary atherosclerosis. As seen in the presence of extremely severe anemia or carboxyhemoglobin, reduced blood oxygen carrying capacity rarely causes myocardial ischemia. Often, two or more ischemic causes coexist, such as left ventricular hypertrophy and increased oxygen demand due to reduced oxygen supply following coronary atherosclerosis.

  Numerous clinical trials have identified factors that increase the risk of cardiovascular disorders. Some of these risk factors such as age, gender, and family history cannot be changed. Other risk factors include: smoking, high blood pressure, high-fat and high-cholesterol diets, diabetes, unexpected exercise, obesity, and stress.

  Fortunately, many of the factors involved can be controlled through lifestyle changes. The risk of cardiovascular disorders in smokers is more than twice that of nonsmokers. When a person quits smoking, the risk of developing disability decreases, regardless of how much he or she has smoked in the past. Serum cholesterol levels are directly related to the prevalence of cardiovascular disorders, and hypertension or hypertension is an important risk factor. Physical activity is alleged to reduce the risk of developing cardiovascular disorders through various mechanisms: this increases myocardial oxygen supply, decreases oxygen demand, and improves myocardial contraction and its electrical stimulation stability To do. Decreased oxygen demand and myocardial motion are reflected in lowering heart rate and blood pressure at rest. Physical activity also increases coronary artery diameter and dilatability, increases collateral arteriogenesis, and reduces the rate of progression of coronary atherosclerosis. Obesity and serum fatty acids are reduced by activity.

  While there may not be significant symptoms of resting cardiovascular disorders, symptoms such as chest tightness may occur with increased activity or stress. Other initial signs that may appear are heartburn, nausea, vomiting, numbness, shortness of breath, severe cold sweat, unexplained fatigue, and anxiety. More serious symptoms of cardiovascular disorders are chest pain (angina), rhythm disturbance (arrhythmia), stroke or heart attack (myocardial infarction). Strokes and heart attacks are the result of arterial blockage of the brain and heart tissue, respectively. Because the symptoms are different, the tests and treatments chosen can vary greatly from patient to patient.

  Diagnostic tests useful for determining the extent and severity of cardiovascular disorders include: electrocardiogram (EKG), stress test, nuclear medicine examination, coronary angiography, resting EKG, EKG multiphase diagnostic information index (EKG) Multiphase Information Diagnosis Indexes), Holter monitor, delayed potential, EKG mapping, echocardiogram, thallium scan, PET, MRI, CT, angiogram and IVUS. Yet other risk factor measurements and useful diagnostics are common and are best applied by those skilled in the medical arts. There are various therapeutic approaches depending on the severity of the disease. For many humans, cardiovascular disorders are managed with lifestyle changes and medications. More serious diagnoses may indicate the need for surgery.

  Surgical approaches for the treatment of ischemic atherosclerosis include bypass grafting, coronary angioplasty, laser angioplasty, atherectomy, endarterectomy and percutaneous transluminal angioplasty (PCTA) Is mentioned. After these approaches, the failure rate due to restenosis, where the occlusion recurs and often worsens, is unusually high (30-50%). Much of restenosis appears to be due to further inflammation, smooth muscle accumulation and thrombus. Still other therapeutic approaches to cardiovascular disease include treatments that recommend angiogenesis in conditions such as ischemic heart and limb disease.

  The non-specific characteristics of most CAD and cardiovascular disorder symptoms make clear diagnosis difficult. More quantitative diagnostic methods suffer from both variability between individuals and between measurements in a single individual. Thus, diagnostic measurements must be standardized and well documented and applied to individuals with a broad history. Furthermore, current diagnostic methods often do not indicate the root cause for a given observation or measurement. Therefore, treatment plans based on specific positive results do not address the causative problem and can even be harmful to the individual.

  Diagnostic methods that rely on nucleotide detection include genetic approaches and expression profiling. For example, genes known to be involved in cardiovascular disorders can be screened for mutations using sequencing, hybridization-based techniques, or general genotyping methods such as PCR. In another example, expression from a known gene can be followed by standard techniques including RTPCR, various hybridization-based techniques, and sequencing. These trial designs often do not allow practitioners to detect differences in mRNA processing and splicing, translation rates, mRNA stability, and post-translational modifications such as proteolytic processing, phosphorylation, glycosylation, and amidation .

  To address the current weaknesses of the diagnostic situation in the field of cardiovascular disorders, the present invention provides specific plasma polypeptides that are differentially increased in plasma from individuals with coronary artery disease compared to control plasma To do. Providing the actual polypeptide species shows differences in mRNA processing and splicing, translation rate, mRNA stability, and post-translational modifications such as proteolytic processing, phosphorylation, glycosylation, and amidation. Accordingly, the polypeptides of the present invention are described as “cardiovascular disorder plasma polypeptides” or “CPPs”. These polypeptide sequences are described as SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25, and these are SEQ ID NOs: 3-5, 8-10, 13-14. , 18-23, and at least one amino acid sequence selected from 26-28 (see FIG. 1-5). These polypeptides are more precisely “cardiovascular disorder plasma polypeptides 2, 9, 17, 20 and 21” (CPP2 corresponds to SEQ ID NO: 1-15, CPP9 corresponds to SEQ ID NO: 6-10, CPP17 Is equivalent to SEQ ID NO: 15-23, CPP20 corresponds to SEQ ID NO: 24-28, and CPP21 corresponds to SEQ ID NO: 11-14) and was obtained from an individual with coronary artery disease (CAD) Includes fragments of CPP and post-translationally modified species that are present at high levels in plasma. Preferred fragments of the invention are those described as SEQ ID NOs: 3-5, 8-10, 13-14, 18-23 and 26-28. Accordingly, the CPPs of the present invention are useful for coronary artery disease (CAD), coronary heart disease (CHD), peripheral vascular disease, cerebral ischemia (stroke), congestive heart failure, atherosclerosis, hypertension and other cardiovascular diseases. Represents an important diagnostic tool for determining risk. CPP is a secreted factor and is itself readily detectable and is useful for drug development, diagnosis, and prevention of cardiovascular disease.

SUMMARY OF THE INVENTION The present invention is directed to compositions relating to secreted polypeptide species that preferentially increase in plasma from individuals with cardiovascular disorders. These polypeptide species are referred to herein as “cardiovascular disorder plasma polypeptides” or CPPs. Such cardiovascular disorder plasma polypeptide comprises an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28, and each CPP2, They are called CPP9, CPP17, CPP20 and CPP21. The compositions include CPP precursors, antibodies specific for CPP, including monoclonal antibodies, and other binding compositions derived therefrom. Further included are methods of making and using these compositions. Precursors of the present invention include unmodified precursors, proteolytic precursors of SEQ ID NO: 1-28, and intermediates obtained from another proteolytic site of the amino acid sequence of SEQ ID NO: 1-28.

  Preferred embodiments of the invention include CPPs having phosphorylation, glycosylation, acetylation, amidation or post-translational modifications such as C-, N- or O-linked carbohydrate groups. In addition, intramolecular or intermolecular interactions such as CPPs with disulfides and hydrogen bonds that produce higher order structures are preferred. Also preferred are CPPs that are the result of differential mRNA processing or splicing. Preferably, CPP represents a post-translationally modified species, structural variant, or splice variant that is present in plasma from an individual having a cardiovascular disorder.

  In another aspect, the invention includes a CPP comprising a sequence that is at least 75% identical to a sequence selected from one of the group consisting of SEQ ID NOs: 1-5 and 11-23. Preferably, the present invention is at least 85%, and more preferably at least 90%, and even more preferably at least 95% identical to any one of the sequences selected from SEQ ID NOs: 1-5 and 11-23 Polypeptides containing sex are included. Most preferably, the invention comprises a polypeptide comprising a sequence that is at least 99% identical to a sequence selected from one of the group consisting of SEQ ID NOs: 1-5 and 11-23.

  In another aspect, the invention includes a CPP comprising a sequence that is at least 85% identical to a sequence selected from the group consisting of SEQ ID NOs: 6-10. Preferably, the present invention provides a polymorph comprising at least 90%, and more preferably at least 95%, and even more preferably at least 97% identity with any one of the sequences selected from SEQ ID NOs: 6-10. Contains peptides. Most preferably, the invention comprises a polypeptide comprising a sequence that is at least 99% identical to a sequence selected from the group consisting of SEQ ID NOs: 6-10.

  In another aspect, the invention includes a CPP comprising a sequence that is at least 95% identical to a sequence selected from the group consisting of SEQ ID NOs: 24-28. Preferably, the present invention provides a polymorph comprising at least 97%, and more preferably at least 98%, and even more preferably at least 99% identity with any one of the sequences selected from SEQ ID NOs: 24-28. Contains peptides. Most preferably, the invention comprises a polypeptide comprising a sequence that is at least 99% identical to a sequence selected from the group consisting of SEQ ID NOs: 24-28.

  In another aspect, the invention includes natural variants of CPP that have a frequency of at least 2% in a selected population. More preferably, such natural variants have a frequency of at least 5% and even more preferably at least 10% in the selected population. Most preferably, such natural variants have a frequency of at least 20% in the selected population. The selected population may be any recognized research population in the field of population genetics. Preferably the selected population is white, black or Asian. More preferably, the selected group is French, German, British, Spanish, Swiss, Japanese, Chinese, Irish, Korean, Singaporean, Icelandic, North American Indian, Israeli, Arab Chinese, Greek, Italian, Polish, Pacific Islander, Finnish, Norwegian, Swedish, Estonian, Austrian or Indian. More preferably, the selected population is Icelandic, Sami, Finnish, Caucasian French, Swiss, Chinese Singaporean, Korean, Japanese, Quebec, North American Pima Indian, Pennsylvania Amish and Amish Menor, Newfoundland, or Polynesian.

  A preferred embodiment of the present invention provides a composition comprising an isolated CPP, ie, a CPP that does not contain a protein or protein isoform having an isoelectric point that is significantly different from or significantly different from the CPP. Affinity and size-based separation chromatography, two-dimensional gel analysis, and mass spectrometry can indicate the isoelectric point and molecular weight of a CPP.

  In a preferred embodiment, the present invention provides a specific polypeptide species comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 3-5, 8-10, 13-14, 18-23, and 26-28. provide. Preferably, the particular polypeptide species further comprises adjacent amino acid sequences from SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25, respectively. Preferred species include i) an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 3-5, 8-10, 13-14, 18-23, and 26-28; ii) have cardiovascular disorders Appears at high levels in plasma from individuals; and iii) in some cases results of proteolytic processing of polypeptides of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25, respectively Is a polypeptide.

  In yet another aspect, the invention provides two or more polypeptides selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28. Provides a combination of

  In yet another aspect, the invention includes a modified CPP. Such modifications include protecting / blocking groups, binding to antibody molecules or other cellular ligands, and detectable labels such as enzymes, fluorescence, isotopes or affinity labels that allow detection and isolation of proteins. Including, but not limited to, specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH4, acetylation, formylation, oxidation, reduction, or metabolic synthesis in the presence of tunicamycin Chemical modification can be performed by known techniques.

  Also provided by the invention are chemically modified derivatives of the polypeptides of the invention that may provide additional benefits such as increased polypeptide solubility, stability and circulation time, or reduced immunogenicity (eg, Water-soluble polymers such as polyethylene glycol, ethylene glycol / propylene glycol copolymers, carboxymethyl cellulose, dextran, polyvinyl alcohol). CPPs are modified at random positions within the molecule or at predetermined positions within the molecule and can contain 1, 2, 3 or more attached chemical groups.

  In another embodiment, the invention provides i) an amino acid selected from one of the groups consisting of the amino acid sequences listed in Table 1 (CPP2, CPP9, CPP17, CPP20 and CPP21) of the test modulator of CPP biological activity. Contacting with the polypeptide comprising; ii) detecting the level of the CPP biological activity; and iii) comparing the level of the CPP biological activity with the level of a control sample lacking the test modulator. A method for identifying at least one modulator of CPP biological activity comprising the steps of: If the difference in the level of CPP protein biological activity is a decrease, the test modulator is at least one inhibitor of CPP biological activity. If the difference in the level of CPP biological activity is an increase, the test substance is an activator of at least one CPP biological activity. For CPP2, the CPP biological activity tested is preferably an increase / decrease in lipase activity.

  Another aspect of the present invention provides: (a) administering a candidate agent to a non-human subject predisposed to or suffering from a cardiovascular disorder; (b) the candidate agent of (a) Administration to a suitable non-human preaffected control animal suffering from cardiovascular disorders; (c) obtained from (a) a non-human test animal or (b) a control animal In a biological sample: (i) a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25; ii) at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 1, 2, 11, 12, 15, 16, or 17. A variant having; (iii) A variant having at least 85% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 6 or 7; (iv) SEQ ID NO: 24, Or a variant having at least 95% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in 25; and (v) a minimum of 10 amino acids in length as described above detecting and / or identifying the level of at least one polypeptide selected from fragments of the polypeptide defined in i), ii), iii), or iv); and step (d) of step (c) Comparing the level of at least one polypeptide comprising the steps of: In which indicate that a modulator of 臓血 tract disorders, to methods for identifying modulators of cardiovascular disorders. A preferred embodiment of the present invention provides that a non-human test animal predisposed or afflicted with a cardiovascular disorder is (i) SEQ ID NO: 1-2, 6-7, 11-12, 15-17. , And a polypeptide comprising an amino acid sequence selected from one of the group consisting of 24-25; (ii) relative to the amino acid sequence shown in SEQ ID NO: 1, 2, 11, 12, 15, 16, or 17 A variant having at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions; (iii) one or more relative to the amino acid sequence shown in SEQ ID NO: 6 or 7 A variant having at least 85% sequence identity with more amino acid substitutions, deletions or insertions; (iv) one relative to the amino acid sequence shown in SEQ ID NO: 24 or 25 or A variant having at least 95% sequence identity with more amino acid substitutions, deletions or insertions; and (v) as defined above in i), ii), iii), or iv) that is at least 10 amino acids long Comprising an increase in plasma levels of at least one polypeptide selected from.

  In yet another aspect of the invention, (a) obtaining a pre-dose biological sample from a subject prior to administration of the drug; (b) in a biological sample from the subject: (i) SEQ ID NO: A polypeptide comprising an amino acid sequence selected from one of the group consisting of 1-2, 6-7, 11-12, 15-17, and 24-25; (ii) SEQ ID NOs: 1, 2, 11, 12 A variant having at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in, 15, 16, or 17; (iii) SEQ ID NO: 6, Or a variant having at least 85% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in FIG. 7; (iv) shown in SEQ ID NO: 24 or 25 A variant having at least 95% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence; and (v) i), ii above, which is at least 10 amino acids long ), Iii), or a fragment of the polypeptide as defined in iv); detecting and / or quantifying the level of at least one polypeptide selected from; and (c) one or more from the subject Obtaining a post-dose biological sample; (d) detecting the level of at least one polypeptide in the post-dose sample or samples; (e) determining the level of at least one polypeptide in the pre-dose sample. Comparing the level of at least one polypeptide in the sample after administration; and (f) adjusting the administration of the drug accordingly. When: step including, methods for monitoring the effectiveness of treatment with drugs subject at risk for or progression is made to develop cardiovascular disorder.

  In another aspect, the invention is selected from one of the group consisting of polynucleotides encoding CPPs of the invention, SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28. Polynucleotides encoding polypeptides having a specific amino acid sequence, oligonucleotides complementary to CPP gene sequences for diagnostic and analytical assays (eg, PCR, hybridization-based techniques), and vectors that express CPPs.

  In another aspect, the present invention provides a vector comprising DNA encoding CPP. The invention also includes host cells containing such vectors and non-human transgenic animals. A method of making a CPP or CPP precursor is also provided. One preferred method is (a) providing a host cell containing the expression vector disclosed above; (b) culturing the host cell under conditions whereby the DNA segment is expressed; and (c) DNA Recovering the protein encoded by the segment. Another preferred method is: (a) providing a host cell capable of expressing CPP; (b) culturing the host cell under conditions that allow expression of the CPP; and (c) the Recovering the CPP. Within one embodiment, the expression vector further comprises a secretion signal sequence operably linked to the DNA segment, the cell secretes the protein into the culture medium, and the protein is recovered from the medium. Particularly preferred methods of making CPPs include chemical synthesis using standard peptide synthesis techniques, as described in the section entitled “Chemical Production of CPP Compositions” and in Example 2.

  In another aspect, the invention includes an isolated antibody specific for any of the polypeptides, peptide fragments, or peptides described above. Preferably, the antibody of the present invention is a monoclonal antibody. More preferred are antibodies that bind exclusively to CPP, ie, antibodies that do not recognize other polypeptides with high affinity. Anti-CPP antibodies have purification, diagnostic, and prognostic applications. A preferred anti-CPP antibody for purification and diagnosis is conjugated to a labeling group. Preferred CPP-related disorders for diagnosis include coronary artery disease (CAD), coronary heart disease (CHD), peripheral vascular disease, cerebral ischemia (stroke), congestive heart failure, atherosclerosis, hypertension, and other Examples include cardiovascular diseases. Diagnostic methods include, but are not limited to, methods that use antibodies or antibody-derived compositions specific for CPP antigens. Diagnostic methods for detecting CPP in specific tissue samples and biological fluids (preferably plasma) and for detecting the expression level of CPP in tissue also form part of the present invention. Compositions comprising one or more of the above-described antibodies together with a pharmaceutically acceptable carrier are also within the scope of the invention, for example for in vivo diagnostic and drug screening assays.

  The present invention further provides a method for the diagnosis of cardiovascular disorders comprising detecting the presence or level of at least one CPP disclosed herein or any combination thereof in a sample of body fluid, preferably plasma. . Further included is a method using a primer and / or messenger RNA complementary to the CPP gene and a CPP composition comprising an anti-CPP antibody for detecting and measuring the amount of CPP in tissue and biological fluids, preferably plasma. It is. These methods are also used for clinical screening, prognosis, therapeutic outcome monitoring, identification of patients most likely to respond to a particular therapeutic treatment, drug screening and development, and identification of new targets for drug treatment. Is appropriate.

  The present invention can be used in the above-listed methods and can include single or multiple preparations or antibodies, optionally with other reagents, labeling groups, substrates, and instructions for use I will provide a. The kit can be used to diagnose a disease, or the kit can be an assay for the identification of new diagnostic and / or therapeutic agents.

  In one embodiment, coronary artery disease (CAD) is defined by the development of at least one symptom. Such symptoms become more severe as the disease progresses. CAD is often accompanied by decreased left ventricular volume or stroke volume. Early symptoms of CAD include elevated plasma levels of cholesterol and low density lipoproteins (particularly oxidized), as well as platelet-rich plasma aggregation. Vascular endothelial cells respond to inflammation and thus form plaques, and levels of inflammation and fibrinogen factor are increased. In addition, CAD or atherosclerosis is characterized by vascular calcification and arteriosclerosis. The resulting partial occlusion of the blood vessels leads to hypertension and ischemic heart disease. Ultimate complete vascular occlusion leads to myocardial infarction, stroke, or gangrene.

  In a preferred embodiment, detection of elevated plasma levels of at least one CPP of the present invention indicates an increased risk that an individual will develop CAD. Preferably, the detection indicates that the individual has the potential to develop CAD that is at least 1.05 times, 1.1 times, 1.15 times, and more preferably at least 1.2 times higher. Alternatively, detection of elevated plasma levels of at least one CPP of the present invention indicates that the individual has CAD. The increased amount of CPP observed in individuals compared to control samples correlates with the certainty of CAD prediction or diagnosis. Because individual plasma CPP levels vary depending on family history and other risk factors, it is preferable to test each individually. In a preferred embodiment, CPP is detected in a human plasma sample by the method of the invention. Particularly preferred techniques are mass spectrometry and immunodetection. Preferably, the prediction or diagnosis of CAD is an increase of at least 1.1 fold, 1.15 fold, 1.2 fold, 1.25 fold and more preferably 1.5 fold in experimental CPP levels compared to controls. based on.

  The invention further includes a method of using a CPP modulating composition for preventing or treating a disorder associated with abnormal expression or processing of the CPP of SEQ ID NO: 1-28 in an individual. Preferred CPP-related disorders include coronary artery disease (CAD), coronary heart disease (CHD), peripheral vascular disease, cerebral ischemia (stroke), congestive heart failure, atherosclerosis, hypertension and other cardiovascular diseases. It is done. A preferred embodiment of the present invention comprises: How to prevent or treat.

  Additional aspects of the invention are also described in the specification and claims.

BRIEF DESCRIPTION OF SEQUENCE LISTING SEQ ID NOs: 1 and 2 describe the amino acid sequences of polypeptides present in plasma samples of individuals with coronary artery disease (hereinafter SEQ ID NO: 2 is referred to as CPP2).
SEQ ID NOs: 3-5 are amino acid sequences of tryptic peptides found by MS-MS and / or MS-MALDI mass spectrometry in plasma samples of individuals with coronary artery disease.
SEQ ID NO: 6 describes the amino acid sequence of eosinophil-derived neurotoxin (EDN, hereinafter CPP9), while SEQ ID NO: 7 is the polypeptide sequence of the mature protein.
SEQ ID NOs: 8, 9 and 10 are the amino acid sequences of tryptic peptides found by MS-MS mass spectrometry in plasma samples of individuals with coronary artery disease.
SEQ ID NO: 11 describes the amino acid sequence of human epididymal secretory protein (HE), while SEQ ID NO: 12 is the polypeptide sequence of the mature protein (hereinafter CPP21).
SEQ ID NOs: 13-14 are the amino acid sequences of tryptic peptides found at high levels by MS-MS mass spectrometry in plasma samples of individuals with coronary artery disease.
SEQ ID NO: 15 describes the amino acid sequence of defensin 1 precursor, while SEQ ID NO: 16 is the polypeptide sequence of the preprotein, and SEQ ID NO: 17 is the sequence of defensin 1 (hereinafter CPP17).
SEQ ID NOs: 18-23 are the amino acid sequences of tryptic peptides that were prominently found by MS-MS mass spectrometry in plasma samples of individuals with coronary artery disease.
SEQ ID NO: 24 describes the amino acid sequence of plasminogen-related protein B precursor, while SEQ ID NO: 25 is the polypeptide sequence of the mature protein (hereinafter CPP20).
SEQ ID NOs: 26-28 are the amino acid sequences of tryptic peptides found by tandem mass spectrometry in plasma samples of individuals with coronary artery disease.

BRIEF DESCRIPTION OF THE FIGURES FIG. 1 shows mature human colipase polypeptide sequences (SEQ ID NOs: 1 and 2) and sequences of tryptic peptides identified by tandem mass spectrometry in the plasma of individuals with coronary artery disease (SEQ ID NOs: 3-5). ). The tryptic peptides of SEQ ID NO: 1 and 2 are underlined.
FIG. 2 shows the sequence of CPP9 (SEQ ID NO: 6) and the peptide sequence (SEQ ID NO: 8-10) found by MS-MS mass spectrometry in the plasma of individuals with coronary artery disease. The tryptic peptides observed by SEQ ID NO: 6 and 7 by tandem mass spectrometry are underlined. The signal peptide is double underlined.
FIG. 3 shows the sequence of the precursor protein (SEQ ID NO: 11) and mature protein (SEQ ID NO: 12, CPP21) and the peptide sequence found by MS-MS mass spectrometry in the plasma of individuals with coronary artery disease (SEQ ID NO: SEQ ID NO: : 13-14). The tryptic peptides observed by tandem mass spectrometry in SEQ ID NOs: 11 and 12 are underlined. The signal peptide is double underlined.
FIG. 4 shows the sequence of CPP17 (SEQ ID NO: 17) and the peptide sequence (SEQ ID NO: 18-23) found by MS-MS mass spectrometry in the plasma of individuals with coronary artery disease. The tryptic peptides observed by tandem mass spectrometry in SEQ ID NOs: 15 and 16 are underlined, representing the precursor and preprotein, respectively. In SEQ ID NO: 15, the signal peptide is double underlined.
FIG. 5 shows the sequence of the precursor (SEQ ID NO: 24) and mature protein (CPP20, SEQ ID NO: 25) of the present invention and the peptide sequence (sequence) found by tandem mass spectrometry in the plasma of an individual with coronary artery disease Number: 26-28). The tryptic peptides observed by tandem mass spectrometry in SEQ ID NOs: 24 and 25 are underlined. In SEQ ID NO: 24, the signal peptide is double underlined.

DETAILED DESCRIPTION OF THE INVENTION The invention described in detail below is for identifying individuals most likely to respond to a particular therapeutic treatment; for monitoring the outcome of cardiovascular disorder therapy; screening for CPP modulators Methods, compositions, and kits useful for screening, diagnosis, and prognosis of cardiovascular disorders in mammalian individuals are provided. The invention also encompasses administration of a therapeutic composition for treating or preventing cardiovascular disorders to a mammalian individual. The individual mammal may be a mammal other than a human, but is preferably a human, more preferably an adult. For clarity of disclosure and not limitation, the present invention will be described with respect to the analysis of plasma samples. However, as will be appreciated by those of skill in the art, the assays and techniques described below may be used with other biological fluid samples (eg, cerebrospinal fluid) from individuals who have or are at risk of developing cardiovascular disorders. , Lymph, bile, serum, saliva or urine) or tissue sample. The methods and compositions of the present invention are useful for screening, diagnosis and prognosis of surviving individuals, but are also useful for post-mortem diagnosis of individuals, for example to identify family members at risk of developing the same disorder. I will.

Definitions The terms “nucleic acid” and “nucleic acid molecule” as used herein were made using DNA molecules (eg, cDNA or genomic DNA) and RNA molecules (eg, mRNA) and nucleotide analogs. It is intended to include analogs of DNA or RNA. The nucleic acid molecule may be single-stranded or double-stranded, but preferably is double-stranded DNA. Throughout this specification, the expression “nucleotide sequence” can be used to denote a polynucleotide or nucleic acid indistinguishably. More precisely, the expression “nucleotide sequence” encompasses the nucleic acid material itself, and thus sequence information that characterizes a particular DNA or RNA molecule biochemically (ie a letter selected from among the four base letters). It is not limited to continuous). In the present specification, the terms “nucleic acid”, “oligonucleotide”, and “polynucleotide” are used interchangeably.

  An “isolated” nucleic acid molecule is one that is separated from other nucleic acid molecules that are present in the natural source of the nucleic acid. Preferably, an “isolated” nucleic acid molecule does not include sequences that naturally flank the nucleic acid in the genomic DNA of the organism from which the nucleic acid is derived (ie, sequences located at the 5 ′ and 3 ′ ends of the nucleic acid). For example, in various embodiments, an isolated CPP nucleic acid molecule is about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0 that naturally flanks the nucleic acid molecule in the genomic DNA of the cell from which the nucleic acid is derived. It can contain less than .1 kb nucleotide sequence. In addition, an “isolated” nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material or culture medium when produced by recombinant techniques, or when chemically synthesized, Contains virtually no chemical precursors or other chemicals. When all or part of a nucleic acid is used as a hybridization probe, CPP nucleic acid molecules can be isolated using standard hybridization and cloning techniques (eg, Sambrook, J., Fritsh, EF, and Maniatis, T Molecular Cloning. A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).

The term “hybridizes to” as used herein is intended to describe conditions for mild stringent or highly stringent hybridization, where Hybridization and wash conditions preferably allow nucleotide sequences that are at least 60% homologous to each other to remain hybridized to each other. Preferably, sequences that are at least about 70%, more preferably at least about 80%, even more preferably at least about 85%, 90%, 95%, or 98% homologous to each other typically remain hybridized to each other. There are certain conditions. Stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, NY (1989), 6.3.1-6.3.6. In a preferred non-limiting example, stringent hybridization conditions for nucleic acid interactions are as follows: hybridization step is 6 × SSC buffer, 5 × Denhardt solution, 0.5% SDS and 100 μg / ml salmon sperm DNA. Performed at 65 ° C. in the presence. The hybridization step is followed by 4 washing steps:
Wash preferably twice for 5 minutes at 65 ° C. in 2 × SSC and 0.1% SDS buffer;
Wash preferably once every 30 minutes at 65 ° C. in 2 × SSC and 0.1% SDS buffer;
Wash preferably once in 10 minutes at 65 ° C. in 0.1 × SSC and 0.1% SDS buffer;
These hybridization conditions are suitable for nucleic acid molecules about 20 nucleotides in length. The hybridization conditions described above are adapted according to the desired nucleic acid length according to techniques well known to those skilled in the art, such as Hames and Higgins SJ (1985) Nucleic Acid Hybridization: A Practical Approach. Hames and Higgins Ed., IRL Press, Adapted by techniques disclosed in Oxford; and Current Protocols in Molecular Biology.

  As used herein, “percent homology” refers to both nucleic acid and amino acid sequences. Amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid “homology”. To determine the percent homology of two amino acid sequences or two nucleic acids, align the sequences for optimal comparison purposes (eg, for optimal alignment with the second amino acid or nucleic acid sequence, Gaps can be introduced into sequences or nucleic acid sequences, and heterologous sequences can be ignored for comparison purposes). The length of the reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, and even more preferably the length of the reference sequence. At least 70%, 80%, 90% or 95%. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. If a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are homologous at that position. The percent homology between the two sequences is a function of the number of identical positions shared by the sequences (ie, percent homology = number of identical positions / total number of positions of 100).

  A mathematical algorithm can be used to achieve sequence comparison between two sequences and determination of percent homology. A preferred non-limiting example of a mathematical algorithm utilized for sequence comparison is the algorithm of Karlin and Altschul (1990) Proc.Natl.Acad.Sci.USA 87: 2264-68, Karlin and Altschul (1993) Proc.Natl.Acad .Sci.USA 90: 5873-77, the entire disclosure of which is hereby incorporated by reference. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul, et al. (1990) J. Mol. Biol. 215: 403-10. To obtain a nucleotide sequence that is homologous to the sequence of the present invention, a BLAST nucleotide search can be performed with the NBLAST program, score = 100, word length = 12. To obtain an amino acid sequence homologous to the polypeptide sequence of the present invention, a BLAST protein search can be performed with the XBLAST program, score = 50, word length = 3. To obtain a gapped alignment for comparative purposes, a gapped BLAST as described in Altschul, et al. (1997) Nucleic Acids Research 25 (17): 3389-3402 can be utilized. When utilizing BLAST and Gapped BLAST, the default parameters of each program (eg, XBLAST and NBLAST) can be used. See http: //www/ncbi.nlm.nih.gov. (the entire disclosure of which is hereby incorporated by reference). Another preferred non-limiting example of a mathematical algorithm utilized for sequence comparison is the algorithm of Myers and Miller, CABIOS (1989), the entire disclosure of which is hereby incorporated by reference. Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program to compare amino acid sequences, the PAM120 weight residue table, gap length penalty 12, and gap penalty 4 can be used.

  The term “polypeptide” refers to a polymer of amino acids, regardless of the length of the polymer; thus, peptides, oligopeptides, and proteins are included in the definition of polypeptide. The term also does not identify or exclude post-translational modifications of the polypeptide, eg, a polypeptide containing a covalent bond of a glycosyl, acetyl, phosphate, amide, lipid, carboxyl, acyl or carbohydrate group is explicitly defined in the term polypeptide. Is included. Also, one or more analogs of amino acids (including non-naturally occurring amino acids, amino acids that occur only in unrelated biological systems, modified amino acids from mammalian systems, etc.), naturally occurring and non-naturally occurring Also included in the definition are polypeptides containing polypeptides having both naturally occurring substitution bonds and other modifications known in the art.

