WO2006005586A2

WO2006005586A2 - New polypeptide species specific to cerebrospinal fluid

Info

Publication number: WO2006005586A2
Application number: PCT/EP2005/007564
Authority: WO
Inventors: Thierry Baussant; Lydie Bougueleret; Isabelle Cusin; Eve Mahe; Anne Niknejad; Samia Reffas; Cedric Saudrais
Original assignee: Geneprot Inc.
Priority date: 2004-07-12
Filing date: 2005-07-12
Publication date: 2006-01-19

Abstract

The invention discloses new human secreted polypeptides which are specific to Human Cerebro-Spinal Fluid. The invention also provides methods of using compositions including the polypeptides, polynucleotides encoding them, and antibodies specific for these polypeptides.

Description

NEW POLYPEPTIDE SPECIES SPECIFIC TO CEREBROSPINAL FLUID

FIELD OF THE INVENTION

The invention relates to polypeptide species secreted specifically in cerebrospinal fluid, isolated polynucleotides encoding such polypeptides, polymorphic variants thereof, and the use of said nucleic acids and polypeptides or compositions thereof for detection assays, disease diagnosis, and therapeutic strategies.

BACKGROUND The non-specific nature of many neurological diseases symptoms often makes definitive diagnosis difficult for medical practitioners. Patient descriptions are often variable or inaccurate. More quantitative diagnostic methods suffer from variability, both between individuals and between readings on a single individual. Thus, diagnostic measures must be standardized and applied to individuals with well-documented and extensive medical histories. Even with these controls, symptoms for entirely different underlying conditions can appear identical. In addition, many serious conditions result from a combination of factors, such as neuropsychiatric diseases (e.g., schizophrenia and bipolar disease, see Johnston- Wilson, et al., Int J Neuropsychopharmacol, 2001, 4:83-92). Current diagnostic methods often do not reveal the underlying cause(s) for a given observation or reading. Therefore, a therapeutic strategy based on a particular positive result likely will not address the causative problem and may even be harmful to the individual.

Methods of diagnosis that rely on nucleotide detection include genetic approaches and expression profiling. For example, genes that are known to be involved in a particular disorder may be screened for mutations using common genotyping techniques such as sequencing, hybridization-based techniques, or PCR. In another example, expression from a known gene may be tracked by standard techniques including RTPCR, various hybridization- based techniques, and sequencing. These strategies often do not enable a practitioner to detect differences in mRNA processing and splicing, translation rate, mRNA stability, and posttranslational modifications such as proteolytic processing, phosphorylation, glycosylation, and amidation.

To address the current weaknesses in the diagnostic state of the art, the invention provides new information relating to the range of polypeptides that are found specifically in human Cerebrospinal Fluid (CSF). Li particular, the inventors have now identified new polypeptide species specific to cerebrospinal fluid which are not detectable in plasma nor serum by proteomic techniques, and which were not previously reported to be detectable in CSF. When dealing with neurological disorders, human CSF is a most useful source of proteins associated with both health and disease. CSF contains active proteins and tell-tale disease markers. Under non-pathological situations, the cells responsible for the protein content of CSF are not to be found in the CSF, thus limiting genomic approaches.

Thus, the invention discloses proteins and polypeptides that have not been previously found in CSF, and that are specific to CSF in that they are detectable by proteomic means in CSF, but undetectable in plasma or serum. The proteins and polypeptides of the invention were not known to be detectable in human CSF before, as they were either only evidenced in solid tissues, or had only been proposed to exist through translation of genomic data. The present inventors have now surprisingly found that these proteins and polypeptides are detectable in human CSF, with the implication that they can be used for example as biomarkers for disease diagnosis, for disease prognosis or for monitoring disease progression. By providing the actual CSF polypeptide species, differences in mRNA processing and splicing, translation rate, mRNA stability, and posttranslational modifications are revealed. Such posttranslational modifications (e.g., proteolytic processing, phosphorylation, glycosylation, and amidation) may, and often do, affect the function of a particular polypeptide. In addition, specific CSF localization points to a novel, previously unknown function for the polypeptides of the invention. These polypeptides are described as "Cerebrospinal Fluid Polypeptides" or CSFPs. These polypeptide sequences are related to the polypeptides with accession numbers listed in Table 1 and include polypeptide species that comprise one or more of the amino acid sequences listed in Table 2. In particular, the present inventors have used experimentally-generated mass spectrometry information to obtain precise sequence information on the polypeptide species found to be circulating in human CSF. The disclosure of the actual sequence circulating, as opposed, for example, to that of an unprocessed precursor, is of prime importance for the design of diagnostic (e.g., to obtain antibodies specific to the circulating peptides) and therapeutic (to know precisely the location of biological activity in the polypeptide sequence) strategies.

The present invention discloses "Cerebrospinal Fluid Polypeptides" (CSFPs), fragments, and post-translationally modified species of CSFPs that are present in, and specific to, human CSF. The CSFPs of the invention represent an important tool for diagnosis and drug development. CSFPs are secreted factors and as such, are easy to detect and target, e.g., with a detectable molecule, protein chip, or modulator. SUMMARY OF THE INVENTION

The present invention is directed to compositions related to polypeptide species secreted specifically in human Cerebrospinal Fluid (CSF). These polypeptide species are designated herein "Cerebrospinal Fluid Polypeptides," or CSFPs. Such Cerebrospinal Fluid Polypeptides comprise an amino acid sequence selected from the list of Table 2.

Compositions include CSFP precursors, antibodies specific for CSFPs, including monoclonal antibodies and other binding compositions derived therefrom. Further included are methods of making and using these compositions. Precursors of the invention include unmodified precursors, proteolytic precursors of the group consisting of the sequences from Table 2, and intermediates resulting from alternative proteolytic sites in the group consisting of the sequences from Table 2.

A preferred embodiment of the invention includes CSFPs having a posttranslational modification, such as a phosphorylation, glycosylation, acetylation, amidation, or a C-, N- or O- linked carbohydrate group. Additionally preferred are CSFPs with intra- or inter- molecular interactions, e.g., disulfide and hydrogen bonds that result in higher order structures. Also preferred are CSFPs that result from differential mRNA processing or splicing. Preferably, the CSFPs represent posttranslationally modified species, structural variants, or splice variants that are present in CSF.

In another aspect, the invention includes CSFPs comprising a sequence which is at least 95 percent identical to a sequence selected from the group of sequences listed in Table 2. Preferably, the invention includes polypeptides comprising at least 97 percent, and more preferably at least 98 percent, and still more preferably at least 99 percent, identity with any one of the sequences selected from Table 2. Most preferably, the invention includes polypeptides comprising a sequence at least 99 percent identical to a sequence selected from the group of sequences listed in Table 2. m another aspect, the invention includes natural variants of CSFPs having a frequency in a selected population of at least two percent. More preferably, such natural variant has a frequency in a selected population of at least five percent, and still more preferably, at least ten percent. Most preferably, such natural variant has a frequency in a selected population of at least twenty percent. The selected population may be any recognized population of study in the field of population genetics. Preferably, the selected population is Caucasian, Negroid, or Asian. More preferably, the selected population is French, German, English, Spanish, Swiss, Japanese, Chinese, Irish, Korean, Singaporean, Icelandic, North American, Israeli, Arab, Turkish, Greek, Italian, Polish, Pacific Islander, Finnish, Norwegian, Swedish, Estonian, Austrian, or Indian. More preferably, the selected population is Icelandic, Saami, Finnish, French of Caucasian ancestry, Swiss, Singaporean of Chinese ancestry, Korean, Japanese, Quebecian, North American Pima Indians, Pennsylvanian Amish and Amish Mennonite, Newfoundlander, or Polynesian. A preferred aspect of the invention provides a composition comprising an isolated

CSFP, i.e., a CSFP free from proteins or protein isoforms having a significantly different isoelectric point or a significantly different apparent molecular weight from the CSFP. The isoelectric point and molecular weight of a CSFP may be indicated by affinity and size-based separation chromatography, 2-dimensional gel analysis, and mass spectrometry. In an additional aspect, the invention includes modified CSFPs. Such modifications include protecting/blocking groups, linkage to an antibody molecule or other cellular ligand, and detectable labels, such as an enzymatic, fluorescent, isotopic or affinity label to allow for detection and isolation of the protein. Chemical modifications may be carried out by known techniques, 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.

Also provided by the invention are chemically modified derivatives of the polypeptides of the invention which may provide additional advantages such as increased solubility, stability and circulating time of the polypeptide, or decreased immunogenicity (e.g., water soluble polymers such as polyethylene glycol, ethylene glycol/propylene glycol copolymers, carboxymethylcellulose, dextran, polyvinyl alcohol). The CSFPs are modified at random positions within the molecule, or at predetermined positions within the molecule and may include one, two, three or more attached chemical moieties.

In another aspect, the invention includes polynucleotides encoding a CSFP of the invention, polynucleotides encoding a polypeptide having an amino acid sequence selected from the group of sequences listed in Table 2, antisense oligonucleotides complementary to such sequences, oligonucleotides complementary to CSFP gene sequences for diagnostic and analytical assays (e.g., PCR, hybridization-based techniques).

In another aspect, the invention provides a vector comprising DNA encoding a CSFP. The invention also includes host cells and transgenic nonhuman animals comprising such a vector.

There is also provided a method of making a CSFP or CSFP precursor. One preferred method comprises the steps of (a) providing a host cell containing an expression vector as disclosed above; (b) culturing the host cell under conditions whereby the DNA segment is expressed; and (c) recovering the protein encoded by the DNA segment. Another preferred method comprises the steps of: (a) providing a host cell capable of expressing a CSFP; (b) culturing said host cell under conditions that allow expression of said CSFP; and (c) recovering said CSFP. Within one embodiment the expression vector further comprises a secretory signal sequence operably linked to the DNA segment, the cell secretes the protein into a culture medium, and the protein is recovered from the medium. An especially preferred method of making a CSFP includes chemical synthesis using standard peptide synthesis techniques, as described in the section titled "Chemical Manufacture of CSFP compositions" and in Example 5. In another aspect, the invention includes isolated antibodies specific for any of the polypeptides, peptide fragments, or peptides described above. Preferably, the antibodies of the invention are monoclonal antibodies. Further preferred are antibodies that bind to a CSFP specifically or exclusively, that is, antibodies that do not recognize other polypeptides with high affinity. Anti-CSFP antibodies have purification, detection, diagnostic and prognostic applications. Preferred anti-CSFP antibodies for purification and detection are attached to a label group. Detection methods include, but are not limited to, those that employ antibodies or antibody-derived compositions specific for a CSFP antigen. A preferred detection method is an enzyme-linked immunosorption assay (ELISA). Compositions comprising one or more antibodies described above, together with a pharmaceutically acceptable carrier are also within the scope of the invention, e.g, for in vivo detection.

Detection methods for identifying CSFPs in specific tissue samples and biological fluids (preferably CSF) form part of the invention. Detection methods for identifying CSFP expression in cell-based samples are also included.

The invention further provides methods that comprise detecting the level of at least one CSFP in a sample of body fluid, preferably CSF. Further included are methods of using CSFP compositions, including primers complementary to CSFP genes and/or messenger RNA and anti- CSFP antibodies, for detecting and measuring quantities of CSFPs in tissues and biological fluids, preferably CSF. In addition, the invention includes detection methods comprising mass spectrometry, retentate chromatography (including protein arrays), and surface enhanced laser desorption/ionization (SELDI) techniques. These methods are also suitable for clinical screening, prognosis, monitoring the results of therapy, identifying patients most likely to respond to a particular therapeutic treatment.

The invention provides kits that may be used in the above-recited methods and that may comprise single or multiple preparations, adsorbant and substrate materials, antibodies, label groups, other reagents, if needed, and directions for use. The kits may be used for diagnosis or for assays to identify new diagnostic agents.

The CSFPs of the invention are also useful candidate therapeutic agents for neurological disorders. Their abilities to modify the course of disease can be assayed by one of skill in the art as further detailled herein, for example in Example 9. The invention provides methods that comprise using a CSFP of the invention as an active compound in the preparation of a pharmaceutical composition for therapeutic use.

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

BRIEF DESCRIPTION OF THE FIGURES

Figure 1 shows the effect of CSFP 1 of the invention on cortical neurons survival, as described in Example 9.

Figure 2 shows the effect of CSFP 83 of the invention on cortical neurons survival, as described in Example 9.

Figure 3 shows the effect of CSFP 135 of the invention on cortical neurons survival, as described in Example 9.

Figure 4 shows the effect of CSFP 152 of the invention on cortical neurons survival, as described in Example 9.

DETAILED DESCRIPTION OF THE INVENTION

The present invention described in detail below provides compositions, methods, and kits useful for screening and diagnosis of human CSF; for identifying individuals most likely to respond to a particular therapeutic treatment; and for monitoring the results of therapy. For clarity of disclosure, and not by way of limitation, the invention will be described with respect to the analysis of CSF samples. However, as one skilled in the art will appreciate, the assays and techniques described below can be applied to other biological fluid samples (e.g. serum, lymph, bile, plasma, saliva or urine) or tissue samples. The methods and compositions of the present invention are useful for screening, diagnosis and prognosis of a living individual, but may also be used for postmortem diagnosis in an individual.

Definitions

As used herein, the term "nucleic acids" and "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA. Throughout the present specification, the expression "nucleotide sequence" may be employed to designate indifferently a polynucleotide or a nucleic acid. More precisely, the expression "nucleotide sequence" encompasses the nucleic material itself and is thus not restricted to the sequence information (i.e. the succession of letters chosen among the four base letters) that biochemically characterizes a specific DNA or RNA molecule. Also, used interchangeably herein are terms "nucleic acids", "oligonucleotides", and "polynucleotides".

An "isolated" nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid. Preferably, an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5¹ and 3¹ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated CSFP nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. Moreover, 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 substantially free of chemical precursors or other chemicals when chemically synthesized. Using all or a portion of the nucleic acid as a hybridization probe, CSFP nucleic acid molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning. A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1989). 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, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non- episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques 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 invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.

As used herein, the term "hybridizes to" is intended to describe conditions for moderate stringency or high stringency hybridization, preferably where the hybridization and washing conditions permit nucleotide sequences at least 60% homologous to each other to remain hybridized to each other. Preferably, the conditions are such that sequences 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. Stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. A preferred, non-limiting example of stringent hybridization conditions for nucleic acid interactions are as follows: the hybridization step is realized at 65⁰C in the presence of 6 x SSC buffer, 5 x Denhardt's solution, 0,5% SDS and lOOμg/ml of salmon sperm DNA. The hybridization step is followed by four washing steps:

- two washings during 5 min, preferably at 65°C in a 2 x SSC and 0.1%SDS buffer; - one washing during 30 min, preferably at 65°C in a 2 x SSC and 0.1% SDS buffer,

- one washing during 10 min, preferably at 65°C in a 0.1 x SSC and 0.1%SDS buffer, these hybridization conditions being suitable for a nucleic acid molecule of about 20 nucleotides in length. It will be appreciated that the hybridization conditions described above are to be adapted according to the length of the desired nucleic acid, following techniques well known to the one skilled in the art, for example be adapted according to the teachings disclosed in Hames B.D. and Higgins SJ. (1985) Nucleic Acid Hybridization: A Practical Approach. Hames and Higgins Ed., IRL Press, Oxford; and Current Protocols in Molecular Biology.

"Percent homology" is used herein to refer to both nucleic acid sequences 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 of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence and non-homologous sequences can be disregarded for comparison purposes). The length of a 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 at least 70%, 80%, 90% or 95% of the length of the reference sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When 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 (i.e., % homology=# of identical positions/total # of positions 100).

The comparison of sequences and determination of percent homology between two sequences can be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264-68, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-77. Such an algorithm is incorporated into the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. MoI. Biol. 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to the sequences of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to the polypeptide sequences of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Research 25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov. Another preferred, non-limiting example of a mathematical algorithim utilized for the comparison of sequences is the algorithm of Myers and Miller, CABIOS (1989). 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 for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.

The term "polypeptide" refers to a polymer of amino acids without regard to the length of the polymer; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide. This term also does not specify or exclude post-translational modifications of polypeptides, for example, polypeptides which include the covalent attachment of glycosyl, acetyl, phosphate, amide, lipid, carboxyl, acyl, or carbohydrate groups are expressly encompassed by the term polypeptide. Also included within the definition are polypeptides which contain one or more analogs of an amino acid (including, for example, non-naturally occurring amino acids, amino acids which only occur naturally in an unrelated biological system, modified amino acids from mammalian systems etc.), polypeptides with substituted linkages, as well as other modifications known in the art, both naturally occurring and non-naturally occurring.

The term "protein" as used herein may be used synonymously with the term "polypeptide" or may refer to, in addition, a complex of two or more polypeptides which may be linked by bonds other than peptide bonds, for example, such polypeptides making up the protein may be linked by disulfide bonds. The term "protein" may also comprehend a family of polypeptides having identical amino acid sequences but different post-translational modifications, particularly as may be added when such proteins are expressed in eukaryotic hosts. An "isolated" or "purified" protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the protein of the invention (i.e., CSFP or biologically active fragment thereof) is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language "substantially free of cellular material" includes preparations of a protein according to the invention in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced. In one embodiment, the language "substantially free of cellular material" includes preparations of a protein according to the invention having less than about 30% (by dry weight) of protein other than the protein of the invention (also referred to herein as a "contaminating protein"), more preferably less than about 20% of protein other than the protein according to the invention, still more preferably less than about 10% of protein other than the protein according to the invention, and most preferably less than about 5% of protein other than the protein according to the invention. When the protein according to the invention or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation.

The language "substantially free of chemical precursors or other chemicals" includes preparations of a protein of the invention in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. Ia one embodiment, the language "substantially free of chemical precursors or other chemicals" includes preparations of a protein of the invention having less than about 30% (by dry weight) of chemical precursors or non-protein chemicals, more preferably less than about 20% chemical precursors or non-protein chemicals, still 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.

The term "recombinant polypeptide" is used herein to refer to polypeptides that have been artificially designed and which comprise at least two polypeptide sequences that are not found as contiguous polypeptide sequences in their initial natural environment, or to refer to polypeptides which have been expressed from a recombinant polynucleotide.

The term "Cerebrospinal Fluid Polypeptide" or "CSFP" refers to a polypeptide comprising the sequence described by any one of the accession numbers listed in Table 1 or any amino acid sequence selected from the group consisting of the sequences from Table 2. Such polypeptide may be post-translationally modified as described herein. CSFPs may also contain other structural or chemical modifications such as disulfide linkages or amino acid side chain interactions such as hydrogen and amide bonds that result in complex secondary or tertiary structures. CSFPs also include mutant polypeptides, such as deletion, addition, swap, or truncation mutants, fusion polypeptides comprising such polypeptides, and polypeptide fragments of at least three, but preferably 8, 10, 12, 15, or 21 contiguous amino acids of the sequences of Table 2. Further included are CSFP proteolytic precursors and intermediates of the sequence selected from the group consisting of the sequences from Table 2. The invention embodies polypeptides encoded by the nucleic acid sequences of CSFP genes or CSFP mRNA species, preferably human CSFP genes and mRNA species, including isolated CSFPs consisting of, consisting essentially of, or comprising the sequences from Table 2. Preferred CSFPs retain at least one biological activity of CSFPs from Table 2.

The term "biological activity" as used herein refers to any function carried out by a CSFP. These include but are not limited to: (1) circulating through the CSF of human individuals; (2) antigenicity, or the ability to bind an anti-CSFP specific antibody; (3) immunogenicity, or the ability to generate an anti-CSFP specific antibody; and (4) interaction with a CSFP target molecule or adsorbant.

A "CSFP-related disorder" or "CSFP-related disease" describes any medical condition known to be associated with a CSFP of the invention. CSFP-related disorders include conditions where the presence of an abnormal level of a CSFP or CSFP polynucleotide is indicative that an individual has or is at risk of developing that condition. CSFP-related disorders also include conditions where the presence of an abnormal form of a CSFP or CSFP polynucleotide (e.g., due to mutation, truncation, increased or decreased biological activity, abnormal posttranslational modification or processing) is indicative that an individual has or is at risk of developing that condition.

A "neurological disorder", as used herein, describes any pathological condition of the Central Nervous System or of the Peripheral Nervous System. By way of example and not limitation, this includes: Alzheimer's disease, Multiple Sclerosis, Amyotrophic Lateral Sclerosis, Parkinson's Disease, head injury, spinal cord injury, seizure, stroke, epilepsy, ischaemia, Huntington's disease, attentiondeficit disorder (ADD), and neuropsychiatric syndromes.

Another aspect of the invention pertains to anti-CSFP antibodies. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen-binding site which specifically binds (immunoreacts with) an antigen, such as CSFP, or a biologically active fragment or homologue thereof. Preferred antibodies bind to a CSFP exclusively 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 which can be generated by treating the antibody with an enzyme such as pepsin. The invention provides polyclonal and monoclonal antibodies that bind a CSFP, or a biologically active fragment or homologue thereof. The term "monoclonal antibody" or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one species of an antigen-binding site capable of immunoreacting with a particular epitope of a CSFP. A monoclonal antibody composition thus typically displays a single binding affinity for a particular CSFP with which it immunoreacts. Preferred CSFP antibodies are attached to a label group.

As used herein, a "label group" is any compound that, when attached to a polynucleotide or polypeptide (including antibodies), allows for detection or purification of said polynucleotide or polypeptide. Label groups may be detected or purified directly or indirectly by a secondary compound, including an antibody specific for said label group.

32 35 3 125

Useful label groups include radioisotopes (e.g., P, S, H, I), fluorescent compounds (e.g., 5-bromodesoxyuridin, umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride, phycoerythrin acetylaminofluorene, digoxigenin), luminescent compounds (e.g., luminol, GFP, luciferin, aequorin), enzymes or enzyme co-factor detectable labels (e.g., peroxidase, luciferase, alkaline phosphatase, galactosidase, or acetylcholinesterase), or compounds that are recognized by a secondary factor such as strepavidin, GST, or biotin. Preferably, a label group is attached to a polynucleotide or polypeptide in such a way as to not interfere with the biological activity of the polynucleotide or polypeptide.

