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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/158—Expression markers

Definitions

• This invention relates to nucleic acid and amino acid sequences of neuron-associated proteins and to the use of these sequences in the diagnosis, treatment, and prevention of cell proliferative disorders including cancer: neuronal and neurological disorders: and autoimmune/inflammation disorders.
• the human nervous system which regulates all bodily functions, is composed of the central nervous system (CNS), consisting of the brain and spinal cord, and the peripheral nervous system (PNS), consisting of afferent neural pathways for conducting nerve impulses from sensory organs to the CNS. and efferent neural pathways for conducting motor impulses from the CNS to effector organs.
• the PNS can be further divided into the somatic nervous system, which regulates voluntary motor activity such as for skeletal muscle, and the autonomic nervous system, which regulates involuntary motor activity for internal organs such as the heart, lungs, and viscera.
• the central nervous system (CNS) is composed of more than 100 billion neurons at the spinal cord level, the lower brain level, and the higher brain or cortical level.
• Neurons transmit electric or chemical signals between cells.
• the spinal cord a thin, tubular extension of the central nervous system within the bony spinal canal, contains ascending sensory and descending motor pathways, and is covered by membranes continuous with those of the brainstem and cerebral hemispheres.
• the spinal cord contains almost the entire motor output and sensory input systems of the trunk and limbs, and neuronal circuits in the cord also control rhythmic movements, such as walking, and a variety of reflexes.
• the lower areas of the brain such as the medulla, pons, mesencephalon, cerebellum, basal ganglia, substantia nigra, hypothalamus, and thalamus control unconscious activities including arterial pressure and respiration, equilibrium, and feeding reflexes, such as salivation.
• Emotions such as anger, excitement, sexual response, and reaction to pain or pleasure, originate in the lower brain.
• the cerebral cortex or higher brain is the largest structure, consisting of a right and a left hemisphere interconnected by the corpus callosum.
• the cerebral cortex is involved in sensory, motor, and integrative functions related to perception, voluntary musculoskeletal movements, and the broad range of activities associated with consciousness, language, emotions, and memory.
• a nerve cell contains four regions, the cell body, axon. dendrites, and axon terminal.
• the cell body contains the nucleus and other organelles.
• the dendrites are processes which extend outward from the cell body and receive signals from sense organs or from the axons of other neurons. These signals are converted to electrical impulses and transmitted to the cell body.
• the axon whose size can range from one millimeter to more than one meter, is a single process that conducts the nerve impulse away from the cell body.
• Cytoskeletal fibers including microtubules and neurofilaments, run the length of the axon and function in transporting proteins, membrane vesicles, and other macromolecules from the cell body along the axon to the axon terminal.
• Some axons are surrounded by a myelin sheath made up of membranes from either an oligodendrocyte cell (CNS) or a Schwann cell (PNS).
• CNS oligodendrocyte cell
• PNS Schwann cell
• Myelinated axons conduct electrical impulses faster than unmyelinated ones of the same diameter.
• the axon terminal is at the tip of the axon away from the cell body.
• CNS-associated proteins have roles in neuronal signaling, cell adhesion, nerve regeneration, axon guidance, neurogenesis, and other functions.
• Certain CNS-associated proteins form an integral part of a membrane or are attached to a membrane.
• neural membrane protein 35 NMP35
• NMP35 neural membrane protein 35
• Synaptophysin (SY) is a major integral membrane protein of small synaptic vesicles. The chromosomal location of SY in human and mouse is on the X chromosome in subbands Xpl 1.22- pl 1.23.
• rds Peripherin or retinal degeneration slow protein
• rds is an integral membrane glycoprotein that is present in the rims of photoreceptor outer segment disks. In mammals, rds is thought to stabilize the disk rim through heterophilic interactions with related nonglycosylated proteins. Rds is a mouse neurological mutation that is characterized by abnormal development of rod and cone photoreceptors followed by their slow degeneration.
• RAPSYN acteylcholine receptor-associated 43 KD protein
• RAPSYN is thought to play a role in anchoring or stabilizing the nicotinic acetylcholine receptor at synaptic sites.
• RAPSYN is involved in membrane association and may link the nicotinic acetylcholine receptor to the underlying postsynaptic cytoskeleton.
• Neuritin is a protein whose gene is known to be induced by neural activity and by neurotrophins which promotes neuritogenesis.
• Neuraxin is a structural protein of the rat central nervous system that is believed to be immunologically related to microtubule-associated protein 5 (MAP5).
• MAP5 microtubule-associated protein 5
• Neuraxin is a novel type of neuron-specific protein which is characterized by an unusual amino acid composition, 12 central heptadecarepeats and putative protein and membrane interaction sites. The gene encoding neuraxin is unique in the haploid rat genome and is conserved in higher vertebrates. Neuraxin is implicated in neuronal membrane-microtubule interactions and is expressed throughout the rodent central nervous system (CNS). (Rienitz, A. et al. (1989) EMBO J.
• NudC a nuclear movement protein, interacts with the lissencephaly gene product Lisl, a protein involved in neuronal migration.
• Lisl a protein involved in neuronal migration.
• People with Miller-Dieker syndrome (MDS) or isolated lissencephaly sequence (ILS) have a hemizygous deletion or mutation in the LIS1 gene. Both conditions are characterized by a smooth cerebral surface, a thickened cortex with four abnormal layers, and misplaced neurons.
• LIS1 is highly expressed in the ventricular zone and the cortical plate.
• CNS-associated proteins can also be phosphoproteins.
• ARPP-21 cyclic AMP-regulated phosphoprotein
• ARPP-21 mRNA is a cytosolic neuronal phosphoprotein that is highly enriched in the striatum and in other dopaminoceptive regions of the brain.
• the steady-state level of ARPP-21 mRNA is developmentally regulated. But, in the neonatal and mature animal, ARPP-21 mRNA is not altered following 6-hydroxydopamine lesions of the substantia nigra or by pharmacologic treatments that upregulate the Dl- or D2-dopamine receptors. (Ehrlich, M. E. et al. (1991) Neurochem.
• CNS-associated signaling proteins may contain PDZ domains.
• PDZ domains have been found in proteins which act as adaptors in the assembly of multifunctional protein complexes involved in signaling events at surfaces of cell membranes.
• PDZ domains are generally found in membrane- associated proteins including neuronal nitric oxide synthase (NOS) and several dystrophin-associated proteins.
• NOS neuronal nitric oxide synthase
• CNS-associated proteins may also contain epidermal growth factor (EGF) domains.
• EGF epidermal growth factor
• Notch proteins are transmembrane proteins which contain extracellular regions of repeated EGF domains. Notch proteins, such as the Drosophila melanogaster neurogenic protein Notch, are generally involved in the inhibition of developmental processes. Other members of the Notch family are the lin-12 and glp-1 genes of Caenorhabditis elegans. Genetic studies indicate that the lin-12 and glp-1 proteins act as receptors in specific developmental cell interactions which may be involved in certain embyronic defects. (Tax, F. E. et al. (1994) Nature 368: 150-154.) Pecanex, a maternal-effect neurogenic locus of D. melanogaster is believed to encode a large transmembrane protein.
• CNS-associated signaling proteins contain WW domains.
• the WW domain is a protein motif with two highly conserved tryptophans. It is present in a number of signaling and regulatory proteins, including Huntingtin interacting protein.
• AD Alzheimer ' s disease
• CNS cerebral spastic syndrome
• AD is a degenerative disorder of the CNS which causes progressive memory loss and cognitive decline during mid to late adult life.
• AD is characterized by a wide range of neuropathologic features including amyloid deposits and intra-neuronal neurofibrillary tangles.
• amyloid deposits and intra-neuronal neurofibrillary tangles.
• at least three genetic loci that confer genetic susceptibility to the disease have been identified. (Schellenberg, G.D. ( 1995) Proc. Natl. Acad. Sci. 92:8552-8559: Sherrington, R. et al. (1995) Nature 375:754-760.)
• NTP Neuronal Thread Proteins
• Astrocytomas and the more malignant glioblastomas, are the most common primary tumors of the brain, accounting for over 65% of primary brain tumors. These tumors arise in glial cells of the astrocyte lineage. Following infection by pathogens, astrocytes function as antigen-presenting cells and modulate the activity of lymphocytes and macrophages. Astrocytomas constitutively express many cytokines and interleukins that are normally produced only after infection by a pathogen (de Micco, C. (1989) J. Neuroimmunol. 25:93-108).
• PR proteins are a family of small (10-20 kDa), protease resistant proteins induced in plants by viral infections, such as tobacco mosaic virus. The synthesis of PR proteins is believed to be part of a primitive immunological response in plants (van Loon, L.C.
• Fe65-like protein (Fe65L2), a new member of the Fe65 protein family, is one of the ligands that interacts with the cytoplasmic domain of Alzheimer beta-amyloid precursor protein (APP).
• Transgenic mice expressing APP are known to simulate some of the prominent behavioral and pathological features of Alzheimer's disease, including age-related impairment in learning and memory, neuronal loss, gliosis, neuritic changes, amyloid deposition, and abnormal tau phosphorylation. Proteins that interact with the cytoplasmic domain of APP provide new insights into the physiological function of APP and, in turn, into the pathogenesis of Alzheimer's disease. (Duilio, A. et al. (1998) Biochem. J. 330:513-519.)
• the synapse Contact from one neuron to another occurs at a specialized site called the synapse.
• the axon terminal from one neuron (the presynaptic cell) sends a signal to another neuron (the postsynaptic cell).
• Synapses may be connected either electrically or chemically.
• An electrical synapse consists of gap junctions connecting the two neurons, allowing electrical impulses to pass directly from the presynaptic to the postsynaptic cell.
• the axon terminal of the presynaptic cell contains membrane vesicles containing a particular neurotransmitter molecule.
• a change in electrical potential at the nerve terminal resulting from the electrical impulse triggers the release of the neurotransmitter from the synaptic vesicle by exocytosis.
• the neurotransmitter rapidly diffuses across the synaptic cleft separating the presynaptic nerve cell from the postsynaptic cell.
• the neurotransmitter then binds receptors and opens transmitter-gated ion channels located in the plasma membrane of the postsynaptic cell, provoking a change in the cell's electrical potential.
• This change in membrane potential of the postsynaptic cell may serve either to excite or inhibit further transmission of the nerve impulse.
• Neurotransmitters comprise a diverse group of some 30 small molecules which include acetylcholine, monoamines such as serotonin, dopamine, and histamine, and amino acids such as gamma-am inobutyric acid (GAB A), glutamate, and aspartate. and neuropeptides such as endorphins and enkephalins.
• GAB A gamma-am inobutyric acid
• neuropeptides such as endorphins and enkephalins.
• GABA is the major inhibitory neurotransmitter in the CNS
• GABA receptors are the principal target of sedatives such as benzodiazepines and barbiturates which act by enhancing GABA-mediated effects (Katzung, B.G. (1995) Basic and Clinical Pharmacology. 6th edition, Appleton & Lange, Norwalk, CT, pp. 338-339).
• Diazepam binding inhibitor also known as endozepine and acyl-Coenzyme (CoA)-binding protein
• DBI is an endogenous GABA receptor ligand which is thought to down-regulate the effects of GABA.
• DBI binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters (* 125950 Diazepam Binding Inhibitor; DBI, Online Mendelian Inheritance in Man (OMIM); PROSITE PDOC00686 Acyl-CoA-binding protein signature).