  The term “protein”, as used herein, can be used interchangeably with the term “polypeptide”, or in addition, two or two that can be linked by bonds other than peptide bonds. It can refer to a complex of more polypeptides, such as those in which the polypeptides constituting the protein can be linked by disulfide bonds. The term “protein” can also include a family of polypeptides having the same amino acid sequence but differing in post-translational modifications that can be added, particularly when such proteins are expressed in eukaryotic hosts.

  An “isolated” or “purified” protein or biologically active portion thereof is derived from the cell or tissue source from which the protein of the invention (ie, CPP or biologically active fragment thereof) is derived. Is substantially free of cellular material or other contaminating proteins, or when chemically synthesized, is substantially free of chemical precursors or other chemicals. The language “substantially free of cellular material” includes a preparation of a protein according to the invention in which the protein is separated from the cellular components of the cell from which it is isolated or recombinantly produced. In one embodiment, the term “substantially free of cellular material” refers to less than about 30% (dry weight) of a protein other than the protein of the invention (also referred to herein as “contaminating protein”). More preferably less than about 20% of a protein other than a protein according to the invention, still more preferably less than about 10% a protein other than a protein according to the invention, and most preferably less than about 5% a protein other than a protein according to the invention. A protein preparation according to the invention having When recombinantly producing a protein according to the present invention or a biologically active portion thereof, preferably it is substantially free of culture medium, ie the culture medium is less than about 20% of the volume of the protein preparation, more preferably Corresponds to less than about 10%, and most preferably less than about 5%.

The language “substantially free of chemical precursors or other chemicals” refers to the preparation of proteins of the invention in which the protein is separated from the chemical precursors or other chemicals involved in the synthesis of the protein. Including things. In one embodiment, the language “substantially free of chemical precursors or other chemicals” refers to less than about 30% (dry weight) chemical precursors or non-protein chemicals, more preferably about 20 % Chemical precursors or non-protein chemicals, even more preferably less than about 10% chemical precursors or non-protein chemicals, and most preferably less than about 5% chemical precursors or non-protein chemicals A protein preparation according to the invention having
As used herein, refers to a polypeptide that is artificially designed using the term “recombinant polypeptide” and that includes at least two polypeptide sequences that are not found in close proximity in the original natural environment. Or a polypeptide expressed from a recombinant polynucleotide.

  The term “cardiovascular disorder plasma polypeptide” or “CPP” refers to a polypeptide comprising a sequence set forth by any one of SEQ ID NOs: 1-28. Such polypeptides may be subjected to post-translational modifications as described herein. CPPs can also contain other structural or chemical modifications such as disulfide bonds or amino acid side chain interactions such as hydrogen and amide bonds leading to complex secondary or tertiary structures. CPPs are also mutant polypeptides such as deletion, addition, exchange, or truncation mutants, fusion polypeptides comprising such polypeptides, and at least three, but preferably and where applicable SEQ ID NO: 1. It also includes polypeptide fragments of 8, 10, 12, 15, or 21 contiguous amino acids of the -28 sequence. The CPP further comprises proteolytic precursors and intermediates of a sequence selected from the group consisting of SEQ ID NOs: 1-28. The present invention relates to a CPP gene or CPP mRNA species, preferably a human CPP gene and mRNA, comprising an isolated CPP composed, consisting essentially of or comprising the sequence of SEQ ID NO: 1-28 The polypeptide encoded by the nucleic acid sequence of the species is embodied. Preferred CPPs have a sequence comprising one of the sequences of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25. Preferred CPP fragments have a sequence comprising one of the sequences of SEQ ID NOs: 3-5, 8-10, 13-14, 18-23, and 26-28. Preferred CPPs retain at least one biological activity of the CPP of SEQ ID NO: 1-28.

  The term “biological activity” as used herein refers to any single function performed by the CPP. These include, but are not limited to: (1) showing that the individual has or will have a cardiovascular disorder; (2) circulating through the bloodstream of an individual with cardiovascular disorder. (3) antigenicity, ie the ability to bind to an anti-CPP-specific antibody; (4) immunogenicity, ie the ability to make an anti-CPP-specific antibody; and for CPP2: (5) a CPP target protein, preferably Interact with lipase; (6) stabilize the active site of lipase; (7) increase lipase activity; (8) interact with CPP target molecules such as phospholipids, micelles or triglycerides. And (9) forming at least one disulfide bond; for CPP9: (5) hydrogen, amide, or preferably disulfide (6) interactions with CPP target molecules, preferably RNA molecules or virions (such as respiratory syncytial virus or RSV); (7) anti-molecular amino acid side chain interactions; Viral activity, and (8) hydrolysis of RNA phosphodiester bonds; for CPP21: (5) forming intramolecular amino acid side chain interactions such as hydrogen, amide, or preferably disulfide bonds; and (6 ) Interacting with CPP target molecules, particularly cholesterol; for CPP17: (5) forming intramolecular amino acid side chain interactions such as hydrogen, amide, or preferably disulfide bonds; (6) CPP target molecules Preferably interacting with bacterial endotoxins; (7) neutralizing bacterial endotoxins; ) Promoting mast cell chemotaxis; (9) undergoing post-translational processing, eg, specific proteolysis; (10) functioning as an antimicrobial defense; and (11) preventing smooth muscle cell contraction. And for CPP20: (5) forming intramolecular amino acid side-chain interactions such as hydrogen, amide, or preferably disulfide bonds; (6) CPP target molecules, particularly kringles such as plasminogen Interacting with domain-containing peptides; and (7) reducing tumor growth.

  A “CPP modulator” as used herein is a molecule that can modulate (ie, increase or decrease) either the expression or biological activity of a CPP of the invention (eg, a polynucleotide, Polypeptide, small molecule or antibody). CPP modulators that enhance CPP expression or activity are described as CPP activators or agonists. Conversely, CPP modulators that suppress CPP expression or activity are described as CPP inhibitors or antagonists. Preferably, the CPP modulator increases / decreases expression or activity by at least 5, 10 or 20%. CPP inhibitors include anti-CPP antibodies, fragments thereof, antisense polynucleotides, and molecules characterized by screening assays as described herein. CPP agonists include polynucleotide expression vectors and molecules characterized by screening assays as described herein.

  “CPP-related disorder” or “CPP-related disease” describes a cardiovascular disorder. Preferred disorders include coronary artery disease (CAD), coronary heart disease (CHD), peripheral vascular disease, cerebral ischemia (stroke), congestive heart failure, atherosclerosis, hypertension and other cardiovascular diseases. Preferably, the likelihood that an individual will develop or already have such a disorder is indicated by a higher than normal plasma level of at least one CPP.

Another aspect of the invention pertains to anti-CPP antibodies. The term “antibody” as used herein refers to an immunoglobulin molecule and an immunologically active portion of an immunoglobulin molecule, ie, an antigen that specifically binds (immunoreacts with) an antigen such as CPP. Refers to a molecule containing a binding site, or a biologically active fragment or homologue thereof. Preferred antibodies bind exclusively to CPP and do not recognize other polypeptides with high affinity. Examples of immunologically active portions of immunoglobulin molecules include F (ab) and F (ab ′) ₂ fragments that can be generated by treating the antibody with an enzyme such as pepsin. The present invention provides polyclonal and monoclonal antibodies that bind to CPP or biologically active fragments or homologues thereof. The terms “monoclonal antibody” or “monoclonal antibody composition” as used herein, an antibody that contains only one species of antigen binding site capable of immunoreacting with a particular epitope of a CPP. Refers to a group of molecules. Thus, a monoclonal antibody composition typically displays a single binding affinity for a particular CPP with which it immunoreacts. Preferred CPP antibodies are conjugated to a labeling group.

A “labeling group” as used herein is any label that, when attached to a polynucleotide or polypeptide (including antibodies), allows detection or purification of the polynucleotide or polypeptide. A compound. The labeling group can be detected or purified directly or indirectly by a secondary compound containing an antibody specific for the labeling group. Useful labeling groups include radioisotopes (eg ³² P, ³⁵ S, ³ H, ¹²⁵ I), fluorescent compounds (eg 5-bromodesoxyuridine, umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotria. Dinylamine fluorescein, dansyl chloride, phycoerythrin acetylaminofluorene, digoxigenin), luminescent compounds (eg luminol, GFP, luciferin, aequorin), enzyme or enzyme cofactor detection label (eg peroxidase, luciferase, alkaline phosphatase, galactosidase, or acetyl) Cholinesterase) or compounds recognized by secondary factors such as streptavidin, GST, or biotin. Preferably, the labeling group is attached to the polynucleotide or polypeptide in a manner that does not interfere with the biological activity of the polynucleotide or polypeptide.

  Radioisotopes can be detected by direct counting of radiation emission, film exposure, or for example by scintillation counting. Enzymatic labels can be detected by determining the conversion of an appropriate substrate into a product that normally causes a fluorescent reaction. Fluorescent and luminescent compounds and reactions can be detected, for example, by radiation emission, fluorescence microscopy, fluorescence activated cell sorting, or luminometer.

  As used herein with respect to antibodies, in a sample containing the target of interest, eg, a biological sample, the antibody recognizes and binds to the target of interest but does not substantially recognize and bind other molecules. In some cases, the antibody is referred to as “selectively binds” or “specifically binds” to the target.

  As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a “plasmid”, which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector in which additional DNA segments can be ligated into the viral genome. Certain vectors are capable of self-replication in the host cell into which they are introduced (eg, bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (eg, non-episomal mammalian vectors) are integrated into the genome of the host cell upon integration into the host cell, and are thereby replicated along with the host genome. Furthermore, a particular vector can direct the expression of a gene to which it is operably linked. Such vectors are referred to herein as “expression vectors”. In general, expression vectors useful in recombinant DNA technology are often in the form of plasmids. In the present specification, “plasmid” and “vector” can be used interchangeably as the plasmid is the most commonly used form of vector. However, the present invention is intended to include such other forms of expression vectors, such as viral vectors that provide equivalent functions (eg, replication defective retroviruses, adenoviruses and adeno-associated viruses).

  As used herein, an “effective amount” describes an amount of an agent, preferably a CPP modulator of the invention, sufficient to have the desired effect. For example, an effective amount of an anti-cardiovascular disorder is the amount of drug required to reduce the symptoms of cardiovascular disorder in an individual by at least 1, 2, 5, 10, 15 or preferably 25%. The term also describes the amount of drug required to ameliorate symptoms caused by cardiovascular disorders in an individual. Common symptoms of cardiovascular disorders include: chest tightness, heartburn, nausea, vomiting, numbness, shortness of breath, severe cold sweat, unexplained fatigue, and anxiety. More serious symptoms of cardiovascular disorders are chest pain (angina), rhythm disturbance (arrhythmia), stroke or heart attack. The effective amount for a particular patient depends on such factors as the method of diagnosing the condition being measured, the status of the condition being treated, the overall health of the patient, the method of administration, and the severity of the side effects. Can be different.

CPP of the present invention
The cardiovascular disorder plasma polypeptides (CPPs) of the present invention are described in the sequences listed as SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25. A CPP comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25 has or develops cardiovascular disorders Secreted and circulated at high levels in the plasma of individuals at risk of

  The CPP further comprises a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 3-5, 8-10, 13-14, 18-23, and 26-28. Such CPPs are also secreted in the plasma and circulate. Preferably such CPPs also comprise yet another amino acid from one of the group of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25. Such additional amino acids are fused in frame with sequences selected to form contiguous amino acid sequences from the proteins of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25. Is done.

  Interestingly, the level of CPP of the present invention is elevated in the plasma of individuals suffering from cardiovascular disorders. As such, the CPPs of the present invention provide a useful diagnostic tool that indicates that increased levels of CPP are an increased risk of developing cardiovascular disorders or the presence of cardiovascular disorders. In addition, CPPs are useful for drug design and in therapeutic planning for the prevention and treatment of cardiovascular disorders.

  CPP2 of SEQ ID NO: 2 represents the sequence of protein colipase. Colipase is a small protein cofactor for pancreatic triglyceride lipase (PTL), which is required for efficient dietary lipid hydrolysis. Mature colipase is 90 amino acids long and has 5 conserved disulfide bonds. The protein is synthesized as a pre-procolipase and has 112 amino acids from which another 5 amino acids are cleaved at the N-terminus and processed into procoliposes. Colipase binds to the C-terminal non-catalytic domain of lipase, thereby contributing to a hydrophobic active binding site; stabilizes activity in the presence of inhibitors such as bile; and enzymes at the oil-water interface It is a secreted protein that is directed. Five residues of colipase: Arg39, Glu40, Glu59, Arg60, and Asn84 form a polar interaction with PTL. In the active conformation, Glu10 and Arg33 also interact with PTL. The lipase-colipase complex is activated by micelles, which also stabilizes the open conformation and exposes hydrophobic active sites. PTL and colipase function in the duodenum and release 50-70% of dietary fatty acids (Crandall WV and Lowe ME, J BIol Chem (2001) 276: 12505-12; van Tilbeurgh H. et al., Biochim Biophys Acta (1999) 1441: 173-84; Pignol D, et al., JBC, (2000) 275: 4220-4224; and Lowe ME, et al., Annu. Rev. Nutr (1997) 17: 141-58) .

  Since colipase is normally present in the duodenum and is active, its presence in human plasma is indicative of a biological abnormality. This is further evidenced by the absence of the CPP of the present invention in normal human plasma. Colipase has been previously observed in the serum of patients with acute pancreatitis (Junge, W. and Leybold, K, Clin. Chim. Acta (1982) 123 (3), 293-302). As such, the CPPs of the present invention are useful in drug design and therapeutic planning for the prevention and treatment of cardiovascular disorders. Interestingly in this regard, therapeutic approaches have been developed for obesity using the lipase inhibitor orlistat (Stemby, B. et al., Clin. Nutr. (2002) 21 (5), 395- 402). Inhibitors are thought to act through a decrease in triglyceride intake and have been observed to cause abnormal fatty stool, which is also associated with a loss of colipase (Gaskin, KJ et al., Gastroenterology (1984) 86 ( 1), 1-7).

  CPP9 full length (SEQ ID NO: 7) forms 4 disulfide bonds; is glycosylated and contains a rare C-linked glycosylation; is the major eosinophilic granule component and breaks down RNA phosphodiester bonds And has antiviral activity. The full length CPP9 has the sequence of non-secretory RNase 2. Ribonucleases catalyze the hydrolysis of phosphodiester bonds in RNA strands. Human ribonucleases include: RNase 1, or secretory / pancreatic, non-secretory RNase 2, or eosinophil-derived neurotoxin (EDN), non-secretory RNase 3, ie acidophilic cationic protein (ECP) , RNase 4, angiogenin, and the recently described RNase k6. RNases 2-4 and 6 belong to the RNase A family and have anti-pathogenic activity (Zhang J and Rosenberg HF, Genetics 2000; 156: 1949-58). EDN, a non-secretory ribonuclease, degrades mRNA by hydrolyzing single-stranded polynucleotides in the 3 'to 5' direction. EDN is the major acidophilic granule protein and is itself found in tissues affected by eosinophils, including pancreas, liver, lung, spleen, and body fluids.

  Increased serum levels of human RNase 1 are indicative of pancreatic cancer (Fernandez-Sales, et al., Eur. J. Biochem., 2000, 267 (5): 1484-94). In particular, intraventricular injection of EDN has been implicated in the promotion of Gordon phenomenon, hypereosinophil syndrome leading to loss of Purkinje cells and cerebellar dysfunction (Newton, DL et al., J. Neurosci., 1994, 14 (2): 538-44). In addition, eosinophils and EDN respond to respiratory diseases caused by single-stranded RNA virus respiratory syncytial virus (RSV; Paramyxoviridae family). Eosinophils are recruited to the lung parenchyma in response to RSV infection. Once replenished, they interact and are directly activated by RSV virions leading to degranulation (Domachowske JW, et al., Nucleic Acids Res 1998 Dec 1; 26 (23): 5327-32). EDN is RNase-dependent and promotes the destruction of extracellular RSV virions by an EDN-specific mechanism.

  CPP21 (SEQ ID NO: 12) of the present invention represents the plasma type of human epididymis secretory protein (HE) 1. HE1, a novel human epididymal gene product isolated by differential screening, predicts abundant small secreted glycopeptides. HE1 is encoded by a well conserved single copy gene (Kirchhoff, et al., Biol Reprod, 1996, 54: 847-56). Genes are widely expressed at the highest levels in testis, kidney, and liver. The HE1 protein is normally present in the lysosomal compartment and constitutes a major component of epididymal fluid secretion.

  The genetic neurodegenerative disease Niemann-Pick C2 type (NPC2) is the result of mutations in the HE1 (or NPC2) gene that cause abnormally high cellular cholesterol accumulation (Naureckiene S et al., Science (2000) 290: 2298 and WO02059369). Niemann-Pick type C disease is associated with impaired intracellular cholesterol and glycolipid transport (Ong YY et al., Exp Brain Res (2001) 141: 218-31). In patients with NPC2, cholesterol is not transported through the late endosome / lysosome system and accumulates in lysosomes, while depriving cells of free cholesterol. As a result, even though excess cholesterol has already accumulated, cells produce additional cholesterol to compensate for the defect (Garver WS et al., Curr Mol Med, (2002) 2: 485-505). The hydrophobic sterol-binding pocket of HE1 interacts with cholesterol with high affinity (K (d) = 30-50 nM) (Ko, et al., Proc. Natl. Acad. Sci. USA, 2003, 100 : 2518-25).

  HE1 has been found in the plasma of patients with coronary artery disease using the method of the present invention. This protein is normally associated with intracellular transport and epididymal secretion and is therefore not expected in the plasma of control individuals. Therefore, HE1 is an important biomarker for cardiovascular disorders.

  CPP17 (SEQ ID NO: 17) is a plasma form of the antimicrobial peptide defensin 1-3. Defensin 1-3 (alpha-defensin) has been cloned from a leukemia cell library and found to be expressed in normal bone marrow and circulating lymphocytes (Daher, et al., PNAS. 85: 7327-7331 (1988) ). Alpha-defensins are constitutively expressed in neutrophils and can constitute up to 5% of cellular proteins. The full-length protein is processed to form a 29-35 amino acid peptide that is released in response to microbial and viral infections. These cationic peptides insert and disrupt the prokaryotic cell membrane (Hill, et al., Science 251: 1481-1485 (1991)). In addition, alpha-defensins reduce HIV replication in response to the CD8 T cell factor CAF (Zhang, et al., Science 298: 995-1000 (2002)).

  Alpha-defensins bind to low density lipoprotein (LDL) particles in the blood and protect against LDL receptor binding and subsequent degradation (Higazi, et al., Blood 96: 1393-1398 (2000) and cited therein). References). Subsequently, alpha-defensins have been found to interact with vesicular smooth muscle cells and prevent contraction (Nassar, et al. Blood 100: 4026-32 (2002)).

  The inventor has shown high levels of alpha-defensin peptides in the plasma of individuals with coronary artery disease. These results provide direct evidence that alpha-defensins are useful plasma biomarkers of disease.

  CPP20 (SEQ ID NO: 25) is a plasma form of plasminogen-related protein B. Plasminogen-related protein B (as well as Plasimilar) has been cloned from chondrocytes and is highly homologous to the N-terminus of plasminogen (Ichinose, Biochemistry 31: 3113-8 (1992)). After removal of the 19 amino acid signal sequence, a 96 amino acid long precursor protein is secreted. Plasminogen-related protein B binds to the kringle domain and is thought to interfere with plasminogen binding to fibrin or alpha2-antiplasmin (Lewis, et al., Eur J Biochem. 259: 618-625 (1999)). Plasminogen-related protein B is expressed in metastatic tumor cells (WO9321341 and Weissbach and Treadwell, Biochem. Biophys. Res. Commun. 186: 1108-1114 (1992)). In addition, Lewis et al. (Anticancer Res 21: 2287-91 (2001)) demonstrated that the protein reduces the growth of tumors implanted in mice but has little effect on plasminogen. Accordingly, the treatment of malignant conditions and the treatment of angiogenesis-related disorders has been described (WO 9946282).

  Using the method of the present invention, plasminogen-related protein B has been found in the plasma of patients with coronary artery disease. This protein normally binds to the extracellular matrix and is not detected in the plasma of control individuals. Thus, plasminogen-related protein B is an important biomarker for cardiovascular disorders.

  The terms “cardiovascular disorder plasma polypeptide” and “CPP” as used herein encompass any and all peptides, polypeptides and proteins of the invention. Polypeptides encoded by the polynucleotides of the present invention, and fusion polypeptides comprising such polypeptides also form part of the present invention. The present invention consists essentially of an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28 Or a human-derived CPP comprising an isolated or purified CPP containing the same. Further, an unmodified precursor, proteolytic precursor and intermediate of a sequence selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28 Also included.

  The present invention embodies isolated, purified and recombinant polypeptides of continuous length of at least 3 amino acids, preferably at least 8 to 10 amino acids, having CPP biological activity. In a preferred embodiment, the contiguous stretch of amino acids includes sites of mutations or functional mutations involving amino acid deletions, additions, exchanges or truncations in the CPP sequence. The invention also relates to polypeptides encoded by the CPP nucleotide sequences of the invention, or their complementary sequences or fragments thereof.

  One aspect of the present invention relates to isolated CPPs and biologically active portions thereof, and polypeptide fragments suitable for use as immunogens that raise anti-CPP antibodies. In one embodiment, the original CPP peptide can be isolated from plasma, cell or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, CPP is produced by recombinant DNA technology. As an alternative to recombinant expression, peptide synthesis techniques can be used to chemically synthesize CPPs as described in the section entitled “Chemical Manufacture of CPP Compositions” and in Example 2.

  Typically, the biologically active portion comprises at least one domain or motif having CPP activity. The biologically active CPP is, for example, at least 1, 2 from a sequence selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28. At least from a sequence comprising 3 or 5 amino acid changes or selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28 Includes 1%, 2%, 3%, 5%, 8%, 10%, or 15% change.

CPP Characterization The polypeptide of the present invention, CPP, is defined by the tryptic peptides of SEQ ID NOs: 3-5, 8-10, 13-14, 18-23, and 26-28 listed in Table 1. As described in Example 1, these peptides were isolated from patients with coronary artery disease and characterized by the MicroProt ™ method. SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25 represent polypeptide species found in CAD plasma from which tryptic peptides have been released.

  Since plasma samples are first separated based on molecular weight, all CPPs of the present invention have a molecular weight of approximately 20 kD or less. High molecular weight polypeptide species are separated and characterized by different methods. As described in Example 1, plasma samples are subjected to a number of chromatographic separations. Details about these chromatographic methods are given in Example 1.

  The first separation is on a cation exchange chromatography column, which is eluted with increasing salt concentration. Collect 18 fractions. The CEX column in Table 1 lists which fractions contain each tryptic peptide and its elution conditions. Separation by cation exchange provides an indication of the overall positive charge of the polypeptide species. Cation exchange is followed by reverse phase HPLC separation. The RP1 column in Table 1 lists which of the 30 fractions eluted each tryptic peptide and its elution conditions. Separation by reverse phase provides an indication of the overall hydrophobicity of the polypeptide species. The last two numbers in the column labeled run number indicate which of the 24 eluted fractions contains the tryptic peptide from the second reverse phase HPLC separation (see Example 1). ). The proteome displays for which sample each tryptic peptide was observed for CPP17. For CPP2, CPP9, CPP20 and CPP21, all observations were made on disease (CAD) samples only. The OLAV score, when present, reflects the intensity of the experimental MS-MS signal above noise, as indicated by the MS-MS data identification software, and thus displays the protein concentration in the sample.

Table 1a-CPP2

Table 1b-CPP9

  For CPP9, the information provided in Table 1b represents a number of characteristics of the polypeptide species present in the plasma of CAD patients. The following represents an illustrative description of the data contained in Table 1b. Table 1b shows that the same tryptic peptide is found in one or more fractions of a given separation. Spacing between several fractions indicates that tryptic peptides are released from different circulating polypeptide species. For example, CPP9 was observed again in a series of 2 to 5 consecutive CEX fractions, and then in a series of 8 to 9 consecutive CEX fractions. This indicates the presence of at least two polypeptide species with different positive charge properties from which tryptic peptides were derived. This indicates that there are additional amino acids or charged modifications (eg, phosphate groups) in one species but not in the other species. Similarly, CPP9 was observed in RP1 fraction 8, and then in a series of 10 to 12 consecutive RP1 fractions. Again, this indicates the presence of at least two polypeptide species with different hydrophobicity indices from which tryptic peptides have been derived. Taken together, these observations indicate that the observed peptide contains three non-sequence specific elution clusters: the first elution cluster contains fragments eluted in CEX fraction 2 and RP1 fraction 8; The cluster contains the fragments eluted in CEX fraction 3-5 and RP1 fraction 10-11; and the third cluster contains the fragments eluted in CEX fraction 8-9 and RP1 fraction 11-12 ; Based on the fractionation information combined for the tryptic peptides of SEQ ID NOs: 3-5, three different forms or species of CPP9 may circulate in the plasma of individuals with CAD. These CPP9 forms may differ in post-translational modifications and / or amino acid lengths. The tryptic peptides of SEQ ID NOs: 8-10 are derived from the polypeptide of SEQ ID NO: 7, which is processed to form different polypeptide species that are present in the plasma of individuals with CAD.

Table 1c-CPP21

Table 1d-CPP17

  For CPP17, the ratio of protein levels in CAD to control plasma samples is calculated by two methods. The first method calculates the CAD / control ratio by the number of fractions from each sample containing CPP17. The result is 2.4 (see Table 1d). Alternatively and more precisely, the weighted ratio is obtained using the OLAV score obtained for each peptide in the mass spectrometry data analysis software. The result is 2.1, indicating that the CPP of the present invention is present in CAD plasma at a level 2.1 times that of the control plasma. As such, CPP provides a useful diagnostic tool that indicates that elevated levels of CPP are at high risk of developing cardiovascular disorders or that cardiovascular disorders are present.

Number of control fractions: 116
Total number of CAD fractions: 279
Total CAD / control: 2.4

OLAV score control: 3720.25
OLAV score Total CAD: 7946.59
Total CAD / control: 2.1

  It is interesting to note that Table 1d displays the tryptic peptide of SEQ ID NO: 18 (ADEVAAAPEQIAADIPEVVVSLAWDESLAPK), which is derived from the preprotein of SEQ ID NO: 16 and itself is not expected to be found in plasma. It is. In addition, this tryptic peptide was identified only in disease plasma. This observation may reflect changes in preprotein processing in the case of disease.

Table 1e-CPP20

CPP Nucleic Acids One aspect of the present invention further relates to purified or isolated nucleic acid molecules that encode CPPs or biologically active portions thereof as described herein, and nucleic acid fragments thereof. To do. The nucleic acids can be used in therapeutic (DNA vaccines) and diagnostic methods, eg, as further described herein, and in drug screening assays.

  The subject of the present invention is a purified, isolated or recombinant nucleic acid encoding CPP, sequences complementary thereto, and fragments thereof. The invention also provides at least 95% nucleotide identity with a polynucleotide encoding CPP, advantageously 99% nucleotide identity with a polynucleotide encoding CPP, preferably 99.5% nucleotide identity, and most preferably Also relates to a purified or isolated nucleic acid molecule comprising a polynucleotide having 99.8% nucleotide identity, or a sequence complementary thereto or a biologically active fragment thereof. Another object of the present invention is to hybridize with a polynucleotide encoding CPP, or a sequence complementary thereto or a variant thereof or a biologically active fragment thereof under stringent hybridization conditions as defined herein. It relates to purified, isolated or recombinant nucleic acids containing soy polynucleotides.

  In another preferred embodiment, the present invention relates to a purified or isolated nucleic acid molecule encoding a portion or variant of CPP, wherein the portion or variant displays CPP biological activity. To do. Preferably the portion or variant is a portion or variant of a naturally occurring CPP or precursor thereof.

  Another subject of the invention essentially comprises an amino acid sequence selected from one of the group of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28, or a fragment thereof A purified, isolated, or recombinant nucleic acid encoding CPP, wherein the isolated nucleic acid molecule is for CPP2: a lipase binding region , Hydrophobic surface, or disulfide bond; for CPP9: substrate RNA binding site, substrate virion binding site (preferably RSV virion), ribonuclease active site, or disulfide bond; for CPP21: cholesterol binding domain, glycosylation site, or Disulfide bond; for CPP17: bacterial endotoxin binding site, Other disulfide bond; with respect CPP20: Kringle binding domain or a disulfide bond; such as, encoding one or more motifs.

  For use in identifying and / or cloning CPP homologues from other CPPs (eg sharing a novel functional domain) and other species, with nucleotide sequences determined from cloning of CPP-encoding genes Designed probes and primers can be created.

  A nucleic acid fragment encoding a “biologically active portion of a CPP” is obtained by isolating a portion of a nucleotide sequence encoding a CPP that encodes a polypeptide having a biological activity of the CPP and the CPP Can be prepared by expressing (eg, by recombinant expression in vitro or in vivo) and evaluating the activity of the coding portion of CPP.

  The invention further encompasses nucleic acid molecules that differ from the CPP nucleotide sequences of the invention due to the degeneracy of the genetic code and encode the same CPPs of the invention.

  It will be appreciated by those skilled in the art that in addition to the CPP nucleotide sequences described above, DNA sequence polymorphisms that lead to changes in the amino acid sequence of CPP may exist within a population (eg, the human population). Such genetic polymorphisms may exist among individuals within a population due to natural allelic variants. Such natural allelic variants typically lead to 1-5% variance in the nucleotide or nucleic acid sequence of the CPP-encoding gene.

  Under stringent hybridization conditions, a nucleic acid molecule corresponding to a natural allelic variant and a homologue of a CPP nucleic acid of the present invention can be converted to a cDNA disclosed herein, or a portion thereof, by standard hybridization techniques. It can be used as a hybridization probe and isolated based on homology to the CPP nucleic acids disclosed herein.

  It will be understood that the present invention includes a polypeptide having an amino acid sequence encoded by any polynucleotide of the present invention.

Use of CPP Nucleic Acids Polynucleotide sequences encoding CPP (or its complement) have a variety of applications including use as hybridization probes in chromosome and gene mapping, and in the production of antisense RNA and DNA. . In addition, as described herein, CPP-encoding nucleic acids are useful as targets for pharmaceutical intervention, eg, for the development of DNA vaccines, and for the preparation of CPPs by recombinant techniques . The polynucleotides described herein, including their sequence variants, can be used in diagnostic assays. Accordingly, diagnostic methods based on the detection of the presence of such polynucleotides in body fluids or tissue samples are a feature of the present invention. Examples of nucleic acid based diagnostic assays according to the present invention include, but are not limited to, hybridization assays such as in situ hybridization, and PCR based assays. As described herein, polynucleotides including polynucleotide extensions, sequence variants and fragments thereof can be used to create hybridization probes or PCR primers for use in such assays. Such probes and primers can detect polynucleotide sequences that are similar to or complementary to the CPP polynucleotides described herein.