Radioisotopes may be detected by direct counting of radioemission, film exposure, or by scintillation counting, for example. Enzymatic labels may be detected by determination of conversion of an appropriate substrate to product, usually causing a fluorescent reaction. Fluorescent and luminescent compounds and reactions may be detected by, e.g., radioemission, fluorescent microscopy, fluorescent activated cell sorting, or a luminometer.

"Adsorbent" refers to any material capable of adsorbing a polypeptide (i.e., a CSFP). The term "adsorbent" is used herein to refer both to a single material ("monoplex adsorbent") (e.g., a compound or functional group) to which a polypeptide is exposed, and to a plurality of different materials ("multiplex adsorbent") to which a sample is exposed. The adsorbent materials in a multiplex adsorbent are referred to as "adsorbent species." For example, an addressable location on a substrate can comprise a multiplex adsorbent characterized by many different adsorbent species (e.g., anion exchange materials, metal chelators, or antibodies), having different binding characteristics. The basis of attraction is generally a function of chemical or biological molecular recognition. Bases for attraction between an adsorbent and a polypeptide include, for example, (1) a salt-promoted interaction, e.g., hydrophobic interactions, thiophilic interactions, and immobilized dye interactions; (2) hydrogen bonding and/or van der Waals forces interactions and charge transfer interactions, such as in the case of a hydrophilic interactions; (3) electrostatic interactions, such as an ionic charge interaction, particularly positive or negative ionic charge interactions; (4) the ability of the polypeptide to form coordinate covalent bonds (i.e., coordination complex formation) with a metal ion on the adsorbent; (5) enzyme-active site binding; (6) reversible covalent interactions, for example, disulfide exchange interactions; (7) glycoprotein interactions; (8) biospecific interactions; or (9) combinations of two or more of the foregoing modes of interaction. That is, the adsorbent can exhibit two or more bases of attraction, and thus be known as a "mixed functionality" adsorbent. CSFPs of the invention

The Cerebrospinal Fluid Polypeptides (CSFPs) of the invention are described in Table 1 and 2. CSFPs comprising an amino acid sequence selected from the group consisting of the sequences from Table 2 and fragments thereof are secreted and circulate in CSF. The CSFPs of the invention are polypeptides that have not previously been found in human CSF, and that are not found in human plasma. As such, they are CSF-specifϊc polypeptides. Thus, the invention introduces a new role or function for these polypeptides.

The terms "Cerebrospinal Fluid Polypeptide" and "CSFP" are used herein to embrace any and all of the peptides, polypeptides and proteins of the present invention. Also forming part of the invention are polypeptides encoded by the polynucleotides of the invention, as well as fusion polypeptides comprising such polypeptides. The invention embodies CSFPs from humans, including isolated or purified CSFPs consisting of, consisting essentially of, or comprising an amino acid sequence selected from the group consisting of the sequences from Table 2. Further included are unmodified precursors, proteolytic precursors and intermediates of the sequence selected from the group consisting of the sequences from Table 2.

The present invention embodies an isolated, purified, and recombinant polypeptide fragment comprising a contiguous span of at least 3 amino acids, preferably at least 8 to 10 amino acids, of an amino acid sequence selected from the group consisting of the sequences from Table 2, wherein said fragment has a CSFP biological activity. In an included embodiment, the contiguous stretch of amino acids comprises the site of a mutation or functional mutation, including a deletion, addition, swap or truncation of the amino acids in the CSFP sequence. The invention also concerns the polypeptide encoded by the CSFP nucleotide sequences of the invention, or a complementary sequence thereof or a fragment thereof. Said polypeptide fragment may represent the actual peptide species that is present in human CSF. Said polypeptide fragment may be used, for example, to generate CSFP-specific antibodies or to design another type of CSFP-specific adsorbant.

One aspect of the invention pertains to isolated CSFPs, and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise anti-CSFP antibodies. In one embodiment, native CSFP peptides can be isolated from CSF, cells or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, CSFPs are produced by recombinant DNA techniques. Alternative to recombinant expression, a CSFP can be synthesized chemically using peptide synthesis techniques, as described in the section titled "Chemical Manufacture of CSFP compositions" and in Example 5.

Typically, biologically active portions comprise a domain or motif with at least one activity of a CSFP. A biologically active CSFP may, for example, comprise at least 1, 2, 3, or 5 amino acid changes from the sequence selected from the group consisting of the sequences from Table 2, or comprise at least 1%, 2%, 3%, 5%, 8%, 10% or 15% change in amino acids from the sequence selected from the group consisting of the sequences from Table 2.

Characterization of CSFPs

The polypeptides of the invention, CSFPs, are defined by the polypeptides of Table 2 and the accession numbers listed in Table 1. These peptides were isolated from human Cerebrospinal Fluid and characterized according to the MicroProt® method, as described in Example 1. For each CSFP, Table 1 provides:

• an accession number in a public database, corresponding to the related polypeptide sequence;

• the Protein Type;

• the amino acid positions defining the observed polypeptide with respect to the polypeptide in the public database; and

• a list of Proteomes where the CSFP was observed. More details on these different Proteomes can be found in Example 1.

For Protein Type, "Parent" denotes a polypeptide sequence whose length is described by the positions listed in the column Amino Acids, but with no other known distinctions from the sequence in the public database. "Fragment" denotes a particular, newly defined, fragment, spanning the positions described in the Amino Acids column. And "Variant" denotes a polypeptide that deviates from the amino acid sequence in the public database. The nature of the variation is described in parenthesis.

Most of the accession numbers listed in Table 1 are references for the the

SwissPROT/TrEMBL databases, both of which are publicly available, for example at: http://www.expasy.ch. CSFP 1 and CSFP 85, however, are defined as sequences appearing in published patent applications, as detailed in Table 1. Moreover, CSFP 83 correspond to a predicted protein sequence obtained by running the Genscan software on a GenBank entry, as detailed in Table 1.

Table 1

The polypeptides of the invention, CSFPs, are defined by the tryptic peptides listed in Table 2. These peptides were isolated from human Cerebrospinal Fluid and characterized according to the MicroProt® method, as described in Example 1.

The CSFPs of the invention are, on average, less than 25kD in molecular weight, as the CSF sample is first separated based on molecular weight. As described in Example 1, the CSF sample is subjected to a number of chromatography separations. Details about these chromatography methods are given in Example 1 and vary for different volumes under study. The CSFPs of the invention have been identified in at least one of 4 different proteomic studies of human CSF, hereinafter designated Proteomes #6, #18, #19 and #20. Details on the sample origins, sample processings and analyses for each of these proteomes are given in Example 1. For each CSFP and for each corresponding tryptic sequence identified, Table 2 indicate the corresponding Proteome number.

The first separation is on a cation exchange chromatography column, which is eluted with increasing salt concentration. Six to fifteen fractions are collected, depending on the Proteome under study (see Example 1 for details). The CEX column in Table 2 lists which fraction contained each tryptic peptide. Separation by cation exchange provides an indication of the overall positive charge of a polypeptide species. Cation exchange is followed by a reverse phase HPLC separation. The RP column in Table 2 lists in which of the 15 fractions (for Proteomes #6, 18 and 19) or in which of the 10 fractions (for Proteome #20) each tryptic peptide eluted. In the case of Proteome #20, a further fractionation by reverse phase was performed, as described in Example 1. Separation by reverse phase provides an indication of the overall hydrophobicity of a polypeptide species. In the last column of Table 2, the tryptic sequences corresponding to the CSFP of interest, in the

Proteome of interest, in the CEX and RP fractions of interest, are listed, with their unique SEQ ID number within brackets.

Table!

CSFP nucleic acids

One aspect of the invention pertains to purified or isolated nucleic acid molecules that encode CSFPs or biologically active portions thereof as further described herein, as well as nucleic acid fragments thereof. Said nucleic acids may be used, for example, in detection methods as further described herein.

An object of the invention is a purified, isolated, or recombinant nucleic acid coding for a CSFP, complementary sequences thereto, and fragments thereof. The invention also pertains to a purified or isolated nucleic acid comprising a polynucleotide having at least 95% nucleotide identity with a polynucleotide coding for a CSFP, advantageously 99 % nucleotide identity, preferably 99.5% nucleotide identity and most preferably 99.8% nucleotide identity with a polynucleotide coding for a CSFP, or a sequence complementary thereto or a biologically active fragment thereof. Another object of the invention relates to purified, isolated or recombinant nucleic acids comprising a polynucleotide that hybridizes, under the stringent hybridization conditions defined herein, with a polynucleotide coding for a CSFP, or a sequence complementary thereto or a variant thereof or a biologically active fragment thereof.

In another preferred aspect, the invention pertains to purified or isolated nucleic acid molecules that encode a portion or variant of a CSFP, wherein the portion or variant displays a CSFP biological activity. Preferably said portion or variant is a portion or variant of a naturally occurring CSFP or precursor thereof.

Another object of the invention is a purified, isolated, or recombinant nucleic acid encoding a CSFP comprising, consisting essentially of, or consisting of the amino acid sequence selected from the group of sequences from Table 2, or fragments thereof, wherein the isolated nucleic acid molecule encodes one or more motifs, such as a target binding site. A nucleic acid fragment encoding a "biologically active portion of a CSFP" can be prepared by isolating a portion of a nucleotide sequence coding for a CSFP, which encodes a polypeptide having a CSFP biological activity, expressing the encoded portion of the CSFP (e.g., by recombinant expression in vitro or in vivo) and assessing the activity of the encoded portion of the CSFP.

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

In addition to the CSFP nucleotide sequences described above, it will be appreciated by those skilled in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of the CSFPs may exist within a population (e.g., the human population). Such genetic polymorphism may exist among individuals within a population due to natural allelic variation. Such natural allelic variations can typically result in 1-5% variance in the nucleotide sequence of a CSFP-encoding gene or nucleic acid sequence.

Nucleic acid molecules corresponding to natural allelic variants and homologues of the CSFP nucleic acids of the invention can be isolated based on their homology to the CSFP nucleic acids disclosed herein using the cDNAs disclosed herein, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions.

It will be appreciated that the invention comprises polypeptides having an amino acid sequence encoded by any of the polynucleotides of the invention.

Uses of CSFP nucleic acids

Polynucleotide sequences (or the complements thereof) encoding CSFPs have various applications, including uses as hybridization probes. In addition, CSFP-encoding nucleic acids are useful for the preparation of CSFPs by recombinant techniques, as described herein. The polynucleotides described herein, including sequence variants thereof, can be used in detection assays. Accordingly, detecting the presence of such polynucleotides in body fluids or tissue samples is a feature of the present invention. Examples of nucleic acid based detection assays in accordance with the present invention include, but are not limited to, hybridization assays (e.g., in situ hybridization or nucleotide arrays) and PCR- based assays. Polynucleotides, including extended length polynucleotides, sequence variants and fragments thereof, as described herein, may be used to generate hybridization probes or PCR primers for use in such assays. Such probes and primers will be capable of detecting polynucleotide sequences, including genomic sequences that are similar, or complementary to, the CSFP polynucleotides described herein. The invention includes primer pairs for carrying out a PCR to amplify a segment of a polynucleotide of the invention. Each primer of a pair is an oligonucleotide having a length of between 15 and 30 nucleotides such that i) one primer of the pair forms a perfectly matched duplex with one strand of a polynucleotide of the invention and the other primer of the pair form a perfectly match duplex with the complementary strand of the same polynucleotide, and ii) the primers of a pair form such perfectly matched duplexes at sites on the polynucleotide that separated by a distance of between 10 and 2500 nucleotides. Preferably, the annealing temperature of each primer of a pair to its respective complementary sequence is substantially the same. Hybridization probes derived from polynucleotides of the invention can be used, for example, in performing in situ hybridization on tissue samples, such as fixed or frozen tissue sections prepared on microscopic slides or suspended cells. Briefly, a labeled DNA or RNA probe is allowed to bind its DNA or RNA target sample in the tissue section on a prepared microscopic, under controlled conditions. Generally, dsDNA probes consisting of the DNA of interest cloned into a plasmid or bacteriophage DNA vector are used for this purpose, although ssDNA or ssRNA probes may also be used. Probes are generally oligonucleotides between about 15 and 40 nucleotides in length. Alternatively, the probes can be polynucleotide probes generated by PCR random priming primer extension or in vitro transcription of RNA from plasmids (riboprobes). These latter probes are typically several hundred base pairs in length. The probes can be labeled by any of a number of label groups and the particular detection method will correspond to the type of label utilized on the probe (e.g., autoradiography, X-ray detection, fluorescent or visual microscopic analysis, as appropriate). The reaction can be further amplified in situ using immunocytochemical techniques directed against the label of the detector molecule used, such as an antibody directed to a fluorescein moiety present on a fluorescently labeled probe. Specific labeling and in situ detection methods can be found, for example, in Howard, G. C, Ed., Methods in Nonradioactive Detection, Appleton & Lange, Norwalk, Conn., (1993), herein incorporated by reference.

Hybridization probes and PCR primers may also be selected from the genomic sequences corresponding to the full-length proteins identified in accordance with the present invention, including promoter, enhancer elements and introns of the gene encoding the naturally occurring polypeptide. Nucleotide sequences encoding a CSFP can also be used to construct hybridization probes for mapping the gene encoding that CSFP and for the genetic analysis of individuals. Individuals carrying variations of, or mutations in the gene encoding a CSEP of the present invention may be detected at the DNA level by a variety of techniques. Nucleic acids used for diagnosis may be obtained from a patient's cells, including, for example, tissue biopsy and autopsy material. Genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR (Saiki, et al. Nature 324: 163-166 (1986)) prior to analysis. RNA or cDNA may also be used for the same purpose. As an example, PCR primers complementary to the nucleic acid of the present invention can be used to identify and analyze mutations in the gene of the present invention. Deletions and insertions can be detected by a change in size of the amplified product in comparison to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to radiolabeled RNA of the invention or alternatively, radiolabeled antisense DNA sequences of the invention. Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and Sl protection or the chemical cleavage method (e.g. Cotton, et al., Proc. Natl Acad. ScL USA 85:4397-4401 (1985)), or by differences in melting temperatures. "Molecular beacons" (Kostrikis L. G. et al., Science 279:1228-1229 (1998)), hairpin-shaped, single-stranded synthetic oligonucleotides containing probe sequences which are complementary to the nucleic acid of the present invention, may also be used to detect point mutations or other sequence changes as well as monitor expression levels of CSFPs.

Nucleotides of the invention, including PCR primers and probes, may be synthesized by conventional means on a commercially available automated DNA synthesizer, e.g. an Applied Biosystems (Foster City, CA) model 380B, 392 or 394 DNA/RNA synthesizer. Preferably, phosphoramidite chemistry is employed, e.g. as disclosed in the following references: Beaucage and Iyer, Tetrahedron, 48: 2223-2311 (1992); Molko et al, U.S. patent 4,980,460; Koster et al, U.S. patent 4,725,677; Caruthers et al, U.S. patents 4,415,732; 4,458,066; and 4,973,679. Primers and probes of the invention can also be prepared by, for example, cloning and restriction of appropriate sequences and direct chemical synthesis by a method such as the phosphodiester method of Narang SA et al (Methods Enzymol 1979; 68:90-98), the phosphodiester method of Brown EL et al (Methods Enzymol 1979; 68:109-151), the diethylphosphoramidite method of Beaucage et al (Tetrahedron Lett 1981, 22: 1859-1862) and the solid support method described in EP 0 707 592.

Detection probes are generally nucleic acid sequences or uncharged nucleic acid analogs such as peptide nucleic acids which are disclosed in WO 92/20702, morpholino analogs which are described in U.S. Patents 5,185,444; 5,034,506 and 5,142,047. If desired, the probe may be rendered "non-extendable" in that additional dNTPs cannot be added to the probe. Ih and of themselves analogs usually are non-extendable and nucleic acid probes can be rendered non-extendable by modifying the 3' end of the probe such that the hydroxyl group is no longer capable of participating in elongation. For example, the 3' end of the probe can be functionalized with the capture or detection label to thereby consume or otherwise block the hydroxyl group.

Any of the polynucleotides of the present invention can be labeled, if desired, by incorporating any label group known in the art to be detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Additional examples include non-radioactive labeling of nucleic acid fragments as described in Urdea et al. (Nucleic Acids Research. 11:4937-4957, 1988) or Sanchez-Pescador et al. (J. Clin. Microbiol. 26(10):1934-1938, 1988). In addition, the probes according to the present invention may have structural characteristics such that they allow the signal amplification, such structural characteristics being, for example, branched DNA probes as those described by Urdea et al (Nucleic Acids Symp. Ser. 24:197-200, 1991) or in the European patent No. EP 0225807 (Chiron).

A label can also be used to capture the primer, so as to facilitate the immobilization of either the primer or a primer extension product, such as amplified DNA, on a solid support. A capture label is attached to the primers or probes and can be a specific binding member which forms a binding pair with the solid's phase reagent's specific binding member (e.g. biotin and streptavidin). Therefore depending upon the type of label carried by a polynucleotide or a probe, it may be employed to capture or to detect the target DNA. Further, it will be understood that the polynucleotides, primers or probes provided herein, may, themselves, serve as the capture label. For example, in the case where a solid phase reagent's binding member is a nucleic acid sequence, it may be selected such that it binds a complementary portion of a primer or probe to thereby immobilize the primer or probe to the solid phase. In cases where a polynucleotide probe itself serves as the binding member, those skilled in the art will recognize that the probe will contain a sequence or "tail" that is not complementary to the target. Ih the case where a polynucleotide primer itself serves as the capture label, at least a portion of the primer will be free to hybridize with a nucleic acid on a solid phase. DNA labeling techniques are well known to the skilled technician.

The probes of the present invention are useful for a number of purposes. They can be notably used in Southern hybridization to genomic DNA. The probes can also be used to detect PCR amplification products. They may also be used to detect mismatches in CSFP- encoding genes or mRNA using other techniques. 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 the walls of wells of a reaction tray, test tubes, polystyrene beads, magnetic beads, nitrocellulose strips, membranes, microparticles such as latex particles, sheep (or other animal) red blood cells, duracytes and others. 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, walls of microtiter wells, glass or silicon chips, sheep (or other suitable animal's) red blood cells and duracytes are all suitable examples. Suitable methods for immobilizing nucleic acids on solid phases include ionic, hydrophobic, covalent interactions and the like. A solid support, as used herein, refers to any material which is insoluble, or can be made insoluble by a subsequent reaction. The solid support can be chosen for its intrinsic ability to attract and immobilize the capture reagent. Alternatively, the solid phase can retain an additional receptor which has the ability to attract and immobilize the capture reagent. The additional receptor can include a charged substance that is oppositely charged with respect to the capture reagent itself or to a charged substance conjugated to the capture reagent. As yet another alternative, the receptor molecule can be any specific binding member attached to the solid support and which has the ability to immobilize the capture reagent through a specific binding reaction. The receptor molecule enables the indirect binding of the capture reagent to a solid support material before the performance of the assay or during the performance of the assay. The solid phase thus can be a plastic, derivatized plastic, magnetic or non-magnetic metal, glass or silicon surface of a test tube, microtiter well, sheet, bead, microparticle, chip, sheep (or other suitable animal's) red blood cells, duracytes and other configurations known to those of ordinary skill in the art. The nucleic acids, polynucleotides, primers and probes of the invention can be attached to or immobilized on a solid support individually or in groups of at least 2, 5, 8, 10, 12, 15, 20, or 25 distinct polynucleotides of the invention to a single solid support. In addition, polynucleotides other than those of the invention may be attached to the same solid support as one or more polynucleotides of the invention.

Any polynucleotide provided herein may be attached in overlapping areas or at random locations on a solid support. Alternatively the polynucleotides of the invention may be attached in an ordered array wherein each polynucleotide is attached to a distinct region of the solid support which does not overlap with the attachment site of any other polynucleotide. Preferably, such an ordered array of polynucleotides is designed to be "addressable" where the distinct locations are recorded and can be accessed as part of an assay procedure. Addressable polynucleotide arrays typically comprise a plurality of different oligonucleotide probes that are coupled to a surface of a substrate in different known locations. The knowledge of the precise location of each polynucleotides location makes these "addressable" arrays particularly useful in hybridization assays. Any addressable array technology known in the art can be employed with the polynucleotides of the invention. One particular embodiment of these polynucleotide arrays is known as the Genechips, and has been generally described in US Patent 5,143,854; PCT publications WO 90/15070 and 92/10092. Preferably, more than one CSFP polynucleotide probe is included in such an array.

Methods for obtaining variant nucleic acids and polypeptides

In addition to naturally-occurring allelic variants of the CSFP sequences that may exist in the population, the skilled artisan will appreciate that changes can be introduced by mutation into the nucleotide sequences coding for CSFPs, thereby leading to changes in the amino acid sequence of the encoded CSFPs, with or without altering the functional ability of the CSFPs.

Several types of variants are contemplated including 1) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue and such substituted amino acid residue may or may not be one encoded by the genetic code, or 2) one in which one or more of the amino acid residues includes a substituent group, or 3) one in which the mutated CSFP is fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol), or 4) one in which the additional amino acids are fused to the CSFP, such as a leader, a signal or anchor sequence, a sequence which is employed for purification of the CSFP, or sequence from a precursor protein. Such variants are deemed to be within the scope of those skilled in the art. The invention provides CSFP chimeric or fusion proteins. As used herein, a CSFP

"chimeric protein" or "fusion protein" comprises a CSFP of the invention or fragment thereof, operatively linked or fused in frame to a non-CSFP polypeptide sequence. In a preferred embodiment, a CSFP fusion protein comprises at least one biologically active portion of a CSFP. In another preferred embodiment, a CSFP fusion protein comprises at least two biologically active portions of a CSFP. For example, in one embodiment, the fusion protein is a GST-CSFP fusion protein in which CSFP domain sequences are fused to the C-terminus of the GST sequences. Such fusion proteins can facilitate the purification of recombinant CSFPs. Ih another embodiment, the fusion protein is a CSFP containing a heterologous signal sequence at its N-terminus, for example, to allow for a desired cellular localization in a certain host cell. In yet another embodiment, the fusion is a CSFP biologically active fragment and an immunoglobulin molecule. Such fusion proteins are useful, for example, to increase the valency of CSFP binding sites. For example, a bivalent CSFP binding site may be formed by fusing biologically active CSFP fragments to an IgG Fc protein.

