WO2002046420A2 - Proteine liee a la nebuline - Google Patents

Proteine liee a la nebuline Download PDF

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WO2002046420A2
WO2002046420A2 PCT/US2001/050876 US0150876W WO0246420A2 WO 2002046420 A2 WO2002046420 A2 WO 2002046420A2 US 0150876 W US0150876 W US 0150876W WO 0246420 A2 WO0246420 A2 WO 0246420A2
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protein
cdna
seq
molecules
antibodies
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PCT/US2001/050876
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WO2002046420A3 (fr
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Randi E. Krasnow
Y Tom Tang
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Incyte Genomics, Inc.
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Publication of WO2002046420A3 publication Critical patent/WO2002046420A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4716—Muscle proteins, e.g. myosin, actin

Definitions

  • This invention relates to a mammalian cDNA which encodes a nebulin-related protein and to the use of the cDNA and the encoded protein in the diagnosis and treatment of heart and muscle disorders, particularly nemaline myopathy, and as a marker of cardiac ontogeny and development.
  • the sarcomere is the contractile unit of muscle cells. Repeating sarcomeric units span the length of myofibrils in muscle cells and contract in an ATP dependent manner in response to Ca 2+ . Composed of thick and thin protein filaments, the sarcomere has a striated appearance with a dark A-band formed from thick myosin filaments and a light I-band formed from thin actin filaments. The Z-line at the center of the I-band marks the separation between adjacent sarcomeres. Other sarcomeric proteins include tropomyosin, troponin, titin, and nebulin.
  • Nebulin is a large sarcomeric protein that interacts with actin filaments in skeletal muscle (Wang et al- (1996) J Biol Chem 271:4304-4314). Nebulin contains 185 or more copies of a 35- residue module that has a SDXXYK consensus sequence and a predicted oc-helical structure. The 35-residue module comprises an actin-binding domain. In the central region of nebulin, the 35- residue modules exhibit a seven module super-repeat pattern. This super-repeat pattern is not present in the C-terminal 100 kDa region of nebulin. The N-terminal region of nebulin contains 8 linker modules and an 8 kDa acidic domain.
  • the C-terminal region is distinct and contains an SH3 domain.
  • nebulin is oriented with its C-terminus located at the Z-line, and its N-terminus at the pointed slow-growing end of thin filaments in the acto-myosin overlap region.
  • the size of nebulin is tissue- and species-specific and is developmentally regulated. Based on the observation that isoform size correlates with the length of thin filaments in skeletal muscle, nebulin is proposed to play a role as a molecular ruler that regulates the length of thin filaments.
  • Each nebulin 35-residue module may associate with one actin monomer; thus, isoforms with different numbers of modules could determine the length of thin filaments.
  • Tropomodulin caps actin at the pointed end of thin filaments and maintains filament length by preventing actin monomer dissociation or addition.
  • Nebulin is absent from cardiac muscle, but related proteins with nebulin-like modules may provide similar functions. Nebulette, for example, is specifically expressed in heart and has a C-terminal region containing twenty-three 35-residue nebulin-like modules (Moncman and Wang (2000) J Muscle Res Cell Motil 21 : 153-169; Millevoi et al. (1998) J Mol Biol 282: 111- 123). The domain structure of nebulette is similar to nebulin, though it is a smaller protein of only 107 kDa. It has an acidic N-terminal domain, a repeat domain containing nebulin-like modules, a linker domain, and an SH3 domain.
  • the repeat domain of nebulette is about one-tenth the size of that of nebulin.
  • the 35-residue modules of nebulette have the consensus motif SD/EXXYK and a subfamily of modules 15-22 share the conserved motif PELXRXK. Unlike nebulin, nebulette modules do not display a super-repeat pattern. Nebulette binds to actin as well as other sarcomeric proteins including myosin, calmodulin, tropomyosin, troponin, and -actinin (Moncman and Wang (1999) Cell Motil Cytoskeleton 44:1-22). The orientation of nebulette in the sarcomere is analogous to that of nebulin with its C-terminus at the Z-line and its N-terminus in the I-band.
  • N-RAP Nebulin-related anchoring protein
  • cardiac and skeletal muscle (Luo et al- (1997) Cell Motil Cytoskeleton 38:75-90). It is a 133 kDa protein found at the ends of myofibrils at muscle myotendon junctions and intercalated disks.
  • the C-terminal region of N- RAP has 27 copies of the 35-residue nebulin-like modules. Seventeen of the modules are organized in a super-repeat pattern.
  • the N-terminal region contains a cysteine-rich LIM domain. LIM domains bind two zinc ions in two adjacent zinc finger-like structures and are known to mediate protein-protein interactions.
  • N-RAP may mediate interactions between actin filaments of myofibrils and other sarcomeric proteins.
  • N-RAP binds to actin, talin, and vinculin (Luo et al. (1999) Biochemistry 38:6135-6143). It interacts with actin and vinculin through its super-repeat region and with talin through its LIM domain.
  • Talin and vinculin are also located at myotendon junctions and together with N-RAP may provide a link between actin filaments of the myofibril and the sarcolemma and transmit tension from the myofibril to the extracellular matrix.
  • sarcomeric proteins are associated with muscle weakness and disease (Laing (1999) Curr Opin Neurol 12:513-518).
  • Autosomal recessive nemaline myopathy in some cases is caused by nebulin deficiency (Pelin et al. (1999) Proc Natl Acad Sci 96:2305-2310).
  • the disease is characterized by the presence of nemaline bodies in muscle fibers.
  • the nemaline bodies contain proteins normally associated with the Z disc and thin filament. Defects in nebulin apparently perturb interactions among sarcomeric proteins and result in the pathological aggregation of proteins in nemaline bodies.
  • Nemaline myopathy is also caused by mutations in tropomyosin and actin.
  • compositions which are useful in the diagnosis and treatment of heart and muscle disorders, particularly nemaline myopathy, and the monitoring of cardiac ontogeny and development.
  • the invention is based on the discovery of a mammalian cDNA which encodes a mammalian nebulin-related protein (NRP) which is useful in the diagnosis and treatment of heart and muscle disorders, particularly nemaline myopathy, and as a marker of cardiac ontogeny and development.
  • NTP mammalian nebulin-related protein
  • the invention provides an isolated mammalian cDNA or a fragment thereof encoding a mammalian protein or a portion thereof selected from the group consisting of an amino acid sequence of SEQ ID NO: 1, a variant having at least 85% identity to the amino acid sequence of SEQ ID NO: 1, an antigenic epitope of SEQ ID NO: 1, an oligopeptide of SEQ ID NO: 1, and a biologically active portion of SEQ ID NO:l.