  The present invention includes primer pairs for performing PCR to amplify a segment of the polynucleotide of the present invention. Each primer pair consists of i) one primer of the pair forms a double strand that is perfectly paired with one strand of the polynucleotide of the invention, and the other primer of the pair is a complementary strand of the same polynucleotide. Forming a perfectly paired duplex, and ii) the primer pair forms such a perfectly paired duplex at sites of the polynucleotide separated by a spacing between 10 and 2500 nucleotides; Is an oligonucleotide having a length between 15 and 30 nucleotides. Preferably, the annealing temperature of each primer pair to its respective complementary sequence is substantially the same.

  Hybridization probes derived from the polynucleotides of the invention can be used to perform in situ hybridization on tissue samples such as fixed or frozen tissue sections or suspended cells prepared on microscope slides. it can. Briefly, under controlled conditions, a labeled DNA or RNA probe can be bound to its DNA or RNA target sample in a prepared tissue section on a microscope. In general, dsDNA probes consisting of the DNA of interest cloned into a plasmid or bacteriophage DNA vector are used for this purpose, but ssDNA or ssRNA probes can also be used. Probes are generally oligonucleotides between about 15 and 40 nucleotides in length. Alternatively, the probe may be a polynucleotide probe made by PCR random priming primer extension or in vitro transcription of RNA from a plasmid (riboprobe). These latter probes are typically hundreds of base pairs in length. The probe can be labeled with any of a number of labeling groups, and the type of label utilized in the probe corresponds to a particular detection method (eg, autoradiography, X-ray, if desired) Detection, fluorescence or visible microscopic analysis). The reaction can be further amplified in situ using immunocytochemical techniques directed against the label of the detection molecule used, such as an antibody directed against the fluorescent moiety present in the fluorescently labeled probe. Finding specific labeling and in situ detection methods, for example in Howard, GC, Ed., Methods in Nonradioactive Detection, Appleton & Lange, Norwalk, Conn., (1993), which is hereby incorporated by reference. Can do.

  Hybridization probes and PCR primers can also be selected from genomic sequences corresponding to full-length proteins identified by the present invention, including promoters, enhancer elements and introns of genes encoding naturally occurring polypeptides. A nucleotide sequence encoding a CPP can also be used to construct hybridization probes for mapping the gene encoding that CPP and for genetic analysis of individuals. An individual carrying a change or mutation in the gene encoding the CPP of the present invention can be detected at the DNA level by various techniques. Nucleic acids used for diagnosis can be obtained from patient cells including, for example, tissue biopsy and dead anatomical material. Genomic DNA can be used directly for detection or can be amplified enzymatically using PCR prior to analysis (Saiki, et al., Nature 324: 163-166 (1986)). RNA or cDNA can also be used for the same purpose. Illustratively, PCR primers complementary to the nucleic acids of the invention can be used to identify and analyze mutations in the genes of the invention. Deletions and insertions can be detected by a change in the size of the amplified product as compared to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to the radiolabeled RNA of the present invention or alternatively to the radiolabeled antisense DNA sequence of the present invention. By nuclease protection assays such as RNase and S1 protection, or by chemical cleavage methods (eg Cotton, et al., Proc. Natl. Acad. Sci. USA 85: 4397-4401 (1985)) or differences in melting points The sequence change at a specific position can also be expressed by. "Molecular index" (Kostrikis LG et al., Science 279: 1228-1229 (1998)), hairpin type, point mutation using a single-stranded synthetic oligonucleotide containing a probe sequence complementary to the nucleic acid of the present invention Alternatively, other sequence changes can be detected and the level of CPP expression can be monitored.

Oligonucleotides and antisense compounds Commercially available automated DNA synthesizers, such as Applied Biosystems (Foster City, Calif.) Model 380B, 392 or 394 DNA / RNA synthesizers or the like, including PCR primers and antisense compounds. It is synthesized by means commonly used in the above apparatus. Preferably, phosphoramidite chemistry is used, for example as disclosed in the following references: Beaucage and Iyer, Tetrahedron, 48: 2223-2311 (1992); Molko et al., US Pat. No. 4,980,460; Koster et al., US Pat. No. 4,725,677; Caruthers et al., US Pat. Nos. 4,415,732; 4,458,066; and 4,973,679; For therapeutic applications, a nuclease resistant backbone is preferred. Many types of modified oligonucleotides that confer nuclease resistance are available, such as phosphorothioates, phosphorodithioates, phosphoramidates, and many documents such as phosphorothioates: Stec et al., US Pat. No. 5,151,510; Hirschbein, US Pat. No. 5,166,387; Bergot, US Pat. No. 5,183,885; Phosphoramidate: froehler et al. International application PCT / US90 / 03138; : Uhlmann and Peyman (cited above). The length of the antisense oligonucleotide must be large enough to ensure that specific binding occurs only at the desired target polynucleotide and not at other accidental sites. Upper limits of the length range include the inconvenience and expense of synthesizing and purifying oligomers longer than about 30-40 nucleotides, greater tolerance for mismatches with longer oligonucleotides than shorter oligonucleotides, etc. , Determined by several factors. Preferably, the antisense oligonucleotide of the present invention has a reaction length of 15 to 40 nucleotides. More preferably, the oligonucleotide portion has a length in the range of about 18 to 25 nucleotides.

Primers and probes such as cloning and restriction of appropriate sequences and the phosphodiester method of Narang SA et al., (Methods Enzymol 1979; 68: 90-98), Brown EL et al., (Methods Enzymol 1979; 68: 109- 151) the phosphodiester method, Beaucage et al., (Tetrahedron Lett 1981, 22: 1859-1862), the diethylphosphoramidite, and methods such as the solid support method described in EP 0707592. The disclosure of which is hereby incorporated by reference in its entirety) primers and probes of the invention can be prepared by any suitable method, including direct chemical synthesis.

  The detection probes are generally nucleic acid sequences such as, for example, peptide nucleic acids disclosed in International Patent Application WO 92/20702, morpholino analogs described in US Pat. Nos. 5,185,444; 5,034,506 and 5,142,047, or uncharged. Sex nucleic acid analog. If desired, the probe can be “non-extendable” by the inability to add another dNTP to the probe. The analogs themselves are usually non-extendable and the nucleic acid probe can be rendered non-extendable by modification of the 3 'end of the probe such that the hydroxyl group can no longer participate in the extension. For example, the 3 'end of the probe can be functionalized with a capture or detection label to thereby consume or otherwise block the hydroxyl group.

  Any of the polynucleotides of the invention can be made by incorporating any labeling group known in the art as desired to be detectable by spectroscopic, photochemical, biochemical, immunochemical or chemical means. Can be labeled. Further examples include Urdea et al., (Nucleic Acids Research. 11: 4937-4957, 1988) or Sanchez-Pescador et al., (J. Clin. Microbiol. 26 (10): 1934-1938, 1988). Non-radioactive labeling of nucleic acid fragments as described in). In addition, the probes according to the invention can have structural properties that allow signal amplification, such as Urdea et al., (Nucleic Acids Symp. Ser. 24: 197-200, 1991). Or branched DNA probes such as those described in EP 0225807 (Chiron).

  A primer can also be used to capture the primer to facilitate immobilization of a primer extension product such as a primer or amplified DNA on a solid support. The capture label can be a specific binding member (eg, biotin and streptavidin) that binds to the primer or probe and forms a binding pair with the specific binding member of the solid phase reagent. Thus, depending on the type of label carried by the polynucleotide or probe, the target DNA can be captured or detected. Furthermore, the polynucleotides, primers or probes provided herein can themselves be provided as capture labels. For example, if the binding member of the solid phase reagent is a nucleic acid sequence, it can be selected to bind to the complementary portion of the primer or probe, thereby immobilizing the primer or probe to the solid phase. One skilled in the art will recognize that if a polynucleotide probe itself is provided as a binding member, the probe will contain a sequence or “tail” that is not complementary to the target. When the polynucleotide primer itself is provided as a capture label, at least a portion of the primer is free to hybridize with the solid phase nucleic acid. DNA labeling techniques are known to those skilled in the art.

  The probes of the present invention are useful for a number of purposes. These can be used in particular in Southern hybridization to genomic DNA. Probes can also be used to detect PCR amplification products. Other techniques can be used to detect mismatches in CPP-encoding genes or mRNAs.

  Any of the nucleic acids, polynucleotides, primers and probes of the present invention can be conveniently immobilized on a solid support. Solid supports are known to those skilled in the art and include well walls of reaction trays, test tubes, polystyrene beads, magnetic beads, nitrocellulose strips, membranes, microparticles such as latex particles, sheep (or other animal) red blood cells, Includes durasite. The solid support is not critical and can be selected by one skilled in the art. Thus, latex particles, microparticles, magnetic or non-magnetic beads, membranes, plastic tubes, microtiter well walls, glass or silicon chips, sheep (or other animal) erythrocytes and durasite are all suitable examples. Suitable methods for immobilizing nucleic acids on the solid phase include ionic, hydrophobic, covalent interactions and the like. A solid support as used herein refers to any material that is insoluble or can be insolubilized by subsequent reaction. The solid support can be selected for its inherent ability to attract and immobilize the capture reagent. Alternatively, the solid phase can hold yet another receptor that has the ability to attract and immobilize the capture reagent. Yet another receptor includes a charged substance that is oppositely charged with respect to the capture reagent itself or a charged substance bound to the capture reagent. As yet another alternative, the receptor molecule may be any specific binding member bound to a solid support, and this has the ability to immobilize the capture reagent via a specific binding reaction. The receptor molecule allows indirect binding of the capture reagent to the solid support material prior to or during the performance of the assay. Thus the solid phase can be plastic, derivatized plastic, magnetic or non-magnetic metal, test tube glass or silicon surface, microtiter wells, sheets, beads, microparticles, chips, sheep (or other animal) erythrocytes, durasite And other forms known to those skilled in the art. At least 2, 5, 8, 10, 12, 15, 20, or 25 different of the nucleic acids, polynucleotides, primers and probes of the present invention individually on a solid support or on a single solid support It can be bound or immobilized with a group of polynucleotides. In addition, polynucleotides other than those of the present invention can be bound to the same solid support as one or more polynucleotides of the present invention.

  Any polypeptide provided herein can be conjugated at overlapping or random locations on a solid support. Alternatively, the polynucleotides of the invention can be bound to an ordered array that is bound to different regions of the solid support that do not overlap with the binding site of any other polynucleotide. Preferably, such an ordered array of polynucleotides is designed so that well-defined positions are recorded and become “addressable” that can be evaluated as part of the assay procedure. An array of addressable polynucleotides typically comprises a plurality of different oligonucleotide probes attached to the surface of the substrate at different known locations. Knowledge of the exact location of each polynucleotide location makes these “addressable” arrays particularly useful in hybridization assays. Addressable array technology known in the art can be used with the polynucleotides of the invention. One particular embodiment of these polynucleotide arrays is known as Genechip and is generally described in US Pat. No. 5,143,854; PCT Publication Nos. WO 90/15070 and 92/10092, the disclosure thereof. Are all incorporated herein by reference.

In addition to naturally occurring allelic variants of CPP sequences that may be present in a population of methods for obtaining variant nucleic acids and polypeptides , mutations are introduced into the nucleotide sequence encoding CPP, thereby increasing the functional capacity of CPP. Those skilled in the art will appreciate that changes can be introduced into the amino acid sequence of the encoded CPP with or without changes.

  Some types of variants include: 1) one or more amino acid residues are replaced with conservative or non-conservative amino acid residues, and such substituted amino acid residues are encoded by the genetic code 2) one or more amino acid residues containing substituents; or 3) another compound, such as a compound in which the mutated CPP increases the half-life of the polypeptide. Additional amino acids such as those fused to (e.g., polyethylene glycol) or 4) leader, signal or anchor sequences, sequences used to purify the CPP, or sequences derived from precursor proteins are fused to the CPP. It is intended to include: Such variants are considered to be within the scope of those skilled in the art.

  For example, nucleotide substitutions can be made that result in amino acid substitutions in the sequence that do not substantially alter the biological activity of the protein. Amino acid residues can be altered from the wild-type sequence encoding CPP or a biologically active fragment thereof or a homologue thereof without altering the biological activity. In general, amino acid residues shared between CPPs of the present invention are expected to be less susceptible to change.

  In another aspect, the invention relates to nucleic acid molecules encoding CPPs that contain changes in amino acid residues that lead to increased biological activity or modification of biological activity. In another aspect, the invention relates to nucleic acid molecules encoding CPPs that contain changes in amino acid residues that are essential for CPP biological activity. Such CPPs differ in amino acid sequence from SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28, and have reduced activity, or one or more CPP biological activities To display the essential lack of.

  Mutations, substitutions, additions or deletions are made to SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24 by standard techniques such as site-directed mutagenesis and PCR-mediated mutagenesis. -28 can be introduced. For example, conservative amino acid substitutions can be made at one or more predicted non-essential amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. A family of amino acid residues having similar side chains has been defined in the art. These families include basic side chains (eg lysine, arginine, histidine), acidic side chains (eg aspartic acid, glutamic acid), uncharged polar side chains (eg glycine, asparagine, glutamine, serine, threonine, tyrosine, Cysteine), nonpolar side chains (eg alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta branched side chains (eg threonine, valine, isoleucine) and aromatic side chains (eg tyrosine, phenylalanine, tryptophan) , Histidine). Thus, a predicted nonessential amino acid residue of CPP, or a biologically active fragment or homologue thereof, can be replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of the CPP coding sequence, such as by saturation mutagenesis, and the resulting mutant can be CPP biological activity Can be screened to identify variants that retain activity. After mutagenesis of nucleotides encoding one of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28, the encoded protein is randomly expressed and Protein activity can be determined in any suitable assay as provided herein.

  The invention or CPP chimera or fusion protein is also provided. A CPP “chimeric protein” or “fusion protein” as used herein is a CPP of the invention that is operably linked to or fused in-frame to a non-CPP polypeptide sequence. Or a fragment thereof. In a preferred embodiment, the CPP fusion protein comprises at least one biologically active portion of CPP. In yet another preferred embodiment, the CPP fusion protein comprises at least two biologically active portions of CPP. For example, in one embodiment, the fusion protein is a GST-CPP fusion protein in which the CPP domain sequence is fused to the C-terminus of the GST sequence. Such fusion proteins can facilitate the purification of recombinant CPP. In yet another embodiment, the fusion protein is a CPP containing a heterologous signal sequence at its N-terminus, eg, to allow desirable cellular localization in a particular host cell. In yet another embodiment, the fusion is a CPP biologically active fragment and an immunoglobulin molecule. Such fusion proteins are useful, for example, to increase the valence of the CPP binding site. For example, a bivalent CPP binding site can be formed by fusing a biologically active CPP fragment to an IgG Fc moiety.

  In subjects using the CPP fusion proteins of the invention as immunogens, anti-CPP antibodies can be produced, CPP or CPP ligands purified, and CPP modulators identified in screening assays.

  In addition, isolated CPP fragments can be obtained by screening recombinantly produced peptides from corresponding nucleic acid fragments encoding such peptides. In addition, fragments can be chemically synthesized using techniques known in the art, such as conventional Merrifield solid phase f-Moc or t-Boc chemistry. For example, the CPPs of the present invention can be appropriately divided into fragments of a desired length that do not include overlapping fragments, or preferably divided into overlapping fragments of a desired length. Fragments can be generated (either recombinantly or by chemical synthesis) and tested, eg, by microinjection assays or in vitro protein binding assays, to identify those peptidyl fragments that have CPP biological activity. In an illustrative embodiment, a peptidyl portion of a CPP, such as a CPP target binding region, can be tested for CPP activity by expressing it as a thioredoxin fusion protein, each containing a separate fragment of CPP ( See, eg, US Pat. Nos. 5,270,181 and 5,292,646; and PCT Publication No. WO 94/02502, the disclosure of which is hereby incorporated by reference.

  In addition, a library of CPP-encoding sequence fragments can be used to generate a CPP fragment variation-rich population for screening and subsequent selection of CPP variants. In one embodiment, a double-stranded PCR fragment of a CPP-encoding sequence is treated with nuclease to denature the double-stranded DNA and regenerate the DNA under conditions that produce nicking only about once per molecule. Form double stranded DNA that can contain sense / antisense pairs from the resulting product, remove the single stranded portion from the double stranded regenerated by treatment with S1 nuclease, and the resulting fragment live By ligating the library to an expression vector, a library of coding sequence fragments can be generated. By this method, an expression library encoding the N-terminal, C-terminal and internal fragments of various sizes of CPP can be derived.

  Whether a change in the amino acid sequence of a peptide leads to a functional CPP homolog can be readily determined by evaluating at least one CPP biological activity of the various peptides. Peptides with one or more substitutions can be easily tested in the same manner.

Chemical Production of CPP Compositions Peptides of the invention are synthesized by standard techniques (eg, Stewart and Young, Solid Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Company, Rockford, IL, 1984). Preferably, a commercially available peptide synthesizer such as Applied Biosystems, Inc. (Foster City, Calif.) Model 430A is used and convergent synthesis studies such as kent et al., US Pat. No. 6,184,344 and Dawson and Kent, Annu. Rev. Biochem., 69: 923-960 (2000), the polypeptides of the present invention can be assembled from multiple, separately synthesized and purified peptides. Starting from the carboxyl terminal residue and adding amino acids in a stepwise fashion until the entire peptide is formed, the peptides of the invention can be assembled by solid phase synthesis on a crosslinked polystyrene support. The following references provide guidance on the chemistry used during the synthesis: Schnolzer et al., Int. J. Peptide Protein Res., 40: 180-193 (1992); Merrifield, J. Amer. Chem. Soc. 85: 2149 (1963); Kent et al., Peptide 1984, Ragnarsson, Ed. (Almquist and Weksell, Stockholm, 1984) pg185; Kent et al., Peptide Chemistrty 84, Izumiya, Ed. (Protein Research Foundation, BH Osaka, 1985) pg 217; Merrifield, Science 232: 341-347 (1986); Kent, Ann. Rev. Biochem. 57: 957-989 (1988), and references cited in these latter two references. .

  Preferably, the chemical synthesis of the polypeptides of the present invention is performed using the original chemical ligation as described in Dawson et al., Science 266: 776-779 (1994) and Kent et al., US Pat. No. 6,184,344. By assembling peptide fragments according to Briefly, the approach provides an N-terminal cysteine with an unoxidized sulfhydryl side chain to the first peptide fragment and a C-terminal thioester to the second peptide fragment. The non-oxidized sulfhydryl side chain of the N-terminal cysteine is then condensed with the C-terminal thioester to produce an intermediate peptide fragment in which the first and second peptide fragments are linked by a β-aminothioester. Intramolecular reconstitution is then performed on the β-aminothioester of the intermediate peptide fragment to produce a peptide fragment product in which the first and second peptide fragments are linked by amide bonds. Preferably, as described below, a cyclic thiazolidine protecting group protects the N-terminal cysteine of the internal fragment from undesired cyclization and / or ligation reactions. Preferably such cyclic thiazolidine protecting group is a thioprolinyl group.

Peptide fragments having a C-terminal thioester can be generated as described in the following references, which are hereby incorporated by reference: Kent et al., US Pat. No. 6,184,344; Tam et al., Proc. Natl. Acad. Sci. 92: 12485-12489 (1995); Blake, Int. J. Peptide Protein Res., 17: 273 (1981); Cann et al., Tetrahedron Letters, 36: 1217-1220 (1995); Hackeng et al., Proc. Natl. Acad. Sci. 94: 7845-7850 (1997); or Hackeng et al., Proc. Natl. Acad. Sci. 96: 10068-10073 (1999) ). Preferably, the method described in Hackeng et al. (1999) is used. Briefly, in Boc chemistry in situ disclosed in Schnolzer et al., Int. J. Peptide Protein Res., 40: 180-193 (1992), which is hereby incorporated by reference. Peptide fragments are typically synthesized on a solid support (described above) on a 0.25 mmol scale by using the sum / HBTU activation procedure. (HBTU is 2- (1H-benzotriazol-1-yl) -1,1,3,3-tetramethyluronium hexafluorophosphate and Boc is tert-butoxycarbonyl). Each synthesis cycle is treated with solvent-free TFA for 1 to 2 minutes, 1 minute DMF flow wash, 10 to 20 minutes of binding time with 1.0 mmol of Boc-amino acid pre-activated in the presence of DIEA, And N ^α -Boc removal by a second DMF flow wash. (TFA is trifluoroacetic acid, DMF is N, N-dimethylformamide, and DIEA is N, N-diisopropylethylamine). N ^α -Boc amino acid (1.1 mmol) is preactivated with 1.0 mmol of HBTU (0.5 M in DMF) for 3 min in the presence of excess DIEA (3 mmol). After each binding step, measure the free amine remaining in a conventional quantitative ninhydrin assay, for example as disclosed in Sarin et al., Anal. Biochem., 117: 147-157 (1981). Determine the yield. After binding of the Gln residue, before and after deprotection with TFA, a DCM flow wash is used to prevent possible high temperature (TFA / DMF) catalyzed pyrrolidone formation. After chain assembly is complete, the peptide fragment is deprotected and cleaved from the resin by treatment with anhydrous HF with 4% p-cresol as a scavenger for 1 hour at 0 ° C. The imidazole side chain 2,4-dinitrophenyl (dnp) protecting group is left on the His residue because the dnp removal procedure is not compatible with the C-terminal thioester group. However, dnp is gradually removed by thiols during the ligation reaction. After cleavage, the peptide fragment is precipitated with ice-cold diethyl ether, dissolved in aqueous acetonitrile and lyophilized.

It is preferred to synthesize the thioester peptide fragment described above on a trityl-linked mercaptopropionic acid-leucine (TAMPAL) resin made as disclosed in Hackeng et al., (1999) or a comparable protocol. Briefly, N ^α -Boc-Leu (4 mmol) was activated with 3.6 mmol of HBTU in the presence of 6 mmol of DIEA and bound to 2 mmol of p-methylbenzhydrylamine (MBHA) resin, or equivalent for 16 minutes. Let Next, 3 mmol of S-trityl mercaptopropionic acid is activated with 2.7 mmol of HBTU in the presence of 6 mmol of DIEA and bound to Leu-MBHA resin for 16 minutes. After removing the trityl protecting group by treating with 3.5% triisopropylsilane and 2.5% H ₂ O in TFA for 1 minute twice, the resulting TAMPAL resin is used as a starting resin for polypeptide chain assembly. be able to. A thioester bond can be formed with any desired amino acid by using a standard in situ neutralizing peptide binding protocol for 1 hour as disclosed in Schnolzer et al., Cited above. Treatment of the final peptide fragment with anhydrous HF yields a C-terminal activated mercaptopropionic acid-leucine (MPAL) thioester peptide fragment.

  Preferably, a thiozolidine protected thioester peptide fragment intermediate is used in the native chemical ligation under the conditions described in Hackeng et al., (1999), or similar conditions. Briefly, 0.1 M phosphate buffer (pH 8.5) containing 6 M guanidine, 4 (vol / vol)% benzyl mercaptan and 4 (vol / vol)% thiophenol is added to the dry peptide ligated, A final peptide concentration of 1-3 mM is obtained with a reduced pH of about 7 from the lyophilized peptide due to the addition of thiol and TFA. Preferably, the ligation reaction is performed at 37 ° C. in a heating block and periodically vortexed to equilibrate the thiol additive. The reaction can be monitored for degree of completion by MALDI-MS or HPLC and electrospray ionization MS.

  After completing or terminating the original chemical ligation reaction, the N-terminal thiazolidine ring of the product is 37 ° C. at pH 3.5-4.5 with a cysteine deprotecting agent such as O-methylhydroxylamine (0.5M). Ring-opening by treatment for 2 hours followed by a 10-fold excess of tris- (2-carboxyethyl) -phosphine to the reaction mixture and any oxidation reaction prior to purification of the product by conventional preparative HPLC. Reduce ingredients completely. Preferably, fractions containing the ligation product are identified by electrospray MS, pooled and lyophilized.

  After synthesis is complete and the final product is purified, the final peptide product is purified using conventional techniques such as Creighton, Meth. Enzymol., 107: 305-329 (1984); White, Meth. Enzymol. 11: 481-484 (1967); Wetlaufer, Meth. Enzymol., 107: 301-304 (1984); Preferably, the final product is refolded by air oxidation, such as by the following method: reduced lyophilized product in 1 M guanidine hydrochloride (or similar chaotropic agent) (pH 8.6) containing 100 mM Tris, 10 mM methionine. (About 0.1 mg / ml). After gently stirring overnight, the refolded product is isolated by reverse phase HPLC using conventional protocols.

Recombinant expression vectors and host cells The polynucleotide sequences described herein can be used in recombinant DNA molecules that direct expression of the corresponding polypeptide in a suitable host cell. Due to the degeneracy of the genetic code, other DNA sequences can encode equivalent amino acid sequences and can be used for cloning and CPP expression. Preferred codons for a particular host cell can be selected and replaced with naturally occurring nucleotide sequences to increase the rate and / or efficiency of expression. Nucleic acids (eg, cDNA or genomic DNA) encoding the desired CPP can be cloned (DNA amplification) or inserted into a replicable vector for expression. Polypeptides can be expressed recombinantly in any of a number of expression systems by methods known in the art (Ausubel et al., Editors, Currennt Protocols in Molecular Biology, John Wiley & Sons, New York, 1990 ). Suitable host cells include yeast, bacteria, primordial bacteria, fungi, and animal cells including insect and mammalian cells, including primary cells including, but not limited to, stem cells including bone marrow stem cells. More specifically, these include, but are not limited to, recombinant bacteriophages, bacteria transformed with plasmid or cosmid DNA expression vectors, and microorganisms such as yeast transformed with yeast expression vectors. It is done. Also included are recombinant insect viruses (such as baculovirus) and insect cells infected with a mammalian expression system. The expressed nucleic acid sequence can be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site using techniques known in the art. Vector components generally include, but are not limited to, one or more signal sequences, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of a suitable vector containing one or more of these components uses standard ligation techniques known to those skilled in the art.
CPPs of the invention are produced by culturing host cells transformed with an expression vector containing a nucleic acid encoding CPP under conditions suitable to induce or induce protein expression. Appropriate conditions for CPP expression will vary with the choice of expression vector and host cell, as confirmed by those skilled in the art. For example, the use of a constitutive promoter in an expression vector may require routine optimization of host cell growth and proliferation, while the use of an inducible promoter requires appropriate growth conditions for induction. In addition, in some embodiments, the timing of collection is important. For example, the baculovirus system used for insect cell expression is a lytic virus, and the choice of harvest time is important for the resulting product.

  A host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the protein include, but are not limited to, glycosyl, acetyl, phosphate, amide, lipid, carboxyl, acyl or carbohydrate groups. Post-translational processing that cleaves the “prepro” form of the protein may also be important for correct insertion, folding and / or function. Illustratively, host cells such as CHO, HeLa, BHK, MDCK, 293, W138, etc. have specific cellular mechanisms and characteristic mechanisms for such post-translational activity, and of introduced foreign proteins Selection can be made to ensure precise modification and processing. Of particular interest are Drosophila melanogaster cells, budding yeast and other yeasts, E. coli, Bacillus subtilis, SF9 cells, C129 cells, 293 cells, Panchabi, BHK, CHO, COS and HeLa cells, fibroblasts, Schwannoma cell lines, immortal cells Mammalian mammalian bone marrow and lymphoid cell lines, Jurkat cells, human cells and other primary cells.

  A nucleic acid encoding a CPP must be “operably linked” by placing it in a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to the DNA of the polypeptide when expressed as a preprotein that participates in the secretion of the polypeptide; If it affects transcription, it is operably linked to the coding sequence; or if the ribosome binding site is located so as to facilitate translation, it is operably linked to the coding sequence. Yes. In general, DNA sequences that are “operably linked” are in close proximity, and in the case of a secretory leader or other polypeptide sequence, are in close proximity and in the reading phase. However, enhancers do not have to be close. Ligation is achieved by ligation at convenient restriction sites. If such sites do not exist, synthetic oligonucleotide adapters or linkers are used according to convention. The promoter sequence encodes either a constitutive or inducible promoter. The promoter can be either a naturally occurring promoter or a hybrid promoter. Hybrid promoters that combine elements of one or more promoters are also known in the art and are useful in the present invention. The expression vector can further comprise additional elements, for example the expression vector can be a two replication system, thus in two organisms, for example mammalian or insect cells for expression and for cloning and amplification. It will be possible to maintain it in a prokaryotic host. Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from plasmid pBR322 is suitable for most gram-negative bacteria; 2: the plasmid origin is suitable for yeast, and the various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are mammalian cells. It is useful as a cloning vector. Furthermore, to incorporate an expression vector, the expression vector contains at least one sequence homologue to the host cell genome, and preferably two homologous sequences that flanking the expression construct. The integrating vector can be directed to a specific location in the host cell by selecting appropriate homologous sequences for vector encapsulation. The construction of integrative vectors is known in the art. In yet another embodiment, the heterologous expression control element can be operably linked to an endogenous gene of the host cell by homologous recombination (described in US Pat. Nos. 6,410,266 and 6,361972, the disclosure of which is All of which are incorporated herein by reference). While this technique allows expression to be controlled to the desired level with selected control elements, it ensures proper processing and modification of the CPP endogenously expressed by the host cell. Useful heterologous expression control elements include, but are not limited to, CMV immediate early promoter, HSV thymidine kinase promoter, early and late SV40 promoters, promoters of retroviral LTRs such as the Rous sarcoma virus (RSV) promoter, and A metallothionein promoter is mentioned.

  Preferably, the expression vector contains a selectable marker gene that allows for selection of transformed host cells. Selection genes are known in the art and will vary with the host cell used. Expression and cloning vectors typically contain a selection gene, also termed a selectable marker. Typical selection genes confer resistance to (a) antibiotics or other toxins such as ampicillin, neomycin, methotrexate or tetracycline; (b) compensate for auxotrophy deficiencies; or (c) essential nutrients not available from complex media For example, Neisseria gonorrhoeae is supplied with a gene encoding D-alanine racemase; it encodes a protein.

  Host cells transformed with a nucleotide sequence encoding CPP can be cultured under conditions suitable for expression and recovery of the encoded protein from cell culture. Depending on the sequence and / or vector used, the protein produced by the recombinant cell can be secreted, membrane bound, or contained within the cell. As will be appreciated by those skilled in the art, expression vectors containing polynucleotides encoding CPPs can be designed with signal sequences that direct secretion of CPPs through prokaryotic or eukaryotic cell membranes. The desired CPP can be produced not only directly but also recombinantly as a fusion polypeptide with a heterologous polypeptide, which is a specific cleavage site at the N-terminus of the signal sequence or mature protein or polypeptide. Other polypeptides having In general, the signal sequence may be a component of the vector, or it may be a part of the CPP-encoding DNA that is inserted into the vector. The signal sequence may be, for example, a prokaryotic signal sequence selected from the group of alkaline phosphatase, penicillinase, lpp, or thermostable enterotoxin II leader. For yeast secretion, the signal sequence can be, for example, a yeast invertase leader, an alpha factor leader (Saccharomyces and Kluyveromyces a factor leader, the latter as described in US Pat. No. 5,010,182), or an acid phosphatase leader, Candida albicans glucoamylase leader (1990). The signal described in European Patent No. 362179 published on April 4, 1990) or WO9113646 published on November 15, 1990 may be used. For mammalian cell expression, mammalian signal sequences, such as signal sequences from secreted polypeptides of the same or related species, and viral secretion leaders can be used to direct protein secretion. Depending on the chosen expression system, the coding sequence is inserted into an appropriate vector, which in turn requires the presence of certain characteristic “control elements” or “regulatory sequences”. Appropriate constructs are generally known in the art (Ausubel, et al., 1990) and in many cases Invitrogen (San Diego, Calif.), Stratagene (La Jolla, Calif.), Gibco BRL (Rockville , Md.) Or Clontech (Palo Alto, Calf.).