In a preferred embodiment, CSFP fusion proteins of the invention are used as immunogens to produce anti-CSFP antibodies in a subject, to purify CSFP, or CSFP ligands and adsorbants.

Furthermore, isolated fragments of CSFPs can also be obtained by screening peptides recombinantly produced from the corresponding fragment of the nucleic acid encoding such peptides. In addition, fragments can be chemically synthesized using techniques known in the art such as conventional Merrifϊeld solid phase f-Moc or t-Boc chemistry. For example, a CSFP of the present invention may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or preferably divided into overlapping fragments of a desired length. The fragments can be produced (recombinantly or by chemical synthesis) and tested to identify those peptidyl fragments with a CSFP biological activity, for example, by microinjection assays or in vitro protein binding assays. Ih an illustrative embodiment, peptidyl portions of a CSFP, such as a CSFP target binding region, can be tested for CSFP activity (e.g., immunogenicity) by expression as thioredoxin fusion proteins, each of which contains a discrete fragment of the CSFP (see, for example, U.S. Patents 5, 270,181 and 5,292,646; and WO94/02502).

Chemical Manufacture of CSFP Compositions

Peptides of the invention are synthesized by standard techniques (e.g. Stewart and Young, Solid Phase Peptide Synthesis, 2nd Ed., Pierce Chemical Company, Rockford, IL, 1984). Preferably, a commercial peptide synthesizer is used, e.g. Applied Biosystems, Inc. (Foster City, CA) model 430A, and polypeptides of the invention may be assembled from multiple, separately synthesized and purified, peptide in a convergent synthesis approach, e.g. Kent et al, U.S. patent 6,184,344 and Dawson and Kent, Annu. Rev. Biochem., 69: 923-960 (2000). Peptides of the invention may be assembled by solid phase synthesis on a cross- linked polystyrene support starting from the carboxyl terminal residue and adding amino acids in a stepwise fashion until the entire peptide has been formed. The following references are guides to the chemistry employed during synthesis: Schnolzer et al, Int. J. Peptide Protein Res., 40: 180-193 (1992); Merrifield, J. Amer. Chem. Soc, Vol. 85, pg. 2149 (1963); Kent et al., pg 185, in Peptides 1984, Ragnarsson, Ed. (Almquist and Weksell, Stockholm, 1984); Kent et al., pg.217 in Peptide Chemistry 84, Izumiya, Ed. (Protein Research Foundation, B.H. Osaka, 1985); Merrifield, Science, Vol. 232, pgs. 341-347 (1986); Kent, Ann. Rev. Biochem, Vol. 57, pgs. 957-989 (1988), and references cited in these latter two references.

Preferably, chemical synthesis of polypeptides of the invention is carried out by the assembly of peptide fragments by native chemical ligation, as described by Dawson et al, Science, 266: 776-779 (1994) and Kent el al, U.S. patent 6,184,344. Briefly, in the approach a first peptide fragment is provided with an N-terminal cysteine having an unoxidized sulfhydryl side chain, and a second peptide fragment is provided with a C-terminal thioester. The unoxidized sulfhydryl side chain of the N-terminal cysteine is then condensed with the C-terminal thioester to produce an intermediate peptide fragment which links the first and second peptide fragments with a β-aminothioester bond. The β-aminothioester bond of the intermediate peptide fragment then undergoes an intramolecular rearrangement to produce the peptide fragment product which links the first and second peptide fragments with an amide bond. Preferably, the N-terminal cysteine of the internal fragments is protected from undesired cyclization and/or concatenation reactions by a cyclic thiazolidine protecting group as described below. Preferably, such cyclic thiazolidine protecting group is a thioprolinyl group. Peptide fragments having a C-terminal thioester may be produced as described in the following references, which are incorporated by reference: Kent et al, U.S. patent 6,184,344; Tarn et al, Proc. Natl. Acad. Sci., 92: 12485-12489 (1995); Blake, Int. J. Peptide Protein Res., 17: 273 (1981); Canne 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 by Hackeng et al (1999) is employed. Briefly, peptide fragments are synthesized on a solid phase support (described below) typically on a 0.25 mmol scale by using the in situ neutralization/HBTU activation procedure for Boc chemistry disclosed by Schnolzer et al, Int. J. Peptide Protein Res., 40: 180-193 (1992), which reference is incorporated herein by reference. (HBTU is 2-(lH-benzotriazol-l- yl)-l,l,3,3-tetramethyluronium hexafluorophosphate and Boc is tert-butoxycarbonyl). Each synthetic cycle consists of N"-Boc removal by a 1- to 2- minute treatment with neat TFA, a 1- minute DMF flow wash, a 10- to 20-minute coupling time with 1.0 mmol of preactivated Boc-amino acid in the presence of DIEA, and a second DMF flow wash. (TFA is trifluoroacetic acid, DMF is N,N-dimethylformamide, and DIEA is N₅N- diisopropylethylamine). ISP-Boc-amino acids (1.1 mmol) are preactivated for 3 minutes with 1.0 mmol of HBTU (0.5 M in DMF) in the presence of excess DIEA (3 mmol). After each coupling step, yields are determined by measuring residual free amine with a conventional quantitative ninhydrin assay, e.g. as disclosed in Sarin et al, Anal. Biochem., 117: 147-157 (1981). After coupling of GIn residues, a DCM flow wash is used before and after deprotection by using TFA, to prevent possible high-temperature (TFA/DMF)-catalyzed pyrrolidone formation. After chain assembly is completed, the peptide fragments are deprotected and cleaved from the resin by treatment with anhydrous HF for 1 hour at O⁰C with as a scavenger. The imidazole side-chain 2,4-dinitrophenyl (dnp) protecting groups remain on the His residues because the dnp-removal procedure is incompatible with C-terminal thioester groups. However, dnp is gradually removed by thiols during the ligation reaction. After cleavage, peptide fragments are precipitated with ice-cold diethylether, dissolved in aqueous acetonitrile, and lyophilized.

Thioester peptide fragments described above are preferably synthesized on a trityl- associated mercaptopropionic acid-leucine (TAMPAL) resin, made as disclosed by Hackeng et al (1999), or comparable protocol. Briefly, ISP-Boc-Leu (4 mmol) is activated with 3.6 mmol of HBTU in the presence of 6 mmol of DIEA and coupled for 16 minutes to 2 mmol of p-methylbenzhydrylamine (MBHA) resin, or the equivalent. 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 coupled for 16 minutes to Leu-MBHA resin. The resulting TAMPAL resin can be used as a starting resin for polypeptide-chain assembly after removal of the trityl protecting group with two 1-minute treatments with 3.5% triisopropylsilane and 2.5% H₂O in TFA. The thioester bond can be formed with any desired amino acid by using standard in situ- neutralization peptide coupling protocols for 1 hour, as disclosed in Schnolzer et al (cited above). Treatment of the final peptide fragment with anhydrous HF yields the C-terminal activated mercaptopropionic acid-leucine (MPAL) thioester peptide fragments.

Preferably, thiazolidine-protected thioester peptide fragment intermediates are used in native chemical ligation under conditions as described by Hackeng et al (1999), or like conditions. Briefly, 0.1 M phosphate buffer (pH 8.5) containing 6 M guanidine, 4% (vol/vol) benzylmercaptan, and 4% (vol/vol) thiophenol is added to dry peptides to be ligated, to give a final peptide concentration of 1-3 mM at about pH 7, lowered because of the addition of thiols and TFA from the lyophilized peptide. Preferably, the ligation reaction is performed in a heating block at 37⁰C and is periodically vortexed to equilibrate the thiol additives. The reaction may be monitored for degree of completion by MALDI-MS or HPLC and electrospray ionization MS.

After a native chemical ligation reaction is completed or stopped, the N-terminal thiazolidine ring of the product is opened by treatment with a cysteine deprotecting agent, such as O-methylhydroxylamine (0.5 M) at pH 3.5-4.5 for 2 hours at 37° C, after which a 10- fold excess of Tris-(2-carboxyethyl)-phosphine is added to the reaction mixture to completely reduce any oxidizing reaction constituents prior to purification of the product by conventional preparative HPLC. Preferably, fractions containing the ligation product are identified by electrospray MS, are pooled, and lyophilized. After the synthesis is completed and the final product purified, the final polypeptide product may be refolded by conventional techniques, e.g. Creighton, Meth. Enzymol., 107: 305-329 (1984); White, Meth. Enzymol., 11: 481-484 (1967); Wetlaufer, Meth. Enzymol., 107: 301-304 (1984); and the like. Preferably, a final product is refolded by air oxidation by the following, or like: The reduced lyophilized product is dissolved (at about 0.1 mg/mL) in I M guanidine hydrochloride (or like chaotropic agent) with 100 mM Tris, 10 mM methionine, at pH 8.6. After gentle overnight stirring, the re-folded product is isolated by reverse phase HPLC with conventional protocols.

Recombinant Expression Vectors and Host Cells The polynucleotide sequences described herein can be used in recombinant DNA molecules that direct the expression of the corresponding polypeptides in appropriate host cells. Because of the degeneracy in the genetic code, other DNA sequences may encode the equivalent amino acid sequence, and maybe used to clone and express the CSFPs. Codons preferred by a particular host cell may be selected and substituted into the naturally occurring nucleotide sequences, to increase the rate and/or efficiency of expression. The nucleic acid (e.g., cDNA or genomic DNA) encoding the desired CSFP may be inserted into a replicable vector for cloning (amplification of the DNA), or for expression. The polypeptide can be expressed recombinantly in any of a number of expression systems according to methods known in the art (Ausubel, et al., editors, Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1990). Appropriate host cells include yeast, bacteria, archebacteria, fungi, and insect and animal cells, including mammalian cells, for example primary cells, including stem cells, including, but not limited to bone marrow stem cells. More specifically, these include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid or cosmid DNA expression vectors, and yeast transformed with yeast expression vectors. Also included, are insect cells infected with a recombinant insect virus (such as baculovirus), and mammalian expression systems. The nucleic acid sequence to be expressed may 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 of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan. The CSFPs of the present invention are produced by culturing a host cell transformed with an expression vector containing a nucleic acid encoding a CSFP, under the appropriate conditions to induce or cause expression of the protein. The conditions appropriate for CSFP expression will vary with the choice of the expression vector and the host cell, as ascertained by one skilled in the art. For example, the use of constitutive promoters in the expression vector may require routine optimization of host cell growth and proliferation, while the use of an inducible promoter requires the appropriate growth conditions for induction. In addition, in some embodiments, the timing of the harvest is important. For example, the baculoviral systems used in insect cell expression are lytic viruses, and thus harvest time selection can be crucial for product yield. 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, which cleaves a "prepro" form of the protein, may also be important for correct insertion, folding and/or function. By way of example, host cells such as CHO, HeLa, BHK, MDCK, 293, W138, etc. have specific cellular machinery and characteristic mechanisms for such post- translational activities and may be chosen to ensure the correct modification and processing of the introduced, foreign protein. Of particular interest are Drosophila melanogaster cells, Saccharomyces cerevisiae and other yeasts, E. coli, Bacillus subtilis, SF9 cells, C129 cells, 293 cells, Neurospora, BHK, CHO, COS, and HeLa cells, fibroblasts, Schwanoma cell lines, immortalized mammalian myeloid and lymphoid cell lines, Jurkat cells, human cells and other primary cells.

The nucleic acid encoding a CSFP must be "operably linked" by placing it into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, "operably linked" DNA sequences are contiguous, and, in the case of a secretory leader or other polypeptide sequence, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. Promoter sequences encode either constitutive or inducible promoters. The promoters may be either naturally occurring promoters or hybrid promoters. Hybrid promoters, which combine elements of more than one promoter, are also known in the art, and are useful in the present invention. The expression vector may comprise additional elements, for example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, for example in mammalian or insect cells for expression and in a procaryotic host for cloning and amplification. 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 the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2: plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells. Further, for integrating expression vectors, the expression vector contains at least one sequence homologous to the host cell genome, and preferably, two homologous sequences which flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art. Li an additional embodiment, a heterologous expression control element may be operably linked with the endogenous gene in the host cell by homologous recombination (described in US Patents 6410266 and 6361972). This technique allows one to regulate expression to a desired level with a chosen control element while ensuring proper processing and modification of CSFP endogenously expressed by the host cell. Useful heterologous expression control elements include but are not limited to CMV immediate early promoter, the HSV thymidine kinase promoter, the early and late SV40 promoters, the promoters of retroviral LTRs, such as those of the Rous Sarcoma Virus (RSV), and metallothionein promoters. Preferably, the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selection genes are well known in the art and will vary with the host cell used. Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available for from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.

Host cells transformed with a nucleotide sequence encoding a CSFP may be cultured under conditions suitable for the expression and recovery of the encoded protein from cell culture. The protein produced by a recombinant cell may be secreted, membrane-bound, or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides encoding the CSFP can be designed with signal sequences which direct secretion of the CSFP through a prokaryotic or eukaryotic cell membrane. The desired CSFP may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide. In general, the signal sequence may be a component of the vector, or it may be a part of the CSFP-encoding DNA that is inserted into the vector. The signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, lpp, or heat-stable enterotoxin II leaders. For yeast secretion the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces a-factor leaders, the latter described in U.S. Pat. No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179 published Apr. 4, 1990), or the signal described in WO 90113646 published Nov. 15, 1990. In mammalian cell expression, mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders. According to the expression system selected, the coding sequence is inserted into an appropriate vector, which in turn may require the presence of certain characteristic "control elements" or "regulatory sequences." Appropriate constructs are known generally in the art (Ausubel, et al., 1990) and, in many cases, are available from commercial suppliers such as mvitrogen (San Diego, Calif.), Stratagene (La Jolla, Calif.), Gibco BRL (Rockville, Md.) or Clontech (Palo Alto, Calif.). Expression in Bacterial Systems

Transformation of bacterial cells may be achieved using an inducible promoter such as the hybrid lacZ promoter of the "BLUESCRIPT" Phagemid (Stratagene) or "pSPORTl" (Gibco BRL). Ih addition, a number of expression vectors may be selected for use in bacterial cells to produce cleavable fusion proteins 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 suitable bacterial promoter is any nucleic acid sequence capable of binding bacterial RNA polymerase and initiating the downstream (3') transcription of the coding sequence of the CSFP gene into mRNA. A bacterial promoter has a transcription initiation region which is usually placed 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 from bacteriophage may 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 the trp and lac promoter sequences. Furthermore, a bacterial promoter 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. The expression vector may also include a signal peptide sequence that provides for secretion of the CSFP in bacteria. The signal sequence typically encodes a signal peptide comprised of hydrophobic amino acids which direct the secretion of the protein from the cell, as is well known in the art. The protein is either secreted into the growth media (gram- positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). The bacterial expression vector may also include a selectable marker gene to allow for the selection of bacterial strains that have been transformed. Suitable selection genes include drug resistance genes such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline. Selectable markers also include biosynthetic genes, such as those in the histidine, tryptophan and leucine biosynthetic pathways. When large quantities of CSFPs are needed, e.g., for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified may be desirable. Such vectors include, but are not limited to, multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene), in which the CSFP coding sequence may be ligated into the vector in-frame with sequences for the amino- terminal Met and the subsequent 7 residues of beta-galactosidase so that a hybrid protein is produced; PIN vectors (Van Heeke & Schuster JBiol Chem 264:5503-5509 1989)); PET vectors (Novagen, Madison Wis.); and the like. Expression vectors for bacteria include the various components set forth above, and are well known in the art. Examples include vectors for Bacillus subtilis, E. coli, Streptococcus cremoris, and Streptococcus lividans, among others. Bacterial expression vectors are transformed into bacterial host cells using techniques well known in the art, such as calcium chloride mediated transfection, electroporation, and others.

Expression in Yeast

Yeast expression systems are well known in the art, and include expression vectors for Saccharomyces cerevisiae, Candida albicans and C. maltosa, Hansenula polymorpha, Kluyveromyces fragilis and K. lactis, Pichia guillermondii and Ppastoris, Schizosaccharomycespom.be, and Yarrowia lipolytica. Examples of suitable promoters for use in yeast hosts include the promoters for 3-phosphoglycerate kinase (Hitzeman et al., J. Biol. Chem. 255:2073 (1980)) or other glycolytic enzymes (Hess et al.,J. Adv. Enzyme Reg. 7:149 (1968); Holland, Biochemistry 17:4900 (1978)), such as enolase, glyceraldehyde-3- phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose- 6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, alpha factor, the ADH2IGAPDH promoter, glucokinase alcohol oxidase, and PGH. (See, for example, Ausubel, et al., 1990; Grant et al., Methods in Enzymology 153:516-544, (1987)). Other yeast promoters, which are inducible have the additional advantage of transcription controlled by growth conditions, include the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors andpromoters for use in yeast expression are further described in EP 73,657. Yeast selectable markers include ADE2. HIS4. LEU2. TRPl. and ALG7, which confers resistance'to tunicamycin; the neomycin phosphotransferase gene, which confers resistance to G418; and the CUPl gene, which allows yeast to grow in the presence of copper ions. Yeast expression vectors can be constructed for intracellular production or secretion of a CSFP from the DNA encoding the CSFP of interest. For example, a selected signal peptide and the appropriate constitutive or inducible promoter may be inserted into suitable restriction sites in the selected plasmid for direct intracellular expression of the CSFP. For secretion of the CSFP, DNA encoding the CSFP can be cloned into the selected plasmid, together with DNA encoding the promoter, the yeast alpha-factor secretory signal/leader sequence, and linker sequences (as needed), for expression of the CSFP. Yeast cells, can then be transformed with the expression plasmids described above, and cultured in an appropriate fermentation media. The protein produced by such transformed yeast can then be concentrated by precipitation with 10% trichloroacetic acid and analyzed following separation by SDS-PAGE and staining of the gels with Coomassie Blue stain. The recombinant CSFP can subsequently be isolated and purified from the fermentation medium by techniques known to those of skill in the art.

Expression in Mammalian Systems

The CSFP may be expressed in mammalian cells. Mammalian expression systems are known in the art, and include retroviral vector mediated expression systems. Mammalian host cells may be transformed with any of a number of different viral-based expression systems, such as adenovirus, where the coding region can be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a nonessential El or E3 region of the viral genome results in a viable virus capable of expression of the polypeptide of interest in infected host cells. A preferred expression vector system is a retroviral vector system such as is generally described in

PCT/US97/01019 and PCT/US97/101048. Suitable mammalian expression vectors contain a mammalian promoter which is any DNA sequence capable of binding mammalian RNA polymerase and initiating the downstream (3') transcription of a coding sequence for CSFP into mRNA. A promoter will have a transcription initiating region, which is usually placed proximal to the 5' end of the coding sequence, and a TATA box, using a located 25-30 base pairs upstream of the transcription initiation site. The TATA box is thought to direct KNA polymerase II to begin RNA synthesis at the correct site. A mammalian promoter will also contain an upstream promoter element (enhancer element), typically located within 100 to 200 base pairs upstream of the TATA box. An upstream promoter element determines the rate at which transcription is initiated and can act in either orientation. Of particular use as mammalian promoters are the promoters from mammalian viral genes, since the viral genes are often highly expressed and have a broad host range. Examples include promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211, 504 published JuI. 5,1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems. Transcription of DNA encoding a CSFP by higher eukaryotes may be increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globin, 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 polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. The enhancer is preferably located at a site 5' from the promoter. Li general, the transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3 ' to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. The 3 ' terminus of the mature mRNA is formed by site-specific post-translational cleavage and polyadenylation.

Examples of transcription terminator and polyadenylation signals include those derived from SV40. Long term, high-yield production of recombinant proteins can be effected in a stable expression system. Expression vectors which contain viral origins of replication or endogenous expression elements and a selectable marker gene may be used for this purpose. Appropriate vectors containing selectable markers for use in mammalian cells are readily available commercially and are known to persons 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. The methods of introducing exogenous nucleic acid into mammalian hosts, as well as other hosts, is well known in the art, and will vary with the host cell used. Techniques include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, viral infection, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.

CSFPs can be purified from culture supernatants of mammalian cells transiently transfected or stably transformed by an expression vector carrying a CSFP-encoding sequence. Preferably, CSFP is purified from culture supernatants of COS 7 cells transiently transfected by the pcD expression vector. Transfection of COS 7 cells with pcD proceeds as follows: One day prior to transfection, approximately 10^ COS 7 monkey cells are seeded onto individual 100 mm plates in Dulbecco's modified Eagle medium (DME) containing 10% fetal calf serum and 2 mM glutamine. 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. The plates are incubated for four hours at

37⁰C, then the DNA-containing medium is removed, and the plates are washed twice with 5 ml of serum-free DME. DME is added back to the plates which are then incubated for an additional 3 hrs at37°C. The plates are washed once with DME, after which DME containing 4% fetal calf serum, 2 mM glutamine, penicillin (100 LVL) and streptomycin (100 μg/L) at standard concentrations is added. The cells are then incubated for 72 hrs at 37⁰C, after which the growth medium is collected for purification of CSFP. Plasmid DNA for the transfections is obtained by growing pcD(SRα), or like expression vector, containing the

CSFP-encoding cDNA insert in E. coli MC1061 (described by Casadaban and Cohen, J. MoI. Biol., Vol. 138, pgs. 179-207 (1980)), or like organism. The plasmid DNA is isolated from the cultures by standard techniques, e.g. Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition (Cold Spring Harbor Laboratory, New York, 1989) or Ausubel et al (1990, cited above).