• ECM extracellular matrix
• Many ECM molecules including fibronectin, vitronectin, members of the laminin, tenascin, collagen, and thrombospondin families, and a variety of proteoglycans, can act either as promoters or inhibitors of neurite outgrowth and extension (Tessier- Lavigne et al., supra).
• Receptors for ECM molecules include integrins, immunoglobulin superfamily members, and proteoglycans. ECM molecules and their receptors have also been implicated in the adhesion, maintenance, and differentiation of neurons (Reichardt, L.F. et al. (1991) Ann. Rev.
• the proteoglycan testican is localized to the post-synaptic area of pyramidal cells of the hippocampus and may play roles in receptor activity, neuromodulation, synaptic plasticity, and neurotransmission (Bonnet, F. et al. (1996) J. Biol. Chem. 271 :4373-4380).
• Other nervous system-associated proteins have roles in neuron signaling, cell adhesion, nerve regeneration, axon guidance, and neurogenesis.
• the neurexophilins are neuropeptide-like proteins which are proteolytically processed after synthesis. They are ligands for the neuron-specific cell surface proteins, the ⁇ -neurexins.
• Neurexophilins and neurexins may participate in a neuron signaling pathway (Missler, M. and T.C. Sudhof ( 1998) J. Neurosci. 18:3630-3638; Missler, M. et al. (1998) J. Biol. Chem. 273:34716-34723).
• Ninjurin is a neuron cell surface protein which plays a role in cell adhesion and in nerve regeneration following injury. Ninjurin is up-regulated after nerve injury in dorsal root ganglion neurons and in Schwann cells (*602062 Ninjurin; NINJ1 OMIM; Araki, T. and Milbrandt, J. (1996) Neuron 17:353-361).
• Mammalian Numb is a phosphotyrosine-binding (PTB) domain-containing protein which may be involved in cortical neurogenesis and cell fate decisions in the mammalian nervous system.
• Numb's binding partner the LNX protein, contains four PDZ domains and a ring finger domain and may participate in a signaling pathway involving Numb.
• PDZ domains have been found in proteins which act as adaptors in the assembly of multifunctional protein complexes involved in signaling events at surfaces of cell membranes (Ponting, C.P. (1997) Bioessays 19:469-479).
• LNX contains a tyrosine phosphorylation site which may be important for the binding of other PTB-containing proteins such as SHC, an adaptor protein which associates with tyrosine- phosphorylated growth factor receptors and downstream effectors (Dho, S.E. et al. (1998) J. Biol. Chem. 273:9179-9187).
• the invention features substantially purified polypeptides. neuron-associated proteins, referred to collectively as “NEUAP” and individually as “NEUAP- 1 ,” “NEUAP-2,” “NEUAP- 3,””NEUAP-4,””NEUAP-5,””NEUAP-6,””NEUAP-7,””NEUAP-8,””NEUAP-9,””NEUAP- 10,”"NEUAP- 1 1 ,” “NEUAP- 12,””NEUAP- 13,””NEUAP- 14,””NEUAP- 15,””NEUAP- 16,””NEUAP- 17,””NEUAP-18,””NEUAP-19,””NEUAP-20,” “NEUAP-21,” “NEUAP-22,” “NEUAP-23,” “NEUAP-24.” “NEUAP-25,” “NEUAP-26,” “NEUAP-27,”, and “NEUAP-28.”
• the invention provides a substantially purified polypeptide comprising an amino acid sequence selected from the group consisting of
• the invention also includes a polypeptide comprising an amino acid sequence that differs by one or more conservative amino acid substitutions from an amino acid sequence selected from the group consisting of SEQ ID NO: 1-27.
• the invention further provides a substantially purified variant having at least 90% amino acid identity to at least one of the amino acid sequences selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof.
• the invention also provides an isolated and purified polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof.
• the invention also includes an isolated and purified polynucleotide variant having at least 90% polynucleotide sequence identity to the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof.
• the invention provides an isolated and purified polynucleotide which hybridizes under stringent conditions to the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof.
• the invention also provides an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide encoding the polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof.
• the invention also provides a method for detecting a polynucleotide in a sample containing nucleic acids, the method comprising the steps of: (a) hybridizing the complement of the polynucleotide sequence to at least one of the polynucleotides of the sample, thereby forming a hybridization complex; and (b) detecting the hybridization complex, wherein the presence of the hybridization complex correlates with the presence of a polynucleotide in the sample.
• the method further comprises amplifying the polynucleotide prior to hybridization.
• the invention also provides an isolated and purified polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:28-54 and fragments thereof.
• the invention further provides an isolated and purified polynucleotide variant having at least 90% polynucleotide sequence identity to the polynucleotide sequence selected from the group consisting of SEQ ID NO:28-54 and fragments thereof.
• the invention also provides an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:28-54 and fragments thereof.
• the invention further provides an expression vector containing at least a fragment of the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1 -27.
• the expression vector is contained within a host cell.
• the invention also provides a method for producing a polypeptide, the method comprising the steps of: (a) culturing the host cell containing an expression vector containing a polynucleotide of the invention under conditions suitable for the expression of the polypeptide; and (b) recovering the polypeptide from the host cell culture.
• the invention also provides a pharmaceutical composition
• a pharmaceutical composition comprising a substantially purified polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof, in conjunction with a suitable pharmaceutical carrier.
• the invention further includes a purified antibody which binds to a polypeptide selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof.
• the invention also provides a purified agonist and a purified antagonist to the polypeptide.
• the invention also provides a method for treating or preventing a disorder associated with decreased expression or activity of NEUAP, the method comprising administering to a subject in need of such treatment an effective amount of a pharmaceutical composition comprising a substantially purified polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof, in conjunction with a suitable pharmaceutical carrier.
• the invention also provides a method for treating or preventing a disorder associated with increased expression or activity of NEUAP, the method comprising administering to a subject in need of such treatment an effective amount of an antagonist of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 1-27 and fragments thereof.
• AD7c-NTP a human neuronal thread protein
• AD7c-NTP Gl 3002527; SEQ ID NO:55
• Figures 2A. 2B, and 2C show the amino acid sequence alignment between NEUAP-2 (2634931 ; SEQ ID NO:2) and a human glioma pathogenesis-related protein, GliPR (Gl 847722; SEQ ID NO:56), produced using the multisequence alignment program of LASERGENE software.
• Table 1 shows polypeptide and nucleotide sequence identification numbers (SEQ ID NOs), clone identification numbers (clone IDs), cDNA libraries, and cDNA fragments used to assemble full- length sequences encoding NEUAP.
• Table 2 shows features of each polypeptide sequence, including potential motifs, homologous sequences, and methods, algorithms, and searchable databases used for analysis of NEUAP.
• Table 3 shows selected fragments of each nucleic acid sequence: the tissue-specific expression patterns of each nucleic acid sequence as determined by northern analysis: diseases, disorders, or conditions associated with these tissues; and the vector into which each cDNA was cloned.
• Table 4 describes the tissues used to construct the cDNA libraries from which cDNA clones encoding NEUAP were isolated.
• Table 5 shows the tools, programs, and algorithms used to analyze NEUAP. along with applicable descriptions, references, and threshold parameters.
• NEUAP refers to the amino acid sequences of substantially purified NEUAP obtained from any species, particularly a mammalian species, including bovine, ovine, porcine, murine, equine, and human, and from any source, whether natural, synthetic, semi-synthetic, or recombinant.
• agonist refers to a molecule which intensifies or mimics the biological activity of NEUAP.
• Agonists may include proteins, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of NEUAP either by directly interacting with NEUAP or by acting on components of the biological pathway in which NEUAP participates.
• allelic variant is an alternative form of the gene encoding NEUAP. Allelic variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. A gene may have none, one, or many allelic variants of its naturally occurring form. Common mutational changes which give rise to allelic variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.
• altered nucleic acid sequences encoding NEUAP include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polypeptide the same as NEUAP or a polypeptide with at least one functional characteristic of NEUAP. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding NEUAP. and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding NEUAP.
• the encoded protein may also be "altered,” and may contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent NEUAP.
• Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of NEUAP is retained.
• negatively charged amino acids may include aspartic acid and glutamic acid
• positively charged amino acids may include lysine and arginine.
• Amino acids with uncharged polar side chains having similar hydrophilicity values may include: asparagine and glutamine; and serine and threonine.
• Amino acids with uncharged side chains having similar hydrophilicity values may include: leucine, isoleucine, and valine; glycine and alanine; and phenylalanine and tyrosine.
• amino acid and amino acid sequence refer to an oligopeptide, peptide, polypeptide, or protein sequence, or a fragment of any of these, and to naturally occurring or synthetic molecules. Where “amino acid sequence " is recited to refer to an amino acid sequence of a naturally occurring protein molecule, “amino acid sequence " and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.
• Amplification relates to the production of additional copies of a nucleic acid sequence. Amplification is generally carried out using polymerase chain reaction (PCR) technologies well known in the art.
• PCR polymerase chain reaction
• Antagonist refers to a molecule which inhibits or attenuates the biological activity of NEUAP.
• Antagonists may include proteins such as antibodies, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of NEUAP either by directly interacting with NEUAP or by acting on components of the biological pathway in which NEUAP participates.
• antibody refers to intact immunoglobulin molecules as well as to fragments thereof, such as Fab, F(ab') 2 , and Fv fragments, which are capable of binding an epitopic determinant.
• Antibodies that bind NEUAP polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen.
• the polypeptide or oligopeptide used to immunize an animal e.g., a mouse, a rat, or a rabbit
• an animal e.g., a mouse, a rat, or a rabbit
• Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.
• antigenic determinant refers to that region of a molecule (i.e., an epitope) that makes contact with a particular antibody.
• an antigenic determinant may compete with the intact antigen (i.e., the immunogen used to elicit the immune response) for binding to an antibody.
• antisense refers to any composition containing a nucleic acid sequence which is complementary to the "sense” strand of a specific nucleic acid sequence. Antisense molecules may be produced by any method including synthesis or transcription. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form duplexes and to block either transcription or translation. The designation “negative” or “minus” can refer to the antisense strand, and the designation “positive” or “plus” can refer to the sense strand.
• biologically active refers to a protein having structural, regulatory, or biochemical functions of a naturally occurring molecule.
• immunologically active refers to the capability of the natural, recombinant, or synthetic NEUAP, or of any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.
• complementarity refers to the natural binding of polynucleotides by base pairing.
• sequence 5' A-G-T 3'
• complementary sequence 3' T-C-A 5'.
• Complementarity between two single-stranded molecules may be "partial,” such that only some of the nucleic acids bind, or it may be "complete,” such that total complementarity exists between the single stranded molecules.
• the degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of the hybridization between the nucleic acid strands. This is of particular importance in amplification reactions, which depend upon binding between nucleic acid strands, and in the design and use of peptide nucleic acid (PNA) molecules.
• PNA peptide nucleic acid
• composition comprising a given polynucleotide sequence and a “composition comprising a given amino acid sequence” refer broadly to any composition containing the given polynucleotide or amino acid sequence.
• the composition may comprise a dry formulation or an aqueous solution.
• Compositions comprising polynucleotide sequences encoding NEUAP or fragments of NEUAP may be employed as hybridization probes.