  • the invention also provides an isolated mammalian cDNA or the complement thereof selected from the group consisting of a nucleic acid sequence of SEQ ID NO:2, a variant having at least 83% identity to the nucleic acid sequence of SEQ ID
  • the invention additionally provides a composition, a substrate, and a probe comprising the cDNA,or the complement of the cDNA, encoding NRP.
  • the invention further provides a vector containing the cDNA, a host cell containing the vector and a method for using the cDNA to make NRP.
  • the invention still further provides a transgenic cell line or organism comprising the vector containing the cDNA encoding NRP.
  • the invention additionally provides a mammalian fragment or the complement thereof selected from the group consisting of SEQ ID NOs: 18-37.
  • the invention provides a substrate containing at least one of these fragments.
  • the invention provides a probe comprising the fragment which can be used in methods of detection, screening, and purification.
  • the probe is a single stranded complementary RNA or DNA molecule.
  • the invention provides a method for using a cDNA to detect the differential expression of a nucleic acid in a sample comprising hybridizing a probe to the nucleic acids, thereby forming hybridization complexes and comparing hybridization complex formation with a standard, wherein the comparison indicates the differential expression of the cDNA in the sample.
  • the method of detection further comprises amplifying the nucleic acids of the sample prior to hybridization.
  • the method showing differential expression of the cDNA is used to diagnose heart and muscle disorders, particularly nemaline myopathy, and the monitoring of cardiac development and ontogeny.
  • the cDNA or a fragment or a complement thereof may comprise an element on an array.
  • the invention additionally provides a method for using a cDNA or a fragment or a complement thereof to screen a library or plurality of molecules or compounds to identify at least one ligand which specifically binds the cDNA, the method comprising combining the cDNA with the molecules or compounds under conditions allowing specific binding, and detecting specific binding to the cDNA, thereby identifying a ligand which specifically binds the cDNA.
  • the molecules or compounds are selected from aptamers, DNA molecules, RNA molecules, peptide nucleic acids, artificial chromosome constructions, peptides, transcription factors, repressors, and regulatory molecules.
  • the invention provides a purified mammalian protein or a portion thereof selected from the group consisting of an amino acid sequence of SEQ ID NO: 1, a variant having at least 85% identity to the amino acid sequence of SEQ ID NO: 1, an antigenic epitope of SEQ ID NO: 1, an oligopeptide of SEQ ID NO: 1 , and a biologically active portion of SEQ ID NO: 1.
  • the invention also provides a composition comprising the purified protein or a portion thereof in conjunction with a pharmaceutical carrier.
  • the invention further provides a method of using the NRP to treat a subject with heart and muscle disorders, particularly nemaline myopathy, comprising administering to a patient in need of such treatment the composition containing the purified protein.
  • the invention still further provides a method for using a protein to screen a library or a plurality of molecules or compounds to identify at least one ligand, the method comprising combining the protein with the molecules or compounds under conditions to allow specific binding and detecting specific binding, thereby identifying a ligand which specifically binds the protein.
  • the molecules or compounds are selected from DNA molecules, RNA molecules, peptide nucleic acids, peptides, proteins, mimetics, agonists, antagonists, antibodies, immunoglobulins, inhibitors, and drugs.
  • the ligand is used to treat a subject with heart and muscle disorders, particularly nemaline myopathy, and to monitor cardiac development and ontogeny.
  • the invention provides a method of using a mammalian protein to screen a subject sample for antibodies which specifically bind the protein comprising isolating antibodies from the subject sample, contacting the isolated antibodies with the protein under conditions that allow specific binding, dissociating the antibody from the bound-protein, and comparing the quantity of antibody with known standards, wherein the presence or quantity of antibody is diagnostic of heart and muscle disorders, particularly nemaline myopathy, and cardiac development.
  • the invention also provides a method of using a mammalian protein to prepare and purify antibodies comprising immunizing a animal with the protein under conditions to elicit an antibody response, isolating animal antibodies, attaching the protein to a substrate, contacting the substrate with isolated antibodies under conditions to allow specific binding to the protein, dissociating the antibodies from the protein, thereby obtaining purified antibodies.
  • the invention provides a purified antibody which binds specifically to a protein which is expressed in heart and muscle disorders, particularly nemaline myopathy, and during cardiac development.
  • the invention also provides a method of using an antibody to diagnose heart and muscle disorders, particularly nemaline myopathy, and for monitoring cardiac development and ontogeny comprising combining the antibody comparing the quantity of bound antibody to known standards, thereby establishing the presence of heart and muscle disorders, particularly nemaline myopathy, and cardiac development.
  • the invention further provides a method of using an antibody to treat heart and muscle disorders, particularly nemaline myopathy comprising administering to a patient in need of such treatment a pharmaceutical composition comprising the purified antibody.
  • the invention provides a method for inserting a marker gene into the genomic DNA of a mammal to disrupt the expression of the endogenous polynucleotide.
  • the invention also provides a method for using a cDNA to produce a mammalian model system, the method comprising constructing a vector containing the cDNA selected from SEQ ID NOs:2-37, transforming the vector into an embryonic stem cell, selecting a transformed embryonic stem, microinjecting the a, transformed embryonic stem cell into a mammalian blastocyst, thereby forming a chimeric blastocyst, transferring the chimeric blastocyst into a pseudopregnant dam, wherein the dam gives birth to a chimeric offspring containing the cDNA in its germ line, and breeding the chimeric mammal to produce a homozygous, mammalian model system.
  • FIGURES AND TABLE Figures 1A, IB, 1C, ID, IE, IF, 1G, IH, II, 1J, IK, IL, IM, IN, 10, IP, 1Q, 1R, IS and IT show the mammalian NRP (SEQ ID NO: 1) encoded by the cDNA (SEQ ID NO:2).
  • the translation was produced using MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco CA).
  • Figures 2A, 2B, 2C, 2D, 2E, 2F, 2G, 2H, 21, 2J, 2K, 2L, 2M, and 2N demonstrate the conserved chemical and structural similarities among the sequences and domains of NRP (6904750, SEQ ID NO:l), mouse N-RAP (g2351568, SEQ ID NO:40), and human nebulin (gl205990, SEQ ID NO:40).
  • the alignment was produced using the MEGALIGN program of LASERGENE software (DNASTAR, Madison WI).
  • Tables 1 and 2 show the northern analysis for NRP produced using the LIFESEQ Gold database (Incyte Genomics, Palo Alto CA).
  • the first column presents the tissue categories; the second column, the number of clones in the tissue category; the third column, the number of libraries in which at least one transcript was found; the fourth column, absolute abundance of the transcript; and the fifth column, percent abundance of the transcript.