Expression in Insect Cells

CSFPs may also be produced in insect cells. Expression vectors for the transformation of insect cells, and in particular, baculovirus-based expression vectors, are well known in the art. In one such system, the CSFP-encoding DNA is fused upstream of an epitope tag contained within a baculovirus expression vector. Autographa californica nuclear polyhidrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda Sf9 cells or in Trichoplusia larvae. The CSFP-encoding sequence is cloned into a nonessential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of a CSFP-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein coat. The recombinant viruses are then used to infect S. frugiperda cells or Trichoplusia larvae in which the CSFP is expressed (Smith et al., J. WoI. 46:584 (1994); Engelhard E K et al., Proc. Nat. Acad. ScL 91:3224-3227 (1994)). Suitable epitope tags for fusion to the CSFP-encoding DNA include poly-his tags and immunoglobulin tags (like Fc regions of IgG). A variety of plasmids may be employed, including commercially available plasmids such as pVL1393 (Novagen). Briefly, the CSFP-encoding DNA or the desired portion of the CSFP-encoding DNA is amplified by PCR with primers complementary to the 5' and 3' regions. The 5' primer may incorporate flanking restriction sites. The PCR product is then digested with the selected restriction enzymes and subcloned into an expression vector. Recombinant baculovirus is generated by co-transfecting the above plasmid and BaculoGoldTM virus DNA (Pharmingen) into Spodopterafrugiperda ("Sf9") cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL), or other methods known to those of skill in the art. Virus is produced by day 4-5 of culture in Sf9 cells at 28⁰C, and used for further amplifications. Procedures are performed as further described in O'Reilley et al., BACULOVIRUSEXPRESSION VECTORS: A LABORATORY MANUAL, Oxford University Press (1994). Extracts may be prepared from recombinant virus-infected Sf9 cells as described in Rupert et al., Nature 362:175-179 (1993). Alternatively, expressed epitope- tagged CSFP can be purified by affinity chromatography, or for example, purification of an IgG tagged (or Fc tagged) CSFP can be performed using chromatography techniques, including Protein A or protein G column chromatography.

Evaluation of Gene Expression

Gene expression may be evaluated in a sample directly, for example, by standard techniques known to those of skill in the art, e.g., Northern blotting to determine the transcription of mRNA, dot blotting (DNA or RNA), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies may be used in assays for detection of polypeptides, nucleic acids, such as specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Such antibodies may be labeled and the assay carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected. Gene expression, alternatively, may be measured by immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to directly evaluate the expression of a CSFP polypeptide or polynucleotide. Antibodies useful for such immunological assays may be either monoclonal or polyclonal, and may be prepared against a native sequence CSFP. Protein levels may also be detected by mass spectrometry. A further method of protein detection is with retentate chromatography (including protein arrays) and surface enhanced laser desorption/ionization (SELDI) techniques. Purification of Expressed Protein

Expressed CSFP may 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 upon what other components are present in the sample. Contaminant components that are removed by isolation or purification are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other solutes. The purification step(s) selected will depend, for example, on the nature of the production process used and the particular CSFP produced. As CSFPs are secreted, they may be recovered from culture medium. Alternatively, the CSFP may be recovered from host cell lysates. If membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g. Triton-X 100) or by enzymatic cleavage. Alternatively, cells employed in expression of CSFP can be disrupted by various physical or chemical means, such as freeze- thaw cycling, sonication, mechanical disruption, or by use of cell lysing agents. Exemplary 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, for example, Sephadex G-75; protein A Sepharose columns to remove contaminants such as IgG; chromatography using metal chelating columns to bind epitope-tagged forms of the CSFP; ethanol precipitation; reverse phase HPLC; chromatofocusing; SDS-PAGE; and ammonium sulfate precipitation. Ordinarily, an isolated CSFP will be prepared by at least one purification step. For example, the CSFP may be purified using a standard anti-CSFP antibody column. Ultrafiltration and dialysis techniques, in conjunction with protein concentration, are also useful (see, for example, Scopes, R., PROTEIN PURIFICATION, Springer-Verlag, New York, N. Y., 1982). The degree of purification necessary will vary depending on the use of the CSFP. In some instances no purification will be necessary. Once expressed and purified as needed, the CSFPs and nucleic acids of the present invention are useful in a number of applications, as detailed herein.

Assessing CSFP activity

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

CSFP biological activities include: (1) circulating through the CSF of human individuals; (2) antigenicity, or the ability to bind an anti-CSFP specific antibody; (3) immunogenicity, or the ability to generate an anti-CSFP specific antibody; (4) interaction with a CSFP target molecule or adsorbant; (5) improving cognitive functions; (6) reducing neuronal loss; (7) increasing neuronal survival; (8) protecting neurons against glutamate or hypoxia injury; (9) improving nerve impulse transmission; (10) enhancing myelin repair; and (11) reducing the inflammatory response.

CSFP biological activity can be assayed by any suitable method known in the art. Antigenicity and immunogenicity may be detected, for example, as described in the sections titled "Anti CSFP antibodies" and "Uses of CSFP antibodies". Circulation in CSF may be detected as described in "Diagnostic and Prognostic Uses".

Determining the ability of the CSFP to bind to or interact with a CSFP target molecule can be accomplished by a method for directly or indirectly determining binding, as is common to the art. Such methods can be cell-based (e.g., such that binding to a membrane-bound CSFP is detected) or cell free. Interaction of a test compound with a CSFP can be detected, for example, by coupling the CSFP or biologically active portion thereof with a label group such that binding of the CSFP or biologically active portion thereof to its cognate target molecule can be determined by detecting the labeled CSFP or biologically active portion thereof in a complex. For example, the extent of complex formation may be measured by immunoprecipitatmg the complex or by performing gel electrophoresis. Determining the ability of the CSFP to bind to a CSFP target molecule may also be accomplished using a technology 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 used herein, "BIA" is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules. Protein array methods are useful for detecting interaction. For example, one member of a receptor/ ligand pair is docked to an adsorbent, and its ability to bind the binding partner is determined in the presence of the test substance. Because of the rapidity with which adsorption can be tested, combinatorial libraries of test substances can be easily screened for their ability to modulate the interaction. In preferred methods, CSFPs are docked to the adsorbent. Binding partners are preferably labeled, thus enabling detection of the interaction. Alternatively, in certain embodiments, a test substance is docked to the adsorbent. The polypeptides of the invention are exposed to the test substance and binding detected.

Assessing the ability of CSFP-related compositions to increase neuronal survival can be performed in vitro, for example according to the procedure described in Example 9. Assessing the ability of CSFP-related compositions to protect neurons against glutamate injury can be performed in vitro, for example according to the following protocol: Preparation of cell cultures

The cortices are dissected under a stereomicroscope from fetal rats (Sprague-Dawley) of embryonic age E 17-El 9 (length of embryos, 18 mm). Cells (4 x 10⁵) are seeded onto 11 mm wells (Costar) that are treated with polyornithine (1 mg/ml) and grown in MEM

(minimum essential medium) tissue culture medium that contains 5% horse serum and 5% fetal calf serum. Cultures are kept at 37°C in 95% air/5% CO2. In order to decrease the number of non-neuronal cells, the antimitotic cytosine arabinoside (ara C) is used at 10^"6 M starting on the third day of culture during 3 days. Culture medium is changed every third day and morphological change of the cells is checked by phase contrast microscopy (Choi, D.W., Neuron, 1, 623, 1988).

Procedure for inducing cell injury (glutamate exposure)

Just prior to glutamate treatment, the culture medium is replaced by 300 μl of a HEPES-buffered control salt solution (HCSS) as described by Regan and Choi (Regan, R.F. and Choi, D.W., Neuroscience, 43, 585, 1991). Cells are incubated for 10 min in the HCSS medium at room temperature. At the end of this incubation, the CSFP-related composition and the reference compound MK-801 are added to the cells at the concentrations indicated (see below) and the cells are incubated for 10 min at room temperature. Thereafter, the cells are incubated for 15 min with 1 mM glutamate at room temperature. Subsequently, this solution is removed and replaced by 250 μl of serum-free MEM and the cells were re- incubated at 37°C for 24h under standard conditions. After morphological examination of the cells, the supernatants from the control and treated cultures are harvested and analysed for LDH activity. Assessment of the ability of CSFP-related compositions to improve cognitive functions can for example be conducted in normal animal where improvements in memory are quantified (e.g., time spent by an animal to recognize an object seen before, Bartolini et al., Pharmacol. Biochem. Behav., 53:277-283, 1996 and Puma C. et al., Eur, Neuropsychopharmacol., 1999 Jun;9(4):323-7). This assessment can also be studied in animal models of the disease, like animal with scopolamine-induced amnesia (Drew et al., Psychopharmacologia 32:171-182, 1973; Maurice et al., Brain Res. 647:44-56, 1994) or animals with basal forebrain lesions (induced for example by stereotaxic injection of ibotenic acid in the nucleus basalis magnocellularis), fimbria-fornix lesions (for example electrolytically-induced), or septum lesions (induced for example by stereotaxic injection of vincristine) where the efficacy of the CSFP-related composition in correcting the chemically- or surgically-induced defect is measured.

Assessing the ability of CSFP-related compositions to enhance myelin repair can be tested in assays such as those involving the study of myelin reformation after lysolecithin-induced demyelination (Larsen PH, et al., J Neurosci. 2003 Dec 3;23(35): 11127- 35).

Assessment of the ability of CSFP-related compositions to reduce the inflammatory response occuring in Multiple Sclerosis can for example be conducted in animal models of the disease, like Experimental Autoimmune Encephalomyelitis.

Anti-CSFP Antibodies

The present invention provides antibodies and binding compositions specific for CSFPs. 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 may be produced in a variety of ways, including hybridoma cultures, recombinant expression in bacteria or mammalian cell cultures, and recombinant expression in transgenic animals. There is abundant guidance in the literature for selecting a particular production methodology, e.g. Chadd and Chamow, Curr. Opin. Biotechnol., 12: 188-194 (2001).

The choice of manufacturing methodology depends on several factors including the antibody structure desired, the importance of carbohydrate moieties on the antibodies, ease of culturing and purification, and cost. Many different antibody structures may be generated using standard expression technology, including full-length antibodies, antibody fragments, such as Fab and Fv fragments, as well as chimeric antibodies comprising components from different species. Antibody fragments of small size, such as Fab and Fv fragments, having no effector functions and limited pharmokinetic activity may be generated in a bacterial expression system. Single chain Fv fragments are highly selective for in vivo tumors, show good tumor penetration and low immunogenicity, and are cleared rapidly from the blood, e.g. Freyre et al, J. Biotechnol., 76: 157-163 (2000). Thus, such molecules are desirable for radioimmunodetection.

Polyclonal Antibodies The anti-CSFP antibodies of the present invention may be polyclonal antibodies.

Such polyclonal antibodies can be produced in a mammal, for example, following one or more injections of an immunizing agent, and preferably, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected into the mammal by a series of subcutaneous or intraperitoneal injections. The immunizing agent may include CSFPs or a fusion protein thereof. It may be useful to conjugate the antigen to a protein 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). The immunization protocol may be determined by one skilled in the art based on standard protocols or by routine experimentation.

Alternatively, a crude protein preparation which has been enriched for a CSFP or a portion thereof can be used to generate antibodies. Such proteins, fragments or preparations are introduced into the non-human mammal in the presence of an appropriate adjuvant. If the serum contains polyclonal antibodies to undesired epitopes, the polyclonal antibodies are purified by immunoaffinity chromatography.

Effective polyclonal antibody production is affected by many factors related both to the antigen and the host species. Also, host animals vary in response to site of inoculations and dose, with both inadequate and excessive doses of antigen resulting in low titer antisera. Small doses (ng level) of antigen administered at multiple intradermal sites appear to be most reliable. Techniques for producing and processing polyclonal antisera are known in the art, see for example, Mayer and Walker (1987). An effective immunization protocol for rabbits can be found in Vaitukaitis, J. et al. J. Clin. Endocrinol. Metab. 33:988-991(1971). Booster injections can be given at regular intervals, and antiserum harvested when antibody titer thereof, as determined semi-quantitatively, for example, by double immunodiffusion in agar against known concentrations of the antigen, begins to fall. See, for example, Ouchterlony, O. et al., Chap. 19 in: Handbook of Experimental Immunology D. Wier (ed) Blackwell ( 1973). Plateau concentration of antibody is usually in the range of 0.1 to 0.2 mg/ml of serum. Affinity of the antisera for the antigen is determined by preparing competitive binding curves, as described, for example, by Fisher, D., Chap.42 in: Manual of Clinical Immunology, 2d Ed. (Rose and Friedman, Eds.) Amer. Soc. For Microbiol., Washington, D. C. (1980).

Monoclonal Antibodies

Alternatively, the anti-CSFP antibodies may be monoclonal antibodies. Monoclonal antibodies may be produced by hybridomas, wherein a mouse, hamster, or other appropriate host animal, is immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent, e.g. Kohler and Milstein, Nature 256:495 (1975). The immunizing agent will typically include the CSFP or a fusion protein thereof and optionally a carrier. Alternatively, the lymphocytes may be immunized in vitro. Generally, spleen cells or lymph node cells are used if non- human mammalian sources are desired, or peripheral blood lymphocytes ("PBLs") are used if cells of human origin are desired. The lymphocytes are fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to produce a hybridoma cell, e.g. 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). hi general, immortalized cell lines are transformed mammalian cells, for example, myeloma cells of rat, mouse, bovine or human origin. The hybridoma cells are cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT), substances which prevent the growth of HGPRT-deficient cells. Preferred immortalized cell lines are those that fuse efficiently, support stable high level production of antibody, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine or human myeloma lines, which can be obtained, for example, from the American Type Culture Collection (ATCC), Rockville, MD. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies, e.g. Kozbor, J. Immunol. 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, pp. 51-63 (1987).

The culture medium (supernatant) in which the hybridoma cells are cultured can be assayed for the presence of monoclonal antibodies directed against a CSFP. Preferably, the binding specificity of monoclonal antibodies present in the hybridoma supernatant is determined by immunoprecipitation or by an in vitro binding assay, such as radio- immunoassay (RIA) or Enzyme-Linked Immuno Sorbent Assay (ELISA). Appropriate techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem. 107:220 (1980). After the desired antibody-producing hybridoma cells are identified, the cells may be cloned by limiting dilution procedures and grown by standard methods (Goding, 1986, supra). Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal. The monoclonal antibodies secreted by selected clones may be isolated or purified from the culture medium or ascites fluid by immunoglobulin purification procedures routinely used by those of skill in the art such as, for example, protein A-Sepharose, hydroxyl-apatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.

The monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No.4,816,567. DNA encoding the monoclonal antibodies of the invention can be isolated from the CSFP-specific hybridoma cells and sequenced, e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies. Once isolated, the DNA may be inserted into an expression vector, which is then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also may be modified, for example, by substituting the coding sequence for the murine heavy and light chain constant domains for the homologous human sequences (Morrison et al., Proc. Nat. Acad. ScL 81:6851-6855 (1984); Neuberger et al., Nature 312:604-608 (1984); Takeda et al., Nature 314:452-454 (1985)), or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. The non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen- combining site of an antibody of the invention to create a chimeric bivalent antibody. The antibodies may also be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, in vitro methods are suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art.

Antibodies and antibody fragments characteristic of hybridomas of the invention can also be produced by recombinant means by extracting messenger RNA, constructing a cDNA library, and selecting clones which encode segments of the antibody molecule. The following are exemplary references disclosing recombinant techniques for producing antibodies: Wall et al., Nucleic Acids Research, Vol. 5, pgs. 3113-3128 (1978); Zakut et al., Nucleic Acids Research, Vol. 8, pgs. 3591-3601 (1980); Cabilly et al., Proc. Natl. Acad. Sci., Vol. 81, pgs. 3273-3277 (1984); Boss et al., Nucleic Acids Research, Vol. 12, pgs. 3791- 3806 (1984); Amster et al., Nucleic Acids Research, Vol. 8, pgs. 2055-2065 (1980); Moore et al., U.S. Patent 4,642,334; Skerra et al, Science, Vol. 240, pgs. 1038-1041(1988); Huse et al, Science, Vol. 246, pgs. 1275-1281 (1989); and U.S. patents 6,054,297; 5,530,101; 4,816,567; 5,750,105; and 5,648,237; which patents are incorporated by reference. In particular, such techniques can be used to produce interspecific monoclonal antibodies, wherein the binding region of one species is combined with non-binding region of the antibody of another species to reduce immunogenicity, e.g. Liu et al., Proc. Natl. Acad. Sci., Vol. 84, pgs. 3439-3443 (1987), and patents 6,054,297 and 5,530,101. Preferably, recombinantly produced Fab and Fv fragments are expressed in bacterial host systems. Preferably, full-length antibodies are produced by mammalian cell culture techniques. More 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 in 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 antigen-antibody complexes with a simple separation of such complexes from unbound material. To titrate anti-peptide serum, peptide conjugated to a carrier different from that used in immunization is adsorbed to the wells of a 96-well microtiter plate. The adsorbed antigen is then allowed to react in the wells with dilutions of anti-peptide serum. Unbound antibody is washed away, and the remaining antigen-antibody complexes are allowed to react with an antibody specific for the IgG of the immunized animal. This second antibody is conjugated to an enzyme such as alkaline phosphatase. A visible colored reaction produced when the enzyme substrate is added indicates which wells have bound antipeptide antibodies. The use of spectrophotometer readings allows better quantification of the amount of peptide-specifϊc antibody bound. High-titer antisera yield a linear titration curve between 1O^-3 and 1O^-5 dilutions.

CSFP peptide carriers

The invention includes immunogens derived from CSFPs, and immunogens comprising conjugates between carriers and peptides of the invention. The term immunogen as used herein refers to a substance which is capable of causing an immune response. The term carrier as used herein refers to any substance which when chemically conjugated to a peptide of the invention permits a host organism immunized with the resulting conjugate to generate antibodies specific for the conjugated peptide. Carriers include red blood cells, bacteriophages, proteins, or synthetic particles such as agarose beads. Preferably, carriers are proteins, such as serum albumin, gamma-globulin, keyhole limpet hemocyanin (KXH), thyroglobulin, ovalbumin, or fibrinogen.

The general technique of linking synthetic peptides to a carrier is described in several references, e.g. Walter and Doolittle, "Antibodies Against Synthetic Peptides," in Setlow et al., eds., Genetic Engineering, Vol. 5, pgs. 61-91 (Plenum Press, N. Y., 1983); Green et al. Cell, Vol. 28, pgs.477-487 (1982); Lerner et al., Proc. Natl. Acad. Sci., Vol. 78, pgs. 3403- 3407 (1981); Shimizu et al., U.S. Patent 4,474,754; and Ganfield et al., U.S. Patent 4,311,639. Accordingly, these references are incorporated by reference. Also, techniques employed to link haptens to carriers are essentially the same as the above-referenced techniques, e.g. chapter 20 in Tijssen, Practice and Theory of Enzyme Immunoassays (Elsevier, New York, 1985). The four most commonly used schemes for attaching a peptide to a carrier are (1) glutaraldehyde for amino coupling, e.g. as disclosed by Kagan and Glick, in Jaffe and Behrman, eds. Methods of Hormone Radioimmunoassay, pgs. 328-329 (Academic Press, N. Y., 1979), and Walter et al. Proc. Natl. Acad. Sci., Vol. 77, pgs. 5197- 5200 (1980); (2) water-soluble carbodiimides for carboxyl to amino coupling, e.g. as disclosed by Hoare et al., J. Biol. Chem., Vol. 242, pgs. 2447-2453 (1967); (3) bis- diazobenzidine (BDB) for tyrosine to tyrosine sidechain coupling, e.g. as disclosed by Bassiri et al., pgs. 46-47, in Jaffe and Behrman, eds. (cited above), and Walter et al. (cited above); and (4) maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) for coupling cysteine (or other sulfhydryls) to amino groups, e.g. as disclosed by Kitagawa et al., J. Biochem. (Tokyo), Vol. 79, pgs. 233-239 (1976), and Lerner et al. (cited above). A general rule for selecting an appropriate method for coupling a given peptide to a protein carrier can be stated as follows: the group involved in attachment should occur only once in the sequence, preferably at the appropriate end of the segment. For example, BDB should not be used if a tyrosine residue occurs in the main part of a sequence chosen for its potentially antigenic character.

Similarly, centrally located lysines rule out the glutaraldehyde method, and the occurrences of aspartic and glutamic acids frequently exclude the carbodiimide approach. On the other hand, suitable residues can be positioned at either end of chosen sequence segment as attachment sites, whether or not they occur in the "native" protein sequence. Internal segments, unlike the amino and carboxy termini, will differ significantly at the "unattached end" from the same sequence as it is found in the native protein where the polypeptide backbone is continuous. The problem can be remedied, to a degree, by acetylating the α- amino group and then attaching the peptide by way of its carboxy terminus. The coupling efficiency to the carrier protein is conveniently measured by using a radioactively labeled peptide, prepared either by using a radioactive amino acid for one step of the synthesis or by labeling the completed peptide by the iodination of a tyrosine residue. The presence of tyrosine in the peptide also allows one to set up a sensitive radioimmune assay, if desirable. Therefore, tyrosine can be introduced as a terminal residue if it is not part of the peptide sequence defined by the native polypeptide. Preferred carriers are proteins, and preferred protein carriers include bovine serum albumin, myoglobulin, ovalbumin (OVA), keyhole limpet hemocyanin (KLH), or the like. Peptides can be linked to KLH through cysteines by MBS as disclosed by Liu et al., Biochemistry, Vol. 18, pgs. 690-697 (1979). The peptides are 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 the dissolution of the peptide is chosen to optimize peptide solubility. The content of free cysteine for soluble peptides is determined by Ellman's method, Ellman, Arch. Biochem. Biophys., Vol. 82, pg. 7077 (1959). For each peptide, 4 mg KLH in 0.25 ml of 10 mM sodium phosphate buffer (pH 7.2) is reacted with 0.7 mg MBS (dissolved in dimethyl formamide) and stirred for 30 min at room temperature. The MBS is added dropwise to ensure that the local concentration of formamide is not too high, as KLH is insoluble in >30% formamide. The reaction product, KLH-MBS, is then passed through Sephadex G-25 equilibrated with 50 mM sodium phosphate buffer (pH 6.0) to remove free MBS, KLH recovery from peak fractions of the column eluate (monitored by OD280) is estimated to be approximately 80%. KLH-MBS is then reacted with 5 mg peptide dissolved in 1 ml of the chosen buffer. The pH is adjusted to 7-7.5 and the reaction is stirred for 3 hr at room temperature. Coupling efficiency is monitored with radioactive peptide by dialysis of a sample of the conjugate against phosphate-buffered saline, and may range from 8% to 60%. Once the peptide-carrier conjugate is available, polyclonal or monoclonal antibodies are produced by standard techniques, e.g. as disclosed by Campbell, Monoclonal Antibody Technology (Elsevier, New York, 1984); Hurrell, ed. Monoclonal Hybridoma Antibodies: Techniques and Applications (CRC Press, Boca Raton, FL, 1982); Schreier et al. Hybridoma Techniques (Cold Spring Harbor Laboratory, New York, 1980); U.S. Patent 4,562,003.