• the probes may be stored in freeze-dried form and may be associated with a stabilizing agent such as a carbohydrate.
• the probe may be deployed in an aqueous solution containing salts (e.g., NaCl), detergents (e.g., sodium dodecyl sulfate; SDS), and other components (e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.).
• Salts e.g., NaCl
• detergents e.g., sodium dodecyl sulfate; SDS
• other components e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.
• Consensus sequence refers to a nucleic acid sequence which has been resequenced to resolve uncalled bases, extended using the XL-PCR kit (Perkin-Elmer, Norwalk CT) in the 5' and/or the 3' direction, and resequenced. or which has been assembled from the overlapping sequences of one or more Incyte Clones and.
• one or more public domain ESTs using a computer program for fragment assembly, such as the GELVIEW fragment assembly system (GCG, Madison Wl). Some sequences have been both extended and assembled to produce the consensus sequence. "Conservative amino acid substitutions" are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative amino acid substitutions.
• Original Residue Conservative Substitution are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative amino acid substitutions.
• Conservative amino acid substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the site of the substitution, and/or (c) the bulk of the side chain.
• a “deletion” refers to a change in the amino acid or nucleotide sequence that results in the absence of one or more amino acid residues or nucleotides.
• derivative refers to the chemical modification of a polypeptide sequence, or a polynucleotide sequence. Chemical modifications of a polynucleotide sequence can include, for example, replacement of hydrogen by an alkyl, acyl, hydroxyl, or amino group.
• a derivative polynucleotide encodes a polypeptide which retains at least one biological or immunological function of the natural molecule.
• a derivative polypeptide is one modified by glycosylation, pegylation, or any similar process that retains at least one biological or immunological function of the polypeptide from which it was derived.
• a “fragment” is a unique portion of NEUAP or the polynucleotide encoding NEUAP which is identical in sequence to but shorter in length than the parent sequence.
• a fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue.
• a fragment may comprise from 5 to 1000 contiguous nucleotides or amino acid residues.
• a fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, may be at least 5, 10, 15, 20, 25, 30, 40, 50. 60, 75, 100, 150, 250 or at least 500 contiguous nucleotides or amino acid residues in length. Fragments may be preferentially selected from certain regions of a molecule.
• a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50% of a polypeptide) as shown in a certain defined sequence.
• a fragment of SEQ ID NO:28-54 comprises a region of unique polynucleotide sequence that specifically identifies SEQ ID NO:28-54, for example, as distinct from any other sequence in the same genome.
• a fragment of SEQ ID NO:28-54 is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish SEQ ID NO:28-54 from related polynucleotide sequences.
• the precise length of a fragment of SEQ ID NO:28-54 and the region of SEQ ID NO:28-54 to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
• a fragment of SEQ ID NO: 1 -27 is encoded by a fragment of SEQ ID NO:28-54.
• a fragment of SEQ ID NO: 1-27 comprises a region of unique amino acid sequence that specifically identifies SEQ ID NO: 1-27.
• a fragment of SEQ ID NO: 1-27 is useful as an immunogenic peptide for the development of antibodies that specifically recognize SEQ ID NO: 1 -27.
• the precise length of a fragment of SEQ ID NO: 1 -27 and the region of SEQ ID NO: 1 -27 to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
• the term “similarity" refers to a degree of complementarity. There may be partial similarity or complete similarity.
• the word "identity” may substitute for the word “similarity.”
• a partially complementary sequence that at least partially inhibits an identical sequence from hybridizing to a target nucleic acid is referred to as “substantially similar.”
• the inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or northern blot, solution hybridization, and the like) under conditions of reduced stringency.
• a substantially similar sequence or hybridization probe will compete for and inhibit the binding of a completely similar (identical) sequence to the target sequence under conditions of reduced stringency. This is not to say that conditions of reduced stringency are such that non-specific binding is permitted, as reduced stringency conditions require that the binding of two sequences to one another be a specific (i.e., a selective) interaction.
• the absence of non-specific binding may be tested by the use of a second target sequence which lacks even a partial degree of complementarity (e.g., less than about 30% similarity or identity). In the absence of non-specific binding, the substantially similar sequence or probe will not hybridize to the second non-complementary target sequence.
• the phrases "percent identity” and "% identity,” as applied to polynucleotide sequences refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.
• NCBI National Center for Biotechnology Information
• BLAST Basic Local Alignment Search Tool
• NCBI National Center for Biotechnology Information
• BLAST Basic Local Alignment Search Tool
• the BLAST software suite includes various sequence analysis programs including "blastn.” that is used to align a known polynucleotide sequence with other polynucleotide sequences from a variety of databases.
• BLAST 2 Sequences are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the "BLAST 2 Sequences” tool Version 2.0.9 (May-07- 1999) set at default parameters. Such default parameters may be, for example:
• Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides.
• Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures, or Sequence Listing, may be used to describe a length over which percentage identity may be measured.
• nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in a nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.
• Percent identity and % identity refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity at the site of substitution, thus preserving the structure (and therefore function) of the polypeptide. Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program (described and referenced above).
• NCBI BLAST software suite may be used.
• BLAST 2 Sequences Version 2.0.9 (May-07- 1999) with blastp set at default parameters.
• Such default parameters may be. for example: Matrix: BLOSUM62
• Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30. at least 40, at least 50, at least 70 or at least 150 contiguous residues.
• Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.
• HACs Human artificial chromosomes
• HACs are linear microchromosomes which may contain DNA sequences of about 6 kb to 10 Mb in size, and which contain all of the elements required for stable mitotic chromosome segregation and maintenance.
• humanized antibody refers to antibody molecules in which the amino acid sequence in the non-antigen binding regions has been altered so that the antibody more closely resembles a human antibody, and still retains its original binding ability.
• Hybridization refers to the process by which a polynucleotide strand anneals with a complementary strand through base pairing under defined hybridization conditions. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under permissive annealing conditions and remain hybridized after the "washing" step(s). The washing step(s) is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid strands that are not perfectly matched.
• Permissive conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency, and therefore hybridization specificity. Permissive annealing conditions occur, for example, at 68°C in the presence of about 6 x SSC, about 1% (w/v) SDS, and about 100 ⁇ g/ml denatured salmon sperm DNA.
• T m thermal melting point
• An equation for calculating T m and conditions for nucleic acid hybridization are well known and can be found in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2 nd ed., vol. 1-3, Cold Spring Harbor Press, Plainview NY; specifically see volume 2, chapter 9.
• High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0.1% SDS, for 1 hour. Alternatively, temperatures of about 65°C, 60°C, 55°C, or 42°C may be used. SSC concentration may be varied from about 0.1 to 2 x SSC, with SDS being present at about 0.1%.
• blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 ⁇ g/ml. Organic solvent, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as for RNA:DNA hybridizations.
• Hybridization particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their encoded polypeptides.
• hybridization complex refers to a complex formed between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary bases.
• a hybridization complex may be formed in solution (e.g., C 0 t or R ⁇ t analysis) or formed between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed).
• insertion and “addition” refer to changes in an amino acid or nucleotide sequence resulting in the addition of one or more amino acid residues or nucleotides, respectively.
• Immuno response can refer to conditions associated with inflammation, trauma, immune disorders, or infectious or genetic disease, etc. These conditions can be characterized by expression of various factors, e.g., cytokines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.
• microarray refers to an arrangement of distinct polynucleotides on a substrate.
• element and “array element” in a microarray context, refer to hybridizable polynucleotides arranged on the surface of a substrate.
• modulate refers to a change in the activity of NEUAP. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional, or immunological properties of NEUAP.
• nucleic acid and nucleic acid sequence refer to a nucleotide, oligonucleotide, polynucleotide, or any fragment thereof. These phrases also refer to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material.
• operably linked refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence.
• a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence.
• operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.
• PNA protein nucleic acid
• PNA refers to an antisense molecule or anti-gene agent which comprises an oligonucleotide of at least about 5 nucleotides in length linked to a peptide backbone of amino acid residues ending in lysine. The terminal lysine confers solubility to the composition. PNAs preferentially bind complementary single stranded DNA or RNA and stop transcript elongation, and may be pegylated to extend their lifespan in the cell.
• Probe refers to nucleic acid sequences encoding NEUAP, their complements, or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences.
• Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands. chemiluminescent agents, and enzymes.
• Primarymers are short nucleic acids, usually DNA oligonucleotides. which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR).
• PCR polymerase chain reaction
• Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 25, 30, 40, 50, 60. 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the tables, figures, and Sequence Listing, may be used.
• PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5. 1991, Whitehead Institute for Biomedical Research, Cambridge MA).
• Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope.
• the Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge MA) allows the user to input a "misprinting library," in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.)
• the PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences.
• this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments.
• the oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.
• a "recombinant nucleic acid” is a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra.
• the term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid.
• a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.
• such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.
• sample is used in its broadest sense.
• a sample suspected of containing nucleic acids encoding NEUAP, or fragments thereof, or NEUAP itself, may comprise a bodily fluid; an extract from a cell, chromosome, organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA, or cDNA, in solution or bound to a substrate; a tissue; a tissue print; etc.
• specific binding and “specifically binding” refer to that interaction between a protein or peptide and an agonist, an antibody, an antagonist, a small molecule, or any natural or synthetic binding composition.
• the interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule.
• a particular structure of the protein e.g., the antigenic determinant or epitope
• the binding molecule e.g., the binding molecule for binding the binding molecule.
• an antibody is specific for epitope "A”
• the presence of a polypeptide containing the epitope A, or the presence of free unlabeled A in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.
• substantially purified refers to nucleic acid or amino acid sequences that are removed from their natural environment and are isolated or separated, and are at least about 60% free, preferably about 75% free, and most preferably about 90% free from other components with which they are naturally associated.
• substitution refers to the replacement of one or more amino acids or nucleotides by different amino acids or nucleotides, respectively.
• Substrate refers to any suitable rigid or semi-rigid support including membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles and capillaries.
• the substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.
• Transformation describes a process by which exogenous DNA enters and changes a recipient cell. Transformation may occur under natural or artificial conditions according to various methods well known in the art, and may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell.
• the method for transformation is selected based on the type of host cell being transformed and may include, but is not limited to, viral infection, electroporation, heat shock, lipofection. and particle bombardment.
• the term "transformed” cells includes stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as transiently transformed cells which express the inserted DNA or RNA for limited periods of time.
• a “variant" of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 40% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07- 1999) set at default parameters.
• Such a pair of nucleic acids may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95% or at least 98% or greater sequence identity over a certain defined length.
• a variant may be described as, for example, an "allelic” (as defined above), “splice,” “species,” or “polymorphic” variant.
• a splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing.
• the corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule.
• Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other.
• a polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.
• Polymorphic variants also may encompass "single nucleotide polymorphisms" (SNPs) in which the polynucleotide sequence varies by one nucleotide base.
• SNPs single nucleotide polymorphisms
• the presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
• a "variant" of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07- 1999) set at default parameters.
• Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% or greater sequence identity over a certain defined length of one of the polypeptides.
• the invention is based on the discovery of new human neuron-associated proteins (NEUAP), the polynucleotides encoding NEUAP. and the use of these compositions for the diagnosis, treatment, or prevention of cell proliferative disorders including cancer; neuronal and neurological disorders; and autoimmune/inflammation disorders.