Expression in bacterial systems Transformation of bacterial cells can be achieved using an inducible promoter such as the hybrid lacZ promoter of “BLUESCRIPT” Phagemid (Stratagene) or “pSPORT1” (Gibco BRL). In addition, cleavage that can be easily detected and / or purified, including but not limited to “BLUESCRIPT” (a-galactosidase; Stratagene) or pGEX (glutathione S-transferase; Promega, Madison, Wis.). A number of expression vectors can be selected for use in bacterial cells to produce possible fusion proteins. A suitable bacterial promoter is any nucleic acid sequence capable of binding bacterial RNA polymerase and initiating downstream (3 ′) transcription of the coding sequence of the CPP gene into mRNA. Bacterial promoters usually have a transcription initiation region located proximal to the 5 ′ end of the coding sequence. This transcription initiation region typically includes an RNA polymerase binding site and a transcription initiation site. Sequences encoding metabolic pathway enzymes provide particularly useful promoter sequences. Examples include promoter sequences derived from sugar metabolizing enzymes such as galactose, lactose and maltose, and sequences derived from biosynthetic enzymes such as tryptophan. Promoters derived from bacteriophages can also be used and are known in the art. In addition, synthetic promoters and hybrid promoters are also useful; for example, the tat promoter is a hybrid of trp and lac promoter sequences. In addition, bacterial promoters can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA polymerase and initiate transcription. An efficient ribosome binding site is also desirable. Expression vectors can also include a signal peptide sequence that provides for secretion of CPP in bacteria. The signal sequence typically encodes a signal peptide consisting of hydrophobic amino acids directed to secrete the protein from the cell, as is known in the art. Proteins are secreted either in the growth medium (gram positive bacteria) or in the periplasmic space located between and outside the cell membrane (gram negative bacteria). Bacterial expression vectors can also include a selectable marker gene that allows for selection of the bacterial strain being transformed. Suitable selection genes include drug resistance genes such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline. Selectable markers can also include biosynthetic genes such as genes for histidine, tryptophan and leucine biosynthetic pathways. For example, if large amounts of CPP are required for antibiotic induction, vectors that direct high level expression of fusion proteins that are easily purified are desirable. Such vectors include, but are not limited to, BLUESCRIPT, in which the CPP coding sequence can be ligated to the vector in frame with a sequence of 7 residues of amino-terminal Met and beta-galactosidase to produce a hybrid protein. Multifunctional E. coli cloning and expression vectors such as (Stratagene); PIN vectors (Van Heeke & Schuster J Biol Chem 264: 5503-5509 (1989)); PET vectors (Novagen, Madison Wis.); Expression vectors for bacteria contain the various components indicated above and are known in the art. Examples include, inter alia, Bacillus subtilis, E. coli, Streptococcus cremoris, and Streptococcus lividans vectors. Bacterial expression vectors are transformed into bacterial host cells using techniques known in the art such as calcium chloride mediated transfection, electroporation and the like.

Expression systems in yeast Examples include Schizosaccharomyces pombe and Yarrowia lipolytica. Examples of suitable promoters for use in yeast hosts include 3-phosphoglycerate kinase promoter (Hitzeman et al., J. Biol. Chem. 255: 2073 (1980)) or enolase, glyceraldehyde-3-phosphate Dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triose phosphate isomerase, phosphoglucose isomerase, alpha factor, ADH21GAPDH promoter, glucokinase alcohol Oxidases and other glycolytic enzymes such as PGH (Hess et al., J. Adv. Enzyme Reg. 7: 149 (1968); Holland, Biochemistry 17: 4900 (1978)). See, for example, Ausubel et al., 1990; Grant et al., Methods in Enzymology 153: 516-544 (1987). Other inducible yeast promoters have additional transcriptional benefits controlled by growth conditions, including alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradation enzymes related to nitrogen metabolism, metallothionein, glyceraldehyde-3- Examples include phosphate dehydrogenase and the promoter region of enzymes that contribute to maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73657. ADE2 that confers resistance to tunicamycin as a yeast selectable marker. HIS4. LEU2. TRP1. And the ALG7; neomycin phosphotransferase gene that confers resistance to G418; and the CUP1 gene that allows yeast to grow in the presence of copper ions. Yeast expression vectors for intracellular production or secretion of CPP from DNA encoding the CPP of interest can be constructed. For example, a selected signal peptide and an appropriate constitutive or inducible promoter can be inserted into an appropriate restriction site of a selected plasmid for direct intracellular expression of CPP. For secretion of CPP, DNA encoding CPP in selected plasmid, DNA encoding promoter, yeast alpha factor secretion signal / leader sequence, and linker sequence (if necessary) for expression of CPP Can be cloned together. Yeast cells can then be transformed with the expression plasmid described above and cultured in a suitable fermentation medium. The protein produced by such transformed yeast can then be concentrated by precipitation with 10% trichloroacetic acid and analyzed after separation by SDS-PAGE and staining of the gel with Coomassie blue dye. Recombinant CPP can subsequently be isolated and purified from the fermentation medium by techniques known to those skilled in the art.

Expression in mammalian systems CPPs can be expressed in mammalian cells. Mammalian expression systems are known in the art and include retroviral vector-mediated expression systems. Transfect mammalian host cells with any of a number of different viral-based expression systems, such as adenovirus, that can ligate the coding region to an adenovirus transcription / translation complex consisting of the late promoter and tripartite leader sequence. Can be converted. Insertion in the non-essential E1 or E3 of the viral genome results in a live virus capable of expressing the polypeptide of interest in the infected host cell. Preferred expression vector systems are retroviral vector systems as generally described in PCT / US97 / 01019 and PCT / US97 / 101048. Suitable mammalian expression vectors contain a mammalian promoter that is any DNA sequence capable of binding mammalian RNA polymerase and initiating downstream (3 ') transcription of the CPP coding sequence into mRNA. . A promoter has a transcription start region, usually located proximal to the 5 'end of the coding sequence, and a TATA box, using 25-30 base pairs located upstream of the transcription start site. The TATA box is thought to cause RNA polymerase II to initiate RNA synthesis at the correct site. Mammalian promoters also typically contain an upstream promoter element (enhancer element) located within 100 to 200 base pairs upstream of the TATA box. The upstream promoter element determines the ratio at which transcription is initiated and can act in either direction. Particularly useful as mammalian promoters are those derived from mammalian viral genes, since viral genes are often highly expressed and have a broad host range. Illustratively, polyoma virus, fowlpox virus (UK 2211504 published July 5, 1989), adenovirus (such as adenovirus 2), bovine papilloma virus, provided that such promoters are compatible with the host cell system. From the genomes of viruses such as avian sarcoma virus, cytomegalovirus, retrovirus, hepatitis B virus and simian virus 40 (SV40), from heterologous mammalian promoters such as actin promoters or immunoglobulin promoters, and heat shock promoters Promoters obtained from Transcription of DNA encoding CPP by higher eukaryotic cells can be increased by inserting an enhancer sequence into the vector. An enhancer is a cis-acting element of about 10 to 300 bp of DNA that acts on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globulin, elastase, albumin, a-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer, the cytomegalovirus early promoter enhancer, the late origin of replication polyoma enhancer, and the adenovirus enhancer. The enhancer is preferably located 5 'from the promoter. In general, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3 'to the translation stop codon, and thus flanking the coding sequence together with the promoter element. The 3 ′ end of the mature mRNA is formed by site-specific post-translational cleavage and polyadenylation. Examples of transcription terminators and polyadenylation signals include those derived from SV40. Long-term, high-yield production of recombinant proteins can be performed in a stable expression system. Expression vectors containing a viral origin of replication or endogenous expression element and a selectable marker gene can be used for this purpose. Suitable vectors containing selectable markers for use in mammalian cells are readily available commercially and are known to those skilled in the art. Examples of such selectable markers include, but are not limited to, herpes simplex virus thymidine kinase and adenine phosphoribosyltransferase for use in tk- or hprt-cells, respectively. Methods for introducing exogenous nucleic acid into mammalian hosts and other hosts are known in the art and will vary with the host used. Techniques include dextran-mediated transfection, calcium phosphate precipitation, polybrene-mediated transfection, protoplast fusion, electroporation, viral infection, encapsulation of polynucleotide (s) in liposomes, and direct microinjection of DNA into the nucleus .

CPP can be purified from the culture supernatant of mammalian cells that have been transformed transiently or stably with an expression vector carrying a CPP coding sequence. Preferably, CPP is purified from the culture supernatant of COS7 cells transiently transfected with a pcD expression vector. Transfection of COS7 cells with pcD proceeds as follows: Approximately 10 ⁶ COS7 monkey cells one day prior to transfection were treated with Dulbecco's Modified Eagle Medium (DEM) containing 10% fetal calf serum and 2 mM glutamine. ) On individual 100 mm plates. To perform the transfection, the medium is aspirated from each plate and replaced with 4 ml of DME containing 50 mM Tris HCl (pH 7.4), 400 mg / ml DEAE-dextran and 50 μg of plasmid DNA. Plates are incubated for 4 hours at 37 ° C., then the DNA-containing medium is removed and washed twice with 5 ml of serum-free DME. DME is added to the original plate, which is then incubated for an additional 3 hours at 37 ° C. The plate is washed once with DME, followed by the addition of DME containing 4% fetal calf serum, 2 mM glutamine, penicillin (100 U / l) and streptomycin (100 μg / l) at standard concentrations. The cells are then incubated at 37 ° C. for 72 hours, after which the growth medium is collected for CPP purification. Plasmid DNA for transfection may be pcD (SRα) or a similar expression vector containing CPP-encoded cDNA insert, E. coli MC1061 (Casadaban and Cohen, J. Mol. Biol. 138: 179-207 (1980)) or It can be obtained by growing in similar organisms. Plasmid DNA is cultured by standard techniques such as Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition (Cold Spring Harbor Laboratory, New York, 1989) or Ausubel et al., (1990, cited above). Isolated from the product.

Insect cell expression CPPs can also be produced in insect cells. Expression vectors for insect cell transformation, and in particular baculovirus-based expression vectors, are known in the art. In one such system, CPP-encoding DNA is fused upstream of an epitope tag contained within a baculovirus expression vector. An exogenous gene is expressed in Spodoptera frugiperda Sf9 cells or Trichopulcia larvae using Autographa californica nuclear polyhedrosis virus (AcNPV) as a vector. The CPP coding sequence is cloned into a nonessential region of the virus such as the polyhedrin gene and placed under the control of the polyhedrin promoter. Sequential insertion of the CPP coding sequence inactivates the polyhedrin gene and generates a recombinant virus that lacks the outer shell of the outer shell protein. The recombinant virus is then used to infect Spodoptera frugiperda cells or Trichopulcia larvae expressing CPP (Smith et al., J. Wol. 46: 584 (1994); Engelhard EK et al., Proc. Natl Acad. Sci. 91: 3224-3227 (1994)). Suitable epitope tags for fusing to CPP-encoded DNA include poly-his tags and immunoglobulin tags (similar to the Fc region of IgG). Various plasmids can be used, including commercially available plasmids such as pVL1393 (Novagen). Briefly, CPP-encoding DNA or a desired portion of CPP-encoding DNA is amplified by PCR using primers complementary to the 5 ′ and 3 ′ regions. The 5 ′ primer can incorporate flanking restriction sites. The PCR product is then digested with selected restriction enzymes and subcloned into an expression vector. Using Lipofectin (commercially available from GIBCO-BRL) or other methods known to those skilled in the art, the plasmid and BaculoGold ™ viral DNA (Pharmingen) can be transformed into Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 1711) Recombinant baculoviruses are produced by co-transfecting with. Virus is produced by culture in Sf9 cells at 28 ° C. for 4-5 days and used for further amplification. Procedures as described further in O'Reilley et al., BACULOVIRUS EXPRESSION VECTORS: A LABORATORY MANUAL, Oxford University Press (1994) are performed. Extracts can be prepared from recombinant virus-infected Sf9 cells as described in Rupert et al., Nature 362: 175-179 (1993). Alternatively, epitope-tagged CPP expressed by affinity chromatography can be purified, or IgG-tagged (or Fc-tagged) CPP using, for example, chromatographic techniques including protein A or protein G column chromatography Can be purified.

Assessment of gene expression , eg, Northern blotting, dot blotting (DNA or DNA blotting) to determine mRNA transcription using standard techniques known to those skilled in the art, eg, appropriate labeled probes based on the sequences provided herein. RNA) or in situ hybridization can directly assess gene expression in a sample. Alternatively, antibodies are used in assays for the detection of nucleic acids such as polypeptides, DNA duplexes, RNA duplexes, and specific duplexes including DNA-RNA hybrid duplexes or DNA-protein duplexes be able to. Such an antibody is labeled and an assay is performed in which the duplex is bound to the surface so that when a duplex is formed on the surface, the presence of the antibody bound to the duplex can be detected. be able to. Alternatively, gene expression can be measured by immunohistochemical staining of cells or tissue sections and cell culture or body fluid assays to directly assess CPP polypeptide or polynucleotide expression. Antibodies useful for such immunological assays can be either monoclonal or polyclonal and can be prepared against the original sequence CPP. Protein levels can also be detected by mass spectrometry. Another method of protein detection uses a protein chip.

Purification of Expressed Protein Expressed CPP can be purified or isolated after expression using any of a variety of methods known to those skilled in the art. The appropriate technique will vary depending on what other components are present in the sample. Contaminant components removed by isolation or purification are materials that typically interfere with the diagnostic or therapeutic use of the polypeptide and can include enzymes, hormones and other solutes. The purification step (s) selected will depend, for example, on the production method used and the nature of the particular CPP produced. Since CPP is secreted, it can be recovered from the culture medium. Alternatively, CPP can be recovered from the host cell lysate. If membrane bound, it can be released using a suitable detergent solution (eg Triton-X 100) or by enzymatic cleavage. Alternatively, the cells used for CPP expression can be disrupted by various physical or chemical means such as repeated freeze-thaw, sonication, mechanical disruption, or by the use of cytolytic agents. Examples of purification methods include, but are not limited to, ion exchange column chromatography; chromatography using silica gel or a cation exchange resin such as DEAE; gel filtration using eg Sephadex G-75; contaminants such as IgG Protein A Sepharose column to remove E. coli; chromatography using metal chelate column to bind to epitope-tagged form of CPP; ethanol precipitation; reverse phase HPLC; chromatofocusing; SDS-PAGE; and ammonium sulfate precipitation . Usually, an isolated CPP is prepared by at least one purification step. For example, CPP can be purified using a standard anti-CPP antibody column. Ultrafiltration and dialysis techniques combined with protein concentration are also useful (see, eg, Scopes, R., PROTEIN PURIFICATION, Springer-Verlag, New York, NY, 1982). The degree of purification required will vary depending on the CPP application. In some cases, no purification is necessary. Once expressed and, if necessary, purified, the CPPs and nucleic acids of the invention are useful in many applications as detailed below.

Transgenic animals Transgenic animals other than humans can also be produced using the host cells of the present invention. For example, in one embodiment, the host cell of the invention is a fertilized egg cell or embryonic stem cell into which a CPP coding sequence has been introduced. Such host cells can then be used to create non-human transgenic animals in which the exogenous CPP sequence has been introduced into the genome, or homologous recombinant animals in which the endogenous CPP sequence has been altered. Such animals are useful for studying the function and / or activity of CPP or fragments thereof, and for identifying and / or evaluating modulators of CPP biological activity. A “transgenic animal” as used herein is a non-human animal, preferably a mammal, more preferably a rat or mouse, in which one or more animal cells contain the transgene. Like rodents. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians and the like. A transgene is an exogenous DNA that is integrated into the genome of a cell from which a transgenic animal develops and remains in the genome of a mature animal, thereby coding in one or more cell types or tissues of the transgenic animal. Directs the expression of chemical gene products. “Homologous recombinant animal” as used herein refers to an endogenous gene and an exogenous DNA molecule introduced into an animal cell, eg, an animal embryo cell, prior to animal development. It is a non-human animal, preferably a mammal, more preferably a mouse, whose endogenous gene has been changed by homologous recombination between them.

  By introducing fertilized egg cells of a CPP-encoding nucleic acid into the male pronucleus, for example by microinjection or retroviral infection, and allowing egg cells to develop in pseudopregnant female foster animals, Can be created. CPP cDNA sequences or fragments thereof can be introduced into the genome of non-human animals as a transgene. Alternatively, non-human homologues of human CPP-encoding genes, such as those derived from mice or rats, can be used as transgenes. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. Tissue specific regulatory sequence (s) can be operably linked to the CPP transgene to direct expression of CPP to specific cells. Methods for generating transgenic animals, particularly animals such as mice, via embryo manipulation and microinjection have become routine in the art, and are both U.S. Pat. 4736866 and 4870009, U.S. Pat. No. 4,873,191 by Wagner et al., And Hogan, B., Manipulating the Mouse Embryo (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1986, all of which is expressly cited) In the present specification))). Similar methods are used for the production of other transgenic animals. A transgene founder can be identified based on the presence of a CPP transgene in its genome and / or expression of CPP mRNA in an animal tissue or cell. The transgene founder can then be used to breed additional animals carrying the transgene. In addition, transgenic animals carrying a transgene encoding CPP can be further bred to other transgenic animals carrying other transgenes.

  In order to create an animal in which the desired nucleic acid has been introduced into the genome by homologous recombination, whereby deletions, additions or substitutions have been introduced to alter, eg functionally disrupt, the CPP coding sequence; A vector containing at least a portion of the CPP coding sequence is prepared. The CPP coding sequence may be a human gene, but more preferably is a non-human homologue of the human CPP coding sequence (eg, a cDNA having a nucleotide sequence encoding CPP isolated by stringent hybridization). For example, a mouse CPP coding sequence can be used to construct a homologous recombination vector suitable for altering an endogenous gene in the mouse genome. In a preferred embodiment, the vector is designed to functionally disrupt the endogenous CPP coding sequence upon homologous recombination (ie, no longer encode a functional protein; also referred to as a “knockout” vector). Alternatively, the endogenous CPP coding sequence is mutated or otherwise altered during homologous recombination, but still encodes a functional protein (eg, changes the upstream regulatory region, thereby changing the endogenous CPP coding Design a vector that alters the expression of the expression sequence. In homologous recombination vectors, the altered portion of the CPP coding sequence is flanked at its 5 ′ and 3 ′ ends by additional nucleic acid sequences of the CPP gene, and the exogenous sequences carried by the vector and the endogenous of embryonic stem cells. Allows homologous recombination to occur with the gene. The added flanking nucleic acid sequence is long enough for successful homologous recombination with the endogenous gene. Typically, several kilobases of flanking DNA (both 5 'and 3' ends) are included in the vector (eg Thomas, KR and Capecchi, MR (1987) Cell 51: 503 (description of homologous recombination vectors). The disclosure of which is incorporated herein by reference))). The vector is introduced into an embryonic stem cell line (eg by electroporation) and cells in which the introduced CPP coding sequence is homologously recombined with the endogenous gene (eg Li, E. et al., ( 1992) Cell 69: 915 (the entire disclosure of which is hereby incorporated by reference)). The selected cells are then injected into animal (eg, mouse) blastocysts to form aggregate chimeras (eg, Bradley, A. Teratocarcinomas and Embryonic Stem Cells. A Practical Approach, EJ Robertson ed. (IRL, Oxford, 1987). ) 113-152 (the entire disclosure of which is hereby incorporated by reference)). The chimeric embryo is then transferred into a suitable pseudopregnant female foster animal and the fetus is born. Using progeny harboring DNA homologously recombined in germ cells, it is possible to breed animals in which all cells of the animal contain the homologous recombinant DNA by germline transmission of the transgene. Methods for constructing homologous recombination vectors and homologous recombination animals are described in Bradley, A. (1991) Current Opinion in Biotechnology 2: 823-829 and Le Mouellec et al., PCT International Publication No. WO 90/11354; Smithies et al., WO 91/01140; Zijlstra et al., WO 92/0968 and Berns et al., WO 93/04169, all of which are incorporated herein by reference. Part.

  In another embodiment, non-human transgenic animals can be generated that contain selected systems that allow for regulated expression of the transgene. An example of such a system is the cre / loxP recombinase system of bacteriophage P1. For a description of the cre / loxP recombinase system, see for example Lakso et al., (1992) PNAS 89: 6232-6236, the entire disclosure of which is hereby incorporated by reference. Another example of the recombinase system is the FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al., (1991) Science 251: 1351-1355, the entire disclosure of which is hereby incorporated by reference) . If the cre / loxP recombinase system is used to regulate transgene expression, animals containing the transgene encoding both the Cre recombinase and the selected protein are required. For example, constructing a “double” transgenic animal by crossing two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase Can provide such animals.

Assessing CPP activity It will be appreciated that the present invention further provides methods for testing or obtaining the activity of functional fragments and variants of CPP and CPP sequences. Such a method involves providing a variant or modified CPP-encoding nucleic acid and assessing whether the encoded polypeptide displays CPP biological activity. Thus, methods for assessing the function of a CPP include: (a) providing the CPP or a biologically active fragment or homologue thereof; and (b) the CPP or biologically under conditions suitable for CPP activity. Testing the active fragment or homologue thereof for CPP biological activity. Cell-free, cell-based and in vivo assays can be used to test CPP activity. For example, the assay can include expressing a CPP nucleic acid in a host cell and observing CPP activity in the cell and other affected cells. In another example, CPP or a biologically active fragment or homologue thereof is contacted with a cell and CPP biological activity is observed.

  For CPP biological activity: (1) the individual has or indicates that the cardiovascular disorder is present; (2) circulates through the blood stream of the individual having the cardiovascular disorder; (3) For antigenicity, ie the ability to bind to an anti-CPP-specific antibody; (4) immunogenicity, ie the ability to make an anti-CPP-specific antibody; and for CPP2: (5) interact with a CPP target protein, preferably a lipase (6) Stabilize the active site of lipase; (7) Increase lipase activity; (8) Interact with CPP target molecules such as phospholipids, micelles or triglycerides; and (9 ) Forming at least one disulfide bond; for CPP9: (5) intramolecular amino acids such as hydrogen, amide, or especially disulfide bonds Forming acid side chain interactions; (6) interactions with CPP target molecules, preferably RNA molecules or virions (such as respiratory syncytial virus or RSV); (7) antiviral activity, and (8 ) Hydrolysis of RNA phosphodiester bonds; for CPP21: (5) forming intramolecular amino acid side chain interactions such as hydrogen, amide, or preferably disulfide bonds; and (6) CPP target molecules, especially Interacting with cholesterol; for CPP17: (5) forming intramolecular amino acid side chain interactions such as hydrogen, amide, or preferably disulfide bonds; (6) CPP target molecules, preferably low density lipoproteins Interaction with proteins or bacterial endotoxins; (7) neutralizing bacterial endotoxins; (8) promoting mast cell chemotaxis; (9) undergoing post-translational processing, eg, specific proteolysis; (10) functioning as an antimicrobial defense; and (11) contraction of smooth muscle cells. As well as for CPP20: (5) forming intramolecular amino acid side chain interactions such as hydrogen, amide, or preferably disulfide bonds; (6) like CPP target molecules, especially plasminogen Interacting with a novel kringle domain-containing peptide; and (7) reducing tumor growth.

  CPP biological activity can be assayed by any suitable method known in the art. Antigenicity and immunogenicity can be detected, for example, as described in the sections entitled “Anti-CPP antibodies” and “Use of CPP antibodies”. Circulation in plasma can be detected as described in “Diagnostic and Prognostic Applications”. For example, in the section entitled “Drug Screening Assays”, interaction with a CPP target molecule can be detected by any of the methods described herein.

  Determination of the ability of a CPP to bind or interact with a CPP target molecule can be accomplished by methods for determining binding directly or indirectly as is common in the art. Such methods may be cell based (eg, detecting binding to membrane bound CPP) or cell free. The binding of a CPP or biologically active portion thereof to its cognate target molecule can be determined, for example, by detecting the labeled CPP or biologically active portion of the complex, eg CPP Alternatively, the interaction of the test compound with CPP can be detected by binding the biologically active moiety to a labeling group. For example, the degree of complex formation can be measured by immunoprecipitation of the complex or by performing gel electrophoresis. Determination of the ability of a CPP to bind to a CPP target molecule can also be accomplished using techniques such as real time biomolecular interaction analysis (BIA). Sjolander, S. and Urbaniczky, C. (1991) Anal. Chem. 63: 2338-2345 and Szabo et al., (1995) Curr. Opin. Struct. Biol. 5: 699-705 As a part of this specification). “BIA”, as used herein, is a technique for studying biospecific interactions in real time that does not label any interactors (eg, BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indicator of real-time reactions between biological molecules.

  For CPP2, lipase activity can be determined by any assay that can detect a lipase-catalyzed hydrolysis reaction. For example, a decrease in the amount of substrate in the test sample, or alternatively, an increase in the amount of product can be measured. A preferred assay is described by Panteghini, et al., (Ann Clin Biochem (2001) 38: 365-370, the entire disclosure of which is hereby incorporated by reference). Briefly, a chromogenic substrate, DGGR, is provided with lipase, bile salts, calcium and colipase in the assay mixture. The lipase activity of the substrate is measured by detecting the formation of the chromophore product methylresorufin at 580 nm. Ideally, the lipase activity is measured in order to stabilize the lipase active site and detect the biological activity of the CPP that increases lipase activity. An example of such a method comprises the steps of: contacting a biological sample with an assay mixture of chromogenic substrate and lipase under conditions appropriate for the activity of lipase; and detecting lipase activity. Preferably, the biological sample is plasma, more preferably plasma from an individual suspected of having a cardiovascular disorder. CPP activity is indicated by an increase in lipase activity when compared to a suitable negative control.

  For CPP9, RNase activity can be assayed by the following illustrative technique. The enzyme was buffer B (1 mM reduced glutathione (Sigma Chemical Co., St Louis, Mo.), 0.5 mM oxidized glutathione, 0.1 mM DTT, 0.5 mM Tris HCl 8.2, 0.01 mM EDTA and 0.1 mM urea. Incubate for 15 minutes at 37 ° C. with 1 ug of yeast tRNA (Sigma) as substrate. Electrophoresis is performed on a 1.5% agarose gel in 0.09 mM Tris-phosphate, 0.002 mM EDTA, and 0.5 μg / ml ethidium bromide. Visualize RNA by UV. RNase activity eliminates full-length RNA. Alternatively, RNase activity can be detected spectrophotometrically. Briefly, the concentration of perchlorate-soluble ribonucleotides made from acid-insoluble yeast tRNA (Sigma) with a given amount of RNase in 40 mM sodium phosphate (pH 7.5) buffer was measured spectrophotometrically at 260 nm. taking measurement. For example, an RNase-containing sample corresponding to approximately 100 mM recombinant RNase is added in a 0.8 ml reaction volume with 10 μl of 4 mg / ml yeast tRNA. An increase in RNase activity results in a decrease in the 260 nm value.

For CPP9, antiviral activity can be detected as follows. Briefly, various concentrations of CPP9-containing samples (or buffer control), virions (2-5 × 10 6) in culture medium (Iskov modified Dulbecco medium containing 10% heat-inactivated fetal calf serum and 2 mM glutamine). Add directly to the suspension containing ³ infectious units / ml) and incubate at room temperature with gentle rotation. After 2 hours of incubation, 200 μl of suspension is present in a confluent monolayer (3-4 × 10 ⁵ cells / monolayer) on a coverslip in a 1 drum shell vial (Viromed, Minneapolis, Minn.). Infect target cells (in the case of respiratory syncytial virus, human respiratory epithelial HEp-2 cells). After spin growth (700 g at 22 ° C.) and incubation for 16 hours (37 ° C., 5% CO ₂ ), primary infected cells were immunized by immunofluorescence staining (mouse anti-RSV blend, FITC labeling; Chemicon International, Temencula, Calif.). Identify. Data are expressed as infectious units ± SD.

For CPP 17, the interaction with LDL particles should be detected according to the method of Higazi, et al., Blood 96: 1393-1398 (2000), the relevant disclosure of which is incorporated herein by reference. Can do. Briefly, the peptide of interest was labeled with radioactive iodine. LDL or BSA control (10 nM) was incubated with 0-5 uM ¹²⁵ I-defensin for 1 hour at 37 ° C. The mixture was applied to a polyacrylamide gel and the amount of radioactivity in the appropriate molecular weight fraction was recorded. Specific LDL binding was defined by an increase in the amount of radioactive peptide bound to LDL compared to BSA. Antimicrobial activity can be detected according to any method known in the art, such as the method described in Porter et al., (Infect. Immun. 65: 2396-2401 (1997)). Briefly, Listeria monocytogenes EGD, E. coli ML35p, Salmonella typhimurium 14028S and 7953S, and Candida albicans 820 are used. Bacterial cultures are collected at mid-growth, washed and resuspended at a dilution of 10 ⁶ bacteria / ml in 10 mM sodium phosphate (pH 7.4), 1% Trypticase Soy Broth. Collect Candida albicans in the same manner but isolated in the stationary phase. Colony forming unit (CFU) assays and radial diffusion assays are performed as described in the presence of test compounds, positive control compounds, or in the absence of compounds. A decrease in the value obtained in either the CFU or radial diffusion assay in the presence of the test compound compared to the compound-free control indicates that the compound has antimicrobial activity.

  For CPP2, CPP9, CPP17, CPP20 and CPP21, intramolecular interactions can be detected by sequence-based structure prediction. Such predictions are generally based on X-ray crystallography or NMR structural data for polypeptides having similar sequences. Detection of intramolecular interactions can also be achieved using SDS-PAGE. For the example of disulfide bonds, the linkage formed between different parts of a given protein leads to a more compact protein, and thus a decrease in apparent molecular weight. Disulfide bonds can be broken by reducing agents such as dithiothreitol (DTT). Thus, a change in apparent molecular weight can be detected by comparing a protein sample treated with a reducing agent by SDS-PAGE to an untreated control. Such methods are common in the art.

For CPP17, antimicrobial activity can be detected according to methods known in the art, such as the method described in Porter, et al., (Infect. Immun. 65: 2396-2401 (1997)). Briefly, Listeria monocytogenes EGD, E. coli ML35p, Salmonella typhimurium 14028S and 7953S, and Candida albicans 820 are used. Bacterial cultures are collected at mid-growth, washed and resuspended at a dilution of 10 ⁶ bacteria / ml in 10 mM sodium phosphate (pH 7.4), 1% Trypticase Soy Broth. Collect Candida albicans in the same manner but isolated in the stationary phase. Colony forming unit (CFU) assays and radial diffusion assays are performed as described in the presence of test compounds, positive control compounds, or in the absence of compounds. A decrease in the value obtained in either the CFU or radial diffusion assay in the presence of the test compound compared to the compound-free control indicates that the compound has antimicrobial activity.