Humanized Antibodies

The anti-CSFP antibodies of the invention may further comprise humanized antibodies or human antibodies. The term "humanized antibody" refers to humanized forms of non-human (e.g., murine) antibodies that are chimeric antibodies, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab'), or other antigen-binding partial sequences of antibodies) which contain some portion of the sequence derived from non- human antibody. Humanized antibodies include human immunoglobulins in which residues from a complementary determining region (CDR) of the human immunoglobulin are replaced by residues from a CDR of a non-human species such as mouse, rat or rabbit having the desired binding specificity, affinity and capacity. In general, the humanized antibody will comprise substantially all of at least one, and generally two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., Nature 321 :522-525 (1986) and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992)). Methods for humanizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acids introduced into it from a source which is non-human in order to more closely resemble a human antibody, while still retaining the original binding activity of the antibody. Methods for humanization of antibodies are further detailed 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 that substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. Heteroconjugate Antibodies

Heteroconjugate antibodies which comprise two covalently joined antibodies, are also within the scope of the present invention. Heteroconjugate antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinkmg agents. For example, immunotoxins may be prepared using a disulfide exchange reaction or by forming a thioether bond.

Bispecific Antibodies

Bispecific antibodies have binding specificities for at least two different antigens. Such antibodies are monoclonal, and preferably human or humanized. One of the binding specificities of a bispecific antibody of the present invention is for a CSFP, and the other one is preferably for a cell-surface protein or receptor or receptor sύbunit. Methods for making bispecific antibodies are known in the art, and in general, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light- chain pairs in hybridoma cells, where the two heavy chains have different specificities, e.g. Milstein and Cuello, Nature 305:537-539 (1983). Given that the random assortment of immunoglobulin heavy and light chains results in production of potentially ten different antibody molecules by the hybridomas, purification of the correct molecule usually requires some sort of affinity purification, e.g. affinity chromatography.

Uses of CSFP antibodies

CSFP antibodies are preferably specific for the CSFPs of the invention and, as such, do not bind peptides derived from other proteins with high affinity. As used herein, the term "heavy chain variable region" means a polypeptide (1) which is from 110 to 125 amino acids in length, and (2) whose amino acid sequence corresponds to that of a heavy chain of an antibody of the invention, starting from the heavy chain's N-terminal amino acid. Likewise, the term "light chain variable region" means a polypeptide (1) which is from 95 to 115 amino acids in length, and (2) whose amino acid sequence corresponds to that of a light chain of an antibody of the invention, starting from the light chain's N-terminal amino acid. As used herein the term "monoclonal antibody" refers to homogeneous populations of immunoglobulins which are capable of specifically binding to CSFPs.

The use of antibody fragments is also well known, e.g. Fab fragments: Tijssen, Practice and Theory of Enzyme Immunoassays (Elsevier, Amsterdam, 1985); and Fv fragments: Hochman et al. Biochemistry, Vol. 12, pgs. 1130-1135 (1973), Sharon et al., Biochemistry, Vol. 15, pgs. 1591-1594 (1976) and Ehrlich et al., U.S. Patent 4,355,023; and antibody half molecules: Auditore- Hargreaves, U.S. Patent 4,470,925.

Preferably, monoclonal antibodies, Fv fragments, Fab fragments, or other binding compositions derived from monoclonal antibodies of the invention have a high affinity to CSFPs. The affinity of monoclonal antibodies and related molecules to CSFPs may be measured by conventional techniques including plasmon resonance, ELISA, or equilibrium dialysis. Affinity measurement by plasmon resonance techniques may be carried out, for example, using a BIAcore 2000 instrument (Biacore AB, Uppsala, Sweden) in accordance with the manufacturer's recommended protocol. Preferably, affinity is measured by ELISA, as described in U.S. patent 6,235,883, for example. Preferably, the dissociation constant between CSFPs and monoclonal antibodies of the invention is less than 10^"5 molar. More preferably, such dissociation constant is less than 10^"8 molar; still more preferably, such dissociation constant is less than 10^"9 molar; and most preferably, such dissociation constant is in the range of 10^"9 to 10^'π molar. The antibodies of the present invention are useful for detecting CSFPs. Such detection methods are advantageously applied to diagnosis of CSFP-related disorders. The antibodies of the invention may be used in most assays involving antigen-antibody reactions. The assays may be homogeneous or heterogeneous. In a homogeneous assay approach, the sample can be a biological sample or fluid such as CSF, serum, urine, whole blood, lymphatic fluid, plasma, saliva, cells, tissue, and material secreted by cells or tissues cultured in vitro. The sample can be pretreated if necessary to remove unwanted materials. The immunological reaction usually involves the specific antibody, a labeled analyte, and the sample suspected of containing the antigen. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both immunological reaction and detection of the extent thereof are carried out in a homogeneous solution. Immunochemical labels which may be employed include free radicals, fluorescent dyes, enzymes, bacteriophages, coenzymes, and so forth.

In a heterogeneous assay approach, the reagents are usually the sample, the specific antibody, and means for producing a detectable signal. The specimen is generally placed on a support, such as a plate or a slide, and contacted with the antibody in a liquid phase. The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal employing means for producing such signal or signal producing system. The signal is related to the presence of the antigen in the sample. Means for producing a detectable signal includes the use of radioactive labels, fluorescent compounds, enzymes, and so forth. Exemplary heterogeneous immunoassays are the radioimmunoassay, immunofluorescence methods, enzyme-linked immunoassays, and the like.

For a more detailed discussion of the above immunoassay techniques, see "Enzyme- Immunoassay," by Edward T. Maggio, CRC Press, Inc., Boca Raton, FIa., 1980. See also, for example, U.S. Pat. Nos. 3,690,834; 3,791,932; 3,817,837; 3,850,578; 3,853,987; 3,867,517; 3,901,654; 3,935,074; 3,984,533; 3,966,345; and 4,098,876, which listing is not intended to be exhaustive. Methods for conjugating labels to antibodies and antibody fragments are well known in the art. Such methods may 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 may be employed is immunoperoxidase labeling. (Sternberger, Immunocytochemistry (1979) pp. 104-169).

One embodiment of an assay employing an antibody of the.present invention involves the use of a surface to which the monoclonal antibody of the invention is attached. The underlying structure of the surface may take different forms, have different compositions and may be a mixture of compositions or laminates or combinations thereof. The surface may assume a variety of shapes and forms and may have varied dimensions, depending on the manner of use and measurement. Illustrative surfaces may be pads, beads, discs, or strips which may be flat, concave or convex. Thickness is not critical, generally being from about 0.1 to 2 mm thick and of any convenient diameter or other dimensions. The surface typically will be supported on a rod, tube, capillary, fiber, strip, disc, plate, cuvette and will typically be porous and polyfunctional or capable of being polyfϊinctionalized so as to permit covalent binding of an antibody and permit bonding of other compounds which form a part of a means for producing a detectable signal. A wide variety of organic and inorganic polymers, both natural and synthetic, and combinations thereof, may be employed as the material for the solid surface. Illustrative polymers include polyethylene, polypropylene, poly(4- methylbutene), polystyrene, polymethracrylate, poly(ethylene terephthalate), rayon, nylon, poly(vinyl butyrate), silicones, polyformaldehyde, cellulose, cellulose acetate, nitrocellulose, and latex. Other surfaces include paper, glasses, ceramics, metals, metaloids, semiconductor materials, cements, silicates or the like. Also included are substrates that form gels, gelatins, lipopolysaccharides, silicates, agarose and polyacrylamides or polymers which form several aqueous phases such as dextrans, polyalkylene glycols (alkylene of 2 to 3 carbon atoms) or surfactants such as phospholipids. The binding of the antibody to the surface may be accomplished by well known techniques, commonly available in the literature (see, for example, "Immobilized Enzymes," Ichiro Chibata, Press, New York (1978) and Cuatrecasas, J. Bio. Chem., 245: 3059 (1970)). In carrying out the assay in accordance with this aspect of the invention, the sample is mixed with aqueous medium and the medium is contacted with the surface having an antibody bound thereto. Labels may be included in the aqueous medium, either concurrently or added subsequently so as to provide a detectable signal associated with the surface. The means for producing the detectable signal can involve the incorporation of a labeled analyte or it may involve the use of a second monoclonal antibody having a label conjugated thereto. Separation and washing steps will be carried out as needed. The signal detected is related to the presence of CSFP in the sample. It is within the scope of the present invention to include a calibration on the same support. A particular embodiment of an assay in accordance with the present invention, by way of illustration and not limitation, involves the use of a support such as a slide or a well of a petri dish. The technique involves fixing the sample to be analyzed on the support with an appropriate fixing material and incubating the sample on the slide with a monoclonal antibody. After washing with an appropriate buffer such as, for example, phosphate buffered saline, the support is contacted with a labeled specific binding partner for the antibody. After incubation as desired, the slide is washed a second time with an aqueous buffer and the determination is made of the binding of the labeled monoclonal antibody to the antigen. If the label is fluorescent, the slide may be covered with a fluorescent antibody mounting fluid on a cover slip and then examined with a fluorescent microscope to determine the extent of binding. On the other hand, the label can be an enzyme conjugated to the monoclonal antibody and the extent of binding can be determined by examining the slide for the presence of enzyme activity, which may be indicated by the formation of a precipitate, color, etc.

A particular example of an assay utilizing the present antibodies is a double determinant ELISA assay. A support such as, e.g., a glass or vinyl plate, is coated with an antibody specific for CSFP by conventional techniques. The support is contacted with the sample suspected of containing CSFP, usually in aqueous medium. After an incubation period from 30 seconds to 12 hours, the support is separated from the medium, washed to remove unbound CSFP with, for example, water or an aqueous buffered medium, and contacted with an antibody specific for CSFP, again usually in aqueous medium. The antibody is labeled with an enzyme directly or indirectly such as, e.g., horseradish peroxidase or alkaline phosphatase. After incubation, the support is separated from the medium, and washed as above. The enzyme activity of the support or the aqueous medium is determined. This enzyme activity is related to the amount of CSFP in the sample. Another antibody-utilizing method of detection includes retentate chromotography methods, as described herein. In this case, the adsorbant is an antibody. Preferably, more than one antibody specific for more than one CSFP of the invention is included on a surface or substrate. The invention also includes kits, e.g., diagnostic assay kits, for carrying out the methods disclosed above. In one embodiment, the kit comprises in packaged combination (a) a monoclonal antibody more specifically defined above and (b) a conjugate of a specific binding partner for the above monoclonal antibody and a label capable of producing a detectable signal. The reagents may also include ancillary agents such as buffering agents and protein stabilizing agents, e.g., polysaccharides and the like. The kit may further include, where necessary, other members of the signal producing system of which system the label is a member, agents for reducing background interference in a test, control reagents, apparatus for conducting a test, and the like. Ih another embodiment, the diagnostic kit comprises a conjugate of monoclonal antibody of the invention and a label capable of producing a detectable signal. Ancillary agents as mentioned above may also be present.

Further, an anti-CSFP antibody (e.g., monoclonal antibody) can be used to isolate CSFPs by standard techniques, such as affinity chromatography or immunoprecipitation. For example, an anti-CSFP antibody can facilitate the purification of natural CSFPs from cells and of recombinantly produced CSFP expressed in host cells. Moreover, an anti-CSFP antibody can be used to isolate CSFP to aid in detection of low concentrations of CSFP (e.g., in CSF, cellular lysate or cell supernatant) or in order to evaluate the abundance and pattern of expression of the CSFP. Anti-CSFP antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a label group.

Detection Using Protein Arrays

Detection and purification of the polypeptides of the invention may be accomplished using retentate chromatography (preferably, protein arrays or chips), as described by U.S. Patent 6225027 and U.S. Patent Application 20010014461. Briefly, retentate chromatography describes methods in which polypeptides (and/ or other sample components) are retained on an adsorbent (e.g., array or chip) and subsequently detected. Such methods involve (1) selectively adsorbing polypeptides from a sample to a substrate under a plurality of different adsorbent/eluant combinations ("selectivity conditions") and (2) detecting the retention of adsorbed polypeptides by desorption spectrometry (e.g., by mass spectrometry). "Desorption spectrometry" refers to a method of detecting a substance (e.g., polypeptide) in which the substance is exposed to energy which desorbs it from a stationary phase into a gas phase, and the desorbed substance or a distinguishable portion of it is directly detected by a detector, without an intermediate capture on a second stationary phase. In conventional chromatographic methods, polypeptides are eluted off of the adsorbent prior to detection. The coupling of adsorption chromatography with detection by desorption spectrometry provides extraordinary sensitivity, the ability to rapidly analyze retained components with a variety of different selectivity conditions, and parallel processing of components adsorbed to different sites (i.e., "affinity sites" or "spots") on the array under different elution conditions.

A preferred embodiment provides adsorbents, either chemical (e.g., ion-affinity or hydrophobic substances) or biospecifϊc (e.g., antibodies or antigen-binding fragments thereof), developed to detect a specific polypeptide, preferably a CSFP. In certain embodiments, a substrate has an array of adsorbent spots selected for a combination of polypeptides, e.g. as diagnostic markers. As few as two and as many as 10, 100, 1000, or more adsorbents can be coupled to a single substrate. The size of the adsorbent site may be varied, depending on experimental design and purpose. However, it does not need to be larger than the diameter of the impinging energy source (e.g., laser spot diameter). The spots can be made of the same or different adsorbents. Ih some cases, it is advantageous to provide the same adsorbent at multiple locations on the substrate to permit evaluation against a plurality of different eluants or so that the bound polypeptide can be preserved for future use or reference, perhaps in secondary processing. By providing a substrate with a plurality of different adsorbents, it is possible to utilize the plurality of binding characteristics provided by the combination of different adsorbents with respect to a single sample (e.g., CSF sample) and thereby bind and detect a wider variety of different polypeptides (preferably CSFPs). The use of a plurality of different adsorbents on a substrate for evaluation of a single sample is essentially equivalent to concurrently conducting multiple chromatographic experiments, each with a different chromatography column, but the present method has the advantage of requiring only a single system. When the substrate includes a plurality of adsorbents, it is particularly useful to provide the adsorbents in predetermined addressable locations. By providing the adsorbents in predetermined addressable locations, it is possible to wash an adsorbent at a first predetermined addressable location with a first eluant and to wash an adsorbent at a second predetermined addressable location with a second eluant. In this manner, the binding characteristics of a single adsorbent for its specified polypeptide can be evaluated in the presence of multiple eluants which each selectively modify each set of adsorbant-polypeptide binding characteristics.

Retentate chromotography may be used in a combinatorial separation method that includes separation and detection of multiple polypeptides in parallel. The method comprises the steps of a) exposing a sample (e.g., a biological fluid such as CSF) to at least two different selectivity conditions, each selectivity condition defined by the combination of an adsorbent and an eluant, to allow retention of a polypeptide by the adsorbent; and b) detecting retained polypeptide under the different selectivity conditions by desorption spectrometry. Each different selectivity condition is defined at a different predetermined, addressable location for parallel processing. The method comprises the steps of i) exposing a sample to a first selectivity condition at a defined location to allow retention of a polypeptide by an adsorbent; ii) detecting retained polypeptide under the first selectivity condition by desorption spectrometry; iii) washing the adsorbent under a second, different selectivity condition at the defined location to allow retention of a polypeptide to the adsorbent at that location; and iv) detecting retained polypeptides under the second selectivity condition by desorption spectrometry.

Polypeptides may be detected by gas phase ion spectrometry, SELDI, or mass spectrometry techniques detailed herein. "Gas phase ion spectrometry" refers to a method of employing an ionization source to generate gas phase ions from a substance presented on a surface and detecting the gas phase ions with a gas phase ion spectrometer. "Surface- enhanced laser desorption/ionisation" or "SELDI" is a method of gas phase ion spectrometry in which the substance-presenting surface plays an active role in desorption and ionization process. SELDI technology is described in, e.g., U.S. Patents 5,719,060 and 6,225,047 (Hutchens and Yip).

These methods are useful for: combinatorial, biochemical separation and purification of the CSFPs; study of differential gene expression; and detection of differences in protein levels between samples (e.g., for diagnosis). WO 03/019193 (Ciphergen) describes the use of such methods for detection of specific kidney disease markers in a fluid sample. A similar approach is taken by Yip and Lomas (Technol Cancer Res Treat, 2002, 1 :273-80) to detect cancer-related polypeptides. CSFPs of the invention or CSFP-binding substances are preferably attached to a label group, and thus directly detected, enabling simultaneous transmission of two or more signals from the same "circuit" (i.e., addressable "chip" location) during a single unit operation. A preferred embodiment of the invention encompasses use of retentate chromotography to identify at least one CSFP in a sample, preferably CSF.

A variation of microchip-based detection utilizes electrophoresis, as described by Chen, et al. (Anal Chem 2002; 74:5146-53). In this method, a flow-through sampling chip is applied to immunoseparation, protein purification, concentration, and detection purposes. This device uses hydrodynamic pressure to drive the sample flow, and a gating voltage is applied to the electrophoretic channel on the microchip. Using this device, the wash/elution step can be integrated on-line with electrophoretic separation and detection on the microchip. Moreover, the electrical field-free bed ensures that protein-adsorbant interaction will not be affected by the electric field during the wash/elution step.

Detection of CSFPs by mass spectrometry

In accordance with the present invention, any instrument, method, process, etc. can be utilized to determine the identity and abundance of proteins in a sample. A preferred method of obtaining identity is by mass spectrometry, where protein molecules in a sample are ionized and then the resultant mass and charge of the protein ions are detected and determined.

To use mass spectrometry to analyze proteins, it is preferred that the protein be converted to a gas-ion phase. Various methods of protein ionization are useful, including, e.g., fast ion bombardment (FAB), plasma desorption, laser desorption, thermal desorption, preferably, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). Many different mass analyzers are available for peptide and protein analysis, including, but not limited to, Time-of-Flight (TOF), ion trap (ITMS), Fourier transform ion cyclotron (FTMS), quadrupole ion trap, and sector (electric and/or magnetic) spectrometers. See, e.g., U.S. Pat. No. 5,572,025 for an ion trap MS. Mass analyzers can be used alone, or in combination with other mass analyzers in tandem mass spectrometers. In the latter case, a first mass analyzer can be use to separate the protein ions (precursor ion) from each other and determine the molecular weights of the various protein constituents in the sample. A second mass analyzer can be used to analyze each separated constituents, e.g., by fragmenting the precursor ions into product ions by using, e.g. an inert gas. Any desired combination of mass analyzers can be used, including, e.g., triple quadrupoles, tandem time-of-flights, ion traps, and/or combinations thereof.

Different kinds of detectors can be used to detect the protein ions. For example, destructive detectors can be utilized, such as ion electron multipliers or cryogenic detectors (e.g., U.S. Patent 5,640,010). Additionally, non-destructive detectors can be used, such as ion traps which are used as ion current pick-up devices in quadrupole ion trap mass analyzers or FTMS.

For MALDI-TOF, a number of sample preparation methods can be utilized including, dried droplet (Karasand Hillenkamp, Anal. Chem., 60:2299-2301 , 1988), vacuum-drying (Winberger et al., In Proceedings of the 41st ASMS Conference on Mass Spectrometry and Allied Topics, San Francisco, May 31-June 4, 1993, pp. 775a-b), crush crystals (Xiang et al., Rapid Comm. Mass Spectrom., 8:199-204,1994), slow crystal growing (Xiang et al., Org. Mass Spectrom, 28:1424-1429, 1993); active film (Mock et al., Rapid Comm. Mass Spectrom.,6:233-238, 1992; Bai et al., Anal. Chem., 66:3423-3430, 1994), pneumatic spray (Kochling et al., Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics; Atlanta, GA, May 21-26, 1995, pi 225); electrospray (Hensel et al., Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics; Atlanta, GA, May 21 -26, 1995, p947); 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 two-layer methods (Dal et al., Anal. Chem., 71:1087-1091, 1999). See also, e.g., Liang et al., Rapid Commun. Mass Spectrom., 10: 1219-1226, 1996; van Adrichemet al., Anal. Chem., 70:923-930, 1998.

For MALDI analysis, samples are prepared as solid-state co-crystals or thin films by mixing them with an energy absorbing compound or colloid (the matrix) in the liquid phase, and ultimately drying the solution to the solid state upon the surface of an inert probe, m some cases an energy absorbing molecule (EAM) is an integral component of the sample presenting surface. Regardless of EAM application strategy, the probe contents are allowed to dry to the solid state prior to introduction into the laser desorption/ionization time-of-flight mass spectrometer (LDIMS).

Ion detection in TOF mass spectrometry is typically achieved with the use of electro- emissive detectors such as electron multipliers (EMP) or microchannel plates (MCP). Both of these devices function by converting primary incident charged particles into a cascade of secondary, tertiary, quaternary, etc. electrons. The probability of secondary electrons being generated by the impact of a single incident charged particle can be taken to be the ion-to- electron conversion efficiency of this charged particle (or more simply, the conversion efficiency). The total electron yield for cascading events when compared to the total number of incident charged particles is typically described as the detector gain. Because generally the overall response time of MCPs is far superior to that of EMPs, MCPs are the preferred electro-emissive detector for enhancing mass/charge resolving power. However, EMPs function well for detecting ion populations of disbursed kinetic energies, where rapid response time and broad frequency bandwidth are not necessary.