• NEUAP new human neuron-associated proteins
• Table 1 lists the Incyte clones used to assemble full length nucleotide sequences encoding NEUAP. Columns 1 and 2 show the sequence identification numbers (SEQ ID NOs) of the polypeptide and nucleotide sequences, respectively. Column 3 shows the clone IDs of the Incyte clones in which nucleic acids encoding each NEUAP were identified, and column 4 shows the cDNA libraries from which these clones were isolated. Column 5 shows Incyte clones and their corresponding cDNA libraries. Clones for which cDNA libraries are not indicated were derived from pooled cDNA libraries.
• column 5 The Incyte clones in column 5 were used to assemble the consensus nucleotide sequence of each NEUAP and are useful as fragments in hybridization technologies.
• the columns of Table 2 show various properties of each of the polypeptides of the invention: column 1 references the SEQ ID NO: column 2 shows the number of amino acid residues in each polypeptide; column 3 shows potential phosphorylation sites; column 4 shows potential glycosylation sites; column 5 shows the amino acid residues comprising signature sequences and motifs; column 6 shows the identity of each polypeptide; and column 7 shows analytical methods and in some cases, searchable databases to which the analytical methods were applied. The methods of column 7 were used to characterize each polypeptide through sequence homology and protein motifs.
• NEUAP- 1 has chemical and structural similarity with a human neuronal thread protein.
• AD7c-NTP (Gl 3002527; SEQ ID NO:55).
• NEUAP- 1 and AD7c-NTP share 24% identity, including a region of NEUAP- 1 between residues S89 and Y127 in which the two proteins share 79% identity as well as two potential phosphorylation sites at SI 17 and S123.
• NEUAP-2 has an SCP-like extracellular protein signature, common to plant PR-1 proteins, between approximately residues S4 and G173.
• the conserved His-Glu-His triad of PR family proteins is found in NEUAP-2 at residues H78, El 09, and HI 28.
• NEUAP-2 has chemical and structural similarity with a human glioma pathogenesis-related protein, GliPR (Gl 847722; SEQ ID NO:56).
• the two proteins share 27% identity, the His-Glu-His triad, and ten of the twelve cysteine residues found in NEUAP-2, including C 163, known to be involved in disulfide bond formation in PR-1 proteins.
• the columns of Table 3 show the tissue-specificity and diseases, disorders, or conditions associated with nucleotide sequences encoding NEUAP.
• the first column of Table 3 lists the nucleotide SEQ ID NOs.
• Column 2 lists fragments of the nucleotide sequences of column 1. These fragments are useful, for example, in hybridization or amplification technologies to identify SEQ ID NO:28-54 and to distinguish between SEQ ID NO:28-54 and related polynucleotide sequences.
• polypeptides encoded by these fragments are useful, for example, as immunogenic peptides.
• Column 3 lists tissue categories which express NEUAP as a fraction of total tissues expressing NEUAP.
• Column 4 lists diseases, disorders, or conditions associated with those tissues expressing NEUAP as a fraction of total tissues expressing NEUAP.
• NDAP-2 in five neuronal tissues.
• Northern analysis shows the expression of NEUAP- 1 in four tissues, three of which are cancerous, including a neuronal teratocarcinoma.
• tissue-specific expression of SEQ ID NO:31 and SEQ ID NO:32 are highly expressed and SEQ ID NO:32 is exclusively expressed in nervous tissue.
• SEQ ID NO:42 SEQ ID NO:46. SEQ ID NO:47, SEQ ID NO: 48, SEQ ID NO:52, SEQ ID NO:55. SEQ ID NO:56. and especially SEQ ID NO:51 in nervous tissues; and the expression of SEQ ID NO:42, SEQ ID NO:46, SEQ ID NO:48, and SEQ ID NO:51 in tissues associated with neurological disorders.
• Column 5 lists the vectors used to subclone each cDNA library.
• the columns of Table 4 show descriptions of the tissues used to construct the cDNA libraries from which cDNA clones encoding NEUAP were isolated.
• Column 1 references the nucleotide SEQ ID NOs
• column 2 shows the cDNA libraries from which these clones were isolated
• column 3 shows the tissue origins and other descriptive information relevant to the cDNA libraries in column 2.
• the invention also encompasses NEUAP variants.
• a preferred NEUAP variant is one which has at least about 80%, or alternatively at least about 90%, or even at least about 95% amino acid sequence identity to the NEUAP amino acid sequence, and which contains at least one functional or structural characteristic of NEUAP.
• the invention also encompasses polynucleotides which encode NEUAP.
• the invention encompasses a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO:28-54. which encodes NEUAP.
• the invention also encompasses a variant of a polynucleotide sequence encoding NEUAP.
• a variant polynucleotide sequence will have at least about 80%, or alternatively at least about 90%, or even at least about 95% polynucleotide sequence identity to the polynucleotide sequence encoding NEUAP.
• a particular aspect of the invention encompasses a variant of a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO:28-54 which has at least about 80%, or alternatively at least about 90%, or even at least about 95% polynucleotide sequence identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO:28-54. Any one of the polynucleotide variants described above can encode an amino acid sequence which contains at least one functional or structural characteristic of NEUAP.
• nucleotide sequences which encode NEUAP and its variants are generally capable of hybridizing to the nucleotide sequence of the naturally occurring NEUAP under appropriately selected conditions of stringency, it may be advantageous to produce nucleotide sequences encoding NEUAP or its derivatives possessing a substantially different codon usage, e.g., inclusion of non- naturally occurring codons. Codons may be selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic host in accordance with the frequency with which particular codons are utilized by the host.
• RNA transcripts having more desirable properties such as a greater half-life, than transcripts produced from the naturally occurring sequence.
• the invention also encompasses production of DNA sequences which encode NEUAP and NEUAP derivatives, or fragments thereof, entirely by synthetic chemistry.
• the synthetic sequence may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art.
• synthetic chemistry may be used to introduce mutations into a sequence encoding NEUAP or any fragment thereof.
• polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, and, in particular, to those shown in SEQ ID NO:28-54 and fragments thereof under various conditions of stringency.
• Hybridization conditions including annealing and wash conditions, are described in "Definitions.”
• DNA sequencing are well known in the art and may be used to practice any of the embodiments of the invention.
• the methods may employ such enzymes as the Klenow fragment of DNA polymerase I, SEQUENASE (US Biochemical, Cleveland OH), Taq polymerase (Perkin- Elmer), thermostable T7 polymerase (Amersham Pharmacia Biotech, Piscataway NJ). or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies, Gaithersburg MD).
• sequence preparation is automated with machines such as the MICRO LAB 2200 liquid transfer system (Hamilton.
• the nucleic acid sequences encoding NEUAP may be extended utilizing a partial nucleotide sequence and employing various PCR-based methods known in the art to detect upstream sequences, such as promoters and regulatory elements.
• restriction-site PCR uses universal and nested primers to amplify unknown sequence from genomic DNA within a cloning vector.
• inverse PCR uses primers that extend in divergent directions to amplify unknown sequence from a circularized template.
• the template is derived from restriction fragments comprising a known genomic locus and surrounding sequences.
• a third method, capture PCR involves PCR amplification of DNA fragments adjacent to known sequences in human and yeast artificial chromosome DNA.
• capture PCR involves PCR amplification of DNA fragments adjacent to known sequences in human and yeast artificial chromosome DNA.
• multiple restriction enzyme digestions and ligations may be used to insert an engineered double-stranded sequence into a region of unknown sequence before performing PCR.
• Other methods which may be used to retrieve unknown sequences are known in the art. (See, e.g., Parker, J.D. et al. (1991) Nucleic Acids Res. 19:3055-3060).
• primers may be designed using commercially available software, such as OLIGO 4.06 Primer Analysis software (National Biosciences, Plymouth MN) or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the template at temperatures of about 68°C to 72°C.
• Genomic libraries may be useful for extension of sequence into 5' non-transcribed regulatory regions.
• Capillary electrophoresis systems which are commercially available may be used to analyze the size or confirm the nucleotide sequence of sequencing or PCR products.
• capillary sequencing may employ flowable polymers for electrophoretic separation, four different nucleotide- specific, laser-stimulated fluorescent dyes, and a charge coupled device camera for detection of the emitted wavelengths.
• Output/light intensity may be converted to electrical signal using appropriate software (e.g., GENOTYPER and SEQUENCE NAVIGATOR, Perkin-Elmer). and the entire process from loading of samples to computer analysis and electronic data display may be computer controlled.
• Capillary electrophoresis is especially preferable for sequencing small DNA fragments which may be present in limited amounts in a particular sample.
• polynucleotide sequences or fragments thereof which encode NEUAP may be cloned in recombinant DNA molecules that direct expression of NEUAP, or fragments or functional equivalents thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be produced and used to express NEUAP.
• nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter NEUAP-encoding sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product.
• DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences.
• oligonucleotide- mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.
• sequences encoding NEUAP may be synthesized, in whole or in part, using chemical methods well known in the art.
• chemical methods See, e.g., Caruthers, M.H. et al. (1980) Nucleic Acids Symp. Ser. 7:215-223; and Horn, T. et al. (1980) Nucleic Acids Symp. Ser. 7:225-232.
• NEUAP itself or a fragment thereof may be synthesized using chemical methods.
• peptide synthesis can be performed using various solid-phase techniques. (See, e.g., Roberge, J.Y. et al.
• Automated synthesis may be achieved using the ABI 431 A peptide synthesizer (Perkin-Elmer). Additionally, the amino acid sequence of NEUAP, or any part thereof, may be altered during direct synthesis and/or combined with sequences from other proteins, or any part thereof, to produce a variant polypeptide.
• the peptide may be substantially purified by preparative high performance liquid chromatography. (See, e.g., Chiez, R.M. and F.Z. Regnier (1990) Methods Enzymol. 182:392-421.) The composition of the synthetic peptides may be confirmed by amino acid analysis or by sequencing. (See. e.g., Creighton. T. (1984) Proteins. Structures and Molecular Properties, WH Freeman, New York NY.) In order to express a biologically active NEUAP, the nucleotide sequences encoding NEUAP or derivatives thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
• an appropriate expression vector i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
• These elements include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5' and 3' untranslated regions in the vector and in polynucleotide sequences encoding NEUAP. Such elements may vary in their strength and specificity. Specific initiation signals may also be used to achieve more efficient translation of sequences encoding NEUAP. Such signals include the ATG initiation codon and adjacent sequences, e.g. the Kozak sequence. In cases where sequences encoding NEUAP and its initiation codon and upstream regulatory sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed.
• exogenous translational control signals including an in- frame ATG initiation codon should be provided by the vector.
• Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers appropriate for the particular host cell system used. (See, e.g., Scharf, D. et al. (1994) Results Probl. Cell Differ. 20: 125-162.)
• a variety of expression vector/host systems may be utilized to contain and express sequences encoding NEUAP. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems.
• the invention is not limited by the host cell employed.
• cloning and expression vectors may be selected depending upon the use intended for polynucleotide sequences encoding NEUAP.
• routine cloning, subcloning, and propagation of polynucleotide sequences encoding NEUAP can be achieved using a multifunctional E. coli vector such as PBLUESCRIPT (Stratagene, La Jolla CA) or PSPORT1 plasmid (Life Technologies). Ligation of sequences encoding NEUAP into the vector ' s multiple cloning site disrupts the lacZ gene, allowing a colorimetric screening procedure for identification of transformed bacteria containing recombinant molecules.