  • Table 2 shows expression of NRP in heart and muscle tissues. The first column lists the library name, the second column, the number of clones sequenced for that library; the third column, the description of the tissue; the fourth column, the absolute abundance of the transcript; and the fifth column, the percent abundance of the transcript.
  • Table 3 shows cardiac and skeletal muscle genes that show strong expression association with NRP.
  • the first column lists the p-value for coexpression with NRP; the second column, the Incyte gene ID; the third column, the Hit ID as determined by BLAST analysis (version 1.4 using default parameters; Altschul (1993) J Mol Evol 36: 290-300; Altschul et al. (1990) J Mol Biol 215:403-410) of the cDNA against GenBank (release 117; National Center for Biotechnology Information (NCBI), Bethesda MD); the fourth column, the hit description; and the fifth column, the source of the gene annotation.
  • BLAST analysis version 1.4 using default parameters; Altschul (1993) J Mol Evol 36: 290-300; Altschul et al. (1990) J Mol Biol 215:403-410) of the cDNA against GenBank (release 117; National Center for Biotechnology Information (NCBI), Bethesda MD); the fourth column, the hit description; and the fifth column, the source of the gene annotation.
  • NRP refers to a substantially purified protein obtained from any mammalian species, including bovine, canine, murine, ovine, porcine, rodent, simian, and preferably the human species, and from any source, whether natural, synthetic, semi-synthetic, or recombinant.
  • Array refers to an ordered arrangement of at least two cDNAs on a substrate. At least one of the cDNAs represents a control or standard sequence, and the other, a cDNA of diagnostic interest. The arrangement of from about two to about 40,000 cDNAs on the substrate assures that the size and signal intensity of each labeled hybridization complex formed between a cDNA and a sample nucleic acid is individually distinguishable.
  • the "complement" of a cDNA of the Sequence Listing refers to a nucleic acid molecule which is completely complementary over its full length and which will hybridize to the cDNA or an mRNA under conditions of high stringency.
  • cDNA refers to an isolated polynucleotide, nucleic acid molecule, or any fragment or complement thereof. It may have originated recombinantly or synthetically, be double-stranded or single-stranded, represent coding and/or noncoding sequence, an exon with or without an intron from a genomic DNA molecule.
  • cDNA encoding a protein refers to a nucleic acid sequence that closely aligns with sequences which encode conserved regions, motifs or domains that were identified by employing analyses well known in the art. These analyses include BLAST (Basic Local t al.).
  • Derivative refers to a cDNA or a protein that has been subjected to a chemical modification. Derivatization of a cDNA can involve substitution of a nontraditional base such as queosine or of an analog such as hypoxanthine. These substitutions are well known in the art. Derivatization of a protein involves the replacement of a hydrogen by an acetyl, acyl, alkyl, amino, formyl, or morpholino group. Derivative molecules retain the biological activities of the naturally occurring molecules but may confer advantages such as longer lifespan or enhanced activity. “Differential expression” refers to an increased, upregulated or present, or decreased, downregulated or absent, gene expression as detected by the absence, presence, or at least twofold changes in the amount of transcribed messenger RNA or translated protein in a sample.
  • “Disorder” refers to conditions, diseases or syndromes in which the cDNAs and NRP are differentially expressed such as heart and muscle disorders, particularly nemaline myopathy, cardiomyopathy, myocarditis, Duchenne's muscular dystrophy, Becker's muscular dystrophy, myotonic dystrophy, central core disease, nemaline myopathy, centronuclear myopathy, lipid myopathy, mitochondrial myopathy, infectious myositis, polymyositis, dermatomyositis, inclusion body myositis, thyrotoxic myopathy, and ethanol myopathy, and cardiac and skeletal muscle developmental and ontogenic disorders.
  • heart and muscle disorders particularly nemaline myopathy, cardiomyopathy, myocarditis, Duchenne's muscular dystrophy, Becker's muscular dystrophy, myotonic dystrophy, central core disease, nemaline myopathy, centronuclear myopathy, lipid myopathy, mitochondrial myopathy, infectious myositis,
  • Fragments refers to a chain of consecutive nucleotides from about 200 to about 700 base pairs in length. Fragments may be used in PCR or hybridization technologies to identify related nucleic acid molecules and in binding assays to screen for a ligand. Nucleic acids and their ligands identified in this manner are useful as therapeutics to regulate replication, transcription or translation.
  • a "hybridization complex” is formed between a cDNA and a nucleic acid of a sample when the purines of one molecule hydrogen bond with the pyrimidines of the complementary molecule, e.g., 5 -A-G-T-C-3'base pairs with 3 -T-C-A-G-5'. The degree of complementarity and the use of nucleotide analogs affect the efficiency and stringency of hybridization reactions.
  • Ligand refers to any agent, molecule, or compound which will bind specifically to a complementary site on a cDNA molecule or polynucleotide, or to an epitope or a protein. Such ligands stabilize or modulate the activity of polynucleotides or proteins and may be composed of inorganic or organic substances including nucleic acids, proteins, carbohydrates, fats, and lipids.
  • Oligomer refers a single stranded molecule from about 18 to about 60 nucleotides in length which may be used in hybridization or amplification technologies or in regulation of replication, transcription or translation. Substantially equivalent terms are amplimer, primer, and oligomer.
  • Portion refers to any part of a protein used for any purpose; but especially, to an epitope for the screening of ligands or for the production of antibodies.
  • Post-translational modification of a protein can involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and the like. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cellular location, cell type, pH, enzymatic milieu, and the like.
  • Probe refers to a cDNA that hybridizes to at least one nucleic acid in a sample. Where targets are single stranded, probes are complementary single strands. Probes can be labeled with reporter molecules for use in hybridization reactions including Southern, northern, in situ, dot blot, array, and like technologies or in screening assays.
  • Protein refers to a polypeptide or any portion thereof.
  • a "portion" of a protein refers to that length of amino acid sequence which would retain at least one biological activity, a domain identified by PFAM or PRINTS analysis or an antigenic epitope of the protein identified using Kyte-Doolittle algorithms of the PROTEAN program (DNASTAR, Madison WI).
  • oligopeptide is an amino acid sequence from about five residues to about 15 residues that is used as part of a fusion protein to produce an antibody.
  • sample refers to any molecule or compound that is separated from its natural environment and is from about 60% free to about 90% free from other components with which it is naturally associated.
  • sample is used in its broadest sense as containing nucleic acids, proteins, antibodies, and the like.
  • a sample may comprise a bodily fluid; the soluble fraction of a cell preparation, or an aliquot of media in which cells were grown; a chromosome, an organelle, or membrane isolated or extracted from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; a cell; a tissue; a tissue print; a fingerprint, buccal cells, skin, or hair; and the like.