  For CPP17, specific proteolysis can be detected by comparing the molecular weight of the sample peptide with a peptide of known molecular weight. Molecular weights can be easily compared according to any method common in the art such as SDS-PAGE, gel chromatography, or mass spectrometry. Preferably, the molecular weight of the test peptide is obtained by mass spectrometry and compared to a database containing the molecular weight of the peptide with post-translational modification. Examples of databases include Genept, SWISSPOT, EMBL, and Protein Sequence Database. Such techniques are described in further detail herein.

For CPP17, chemotaxis activity can be assessed as described for T cells in US Pat. No. 5,837,247. Briefly, lymphocyte migration was assessed using a 48 well microchemotaxis chamber (Neuro Probe Inc. Cabin John, Md.). 25 ul of the sample to be tested, diluted with chemotactic solvent, was placed in the lower compartment and 50 ul of cell suspension (at 5 × 10 ⁶ cells / ml) was placed in the upper compartment. The two compartments were separated by a polycarbonate filter (5 μm pore size for T cells, larger for other lymphocytes) coated overnight at 4 ° C. with 10 ug / ml type IV collagen. The apparatus was incubated for 3 hours at 37 ° C. in humidified air containing 5% CO ₂ . At the end of the incubation period, the filters were removed, fixed and stained with LeukoStat (Fisher Scientific, Pittsburgh, Pa.). The number of cells that migrated through the filter per high power field was counted by light microscopy. Results are expressed as mean (± SD) values of triplicate triplicates and represent at least 3 experiments. The statistical significance of the number of cell migration in response to stimulation relative to the control medium was calculated using Student's t test. For in vivo assays, BALB / C and CB-17 scid / scid (SCID) mice were obtained from the Animal Production Area (NCI-FCCRDC, Frederick, Md.). 8-12 week old mice were used and maintained in aseptic conditions. SCID mice were treated with anti-ASGM-1 and injected with 1 × 10 ⁸ huPBL intraperitoneally. Immediately thereafter, 0.1 ml of PBS containing a purified preparation of 1.0 ug of compound or 0.1 ml of control PBS was injected daily subcutaneously at the same injection site. The injection sites were examined histologically either at 4 hours after the first or 24 hours up to 4 hours after the second injection. Experiments were performed with 2 specimens of 3 to 4 mice per group.

  As for CPP17, as described in Nassar, et al., (Blood 100: 4026-32 (2002)) or European Patent No. 05828631 B1, the relevant disclosure of which is hereby incorporated by reference. In addition, vascular smooth muscle contraction can be measured. Generally, rat or other suitable animal aortic ring tissue sections are used in the assay. Tissue slices are treated with epinephrine, for example, a potent contractile stimulant, and lengths are measured in the presence and absence of the test substance. An increase in section length relative to the negative control indicates that the substance has reduced contractile activity.

For CPP20, tumor growth can be assayed using any method known in the art. For example, in experiments detailed in WO 99/46282 (the relevant disclosure of which is incorporated herein by reference), C57B16 / J mice were transplanted with Lewis lung carcinoma. A suspension of 10 ⁶ tumor cells in 100 μl PBS was injected subcutaneously into the back of the mice. Tumors were measured with a dial caliper and volume was determined using the general formula for volume of ellipsoidal spheres (width ² x length x 0.52). When the tumor volume reached approximately 160 mm 3, the mice were randomly divided into two groups. One group was treated with the test substance and the other group received a PBS control. Tumor growth was monitored over 11 days.

  One skilled in the art can diagnose cardiovascular disorders by any method appropriately determined for the individual. Further examples of symptoms and diagnosis can be found in the background section and are best determined by those skilled in the art based on the patient's specific profile.

  Intramolecular interactions can be detected by sequence-based structure prediction. Such predictions are generally based on X-ray crystallography or NMR structural data for polypeptides having similar sequences. Detection of intramolecular interactions can also be achieved using SDS-PAGE. For the example of disulfide bonds, the linkage formed between different parts of a given protein leads to a more compact protein, and thus a decrease in apparent molecular weight. Disulfide bonds can be broken by reducing agents such as dithiothreitol (DTT). Thus, a change in apparent molecular weight can be detected by comparing a protein sample treated with a reducing agent by SDS-PAGE to an untreated control. Such methods are common in the art.

Anti-CPP Antibodies The present invention provides antibodies and binding compositions specific for CPP. Such antibodies and binding compositions include polyclonal antibodies, monoclonal antibodies, Fab and single chain Fv fragments thereof, bispecific antibodies, heteroconjugates, and humanized antibodies. Such antibodies and binding compositions can be generated in a variety of ways, including hybridoma culture, recombinant expression in bacterial or mammalian cell culture, and recombinant expression in transgenic animals. There are many guides in the literature for selecting specific production methods, such as Chad and Chamow, Curr. Opin. Biotechnol., 12: 188-194 (2001).

  The choice of manufacturing method depends on several factors including the desired antibody structure, the importance of the carbohydrate moiety on the antibody, ease of culture and purification, and cost. Standard expression techniques can be used to create many different antibody structures, including full-length antibodies, antibody fragments such as Fab and Fv fragments, and chimeric antibodies containing components from different species. Small antibody fragments such as Fab and Fv fragments that have no effector function and limited pharmacokinetic activity can be made in bacterial expression systems. Single chain Fv fragments are highly selective for in vivo tumors, exhibit good tumor penetration and low immunogenicity, and are rapidly cleared from the blood (eg, Freyre et al., J. Biotechnol., 76 : 157-163 (2000)). Such molecules are therefore desirable for radioimmunodetection.

Polyclonal antibody The anti-CPP antibody of the present invention may be a polyclonal antibody. Such polyclonal antibodies can be generated in mammals, for example after one or more injections of an immunizing agent, and preferably an adjuvant. The mammal is injected with the immunizing agent and / or adjuvant, typically by a series of subcutaneous or intraperitoneal injections. The immunizing agent can include CPP or a fusion protein thereof. It may be useful to bind an antigen to a protein that is known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), methylated bovine serum albumin (mBSA), bovine serum albumin (BSA), hepatitis B surface antigen, serum albumin Bovine thyroglobulin, and soybean trypsin inhibitor. Adjuvants include, for example, Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl lipid A, synthetic trehalose dicoryno-mycolate). One skilled in the art can determine the immunization protocol based on standard protocols or by routine experimentation.

  Alternatively, antibodies can be made using a crude protein preparation enriched with CPP or a portion thereof. Such a protein, fragment or preparation is introduced into a non-human mammal in the presence of a suitable adjuvant. If the serum contains polyclonal antibodies against unwanted epitopes, the polyclonal antibodies are purified by immunoaffinity chromatography.

  Efficient polyclonal antibody production is affected by many factors related to both the antigen and the host species. Host animals also vary in response to the site and dose of inoculation, leading to low titer antisera as a result of insufficient and excessive doses of antigen. Small doses (ng level) of antigen administration at multiple intradermal sites appear to be most reliable. Techniques for generating and processing polyclonal antisera are known in the art, see for example, Mayer and Walker (1987), the disclosure of which is hereby incorporated by reference in its entirety. Effective immunization protocols for rabbits include Vaitukaitis, J. et al., J. Clin. Endocrinol. Metab. 33: 988-991 (1971) (the disclosure of which is incorporated herein by reference in its entirety) ) Can be found. When booster injections are administered at regular intervals and the antibody titer begins to decrease against a known concentration of antigen, for example by double immunodiffusion in agar, as determined semi-quantitatively, antiserum Can be collected. See, for example, Ouchterlony, O. et al., Handbook of Experimental Immunology D. Wier (ed) Blackwell (1973) Chap. Antibody plateau concentrations are usually in the range of 0.1 to 0.2 mg / ml of serum. Prepare competitive binding curves as described, for example, in Fisher, D., Manual of Clinical Immunology, 2d Ed (Rose and Friedman, Eds.) Amer. Soc. For Microbiol., Washington, DC, Chap42 (1980). To determine the affinity of the antiserum for the antigen.

The monoclonal antibody or anti-CPP antibody may be a monoclonal antibody. Mice, hamsters, or other suitable animals can be immunized with an immunizing agent to generate antibodies that specifically bind to the immunizing agent, or monoclonal antibodies can be generated by hybridomas that induce lymphocytes ( For example, Kohler and Milstein, Nature 256: 495 (1975)). The immunizing agent typically includes CPP or a fusion protein thereof and optionally a carrier. Alternatively, lymphocytes can be immunized in vitro. In general, spleen cells or lymph node cells are used when a non-human mammalian source is desired, or peripheral blood lymphocytes ("PBL") are used when cells of human origin are desired. Lymphocytes are fused with immortalized cells using a suitable fusing agent such as polyethylene glycol to produce hybridoma cells (eg Goding, MONOCLONAL ANTIBODIES: PRINCIPLES AND PRACTICE, Academic Press, pp. 59-103 (1986); Liddell and Cryer, A Practical Guide to Monoclonal Antibodies (John Wiley & Sons, New York, 1991); Malik and Lillenoj, Editors, Antibody Techniques (Academic Press, New York, 1994) Generally, immortalized cells are transformed. Suitable mammalian cells, such as myeloma cells of rat, mouse, bovine or human origin, preferably containing one or more substances that inhibit the growth or survival of unfused immortalized cells. Hybridoma cells are cultured in culture medium, eg, if the parent cell lacks the enzyme hypoxanthine guanine phosphoribosyltransferase (HGPRT) The culture medium for mammary typically contains hypoxanthine, aminopterin, and thymidine (HAT), a substance that inhibits the growth of HGPRT-deficient cells.Preferred immortal cell lines fuse efficiently and stabilize antibodies. The preferred immortal cell line is a mouse or human myeloma cell line, such as the American Type Culture Collection (ATCC). Human myeloma cells and mouse-human heteromyeloma cell lines have also been described for the production of human monoclonal antibodies (eg Kozbor, J. Immunol. 133: 3001 (1984)). Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, pp. 51-63 (1987)).

  Culture medium (supernatant) for culturing hybridoma cells can be assayed for the presence of monoclonal antibodies directed against CPP. Preferably, the binding specificity of the monoclonal antibody present in the hybridoma supernatant is determined by immunoprecipitation or by an in vitro binding assay such as a radioimmunoassay (RIA) or enzyme-linked immunosorbent assay (ELISA). Suitable techniques and assays are known in the art. The binding affinity of a monoclonal antibody can be determined, for example, by the Scatchard analysis of Munson and Pollard, Anal. Biochem. 107: 220 (1980). After identifying the desired antibody-producing hybridoma, the cells can be cloned by limiting dilution and grown by standard methods (Goding, 1986, supra). Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium (DEM) and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as mammalian ascites. Monoclonal antibodies secreted by selected clones can be obtained by immunoglobulin purification procedures commonly used by those skilled in the art, such as protein A-sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography. It can be isolated or purified from culture medium or ascites.

  Monoclonal antibodies can also be made by recombinant DNA methods, such as those described in US Pat. No. 4,816,567. Isolating DNA encoding a monoclonal antibody of the invention from CPP-specific hybridoma cells, for example by using oligonucleotide probes capable of specifically binding to the genes encoding the heavy and light chains of the murine antibody; and Can be sequenced. Once isolated, the DNA can be inserted into an expression vector which is then hosted, such as monkey COS cells, Chinese hamster ovary (CHO) cells or myeloma cells that would otherwise not produce immunoglobulin proteins. Cells are transfected to synthesize monoclonal antibodies in recombinant host cells. For example, by replacing the coding sequences of the mouse heavy and light chain constant domains with homologous human sequences (Morrison et al., Proc. Natl. Acad. Sci. 81: 6851-6855 (1984); Neuberger et al., Nature 312: 604-608 (1984); Takeda et al., Nature 314: 452-454 (1985)), or covalently linking all or part of a non-immunoglobulin polypeptide coding sequence to an immunoglobulin coding sequence. To modify the DNA. A non-immunoglobulin polypeptide can be substituted with the constant domain of an antibody of the invention or with the variable domain of one antigen binding site of an antibody of the invention to create a chimeric bivalent antibody. The antibody may also be a monovalent antibody. Methods for preparing monovalent antibodies are known in the art. For example, in vitro methods are suitable for preparing monovalent antibodies. Conventional techniques known in the art can be used to achieve digestion of the antibody to produce its fragments, particularly Fab fragments.

  Antibodies and antibody fragments characteristic of the hybridomas of the invention can also be generated by recombinant means by extracting messenger RNA, constructing a cDNA library, and selecting clones that encode segments of the antibody molecule. it can. The following are illustrative references disclosing recombinant techniques for generating antibodies: Well et al., Nucleic Acids Research, 5: 3113-3128 (1978); Zakut et al., Nucleic Acids Research, 8 : 3591-3601 (1980); Cabilly et al., Proc. Natl. Acad. Sci. 81: 3273-3277 (1984); Bose et al., Nucleic Acids Research, 12: 3791-3806 (1984); Amster et al., Nucleic Acids Research, 8: 2055-2065 (1980); Moore et al., US Pat. No. 4,642,334; Skerra et al., Science 240: 1038-1041 (1988); Huse et al., Science 246: 1275-1281 (1989); and US Pat. Nos. 6,054,297; 5,530,101; 4,816,567; 5,750,105; and 5,648,237, which are hereby incorporated by reference. In particular, such techniques can be used to generate interspecies monoclonal antibodies in which the binding region of one species is combined with the non-binding region of another species' antibody to reduce immunogenicity (eg, Liu et al. Proc. Natl. Acad. Sci. 84: 3439-3443 (1987) and patents 6054297 and 5530101). Preferably, recombinantly produced Fab and Fv fragments are expressed in bacterial host systems. Preferably, full length antibodies are produced by mammalian cell culture techniques. Most preferably, full length antibodies are expressed in Chinese hamster ovary (CHO) cells or NSO cells.

Both polyclonal and monoclonal antibodies can be screened by ELISA. As with other solid phase immunoassays, the test is based on the tendency of macromolecules to adsorb nonspecifically to plastic. The irreversibility of this reaction without loss of immunological activity allows the formation of an antigen-antibody complex that can be easily separated from unbound material. In order to determine the titer of the anti-peptide serum, peptides bound to a carrier different from that used for immunization are adsorbed to the wells of a 96-well microtiter plate. The adsorbed antigen is then reacted with a dilution of anti-peptide serum in the well. Unbound antibody is washed away and the remaining antigen-antibody complex is reacted with antibodies specific for IgG of the immunized animal. This second antibody is conjugated to an enzyme such as alkaline phosphatase. The visible color reaction produced when the enzyme substrate is added indicates which well is bound to the anti-peptide antibody. Use of a spectrophotometer reading allows for better quantification of the amount of peptide-specific antibody binding. High titer antiserum produces a linear titer curve between 10 ⁻³ and 10 ⁻⁵ dilution.

CPP Peptide Carriers The present invention includes immunogens derived from CPP and immunogens comprising conjugates between the carrier and the peptides of the present invention. The term immunogen, as used herein, refers to a substance that can elicit an immune response. The term carrier, as used herein, creates an antibody specific for a peptide bound to a host organism immunized with the resulting conjugate when chemically bound to a peptide of the invention. Refers to any substance to be made. Carriers include synthetic particles such as red blood cells, bacteriophages, proteins, or agarose beads. Preferably, the carrier is a protein such as serum albumin, gamma globulin, keyhole limpet hemocyanin (KLH), thyroglobulin, ovalbumin, fibrinogen and the like.

General techniques for linking synthetic peptides to carriers are described in several literatures, such as Walter and Doolittle, Setlow et al., Eds., Gentetic Engineering, 5: 61-95 (Plenum Press, NY, 1983). Antibodies to "; Green et al., Cell 28: 477-487 (1982); Lerner et al., Proc. Natl. Acad. Sci. 78: 3403-3407 (1981); Shimizu et al., US Pat. No. 4,474,754. And Ganfield et al., US Pat. No. 4,311,639. Accordingly, these references are hereby incorporated by reference. The technique used to link the hapten to the carrier is the technique referred to above, such as Tijssen, Practice and Theory of Enzyme Immunoassays (Elsevier, New York, 1985),
Essentially identical to chapter 20. The four most commonly used schemes for conjugating peptides to carriers are (1) Kagan and Glick, page.328-, eg, Jaffe and Behrman, eds. Methods of Hormone Radioimmunoassay, (Academic Press, NY, 1979). 329 and Walter et al., Proc. Natl. Acad. Sci., Vol. 77: 5197-5200 (1980); glutaraldehyde for amino linkages; (2) eg Hoare et al., 242: 2447-2453 (1967), water-soluble carbodiimides for the attachment of carboxyls to amino acids; (3) Bassili et al., Jaffe and Behrman, eds. (Cited above). bis-diazobedidine (BDB) for tyrosine side chain binding of tyrosine as disclosed in al., page. 46-47 and Walter et al. (cited above); and (4) Kitagawa et al., Cis as disclosed in J. Biochem. (Tokyo) 79: 233-239 (1976), and Lerner et al., Cited above. It is in (or other sulfhydryl) maleimidobenzoyl--N- hydroxysuccinimide ester for binding to the amino group of (MBS). General rules for the selection of an appropriate method for conjugation of a given peptide to a protein carrier can be stated as follows: the group involved in the conjugation is only once in the sequence, preferably of the segment Should occur at the appropriate end. For example, BDB should not be used if tyrosine residues occur in the major part of the sequence selected for its potential antigenic properties. Similarly, the centrally located lysine is excluded from the glutaraldehyde method and the carbodiimide approach is often excluded due to the presence of aspartic acid and glutamic acid. On the other hand, suitable residues can be located at either end of the sequence segment selected as the binding site, whether or not it occurs in the “original” protein sequence. Unlike the amino and carboxy termini, the internal segment is “unbound” and is significantly different from the same sequence found in the original protein where the polypeptide backbone is continuous. The problem can be remedied to some extent by acetylating the α-amino group and then attaching the peptide via its carboxy terminus. Binding efficiency to the carrier protein is conveniently measured using radioactively labeled peptides prepared either by using radioactive amino acids in one step of the synthesis or by labeling the finished peptide by iodination of tyrosine residues. The The presence of tyrosine in the peptide also makes it possible to set up a more sensitive radioimmunoassay if desired. Thus, if tyrosine is not part of the peptide sequence defined by the original polypeptide, tyrosine can be introduced as a terminal residue.

  Preferred carriers are proteins, and preferred protein carriers include bovine serum albumin, myoglobulin, ovalbumin (OVA), keyhole limpet hemocyanin (KLH) and the like. As disclosed in Liu et al., Biochemistry, 18: 690-697 (1979), the peptide can be linked to KLH via cysteine by MBS. The peptide is dissolved in phosphate buffered saline (pH 7.5), 0.1 M sodium borate buffer (pH 9.0), or 1.0 M sodium acetate buffer (pH 4.0). The pH for peptide dissolution is selected to optimize peptide solubility. The free cysteine content of the soluble peptide is determined by the Ellman method (Ellman, Arch. Biochem. Biophys. 82: 7077 (1959)). For each peptide, 4 mg of KLM in 0.25 ml of 10 mM sodium phosphate buffer (pH 7.2) is reacted with 0.7 mg of MBS (dissolved in dimethylformamide) and stirred at room temperature for 30 minutes. Since KLH is insoluble in> 30% formamide, MBS is added dropwise to confirm that the local concentration of formamide is not very high. The reaction product KLH-MBS was then passed through Sephadex G-25 equilibrated with 50 mM sodium phosphate buffer (pH 6.0) to remove free MBS, and KLH was recovered from the peak fraction of the column eluate (by OD280). Monitoring) is expected to be approximately 80%. KLH-MBS is then reacted with 5 mg of peptide dissolved in 1 ml of the selected buffer. The pH is adjusted to 7-7.5 and the reaction is stirred at room temperature for 3 hours. By dialysis of the conjugate sample against phosphate buffered saline, the binding efficiency is monitored with the radioactive peptide and can range from 8% to 60%. Once a peptide-carrier conjugate is utilized, for example, Campbell, Monoclonal Antibody Technology (Elsevier, New York, 1984); Hurrell, ed. Monoclonal Hybridoma Antibodies: Techniques and Applications (CRC Press, Boca Raton, FL, 1982); Polyclonal or monoclonal antibodies are generated by standard techniques as disclosed in Schreier et al., Hybridoma Techniques (Cold Spring Harbor Laboratory, New York, 1980); US Pat. No. 4,456,2003. In particular, US Pat. No. 4,456,2003 is hereby incorporated by reference.

Humanized antibodies The anti-CPP antibodies of the present invention may further comprise humanized antibodies or human antibodies. The term “humanized antibody” refers to a chimeric antibody, immunoglobulin chain or (Fv, Fab, Fab ′, F (ab ′), or other antigen of an antibody that contains some of the sequence derived from a non-human antibody. Refers to a humanized form of a non-human (eg mouse) antibody that is a fragment thereof (such as a binding subsequence). For humanized antibodies, residues from the complementarity determining regions (CDRs) of human immunoglobulins are derived from CDRs of non-human species such as mice, rats or rabbits with the desired binding specificity, affinity and ability. Includes human immunoglobulins that are replaced by residues. In general, a humanized antibody will contain substantially all of at least one and generally two variable domains, wherein all or substantially all of the CDR regions correspond to those of non-human immunoglobulin. And all or substantially all of the FR region is of human immunoglobulin consensus sequence. Humanized antibodies also optimally comprise at least a portion of an immunoglobulin, typically the constant region (Fc) of a human immunoglobulin (Jones et al., Nature 321: 522-525 (1986) and Presta, Curr .Op.Struct.Biol. 2: 593-596 (1992)). Methods for humanized non-human antibodies are known in the art. Generally, to more closely resemble a human antibody, a humanized antibody has one or more amino acids introduced into it from a source that is non-human, but still retains the unique binding activity of the antibody. Yes. Methods for humanization of antibodies are described in Jones et al., Nature 321: 522-525 (1986); Riechmann et al., Nature 332: 323-327 (1988); and Verhoeyen et al., Science 239: 1534- 1536 (1988). Such “humanized” antibodies are chimeric antibodies in which substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species.

Heteroconjugate antibodies Heteroconjugate antibodies comprising two covalently bound antibodies are also within the scope of the present invention. Heteroconjugate antibodies can be prepared in vitro using known methods of protein synthesis chemistry, including those related to cross-linking agents. For example, immunotoxins can be prepared using a disulfide exchange reaction or by forming a thioester bond.

Bispecific antibodies Bispecific antibodies have binding specificities for at least two different antigens. Such antibodies are monoclonal and are preferably human or humanized antibodies. One of the binding specificities of the bispecific antibody of the invention is with respect to CPP, and the other is preferably with respect to cell surface proteins or receptors or receptor subunits. Methods for making bispecific antibodies are known in the art, and generally recombinant production of bispecific antibodies involves two immunoglobulin heavy chains where the two heavy chains have different specificities. / Based on co-expression of light chain pairs in hybridoma cells (eg Milstein and Cuello, Nature 305: 537-539 (1983)). If the random combination of immunoglobulin heavy and light chains leads to the generation of potentially 10 different antibody molecules by the hybridoma, accurate molecular purification usually involves some kind of affinity purification, eg affinity Requires chromatography.

Use of CPP antibodies CPP antibodies are preferably specific for the CPPs of the present invention and as such do not bind with high affinity to peptides derived from other proteins. The term “heavy chain variable region” as used herein is (1) 110 to 125 amino acids long and (2) its amino acid sequence starts from the N-terminal amino acid of the heavy chain. Means a polypeptide corresponding to the heavy chain sequence of the antibody of the present invention. Similarly, the term “light chain variable region” is (1) 95 to 115 amino acids long, and (2) the amino acid sequence starts from the N-terminal amino acid of the light chain and is the sequence of the light chain of the antibody of the invention Means a polypeptide corresponding to. The term “monoclonal antibody” as used herein refers to a homogeneous population of immunoglobulins that can specifically bind to CPP.

  CPP antibodies can be used as functional modulators, preferably as antagonists. Preferably, the antibody modulator of the present invention is derived from a monoclonal antibody specific for CPP. Monoclonal antibodies that can block or neutralize CPP are selected for their ability to block CPP biological activity.

  The use of antibody fragments is also well known; for example, Fab fragment: Tijssen, Practice and Theory of Enzyme Immunoassays (Elsevier, Amsterdam, 1985); and Fv fragment: Hochman et al., Biochemistry, 12: 1130-1135 (1973), Sharon et al., Biochemistry, 15: 1591-1594 (1976) and Ehrlich et al., US Pat. No. 4,355,023; and antibody half-molecules: Auditore-Hargreaves, US Pat. No. 4,470,925.

Preferably, the monoclonal antibody, Fv fragment, Fab fragment, or other binding composition derived from the monoclonal antibody of the present invention has a high affinity for CPP. The affinity of monoclonal antibodies and related molecules for CPP can be measured by conventional techniques including plasmon resonance, ELISA, or equilibrium dialysis. For example, using a BIAcore 2000 instrument (Biacore AB, Uppsala, Sweden), affinity measurement by plasmon resonance technique can be performed according to the protocol recommended by the manufacturer. For example, affinity is measured by ELISA, preferably as described in US Pat. No. 6,235,883. Preferably, the dissociation constant between the CPP and the monoclonal antibody of the invention is less than 10 ⁻⁵ molar. More preferably, such a dissociation constant is less than 10 ⁻⁸ molar; even more preferably, such a dissociation constant is less than 10 ⁻⁹ molar; and most preferably, such a dissociation constant is from 10 ⁻⁹ to 10 ^−. The range is ¹¹ molar.

  In addition, the antibodies of the present invention are useful for detecting CPP. Such a detection method is advantageously applied to the diagnosis of cardiovascular disorders, particularly coronary artery disease. The antibodies of the present invention can be used in most assays involving antigen-antibody reactions. The assay may be homogeneous or heterogeneous. In homogeneous assay studies, the sample may be a biological sample or fluid such as serum, urine, whole blood, lymph, plasma, saliva, cells, tissues, and materials secreted by cells or tissues cultured in vitro. . If necessary, the sample can be pretreated to remove unwanted material. Immunological reactions usually require a sample suspected of containing a specific antibody, a labeled analyte, and an antigen. The signal resulting from the label is modified directly or indirectly upon binding of the antibody to the labeled analyte. Both immunological reactions and the extent of detection are performed in homogeneous solutions. Immunochemical labels that can be used include free radicals, fluorescent dyes, enzymes, bacteriophages, coenzymes and the like.

  In heterogeneous assay studies, reagents are usually a sample, a specific antibody, and a means for generating a detectable signal. The specimen is typically placed on a support such as a plate or slide and contacted with the liquid phase antibody. The support is then separated from the liquid phase and either the support phase or the liquid phase is tested for a detectable signal using a means or signal generation system for generating such a signal. This signal is related to the presence of the antigen in the sample. Means for generating a detectable signal include the use of radioactive labels, fluorescent compounds, enzymes, and the like. Examples of heterogeneous immunoassays are radioimmunoassays, immunofluorescence methods, enzyme linked immunoassays and the like.

  See Edward T. Maggio, “Enzyme-Immunoassay” CRC Press, Inc., Boca Raton, Fla., 1980, for a more detailed discussion of the immunoassay techniques described above. See also, for example, U.S. Pat. Nos. 3,690,834; 3,791,932; 3,817,837; 3,850,578; 3,835,987; 3,867,517; 3,901,654; 3,935,054; 3,984,533; (This list is not intended to be exhaustive). Methods for attaching labels to antibodies and antibody fragments are well known in the art. Such methods can be found in U.S. Pat. Nos. 4,220,450; 4,235,869; 3,935,974; and 3,966,345. Another example of a technique in which the antibodies of the invention can be used is immunoperoxidase labeling (Sternberger, Immunocytochemistry (1979) pp. 104-169). Alternatively, antibodies can be conjugated to radioactive materials or drugs to form radiopharmaceuticals or drugs, respectively (Carrasquillo, et al., Cancer Treatment Reports (1984) 68: 317-328).

One embodiment of an assay using the antibodies of the invention involves the use of a surface to which the monoclonal antibodies of the invention are bound. The underlying structure of the surface takes various forms, has various compositions, and may be a mixture of compositions or sheets or combinations thereof. The surface may take a variety of shapes and forms and may vary in size depending on the use and mode of measurement. Illustrative surfaces may be pads, beads, disks, or strips that may be flat, concave, or convex. Thickness is not critical and is generally about 0.1 to 2 mm thick and is any convenient diameter or other dimension. The surface is typically supported by rods, tubes, capillaries, fibers, strips, disks, plates, cuvettes and is typically porous and multifunctional or allows for covalent attachment of antibodies and detection It can be multifunctional to allow the binding of other compounds that form part of the means for generating possible signals. A variety of organic and inorganic polymers, both natural and synthetic, and combinations thereof can be used as materials for solid surfaces. Illustrative polymers include polyethylene, polypropylene, poly (4-methylbutene), polystyrene, polymethacrylate, poly (ethylene terephthalate), rayon, nylon, poly (vinyl butyrate), silicon, polyformaldehyde, cellulose, Examples include cellulose acetate, nitrocellulose, and latex. Other surfaces include paper, glass, ceramic, metal, metalloid, semiconductor material, cement, silicate and the like. Substances that form polymers that form several aqueous phases, such as gels, gelatins, lipopolysaccharides, silicates, agarose and polyacrylamides, or dextrans, polyalkylene glycols (alkylenes of 2 to 3 carbon atoms), Or surfactants such as phospholipids are also included. Antibody binding to the surface can be achieved by well-known techniques commonly available in the literature (eg Ichiro Chibata, “Immobillized Enzymes” Press, New York (1978) and Cuatrecasas, J. Bio. Chem., 245 : 3059 (1970)). When performing an assay according to this aspect of the invention, the sample is mixed with an aqueous solvent and the solvent is contacted with the surface to which the antibody is bound. The label can be simultaneously included or subsequently added to the aqueous solvent so as to provide a detectable signal associated with the surface. Means for generating a detectable signal may require the incorporation of a labeled analyte or require the use of a second monoclonal antibody having a label attached thereto. Separation and washing steps are performed as necessary. The detected signal is related to the presence of CPP in the sample. It is within the scope of the present invention to assay on the same support. A particular embodiment of the assay according to the present invention is for purposes of illustration and not limitation, but involves the use of a support such as a slide or well of a petri dish. The technique involves immobilizing a sample to be analyzed on a support with appropriate immobilization material and incubating the feed on a slide with monoclonal antibodies. After washing with a suitable buffer, eg, phosphate buffered saline, the support is contacted with the labeled, specific binding partner of the antibody. After optional incubation, the slide is washed twice with aqueous buffer and a determination of the binding of the labeled monoclonal antibody to the antigen is made. If the label is fluorescent, the slide can be covered with a fluorescent antibody mounting solution over a coverslip and then examined with a fluorescent microscope to determine the extent of binding. On the other hand, an enzyme with a label attached to a monoclonal antibody can be used, and the extent of binding can be determined by testing the slide for the presence of enzyme activity that can be demonstrated by the formation of precipitates, coloration, and the like. A specific example of an assay utilizing this antibody is the double-determined ELISA assay. A support such as a glass or vinyl plate is coated with an antibody specific for CPP by conventional techniques. A sample suspected of containing CPP, usually in an aqueous solvent, is contacted with the support. After an incubation period of 30 seconds to 12 hours, the support is separated from the solvent, washed with, for example, water or an aqueous buffer solvent to remove unbound CPP, and again typically CPP specific in aqueous solvent. Contact with antibody. The antibody is directly or indirectly labeled with an enzyme such as horseradish peroxidase or alkaline phosphatase. After incubation, the support is separated from the solvent and washed as described above. The enzyme activity of the support or aqueous solvent is determined. This enzyme activity is related to the amount of CPP in the sample.
See, for example, Kurokawa, E. et al., Clin. Chim. Acta (1983), 128 (1): 83-93 for an example of an immunoassay for detecting the CPP9 polypeptide of the present invention.