• these vectors may be useful for in vitro transcription, dideoxy sequencing, single strand rescue with helper phage, and creation of nested deletions in the cloned sequence.
• vectors which direct high level expression of NEUAP may be used.
• vectors containing the strong, inducible T5 or T7 bacteriophage promoter may be used.
• Yeast expression systems may be used for production of NEUAP.
• a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase. and PGH promoters, may be used in the yeast Saccharomyces cerevisiae or Pichia pastoris.
• such vectors direct either the secretion or intracellular retention of expressed proteins and enable integration of foreign sequences into the host genome for stable propagation.
• Plant systems may also be used for expression of NEUAP. Transcription of sequences encoding NEUAP may be driven viral promoters, e.g., the 35S and 19S promoters of CaMV used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 3:17-31 1 ). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used. (See, e.g., Coruzzi, G. et al. (1984) EMBO J. 3: 1671-1680; Brogue, R. et al.
• a number of viral-based expression systems may be utilized.
• sequences encoding NEUAP may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential El or E3 region of the viral genome may be used to obtain infective virus which expresses NEUAP in host cells.
• transcription enhancers such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.
• SV40 or EBV- based vectors may also be used for high-level protein expression.
• HACs Human artificial chromosomes
• HACs may also be employed to deliver larger fragments of DNA than can be contained in and expressed from a plasmid.
• HACs of about 6 kb to 10 Mb are constructed and delivered via conventional delivery methods (liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes. (See, e.g., Harrington, J.J. et al. ( 1997) Nat. Genet. 15:345-355.)
• sequences encoding NEUAP can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for about 1 to 2 days in enriched media before being switched to selective media.
• the purpose of the selectable marker is to confer resistance to a selective agent, and its presence allows growth and recovery of cells which successfully express the introduced sequences.
• Resistant clones of stably transformed cells may be propagated using tissue culture techniques appropriate to the cell type.
• Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the he ⁇ es simplex virus thymidine kinase and adenine phosphoribosyltransferase genes, for use in tk and apr cells, respectively. (See, e.g., Wigler, M. et al. (1977) Cell 1 1 :223-232; Lowy, I. et al. (1980) Cell 22:817-823.) Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection.
• dhfr confers resistance to methotrexate
• neo confers resistance to the aminoglycosides neomycin and G-418
• als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively.
• Additional selectable genes have been described, e.g., trpB and hisD, which alter cellular requirements for metabolites.
• Visible markers e.g., anthocyanins, green fluorescent proteins (GFP; Clontech), ⁇ glucuronidase and its substrate ⁇ -glucuronide, or luciferase and its substrate luciferin may be used. These markers can be used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system. (See, e.g., Rhodes, CA. (1995) Methods Mol. Biol. 55: 121-131.)
• marker gene expression suggests that the gene of interest is also present, the presence and expression of the gene may need to be confirmed.
• sequence encoding NEUAP is inserted within a marker gene sequence
• transformed cells containing sequences encoding NEUAP can be identified by the absence of marker gene function.
• a marker gene can be placed in tandem with a sequence encoding NEUAP under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.
• host cells that contain the nucleic acid sequence encoding NEUAP and that express NEUAP may be identified by a variety of procedures known to those of skill in the art.
• DNA-DNA or DNA-RNA hybridizations include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences.
• Immunological methods for detecting and measuring the expression of NEUAP using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell sorting (FACS).
• ELISAs enzyme-linked immunosorbent assays
• RIAs radioimmunoassays
• FACS fluorescence activated cell sorting
• a two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on NEUAP is preferred, but a competitive binding assay may be employed.
• These and other assays are well known in the art. (See, e.g., Hampton. R. et al. (1990) Serological Methods, a Laboratory Manual. APS Press, St. Paul MN, Sect. IV; Coligan, J.E. et al. (1997) Current Protocols in Immunology. Greene Pub. Associates and Wiley-Interscience, New York NY; and Pound. J.D. (1998) Immunochemical Protocols.
• NEUAP nucleic acid and amino acid assays.
• Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding NEUAP include oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide.
• the sequences encoding NEUAP, or any fragments thereof may be cloned into a vector for the production of an mRNA probe.
• RNA polymerase such as T7, T3, or SP6 and labeled nucleotides.
• T7, T3, or SP6 RNA polymerase
• reporter molecules or labels which may be used for ease of detection include radionuclides. enzymes, fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
• Host cells transformed with nucleotide sequences encoding NEUAP may be cultured under conditions suitable for the expression and recovery of the protein from cell culture.
• the protein produced by a transformed cell may be secreted or retained intracellularly depending on the sequence and/or the vector used.
• expression vectors containing polynucleotides which encode NEUAP may be designed to contain signal sequences which direct secretion of NEUAP through a prokaryotic or eukaryotic cell membrane.
• a host cell strain may be chosen for its ability to modulate expression of the inserted sequences or to process the expressed protein in the desired fashion.
• modifications of the polypeptide include, but are not limited to. acetylation. carboxylation, glycosylation. phosphorylation, lipidation, and acylation.
• Post-translational processing which cleaves a "prepro” or "pro” form of the protein may also be used to specify protein targeting, folding, and/or activity.
• Different host cells which have specific cellular machinery and characteristic mechanisms for post-translational activities (e.g., CHO. HeLa. MDCK, HEK293, and WI38) are available from the American Type Culture Collection (ATCC, Manassas VA) and may be chosen to ensure the correct modification and processing of the foreign protein.
• ATCC American Type Culture Collection
• natural, modified, or recombinant nucleic acid sequences encoding NEUAP may be ligated to a heterologous sequence resulting in translation of a fusion protein in any of the aforementioned host systems.
• a chimeric NEUAP protein containing a heterologous moiety that can be recognized by a commercially available antibody may facilitate the screening of peptide libraries for inhibitors of NEUAP activity.
• Heterologous protein and peptide moieties may also facilitate purification of fusion proteins using commercially available affinity matrices. Such moieties include, but are not limited to, glutathione S-transferase (GST), maltose binding protein (MBP).
• thioredoxin Trx
• CBP calmodulin binding peptide
• 6-His FLAG, c-myc, and hemagglutinin (HA).
• GST, MBP, Trx. CBP, and 6-His enable purification of their cognate fusion proteins on immobilized glutathione, maltose, phenylarsine oxide, calmodulin. and metal- chelate resins, respectively.
• FLAG, c-myc, and hemagglutinin (HA) enable immunoaffinity purification of fusion proteins using commercially available monoclonal and polyclonal antibodies that specifically recognize these epitope tags.
• a fusion protein may also be engineered to contain a proteolytic cleavage site located between the NEUAP encoding sequence and the heterologous protein sequence, so that NEUAP may be cleaved away from the heterologous moiety following purification.
• Methods for fusion protein expression and purification are discussed in Ausubel (1995. supra, ch. 10).
• a variety of commercially available kits may also be used to facilitate expression and purification of fusion proteins.
• synthesis of radiolabeled NEUAP may be achieved in vitro using the TNT rabbit reticulocyte lysate or wheat germ extract system (Promega). These systems couple transcription and translation of protein-coding sequences operably associated with the T7, T3, or SP6 promoters. Translation takes place in the presence of a radiolabeled amino acid precursor, for example, 35 S-methionine.
• NEUAP fragments of NEUAP may be produced not only by recombinant means, but also by direct peptide synthesis using solid-phase techniques. (See, e.g., Creighton. supra, pp. 55-60.) Protein synthesis may be performed by manual techniques or by automation. Automated synthesis may be achieved, for example, using the ABI 431 A peptide synthesizer (Perkin-Elmer). Various fragments of NEUAP may be synthesized separately and then combined to produce the full length molecule. THERAPEUTICS
• NEUAP Chemical and structural similarity, e.g., in the context of sequences and motifs, exists between regions of NEUAP and neuron-associated proteins.
• the expression of NEUAP is closely associated with nervous tissue, neurological disorders, cell proliferation including cancer, inflammation, and the immune response. Therefore, NEUAP appears to play a role in cell proliferative disorders including cancer; neuronal and neurological disorders; and autoimmune/inflammation disorders.
• NEUAP In the treatment of disorders associated with decreased NEUAP expression or activity, it is desirable to increase the expression or activity of NEUAP.
• NEUAP or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of NEUAP.
• disorders include, but are not limited to, a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms. Alzheimer ' s disease, Pick's disease, Huntington's disease, dementia.
• Parkinson ' s disease and other extrapyramidal disorders amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis.
• viral central nervous system disease prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann- Straussler-Scheinker syndrome; fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorders of the central nervous system, cerebral palsy, neuroskeletal disorders, autonomic nervous system disorders, cranial nerve disorders, spinal cord diseases, muscular dystrophy and other neuromuscular disorders, peripheral nervous system disorders, dermatomyositis and polymyositis; inherited, metabolic, endocrine, and toxic myopathies; myasthenia gravis, periodic paralysis; mental disorders including mood, anxiety, and schizophrenic disorders; seasonal affective disorder (SAD); akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias.
• SAD
• a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria.
• MCTD mixed connective tissue disease
• polycythemia vera psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; and an autoimmune/inflammatory disorder such as acquired immunodeficiency syndrome (AIDS), Addison ' s disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyenodocrin
• Sj ⁇ gren's syndrome systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic pu ⁇ ura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extraco ⁇ oreal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma.
• a vector capable of expressing NEUAP or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of NEUAP including, but not limited to, those described above.
• a pharmaceutical composition comprising a substantially purified NEUAP in conjunction with a suitable pharmaceutical carrier may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of NEUAP including, but not limited to, those provided above.
• an agonist which modulates the activity of NEUAP may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of NEUAP including, but not limited to, those listed above.
• an antagonist of NEUAP may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of NEUAP.
• disorders include, but are not limited to. those cell proliferative disorders including cancer; neuronal and neurological disorders; and autoimmune/inflammation disorders described above.
• an antibody which specifically binds NEUAP may be used directly as an antagonist or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissues which express NEUAP.
• a vector expressing the complement of the polynucleotide encoding NEUAP may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of NEUAP including, but not limited to, those described above.
• any of the proteins, antagonists, antibodies, agonists, complementary sequences, or vectors of the invention may be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles.
• the combination of therapeutic agents may act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.
• NEUAP An antagonist of NEUAP may be produced using methods which are generally known in the art.
• purified NEUAP may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind NEUAP.
• Antibodies to NEUAP may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are generally preferred for therapeutic use.
• various hosts including goats, rabbits, rats, mice, humans, and others may be immunized by injection with NEUAP or with any fragment or oligopeptide thereof which has immunogenic properties.
• various adjuvants may be used to increase immunological response.
• adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols. polyanions. peptides. oil emulsions, KLH, and dinitrophenol.
• BCG Bacilli Calmette-Guerin
• Corvnebacterium parvum are especially preferable. It is preferred that the oligopeptides, peptides, or fragments used to induce antibodies to
• NEUAP have an amino acid sequence consisting of at least about 5 amino acids, and generally will consist of at least about 10 amino acids. It is also preferable that these oligopeptides, peptides, or fragments are identical to a portion of the amino acid sequence of the natural protein and contain the entire amino acid sequence of a small, naturally occurring molecule. Short stretches of NEUAP amino acids may be fused with those of another protein, such as KLH. and antibodies to the chimeric molecule may be produced.