  • Specific binding refers to a special and precise interaction between two molecules which is dependent upon their structure, particularly their molecular side groups. For example, the intercalation of a regulatory protein into the major groove of a DNA molecule, the hydrogen bonding along the backbone between two single stranded nucleic acids, or the binding between an epitope of a protein and an agonist, antagonist, or antibody.
  • Similarity refers to the quantification (usually percentage) of nucleotide or residue matches between at least two sequences aligned using a standardized algorithm such as Smith-Waterman alignment (Smith and Waterman (1981) J Mol Biol 147:195- 197) or BLAST2 (Altschul et al. (1997) Nucleic Acids Res 25:3389-3402).
  • BLAST2 may be used in a standardized and reproducible way to insert gaps in one of the sequences in order to optimize alignment and to achieve a more meaningful comparison between them.
  • Substrate refers to any rigid or semi-rigid support to which cDNAs or proteins are bound and includes membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, capillaries or other tubing, plates, polymers, and microparticles with a variety of surface forms including wells, trenches, pins, channels and pores.
  • “Variant” refers to molecules that are recognized variations of a cDNA or a protein encoded by the cDNA. Splice variants may be determined by BLAST score, wherein the score is at least 100, and most preferably at least 400. Allelic variants have a high percent identity to the cDNAs and may differ by about three bases per hundred bases. "Single nucleotide polymorphism” (SNP) refers to a change in a single base as a result of a substitution, insertion or deletion. The change may be conservative (purine for purine) or non-conservative (purine to pyrimidine) and may or may not result in a change in an encoded amino acid or its secondary, tertiary, or quaternary structure.
  • SNP single nucleotide polymorphism
  • the invention is based on the discovery of a cDNA which encodes NRP and on the use of the cDNA, or fragments thereof, and protein, or portions thereof, directly or as compositions in the characterization, diagnosis, and treatment of heart and muscle disorders.
  • Nucleic acids encoding the NRP of the present invention were first identified in Incyte Clone 6904750H1 from the thigh muscle tissue cDNA library (MUSLTDR02) using a computer search for amino acid sequence alignments.
  • the full length polynucleotide sequence of the present invention was assembled using a combination of cDNA sequences and predicted coding (exon) sequences derived from genomic DNA.
  • Table 1 shows expression of the transcript across the tissue categories (also shown in Example VII). The transcript is expressed predominantly in the cardiovascular system and the musculoskeletal system. Table 2 shows expression of the transcript in tissues from heart and skeletal muscle. NRP is expressed in adult heart tissue but shows no detectable expression in fetal heart tissue. Therefore, the cDNA is useful in diagnostic assays for heart and muscle disorders, and cardiac development and ontogeny. A fragment thereof the cDNA from about nucleotide 4820 to about nucleotide 4870 is also useful in diagnostic assays.
  • the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO: 1.
  • NRP is 1695 amino acids in length and has one potential amidation site at El 155, six potential N-glycosylation sites at N61, N487, N745, N988, N1231, and N1625; one potential cyclic AMP-dependent protein kmase phosphorylation site at SI 161, twenty-three potential casein kinase ⁇ phosphorylation sites at S20, T78, S152, S189, T206, S455, S578, S613, S694, S699, S730, S753, S821, S937, S1046, S1099, S1112, S1289, S1342, T1423, S1532, S1550, and S1567; twelve potential protein kinase C phosphorylation sites at S679, S747, S922, S937, SI 175, S1240, S1289, S1399, S1418, S1476, T1503, and S9
  • BLOCKS and PRINTS analyses indicate that the regions of NRP from residues K583 to 1602, H604 to K619, H865 to Y883, W897 to Q913, S1021 to Q1040, D1049 to Y1068, K1069 to L1088, H1090 to HI 105, FI 140 to Gl 156, and D1535 to Y1554 are similar to a nebulin signature (PRINTS: p ⁇ 1.8 x 10 "n ).
  • PFAM analysis indicates that the regions of NRP from residues S205 to G237, F311 to G343, S454 to L486, T489 to G521, D529 to G557, T693 to H725, T728 to A760, D768 to G796, W903 to F935, T936 to H968, T971 to D1003, K1007 to G1039, R1045 to A1077, T1179 to H1211, T1214 to A1246, H1323 to A1355, S1294 to F1421, T1422 to L1453, and T1457 to A1489 are similar to nebulin-repeat domains.
  • NRP has chemical and structural similarity with mouse N-RAP (g2351568, SEQ ID NO:39) and human nebulin (gl205990, SEQ ID NO:40).
  • NRP and mouse N-RAP share about 80% identity and NRP and human nebulin share about 36% identity.
  • a useful antigenic epitope extends from T1252 to D1327 of SEQ ID NO: 1; oligopeptides useful for distinguishing NRP from the nearest homolog extend from G277 to G297 and from D 1360 to R1376 of SEQ ID NO:l; and biologically active portions of NRP, the LLVI domain, residue C6 to H57 of SEQ ID NO: 1, and a nebulin-repeat domain, residue K1007 to G1039 of SEQ ID NO: 1.
  • An antibody which specifically binds NRP is useful in an assay to diagnose heart and muscle disorders, particularly nemaline myopathy, and for monitoring cardiac development and ontogeny.
  • Mammalian variants of the cDNA encoding NRP were identified using BLAST2 with default parameters and the ZOOSEQ databases (Incyte Genomics). These preferred variants have from about 83% to about 100% identity as shown in the table below.
  • the first column shows the SEQ ID for the human cDNA (SEQ ID H ); the second column, the SEQ ID for the variant cDNAs (SEQ ID var ); the third column, the clone number for the variant cDNAs (Clone var ); the fourth column, the library name; the fifth column, the alignment of the variant cDNA to the human cDNA; and the sixth column, the percent identity to the human cDNA.
  • cDNAs are particularly useful for producing transgenic cell lines or organisms which model human disorders and upon which potential therapeutic treatments for such disorders may be tested.
  • the cDNA and fragments thereof may be used in hybridization, amplification, and screening technologies to identify and distinguish among SEQ ID NO:2 and related molecules in a sample.
  • the mammalian cDNAs may be used to produce transgenic cell lines or organisms which are model systems for human heart and muscle disorders, particularly nemaline myopathy and upon which the toxicity and efficacy of potential therapeutic treatments may be tested. Toxicology studies, clinical trials, and subject/patient treatment profiles may be performed and monitored using the cDNAs, proteins, antibodies and molecules and compounds identified using the cDNAs and proteins of the present invention. Characterization and Use of the Invention cDNA libraries
  • mRNA was isolated from mammalian cells and tissues using methods which are well known to those skilled in the art and used to prepare the cDNA libraries.