  The invention also includes kits for carrying out the methods disclosed above, such as diagnostic assay kits. In one embodiment, the kit comprises (a) a monoclonal antibody as specifically defined above, and (b) a specific binding partner of said monoclonal antibody and a conjugate of a label capable of producing a detectable signal. Including. Reagents can also include adjuvants such as buffers and protein stabilizers, such as polysaccharides. The kit may further include, if necessary, other members of the signal generating system, the label being a member of the system, agents for reducing background interference of the test, control reagents, devices for performing the test, etc. it can. In another embodiment, the diagnostic kit comprises a conjugate of the monoclonal antibody of the invention and a label capable of producing a detectable signal. Adjuvants as described above may also be present.

  In addition, CPPs can be isolated using anti-CPP antibodies (eg, monoclonal antibodies) by standard techniques such as affinity chromatography or immunoprecipitation. For example, anti-CPP antibodies can facilitate the purification of native CPP from cells and recombinantly produced CPP expressed in host cells. In addition, to help detect low concentrations of CPP (eg, in plasma, cell lysate or cell supernatant) or to assess the abundance and pattern of CPP expression, CPP isolation using anti-CPP antibodies can do. Anti-CPP antibodies can be used in diagnosis to monitor protein levels in tissues as part of a clinical trial procedure, eg, to determine the effectiveness of a given treatment plan. Detection can be facilitated by coupling (ie, physically linking) the antibody to a labeling group.

Retentate chromatography (preferably a protein array or chip) as described in Protein Array U.S. Pat. No. 6,225,027 and U.S. Patent Application No. 2001014461, the entire disclosure of which is hereby incorporated by reference. Can be used to achieve detection, purification, and screening of the polypeptides of the invention. Briefly, retentate chromatography describes a method in which a polypeptide (and / or other sample component) is retained on an absorbent (eg, an array or chip) and subsequently detected. Such methods include (1) selectively adsorbing a polypeptide from a sample to a substrate under a plurality of different adsorbent / eluent combinations (“selection conditions”); and (2) by desorption spectroscopy ( Detecting retention of adsorbed polypeptide (eg, by mass spectrometry). In conventional chromatographic methods, the adsorbent polypeptide is eluted prior to detection. Combined with adsorption chromatography detection by desorption spectroscopy, extraordinary sensitivity, ability to rapidly analyze retained components under a variety of different selection conditions, and adsorption to different sites on the array under different elution conditions Parallel processing of the components is provided.

  These methods include: combinatorial, biochemical separation and CPP purification; differential gene expression studies; detection of differences at the protein level (eg for diagnostics); and detection of molecular recognition events (eg for screening and drug discovery); Useful for. Thus, the present invention provides a molecular discovery and diagnostic device characterized by including both parallel and multiple polypeptide processing capabilities. The polypeptides and CPP binding agents of the invention are preferably conjugated to a labeling group and are therefore detected directly and from the same “circuit” (ie, addressable “chip” location) to 2 during single unit operation. Allows simultaneous transmission of one or more signals.

Detection of CPP by Mass Spectrometry In accordance with the present invention, any device, method, process, etc. can be utilized to determine the identity and abundance of a protein in a sample. A preferred method of obtaining identity is by mass spectrometry, which ionizes protein molecules in the sample and then detects and determines the mass and charge of the resulting protein.

  In order to use mass spectrometry to analyze the protein, it is preferred to convert the protein to a gas-ion phase. Various methods of protein ionization are useful, including, for example, fast ion irradiation (FAB), plasma desorption, laser desorption, thermal desorption, preferably electrospray ionization (ESI) and matrix-assisted laser desorption / ionization (MALDI). is there. A variety of mass analyzers including but not limited to time of flight (TOF), ion trap (ITMS), Fourier transform ion cyclotron (FTMS), quadrupole ion trap, and sector (electric / magnetic) spectrometers Are available for peptide and protein analysis. See, for example, US Pat. No. 5,572,025 for ion trap MS. The mass analyzer can be used in a tandem mass analyzer alone or in combination with other mass analyzers. In the latter case, the first mass analyzer is used to separate protein ions (precursor ions) from each other and to determine the molecular weight of the various protein components in the sample. A second mass analyzer can be used to analyze each separate component, for example by using an inert gas, for example by fragmenting precursor ions into product ions. Any desired combination of mass analyzers can be used including, for example, triple quadrupole, tandem time-of-flight, ion trap, and / or combinations thereof.

  A variety of detectors can be used to detect protein ions. For example, destructive detectors such as ion electron multipliers or cryogenic detectors (eg, US Pat. No. 5,641,010) can be utilized. In addition, a non-destructive detector such as a quadrupole ion trap mass analyzer or an ion trap used as an FTMS ion current pick-up device can be used.

  Regarding MALDI-TOF, dry droplets (Karasand Hillenkamp, Anal. Chem., 60: 2299-2301, 1988), vacuum drying (Winberger et al., Proceedings of the 41st ASMS Conference on Mass Spectrometry and Allied Topics, San Francisco, May 31-June 4,1993, pp.775a-b), crystal grinding (Xiang et al., Rapid Coumm. Mass Spectrom., 8: 199-204, 1994), slow crystal growth (Xiang et al., Org, Mass Spectrom, 28: 1424-1429, 1993); active film (Mock et al., Rapid Coumm. Mass Spectrom., 6: 233-238, 1992; Bai et al., Anal. Chem. 66: 3423- 3430, 1994), air spray (Kochling et al., Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, Atlanta, GA, May 21-May 26, 1995, pp. 1225); electrospray (Hensel et al. , Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics, Atlanta, GA, May 21-May 26, 1995, pp.947); fast solvent evaporation (Vorm et al., Anal. Chem. 66: 3281-3287, 1994); sandwich (Li et al., J .Am.Chem.soc. 11 (8): 11662-11663, 1996); and many sample preparation methods including the two-layer method (Dal et al., Anal. Chem. 71: 1087-1091, 1999) can do. See also Liang et al., Rapid Commun. Mass Spectrom., 10: 1219-1226, 1996; van Adrichem et al., Anal. Chem. 70: 923-930, 1998.

  For MALDI analysis, the solid state co-crystal is obtained by mixing the sample with an energy absorbing compound or colloid (matrix) in the liquid phase and finally drying the solution to the solid state on the surface of the inert probe. Alternatively, it is prepared as a thin film. In some cases, energy absorbing molecules (EAM) are an integral component of the sample presentation surface. Regardless of the EAM application plan, the probe contents are dried to a solid state prior to introduction into a laser desorption / ionization time-of-flight mass spectrometer (LDIMS).

  Ion detection in TOF mass spectrometry is typically accomplished using an electrical radiation detector such as an electron multiplier (EMP) or microchannel plate (MCP). Both of these devices function by converting primary incident charged particles into a series of secondary, tertiary, quaternary, etc. electrons. The possibility of secondary electrons created by the impact of a single incident charged particle can be considered to be the ion-to-electron conversion efficiency (or more simply, conversion efficiency) of this charged particle. All electrons generated in a cascade event are typically described as detector acquisition when compared to the total number of incident charged particles. In general, the overall response time of MCP is much better than that of EMP, so MCP is the preferred electron emission detector for mass / charge resolution enhancement. However, EMP works well to detect the spent kinetic energy of an ion population, in which case fast response time and wide frequency bandwidth are not required.

  In a preferred embodiment, a liquid chromatography tandem mass spectrometer (LC-TMS) is used for analysis of digested proteins. This system provides a further stage of sample separation by liquid chromatography followed by the use of a tandem mass spectrometer.

  In a preferred embodiment, the protein eluted from the column according to the system described in Example 1 is analyzed using both MS and MS-MS analysis. For example, a few intact proteins eluting from RP2 can be sent to on-line detection using LC-ESI MS. The protein is aliquoted into a number of plates allowing preparation for MALDI-MS and ESI-MS, with or without trypsin, and preparation of MALDI plates with various matrices. Thus, in addition to information about intact mass, the method allows analysis to be performed both by peptide mass fingerprinting and MS-MS techniques.

  The methods for separating and fractionating proteins described herein provide individual proteins or fractions containing a small number of identified proteins. These proteins can be identified by mass spectral determination of the molecular weight of the proteins and peptides resulting from the fragmentation. By using the available information in the protein sequence database, a comparison can be made between the proteolytic peptide mass pattern created in silico and the experimentally observed mass. Based on the number of matches between theoretical and experimental proteolytic fragments (among other criteria), a “hit list” is compiled to rank candidate proteins in the database. Based on peptide mapping and sequence database search schemes, several websites providing software for online protein identification can be accessed (eg http://www.expasy.ch). Peptide mapping and sequencing methods using MS are described in WO 95/252919, US Pat. No. 5,538,897, US Pat. No. 5,869,240, US Pat. No. 5,572,259 and US Pat. No. 5,696,376. See also Yates, J. Mass Spec., 33: 1 (1998).

  Data collected from the mass analyzer includes the intensity and mass to charge ratio for each detection event. Spectral data can be recorded in any suitable form including, for example, graphs, numbers, or electronic forms in either digital or analog form. Preferably, the spectrum is recorded on a storage medium including, for example, magnetism such as floppy disk, tape or hard disk; optics such as CD-ROM or laser disk; or ROM-CHIP.

  The mass spectrum of a given sample provides information regarding protein strength, mass to charge ratio, and molecular weight. In a preferred embodiment of the invention, the molecular weight of the protein in the sample is used as a match criterion for querying the database. Usually, for example, by subtracting the mass of the ionized proton for a monovalent protonated molecular ion, the measured mass-to-charge ratio is multiplied by the number of charged polyvalent ions, and the molecular weight is conveniently reduced by subtracting the number of ionized protons. calculate.

  Various databases are useful in accordance with the present invention. Useful databases include databases that contain genomic sequences, expressed gene sequences, and / or expressed protein sequences. Preferred databases include the molecular weights of nucleotide sequence-derived proteins present in known organisms, organs, tissues or cell types. There are many algorithms for identifying open leading frames (ORFs) and converting nucleotide sequences into protein sequences and molecular weight information. Several publicly accessible databases are available including the SwissPROT / TrEMBL database (http://www.expasy.ch).

  A mass analyzer is typically equipped with commercially available software that identifies peaks above a certain threshold level and calculates the mass, charge and intensity of the detected ions. The correlation of molecular weight with a given output peak can be achieved directly from the spectral data, i.e. where the charge of the ion is 1, and thus the molecular weight is equal to the calculated value minus the mass of the ionized proton. However, protein ions can be complexed with various counter ions and adducts such as N, C, and K ′. In such cases, it is expected that a given protein ion will exhibit multiple peaks, such as triplets, representing different ionic states (or species) of the same protein. Thus, it may be necessary to analyze and process the spectral data to determine the family of peaks that originate from the same protein. Usually, this analysis can be performed as described, for example, in Mann et al., Anal. Chem. 61: 1702-1708 (1989).

  Post-translational processing may have to be considered in order to match the molecular weight calculated from the mass spectrometer to the molecular weight predicted from a database such as a genome or expressed gene database. There are various processing events that modify protein structure, including proteolytic processing, removal of N-terminal methionine, acetylation, methylation, glycosylation, phosphorylation, and the like.

  The database can be queried for a range of proteins that match the molecular weight of the unknown protein. The range window can be determined by the accuracy of the apparatus, the method of preparing the sample, and the like. Based on the number of spectral hits (where hits are matches), the unknown protein or peptide is identified or classified.

  The method of identifying one or more CPPs with a mass analyzer is useful for the diagnosis and prognosis of cardiovascular disorders. Preferably, such a method is used to detect one or more CPPs present in human plasma. Illustrative techniques are U.S. Patent Application Nos. 02/0060290, 02/0137106, 02/0138208, 02/0142343, 02/0155509, the entire disclosure of which is hereby incorporated by reference. It is described in.

Diagnostic and Prognostic Applications The nucleic acid molecules, proteins, protein homologs, and antibodies described herein can be used in one or more of the following ways: diagnostic assays, prognostic assays, clinical trial monitoring And in pharmacogenetics; and in drug screening as further described herein.
The present invention provides diagnostic and prognostic assays for detecting CPP nucleic acids and proteins as further described. Also provided are diagnostic and prognostic assays for detecting interactions between CPP and CPP target molecules, particularly natural agonists and antagonists.

  The present invention provides a method for identifying polypeptides that are differentially expressed between two or more samples. “Differential expression” refers to differences in polypeptide quality or quantity between samples. Such differences can occur at any stage of protein expression from transcription by post-translational modification. For example, using protein array methods, two samples are bound to affinity spots on different sets of adsorbents (eg chips) and the recognition maps are compared and retained differentially by the two sets of adsorbents The polypeptide to be identified is identified. Differential retention includes quantitative retention of the polypeptide and qualitative differences. For example, differences in protein post-translational modifications can be detected as differences in binding properties (eg, glycosylated proteins bind differentially to lectin adsorbents) or mass differences (eg, post-translational cleavage products). Can make a difference. In certain embodiments, the adsorbent can have an array of affinity spots selected for a combination of diagnostic markers for a disease or syndrome.

  Identifying differences in polypeptide levels between samples (eg CPP differentially expressed in plasma samples) by exposing samples to various conditions for analysis by desorption spectroscopy (eg mass spectrometry) can do. Unknown proteins can be identified by detecting physicochemical characteristics (eg, molecular weight), and this information can be used to search a database for proteins with similar profiles.

  A preferred method for detecting CPP utilizes mass spectrometry techniques. Such methods provide information about the size and characteristics of particular CPP isoforms present in a sample, eg, a biological sample presented for diagnosis or prognosis. The mass spectrometry technique is detailed in the section entitled “Detection of CPP by mass spectrometry”. Example 1 outlines a preferred detection scheme in which biological samples are separated by chromatography prior to characterization by mass spectrometry. The invention: fractionating a biological sample (eg plasma, serum, lymph fluid, cerebrospinal fluid, cell lysate of a particular tissue) by at least one chromatography step; subjecting the fraction to mass spectrometry; And comparing the characteristics of the polypeptide species observed by mass spectrometry with the characteristics of known CPP polypeptides (eg CPP2, CPP9, CPP17, CPP20 and CPP21 as disclosed in Table 1). A method for detecting CPP in a biological sample is provided.

  The isolated nucleic acid molecule of the present invention can be used to detect genetic changes in, for example, CPP mRNA or CPP-encoding genes (eg, in a biological sample) and to further reduce CPP activity, as described further below. Can be adjusted. In addition, CPPs can be used to screen naturally occurring CPP target molecules and to screen for drugs or compounds that modulate CPP activity. Furthermore, the anti-CPP antibodies of the invention can be used to detect and isolate CPPs, modulate CPP bioavailability, and modulate CPP activity.

  Accordingly, one embodiment of the present invention is the use of a molecule of the present invention (eg CPP, CPP nucleic acid, or CPP modulator) to diagnose and / or prognose a disorder exhibiting any of the CPP activities described above, for example Related to the method. In another embodiment, the present invention provides a method of using a molecule of the present invention for the diagnosis and / or prognosis of a subject, preferably a human subject, whose pathology is disrupted, eg, any of the aforementioned activities. Involved.

  For example, the invention contacts a) the biological sample with: i) a polynucleotide that hybridizes to a CPP nucleic acid under stringent conditions; or ii) a detectable polypeptide (eg, an antibody) that selectively binds to the CPP. And b) detecting the presence or absence of hybridization between the polynucleotide and mRNA species in the sample, or the presence or absence of binding of the detectable polypeptide to a polypeptide in the sample. A method for determining whether a CPP is expressed in a biological sample. Detection of the hybridization or the binding indicates that the CPP is expressed in the sample. Preferably, the polynucleotide is a primer and the hybridization is detected by detecting the presence of an amplification product comprising the primer sequence, or the detectable polypeptide is an antibody.

  In certain embodiments, the detection is a polymerase chain reaction (PCR) such as anchor PCR or RACE PCR (eg, US Pat. Nos. 4,683,195 and 4,683,202, the disclosures of which are hereby incorporated by reference in their entirety). Or alternatively, ligation chain reaction (LCR) (eg Landegren et al., (1988) Science 241: 1077-1080; and Nakazawa et al., (1994) PNAS 91: 360-364 (disclosure thereof). All of which are hereby incorporated by reference), and the latter may be particularly useful for detecting point mutations in CPP-encoding genes (Abravaya et al ., (1995) Nucleic Acids Res. 23: 675-682, the entire disclosure of which is hereby incorporated by reference.

  a) providing a biological sample from the mammal; and b) the amount of CPP or CPP RNA species encoding CPP in the biological sample is detected or predicted in a control sample A method for determining whether the expression level of a CPP in a mammal, preferably a human, is increased or decreased is also envisaged. An increase in the amount of the CPP or CPP RNA species in the biological sample compared to the level detected or predicted from the control sample is an increase in the level of CPP expression in the mammal. And a decrease in the amount of the CPP or CPP RNA species in the biological sample compared to the level detected or predicted from the control sample is CPP in the mammal It shows that the expression level is decreasing.

  The invention also relates to the field of predictive medicine using diagnostic assays, prognostic assays, and clinical trial monitoring for prognostic purposes. Accordingly, one aspect of the present invention is to determine whether an individual is suffering from or at risk of developing a disorder associated with abnormal CPP expression or activity. Relates to diagnostic assays for determining CPP and / or nucleic acid expression and CPP activity in the context of biological samples (eg blood, plasma, cells, tissues). The present invention also provides a prognostic (or predictive) assay for determining whether an individual is at risk of developing a disorder associated with CPP, nucleic acid expression or activity. For example, mutations in a CPP-encoding gene in a biological sample can be assayed. Thereby, such assays can be used for prognostic or predictive purposes to treat an individual prophylactically prior to the onset of a disorder characterized by or associated with CPP expression or activity.

The term “biological sample” is intended to include tissues, cells and biological fluids isolated from an individual, as well as tissues, cells and fluids present within an individual. That is, CPP mRNA, protein or genomic DNA in a biological sample can be detected in vitro and in vivo using the detection method of the present invention. Preferred biological samples are lymph, cerebrospinal fluid, blood and especially plasma. For example, in vitro techniques for detection of CPP mRNA include Northern hybridization and in situ hybridization. In vitro techniques for detection of CPP include mass spectrometry, enzyme-linked immunosorbent assay (ELISA), Western blot, immunoprecipitation and immunofluorescence. In vitro techniques for detection of CPP-encoded genomic DNA include Southern hybridization. Furthermore, in vivo techniques for detection of CPP include introducing labeled anti-CPP antibodies into the individual.
For examples of immunoassays for detecting CPP9 polypeptides of the invention, see Kurokawa, E. et al., Clin. Chim. Acta. (1983), 128 (1): 83-93.
In a preferred embodiment, the subject method generally comprises (i) a mutation of a gene encoding one of the subject CPPs in a tissue sample of an individual (eg, a human patient); or (ii) a misexpression of a CPP-encoding gene. Including detection of the presence or absence of a genetic lesion characterized by at least one of the following: To illustrate: (i) deletion of one or more nucleotides from a CPP-encoding gene, (ii) addition of one or more nucleotides to the gene, (iii) one or more of the genes More nucleotide substitutions, (iv) whole chromosome rearrangements or gene amplifications, (v) global changes in the level of messenger RNA transcripts of genes, (vi) gene methylation patterns such as genomic DNA methylation patterns Of (vii) the presence of a non-wild type splicing pattern of the messenger RNA transcript of the gene, and (viii) a reduced level of expression indicative of a lesion in the regulatory element, or reduced stability of the CPP-encoded transcript; Such genetic lesions can be detected by confirming the presence of at least one of these.

  In yet another illustrative embodiment, one or more restriction endonucleases that are sensitive to methylation and whose recognition site is present in a CPP-encoding gene (including flanking and intron sequences) may be By digesting the genomic DNA derived from the sample, an abnormality in the methylation pattern of the CPP nucleic acid can be detected. See, for example, Buiting et al., (1994) Human Mol Genet 3: 893-895. Digested DNA is separated by gel electrophoresis and hybridized with probes derived from, for example, genomic or cDNA sequences. By comparing the restriction pattern generated from the sample DNA with a known standard pattern of methylation, the methylation status of the CPP-encoding gene can be determined.

  In yet another embodiment, a diagnostic assay is provided that detects the ability of CPP to bind to a cell surface or extracellular protein. For example, a CPP variant that is expressed at a significant level in a cell but lacks binding to a CPP target protein (either has a reduced or enhanced binding affinity for the target) It is desirable to detect. Such mutants can arise, for example, from mutations, such as point mutants, and would be unrealistic to detect by diagnostic DNA sequencing techniques or by the immunoassays described above. Thus, the present invention further generally under conditions that allow one or more CPP-encoding genes to be cloned from a sample tissue and to detect the interaction between the recombinant gene product and the target protein. A diagnostic screening assay is contemplated that involves expressing the cloned gene. As will be apparent from the description of the various drug screening assays presented herein, a variety of techniques can be used to determine the ability to bind to other components of the CPP. These techniques can be used to detect mutations in CPP-encoding genes that give rise to mutant proteins with high or low binding affinity for CPP target proteins relative to wild-type CPP. Conversely, by replacing the CPP target protein and CPP that are “bait” and those derived from patient samples, the subject assay is used to compare to the wild-type form of the CPP target protein. Thus, CPP target protein variants with high or low binding affinity for CPP can also be detected.

In an illustrative embodiment, the target protein can be provided as an immobilized protein ("target"), such as by use of a GST fusion protein and a glutathione treated microtiter plate, as described herein.
In another embodiment, the method further measures the level of CPP, mRNA, or genomic DNA in the biological sample, and the level of CPP, mRNA, or genomic DNA in the control sample is determined from CPP, mRNA in the test sample. Or obtaining a control biological sample from a control subject for comparison with the level of genomic DNA, contacting the control sample with a compound or agent capable of detecting CPP, mRNA, or genomic DNA. The invention also encompasses kits for detecting the presence of CPP, mRNA, or genomic DNA in a biological sample. For example, the kit: a labeled compound or agent capable of detecting CPP, mRNA, or genomic DNA in a biological sample; a means for determining the amount of CPP in the sample; and standardizing the amount of CPP in the sample Means for comparing with can be included. The compound or drug can be packaged in a suitable container. The kit can further include instructions for using the kit to detect CPP or nucleic acid.

CPP Cluster In one aspect of the invention, a method for the diagnosis of a cardiovascular disorder is one or more of the invention in a test biological sample combined with the detection of another cardiovascular disorder plasma polypeptide (CPP). Including detecting the presence or level of more CPPs. Other particularly preferred CPPs for use in the diagnosis of cardiovascular disorders in combination with the CPPs of the present invention are listed in Table 2.

Table 2

  Table 2 details, for each CPP, the sequences detected by mass spectrometry according to the procedure described in Example 1. In addition, Table 2 shows the CEX, RP1, and RP2 chromatographic fractions where each sequence was found.

  All CPPs listed in Table 2 were identified as being differentially expressed between individuals with cardiovascular disorders and control individuals using the procedure described in Example 1. In particular, each CPP listed in Table 2 was found to differ between control and disease samples as detailed in Table 3 below.

Table 3

  A person skilled in the art will work with many additional CPPs from Table 2 that are selected using an appropriate analysis of the levels of CPPs from Table 2 measured in many diseased and control individuals by the method of Example 1. The CPP of the present invention can be used. A plan to find such a combination of CPPs should consider each CPP as one variable and treat the disease as an associated, multivariate effect caused by the interaction of these variables.

  Linear discriminant analysis (LDA) is one such analytical procedure that can be used to detect a significant association between a cluster of variables (ie, CPP) and cardiovascular disease. In performing an LDA, a series of weights are associated with each variable (ie, CPP), so that subjects with and without cardiovascular disease have a linear combination of weight and variable measurements. By discriminating, the state of the disease can be identified. With enhancements to LDA, the discriminating power of the model can be optimized by including (or excluding) variables in stages. The result of LDA is therefore a cluster of CPPs that can be used without limitation for diagnosis, prognosis, treatment or drug development. Other enhanced LDA versions, such as Flexible Discriminanat Analysis, allow the disease state to be distinguished from the normal state using a variable nonlinear combination. The results of discriminant analysis can be confirmed by a post-hoc test and also by repeated analysis using alternative techniques such as a classification tree.

"Drug screening assay"
The present invention relates to methods for identifying candidate modulators (eg, small molecules and peptides, antibodies, peptidomimetics or other drugs) that bind to CPP and have a modulating effect on CPP expression or preferably CPP biological activity. (Also referred to as “screening assay” as used herein). In some embodiments, combinatorial chemistry can be used to create small molecules or to obtain natural product libraries. The assay may be a cell based or non-cell based assay. The drug screening assay may be a binding assay or more preferentially a functional assay, as further described.

  When the present invention is used in drug development to determine the ability of a CPP modulator or drug candidate to elicit an anti-cardiovascular disorder response, for example, the body fluid analyzed for the level of at least one CPP is derived from a non-human mammal. Is preferred. Mammals other than humans are preferably those in which induction of an anti-cardiovascular disorder response by endogenous and / or exogenous agents is predictive of induction of such a response in humans. Rodents (mouse, rat, etc.) and primates are particularly suitable for use in this aspect of the invention.

  As further described herein, CPP activity is used in screening assays to at least 5%, more preferably at least 10%, even more preferably at least 30%, even more preferably at least 50%, even more so Agents that have been found to adjust to preferably at least 70%, more preferably at least 90%, can be selected for further testing as prophylactic and / or therapeutic anti-cardiovascular agents.

  In another aspect, as further described herein, CPP expression is at least 5%, more preferably at least 10%, even more preferably at least 30%, even more preferably at least using screening assays. Agents found to adjust up to 50%, even more preferably up to at least 70%, more preferably up to at least 90% are selected for further testing as prophylactic and / or therapeutic anti-cardiovascular agents be able to.

  Agents found to modulate CPP activity alone, or in combination with other appropriate agents or treatments, for example, adjust cardiovascular disorder treatment plans or reduce cardiovascular disorder symptoms be able to.

  Protein array methods are useful for screening and drug discovery. For example, one member of a receptor / ligand pair is docked to an absorbent and its ability to bind to a binding partner in the presence of a test substance is determined. Because of the rapid adsorption that can be tested, a combinatorial library of test substances can be easily screened for its ability to modulate interactions. In a preferred screening method, CPP is docked to the adsorbent. The binding partner is preferably labeled, thus allowing detection of the interaction.

  Alternatively, in certain embodiments, the test substance is docked to the adsorbent. The polypeptide of the present invention is exposed to a test substance and screened for binding.

  In another embodiment, the assay is a cell-based assay in which cells expressing CPP or a biologically active portion thereof are contacted with a test compound and the ability of the test compound to modulate CPP activity is determined. Determination of the ability of a test compound to modulate CPP activity can be accomplished by monitoring the biological activity of the CPP or biologically active portion thereof. The cell can be, for example, of mammalian origin, insect origin, bacterial origin, or yeast cell.

  In one embodiment, the present invention provides an assay for screening candidate or test compounds that are target molecules of CPP or biologically active portion thereof. In another embodiment, the invention provides an assay for screening candidate or test compounds that bind to or modulate the activity of CPP or biologically active portion thereof. Biological libraries, spatially addressable parallel solid or liquid phase libraries; synthetic library methods requiring deconvolution; one bead one compound library method; and synthetic libraries using affinity chromatography selection Any of a number of combinatorial methods known in the art, including methods, can be used to obtain the test compounds of the present invention. Biological library approaches are used with peptide libraries, but the other four approaches can be applied to small molecule libraries of peptides, non-peptide oligomers or compounds (Lam, KS (1997) Anticancer Drug Des 12: 145 (the entire disclosure of which is hereby incorporated by reference)).

  Examples of methods for the synthesis of molecular libraries are known in the art, for example: DeWitt et al., (1993) Proc.Natl.Acad.Sci.USA 90: 6909; Erb et al., (1994) Proc.Natl Acad. Sci. USA 91: 11422; Zuckermann et al., (1994) J. Med. Chem. 37: 2678; Cho et al., (1993) Science 261: 1303; Carrell et al., Angew. Chem. Int. Ed. Engl. 33: 2059 and 2061; and Gallop et al., (1994) J. Med. Chem. 37: 1233, the entire disclosure of which is hereby incorporated by reference. Can do.

  Compound libraries are in solution (eg Houghten (1992) Biotechniques 13: 412-421) or beads (Lam (1991) Nature 354: 82-84), chips (Fodor (1993) Nature 364: 555-556), bacteria (Ladner US Pat. No. 5,223,409), spores (Ladner US Pat. No. '409), on plasmid (Cull et al., (1992) Proc. Natl. Acad. Sci. USA 89: 1865-1869), or on phage (Scott and Smith (1990) Science 249: 386-390); (Devin (1990) Science 249: 404-406); (Cwirla et al., (1990) Proc. Natl. Acad. Sci. 87: 6378-6382 (Felici (1991) J. Mol. Biol. 222: 301-310); (Ladner supra) (the entire disclosure of which is hereby incorporated by reference).

  The binding of the CPP or biologically active portion thereof to its cognate target molecule can be determined by detecting the labeled CPP or biologically active portion thereof in the complex, for example CPP or Determination of the ability of a test compound to modulate CPP activity can also be accomplished by attaching that biologically active moiety to a labeling group. For example, the degree of complex formation can be measured by immunoprecipitation of the complex or by performing gel electrophoresis.

  It is also within the scope of the present invention to determine the ability of a compound to interact with its cognate target molecule without labeling any reactant. For example, a microphysiometer can be used to detect an interaction between a compound and its cognate target molecule without labeling the compound or the target molecule. McConnell, H.M. et al., (1992) Science 257: 1906-1912 (the entire disclosure of which is hereby incorporated by reference). A microphysiometer, such as a site sensor, is an analytical device that measures the rate at which cells acidify their environment using light addressable potential measurement (LAPS). This change in acidification rate can be used as an indicator of the interaction between the compound and the receptor.

  In a preferred embodiment, the assay comprises: contacting a cell expressing CPP or a biologically active portion thereof with a target molecule to form an assay mixture, contacting the assay mixture with a test compound, and the test compound is CPP Or determining the ability to modulate the activity of the biologically active portion thereof. Determining the ability of a test compound to modulate the activity of a CPP or biologically active portion thereof is: the ability of a test compound to modulate the biological activity of a CPP-expressing cell (eg, as discussed above, CPP Determining the interaction with the target molecule).