• Monoclonal antibodies to NEUAP may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to. the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique. (See, e.g., Kohler, G. et al. ( 1975) Nature 256:495-497; Kozbor. D. et al. ( 1985) J.
• Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature. (See, e.g., Orlandi, R. et al. ( 1989) Proc. Natl. Acad. Sci. USA
• Antibody fragments which contain specific binding sites for NEUAP may also be generated.
• fragments include, but are not limited to. F(ab') 2 fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F(ab')2 fragments.
• Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity. (See, e.g., Huse, W.D. et al. ( 1989) Science 246: 1275- 1281.)
• immunoassays may be used for screening to identify antibodies having the desired specificity.
• Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art.
• Such immunoassays typically involve the measurement of complex formation between NEUAP and its specific antibody.
• a two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering NEUAP epitopes is generally used, but a competitive binding assay may also be employed (Pound, supra).
• Various methods such as Scatchard analysis in conjunction with radioimmunoassay techniques may be used to assess the affinity of antibodies for NEUAP.
• K a is defined as the molar concentration of NEUAP-antibody complex divided by the molar concentrations of free antigen and free antibody under equilibrium conditions.
• the K a determined for a preparation of monoclonal antibodies, which are monospecific for a particular NEUAP epitope, represents a true measure of affinity.
• High-affinity antibody preparations with K a ranging from about 10 9 to 10 12 L/mole are preferred for use in immunoassays in which the NEUAP-antibody complex must withstand rigorous manipulations.
• Low-affinity antibody preparations with K a ranging from about 10 6 to 10 7 L/mole are preferred for use in immunopurification and similar procedures which ultimately require dissociation of NEUAP, preferably in active form, from the antibody (Catty, D. (1988) Antibodies. Volume 1: A Practical Approach. IRL Press, Washington, DC; Liddell. J.E. and Cryer. A. (1991 ) A Practical Guide to Monoclonal Antibodies, John Wiley & Sons, New York NY).
• polyclonal antibody preparations may be further evaluated to determine the quality and suitability of such preparations for certain downstream applications.
• a polyclonal antibody preparation containing at least 1 -2 mg specific antibody/ml, preferably 5-10 mg specific antibody/ml is generally employed in procedures requiring precipitation of NEUAP- antibody complexes.
• Procedures for evaluating antibody specificity, titer, and avidity, and guidelines for antibody quality and usage in various applications, are generally available. (See, e.g., Catty, supra, and Coligan et al. supra.)
• the polynucleotides encoding NEUAP. or any fragment or complement thereof may be used for therapeutic pu ⁇ oses.
• the complement of the polynucleotide encoding NEUAP may be used in situations in which it would be desirable to block the transcription of the mRNA.
• cells may be transformed with sequences complementary to polynucleotides encoding NEUAP.
• complementary molecules or fragments may be used to modulate NEUAP activity, or to achieve regulation of gene function.
• sense or antisense oligonucleotides or larger fragments can be designed from various locations along the coding or control regions of sequences encoding NEUAP.
• Expression vectors derived from retroviruses, adenoviruses, or he ⁇ es or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. Methods which are well known to those skilled in the art can be used to construct vectors to express nucleic acid sequences complementary to the polynucleotides encoding NEUAP. (See. e.g., Sambrook. supra: Ausubel, 1995, supra.)
• Genes encoding NEUAP can be turned off by transforming a cell or tissue with expression vectors which express high levels of a polynucleotide, or fragment thereof, encoding NEUAP. Such constructs may be used to introduce untranslatable sense or antisense sequences into a cell. Even in the absence of integration into the DNA. such vectors may continue to transcribe RNA molecules until they are disabled by endogenous nucleases. Transient expression may last for a month or more with a non-replicating vector, and may last even longer if appropriate replication elements are part of the vector system.
• modifications of gene expression can be obtained by designing complementary sequences or antisense molecules (DNA, RNA, or PNA) to the control, 5', or regulatory regions of the gene encoding NEUAP.
• Oligonucleotides derived from the transcription initiation site e.g., between about positions -10 and +10 from the start site, may be employed.
• inhibition can be achieved using triple helix base-pairing methodology.
• Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature. (See, e.g., Gee, J.E. et al.
• a complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.
• Ribozymes enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA.
• the mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage.
• engineered hammerhead motif ribozyme molecules may specifically and efficiently catalyze endonucleolytic cleavage of sequences encoding NEUAP.
• RNA sequences of between 15 and 20 ribonucleotides, corresponding to the region of the target gene containing the cleavage site, may be evaluated for secondary structural features which may render the oligonucleotide inoperable.
• the suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.
• RNA molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis.
• RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding NEUAP. Such DNA sequences may be incorporated into a wide variety of vectors with suitable RNA polymerase promoters such as T7 or SP6.
• these cDNA constructs that synthesize complementary RNA, constitutively or inducibly, can be introduced into cell lines, cells, or tissues.
• RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to. the addition of flanking sequences at the 5' and/or 3' ends of the molecule, or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine.
• vectors may be introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient. Delivery by transfection, by liposome injections, or by polycationic amino polymers may be achieved using methods which are well known in the art. (See, e.g., Goldman, C.K. et al. (1997) Nat. Biotechnol. 15:462-466.) Any of the therapeutic methods described above may be applied to any subject in need of such therapy, including, for example, mammals such as humans, dogs, cats, cows, horses, rabbits, and monkeys.
• An additional embodiment of the invention relates to the administration of a pharmaceutical or sterile composition, in conjunction with a pharmaceutically acceptable carrier, for any of the therapeutic effects discussed above.
• Such pharmaceutical compositions may consist of NEUAP, antibodies to NEUAP, and mimetics, agonists, antagonists, or inhibitors of NEUAP.
• the compositions may be administered alone or in combination with at least one other agent, such as a stabilizing compound, which may be administered in any sterile, biocompatible pharmaceutical carrier including, but not limited to, saline, buffered saline, dextrose, and water.
• the compositions may be administered to a patient alone, or in combination with other agents, drugs, or hormones.
• compositions utilized in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial. intramedullary, intrathecal, intraventricular, transdermal. subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.
• these pharmaceutical compositions may contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Further details on techniques for formulation and administration may be found in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing. Easton PA).
• compositions for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.
• Pharmaceutical preparations for oral use can be obtained through combining active compounds with solid excipient and processing the resultant mixture of granules (optionally, after grinding) to obtain tablets or dragee cores. Suitable auxiliaries can be added, if desired.
• Suitable excipients include carbohydrate or protein fillers, such as sugars, including lactose, sucrose, mannitol, and sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose, such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose; gums, including arabic and tragacanth; and proteins, such as gelatin and collagen.
• disintegrating or solubilizing agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, and alginic acid or a salt thereof, such as sodium alginate.
• Dragee cores may be used in conjunction with suitable coatings, such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol. and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
• suitable coatings such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol. and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
• Dyestuffs or pigments may be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e.. dosage.
• compositions which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating, such as glycerol or sorbitol.
• Push-fit capsules can contain active ingredients mixed with fillers or binders, such as lactose or starches, lubricants, such as talc or magnesium stearate, and, optionally, stabilizers.
• the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers.
• Pharmaceutical formulations suitable for parenteral administration may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution.
• Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol. or dextran. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils, such as sesame oil. or synthetic fatty acid esters, such as ethyl oleate, triglycerides, or liposomes. Non-lipid polycationic amino polymers may also be used for delivery. Optionally, the suspension may also contain suitable stabilizers or agents to increase the solubility of the compounds and allow for the preparation of highly concentrated solutions.
• penetrants appropriate to the particular barrier to be permeated are used in the formulation.
• penetrants are generally known in the art.
• compositions of the present invention may be manufactured in a manner that is known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes.
• the pharmaceutical composition may be provided as a salt and can be formed with many acids, including but not limited to, hydrochloric, sulfuric, acetic, lactic, tartaric, malic, and succinic acids. Salts tend to be more soluble in aqueous or other protonic solvents than are the corresponding free base forms.
• the preparation may be a lyophilized powder which may contain any or all of the following: 1 mM to 50 mM histidine, 0.1% to 2% sucrose, and 2% to 7% mannitol, at a pH range of 4.5 to 5.5. that is combined with buffer prior to use.
• compositions After pharmaceutical compositions have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition.
• labeling would include amount, frequency, and method of administration.
• Pharmaceutical compositions suitable for use in the invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended pu ⁇ ose. The determination of an effective dose is well within the capability of those skilled in the art.
• the therapeutically effective dose can be estimated initially either in cell culture assays, e.g., of neoplastic cells, or in animal models such as mice, rats, rabbits, dogs, or pigs. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
• a therapeutically effective dose refers to that amount of active ingredient, for example NEUAP or fragments thereof, antibodies of NEUAP, and agonists, antagonists or inhibitors of NEUAP, which ameliorates the symptoms or condition.
• Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating the ED J0 (the dose therapeutically effective in 50% of the population) or LD 50 (the dose lethal to 50% of the population) statistics.
• the dose ratio of toxic to therapeutic effects is the therapeutic index, which can be expressed as the LD 5O /ED 50 ratio.
• Pharmaceutical compositions which exhibit large therapeutic indices are preferred.
• the data obtained from cell culture assays and animal studies are used to formulate a range of dosage for human use.
• the dosage contained in such compositions is preferably within a range of circulating concentrations that includes the ED 50 with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, the sensitivity of the patient, and the route of administration.
• Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation.
• Normal dosage amounts may vary from about 0.1 ⁇ g to 100.000 ⁇ g, up to a total dose of about 1 gram, depending upon the route of administration.
• Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc. DIAGNOSTICS
• antibodies which specifically bind NEUAP may be used for the diagnosis of disorders characterized by expression of NEUAP, or in assays to monitor patients being treated with NEUAP or agonists, antagonists, or inhibitors of NEUAP.
• Antibodies useful for diagnostic pu ⁇ oses may be prepared in the same manner as described above for therapeutics. Diagnostic assays for NEUAP include methods which utilize the antibody and a label to detect
• NEUAP in human body fluids or in extracts of cells or tissues.
• the antibodies may be used with or without modification, and may be labeled by covalent or non-covalent attachment of a reporter molecule.
• reporter molecules A wide variety of reporter molecules, several of which are described above, are known in the art and may be used.
• protocols for measuring NEUAP including ELISAs. RIAs, and FACS, are known in the art and provide a basis for diagnosing altered or abnormal levels of NEUAP expression.
• Normal or standard values for NEUAP expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, for example, human subjects, with antibody to NEUAP under conditions suitable for complex formation. The amount of standard complex formation may be quantitated by various methods, such as photometric means.
• the polynucleotides encoding NEUAP may be used for diagnostic pu ⁇ oses.
• the polynucleotides which may be used include oligonucleotide sequences, complementary RNA and DNA molecules, and PNAs.
• the polynucleotides may be used to detect and quantify gene expression in biopsied tissues in which expression of NEUAP may be correlated with disease.
• the diagnostic assay may be used to determine absence, presence, and excess expression of NEUAP, and to monitor regulation of NEUAP levels during therapeutic intervention.