  • the Incyte clones listed above were isolated from mammalian cDNA libraries. Three library preparations representative of the invention are described in the EXAMPLES below.
  • the consensus sequences were chemically and/or electronically assembled from fragments including Incyte clones and extension and/or shotgun sequences using computer programs such as PHRAP (P Green, University of Washington, Seattle WA), and AUTO ASSEMBLER application (Applied Biosystems, Foster City CA). Clones, extension and/or shotgun sequences are electronically assembled into clusters and/or master clusters.
  • Sequencing Methods for sequencing nucleic acids are well known in the art and may be used to practice any of the embodiments of the invention. These methods employ enzymes such as the Klenow fragment of DNA polymerase I, SEQUENASE, Taq DNA polymerase and thermostable T7 DNA polymerase (Amersham Pharmacia Biotech (APB), 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 MICROLAB 2200 system (Hamilton, Reno NV) and the DNA ENGINE thermal cycler (MJ Research, Watertown MA).
  • Machines commonly used for sequencing include the ABI PRISM 3700, 377 or 373 DNA sequencing systems (Applied Biosystems), the MEGABACE 1000 DNA sequencing system (APB), and the like.
  • the sequences may be analyzed using a variety of algorithms well known in the art and described in Ausubel et al. (1997; Short Protocols in Molecular Biology. John Wiley & Sons, New York NY, unit 1.1) and in Meyers (1995; Molecular Biology and Biotechnology. Wiley VCH, New York NY, pp. 856-853).
  • Shotgun sequencing may also be used to complete the sequence of a particular cloned insert of interest. Shotgun strategy involves randomly breaking the original insert into segments of various sizes and cloning these fragments into vectors. The fragments are sequenced and reassembled using overlapping ends until the entire sequence of the original insert is known. Shotgun sequencing methods are well known in the art and use thermostable DNA polymerases, heat-labile DNA polymerases, and primers chosen from representative regions flanking the cDNAs of interest. Incomplete assembled sequences are inspected for identity using various algorithms or programs such as CONSED (Gordon (1998) Genome Res 8: 195-202) which are well known in the art.
  • Contaminating sequences including vector or chimeric sequences or deleted sequences can be removed or restored, respectively, organizing the incomplete assembled sequences into finished sequences.
  • Extension of a Nucleic Acid Sequence The sequences of the invention may be extended using various PCR-based methods known in the art. For example, the XL-PCR kit (Applied Biosystems), nested primers, and commercially available cDNA or genomic DNA libraries may be used to extend the nucleic acid sequence.
  • primers may be designed using commercially available software, such as OLIGO primer analysis software (Molecular Biology Insights, Cascade CO) to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to a target molecule at temperatures from about 55C to about 68C.
  • OLIGO primer analysis software Molecular Biology Insights, Cascade CO
  • a probe may be designed or derived from unique regions such as the 5' regulatory region or from a nonconserved region (i.e., 5' or 3' of the nucleotides encoding the conserved catalytic domain of the protein) and used in protocols to identify naturally occurring molecules encoding the NRP, allelic variants, or related molecules.
  • the probe may be DNA or RNA, may be single stranded and should have at least 50% sequence identity to any of the nucleic acid sequences, SEQ ID NOs:2-37.
  • Hybridization probes may be produced using oligolabeling, nick translation, end-labeling, or PCR amplification in the presence of a reporter molecule.
  • a vector containing the cDNA or a fragment thereof may be used to produce an mRNA probe in vitro by addition of an RNA polymerase and labeled nucleotides. These procedures may be conducted using commercially available kits such as those provided by APB.
  • the stringency of hybridization is determined by G+C content of the probe, salt concentration, and temperature. In particular, stringency can be increased by reducing the concentration of salt or raising the hybridization temperature. In solutions used for some membrane based hybridizations, addition of an organic solvent such as formamide allows the reaction to occur at a lower temperature.
  • Hybridization can be performed at low stringency with buffers, such as 5xSSC with 1% sodium dodecyl sulfate (SDS) at 60C, which permits the formation of a hybridization complex between nucleic acid sequences that contain some mismatches. Subsequent washes are performed at higher stringency with buffers such as 0.2xSSC with 0.1% SDS at either 45C (medium stringency) or 68C (high stringency). At high stringency, hybridization complexes will remain stable only where the nucleic acids are completely complementary.
  • buffers such as 5xSSC with 1% sodium dodecyl sulfate (SDS) at 60C
  • formamide can be added to the hybridization solution to reduce the temperature at which hybridization is performed, and background signals can be reduced by the use of other detergents such as Sarkosyl or TRITON X-100 (Sigma-Aldrich, St. Louis MO) and a blocking agent such as denatured salmon sperm DNA. Selection of components and conditions for hybridization are well known to those skilled in the art and are reviewed in Ausubel (supra) and Sambrook et al. (1989) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Press, Plainview NY.
  • Arrays may be prepared and analyzed using methods known in the art. Oligonucleotides may be used as either probes or targets in an array. The array can be used to monitor the expression level of large numbers of genes simultaneously and to identify genetic variants, mutations, and single nucleotide polymorphisms. Such information may be used to determine gene function; to understand the genetic basis of a condition, disease, or disorder; to diagnose a condition, disease, or disorder; and to develop and monitor the activities of therapeutic agents. (See, e.g., Brennan et al. (1995) USPN 5,474,796; Schena et al. (1996) Proc Natl Acad Sci 93: 10614-10619; Baldeschweiler et al.
  • Hybridization probes are also useful in mapping the naturally occurring genomic sequence.
  • the probes may be hybridized to: 1) a particular chromosome, 2) a specific region of a chromosome, or 3) an artificial chromosome construction such as human artificial chromosome (HAC), yeast artificial chromosome (YAC), bacterial artificial chromosome (BAC), bacterial PI construction, or single chromosome cDNA libraries.
  • HAC human artificial chromosome
  • YAC yeast artificial chromosome
  • BAC bacterial artificial chromosome
  • PI construction single chromosome cDNA libraries.
  • Any one of a multitude of cDNAs encoding NRP may be cloned into a vector and used to express the protein, or portions thereof, in host cells.
  • the nucleic acid sequence can be engineered by such methods as DNA shuffling (USPN 5,830,721) and site-directed mutagenesis to create new restriction sites, alter glycosylation patterns, change codon preference to increase expression in a particular host, produce splice variants, extend half-life, and the like.
  • the expression vector may contain transcriptional and translational control elements (promoters, enhancers, specific initiation signals, and polyadenylated 3' sequence) from various sources which have been selected for their efficiency in a particular host.
  • the vector, cDNA, and regulatory elements are combined using in vitro recombinant DNA techniques, synthetic techniques, and/or in vivo genetic recombination techniques well known in the art and described in Sambrook (supra, ch.4, 8, 16 and 17).