  In another preferred embodiment, the assay comprises contacting a cell that responds to CPP or biologically active portion thereof with CPP or biologically active portion thereof to form an assay mixture and testing the assay mixture. Contacting the compound and determining the ability of the test compound to modulate the activity of the CPP or biologically active portion thereof. Determining the ability of a test compound to modulate the activity of a CPP or biologically active portion thereof includes determining the ability of a test compound to modulate the biological activity of a CPP-responsive cell.

  In another embodiment, the assay comprises contacting a cell expressing a CPP target molecule (ie, a molecule with which CPP interacts) with a test compound and determining the ability of the test compound to modulate the activity of the CPP target molecule. Including cell-based assays. Achieving a determination of the ability of a test compound to modulate the activity of a CPP target molecule, for example by assessing the activity of the target molecule or assessing the ability of a CPP to bind to or interact with a CPP target molecule it can.

  Determination of the ability of a CPP to bind to or interact with a CPP target molecule can be accomplished, for example, by one of the methods described above for determining binding directly or indirectly. In a preferred embodiment, the assay comprises contacting a CPP or biologically active portion thereof with a known compound that binds to the CPP (eg, a CPP antibody or target molecule) to form an assay mixture, Contacting the CPP with the test compound before or after and determining the ability of the test compound to interact with the CPP. Determining the ability of a test compound to interact with a CPP includes determining the ability of the test compound to preferentially bind to CPP or a biologically active portion thereof as compared to a known compound. Determining the ability of a CPP to bind to a CPP target molecule can also be accomplished using techniques such as real time biomolecular interaction analysis (BIA). Sjolander, S. and Urbaniczky, C. (1991) Anal. Chem. 63: 2338-2345 and Szabo et al., (1995) Curr. Opin. Struct. Biol. 5: 699-705 (all disclosures cited) As a part of this specification). “BIA” as used herein is a technique for studying biospecific interactions in real time without labeling any of the reactants (eg, BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indicator of real-time reactions between biological molecules.

  In another embodiment, the assay comprises contacting a CPP or biologically active portion thereof with a test compound and determining the ability of the test compound to modulate the activity of the CPP or biologically active portion thereof. It is a free assay. In a preferred embodiment, determining the ability of a CPP to modulate or interact with a CPP target molecule can be accomplished by determining the activity of the target molecule. For example, the target molecule is contacted with CPP or a fragment thereof, and the induction of the target cellular secondary messengers (eg cAMP, STAT3, Akt, intracellular Ca2 +, diacylglycerol, IP3, etc.) is measured and the target for the appropriate substrate Detecting the catalytic / enzymatic activity of the gene and detecting induction of a reporter gene (including a target responsive regulatory element operably linked to a detectable marker, eg, a nucleic acid encoding luciferase) or target modulation The activity of the target molecule can be determined by detecting the cellular response that has been made, such as signal transduction or protein: protein interactions.

  The cell-free assays of the present invention are suitable for use in both soluble and / or membrane-bound forms of isolated proteins (eg, CPP or biologically active portions thereof or molecules to which CPP targets bind). . For cell-free assays using an isolated protein in membrane-bound form, it may be desirable to utilize a solubilizer so that the membrane-bound form of the isolated protein is maintained in solution. Examples of such solubilizers include n-octyl glucoside, n-dodecyl glucoside, n-dodecyl maltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton ™ X-100, Triton (Trademark) X-114, Thesit (trademark), isotridecipoly (ethylene glycol ether) n, sulfonic acid 3-[(3-coramidopropyl) dimethylaminio] -1-propane (CHAPS), sulfonic acid 3-[( Non-ionic detergents such as 3-coramidopropyl) dimethylaminio] -2-hydroxy-1-propane (CHAPSO) or N-dodecyl sulfonate N, N-dimethyl-3-ammonio-1-propane Is mentioned.

  In one or more embodiments of the above-described assay method of the present invention, to accommodate assay automation, at the same time to facilitate separation of complex forms from uncomplexed forms of one or both proteins or CPP or its It may be desirable to immobilize any of the target molecules. Binding of the test compound to the CPP or interaction of the CPP with the target molecule in the presence and absence of the candidate compound is described in any container suitable for containing the reactants and described herein. This can be achieved by any fixation protocol. Alternatively, the complex can be dissociated from the matrix and the level of CPP binding or activity determined using standard techniques.

  Other techniques for immobilizing proteins on a matrix can also be used in the screening assays of the present invention. For example, either a CPP or CPP target molecule can be immobilized utilizing a conjugate of biotin and streptavidin. Biotinylated CPP or target molecule was prepared from biotin-NHS (N-hydroxysuccinimide) using techniques well known in the art (eg, biotinylation kit, Pierce Chemicals, Rockford, Ill.) And coated with streptavidin Can be fixed to a well (Pierce Chemical) of a 96-well plate. Alternatively, an antibody that reacts with CPP or a target molecule but does not interfere with binding of CPP to its target molecule can be derivatized to the well of the plate, and unbound target or CPP can be captured in the well by antibody binding. Methods for detecting such complexes include, in addition to those described above for GST-immobilized complexes, immunodetection of complexes using antibodies that react with CPP or target molecules, and associated with CPP or target molecules. Enzyme binding assays that rely on detection of enzyme activity.

  In another embodiment, a cell is contacted with a candidate compound and a modulator of CPP expression is identified in a method that determines the expression of CPP mRNA or protein in the cell. The level of CPP mRNA or protein expression in the presence of the candidate compound is compared to the level of CPP mRNA or protein expression in the absence of the candidate compound. The candidate compound can then be identified as a modulator of CPP expression based on this comparison. For example, a candidate compound is identified as a stimulator of CPP mRNA or protein expression if the expression of the CPP mRNA or protein is greater in the presence of the candidate compound than in the absence (statistically significantly greater). Alternatively, a candidate compound is identified as an inhibitor of CPP mRNA or protein expression if the expression of CPP mRNA or protein is less in the presence of the candidate compound (statistically significantly less). The level of CPP mRNA or protein expression in a cell can be determined by the methods for detecting CPP mRNA or protein described herein.

  In yet another aspect of the invention, CPP is used as a “bait protein” in two-hybrid assays or three-hybrid assays (eg, US Pat. No. 5,283,317; Zervos et al., (1993) Cell 72: 223-232; Madura et al., (1993) J. Biol. Chem. 268: 12046-12054; Bartel et al., (1993) Biotechniques 14: 920-924; Iwabuchi et al., (1993) Oncogene 8: 1693-1696; And Brent WO 94/10300 (the entire disclosure of which is hereby incorporated by reference), binds or interacts with CPP ("CPP binding protein" or "CPP-bp"), and is associated with CPP activity. Other proteins involved can be identified. Such CPP binding proteins may also be involved in signal propagation by CPP or CPP targets, for example as downstream elements of CPP-mediated signaling pathways.

  The two-hybrid system is based on the modular properties of most transcription factors consisting of separable DNA binding and activation domains. Briefly, the assay utilizes two different DNA constructs, in which a gene encoding CPP or a fragment thereof is fused to a gene encoding the DNA binding domain of a known transcription factor (eg, GAL-4). Let In the other construct, a DNA sequence from a library of DNA sequences that encodes an unidentified protein ("prey" or "sample") is fused to a gene encoding an activation domain of a known transcription factor. When “bait” and “prey” proteins can interact in vivo to form a CPP-dependent complex, the DNA binding and activation domains of transcription factors become in close proximity. This approach allows transcription of a reporter gene (eg, LacZ) that is operably linked to a transcriptional regulatory site that is responsive to a transcription factor. Reporter gene expression can be detected and cell colonies containing functional transcription factors can be isolated and used to obtain cloned genes encoding proteins that interact with CPP. it can.

  The present invention further relates to novel agents identified by the screening assays described above and methods for producing such agents through the use of these assays. Accordingly, in one embodiment, the invention includes a compound or agent obtainable by a method comprising any one step of the screening assays described above (eg, cell based assays or cell free assays).

  Accordingly, it is within the scope of this invention to further use an agent identified as described herein in an appropriate animal model. For example, agents identified as described herein (eg, CPP modulators or CPP binding partners) can be used in animal models to determine the efficacy, toxicity, or treatment side effects of such agents. Alternatively, agents identified as described herein can be used in animal models to determine the mechanism of action of such agents. Furthermore, the present invention relates to the use of novel agents identified by the screening assays described above for treatment as described herein.

  The present invention also relates to the use of novel agents identified by the screening assays described above for diagnosis, prognosis, prevention, and treatment as described herein. Accordingly, the use of such agents in the design, formulation, synthesis, manufacture, and / or production of a drug or pharmaceutical composition for use in diagnosis, prognosis, or treatment as described herein is within the scope of the present invention. Is within. For example, in one embodiment, the present invention includes a method of synthesizing or producing a drug or pharmaceutical composition with reference to the structure and / or properties of a compound obtainable by one of the screening assays described above. For example, based on the structure and / or properties of a compound obtained by contacting a cell expressing a CPP target molecule with a test compound and determining the ability of the test compound to bind to or modulate the activity of the CPP target molecule Thus, a drug or pharmaceutical composition can be synthesized. In another illustrative embodiment, the invention contacts a CPP or biologically active portion thereof with a test compound and the test compound binds to or binds to the CPP or biologically active portion thereof. It includes a method of synthesizing a drug or pharmaceutical composition based on the structure and / or properties of a compound obtained by a method for determining the ability to modulate activity.

Animal-based drug screening It is also advantageous to perform drug screening assays in vivo. In vivo screening assays are performed on non-human animals to find effective CPP modulators that may play a role in cardiovascular disease. Animal based model systems for cardiovascular disease include, but are not limited to, non-recombinant animals and transgenic animals.

  Examples of non-recombinant animal models of cardiovascular disease include genetic models. Such genetic cardiovascular disease models include apoB or apoR deficient pigs (Rapacz, et al., 1986, Science 234: 1573-1577) and Watanabe hereditary high fat plasma (WHHL) rabbits (Kita et al., 1987 Proc. Natl. Acad. Sci. USA 84: 5928-5931). Non-recombinant, non-genetic animal models of atherosclerosis can include, for example, porcine, rabbit, or rat models, where the animal is chemically damaged by, for example, LDL supplementation to the diet or balloon catheter Exposed to any mechanical damage due to angiogenesis.

  As shown in the art (Ferns, GAA et al., (1991) Science, 253: 1129-1132), a rat carotid artery injury model of restenosis would be useful in showing potential therapeutic effects . An example of this model is described in US Pat. No. 6,500,909, the disclosure of which is hereby incorporated by reference. Briefly, the protocol approved by the National Institute of Aging Animal Experiment Committee is 6 months Wistar from a GRC colony anesthetized intraperitoneally with 20 mg / kg body weight pentobarbital, 2 mg / kg body weight ketamine and 4 mg / kg body weight xylazine. Rats were used. The left external carotid artery was cannulated with a 2-French Fogarty embolectomy catheter, inflated with saline, and passed through the common carotid artery three times up and down to create an expandable deendothelial injury. With an appropriate solution such as DMSO: Cremophor EL: absolute ethanol: phosphate buffered saline 1: 2: 2: 165 by intraperitoneal injection starting 2 hours after the injury, by an appropriate dose of test substance or vehicle alone. Animals were treated (based on body weight per day). The test substance or vehicle alone was administered as an intraperitoneal injection once a day for the next 4 days. After 11 days, animals (8 treatments, 10 vehicle treatments) were anesthetized as described above and the carotid arteries were isolated, fixed in 10% buffered formalin and embedded in paraffin. The carotid artery cross-section was mounted on a microscope slide and stained with hematoxylin and eosin dye. An image of the carotid artery was projected onto a digital board and the intima and media cross-sectional areas were measured. The decrease (thickening) of the neointimal area indicates that the test substance is an effective anti-restenosis agent.

In a causal relationship, interference of bile acid recirculation from the lumen of the intestinal tract is found to reduce serum cholesterol levels. Epidemiological data has been accumulated showing that such a decrease leads to an improvement in the pathology of atherosclerosis (Stedronsky, Biochimica et Biophysica Acta, 1210: 255-287 (1994)). Inhibition of cholesteryl ester transfer protein (CETP) has been shown to effectively modify the plasma HDL / LDL ratio and is expected to inhibit the progression and / or formation of certain cardiovascular diseases. Inhibition of CETP leads to increased plasma HDL cholesterol and decreased plasma LDL cholesterol, thereby providing a therapeutically beneficial plasma lipid profile (McCarthy, Medicinal Res. Revs., 13: 139-159 (1993)). ^In vivo assays for compounds that block rat ileal uptake of ¹⁴ C-taurocholic acid into bile are disclosed in US Pat. No. 6,489,366 and Une, et al., Biochimica et Biophysica Acta, 833: 196-202 (1985). , The disclosure of which is incorporated herein by reference.

Briefly, male Wistar rats (200-300 g) are anesthetized with inactin (100 mg / kg). The bile duct is cannulated with a 10 inch long PE10 tube. Expose the small intestine and place on a gauze pad. A cannula (1/8 "luer lock, tapered female adapter) is inserted 12 cm from the small intestine and caecum junction. A slit is cut 4 cm from this same junction (using an 8 cm long ileum) Flush the intestine with 20 ml of warm Dulbecco's phosphate buffered saline (PBS) (pH 6.5). A 20 cm long silicone tube (inner diameter 0.02 "x outer diameter 0) at the distal opening. The proximal cannula is connected to a peristaltic pump and the intestine is flushed with warm PBS for 20 minutes at 0.25 ml / min. The temperature of the intestinal part is continuously monitored. the 2.0 ml ⁽¹⁴ C-taurocholate 0.05mCi / ml with 5mM non-radioactive labels taurocholate) control sample was loaded on intestinal segments in 3ml syringe at the start, and bile Control samples are injected at a rate of 0.25 ml / min for 21 minutes Bile sample fractions are collected every 3 minutes for the first 27 minutes of the procedure 21 minutes after sample injection, the ileal loop Is rinsed with 20 ml of warm PBS (using a 30 ml syringe), and then the loop is rinsed with warm PBS at 0.25 ml / min for 21 minutes, starting a second perfusion as described above, but with the test compound administered as well ( 21 minutes followed by a 21 minute wash), and bile is sampled every 3 minutes for the first 27 minutes, optionally a third perfusion containing the control sample is performed as described above.

  In addition, measurement of liver cholesterol concentration is a useful assay for determining the effectiveness of a test substance against cardiovascular disorders. In this assay, liver tissue is weighed and homogenized in chloroform: methanol (2: 1). After homogenization and centrifugation, the supernatant is separated and dried under nitrogen. The residue is dissolved in isopropanol and cholesterol oxidase and as described in Allain, CA et al., Clin. Chem., 20: 470 (1974) (incorporated herein by reference). Cholesterol content is measured enzymatically using a combination of peroxidases.

  Similarly, serum cholesterol can be determined as follows. Total serum cholesterol is measured enzymatically using a commercial kit from Wako Fine Chemicals (Richmond, VA); Cholesterol C11, catalog number 276-64909. With this same kit, HDL cholesterol can be assayed after precipitation of VLDL and LDL with Sigma Chemical Co. HDL cholesterol reagent, catalog number 352-3 (dextran sulfate method). Total serum triglyceride (blank) (TGI) is also assayed enzymatically with Sigma Chemical Co. GPO-Trinder, catalog number 337-B. VLDL and LDL (VLDL + LDL) cholesterol concentrations are calculated as the difference between total cholesterol and HDL cholesterol. In contrast to the control, a decrease in VLDL + LDL in the test article treated sample indicates an effective anti-cardiovascular disorder agent.

A canine model for evaluating lipid-lowering drugs can also be utilized, for example, as described in US Pat. No. 6,489,366.
Briefly, it was obtained from a vendor such as Marshall Farm, and male beagle dogs weighing 6-12 kg were fed once a day for 2 hours and allowed free access to water. Administration group consisting of 6 to 12 dogs randomly: vehicle, intragastric administration; 1 mg / kg, intragastric administration; 2 mg / kg, intragastric administration; 4 mg / kg, intragastric administration; 2 mg / kg, oral administration (powder in capsule); Intragastric administration of a therapeutic substance dissolved in an aqueous solution (eg, 0.2% Tween 80 solution [polyoxyethylene monooleate, Sigma Chemical Co., St. Louis, MO]) can be performed using a gastric tube. . Before initiating dosing, blood samples can be taken from the cephalic vein before feeding in the morning to assess serum cholesterol (total and HDL) and triglycerides. Animals are dosed in the morning for several consecutive days before food. Allow the animals to eat for 2 hours, after which all remaining food is removed. Feces can be collected at the end of the study for 2 days and analyzed for bile acid or lipid content. A blood sample is also taken at the end of the treatment period and compared to serum lipid levels prior to testing. Statistical significance is determined at p <0.05 using a standard student t test.

  Serum lipid measurement is measured similarly. Blood is collected from the cephalic vein of a fasted dog into a serum separator tube (Vacutainer SST, Becton Dickinson and Co., Franklin Lakes, NJ). The blood is centrifuged at 2000 rpm for 20 minutes and the serum is decanted. Measuring total cholesterol in a 96-well format using the Wako Enzyme Diagnostic Kit (Cholesterol CII) (Wako Chemicals, Richmond, VA) which produces hydrogen peroxide measured by colorimetry using the cholesterol oxidase reaction it can. Prepare a 0.5-10 ug cholesterol standard curve in the first two columns of the plate. Serum samples (20-40 ul, depending on expected lipid concentration) or known serum control samples are added in duplicate to separate wells. Add water to bring the volume of each well to 100ul. A 100 ul aliquot of color reagent is added to each well and after incubation at 37 ° C. for 15 minutes, the plate is read at 500 nm.

  HDL cholesterol can be assayed using Sigma kit number 352-3 (Sigma Chemical Co., St. Louis, Mo.) that selectively precipitates LDL and VLDL utilizing dextran sulfate and Mg ions. A volume of 150 ul of each serum sample is added to individual microtubes, followed by 15 ul of HDL cholesterol reagent (Sigma 352-3). Samples are mixed and centrifuged at 5000 rpm for 5 minutes. A 50 ul aliquot of the supernatant is then mixed with 200 ul of saline and assayed using the same procedure as for total cholesterol measurement.

  Triglycerides are measured using a Sigma kit 337 in a 96 well plate format. This procedure measures glycerol, followed by its release by reaction of triglycerides with lipoprotein lipase. A standard curve is generated using a glycerol (Sigma 339-11) standard solution in the range of 1 to 24 ug. Serum samples (20-40 ul, depending on expected lipid concentration) are added to wells in duplicate. Water is added to bring the volume in each well to 100 ul, and 100 ul of color reagent is also added to each well. After mixing and incubating for 15 minutes, the plate is read at 540 nm and triglyceride values are calculated from a standard curve. Run on homotypic plates with blank enzyme reagent and correct for any endogenous glycerol in the serum sample.

  Effects on serum glucose and serum insulin in db / db mice (C578BL / KsJ-db / db Jcl) as described in US Pat. No. 6,462,046, the disclosure of which is hereby incorporated by reference. Test compounds can be evaluated for their effects. The compound is dissolved in a vehicle (eg consisting of 2% Tween 80 in distilled water) and administered orally. Dosage is determined by body weight. All aspects of the study, including experiments and animal disposal, are performed in general accordance with the International Guidelines for Biomedical Research involving Animals (CIOMS Publication No. ISBN 9290360194, 1985). Serum glucose is determined using a glucose HA assay kit (Wako, Japan) and insulin is determined using an ELISA mouse insulin assay kit (SPI bio, France). A suitable positive control is troglitazone (Helios Pharmaceutical, Louisville, Ky).

  The animals are divided into 20 groups of 4 animals each. The animal weighs 52 ± 5 g and is 8-10 weeks old. During the experiment, animals have free access to laboratory food (Fwusow Industry Co., Taiwan) and water. Prior to any treatment, a blood sample (pretreatment blood) is taken from each animal. The vehicle group, the four groups of animals, receives only vehicle. Each vehicle group is orally dosed with 100, 30, 10 or 1 ml / kg body weight vehicle. Troglitazone solution (Tween 80/10 ml / kg body weight in water) is orally administered to 4 groups of positive controls at doses of 100, 30, 10, and 1 ml / kg body weight, respectively. The test compound is similarly administered as a solution to four groups of animals, each group receiving a different dose of the compound. Vehicle, positive control and test compound solutions are administered to groups 24 hours and 48 hours immediately after taking pre-treatment blood. Blood is taken 1.5 hours after the last dose (post-treatment blood). Serum glucose is determined enzymatically (mutaratose-GOD) and insulin levels are determined by ELISA (mouse insulin assay kit). An average SEM for each group is calculated and comparison between pre-treatment blood and post-treatment blood yields serum glucose and percent insulin inhibition. Relative to pre-treatment blood, the percentage of serum glucose and insulin level reduction in post-treatment blood is determined, and an unpaired student t-test is applied to the comparison between the control and test solution groups and the vehicle group. Significance was considered as p <0.05. Troglitazone, an effective anti-cardiovascular disorder agent, leads to a decrease in glucose levels (25 ± 2%) at 10 mg / kg body weight.

  US Pat. No. 6,121,319, the disclosure of which is hereby incorporated by reference, describes an assay for the progression of atherosclerosis in hypercholesterolemic rabbits. Rabbits are sacrificed and the aorta is obtained. Stain the aorta with Sudan-4 and analyze the extent of staining. Graph the percent of aortic surface area covered by injury in test article-treated and untreated lipid-fed rabbits. The rabbit aorta treated with an effective anti-atherosclerotic agent is less stained, indicating a reduction in atherosclerosis. In addition, aortic sections are immunostained for VCAM-1 expression or macrophage accumulation using antibodies to VCAM-1 or Ram-11 antigens. A decrease in VCAM-1 expression or macrophage accumulation is indicative of an effective drug compared to a control treated sample.

  LDL cholesterol reduction can also be determined in a primate model. For example, cynomolgus monkeys are hypercholesterolemic by giving a high fat cholesterol diet prior to administration of the test compound. The monkeys are then orally dosed with the test compound or control vehicle for 2 weeks. The decrease in monkey serum LDL cholesterol percentage during this period is indicative of an effective anti-atherosclerotic agent.

Pharmaceutical compositions When the polypeptide of the invention is expressed in a soluble form, for example as a secreted product of transformed yeast or mammalian cells, ammonium sulfate precipitation, ion exchange chromatography, gel filtration, electrophoresis, affinity chromatography For example, “Enzyme Purification and Related Technologies” Methods in Enzymology, 22: 233-577 (1977), and Scopes, R., Protein Purification, which provide guidance for such purification, according to standard procedures in the art, including : They can be purified according to Principles and Practice (Springer-Verlag, New York, 1982). Similarly, if the polypeptide of the invention is expressed in an insoluble form, for example as an aggregate or inclusion body, separating the inclusion body from host cells disrupted by centrifugation, solubilizing the inclusion body with a chaotropic agent and a reducing agent Diluting solubilized mixtures and purifying them by appropriate techniques including reducing the concentration of chaotropic and reducing agents so that the polypeptide assumes a biologically active conformation. Can do. The latter procedure is disclosed in the following literature, which is hereby incorporated by reference: Winkler et al., Biochemistry, 25: 4041-4045 (1986); Winkler et al., Biotechnology, 3 : 992-998 (1985); Koths et al., US Pat. No. 4,569,790; and European Patent Applications Nos. 86306917.5 and 86306353.3.

  Compounds including small molecules, peptides, CPP nucleic acid molecules, and anti-CPP antibodies of the invention that can modulate CPP or CPP biological activity can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically include a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” as used herein refers to any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, and the like that are compatible with pharmaceutical administration. Intended to include tonicity and absorption delaying agents and the like. The use of such solvents and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional solvent or agent is incompatible with the active compound, its use in the composition is contemplated. Supplementary active compounds can also be incorporated into the compositions.

  A composition of the invention is formulated to be compatible with its intended route of administration. Illustrative routes of administration include parenteral, such as intravenous, intradermal, subcutaneous, oral (eg inhalation), transdermal (topical), transmucosal and rectal administration. Solutions or suspensions used for parenteral, intradermal or subcutaneous application may contain the following components: water for injection, saline solution, non-volatile oil, polyethylene glycol, glycerin, propylene glycol or other synthetic solvents Aseptic diluents such as; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; acetates, citrates or phosphates Buffers such as and drugs for tonicity adjustment such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

  Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. Suitable carriers for intravenous administration include physiological saline, bacteriostatic water, Cremophor EL® (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lectin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. A variety of antibacterial and antifungal agents such as parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, etc. can achieve protection of microbial action. In many cases, it will be preferable to include isotonic agents, for example, mannitol, sorbitol, sugars such as sodium chloride, polyalcohols in the composition. Inclusion of agents in the composition that delay absorption, for example, aluminum monostearate and gelatin can result in prolonged absorption of the injectable composition.

  If the active compound is a protein, such as an anti-CPP antibody, by incorporating the required amount of the active compound with one or a combination of the above-listed components in a suitable solvent, followed by sterile filtration if necessary A sterile injectable solution can be prepared. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred method of preparation is vacuum and lyophilization from the pre-sterilized filtered solution resulting in a powder of the active ingredient plus any further desired ingredients .

  Oral compositions generally include an inert diluent or an edible carrier. These can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, eg, a gas such as carbon dioxide, or a nebulizer. Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be passed are used in the formulation. Such penetrants are generally known in the art and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art. Most preferably, the active compound is delivered to the subject by intravenous injection.

  In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microcapsule delivery systems. Biodegradable, biocompatible polymers such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid can be used. Methods for preparing such formulations will be apparent to those skilled in the art. Commercial materials are also available from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in US Pat. No. 4,522,811, the entire disclosure of which is hereby incorporated by reference.

  In another embodiment, the active compound can be coated on a microchip drug delivery device. Such devices are useful for the controlled delivery of proteinaceous compositions to an individual's bloodstream, cerebrospinal fluid, lymph fluid, or tissue without subjecting such compositions to digestion or to an individual. . Methods for using the microchip drug delivery device are described in US Pat. Nos. 6,123,861, 597898 and US Patent Application No. 2002201176A1, the entire disclosure of which is hereby incorporated by reference.

  It is especially advantageous to formulate oral or preferably parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form, as used herein, refers to physically discrete units suitable for uniformity of dosage for the subject being treated; each unit is calculated to produce the desired therapeutic effect. A predetermined amount of active compound together with the required pharmaceutical carrier. The specifications for the dosage unit forms of the present invention are determined by the unique properties of the active compound and the specific therapeutic effect achieved, as well as inherent limitations in the field of formulating such active compounds for the treatment of individuals, and It depends directly on it.

  Standard toxicity in cell cultures or experimental animals to determine the toxic and therapeutic effects of such compounds, eg LD50 (a lethal dose to 50% of the population) and ED50 (a therapeutically effective dose to 50% of the population). It can be determined by pharmaceutical procedures. The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50 / ED50. Compounds that exhibit large therapeutic indices are preferred. Compounds that exhibit toxic side effects can be used, but care should be taken in the design of delivery systems that target such compounds to affected tissue sites in order to minimize the potential for damage to uninfected cells and thereby reduce side effects Have to pay.

Data obtained from cell culture assays and animal studies can be used to calculate dosage ranges for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. The dose is formulated in animal models to achieve circulation and is used to more accurately determine useful doses in humans. For example, plasma levels can be measured by high performance liquid chromatography.
The pharmaceutical composition can be included in a container, pack or dispenser together with instructions for administration.

Cardiovascular Disease Therapy The CPP modulators and anti-CPP antibodies of the present invention can be used for the treatment or prevention of CPP-related disorders. Accordingly, in one aspect, the invention relates to a pharmaceutical composition containing an antibody, antibody fragment, or peptide modulator of CPP, preferably containing a pharmaceutically acceptable carrier or diluent. The carrier or diluent is preferably adapted for oral, intravenous, intramuscular or subcutaneous administration. The pharmaceutical composition can comprise or consist essentially of any of the CPP modulators, anti-CPP antibodies, or anti-CPP antibody fragments described herein.
Many drugs are useful for the treatment and prevention of cardiovascular disorders. Such agents can be advantageously used in combination with CPP related compositions.

  For example, cell cycle inhibitors and proto-oncogenes (Simari and Nabel, Semin. Intervent. Cardiol. 1: 77-83 (1996)); NO (nitrogen monoxide) donor drugs; pro-apoptotic agents such as bcl-x (Pollman et al., Nature Med. 2: 222-227 (1998)); herpesvirus thymidine kinase (tk) gene and systemic ganciclovir (Ohno et al., Science 265: 781-784 (1994); Guzman et al., Proc. Natl. Acad. Sci. USA 91: 10732-10736 (1994); Chang et al., Mol. Med. 1: 172-181 (1995); and Simari et al., Circulation 92: 1-501 (1995) )) Has been used to treat atherosclerosis, restenosis and neointimal smooth muscle proliferation. The disclosures of the above references are hereby incorporated by reference.

  Antithrombotic agents useful in combination with the compositions of the invention include, for example, inhibitors of IIb / IIIa integrin; tissue factor inhibitors; and antithrombin agents. Vukmir, Am. J. Emer. Med. 13: 459-470 (1995); Grant, PACE 20: 432-444 (1997); Assmann I., Curr. Med. Res. Opin. 13: 325-343 (1995) ); And Lipka et al., Am. Heart J. 130: 632-640 (1995), the disclosure of which is hereby incorporated by reference in its entirety. Agents), sympathetic nerve antagonists (Group II agents), antifibrillators (Group III agents) calcium channel agents (Group IV agents) or anionic antagonists (Group V agents) can also be used. Illustrative examples of Group I agents include: procainamide; quinidine or disopyramide; lidocaine; phenytoin; tocainide or mexiletine; encainide; flecainide; lorcainide; Sympathetic antagonists include: propranolol, esmolol, metoprolol, ateneral, or acebutolol. Illustrative antifibrillators are bretylium, amiodarone, sotalol (II) or N-acetylprocainamide. Group IV agents include verapamil, diltiazem and bepridil, and anionic antagonists such as alinidine.

  Congestive heart failure treatments include Embrel ™ (Immunex Corp .; Seattle, Wash.), TNF inhibitors such as TBC11251 or ACE (angiotensin converting enzyme) inhibitors such as Natrecor (Nesiritide; Scios, Inc.) Is mentioned. Recombinant VEGF isoforms such as rhVEGF developed by Genentech, for example an angiogenic agent; nucleic acid molecules encoding 121 amino acid isoforms of VEGF (BioByPass ™; Gen Vec / Parke Davis); or encoding VEGF-2 Nucleic acids (Vascular Genetics, Inc.); a recombinant form of FGF-2 developed by FIBLAST ™, Scios, Inc. (Mountain View, Calif.) And Wyeth Ayerst Laboratories (Radnor, Pa.), GENERX (Trademark) or Collateral Therapeutics (San Diego, Calif.) And Schering AG (Miller and Abrams, Gen. Engin. News 18: 1 (1998), the entire disclosure of which is hereby incorporated by reference) The adenoviral gene therapy vector encoding FGF-4 developed by) is also useful in combination with the CPP-related composition of the present invention. Finally, amlodipine (Marche et al., Int. J. Cardiol. 62 (suppl.): S17-S22 (1997); Schachter, Int. J. Cardiol. 62 (suppl.): S85-S90 (1997)) Nicardipine, nifedipine; propanolol; isosorbide nitrate; diltiazem; and isradipine (Nayler (Ed.) Calcium Antagonists pages 157-260 London: Academic Press (1988); Schachter, Int. J. Cardiol. 62 (suppl.): S9-S15 (1997)) are also advantageous treatments for cardiovascular disorders.