• hybridization with PCR probes which are capable of detecting polynucleotide sequences, including genomic sequences, encoding NEUAP or closely related molecules may be used to identify nucleic acid sequences which encode NEUAP.
• the specificity of the probe whether it is made from a highly specific region, e.g.. the 5' regulatory region, or from a less specific region, e.g., a conserved motif, and the stringency of the hybridization or amplification will determine whether the probe identifies only naturally occurring sequences encoding NEUAP, allelic variants, or related sequences.
• Probes may also be used for the detection of related sequences, and may have at least 50% sequence identity to any of the NEUAP encoding sequences.
• the hybridization probes of the subject invention may be DNA or RNA and may be derived from the sequence of SEQ ID NO:28-54 or from genomic sequences including promoters, enhancers, and introns of the NEUAP gene.
• Means for producing specific hybridization probes for DNAs encoding NEUAP include the cloning of polynucleotide sequences encoding NEUAP or NEUAP derivatives into vectors for the production of mRNA probes. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides.
• Hybridization probes may be labeled by a variety of reporter groups, for example, by radionuclides such as 32 P or 35 S, or by enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.
• Polynucleotide sequences encoding NEUAP may be used for the diagnosis of disorders associated with expression of NEUAP.
• disorders include, but are not limited to, a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer ' s disease, Pick's disease.
• MCTD mixed connective tissue disease
• polycythemia vera polycythemia vera
• psoriasis primary thrombocythemia
• cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma.
• AIDS acquired immunodeficiency syndrome
• autoimmune polyenodocrinopathy-candidiasis-ectodermal dystrophy APECED
• bronchitis cholecystitis
• contact dermatitis Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythema nodosum.
• osteoporosis pancreatitis, polymyositis, psoriasis, Reiter ' s syndrome, rheumatoid arthritis, scleroderma, Sj ⁇ gren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic pu ⁇ ura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extraco ⁇ oreal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma.
• the polynucleotide sequences encoding NEUAP may be used in Southern or northern analysis, dot blot, or other membrane-based technologies: in PCR technologies; in dipstick, pin, and multiformat ELISA- like assays; and in microarrays utilizing fluids or tissues from patients to detect altered NEUAP expression. Such qualitative or quantitative methods are well known in the art.
• the nucleotide sequences encoding NEUAP may be useful in assays that detect the presence of associated disorders, particularly those mentioned above.
• the nucleotide sequences encoding NEUAP may be labeled by standard methods and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes.
• the sample is washed and the signal is quantified and compared with a standard value. If the amount of signal in the patient sample is significantly altered in comparison to a control sample then the presence of altered levels of nucleotide sequences encoding NEUAP in the sample indicates the presence of the associated disorder.
• assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or to monitor the treatment of an individual patient. In order to provide a basis for the diagnosis of a disorder associated with expression of
• NEUAP a normal or standard profile for expression is established. This may be accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with a sequence, or a fragment thereof, encoding NEUAP, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained from normal subjects with values from an experiment in which a known amount of a substantially purified polynucleotide is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a disorder. Deviation from standard values is used to establish the presence of a disorder.
• hybridization assays may be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in the normal subject.
• the results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.
• the presence of an abnormal amount of transcript (either under- or overexpressed) in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms.
• a more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the cancer.
• Additional diagnostic uses for oligonucleotides designed from the sequences encoding NEUAP may involve the use of PCR. These oligomers may be chemically synthesized, generated enzymatically, or produced in vitro.
• Oligomers will preferably contain a fragment of a polynucleotide encoding NEUAP, or a fragment of a polynucleotide complementary to the polynucleotide encoding NEUAP, and will be employed under optimized conditions for identification of a specific gene or condition. Oligomers may also be employed under less stringent conditions for detection or quantification of closely related DNA or RNA sequences.
• Methods which may also be used to quantify the expression of NEUAP include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and interpolating results from standard curves.
• radiolabeling or biotinylating nucleotides include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and interpolating results from standard curves.
• the speed of quantitation of multiple samples may be accelerated by running the assay in a high-throughput format where the oligomer of interest is presented in various dilutions and a spectrophotometric or colorimetric response gives rapid quantitation.
• oligonucleotides or longer fragments derived from any of the polynucleotide sequences described herein may be used as targets in a microarray.
• the microarray can be used to monitor the expression level of large numbers of genes simultaneously and to identify genetic variants, mutations, and polymo ⁇ hisms. This information may be used to determine gene function, to understand the genetic basis of a disorder, to diagnose a disorder, and to develop and monitor the activities of therapeutic agents.
• Microarrays may be prepared, used, and analyzed using methods known in the art.
• methods known in the art See, e.g., Brennan, T.M. et al. (1995) U.S. Patent No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93 : 10614- 10619; Baldeschweiler et al. ( 1995) PCT application W095/251 1 16: Shalon. D. et al. (1995) PCT application WO95/35505; Heller, R.A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2150- 2155; and Heller, M.J. et al. (1997) U.S. Patent No. 5,605,662.
• nucleic acid sequences encoding NEUAP may be used to generate hybridization probes useful in mapping the naturally occurring genomic sequence.
• the sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial PI constructions, or single chromosome cDNA libraries.
• HACs human artificial chromosomes
• YACs yeast artificial chromosomes
• BACs bacterial artificial chromosomes
• PI constructions or single chromosome cDNA libraries.
• Fluorescent in situ hybridization may be correlated with other physical chromosome mapping techniques and genetic map data.
• FISH Fluorescent in situ hybridization
• Examples of genetic map data can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site. Correlation between the location of the gene encoding NEUAP on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder.
• the nucleotide sequences of the invention may be used to detect differences in gene sequences among normal, carrier, and affected individuals.
• In situ hybridization of chromosomal preparations and physical mapping techniques may be used for extending genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of a particular human chromosome is not known. New sequences can be assigned to chromosomal arms by physical mapping. This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques.
• any sequences mapping to that area may represent associated or regulatory genes for further investigation.
• the nucleotide sequence of the subject invention may also be used to detect differences in the chromosomal location due to translocation, inversion, etc., among normal, carrier, or affected individuals.
• NEUAP its catalytic or immunogenic fragments, or oligopeptides thereof can be used for screening libraries of compounds in any of a variety of drug screening techniques.
• the fragment employed in such screening may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The formation of binding complexes between NEUAP and the agent being tested may be measured.
• Another technique for drug screening provides for high throughput screening of compounds having suitable binding affinity to the protein of interest.
• This method large numbers of different small test compounds are synthesized on a solid substrate. The test compounds are reacted with NEUAP, or fragments thereof, and washed. Bound NEUAP is then detected by methods well known in the art. Purified NEUAP can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.
• nucleotide sequences which encode NEUAP may be used in any molecular biology techniques that have yet to be developed, provided the new techniques rely on properties of nucleotide sequences that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.
• RNA was purchased from Clontech or isolated from tissues described in Table 4. Some tissues were homogenized and lysed in guanidinium isothiocyanate. while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated from the lysates with either isopropanol or sodium acetate and ethanol, or by other routine methods.
• poly(A+) RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles (QIAGEN, Chatsworth CA), or an OLIGOTEX mRNA purification kit (QIAGEN).
• RNA was provided with RNA and constructed the corresponding cDNA libraries. Otherwise. cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, units 5.1 -6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes.
• cDNA was size-selected (300- 1000 bp) using SEPHACRYL S I 000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis.
• cDNAs were ligated into compatible restriction enzyme sites of the polyl inker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Stratagene), PSPORT1 plasmid (Life Technologies), or pINCY (Incyte Pharmaceuticals. Palo Alto CA).
• Recombinant plasmids were transformed into competent E. coli cells including XLl -Blue, XLl-BlueMRF, or SOLR from Stratagene or DH5 ⁇ , DH10B, or ElectroMAX DH 10B from Life Technologies.
• Plasmids were purified using at least one of the following: a Magic or WIZARD Minipreps DNA purification system (Promega); an AGTC Miniprep purification kit (Edge Biosystems. Gaithersburg MD); and QIAWELL 8 Plasmid, QIAWELL 8 Plus Plasmid, QIAWELL 8 Ultra Plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit from QIAGEN. Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4°C
• plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format (Rao, V.B. (1994) Anal. Biochem. 216: 1- 14). Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Eugene OR) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).
• PICOGREEN dye Molecular Probes, Eugene OR
• FLUOROSKAN II fluorescence scanner Labsystems Oy, Helsinki, Finland.
• cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 (Perkin-Elmer) thermal cycler or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific) or the MICROLAB 2200 (Hamilton) liquid transfer system.
• cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Perkin-Elmer).
• Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (Perkin-Elmer) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel. 1997, supra, unit 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example V.
• Table 5 summarizes the tools, programs, and algorithms used and provides applicable descriptions, references, and threshold parameters.
• the first column of Table 5 shows the tools, programs, and algorithms used, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are inco ⁇ orated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).
• polynucleotide sequences were validated by removing vector, linker, and polyA sequences and by masking ambiguous bases, using algorithms and programs based on BLAST, dynamic programing, and dinucleotide nearest neighbor analysis. The sequences were then queried against a selection of public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases, and BLOCKS, PRINTS, DOMO, PRODOM. and PFAM to acquire annotation using programs based on BLAST, FASTA, and BLIMPS.
• the sequences were assembled into full length polynucleotide sequences using programs based on Phred, Phrap, and Consed, and were screened for open reading frames using programs based on GeneMark.
• BLAST, and FASTA The full length polynucleotide sequences were translated to derive the corresponding full length amino acid sequences, and these full length sequences were subsequently analyzed by querying against databases such as the GenBank databases (described above). SwissProt, BLOCKS, PRINTS, DOMO, PRODOM, Prosite, and Hidden Markov Model (HMM)-based protein family databases such as PFAM.
• HMM is a probabilistic approach which analyzes consensus primary structures of gene families. (See, e.g., Eddy. S.R. ( 1996) Curr. Opin. Struct. Biol. 6:361 -365.)
• Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook. supra, ch. 7; Ausubel, 1995. supra, ch. 4 and 16.)
• % sequence identity x % maximum BLAST score 100 The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. For example, with a product score of 40, the match will be exact within a 1 % to 2% error, and, with a product score of 70, the match will be exact. Similar molecules are usually identified by selecting those which show product scores between 15 and 40, although lower scores may identify related molecules.
• the results of northern analyses are reported as a percentage distribution of libraries in which the transcript encoding NEUAP occurred.
• Analysis involved the categorization of cDNA libraries by organ/tissue and disease.
• the organ/tissue categories included cardiovascular, dermatologic, developmental, endocrine, gastrointestinal, hematopoietic/immune, musculoskeletal, nervous, reproductive, and urologic.
• the disease/condition categories included cancer, inflammation, trauma, cell proliferation, neurological, and pooled. For each category, the number of libraries expressing the sequence of interest was counted and divided by the total number of libraries across all categories. Percentage values of tissue-specific and disease- or condition-specific expression are reported in Table 3. V. Extension of NEUAP Encoding Polynucleotides
• the full length nucleic acid sequences of SEQ ID NO:28-54 were produced by extension of an appropriate fragment of the full length molecule using oligonucleotide primers designed from this fragment.
• One primer was synthesized to initiate 5' extension of the known fragment, and the other primer, to initiate 3' extension of the known fragment.