  • a variety of host systems may be transformed with an expression vector. These include, but are not limited to, bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems transformed with baculovirus expression vectors; plant cell systems transformed with expression vectors containing viral and/or bacterial elements, or animal cell systems (Ausubel supra, unit 16).
  • an adenovirus transcription/translation complex may be utilized in mammalian cells. After sequences are ligated into the El or E3 region of the viral genome, the infective virus is used to transform and express the protein in host cells.
  • the Rous sarcoma virus enhancer or SV40 or EBV-based vectors may also be used for high-level protein expression.
  • Routine cloning, subcloning, and propagation of nucleic acid sequences can be achieved using the multifunctional PBLUESCRIPT vector (Stratagene, La Jolla CA) or PSPORT1 plasmid (Life Technologies). Introduction of a nucleic acid sequence into the multiple cloning site of these vectors disrupts the lacZ gene and allows colorimetric screening for transformed bacteria. In addition, 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.
  • the vector can be stably transformed into cell lines along with a selectable or visible marker gene on the same or on a separate vector. After transformation, cells are allowed to grow for about 1 to 2 days in enriched media and then are transferred to selective media. Selectable markers, antimetabolite, antibiotic, or herbicide resistance genes, confer resistance to the relevant selective agent and allow growth and recovery of cells which successfully express the introduced sequences. Resistant clones identified either by survival on selective media or by the expression of visible markers, such as anthocyanins, green fluorescent protein (GFP), ⁇ glucuronidase, luciferase and the like, may be propagated using culture techniques. Visible markers are also used to quantify the amount of protein expressed by the introduced genes.
  • visible markers such as anthocyanins, green fluorescent protein (GFP), ⁇ glucuronidase, luciferase and the like, may be propagated using culture techniques. Visible markers are also used to quantify the amount of protein expressed by the introduced genes.
  • Verification that the host cell contains the desired mammalian cDNA is based on DNA-DNA or DNA-RNA hybridizations or PCR amplification techniques.
  • the host cell may be chosen for its ability to modify a recombinant protein in a desired fashion. Such modifications include acetylation, carboxylation, glycosylation, phosphorylation, lipidation, acylation and the like.
  • Post-translational processing which cleaves a "prepro" form may also be used to specify protein targeting, folding, and/or activity.
  • Different host cells available from the ATCC Manassas VA
  • Different host cells available from the ATCC Manassas VA
  • Heterologous moieties engineered into a vector for ease of purification include glutathione S-transferase (GST), 6xHis, FLAG, MYC, and the like.
  • GST and 6-His are purified using commercially available affinity matrices such as immobilized glutathione and metal-chelate resins, respectively.
  • FLAG and MYC are purified using commercially available monoclonal and polyclonal antibodies.
  • a sequence encoding a proteolytic cleavage site may be part of the vector located between the protein and the heterologous moiety. Methods for recombinant protein expression and purification are discussed in Ausubel (supra, unit 16) and are commercially available. Chemical Synthesis of Peptides
  • Proteins or portions thereof may be produced not only by recombinant methods, but also by using chemical methods well known in the art.
  • Solid phase peptide synthesis may be carried out in a batchwise or continuous flow process which sequentially adds ⁇ -amino- and side chain- protected amino acid residues to an insoluble polymeric support via a linker group.
  • a linker group such as methylamine-derivatized polyethylene glycol is attached to poly(styrene-co- divinylbenzene) to form the support resin.
  • the amino acid residues are N- -protected by acid labile Boc (t-butyloxycarbonyl) or base-labile Fmoc (9-fluorenylmethoxycarbonyl).
  • the carboxyl group of the protected amino acid is coupled to the amine of the linker group to anchor the residue to the solid phase support resin.
  • Trifluoroacetic acid or piperidine are used to remove the protecting group in the case of Boc or Fmoc, respectively.
  • Each additional amino acid is added to the anchored residue using a coupling agent or pre-activated amino acid derivative, and the resin is washed.
  • the full length peptide is synthesized by sequential deprotection, coupling of derivitized amino acids, and washing with dichloromethane and or N, N-dimethylformamide. The peptide is cleaved between the peptide carboxy terminus and the linker group to yield a peptide acid or amide.
  • oligopeptide, peptide, or portion of protein used to induce antibodies should consist of at least about five amino acids, more preferably ten amino acids, which are identical to a portion of the natural protein. Oligopeptides may be fused with proteins such as KLH in order to produce antibodies to the chimeric molecule.
  • Monoclonal antibodies may be prepared using any technique which provides for the production of antibodies 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 et al. (1975) Nature 256:495-497; Kozbor et al. (1985) J. Immunol Methods 81:31-42; Cote et al. (1983) Proc Natl Acad Sci 80:2026-2030; and Cole et al. (1984) Mol Cell Biol 62:109-120.)
  • single chain antibodies may be adapted, using methods known in the art, to produce epitope specific single chain antibodies.
  • Antibody fragments which contain specific binding sites for epitopes of the protein 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 et al. (1989) Science 246: 1275-1281.) The NRP or a portion thereof may be used in screening assays of phagemid or B- lymphocyte immunoglobulin libraries to identify antibodies having the desired specificity.
  • reporter molecules and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid, amino acid, and antibody assays.
  • Synthesis of labeled molecules may be achieved using commercially available kits (Promega,
  • a labeled nucleotide such as 32 P-dCTP (APB), Cy3-dCTP or
  • Cy5-dCTP (Operon Technologies, Alameda CA), or amino acid such as 35 S-methionine (APB).
  • Nucleotides and amino acids may be directly labeled with a variety of substances including fluorescent, chermluminescent, or chromogenic agents, and the like, by chemical conjugation to amines, thiols and other groups present in the molecules using reagents such as BIODIPY or F ⁇ TC
  • the cDNAs, fragments, oligonucleotides, complementary RNA and DNA molecules, and PNAs may be used to detect and quantify differential gene expression, absence/presence vs. excess, expression of mRNAs or to monitor mRNA levels during therapeutic intervention.
  • antibodies which specifically bind NRP may be used to quantitate the protein.
  • Disorders associated with differential expression include heart and muscle disorders, particularly nemaline myopathy.
  • the diagnostic assay may use hybridization or amplification technology to compare gene expression in a biological sample from a patient to standard samples in order to detect differential gene expression. Qualitative or quantitative methods for this comparison are well known in the art.
  • the cDNA or probe may be labeled by standard methods and added to a biological sample from a patient under conditions for the formation of hybridization complexes. After an incubation period, the sample is washed and the amount of label (or signal) associated with hybridization complexes, is quantified and compared with a standard value. If complex formation in the patient sample is significantly altered (higher or lower) in comparison to either a normal or disease standard, then differential expression indicates the presence of a disorder.