  Although the present invention has been generally described, further understanding can be obtained by reference to specific specific embodiments that are provided for purposes of illustration only and are not intended to be limiting unless otherwise specified. .

Example 1:
Characterization of CPP levels in experimental and control populations Subjects enrolled in the Duke Data Bank for Cardiovascular Disease were selected based on coronary artery disease (CAD). All 241 CAD patients and control individuals were further matched for gender, age, and ethnicity, and individuals with plasma abnormalities were excluded. 53 CAD patients and 53 control individuals were defined. Six liters of plasma from each set was pooled. An aliquot of plasma from each individual is maintained, thus allowing a positive result of the pooled sample to be confirmed for each member of the population. Such confirmation is valuable in dispelling the possibility of confusing individual effects with abnormal levels of specific polypeptides that are unrelated to cardiovascular disorders. 2 and 1/2 liters of pooled plasma from each population were subjected to separation by a multi-stage chromatography process according to the MicroProt ™ method as follows:

Step 1: 125 ml HSA / IgG depleted frozen plasma was thawed and filtered through a 0.45 μm sterile filter in a sterile hood.
Two filtrates, each in 300 ml HSA ligand Sepharose fast flow column (Amersham, Upsala, Sweden), 5 cm id, 15 cm length; and 100 ml protein G Sepharose fast flow column (Amersham, Upsala, Sweden), 5 cm id, 5 cm length The column was injected.
The column was equilibrated with 50 mM PO4 buffer (pH 7.1), 0.15 M NaCl and washed. The flow rate was 5 ml / min.
The non-retained fraction (350 ml) was frozen until the second step. Run 20 times.

Step 2: Gel Filtration / Reverse Phase Capture Step The sample from step 1 was thawed and filtered through a 0.45 μm sterile filter in a sterile hood.
The filtrate was injected into two in-line gel filtration columns: a 2 × 9.5 liter Superdex 75 (Amersham, UK) column, 4 cm inner diameter, 62 cm long. The column was equilibrated with 50 mM PO4 buffer (pH 7.4), 0.1 M NaCl, 8 M urea. Hydrophobic impurities were retained on a reverse phase pre-column: 150 ml PLRPS (Polymer Labs, UK). The precolumn was replaced for sample injection. Gel filtration was performed at a flow rate of 40 ml / min.
Low molecular weight protein (<20 kDa) was adapted to a serial reverse phase capture column: 50 ml PLRPS 100 angstrom (Polymer Labs, UK). The gel filtration eluate was sent to the reverse-phase capture column by switching the 3-way valve controlling the injection with the PLRPS column with a cut-off of 33 mAU (280 nm). This cut-off value is obtained by first using SDS-PAGE to provide an estimated range of OD values, and then by evaluating three cut-off values (high, medium and low values of the OD range). ) Established. The final cut-off value was chosen to maximize the resulting low molecular weight protein and to have at least 85% low molecular weight protein portion. Low molecular weight proteins and peptides were eluted from the reverse phase capture PLRPS column with a 1 column volume gradient of 0.1% TFA, 80% CH3CN in water. The eluate fraction (50 ml) was frozen until the next step. Run 20 times. At the end of this step, all reverse phase eluates were thawed, pooled (1 liter) and divided into 7 polypropylene containers (143 ml). The container was maintained at -20 degrees until used in the next step.

Step 3: The sample from cation exchange step 2 (147 ml) was thawed and mixed with an equal volume of cation exchange buffer A (Gly / HCl buffer 50 mM, pH 2.7, urea 8M).
Samples were injected into a 100 ml Source 15S column (Amersham, Upsala, Sweden), 35 mm ID, 100 mm length. The column was equilibrated with buffer A and washed. The flow rate was 10 ml / min.
Proteins and peptides were eluted with a step gradient from 100% buffer A to 100% buffer B (buffer A containing 1 M NaCl):
7.5% B (75 mM NaCl) 3 column volume 10% B (100 mM NaCl) 3 column volume 17.5% B (175 mM NaCl) 3 column volume 22.5% B (225 mM NaCl) 2 column volume 27.5% B (275 mM NaCl) 2 column volume 100% B (1M NaCl) 2 column volume 45-60 fractions were collected based on the peak. Run 7 times. After achieving 7 runs, the fractions during and between runs were pooled to obtain 18 fractions. Fractions were maintained at -20 degrees until used in the next step.

Step 4: Reduction / alkylation and reverse phase HPLC fractionation 1
After adjusting the pH to 8.5 with concentrated Tris HCl, each of the 18 cation exchange fractions was reduced with dithiothreitol (DTE, 30 mM at 37 ° C. for 3 hours) and iodoacetamide (120 mM at 25 ° C. in the dark). 1 hour). The latter reaction was stopped by addition of DTE (30 mM) followed by acidification (TFA, 0.1%). Subsequently, the fraction was injected into an Uptispher C8, 5 μm, 300 Å column (Interchim, French) inner diameter 21 mm, length 150 mm, and injection was performed at a flow rate of 10 ml / min.
The C8 column was equilibrated with 0.1% TFA in water (solution A) and washed. Proteins and peptides were eluted at 60 minutes using a biphasic gradient from 100% A to 100% B (0.1% TFA in water, 80% CH3CN). The flow rate was 20 ml / min. 40 ml of 30 fractions were collected.
Based on the optical density (OD) measured at 280 nm of each fraction reflecting the protein concentration of that fraction, an aliquot of similar protein content was created for each fraction.
One per fraction, add 500 μl of 10% glycerol in water to each fraction to prevent excessive drying, then dry with SpeedVac (Savant, Fischer, Geneva), otherwise all aliquots for further use Was frozen and maintained. The dried fraction was maintained at −20 ° C. until used in the next step.

Step 5: Reversed phase HPLC fractionation 2
The dried sample from step 4 is resuspended in 1 ml of solution A (0.03% TFA in water) and made to a Vydac LCMS C4 column, 5 micrometers, 300 Angstrom (Vydac, USA) ID 4.6 mm, length 150 mm. Injected. The flow rate was 0.8 ml / min.
The C4 column was equilibrated with solution A and washed, and the protein and peptide were eluted using a biphasic gradient adapted to the elution position of the reverse phase HPLC fraction 1 sample. Uncorrected mass data was acquired using an electrospray ion trap mass spectrometer. Sixteen different gradients were used with CH3CN concentration range RP1 fraction equivalent solvent concentration ± 5%. For proteins eluted with RP1 at a solvent concentration equal to or greater than 30% CH3CN, the starting elution conditions for the RP2 gradient were set at CH3CN percentage, RP1 elution concentration minus 30%. Twenty-four eluted fractions were collected in deep well plates and adapted to different optimized collection forms designed for optimal SpeedVac enrichment and further robotic processing.

Step 6: After mass detection reverse phase HPLC fractionation 2, approximately 13000 fractions were collected in 96 well deep well plates (DWP). A small portion (2.5%) of the volume was diverted to online analysis using LC-ESI-MS (Bruker Esquire). An aliquot of undigested protein was mixed with a MALDI matrix and spotted on a MALDI plate along with a mass calibration standard and a sensitivity standard. An automatic spotting device (Bruker MALDI sample preparation robot) was used. Two different MALDI matrices were used: sinapic acid (SA), also known as sinapinic acid, trans-3,5-dimethoxy-4-hydroxycinnamic acid, and alpha-cyano-4-. Hydroxycinnamic acid (HCCA). The MALDI plate was subjected to mass detection using a Bruker Reflex III MALDI MS instrument. 96 well plates were stored at + 4 ° C.

  A 96-well plate (DWP) was collected and subjected to two consecutive concentration steps. By drying with SpeedVac, the volume was concentrated from 0.8 ml to about 50 μl per well and then redissolved to approximately 200 μl and reconcentrated to about 50 μl per well and stored at + 4 ° C. The protein was then digested by rebuffering, adding trypsin to the wells, sealing and incubation of the plate at 37 ° C. for 12 hours, followed by quenching (adding formic acid to lower the pH to 2.0). The concentration of trypsin added to the wells was adjusted based on the OD at 280 nm recorded for each specific fraction. This ensures optimal use of trypsin and complete digestion of the most concentrated fraction. An automatic spotting device (Bruker MALDI sample preparation robot) was used to load a constant volume from each well, premixed with the HCCA matrix, along with sensitive and mass calibration standards, on a MALDI plate. MALDI plates were analyzed using a Bruker Reflex III MALDI MS instrument. The content from each well of the 96-well plate was analyzed by LC-ESI-MS-MS Bruker Esquire ESI ion trap MS instrument.

Step 7: Detection and identification of low abundance peptides in human plasma The separated fractions are further subjected to mass spectrometry for separation and detection (both matrix-assisted laser desorption / ionization (MALDI) and MS-MS).
Uncorrected mass data, peptide mass fingerprint and peptide sequence data were integrated for protein identification and characterization. Proteins were identified using Mascot software (Matrix Science Ltd, London, UK), and results from peptide identification were confirmed by manual analysis of the spectra.
Of the proteins identified by this method, calgranulin A (S100 calcium binding protein A8 with SwissProt accession number P05109) is expressed more in samples pooled from controls than in samples pooled from CAD patients. (Eg, peptides from a protein are observed in twice as many control fractions as compared to the disease fraction, and the cumulative score obtained during mass spectral identification of this protein is the control sample About 2.5 times higher). Calgranulin A has been characterized as a pro-inflammatory protein (Odink et al., Nature 330 (6143): 80-82 (1987) and many subsequent references). This is expressed by leaching of myeloid cells during the inflammatory response, where it binds to the glycosaminoglycan structure of epithelial cells (Robinson, et al., JBC 277: 3658-3665 (2002)). Interestingly, PCT Publication No. WO 00/61472 discloses the use of calgranulin A for the treatment of heart failure caused, for example, by atherosclerosis. In addition, PCT Publication No. WO 00/18970 discloses the use of calgranulin A as an inhibitor of vascular membrane growth for the prevention of myocardial infarction and hypertension. Thus, the protein separation and identification studies described herein are effective in providing proteins that have a beneficial effect in the treatment of the disease being studied when detected at higher levels in control samples than in disease samples. It seems to be.

  Conversely, the identification of the matrix Gla protein (SwissProt accession number P08493) is the protein separation and identification described in this example because it is overexpressed in samples pooled from CAD patients by comparison with samples pooled from controls. Enabled by the method (eg, peptides from the protein are almost twice as high in the disease fraction compared to the control fraction, and the cumulative score obtained during mass spectral identification of this protein is related to the disease sample. 2 times higher). MGP is a vitamin K-dependent protein related to the organic matrix of bone and cartilage. Mori et al., Demonstrated that MGP can prevent vascular calcification (FEBS Letters 433: 19-22 (1998)). MGP levels are elevated in atheroma plaques as a possible feedback response to vascular calcification. PCT Publication Nos. WO01 / 02863 and WO01 / 25427 describe MGP as a biomarker for atherosclerosis and cardiovascular disorders. Thus, the protein separation and identification studies described herein would be useful in providing proteins with recognized uses in the diagnosis of the disease being studied.

The tryptic peptides of SEQ ID NOs: 3-5, 8-10, 13-14, 18-23, and 26-28 listed in FIG. 1 and Table 1 were observed only in coronary artery disease samples by tandem mass spectrometry.
The presence of trypsin peptide is present at high levels in a starting plasma sample of an individual having a polypeptide comprising the amino acid sequence of SEQ ID NO: 3 (SNCCQHSSSALGLAR), SEQ ID NO: 4 (CTSMASENSECSV) or SEQ ID NO: 5 (TIVGSINTNFGICGGAGR) It shows that. Such polypeptides include those represented by the sequences of SEQ ID NO: 1 and 2 (CPP2).

The presence of trypsin peptide is present at high levels in a starting plasma sample of an individual with a polypeptide comprising the amino acid sequence of SEQ ID NO: 8 (YAQTPANMFYIVACDNR), SEQ ID NO: 9 (RDPPQYPVPVPVHLDR) or SEQ ID NO: 10 (DPPQYPVPVPVHLDR) It shows that. Such polypeptides include those represented by the sequences of SEQ ID NOs: 6 and 7 (CPP9).
The presence of trypsin peptide indicates that a polypeptide comprising the amino acid sequence of SEQ ID NO: 13 (AVVHGILMG VPVPFPIPEPDGCK) or SEQ ID NO: 14 (SGINPPIQK) was present at high levels in the starting plasma sample of individuals with CAD. Such polypeptides include those represented by the sequences of SEQ ID NOs: 11 and 12 (CPP21).

The presence of trypsin peptide is present at high levels in a starting plasma sample of an individual having a polypeptide comprising the amino acid sequence of SEQ ID NO: 26 (EPLDDYVNTQGPSLFSVTK), SEQ ID NO: 37 (CEEDKEFTCR) or SEQ ID NO: 28 (AFQYHSK) It shows that. Such polypeptides include those represented by the sequences of SEQ ID NOs: 24 and 25 (CPP20).
Finally, the tryptic peptides SEQ ID NO: 18-23 listed in FIG. 4 and Table 1d were observed at high levels in coronary artery disease samples by tandem mass spectrometry. The presence of trypsin peptides is SEQ ID NO: 18 (ADEVAAAPEQIAADIPEVVVSLAWDESLAPK), SEQ ID NO: 19 (IPACIAGER), SEQ ID NO: 20 (RYGTCIYQGR), SEQ ID NO: 21 (YGTCIYQGR), SEQ ID NO: 22 (YGTCIFQG). It shows that a polypeptide comprising the amino acid sequence of (LWAFCC) was present at high levels in the starting plasma sample of individuals with CAD. Such polypeptides include those represented by the sequences of SEQ ID NOs: 15, 16, and 17 (CPP17). Tryptic peptides were reduced in non-CAD control samples.

CPP2, CPP9, CPP20 and CPP21 tryptic peptides were not detected in non-CAD control samples, and they were detected at very low levels for CPP17. In addition, the tryptic peptide of SEQ ID NO: 18 from CPP17, derived from the preprotein of SEQ ID NO: 16, and it is predicted not to be found in plasma itself and was observed only in diseased plasma (Table 1d). This observation may reflect changes in preprotein processing in the case of disease.
The method of protein separation and identification according to the present invention is very sensitive. The Microprot ™ method can detect very low abundance proteins with plasma concentrations in the hundreds of pM range. The accuracy was confirmed during the implementation of the method described here. Proteins with a well-characterized role, particularly in atherosclerosis and CAD, were differentially detected in CAD and control samples (supra). Thus, due to the absence of some of the listed peptides in the control plasma, the corresponding CPP (CPP2, CPP9, CPP20 and CPP21) is usually present at negligibly low levels in the plasma, if any. Is shown.

Example 2:
Chemical Synthesis of CPP In this example, the CPP of the present invention is synthesized. Peptide fragment intermediates are first synthesized and then assembled into the desired polypeptide.
Initially a CPP can be prepared with, for example, 5 fragments selected to have a Cys residue at the N-terminus of the ligated fragment. Fragment 1 is first coupled to fragment 2 to give a first product, and after preparative HPLC purification, the first product is then coupled to fragment 3 to give a second product. After preparative HPLC purification, the second product is coupled to fragment 4 to give a third product. Finally, after preparative HPLC purification, the third product is coupled to fragment 5 to yield the desired polypeptide, which is purified and refolded.

Thioester formation Fragments 2, 3, 4 and 5 are synthesized on a thioester making resin as described above. For this purpose, the following resin is prepared: S-acetylthioglycolic acid pentafluorophenyl ester is coupled to Leu-PAM resin essentially under the conditions described in HackengB et al., (1999). Let In the first case, after removing the acetyl protecting group by treatment with 10% mercaptoethanol, 10% piperidine in DMF for 30 minutes, the resulting resin was used as a starting resin for elongation of the peptide chain on a 0.2 mmol scale. Use. Instead of the conventional N ^alpha or Cys having a S ^beta protection, Boc-thioproline (Boc-SPr, i.e. Boc-L-thioproline) by binding to each strand of the end of, N-terminal Cys residue from fragment 2 5 protecting the N ^alpha group (e.g. Brik et al, J.Org.Chem, 65: .. 3829-3835 (2000)).

Peptide synthesis
In situ neutralization / 2- (1H-benzotriazole-1 for stepwise Boc chemical chain extension as described in Schnolzer et al., J. Peptide Protein Res., 40: 180-193 (1992). -Ill) Perform solid phase synthesis on Applied Biosystems' specially modified 433A peptide synthesizer using the 1,1,1,3,3-tetramethyluronium hexafluorophosphate (HBTU) activation protocol . Each synthesis cycle consists of 1 to 2 minutes treatment with solvent free TFA, 1 minute DMF flow wash, 10 minutes binding time with 2.0 mmol of Boc-amino acid pre-activated in the presence of excess DIEA, and It consists of N ^α -Boc-removal by a second DMF flow wash. Nα-Boc-amino acid (2 mmol) is preactivated for 3 minutes with 1.8 mmol HBTU (0.5 M in DMF) in the presence of excess DIEA (6 mmol). After conjugation of Gln residues, before and after deprotection with TFA, a dichloromethane flow wash is used to prevent possible high temperature (TFA / DMF) -catalyzed pyrrolidone carboxylic acid formation. Side chain protected amino acids are Boc-Arg (p-toluenesulfonyl) -OH, Boc-Asn (xanthyl) -OH, Boc-Asp (O-cyclohexyl) -OH, Boc-Cys (4-methylbenzyl) -OH, Boc -Glu (O-cyclohexyl) -OH, Boc-His (dinitrophenylbenzyl) -OH, Boc-Lys (2-Cl-Z) -OH, Boc-Ser (benzyl) -OH, Boc-Thr (benzyl)- OH, Boc-Trp (cyclohexylcarbonyl) -OH and Boc-Tyr (2-Br-Z) -OH (Orpagen Pharma, Heidelberg, Germany). Other amino acids are used without side chain protection. C-terminal fragment 1 is synthesized with Boc-Leu-O—CH ₂ —Pam resin (0.71 mmol / g of loaded resin), but for fragments 2 to 5, machine-assisted synthesis is performed with Boc-Xas-S—CH. Start with _2- CO-Leu-Pam resin. This resin is obtained by coupling S-acetylthioglycolic acid pentafluorophenyl ester to Leu-PAM resin under standard conditions. After removal of the acetyl protecting group by treatment with 10% mercaptoethanol, 10% piperidine in DMF for 30 minutes, the resulting resin is used as a starting resin for peptide chain elongation on a 0.2 mmol scale.

After completing chain assembly, the peptide fragment is deprotected and cleaved from the resin by treatment with anhydrous hydrogen fluoride at 0 ° C. for 1 hour using 5% p-cresol as a scavenger. In all cases except fragment 1, the imidazole side chain 2,4-dinitrophenyl (DNP) protecting group remains in the His residue because the DNP removal procedure is not compatible with the C-terminal thioester group. However, DNP is gradually removed by thiols during the ligation reaction, yielding an unprotected His. After cleavage, the peptide fragment is precipitated with ice-cold diethyl ether, dissolved in aqueous acetonitrile and lyophilized. By using a linear gradient of buffer B (acetonitrile / 0.1% trifluoroacetic acid) in buffer A (H ₂ O / 0.1% trifluoroacetic acid) and UV detection at 214 nm on a C18 column (Waters). The peptide fragment is purified by RP-HPLC. Samples are analyzed by electrospray mass spectrometry (ESMS) using an Esquire apparatus (Brueker, Bremen, Germany) or similar apparatus.

As described more fully below the original chemical ligation, ligation of the unprotected fragment is performed as follows: 6M hydrochloric acid to obtain a final peptide concentration of 1-8 mM at pH ˜7. Dissolve the dried peptide in equimolar amounts in guanidine (GuHCl), 0.2M phosphate (pH 7.5) and add 1% benzyl mercaptan, 1% thiophenol. Reactions are usually performed overnight and monitored by HPLC and electrospray mass spectrometry. The ligation product is subsequently processed to remove any protecting groups still present. The opening of the N-terminal thiazolidine ring requires the addition of solid methoxamine to a final concentration of 0.5 M at pH 3.5 and an additional 2 hours incubation at 37 ° C. A 10-fold excess of tris (2-carboxyethyl) phosphine is added prior to preparative HPLC purification. Fractions containing polypeptide chains are identified by ESMS, pooled and lyophilized.

Ligation of fragments 4 and 5 is performed in 6M GuHCl at pH 7.0. The concentration of each reaction is 8 mM, and 1% benzyl mercaptan and 1% thiophenol are added to create a reducing environment and promote the ligation reaction. After stirring overnight at 37 ° C., a nearly quantitative ligation reaction is observed. To open the N-terminal thiazolidine ring, at this point in the reaction, CH ₃ —O—NH ₂ . HCl is added to the solution to obtain a final concentration of 0.5M and the pH is adjusted to 3.5. After 2 hours incubation at 37 ° C., the completion of the reaction is confirmed using ESMS. The reaction mixture was subsequently treated with a 10-fold excess of tris (2-carboxyethylphosphine) on the peptide fragment and after 15 minutes preparative HPLC (eg C4, 20-60% CH ₃ CN, 0.5 per minute). %) Is used to purify the ligation product, lyophilized and stored at −20 ° C.
Repeat the same procedure with minor modifications for the rest of the ligation.

Polypeptide folding Refolding is performed by air oxidation by dissolving reduced lyophilized protein (approximately 0.1 mg / ml) in 1 M GuHCl, 100 mM Tris, 10 mM methionine (pH 8.6). After gentle stirring overnight, the protein solution is purified by RP-HPLC as described above.

Example 3
Preparation of CPP antibody composition Obtain substantially pure CPP or a portion thereof. The protein concentration in the final preparation is adjusted to a level of a few micrograms per ml, for example by concentrating with an Amicon filter device. Monoclonal or polyclonal antibodies against the protein are then prepared as described in the sections entitled “Monoclonal antibodies” and “Polyclonal antibodies”.

  Briefly, mice are inoculated with several micrograms of CPP or a portion thereof over several weeks to produce anti-CPP monoclonal antibodies. The mice are then sacrificed and spleen antibody-producing cells are isolated. The spleen cells are fused with mouse myeloma cells by means of polyethylene glycol and the excess unfused cells are destroyed beyond the growth of the system on selective medium containing aminopterin (HAT medium). The well fused cells are diluted and an aliquot of the dilution is placed in a well of the microtiter plate where the culture is allowed to continue to grow. First, as described in Engvall, E., Meth. Enzymol. 70: 419 (1980) (the disclosure of which is hereby incorporated by reference in its entirety), the wells are prepared by immunoassay procedures such as ELISA. Antibody-producing clones are identified by detection of antibodies in the supernatant. Selected positive clones can be expanded and the monoclonal antibody product collected for use. Detailed procedures for monoclonal antibody production are described in Davis, L. et al., Basic Methods in Molecular Biology Elsvier, New York, Section 21-2, the entire disclosure of which is hereby incorporated by reference. Has been.

For the production of polyclonal antibodies by immunization, a polyclonal antiserum containing antibodies against heterologous epitopes of CPP or part thereof is prepared by immunizing mice with CPP or part thereof, and this is modified or unmodified to immunize. The originality can be enhanced. Any suitable non-human animal can be selected, preferably non-human mammals including rats, rabbits, goats or horses.
Antibody preparations prepared according to either monoclonal or polyclonal protocols are useful for quantitative immunoassays to determine CPP concentrations in biological samples; or they can be used semi-quantitatively or qualitatively to biological samples Identify the presence of the antigen in it. Antibodies can also be used in therapeutic compositions to kill cells that express the protein or to reduce the level of protein in the body.

FIG. 1 shows the mature human colipase polypeptide sequence (SEQ ID NO: 1 and 2) and the tryptic peptide sequence (SEQ ID NO: 3-5) identified by tandem mass spectrometry in the plasma of individuals with coronary artery disease. The tryptic peptides of SEQ ID NO: 1 and 2 are underlined. FIG. 2 shows the sequence of CPP9 (SEQ ID NO: 6) and the peptide sequence (SEQ ID NO: 8-10) found by MS-MS mass spectrometry in the plasma of individuals with coronary artery disease. The tryptic peptides observed by tandem mass spectrometry in SEQ ID NOs: 6 and 7 are underlined. The signal peptide is double underlined. FIG. 3 shows the sequence of the precursor protein (SEQ ID NO: 11) and mature protein (SEQ ID NO: 12, CPP21) and the peptide sequence found by MS-MS mass spectrometry in the plasma of individuals with coronary artery disease (SEQ ID NO: SEQ ID NO: : 13-14). The tryptic peptides observed by tandem mass spectrometry in SEQ ID NOs: 11 and 12 are underlined. The signal peptide is double underlined. FIG. 4 shows the sequence of CPP17 (SEQ ID NO: 17) and the peptide sequence (SEQ ID NO: 18-23) found by MS-MS mass spectrometry in the plasma of individuals with coronary artery disease. The tryptic peptides observed by tandem mass spectrometry in SEQ ID NOs: 15 and 16 are underlined, representing the precursor and preprotein, respectively. In SEQ ID NO: 15, the signal peptide is double underlined. FIG. 5 shows the sequence of the precursor (SEQ ID NO: 24) and mature protein (CPP20, SEQ ID NO: 25) of the present invention, as well as the peptide sequence (sequence) found by tandem mass spectrometry in the plasma of individuals with coronary artery disease Number: 26-28). The tryptic peptides observed by tandem mass spectrometry in SEQ ID NOs: 24 and 25 are underlined. In SEQ ID NO: 24, the signal peptide is double underlined.

[Sequence Listing]

Claims (16)

(A)
i) a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25;
ii) at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 1, 2, 11, 12, 15, 16, or 17 A mutant having sex;
iii) variants having at least 85% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 6 or 7;
iv) a variant having at least 95% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 24 or 25; and v) lowest A fragment of the polypeptide as defined in i), ii), iii), or iv) above which is 10 amino acids in length;
Detecting and / or quantifying the level of a polypeptide selected from in a biological sample from the subject;
(B) comparing the level to that of a control sample;
A method of screening and / or diagnosing cardiovascular disorders in a subject, wherein said increased level relative to a control level is indicative of a cardiovascular disorder. (A)
i) a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25;
ii) at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 1, 2, 11, 12, 15, 16, or 17 A mutant having sex;
iii) variants having at least 85% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 6 or 7;
iv) a variant having at least 95% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 24 or 25; and v) lowest A fragment of the polypeptide as defined in i), ii), iii), or iv) above which is 10 amino acids in length;
Detecting and / or quantifying the level of a polypeptide selected from in a biological sample from the subject;
(B) comparing the level to that of a control sample;
A method of predicting cardiovascular disorders in a subject, wherein an increase in the level relative to a control level indicates a risk of developing the cardiovascular disorder.   3. The method of claim 1 or 2, wherein the level of two or more polypeptides of claim 1 or 2 is detected and / or quantified in a biological sample from the subject.   4. The method according to any one of claims 1 to 3, wherein the cardiovascular disorder is coronary artery disease (CAD).   The method according to claim 1, wherein the biological sample is plasma.   6. The method according to any one of claims 1 to 5, wherein the polypeptide is detected and / or quantified by mass spectrometry.   6. The method according to any of claims 1 to 5, wherein the polypeptide is detected and / or quantified by an enzyme linked immunosorbent assay.   An amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28, wherein the polypeptide is fused to a heterologous polypeptide sequence; An isolated polypeptide comprising.   An anti-cardiovascular disorder that selectively binds to a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28 Plasma polypeptide (CPP) antibody. i) contacting the antibody of claim 8 with a biological sample under conditions that allow antibody binding; and ii); removing contaminants;
A method of binding an antibody to a cardiovascular disorder plasma polypeptide (CPP) comprising the steps of:   The method of claim 10, wherein the antibody is conjugated to a labeling group.   The method of claim 10, wherein the sample is human plasma. i) selected from one of the group consisting of SEQ ID NOs: 1-5, 6-10, 11-14, 15-23, and 24-28 under sample conditions permitting at least one CPP biological activity Contacting a test compound with a CPP comprising the amino acid sequence;
ii) determining the level of at least one said biological activity of CPP;
iii) comparing the level to the level of a control sample lacking the test compound; and iv) causing a change in the level for further testing as a CPP modulator for the prevention and / or therapeutic treatment of cardiovascular disorders. Selecting a test compound;
A method of identifying a cardiovascular disorder plasma polypeptide (CPP) modulator comprising the steps of: (A) administering the candidate agent to a non-human test animal that is predisposed to or afflicted with a cardiovascular disorder;
(B) administering the candidate agent of (a) to a suitable non-human predisposed subject animal who is not predisposed to cardiovascular disorders;
(C) In a biological sample obtained from a non-human test animal of (a) or a control animal of (b):
i) a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25;
ii) at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 1, 2, 11, 12, 15, 16, or 17 A mutant having sex;
iii) variants having at least 85% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 6 or 7;
iv) a variant having at least 95% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 24 or 25; and v) lowest A fragment of the polypeptide as defined in i), ii), iii), or iv) above which is 10 amino acids in length;
Detecting and / or identifying the level of at least one polypeptide selected from: and (d) comparing the level of at least one polypeptide of step (c);
A method of identifying a modulator of cardiovascular disorder, wherein a change in the level of at least one polypeptide indicates that the candidate agent is a modulator of cardiovascular disorder. Non-human test animals predisposed to or afflicted with cardiovascular disorders include:
i) a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25;
ii) at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 1, 2, 11, 12, 15, 16, or 17 A mutant having sex;
iii) variants having at least 85% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 6 or 7;
iv) a variant having at least 95% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 24 or 25; and v) lowest A fragment of the polypeptide as defined in i), ii), iii), or iv) above which is 10 amino acids in length;
15. The method of claim 14, comprising increasing plasma levels of at least one polypeptide selected from. (A) obtaining a pre-dose biological sample from a subject prior to administration of the drug;
(B) in a biological sample from the subject:
i) a polypeptide comprising an amino acid sequence selected from one of the group consisting of SEQ ID NOs: 1-2, 6-7, 11-12, 15-17, and 24-25;
ii) at least 75% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 1, 2, 11, 12, 15, 16, or 17 A mutant having sex;
iii) variants having at least 85% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 6 or 7;
iv) a variant having at least 95% sequence identity with one or more amino acid substitutions, deletions or insertions relative to the amino acid sequence shown in SEQ ID NO: 24 or 25; and v) lowest A fragment of the polypeptide as defined in i), ii), iii), or iv) above which is 10 amino acids in length;
Detecting and / or quantifying the level of at least one polypeptide selected from:
(C) obtaining one or more post-dose biological samples from the subject;
(D) detecting the level of at least one polypeptide in the sample or samples after administration;
(E) comparing the level of at least one polypeptide in the pre-dose sample with the level of at least one polypeptide in the post-dose sample; and (f) adjusting the administration of the drug accordingly.
A method for monitoring the effectiveness of treatment with a drug in a subject having or at risk of developing a cardiovascular disorder.

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