In a preferred aspect, for the analysis of digested proteins, a liquid-chromatography tandem mass spectrometer (LC-TMS) is used. This system provides an additional stage of sample separation via use of a liquid chromatograph followed by tandem mass spectrometry. Electrospray ionization (ESI) and MALDI are commonly used ionization techniques for interfacing capillary electrophoresis (CE) to MS (Moini, M., Anal Bioanal Chem, 2002; 373:466-80). CE has the advantage of high sensitivity and separation efficiency. The high concentration detection limit of CE has been addressed by development of sample concentration and sample focusing methods. In addition, a wide variety of techniques such as capillary zone electrophoresis, capillary isoelectric focusing, and on-column transient isotachophoresis have now been interfaced to MS. Deterding, et al. (Electrophoresis 2002; 23:2296-305) describe successful application of CE-MS techniques for identification of apolipoprotein species from plasma samples. Thus, it is envisioned that these methods are similarly applied to detect CSFPs, in particular, in human CSF samples. iti preferred aspects, a protein eluted from a column according to the system described in Example 1 is analyzed using both MS and MS-MS analysis. For example, a small portion of intact proteins eluting from RP2 may be diverted to online detection using LC-ESI MS. The proteins are aliquoted on a number of plates allowing digestion or not with trypsin, preparation for MALDI-MS as well as for ESI-MS, as well as preparation of the MALDI plates with different matrices. The methods thus allow, in addition to information on intact mass, to conduct an analysis by both peptide mass fingerprinting and MS-MS techniques. The methods described herein of separating and fractionating proteins provide individual proteins or fractions containing small numbers of distinct proteins. These proteins can be identified by mass spectral determination of the molecular masses of the protein and peptides resulting from the fragmentation thereof. Making use of available information in protein sequence databases, a comparison can be made between proteolytic peptide mass patterns generated in silico, and experimentally observed peptide masses. A "hit-list" can be compiled, ranking candidate proteins in the database, based on (among other criteria) the number of matches between the theoretical and experimental proteolytic fragments. Several Web sites are accessible that provide software for protein identification on-line, based on peptide mapping and sequence database search strategies (e.g., http://www.expasy.ch). Methods of peptide mapping and sequencing using MS are described in WO 95/252819, U.S. Pat. No. 5,538,897, U.S. Pat. No. 5,869,240, U.S. Pat. No. 5,572,259, and U.S. Pat. No. 5,696,376. See, also, Yates, J. Mass Spec, 33:1 (1998).

Data collected from a mass spectrometer typically comprises the intensity and mass to charge ratio for each detected event. Spectral data can be recorded in any suitable form, including, e.g., in graphical, numerical, or electronic formats, either in digital or analog form. Spectra are preferably recorded in a storage medium, including, e.g., magnetic, such as floppy disk, tape, or hard disk; optical, such as CD-ROM or laser-disc; or, ROM-CHIPS. The mass spectrum of a given sample typically provides information on protein intensity, mass to charge ratio, and molecular weight. In preferred embodiments of the invention, the molecular weights of proteins in the sample are used as a matching criterion to query a database. The molecular weights are calculated conventionally, e.g., by subtracting the mass of the ionizing proton for singly-charged protonated molecular ions, by multiplying the measured mass/charge ratio by the number of charges for multiply-charged ions and subtracting the number of ionizing protons.

Various databases are useful in accordance with the present invention. Useful databases include, databases containing genomic sequences, expressed gene sequences, and/or expressed protein sequences. Preferred databases contain nucleotide sequence-derived molecular masses of proteins present in a known organism, organ, tissue, or cell-type. There are a number of algorithms to identify open reading frames (ORF) and convert nucleotide sequences into protein sequence and molecular weight information. Several publicly accessible databases are available, including, the SwissPROT/TrEMBL database (http://www.expasy.ch).

Typically, a mass spectrometer is equipped with commercial software that identifies peaks above a certain threshold level, calculates mass, charge, and intensity of detected ions. Correlating molecular weight with a given output peak can be accomplished directly from the spectral data, i.e., where the charge on an ion is one and the molecular weight is therefore equal to the numerator value minus the mass of the ionizing proton. However, protein ions can be complexed with various counter-ions and adducts, such as N, C, and K. In such a case, it would be expected that a given protein ion would exhibit multiple peaks, such as a triplet, representing different ionic states (or species) of the same protein. Thus, it may be necessary to analyze and process spectral data to determine families of peaks arising from the same protein. This analysis can be carried out conventionally, e.g., as described by Mann et al., anal. Chem., 61:1702-1708 (1989). In matching a molecular mass calculated from a mass spectrometer to a molecular mass predicted from a database, such as a genomic or expressed gene database, post- translation processing may have to be considered. There are various processing events which modify protein structure, including, proteolytic processing, removal of N-terminal methionine, acetylation, methylation, glycosylation, phosphorylation, etc.

A database can be queried for a range of proteins matching the molecular mass of the unknown. The range window can be determined by the accuracy of the instrument, the method by which the sample was prepared, etc. Based on the number of hits (where a hit is match) in the spectrum, the unknown protein or peptide is identified or classified. Methods of identifying one or more CSFP by mass spectrometry are useful for diagnosis and prognosis. Preferably, such methods are used to detect one or more CSFP present in human CSF. Exemplary techniques are described in U.S. Patent Applications 02/0060290, 02/0137106, 02/0138208, 02/0142343, 02/0155509.

Diagnostic and Prognostic Uses

The nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more of the following methods: diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenetics as further described herein.

The invention provides diagnostic and prognostic assays for detecting CSFP nucleic acids and proteins, as further described. Also provided are diagnostic and prognostic assays for detecting interactions between CSFPs and CSFP target molecules, particularly natural agonists and antagonists.

The present invention provides methods for identifying polypeptides that are differentially expressed between two or more samples. "Differential expression" refers to differences in the quantity or quality of a polypeptide between samples. Such differences could result at any stage of protein expression from transcription through post-translational modification. For example, using protein array methods, two samples are bound to affinity spots on different sets of adsorbents (e.g., chips) and recognition maps are compared to identify polypeptides that are differentially retained by the two sets of adsorbents. Differential retention includes quantitative retention as well as qualitative differences in the polypeptide. For example, differences in post-translational modification of a protein can result in differences in recognition maps detectable as differences in binding characteristics (e.g., glycosylated proteins bind differently to lectin adsorbents) or differences in mass (e.g., post-translational cleavage products). In certain embodiments, an adsorbent can have an array of affinity spots selected for a combination of markers diagnostic for a disease or syndrome.

Differences in polypeptide levels between samples (e.g., differentially expressed CSFPs in CSF samples) can be identified by exposing the samples to a variety of conditions for analysis by desorption spectrometry (e.g., mass spectrometry). Proteins can be identified by detecting physicochemical characteristics (e.g., molecular mass), and this information can be used to search databases for proteins having similar profiles.

Preferred methods of detecting a CSFP utilize mass spectrometry techniques. Such methods provide information about the size and character of the particular CSFP isoform that is present in a sample, e.g., a biological sample submitted for diagnosis or prognosis. Mass spectrometry techniques are detailed in the section titled "Detection of CSFPs by mass spectrometry". Example 1 outlines a preferred detection scheme, wherein a biological sample is separated by chromatography before characterization by mass spectrometry. The invention provides a method of detecting a CSFP in a biological sample comprising the steps of: fractionating a biological sample (e.g., plasma, serum, lymph, cerebrospinal fluid, cell lysate of a particular tissue) by at least one chromatographic step; subjecting a fraction to mass spectrometry; and comparing the characteristics of polypeptide species observed in mass spectrometry with known characteristics of CSFP polypeptides.

An especially preferred method includes detection of at least one CSFP using retentate chromotography methods, including, for example, protein arrays or chips. Such methods are described in the section titled "Detection Using Protein Arrays." Preferably, said more than one CSFP is detected in a biological sample, preferably CSF. A favored embodiment provides a protein chip capable of detecting a CSFP on an addressable array representing proteins present in human CSF. Accordingly one embodiment of the present invention involves a method of use (e.g., a diagnostic or prognostic assay) wherein a molecule of the present invention (e.g., a CSFP, CSFP nucleic acid, or antibody) is used to diagnose or prognose a CSFP-related disorder or one in which any of the aforementioned CSFP activities is indicated. In another embodiment, the present invention involves a method of use wherein a molecule of the present invention is used, for example, for the diagnosis or prognosis of subjects, preferably a human subject, in which any of the aforementioned activities is pathologically perturbed.

For example, the invention encompasses a method of determining whether a CSFP is expressed within a biological sample comprising: a) contacting said biological sample with: i) a polynucleotide mat hybridizes under stringent conditions to a CSFP nucleic acid; or ii) a detectable polypeptide (e.g. antibody) that selectively binds to a CSFP; and b) detecting the presence or absence of hybridization between said polynucleotide and an RNA species within said sample, or the presence or absence of binding of said detectable polypeptide to a polypeptide within said sample. Detection of said hybridization or of said binding indicates that said CSFP is expressed within said sample. Preferably, the polynucleotide is a primer, and wherein said hybridization is detected by detecting the presence of an amplification product comprising said primer sequence, or the detectable polypeptide is an antibody.

Ih certain embodiments, detection involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Pat. Nos.4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegren et al. (1988) Science 241:1077-1080; andNakazawa et al. (1994) PNAS 91:360-364), the latter of which can be particularly useful for detecting point mutations in the CSFP-encoding-gene (see Abravaya et al. (1995) Nucleic Acids Res. 23:675-682).

Also envisioned is a method of determining whether a mammal, preferably human, has an elevated or reduced level of expression of a CSFP, comprising: a) providing a biological sample from said mammal; and b) comparing the amount of a CSFP or of a CSFP RNA species encoding a CSFP within said biological sample with a level detected in a control sample. An increased amount of said CSFP or said CSFP RNA species within said biological sample compared to said level detected in or expected from said control sample indicates that said mammal has an elevated level of CSFP expression, and a decreased amount of said CSFP or said CSFP RNA species within said biological sample compared to said level detected in or expected from said control sample indicates that said mammal has a reduced level of expression of a CSFP.

The present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, and monitoring clinical trials are used for prognostic purposes. Accordingly, one aspect of the present invention relates to diagnostic assays for determining CSFP and/or nucleic acid expression as well as CSFP activity, in the context of a biological sample (e.g., CSF, blood, plasma, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant CSFP expression or activity. The invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with a CSFP, nucleic acid expression or activity. For example, mutations in a CSFP-encoding gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive purpose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with CSFP 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, the detection methods of the invention can be used to detect a CSFP mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo. Prefered biological samples are biological fluids such as cell lysate, lymph, blood plasma, blood, and especially cerebrospinal fluid. For example, in vitro techniques for detection of a CSFP mRNA include Northern hybridizations and in situ hybridizations, hi vitro techniques for detection of a CSFP include mass spectrometry, Enzyme Linked Immuno Sorbent Assays

(ELISAs), Western blots, immunoprecipitations and immunofluorescence. In vitro techniques for detection of a CSFP-encoding genomic DNA include Southern hybridizations. Furthermore, in vivo techniques for detection of a CSFP include introducing into an individual a labeled anti- CSFP antibody.

Drug Screening Assays

The invention provides a method (also referred^" to herein as a "screening assay") for identifying candidate modulators (e.g., small molecules, peptides, antibodies, peptidomimetics or other drugs) which bind to CSFPs, have a modulatory effect on, for example, CSFP expression or preferably CSFP biological activity, m some embodiments small molecules can be generated using combinatorial chemistry or can be obtained from a natural products library. Assays may be cell based or non-cell based assays. Drug screening assays may be binding assays or more preferentially functional assays, as further described.

Agents that are found, using screening assays as further described herein, to modulate CSFP activity by at least 5%, more preferably by at least 10%, still more preferably by at least 30%, still more preferably by at least 50%, still more preferably by at least 70%, even more preferably by at least 90 %, may be selected for further testing as a prophylactic and/or therapeutic agent.

In another aspect, agents that are found, using screening assays as further described herein, to modulate CSFP expression by at least 5%, more preferably by at least 10%, still more preferably by at least 30%, still more preferably by at least 50%, still more preferably by at least 70%, even more preferably by at least 90 %, may be selected for further testing as a prophylactic and/or therapeutic agent. Protein array methods are useful for screening and drug discovery. For example, one member of a receptor/ ligand pair is docked to an adsorbent, and its ability to bind the binding partner is determined in the presence of the test substance. Because of the rapidity with which adsorption can be tested, combinatorial libraries of test substances can be easily screened for their ability to modulate the interaction. In preferred screening methods, CSFPs are docked to the adsorbent. Binding partners are preferably labeled, thus enabling detection of the interaction. Alternatively, in certain embodiments, a test substance is docked to the adsorbent. The polypeptides of the invention are exposed to the test substance and screened for binding. In other embodiments, an assay is a cell-based assay in which a cell which expresses a CSFP or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate CSFP activity determined. Determining the ability of the test compound to modulate CSFP activity can be accomplished by monitoring the bioactivity of the CSFP or biologically active portion thereof. The cell, for example, can be of mammalian origin, insect origin, bacterial origin or a yeast cell.

In one embodiment, the invention provides assays for screening candidate or test compounds which are target molecules of a CSFP or biologically active portion thereof. In another embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of a CSFP or biologically active portion thereof. The test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection. The biological library approach is used with peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K. S. (1997) Anticancer Drug Des. 12:145, the disclosure of which is incorporated herein by reference in its entirety).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 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. (1994) Angew. Chem. Int. Ed. Engl. 33:2059 and 2061; and in Gallop et al. (1994) J. Med. Chem. 37:1233, the disclosures of which are incorporated herein by reference in their entireties. Libraries of compounds may be presented in solution (e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (Ladner U.S. Pat. No. 5,223,409), spores (Ladner U.S. Pat. No. '409), plasmids (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. MoI. Biol. 222:301-310); (Ladner supra).

Determining the ability of the test compound to modulate CSFP activity can also be accomplished, for example, by coupling the CSFP or biologically active portion thereof with a label group such that binding of the CSFP or biologically active portion thereof to its cognate target molecule can be determined by detecting the labeled CSFP or biologically active portion thereof in a complex. For example, the extent of complex formation may be measured by immunoprecipitating the complex or by performing gel electrophoresis.

It is also within the scope of this invention to determine the ability of a compound to interact with its cognate target molecule without the labeling of any of the interactants. For example, a microphysiometer can be used to detect the interaction of a compound with its cognate target molecule without the labeling of either the compound or the target molecule. McConnell, H. M. et al. (1992) Science 257:1906-1912, the disclosure of which is incorporated by reference in its entirety. A microphysiometer such as a cytosensor is an analytical instrument that measures the rate at which a cell acidifies its environment using a Light-Addressable Potentiometric Sensor (LAPS). Changes in this acidification rate can be used as an indicator of the interaction between compound and receptor.

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

In another preferred embodiment, the assay comprises contacting a cell which is responsive to a CSFP or biologically active portion thereof with a CSFP or biologically active portion thereof, to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to modulate the activity of the CSFP or biologically active portion thereof. Determining the ability of the test compound to modulate the activity of the CSFP or biologically active portion thereof comprises determining the ability of the test compound to modulate a biological activity of the CSFP- responsive cell. In another embodiment, an assay is a cell-based assay comprising contacting a cell expressing a CSFP target molecule (i.e. a molecule with which CSFPs interact) with a test compound and determining the ability of the test compound to modulate the activity of the CSFP target molecule. Determining the ability of the test compound to modulate the activity of a CSFP target molecule can be accomplished, for example, by assessing the activity of a target molecule, or by assessing the ability of the CSFP to bind to or interact with the CSFP target molecule.

Determining the ability of the CSFP to bind to or interact with a CSFP target molecule, for example, can be accomplished by one of the methods described above for directly or indirectly determining binding. In a preferred embodiment, Ihe assay includes contacting the CSFP or biologically active portion thereof with a known compound which binds said CSFP (e.g., a CSFP antibody or target molecule) to form an assay mixture, contacting the CSFP with a test compound before or after said known compound, and determining the ability of the test compound to interact with the CSFP. Determining the ability of the test compound to interact with a CSFP comprises determining the ability of the test compound to preferentially bind to the CSFP or biologically active portion thereof as compared to the known compound. Determining the ability of the CSFP to bind to a CSFP target molecule can also be accomplished using a technology 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, the disclosures of which are incorporated herein by reference in their entireties. As used herein, "BIA" is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.

In another embodiment, the assay is a cell-free assay in which a CSFP or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate the activity of the CSFP or biologically active portion thereof is determined. In a preferred embodiment, determining the ability of the CSFP to modulate or interact with a CSFP target molecule can be accomplished by determining the activity of the target molecule. For example, the activity of the target molecule can be determined by contacting the target molecule with the CSFP or a fragment thereof and measuring induction of a cellular second messenger of the target (e.g., cAMP, STAT3, Akt, intracellular Ca2+, diacylglycerol, IP3, etc.), detecting catalytic/enzymatic activity of the target for an appropriate substrate, detecting the induction of a reporter gene (comprising a target- responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase), or detecting a target-regulated cellular response, for example, signal transduction or protein:protein interactions.

The cell-free assays of the present invention are amenable to use of both soluble and/or membrane-bound forms of isolated proteins (e.g. CSFPs or biologically active portions thereof or molecules to which CSFPs targets bind). In the case of cell-free assays in which a membrane-bound form an isolated protein is used it may be desirable to utilize a solubilizing agent such that the membrane-bound form of the isolated protein is maintained in solution. Examples of such solubilizing agents include non-ionic detergents such as n- octylglucoside, n-dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton TM X-100, Triton TM X-114, Thesit TM,

Isotridecypoly(ethylene glycol etheτ)n,3-[(3-cholamidopropyl)dimethylamminio]- 1-propane sulfonate (CHAPS), 3-[(3-cholamidopropyl)dimethylamminio]-2-hydroxy-l-propane sulfonate (CHAPSO), or N-dodecyl=N,N-dimethyl-3-ammonio- 1-propane sulfonate.

In more than one embodiment of the above assay methods of the present invention, it may be desirable to immobilize either a CSFP or its target molecule to facilitate separation of complexed from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of a test compound to a CSFP, or interaction of a CSFP with a target molecule in the presence and absence of a candidate compound, can be accomplished in any vessel suitable for containing the reactants and by any immobilization protocol described herein. Alternatively, the complexes can be dissociated from the matrix, and the level of CSFP binding or activity determined using standard techniques.

Other techniques for immobilizing proteins on matrices can also be used in the screening assays of the invention. For example, either a CSFP or a CSFP target molecule can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylated CSFP or target molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, Hl.), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with CSFP or target molecules but which do not interfere with binding of the CSFP to its target molecule can be derivatized to the wells of the plate, and unbound target or CSFP trapped in the wells by antibody conjugation. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the CSFP or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the CSFP or target molecule.

In another embodiment, modulators of CSFP expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of CSFP mRNA or protein in the cell is determined. The level of expression of CSFP mRNA or protein in the presence of the candidate compound is compared to the level of expression of CSFP mRNA or protein in the absence of the candidate compound. The candidate compound can then be identified as a modulator of CSFP expression based on this comparison. For example, when expression of CSFP mRNA or protein is greater (statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of CSFP mRNA or protein expression. Alternatively, when expression of CSFP mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of CSFP mRNA or protein expression. The level of CSFP mRNA or protein expression in the cells can be determined by methods described herein for detecting CSFP mRNA or protein. In yet another aspect of the invention, the CSFP can be used as "bait proteins" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. 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 WO94/10300, the disclosures of which are incorporated herein by reference in their entireties), to identify other proteins, which bind to or interact with CSFPs ("CSFP-binding proteins" or "CSFP-bp") and are involved in CSFP activity. Such CSFP-binding proteins are also likely to be involved in the propagation of signals by the CSFP or CSFP targets as, for example, downstream elements of a CSFP-mediated signaling pathway.

The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. Ih one construct, the gene that codes for a CSFP or a fragment thereof is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). 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 that codes for the activation domain of the known transcription factor. If the "bait" and the "prey" proteins are able to interact, in vivo, forming a CSFP -dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with the CSFP.

This invention further pertains to novel agents identified by the above-described screening assays and to processes for producing such agents by use of these assays. Accordingly, in one embodiment, the present invention includes a compound or agent obtainable by a method comprising the steps of any one of the aforementioned screening assays (e.g., 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, an agent identified as described herein (e.g., a CSFP modulating agent, or a CSFP -binding partner) can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent. Alternatively, an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent. Furthermore, flu^'s invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein.

The present invention also pertains to uses of novel agents identified by the above- described screening assays for diagnoses, prognoses, prevention, and treatments as described herein. Accordingly, it is within the scope of the present invention to use 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. For example, in one embodiment, the present invention includes a method of synthesizing or producing a drug or pharmaceutical composition by reference to the structure and/or properties of a compound obtainable by one of the above-described screening assays. For example, a drug or pharmaceutical composition can be synthesized based on the structure and/or properties of a compound obtained by a method in which a cell which expresses a CSFP target molecule is contacted with a test compound and the ability of the test compound to bind to, or modulate the activity of, the CSFP target molecule is determined. In another exemplary embodiment, the present invention includes a method of synthesizing or producing a drug or pharmaceutical composition based on the structure and/or properties of a compound obtainable by a method in which a CSFP or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to, or modulate, the activity of the CSFP or biologically active portion thereof is determined.

Pharmaceutical Compositions

When polypeptides of the present invention are expressed in soluble form, for example as a secreted product of transformed yeast or mammalian cells, they can be purified according to standard procedures of the art, including steps of ammonium sulfate precipitation, ion exchange chromatography, gel filtration, electrophoresis, affinity chromatography, according to, e.g., "Enzyme Purification and Related Techniques," Methods in Enzymology, 22:233-577 (1977), and Scopes, R., Protein Purification: Principles and Practice (Springer-Verlag, New York, 1982) provide guidance in such purifications. Likewise, when polypeptides of the invention are expressed in insoluble form, for example as aggregates or inclusion bodies, they can be purified by appropriate techniques, including separating the inclusion bodies from disrupted host cells by centrifugation, solύbilizing the inclusion bodies with chaotropic and reducing agents, diluting the solubilized mixture, and lowering the concentration of chaotropic agent and reducing agent so that the polypeptide takes on a biologically active conformation. The latter procedures are disclosed in the following references, which are incorporated by reference: Winkler et al, Biochemistry, 25: 4041-4045 (1986); Winkler et al, Biotechnology, 3: 992-998 (1985); Koths et al, U.S. patent 4,569,790; and European patent applications 86306917.5 and 86306353.3.

Compounds capable of detecting or modulating a CSFP or a CSFP biological activity, including small molecules, peptides, CSFP nucleic acid molecules, and anti- CSFP antibodies of the invention, can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically comprise a pharmaceutically acceptable carrier. As used herein the language "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions. A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. 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. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL® (BASF, Parsippany, NJ.) 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 lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.