  • normal and disease expression profiles are established. This is accomplished by combining a sample taken from normal subjects, either animal or human, with a cDNA under conditions for hybridization to occur. Standard hybridization complexes may be quantified by comparing the values obtained using normal subjects with values from an experiment in which a known amount of a substantially purified sequence is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who were diagnosed with a particular condition, disease, or disorder. Deviation from standard values toward those associated with a particular disorder is used to diagnose that disorder.
  • Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies and in clinical trial or to monitor the treatment of an individual patient. Once the presence of a condition is established and a treatment protocol is initiated, diagnostic 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 a 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.
  • Detection and quantification of a protein 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
  • NRP nebulin-repeat domains
  • mouse N-RAP g2351568, SEQ ID NO:39
  • human nebulin gl205990, SEQ ID NO:40
  • differential expression is associated with heart and muscle tissues as shown in Tables 1 and 2.
  • NRP is expressed in adult heart tissue but shows no detectable expression in fetal heart tissue. Defects in sarcomeric proteins are associated with heart and muscle disorders. In particular, mutations in nebulin cause nemaline myopathy. Since NRP contains nebulin-like domains, mutations in NRP may also cause nemaline myopathy.
  • NRP like other sarcomeric proteins, may be incorporated into nemaline bodies and provide a diagnostic marker of nemaline myopathy.
  • Vectors expressing NRP may be used in gene therapy to transfer NRP to heart and skeletal muscle cells to treat heart and muscle disorders, particularly nemaline myopathy.
  • NRP may also be used as a marker of cardiac ontogeny and development.
  • the an inhibitor, antagonist or antibody of the protein may be administered to a subject to treat a condition associated with increased expression or activity.
  • a pharmaceutical composition comprising an inhibitor, antagonist or antibody in conjunction with a pharmaceutical carrier may be administered to a subject to treat a condition associated with the increased expression or activity of the endogenous protein.
  • a vector expressing the complement of the cDNA or fragments thereof may be administered to a subject to treat the disorder. In the treatment of heart and muscle disorders associated with decreased expression of the protein, it is desirable to increase expression or protein activity.
  • the protein, an agonist or enhancer may be administered to a subject to treat a condition associated with decreased expression or activity.
  • a pharmaceutical composition comprising the protein, an agonist or enhancer in conjunction with a pharmaceutical carrier may be administered to a subject to treat a condition associated with the decreased expression or activity of the endogenous protein.
  • a vector expressing cDNA may be administered to a subject to treat the disorder.
  • any of the cDNAs, complementary molecules, or fragments thereof, proteins or portions thereof, vectors delivering these nucleic acid molecules or expressing the proteins, and their ligands may be administered in combination with other therapeutic agents. Selection of the agents for use in combination therapy may be made by one of ordinary skill in the art according to conventional pharmaceutical principles. A combination of therapeutic agents may act synergistically to affect treatment of a particular disorder at a lower dosage of each agent. Modification of Gene Expression Using Nucleic Acids Gene expression may be modified by designing complementary or antisense molecules (DNA, RNA, or PNA) to the control, 5', 3', or other regulatory regions of the gene encoding NRP. Oligonucleotides designed with reference to the transcription initiation site are preferred.
  • inhibition can be achieved using triple helix base-pairing which inhibits the binding of polymerases, transcription factors, or regulatory molecules (Gee et al. In: Huber and Carr (1994) Molecular and Immunologic Approaches, Futura Publishing, Mt. Kisco NY, pp. 163-177).
  • a complementary molecule may also be designed to block translation by preventing binding between ribosomes and mRNA.
  • a library or plurality of cDNAs or fragments thereof may be screened to identify those which specifically bind a regulatory, nontranslated sequence.
  • 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 at sites such as GUA, GUU, and GUC. Once such sites are identified, an oligonucleotide with the same sequence may be evaluated for secondary structural features which would render the oligonucleotide inoperable.
  • the suitability of candidate targets may also be evaluated by testing their hybridization with complementary oligonucleotides using ribonuclease protection assays.
  • RNA molecules may be modified to increase intracellular stability and half -life by addition of flanking sequences at the 5' and/or 3' ends of the molecule or by the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. Modification is inherent in the production of PNAs and can be extended to other nucleic acid molecules.
  • the cDNA encoding NRP may be used to screen a library of molecules or compounds for specific binding affinity.
  • the libraries may be aptamers, DNA molecules, RNA molecules, PNAs, peptides, proteins such as transcription factors, enhancers, repressors, and other ligands which regulate the activity, replication, transcription, or translation of the cDNA in the biological system.
  • the assay involves combining the cDNA or a fragment thereof with the library of molecules under conditions allowing specific binding, and detecting specific binding to identify at least one molecule which specifically binds the single stranded or, if appropriate, double stranded molecule.
  • the cDNA of the invention may be incubated with a plurality of purified molecules or compounds and binding activity determined by methods well known in the art, e.g., a gel-retardation assay (USPN 6,010,849) or a reticulocyte lysate transcriptional assay.
  • the cDNA may be incubated with nuclear extracts from biopsied and/or cultured cells and tissues. Specific binding between the cDNA and a molecule or compound in the nuclear extract is initially determined by gel shift assay and may be later confirmed by recovering and raising antibodies against that molecule or compound. When these antibodies are added into the assay, they cause a supershift in the gel-retardation assay.
  • the cDNA may be used to purify a molecule or compound using affinity chromatography methods well known in the art.
  • the cDNA is chemically reacted with cyanogen bromide groups on a polymeric resin or gel. Then a sample is passed over and reacts with or binds to the cDNA. The molecule or compound which is bound to the cDNA may be released from the cDNA by increasing the salt concentration of the flow- through medium and collected.
  • the protein or a portion thereof may be used to purify a ligand from a sample.
  • a method for using a mammalian protein or a portion thereof to purify a ligand would involve combining the protein or a portion thereof with a sample under conditions to allow specific binding, detecting specific binding between the protein and ligand, recovering the bound protein, and using an appropriate chaotropic agent to separate the protein from the purified ligand.
  • NRP or a portion thereof may be used to screen a plurality of molecules or compounds in any of a variety of screening assays. The portion of the protein employed in such screening may be free in solution, affixed to an abiotic or biotic substrate (e.g.
  • viable or fixed prokaryotic host cells that are stably transformed with recombinant nucleic acids that have expressed and positioned a peptide on their cell surface can be used in screening assays.
  • the cells are screened against a plurality or libraries of ligands and the specificity of binding or formation of complexes between the expressed protein and the ligand may be measured. Specific binding between the protein and molecule may be measured.