• the initial primers were designed using OLIGO 4.06 software (National Biosciences), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68 °C to about 72 °C. Any stretch of nucleotides which would result in hai ⁇ in structures and primer-primer dimerizations was avoided.
• Selected human cDNA libraries were used to extend the sequence. If more than one extension was necessary or desired, additional or nested sets of primers were designed.
• the concentration of DNA in each well was determined by dispensing 100 ⁇ l PICOGREEN quantitation reagent (0.25% (v/v) PICOGREEN: Molecular Probes, Eugene OR) dissolved in IX TE and 0.5 ⁇ l of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Costar, Acton MA), allowing the DNA to bind to the reagent.
• the plate was scanned in a Fluoroskan II (Labsystems Oy, Helsinki, Finland) to measure the fluorescence of the sample and to quantify the concentration of DNA.
• a 5 l to 10 l aliquot of the reaction mixture was analyzed by electrophoresis on a 1 % agarose mini-gel to determine which reactions were successful in extending the sequence.
• the extended nucleotides were desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison Wl), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Pharmacia Biotech).
• CviJI cholera virus endonuclease Molecular Biology Research, Madison Wl
• sonicated or sheared prior to religation into pUC 18 vector
• the digested nucleotides were separated on low concentration (0.6 to 0.8%) agarose gels, fragments were excised, and agar digested with Agar ACE (Promega).
• Extended clones were religated using T4 ligase (New England Biolabs, Beverly MA) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells were selected on antibiotic-containing media, individual colonies were picked and cultured overnight at 37°C in 384- well plates in LB/2x carb liquid media.
• Step 1 94°C, 3 min: Step 2: 94°C 15 sec: Step 3 : 60°C, 1 min; Step 4: 72°C, 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72°C. 5 min; Step 7: storage at 4°C DNA was quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries were reamplified using the same conditions as described above.
• nucleotide sequences of SEQ ID NO:28-54 are used to obtain 5' regulatory sequences using the procedure above, oligonucleotides designed for such extension, and an appropriate genomic library.
• Hybridization probes derived from SEQ ID NO:28-54 are employed to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base pairs, is specifically described, essentially the same procedure is used with larger nucleotide fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 software (National Biosciences) and labeled by combining 50 pmol of each oligomer. 250 ⁇ Ci of [ ⁇ - 32 P] adenosine triphosphate (Amersham Pharmacia Biotech), and T4 polynucleotide kinase (DuPont NEN, Boston MA).
• the labeled oligonucleotides are substantially purified using a SEPHADEX G-25 superfine size exclusion dextran bead column (Amersham Pharmacia Biotech). An aliquot containing 10 7 counts per minute of the labeled probe is used in a typical membrane-based hybridization analysis of human genomic DNA digested with one of the following endonucleases: Ase I. Bgl II, Eco RI, Pst I. Xba I, or Pvu II (DuPont NEN).
• the DNA from each digest is fractionated on a 0.7% agarose gel and transferred to nylon membranes (Nytran Plus, Schleicher & Schuell, Durham NH). Hybridization is carried out for 16 hours at 40 °C To remove nonspecific signals, blots are sequentially washed at room temperature under conditions of up to, for example, 0.1 x saline sodium citrate and 0.5% sodium dodecyl sulfate. Hybridization patterns are visualized using autoradiography or an alternative imaging means and compared. VII. Microarrays
• a chemical coupling procedure and an ink jet device can be used to synthesize array elements on the surface of a substrate.
• An array analogous to a dot or slot blot may also be used to arrange and link elements to the surface of a substrate using thermal, UV, chemical, or mechanical bonding procedures.
• a typical array may be produced by hand or using available methods and machines and contain any appropriate number of elements.
• nonhybridized probes are removed and a scanner used to determine the levels and patterns of fluorescence. The degree of complementarity and the relative abundance of each probe which hybridizes to an element on the microarray may be assessed through analysis of the scanned images.
• Full-length cDNAs, Expressed Sequence Tags (ESTs), or fragments thereof may comprise the elements of the microarray. Fragments suitable for hybridization can be selected using software well known in the art such as LASERGENE software (DNASTAR). Full-length cDNAs, ESTs, or fragments thereof corresponding to one of the nucleotide sequences of the present invention, or selected at random from a cDNA library relevant to the present invention, are arranged on an appropriate substrate, e.g., a glass slide. The cDNA is fixed to the slide using, e.g., UV cross-linking followed by thermal and chemical treatments and subsequent drying. (See, e.g., Schena, M. et al.
• Fluorescent probes are prepared and used for hybridization to the elements on the substrate.
• the substrate is analyzed by procedures described above.
• NEUAP-encoding sequences Sequences complementary to the NEUAP-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring NEUAP. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using OLIGO 4.06 software (National Biosciences) and the coding sequence of NEUAP. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5' sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the NEUAP-encoding transcript.
• NEUAP expression and purification of NEUAP is achieved using bacterial or virus-based expression systems.
• cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription.
• promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element.
• Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL21(DE3).
• Antibiotic resistant bacteria express NEUAP upon induction with isopropyl beta-D- thiogalactopyranoside (IPTG).
• NEUAP in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus.
• AcMNPV Autographica californica nuclear polyhedrosis virus
• the nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding NEUAP by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription.
• Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases.
• NEUAP is synthesized as a fusion protein with, e.g., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates.
• GST a 26- kilodalton enzyme from Schistosoma japonicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech). Following purification, the GST moiety can be proteolytically cleaved from NEUAP at specifically engineered sites.
• NEUAP an 8-amino acid peptide
• Mabs to recombinant NEUAP may be prepared by methods well known in the art, and used to detect the expression of NEUAP in tissues by western blot analysis. Western blot analysis is carried out as described by de la Monte et al. (1996) J. Neuropathol. Exp. Neurol. supra. Cytosolic protein extracts of tissues are prepared and electrophoresed in SDS-PAGE Laemmli gels, and immunoblotted using Mabs raised against NEUAP. Antibody binding is detected with horseradish peroxidase-conjugated secondary antibody (IgG), and enhanced chemiluminesence reagents (Amersham Corp, Arlington Heights, IL).
• IgG horseradish peroxidase-conjugated secondary antibody
• IgG enhanced chemiluminesence reagents
• the amount of MAb immunoreactivity measured is proportional to the activity of NEUAP in the tissue preparation.
• NEUAP, or biologically active fragments thereof are labeled with l25 I Bolton-Hunter reagent (see. eg., Bolton et al. ( 1973) Biochem. J. 133:529).
• Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled NEUAP. washed, and any wells with labeled NEUAP complex are assayed. Data obtained using different concentrations of NEUAP are used to calculate values for the number, affinity, and association of NEUAP with the candidate molecules.
• NEUAP function is assessed by expressing the sequences encoding NEUAP at physiologically elevated levels in mammalian cell culture systems.
• cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression.
• Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen, Carlsbad CA), both of which contain the cytomegalovirus promoter.
• 5- 10 ⁇ g of recombinant vector are transiently transfected into a human cell line, for example, an endothelial or hematopoietic cell line, using either liposome formulations or electroporation.
• a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector.
• Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; Clontech), CD64. or a CD64-GFP fusion protein.
• FCM Flow cytometry
• FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod. M.G. ( 1994) Flow Cvtometrv. Oxford, New York NY.
• NEUAP The influence of NEUAP on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding NEUAP and either CD64 or CD64-GFP.
• CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG).
• Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Lake Success NY).
• mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding NEUAP and other genes of interest can be analyzed by northern analysis or microarray techniques.
• NEUAP substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e.g., Harrington. M.G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols.
• PAGE polyacrylamide gel electrophoresis
• NEUAP amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding oligopeptide is synthesized and used to raise antibodies by means known to those of skill in the art.
• LASERGENE software DNASTAR
• Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art. (See, e.g., Ausubel. 1995, supra, ch. 1 1.)
• oligopeptides of about 15 residues in length are synthesized using an ABI 431A peptide synthesizer (Perkin-Elmer) using fmoc-chemistry and coupled to KLH (Sigma-Aldrich. St. Louis MO) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity.
• ABI 431A peptide synthesizer Perkin-Elmer
• KLH Sigma-Aldrich. St. Louis MO
• MBS N-maleimidobenzoyl-N-hydroxysuccinimide ester
• Rabbits are immunized with the oligopeptide- KLH complex in complete Freund's adjuvant.
• Resulting antisera are tested for antipeptide and anti- NEUAP activity by, for example, binding the peptide or NEUAP to a substrate, blocking with 1% BSA, reacting with rabbit antisera. washing, and reacting with radio-iodinated goat anti-rabbit IgG.
• Naturally occurring or recombinant NEUAP is substantially purified by immunoaffmity chromatography using antibodies specific for NEUAP.
• An immunoaffmity column is constructed by covalently coupling anti-NEUAP antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.
• NEUAP Media containing NEUAP are passed over the immunoaffmity column, and the column is washed under conditions that allow the preferential absorbance of NEUAP (e.g., high ionic strength buffers in the presence of detergent).
• the column is eluted under conditions that disrupt antibody/NEUAP binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and NEUAP is collected.
• BRSTNOT24 Library was constructed using RNA isolated from diseased breast tissue removed from a 46-year-old Caucasian female during bilateral subcutaneous mammectomy. Pathology indicated nonproliferative fibrocystic disease bilaterally. Family history included breast cancer, benign hypertension, and atherosclerotic coronary artery disease.
• BRADDIR01 Library was constructed using RNA isolated from diseased choroid plexus tissue of the lateral ventricle, removed from the brain of a 57-year-old Caucasian male, who died from a cerebrovascular accident. Patient history included Huntington's disease and emphysema.
• BRAHNOT01 Library was constructed using RNA isolated from posterior hippocampus tissue removed from a 35-year-old Caucasian male who died from cardiac failure. Pathology indicated moderate leptomeningeal fibrosis and multiple microinfarctions of the cerebral neocortex. Microscopically, the cerebral hemisphere revealed moderate fibrosis of the leptomeninges with focal calcifications. There was evidence of shrunken and slightly eosinophilic pyramidal neurons throughout the cerebral hemispheres. In addition, scattered throughout the cerebral cortex, there were multiple small microscopic areas of cavitation with surrounding gliosis. Patient history included dilated cardiomyopathy, congestive heart failure, cardiomegaly and an enlarged spleen and liver.
• ABI FACTURA A program that removes vector sequences and masks Perkin-Elmer Applied Biosystems, ambiguous bases in nucleic acid sequences. Foster City, CA.
• AB1/PARACEL FDF A Fast Data Finder useful in comparing and annotating Perkin-Elmer Applied Biosystems, Mismatch ⁇ 50% amino acid or nucleic acid sequences. Foster City, CA; Paracel Inc., Pasadena, CA.
• ABI AutoAssembler A program that assembles nucleic acid sequences. Perkin-Elmer Applied Biosystems, Foster City, CA.
• Phred A base-calling algorithm that examines automated Ewing, B. et al. (1998) Genome sequencer traces with high sensitivity and probability. Res. 8: 175-185; Ewing, B. and P. Green (1998) Genome Res. 8: 186- 194.
• Motifs A program that searches amino acid sequences for patterns Bairoch et al. supra; Wisconsin that matched those defined in Prosite. Package Program Manual, version 9, page M51-59, Genetics Computer Group, Madison, Wl.

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