Where the active compound is a protein, e.g., an anti-CSFP antibody, sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and other required ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an edible carrier. They 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, e.g., 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 permeated 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, active compound is delivered to a 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 microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Lie. 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 U.S. Pat. No.4,522,811, the disclosure of which is incorporated herein by reference in its entirety. In a further embodiment, the active compound may be coated on a microchip drug delivery device. Such devices are useful for controlled delivery of proteinaceous compositions into the bloodstream, cerebrospinal fluid, lymph, or tissue of an individual without subjecting such compositions to digestion or subjecting the individual to injection. Methods of using microchip drug delivery devices are described in US Patents 6123861, 5797898 and US Patent application 20020119176A1, disclosures of which are hereby incorporated in their entireties.

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 suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.

Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage 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 may 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. A dose may be formulated in animal models to achieve a given circulating concentration, subsequently used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration. Disclosures of the references cited throughout the specification are incorporated by reference in their entireties. Having generally described this invention, a further understanding can be obtained by reference to certain specific examples provided herein for purposes of illustration only, and are not intended to be limiting unless otherwise specified.

EXAMPLES

Example 1: Characterization of CSFP in human Cerebrospinal Fluid The CSFPs of the invention were identified for the first time in the CSF from human patients, in one or more of four studies. These four studies were analyzing samples from:

• Proteome #6: Normal Pressure Hydrocephalus patients.

• Proteome #18:

• Proteome #19: • Proteome #20:

Tables 1 and 2, in the Detailed Description of the Invention, set out for each CSFP of the invention, the Proteomes from the list above where the CSFP has been observed.

The samples analyzed in Proteome #6 were obtained from 3 patients with Normal Pressure Hydrocephalus. 4 ml of CSF per patient were pooled together, such that the total 12 mis were analyzed according to the process described in details below.

The samples analyzed in Proteome #18 were obtained from 11 Alzheimer's patients and matched controls. CSF samples from patients were pooled together, and 10 mis of the pool were analyzed according to the process described in details below. Similarly, CSF samples from matched controls were pooled together, and 10 mis of the pool were analyzed according to the process described in details below.

The samples analyzed in Proteome #19 were obtained from patients with Fronto-Temporal dementia, from patients with Lewy's bodies dementia, from patients with Vascular dementia, and from matched controls. For each group, a pooled volume of 10 mis of CSF was analyzed according to the process described in details below. For Fronto-Temporal dementia, 3 patients were used. For Lewy's bodies dementia, 2 patients were used. For Vascular dementia, 2 patients were used. Finally, 4 matched controls were used. The samples analyzed in Proteome #20 were obtained from 11 Alzheimer's patients and matched controls. CSF samples from patients were pooled together, and 59 mis of the pool were analyzed process described in details below. Similarly, CSF samples from matched controls were pooled together, and 59 mis of the pool were analyzed process described in details below.

Step 1 : Transthyretin, transferrin, IgG and human albumin depletion To remove the CSF-abundant protein transferrin, an immunodepletion technique has been used, which is based on addition of anti-transferrin IgG, followed by incubation and retention of the transferrin-IgG complex on the protein G column used to deplete CSF IgG. Similarly, transthyretin which represents about 10% of total protein content in CSF, and which is the major component of low molecular weight protein fraction, was depleted by the immunodepletion technique.

Anti-transferrin and anti-transthyretin IgG were purified from commercial goat serum (Strategic Biosolution, USA) by affinity chromatography on Protein G Sepharose (Amersham, Uppsala, Sweden) accordingly to the chromatography gel manufacturer instructions.

4 mg of anti-Transthyretin IgG and 2 mg of anti-transferrin IgG were added to 12 ml of CSF.

After 2 hours incubation at +4°C, the CSF solution was applied to a Protein G Sepharose column (0.5 cm X 17 cm) coupled to an HSA ligand Sepharose column (Amersham, Uppsala,

Sweden) (0.5 cm X 13 cm).

After CSF injection, the two in-line columns are washed with Phosphate buffer 20 mM, NaCl

50 mM, pH 7.1, with a 1.5 ml/min flow rate, using an Akta Explorer chromatography system

(Amersham, Uppsala, Sweden) equipped with 10 ml/min pumps. The non-retained protein fraction is used for the subsequent chromatography steps and frozen at -20⁰C until use. The depletion columns are regenerated with Citrate buffer 20 mM, pH 2.5.

Step 2: Concentration of depleted CSF by reverse phase capture

The non-retained, depleted, fraction is defrost, adjusted to 0.2% TFA concentration with a . 10% TFA solution in water, and injected on a PLRPS 300A HPLC column (Polymer

Laboratories, UK) (0.46 cm X 5 cm) at 1 ml/min. The column was washed with 0.2% TFA in 5% CH3CN. Proteins are eluted with a one-column volume gradient from 0% to 100% of 0.2% TFA in 80% CH3CN. The eluted fraction is used for the subsequent chromatography steps and frozen at -2O⁰C until use.

Step 3: In line Gel Filtration and cation exchange chromatography The reverse phase capture eluate is defrost, concentrated to 0.5 ml by vacuum concentration in a Speed Vac concentrator and injected on a Biosec SEC3000 HPLC column (0.7 cm X 60 cm) coupled with a Source 15S column (0.3 cm X 5 cm) at 0.6 ml/min. The two in-line columns were equilibrated with 0.2% TFA in 30% CH3CN. The two in-line columns are disconnected during injection and elution of high molecular weight proteins. When an elution volume corresponding to an apparent molecular weight cut off of 25kDa is reached, the two columns are connected and washed with equilibration solution. Proteins adsorbed on the source 15S column are eluted with a biphasic linear gradient from 0% to 30% of Gly/HCl buffer 20 mMin, 8M urea, IM NaCl, pH2.7 (buffer B), in 2 ml followed by a 30% to 100% buffer B in 2 ml. Elution flow rate was 0.2 ml/min. 15 fractions were collected, based on time. For Proteomes ID 18, 19 & 20, only the 6 fractions containing proteins (positive UV adsorption signal for 280 run wavelength) were used for the following step.

Step 4 (For Proteomes ID 6, 18 &19): Reduction/Alkylation and Reverse Phase HPLC Fractionation

After adjusting the pH to 8.5 with concentrated tris-HCl, each one of the 15 cation exchange fractions (or each one of the 6 cation exchange fractions for Proteomes ID 18, 19 & 20) was reduced with dithioerythritol (DTE, 30 mM, 2 hours at 37°C) and alkylated with iodoacetamid (120 mM, 30 min at 37⁰C in the dark, under agitation). The latter reaction was stopped with the addition of DTE (30 mM) followed by acidification (TFA, 0.1%). The fractions were then injected on a Vydac C4, 3 μm, 300 angstroms column (Vydac, CA, USA), 4.6 mm ID, and 100 mm length. C4 column was equilibrated and washed with 0.05 % TFA in water (solution A). Proteins and peptides were eluted with a biphasic gradient from 100% A until 100% B (0.1% TFA, 80% CH3CN in water) in 15 min. Flow rate was 0.8 ml/min. 15 fractions of 0.6 ml were collected.

Step 4a (For Proteome ID 20): Reduction/Alkylation and First Dimension Reverse Phase HPLC Fractionation

After adjusting the pH to 8.5 with concentrated tris-HCl, each one of the 6 cation exchange fractions was reduced with dithioerythritol (DTE, 30 mM, 2 hours at 37°C) and alkylated with iodoacetamid (120 mM, 30 min at 37°C in the dark, under agitation). The latter reaction was stopped with the addition of DTE (30 mM) followed by acidification (TFA, 0.1%). The fractions were then injected on a Uptispher C8, 3 urn, 300 angstroms column (Interchim, Montlucon, France), 4.6 mm ID, and 100 mm length. C8 column was equilibrated and washed with 0.1 % TFA in water (solution A). Proteins and peptides were eluted with a biphasic gradient from 100% A until 100% B (0.1% TFA, 80% CH3CN in water) in 15 min. Flow rate was 0.8 ml/min. 10 fractions of 1.2 ml were collected. The fractions were dried under reduced pressure after addition of 120 μl of glycerol 10% in water (w/w).

Step 4b (For Proteome ID 20): Second Dimension Reverse Phase HPLC Fractionation Dried fractions of the Step 4a were injected on a Vydac C4, 3 μm, 300 angstroms column (Vydac, CA, USA)₃ 4.6 mm ID, and 100 mm length. C4 column was equilibrated and washed with 0.05 % TFA in water (solution A). Proteins and peptides were eluted with a biphasic gradient from 100% A until 100% B (0.1% TFA, 80% CH3CN in water) in 15 min. Flow rate was 0.8 ml/min. 15 fractions of 0.6 ml were collected.

Step 5: Mass detection

225 fractions (for Proteome ID 6), or 90 fractions (for Proteomes ID 18&19), or 900 fractions (for Proteome ID 20) were collected following reverse phase HPLC fractionation into 96-well deep well plates (DWP). For Proteome ID 6, a small proportion (2.5 %) of the volume is diverted to online analysis using LC-ESI-MS (Bruker Esquire).

For all Proteomes, 96-well plates (DWP) are recovered and subjected to concentration step. Volumes are concentrated from 0.8 ml to about 50 microl per well by drying with a SpeedVac and proteins are then digested by re-buffering, adding trypsin to the wells, sealing and incubating the plates at 37 C for 12 hours. The concentration of trypsin to be added to the wells was adjusted based on the OD at 210 nm recorded for each particular fraction. This ensures an optimal use of trypsin and a complete digestion of the most concentrated fractions. Contents from each well of the 96 well plates are analyzed by LC- ESI-MS-MS on Bruker Esquire ESI Ion-Trap MS devices.

Step 6: Protein identification

The mass spectra collected in step 5 above (a total in excess of 88,700 spectra for Proteome #6, in excess of 55,493 spectra for Proteome #18, in excess of 105,869 spectra for Proteome #19, and in excess of 209,303 spectra for Proteome #20) were processed as described in the International Patent Application published as WO 04/013635, on the following databanks: human subsection of SwissProt, TrEMBL, TrEMBLNew, GeneSeqP, and predicted peptides from the human genome. For Proteome #6, this resulted in the identification of 678 database hits, corresponding to 566 non redundant protein sequences. For Proteome #18, this resulted in the identification of 6138 database hits, corresponding to 3637 non redundant protein sequences.

For Proteome #19, this resulted in the identification of 7805 database hits, corresponding to 4150 non redundant protein sequences. For Proteome #20, this resulted in the identification of 7449 database hits, corresponding to 4237 non redundant protein sequences.

Example 2: Manual analysis of mass spectrometry data to accurately identify the polypeptide sequences circulating in CSF The process described in Example 1 above allowed the inventors to generate a list of tryptic sequences for each proteome, in each CEX and RP fraction. This list is summarized in Table 2.

By careful review of this list, and in particular of the elution conditions for each tryptic peptide, together with sequence information available in databases, the inventors have been able to precisely determine, for each CSFP, the polypeptide sequence of the circulating species. This is indicated in the fourth column of Table 1, as the start and finish amino acids defining the polypeptide of the invention with respect to the publicly available sequence (with an accession number given in column 2). More precisely, the Protein Type, as indicated in column 3 of Table 1, teaches whether each polypeptide of the invention was previously disclosed as an entity (for these CSFPs, the Protein Type is "Parent"), and in this case the present invention now discloses that the polypeptide is circulating in human CSF, specific to CSF, and detectable by proteomic means, or whether the polypeptide of the invention was not previously disclosed as an entity (for these CSFPs, the Protein Type is "Fragment"), and in this case the present invention now discloses the new polypeptide sequence in addition to its circulation in human CSF, specificity to CSF, and detectability by proteomic means.

Example 3: Comparative analysis of the proteins identifed in human CSF with proteins identified in human plasma and serum

The present inventors have analyzed further the proteins identified in the studies of human CSF described above in Examples 1 and 2 by comparison with results obtained with human biofiuids derived from blood. In particular, the inventors have used a total of 7 proteomic studies performed on human blood-derived samples of plasma and serum. Among these 7 blood-derived proteomic studies, a total of 1920 non-redundant proteins were identified. The present inventors have thus performed a comparison of the CSF and blood proteins to identify CSF-specific proteins. Bioinformatic alignments using the BLAST algorithm (Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. USA 87:2264-68; Karlin and Altschul, 1993, Proc. Natl. Acad. Sci. USA 90:5873-77) were performed between the sequences of the CSF proteins identified by the process of Example 1 and the 1920 sequences identified in blood-derived samples. In this analysis, two sequences were considered identical if an alignment of at least 15 amino-acids, and at least 90% identity percentage was found. Only the proteins unique to the CSF were retained and are listed in Tables 1 and 2.

Example 4: Comparative analysis between the CSF-specific proteins identifed with the method of Example 3 and CSF proteins previously observed by Proteomics The present inventors performed a comparison between the CSF-specific proteins identified in Example 3 above and listed in Tables 1 and 2 and CSF proteins published in a representative selection of the scientific litterature (Sickmann, A. et al., J.Chromatogr. B Analyt. Technol. Biomed. Life Sci 2002 May 5: 771(1-2): 167-196; Yuan, X. et al.,

Electrophoresis 2002 April: 23 (7-8): 1185-1196; Jiang, L. et al., Amino Acids 2003 July: 25(1): 49-57; Wenner, B.R. et al., J. Proteome. Res. 2004 January: 3(1): 97-103; Maccarrone, G. et al., Electrophoresis 2004 July: 25(14): 2402-2412). A databank in a BLAST-compatible format containing the sequences already identified in CSF by proteomics techniques, as reported in the scientific litterature, was constructed. Sequence homology searches were performed with the list of proteins from Tables 1 and 2, using the following criteria: two sequences were considered identical if an alignment of at least 15 amino-acids, and at least 90% identity percentage was found. As a result, the following CSFPs were found to have been identified, with the same sequence as that listed in the fourth column of Table 1, in one or more scientific publication: CSFP 40 , CSFP 127, CSFP 130, CSFP 131, CSFP 133, CSFP 134, CSFP 136, CSFP 138, CSFP 140, CSFP 144, CSFP 149, CSFP 150, CSFP 156, and CSFP 160.

Example 5: Chemical Synthesis of CSFPs In this example, a CSFP of the invention is synthesized. Peptide fragment intermediates are first synthesized and then assembled into the desired polypeptide.

A CSFP can initially be prepared in, e.g. 5 fragments, selected to have a Cys residue at the N-terminus of the fragment to be coupled. Fragment 1 is initially coupled to fragment 2 to give a first product, then after preparative HPLC purification, the first product is 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 give the desired polypeptide, which is purified and refolded. Thioester formation

Fragments 2, 3, 4, and 5 are synthesized on a thioester generating resin, as described above. For this purpose the following resin is prepared: S-acetylthioglycolic acid pentafluorophenylester is coupled to a Leu-PAM resin under conditions essentially as described by Hackeng et al (1999). In the first case, the resulting resin is used as a starting resin for peptide chain elongation on a 0.2 mmol scale after removal of the acetyl protecting group with a 30 min treatment with 10% mercaptoethanol, 10% piperidine in DMF. The N" of the N-terminal Cys residues of fragments 2 through 5 are protected by coupling a Boc- thioproline (Boc-SPr, i.e. Boc-L-thioproline) to the terminus of the respective chains instead of a Cys having conventional N" or S^ protection, e.g. Brik et al, J. Org. Chem., 65: 3829- 3835 (2000).

Peptide synthesis

Solid-phase synthesis is performed on a custom-modified 433 A peptide synthesizer from Applied Biosystems, using in situ neutralization/2-(lH-benzotriazol-l-yl)-l, 1,1,3,3- tetramethyluronium hexafluoro-phosphate (HBTU) activation protocols for stepwise Boc chemistry chain elongation, as described by Schnolzer et al, hit. J. Peptide Protein Res., 40: 180-193 (1992). Each synthetic cycle consists of ISP'-Boc -removal by a 1 to 2 min treatment with neat TFA, a 1-min DMF flow wash, a 10-min coupling time with 2.0 mmol of preactivated Boc-amino acid in the presence of excess DIEA and a second DMF flow wash. Nα-Boc-amino acids (2 mmol) are preactivated for 3min with 1.8mmol HBTU (0.5M in DMF) in the presence of excess DIEA (6mmol). After coupling of GIn residues, a dichloromεthane flow wash is used before and after deprotection using TFA, 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 on Boc-Leu-O-CH₂-Pam resin (0.71mmol/g of loaded resin), while for Fragments 2 through 5 machine-assisted synthesis is started on the Boc-Xaa- S-CH₂-CO-Leu-Pam resin. This resin is obtained by the coupling of S-acetylthioglycolic acid pentafluorophenylester to a Leu-PAM resin under standard conditions. The resulting resin is used as a starting resin for peptide chain elongation on a 0.2 mmol scale after removal of the acetyl protecting group with a 30min treatment with 10% mercaptoethanol, 10% piperidine in DMF.

After chain assembly is completed, the peptide fragments are deprotected and cleaved from the resin by treatment with anhydrous hydrogen fluoride for lhr at 0⁰C with 5% p-cresol as a scavenger. In all cases except Fragment 1, the imidazole side chain 2,4- dinitrophenyl (DNP) protecting groups remain on His residues because the DNP-removal procedure is incompatible with C-terminal thioester groups. However DNP is gradually removed by thiols during the ligation reaction, yielding unprotected His. After cleavage, peptide fragments are precipitated with ice-cold diethylether, dissolved in aqueous acetonitrile and lyophilized. The peptide fragments are purified by RP-HPLC with a Cl 8 column from Waters by using linear gradients of buffer B (acetonitile/0.1% trifluoroacetic acid) in buffer A (H₂O/0.1% trifluoroacetic acid) and UV detection at 214nm. Samples are analyzed by electrospray mass spectrometry (ESMS) using an Esquire instrument (Brucker, Bremen , Germany), or like instrument. Native chemical ligations

As described more fully below, the ligation of unprotected fragments is performed as follows: the dry peptides are dissolved in equimolar amounts in 6M guanidine hydrochloride (GuHCl), 0.2M phosphate, pH 7.5 in order to get a final peptide concentration of 1-8 mM at a pH around 7, and 1% benzylmercaptan, 1% thiophenol is added. Usually, the reaction is carried out overnight and is monitored by HPLC and electrospray mass spectrometry. The ligation product is subsequently treated to remove protecting groups still present. Opening of the N-terminal thiazolidine ring further required the addition of solid methoxamine to a 0.5M final concentration at pH3.5 and a further incubation for 2h at 37°C. A 10-fold excess of Tris(2-carboxyethyl)phosphine is added before preparative HPLC purification. Fractions containing the polypeptide chain are identified by ESMS, pooled and lyophilized.

The ligation of fragments 4 and 5 is performed at pH7.0 in 6 M GuHCl. The concentration of each reactant is 8mM, and 1% benzylmercaptan and 1% thiophenol were added to create a reducing environment and to facilitate the ligation reaction. An almost quantitative ligation reaction is observed after overnight stirring at 37°C. At this point in the reaction, CH₃-O-NH₂.HCI is added to the solution to get a 0.5M final concentration, and the pH adjusted to 3.5 in order to open the N-terminal thiazolidine ring. After 2h incubation at 37°C, ESMS is used to confirm the completion of the reaction. The reaction mixture is subsequently treated with a 10-fold excess of Tris(2-carboxyethylphosphine) over the peptide fragment and after 15min, the ligation product is purified using the preparative HPLC (e.g., C4, 20-60% CH₃CN, 0.5% per min), lyophilised, and stored at -20°C. The same procedure is repeated for the remaining ligations with slight modifications.

Polypeptide Folding

The full length peptide is refolded by air oxidation by dissolving the reduced lyophilized protein (about 0.1 mg/mL) in IM GuHCl; 10OmM Tris, 1OmM methionine, pH 8.6 After gentle stirring overnight, the protein solution is purified by RP-HPLC as described above.

Example 6: Synthesis of CSFP 1, CSFP 83, CSFP 135 and CSFP 152

Synthesis of CSFP 1 and CSFP 152: The two peptides were prepared by SPPS on a 0.2mmol scale using machine assisted protocols on a custom-modified Applied Biosystems model 433A peptide synthesizer, using in situ neutralization/HCTU activation procedure for Boc chemistry as described (Schnolzer et al., Int. J. Peptide Protein Res., 40: 180-193, 1992). The two peptides were synthesized on the appropriate Boc-amino acyl -Pam preloaded resin. After chain assembly was completed, the peptides were deprotected and cleaved from the resin by treatment with anhydrous HF for Ih at O⁰C with 5% p-cresol as scavenger. The peptides were precipitated with diethyl ether, dissolved in aqueous acetonitrile, lyophilized and purified by preparative RP-HPLC on a Waters 600 HPLC module using a Vydac C8 5um 300A, 22x250mm column. Peptide identity was confirmed by ESI-MS with a Bruker Esquire 3000 Ion Trap (Bruker Daltonics, Bremen, DE).

Analytical RP-HPLC of all the products was performed on a Waters 2690 HPLC module with a 214nm UV detection, using a Symmetry 300 Cl 8 column, with a linear gradient of buffer B in buffer A over 30 min at lmL/min. Buffer A= 0.1%TFA in water; buffer B= 0.1% TFA in ACN. Data were recorded and analyzed using the software system Millennium 32.

In the case of CSFP 1, 50 mg pure material was obtained from the purification of 270mg crude peptide. The synthesized sequence was:

GLTLWPRLASNPFLLPWPPGITGMSHHSQLHCGFGLRFFDD (SEQ ID NO: 267) Number of residues: 41

Theoretical relative molecular mass, reduced form: 4620.38 Theoretical relative molecular mass, refolded form: 4620.38

Analytical data:

Experimental relative molecular mass, refolded form: 4620.25

Protein purity: 95.72 % (by RP-HPLC analysis, column Waters Symmetry 300A, Cl 8, 5μm, UV detection 214nm).

Material available as a TFA salt; estimated net protein content: 70-80%. Readily soluble in water at 5 mg/ml.

m the case of CSFP 152, 680 mg crude material was obtained after cleavage from the resin and purification of 1 OOmg yielded 18mg pure material.

The synthesized sequence was:

TYPPENl^GQSNYSFVDNLNLLKAITEKEKIEKERQSIRSSPLDNKLNVEDVDS

TKNRK (SEQ ID No: 268)

Number of residues: 59 Theoretical relative molecular mass, reduced form: 6820.65

Analytical data:

Experimental relative molecular mass, reduced form: 6819.78

Protein purity: 91.17 % (by RP-HPLC analysis, column Waters Symmetry 300A, C18, 5μm, UV detection 214nm).

Material available as a TFA salt; estimated net protein content: 70-80%. Readily soluble in water at 2 mg/ml.

Synthesis of CSFP 83: CSFP 83 was prepared by polymer-supported organic synthesis of three fragments equivalent to the whole sequence after cleavage between residues 36 and 37on the one hand and residues 90 and 91 on the other hand. These three fragments numbered 1 to 3 by starting from the C-ter were selected in such a way that fragments 1 and 2 have a Cys residue at the N- terminus. Fragments 2 and 3 were synthesized as thioesters to be able to assemble them through native chemical ligation (Dawson et al., 1994, Science, 266, 776-779). Fragment 1 is initially coupled to fragment 2 to give a first product, then after deprotection of N-terminal Cys and preparative HPLC purification, the first product is coupled to fragment 3 to give the desired polypeptide, which is purified and refolded.

• Fragment synthesis

Boc chemistry was used as described (Schnolzer et al., Int. J. Peptide Protein Res., 40: 180- 193, 1992). Solid-phase synthesis is performed on a custom-modified 433 A peptide synthesizer from Applied Biosystems, using in situ neutralization/0-(lH-6- Chlorobenzotriazol-l-yl)-l,l,l,3,3-tetramethyluronium hexafluoro-phosphate (HCTU) activation protocols for stepwise Boc chemistry chain elongation, as described by Schnolzer et al, Int. J. Peptide Protein Res., 40: 180-193 (1992). Each synthetic cycle consists of N"- Boc -removal by a 1 to 2 min treatment with neat TFA, a 1-min DMF flow wash, a 10-min coupling time with 2.0 mmol of preactivated Boc-amino acid in the presence of excess DEEA and a second DMF flow wash. Nα-Boc-amino acids (2 mmol) are preactivated for 3min with l.δmmol HCTU (0.5M in DMF) in the presence of excess DIEA (6mmol). After coupling of GIn residues, a dichloromethane flow wash is used before and after deprotection using TFA, 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(2,4-dinitrophenyl)-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 (Orpegen Pharma, Heidelberg, Germany). The N" of the N-terminal Cys residues of fragments 2 was protected by coupling a Boc-thioproline (Boc-SPr, i.e. Boc-L-thioproline) to the terminus of the respective chains instead of a Cys having conventional N" or S^β protection (Brik et al., 2000 J. Org. Chem., 65: 3829-3835). Other amino acids are used without side chain protection. C-terminal Fragment 1 is synthesized on a preloaded Boc-amino acyl PAM resin — (0.4-0.7mmol/g) at a 0.2mmol scale. Fragments 2 and 3 were synthesized on a thioester generating resin, as described (Hackeng et al., 1999, PNAS-USA, 96, 10068-10073). Synthesis is started on the Boc-Xaa-S-CH₂-CO- Leu-Pam resin. This resin is obtained by the coupling of S-trityl-mercaptoacetic acid to a Leu-PAM resin under standard conditions. The resulting resin is used as a starting resin for peptide chain elongation on a 0.2 mmol scale after removal of the trityl protecting group with a 2xl5min treatment with 95% TFA, 2.5% H₂0, 2.5% TIS. After chain assembly is completed, the peptide fragments are deprotected and cleaved from the resin by treatment with anhydrous hydrogen fluoride for lhr at O⁰C with 5% p-cresol as a scavenger. In all cases except Fragment 1, the imidazole side chain 2,4-dinitrophenyl (DNP) protecting groups remain on His residues because the DNP-removal procedure is incompatible with C-terminal thioester groups. However DNP is gradually removed by thiols during the ligation reaction, yielding unprotected His. After cleavage, peptide fragments are precipitated with ice-cold diethylether, dissolved in aqueous acetonitrile and lyophilized. The peptide fragments are purified by RP-HPLC with a Cl 8 Vydac column by using linear gradients of buffer B (acetonitile/0.1% trifluoroacetic acid) in buffer A (H₂O/0.1% trifluoroacetic acid) and UV detection at 214nm. Samples are analyzed by electrospray mass spectrometry (ESI-MS) using a Bruker Esquire 3000 Ion Trap (Bruker Daltonics, Bremen, DE).

• Native chemical ligation

As described more fully below, the ligation of unprotected fragments is performed as follows: the dry peptides are dissolved in equimolar amounts in 6M guanidine hydrochloride (GuHCl), 0.2M phosphate, pH 7.5 in order to get a final peptide concentration of 1-8 mM at a pH around 7, 1% thiophenol is added. Usually, the reaction is carried out overnight and is monitored by HPLC and electrospray mass spectrometry. The ligation product is subsequently treated to remove protecting groups still present. Opening of the N-terminal thiazolidine ring further required the addition of solid methoxamine to a 0.5M final concentration at pH3.5 and a further incubation for 2h at 37°C. A 10-fold excess of Tris(2- carboxyethyl)phosphine is added before preparative HPLC purification. Fractions containing the polypeptide are identified by ESI-MS, pooled and freeze-dried.

• Polypeptide Folding The full length peptide is refolded by air oxidation by dissolving the reduced lyophilized protein in 4M Urea, 0.1M Tris.HCl, 20 mM Met, 0.1% maltoside, pH=8.2, at about 0.1 mg/mL. After gentle stirring overnight, the protein solution was purified by RP-HPLC as described above.

For CSFP 83, 15mg full length linear peptide was obtained resulting in 4.7 mg folded material. The synthesized sequence was: MKPRTLTSLESNKRGKTSTEQMQNKEWSFVLVIETQCMRGNRVERRMLPDG VffiDRLLSQKFVPPNSTQPCEVRSTALRSQLPSVNDSPMCMASWVSLASESNIL DTPCQFGCSEKQMSKL (SEQ ID NO: 269) Number of residues: 121 Theoretical relative molecular mass, reduced form: 13698.91 Theoretical relative molecular mass, refolded form: 13694.88

Analytical data:

Experimental relative molecular mass, refolded form: 13695.63 Protein purity: 80.08 % (by RP-HPLC analysis, column Waters Symmetry 300A, Cl 8, 5μm, UV detection 214nm).

Synthesis of CSFP 135:

CSFP 135 was prepared by polymer-supported organic synthesis of two fragments equivalent to the whole sequence after cleavage between residues A²⁸ and Cys²⁹. These two fragments numbered 1 and 2 by starting from the C-ter were selected in such a way that fragment 1 has a N-terminal Cys residue. Fragment 2 was synthesized as thioester to be able to assemble them through native chemical ligation (Dawson et al., 1994, Science, 266, 776-779). Fragment 1 is coupled to fragment 2 to give the full length polypeptide, which is then purified and refolded.

• Fragment synthesis Boc chemistry was used as described (Schnδlzer et al., Int. J. Peptide Protein Res., 40: 180- 193, 1992). Solid-phase synthesis is performed on a custom-modified 433A peptide synthesizer from Applied Biosystems, using in situ neutralization/0-(lH-6- Chlorobenzotriazol-l-yl)-l,l,l,3,3-tetramethyluronium hexafluoro-phosphate (HCTU) activation protocols for stepwise Boc chemistry chain elongation, as described by Schnδlzer et al, Int. J. Peptide Protein Res., 40: 180-193 (1992). Each synthetic cycle consists of N"- Boc -removal by a 1 to 2 min treatment with neat TFA, a 1-min DMF flow wash, a 10-min coupling time with 2.0 mmol of preactivated Boc-amino acid in the presence of excess DIEA and a second DMF flow wash. Nα-Boc-amino acids (2 mmol) are preactivated for 3min with 1.8mmol HCTU (0.5M in DMF) in the presence of excess DIEA (6mmol). After coupling of GIn residues, a dichloromethane flow wash is used before and after deprotection using TFA, 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(2,4-dinitrophenyl)-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 (Orpegen Pharma, Heidelberg, Germany). The N" of the N-terminal Cys residues of fragments 2 was protected by coupling a Boc-thioproline (Boc-SPr, i.e. Boc-L-thioproline) to the terminus of the respective chains instead of a Cys having conventional N" or S^p protection (Brik et al., 2000 J. Org. Chem., 65: 3829-3835). Other amino acids are used without side chain protection. C-terminal Fragment 1 is synthesized on a preloaded Boc-amino acyl PAM resin ~(0.4-0.7mmol/g) at a 0.2mmol scale.

Fragments 2 is synthesized on a thioester generating resin, as described (Hackeng et al., 1999, PNAS-USA, 96, 10068-10073). Synthesis is started on the Boc-Xaa-S-CH₂-CO-Leu- Pam resin. This resin is obtained by the coupling of S-trityl-mercaptoacetic acid to a Leu- PAM resin under standard conditions. The resulting resin is used as a starting resin for peptide chain elongation on a 0.2 ππnol scale after removal of the trityl protecting group with a 2xl5min treatment with 95% TFA, 2.5% H₂0, 2.5% TIS. After chain assembly is completed, the peptide fragments are deprotected and cleaved from the resin by treatment with anhydrous hydrogen fluoride for lhr at O⁰C with 5% p-cresol as a scavenger. In all cases except for Fragment 1, the imidazole side chain 2,4-dinitrophenyl (DNP) protecting groups remain on His residues because the DNP-removal procedure is incompatible with C-terminal thioester group. However DNP is gradually removed by thiols during the ligation reaction, yielding unprotected His. After cleavage, peptide fragments are precipitated with ice-cold diethylether, dissolved in aqueous acetonitrile and lyophilized. The peptide fragments are purified by RP-HPLC with a Cl 8 Vydac column by using linear gradients of buffer B (acetonitile/0.1% trifluoroacetic acid) in buffer A (H₂O/0.1% trifluoroacetic acid) and UV detection at 214nm. Samples are analyzed by electrospray mass spectrometry (ESI-MS) using a Bruker Esquire 3000 Ion Trap (Bruker Daltonics, Bremen, DE).

• Native chemical ligation

The ligation of unprotected fragments is performed as follows: the dry peptides are dissolved in equimolar amounts in 6M guanidine hydrochloride (GuHCl), 0.2M phosphate, pH 7.5 in order to get a final peptide concentration of 1-8 mM at a pH around 7, 1% thiophenol is added. Usually, the reaction is carried out overnight at 37°C and is monitored by HPLC and electrospray mass spectrometry. The ligation product is subsequently treated to remove protecting groups still present. Opening of the N-terminal thiazolidine ring further required the addition of solid methoxamine to a 0.5M final concentration at pH3.5 and a further incubation for 2h at 37°C. A 10-fold excess of Tris (2-carboxyethyl) phosphine is added before preparative HPLC purification. Fractions containing the polypeptide are identified by ESI-MS₅ pooled and freeze-dried.

• Polypeptide Folding The full length peptide is refolded by air oxidation: the reduced lyophilized protein is resuspended in 6M guanidine at 10mg/ml and diluted 50 times in 0.2M Tris.HCl, IM GuCL, 40 mM Met, pH 8.0, to get a final protein concentration of about about 0.2 mg/mL. After gentle stirring overnight at room temperature in an open flask, formation of the 3 disulfide bridges was assessed by ESI-MS and the folded protein was purified by RP-HPLC as described above.

For CSFP 135, 140mg Fragment 1 and 144 mg Fragment 2 were obtained. Ligation resulted in 90 mg full-length peptide from which 39 mg folded material could be obtained. The synthesized sequence was: GHPDVAACPGSLDCALKRRARCPPGAHACGPCLQPFQEDQQGLCVPRMRRP PGGGRPQPRLEDEIDFLAQELAR (SEQ ID NO: 270) Number of residues: 74

Theoretical relative molecular mass, reduced form: 8015.27 Theoretical relative molecular mass, refolded form: 8009.22

Analytical data:

Experimental relative molecular mass, refolded form: 8009.58

Protein purity: 97.92 % (by RP-HPLC analysis, column Waters Symmetry 300A, Cl 8, 5μm, UV detection 214nm).

Example 7: Preparation of CSFP antibody compositions

Substantially pure CSFP or a portion thereof is obtained. The concentration of protein in the final preparation is adjusted, for example, by concentration on an Amicon filter device, to the level of a few micrograms per ml. Monoclonal or polyclonal antibodies to the protein are then prepared as described in the sections titled "Monoclonal antibodies" and "Polyclonal antibodies."

Briefly, to produce an anti-CSFP monoclonal antibody, a mouse is repetitively inoculated with a few micrograms of the CSFP or a portion thereof over a period of a few weeks. The mouse is then sacrificed, and the antibody producing cells of the spleen isolated. The spleen cells are fused by means of polyethylene glycol with mouse myeloma cells, and the excess unfused cells destroyed by growth of the system on selective media comprising aminopterin (HAT media). The successfully fused cells are diluted and aliquots of the dilution placed in wells of a microtiter plate where growth of the culture is continued.

Antibody-producing clones are identified by detection of antibody in the supernatant fluid of the wells by immunoassay procedures, such as ELISA, as originally described by Engvall, E., Meth. Enzymol. 70: 419 (1980). Selected positive clones can be expanded and their monoclonal antibody product harvested for use. Detailed procedures for monoclonal antibody production are described in Davis, L. et al. Basic Methods in Molecular Biology Elsevier, New York. Section 21-2.

For polyclonal antibody production by immunization, polyclonal antiserum containing antibodies to heterogeneous epitopes in the CSFP or a portion thereof are prepared by immunizing a mouse with the CSFP or a portion thereof, which can be unmodified or modified to enhance immunogenicity. Any suitable nonhuman animal, preferably a non-human mammal, may be selected including rat, rabbit, goat, or horse.

Antibody preparations prepared according to either the monoclonal or the polyclonal protocol are useful in quantitative immunoassays which determine concentrations of CSFP in biological samples; or they are also used semi-quantitatively or qualitatively to identify the presence of antigen in a biological sample. The antibodies may also be used in therapeutic compositions for killing cells expressing the protein or reducing the levels of the protein in the body.

Example 8: Differential expression of CSFPs 157, 158, 159 and 160 in Alzheimer's Disease The present inventors have measured the levels of some CSFPs of the invention in the CSF of Alzheimer's patients, and compared them to the levels measured in matched healthy controls. Interestingly, CSFPs 157, 158, 158 and 160 were found to vary significantly in abundance between the two sample sets. The Table 3 below shows the magnitude and details of these variations. In addition to the experimental parameters listed in Table 2 above, Table 3 provides in the second column the indication of the Proteome (Disease or Control), as well as next to each tryptic sequence, the identification score obtained for that tryptic sequence. Olav scores are indicated within parenthesis; these scores reflect, among other things, the strength of the experimental MS-MS signal over noise as detected by the MS-MS data identification software, and thus indicate the protein concentration in the sample.

Table 3

Where applicable, the ratio of protein levels in Alzheimer's disease versus control CSF samples is calculated by two methods. The first method calculates the AD / Control ratio by the number of fractions from each sample containing the CSFP. For example, for CSFP 157, this calculation is 3 / 1 (see Table 3), indicating a 3-fold increase in CSFP 157 in Alzheimer's disease CSF. Alternatively, and more accurately, the Olav scores obtained for each peptide in the mass spectrometry data analysis software are used to give a weighted ratio. For CSFP 157, the calculation is 204 / 96, resulting in 2.1. Thus, CSFP 157 is present at a 2.1-fold higher level in AD CSF compared to control CSF.

Similarly, CSFP 158 is present at a 2.0-fold lower level in diseased patients (calculation based on number of fractions), or at a 2.6-fold lower level in diseased patients (calculation based on Scores).

CSFP 160 is present at a 3.0-fold lower level in diseased patients (calculation based on number of fractions), or at a 2.1— fold lower level in diseased patients (calculation based on Scores). Finally CSFP 159 was detected only in control CSF samples. The MicroProt® process is able to detect very low abundance proteins with a CSF concentration in the range of a few hundreds of pM. Thus, these polypeptides are present at vanishingly low levels, if at all, in the CSF from individuals with Alzheimer's disease.

Example 9: In vitro effects of CSFP 1, CSFP 83, CSFP 135 and CSFP 152 on cortical neurons survival

Primary cultures of rat cortical neurons

A female rat of 17 days gestation was killed by cervical dislocation; the fetuses were removed from the uterus. Their brains were removed and placed in ice-cold medium of Leibovitz (Ll 5, Gibco, Invitrogen, Cergy-Pontoise, France). Cortex were dissected and meninges were carefully removed. The cortical neurons were dissociated by trypsinization for 30 min at 37°C (trypsin-EDTA Gibco) in presence of DNAse I (Roche, Meylan). The reaction was stopped by addition of medium of Eagle modified by Dulbecco (DMEM ; Gibco) with 10 % of fetal bovine serum (FBS ; Gibco). The suspension was triturated with a 10-ml pipette and using a needle syringe 21G and centrifuged at 350 x g for 10 min at room temperature. The pellets of dissociated cells were resuspended in culture medium containing Neurobasal medium (Gibco) with 2% of B27 supplement (Gibco) and 0.5 mM of glutamine (Gibco). Viable cells were counted in a Neubauer cytometer using the trypan blue exclusion test (Sigma ref T8154) and seeded on the basis of 4 000 cells per well in 96 well-plates (TPP) precoated with poly-L-lysine. Cells were allowed to adhere 2-3h and maintained in a humidified incubator at 37°C in 5 % CO₂-95 air atmosphere. Test compounds were then added to the medium.

Stock solutions were prepared in distilled water (Gibco) as follows: at 1 mM for CSFP 1, at 0.2 mM for CSFP 152, at 0.1 mM for CSFP 83 and at 0.5 mM for CSFP 135. BDNF (Tebu, Peprotech) was tested at 50 ng/ml as a reference compound. All dilutions were made in culture medium. Final concentration of water was fixed at 1%.

Evaluation of survival

After 3 days of treatment, neuronal survival was assayed by measuring acid phosphatase activity according to a method known in the art. Briefly, after removal of the culture medium, cells were rinsed with 100 μl of PBS (Phosphatase Buffer Saline, Gibco), after 100 μl of buffer containing 0.1 M sodium acetate (pH 5.5), 0.1% Triton XlOO and lmg/ml p- nitrophenyl phosphate (Sigma) was added. Reaction was stopped by addition of 10 μl of IN NaOH. Enzyme activity was measured at 405 nm in a microplate reader (Labsystems Multiskan Bichromatic).

Data analysis A global analysis of the data was done using a one way analysis of variance (ANOVA).

Where applicable, Fisher's PLSD test was used for multiple pairwise comparison. The level of significance was set at p < 0.05.

*** significant from control group (p < 0.001, Fisher's test) ** significant from control group (p < 0.01, Fisher's test) * significant from control group (p < 0.05, Fisher's test)

Results

BDNF, used (at 50 ng/ml) as reference compound, significantly enhanced cortical neurons survival.

The experiment was run in duplicate (resp. triplicate for CSFP 135), on 2 (resp. 3 for CSFP 135) different primary cells cultures.

The results for CSFP 1 are shown in Figure 1. CSFP 1 displays a very significant effect on cortical neurons survival. The results for CSFP 83 are shown in Figure 2. CSFP 83 displays a significant effect on cortical neurons survival.

The results for CSFP 135 are shown in Figure 3. CSFP 135 displays an intermediate effect on cortical neurons survival. The results for CSFP 152 are shown in Figure 4. CSFP 152 displays a significant effect on cortical neurons survival.

Claims

1. A method of detecting one or more Cerebrospinal Fluid Polypeptide(s) selected from the group consisting of: CSFPs 1-4, 7, 9, 10, 18, 38, 50-126, 128, 129, 132, 135, 137, 139, 141-143, 145-148, 151-155, 157-159, comprising the steps of: i) contacting a biological sample with a CSFP-binding adsorbent; and ii) detecting and/ or quantifying binding of a CSFP to the CSFP-binding adsorbent.

2. The method of claim 1, wherein said biological sample is a Cerebrospinal Fluid sample.

3. The method of claim 1, wherein said CSFP-binding adsorbent is a CSFP-specific antibody.

4. The method of claim 1, wherein the CSFP-binding adsorbent is attached to a substrate.

5. The method of claim 1 , wherein said detecting and/ or quantifying comprises a method selected from the group consisting of: radioimmunoassay, enzyme-linked immunoadsorption assay, retentate chromatography, protein array, surface enhanced laser desorption/ionisation, and mass spectrometry.

6. A protein array comprising an adsorbant specific for at least one Cerebrospinal Fluid Polypeptide selected from the group consisting of: CSFPs 1-4, 7, 9, 10, 18, 38, 50-126, 128, 129, 132, 135, 137, 139, 141-143, 145-148, 151-155, 157-159.

7. A method of detecting an abnormal concentration of at least one Cerebrospinal Fluid Polypeptide selected from the group consisting of: CSFPs 1-4, 7, 9, 10, 18, 38, 50-126,

128, 129, 132, 135, 137, 139, 141-143, 145-148, 151-155, 157-159, in an individual comprising the steps of: i) obtaining a sample from said individual; ii) determining a first level of said at least one CSFP in said sample; and iii) comparing said level to that of a control sample; wherein a difference between the first level and the control level is diagnostic of an abnormal concentration of a CSFP. 8. An isolated polypeptide having the amino acid sequence of a Cerebrospinal Fluid

Polypeptide (CSFP) selected from the group of CSFPs 2-4, 50-53, 55-62, 66, 67, 71, 75, 78-83, 88, 89, 94, 97-100, 102-105, 107, 109, 112, 113, 117-120, 123-125, 128, 129, 132, 135, 137, 139, 141-143, 145-148, 151-155, 159, 159.

9. An isolated polynucleotide encoding the polypeptide of claim 8.

10. The use of at least one polypeptide selected from: CSFP 1, CSFP 83, CSFP 135 and

CSFP 152 in the preparation of a medicament for the prophylaxis and/or treatment of a neurological disorder.