  • the assay may be used to identify DNA molecules, RNA molecules, peptide nucleic acids, peptides, proteins, mimetics, agonists, antagonists, antibodies, immunoglobulins, inhibitors, and drugs or any other ligand, which specifically binds the protein.
  • this invention comtemplates a method for high throughput screening using very small assay volumes and very small amounts of test compound as described in USPN 5,876,946, incorporated herein by reference. This method is used to screen large numbers of molecules and compounds via specific binding.
  • this invention also contemplates the use of competitive drug screening assays in which neutralizing antibodies capable of binding the protein specifically compete with a test compound capable of binding to the protein or oligopeptide or portion thereof.
  • Molecules or compounds identified by screening may be used in a mammalian model system to evaluate their toxicity, diagnostic, or therapeutic potential.
  • Pharmacology Pharmaceutical compositions are those substances wherein the active ingredients are contained in an effective amount to achieve a desired and intended purpose. The determination of an effective dose is well within the capability of those skilled in the art. For any compound, the therapeutically effective dose may be estimated initially either in cell culture assays or in animal models. The animal model is also used to achieve a desirable concentration range and route of administration. Such information may then be used to determine useful doses and routes for administration in humans.
  • a therapeutically effective dose refers to that amount of protein or inhibitor which ameliorates the symptoms or condition.
  • Therapeutic efficacy and toxicity of such agents may be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED 50 (the dose therapeutically effective in 50% of the population) and LD 50 (the dose lethal to 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index, and it may be expressed as the ratio, LD 50 /ED S0 .
  • Pharmaceutical compositions which exhibit large therapeutic indexes are preferred. The data obtained from cell culture assays and animal studies are used in formulating a range of dosage for human use. Model Systems
  • Animal models may be used as bioassays where they exhibit a phenotypic response similar to that of humans and where exposure conditions are relevant to human exposures. Mammals are the most common models, and most infectious agent, cancer, drug, and toxicity studies are performed on rodents such as rats or mice because of low cost, availability, lifespan, reproductive potential, and abundant reference literature. Inbred and outbred rodent strains provide a convenient model for investigation of the physiological consequences of under- or over- expression of genes of interest and for the development of methods for diagnosis and treatment of diseases. A mammal inbred to over-express a particular gene (for example, secreted in milk) may also serve as a convenient source of the protein expressed by that gene. Toxicology
  • Toxicology is the study of the effects of agents on living systems. The majority of toxicity studies are performed on rats or mice. Observation of qualitative and quantitative changes in physiology, behavior, homeostatic processes, and lethality in the rats or mice are used to generate a toxicity profile and to assess potential consequences on human health following exposure to the agent. Genetic toxicology identifies and analyzes the effect of an agent on the rate of endogenous, spontaneous, and induced genetic mutations. Genotoxic agents usually have common chemical or physical properties that facilitate interaction with nucleic acids and are most harmful when chromosomal aberrations are transmitted to progeny.
  • Toxicological studies may identify agents that increase the frequency of structural or functional abnormalities in the tissues of the progeny if administered to either parent before conception, to the mother during pregnancy, or to the developing organism. Mice and rats are most frequently used in these tests because their short reproductive cycle allows the production of the numbers of organisms needed to satisfy statistical requirements.
  • Acute toxicity tests are based on a single administration of an agent to the subject to determine the symptomology or lethality of the agent. Three experiments are conducted: 1) an initial dose-range-finding experiment, 2) an experiment to narrow the range of effective doses, and 3) a final experiment for establishing the dose-response curve.
  • Subchronic toxicity tests are based on the repeated administration of an agent. Rat and dog are commonly used in these studies to provide data from species in different families. With the exception of carcinogenesis, there is considerable evidence that daily administration of an agent at high-dose concentrations for periods of three to four months will reveal most forms of toxicity in adult animals.
  • Transgenic rodents that over-express or under-express a gene of interest may be inbred and used to model human diseases or to test therapeutic or toxic agents.
  • the introduced gene may be activated at a specific time in a specific tissue type during fetal or postnatal development. Expression of the transgene is monitored by analysis of phenotype, of tissue-specific mRNA expression, or of serum and tissue protein levels in transgenic animals before, during, and after challenge with experimental drug therapies.
  • Embryonic (ES) stem cells isolated from rodent embryos retain the potential to form embryonic tissues. When ES cells are placed inside a carrier embryo, they resume normal development and contribute to tissues of the live-born animal. ES cells are the preferred cells used in the creation of experimental knockout and knockin rodent strains.
  • Mouse ES cells such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and are grown under culture conditions well known in the art. Vectors used to produce a transgenic strain contain a disease gene candidate and a marker gen, the latter serves to identify the presence of the introduced disease gene.
  • the vector is transformed into ES cells by methods well known in the art, and transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain.
  • the blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains.
  • ES cells derived from human blastocysts may be manipulated in vitro to differentiate into at least eight separate cell lineages. These lineages are used to study the differentiation of various cell types and tissues in vitro, and they include endoderm, mesoderm, and ectodermal cell types which differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes. Knockout Analysis
  • a region of a mammalian gene is enzymatically modified to include a non-mammalian gene such as the neomycin phosphotransferase gene (neo; Capecchi (1989) Science 244:1288-1292).
  • the modified gene is transformed into cultured ES cells and integrates into the endogenous genome by homologous recombination. The inserted sequence disrupts transcription and translation of the endogenous gene.
  • Transformed cells are injected into rodent blastulae, and the blastulae are implanted into pseudopregnant dams.
  • Transgenic progeny are crossbred to obtain homozygous inbred lines which lack a functional copy of the mammalian gene.
  • the mammalian gene is a human gene. Knockin Analysis
  • ES cells can be used to create knockin humanized animals (pigs) or transgenic animal models (mice or rats) of human diseases.
  • knockin technology a region of a human gene is injected into animal ES cells, and the human sequence integrates into the animal cell genome.
  • Transformed cells are injected into blastulae and the blastulae are implanted as described above.
  • Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on treatment of the analogous human condition. These methods have been used to model several human diseases.
  • NHPs are the first choice test animal.
  • NHPs and individual humans exhibit differential sensitivities to many drugs and toxins and can be classified as a range of phenotypes from "extensive metabolizers" to "poor metabolizers” of these agents.
  • the cDNAs which encode the mammalian protein may be used in any molecular biology techniques that have yet to be developed, provided the new techniques rely on properties of cDNAs that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.
  • the MUSLTDR02 library was constructed using RNA isolated from the right lower thigh muscle tissue removed from a 58-year-old Caucasian male during a wide resection of the right posterior thigh.
  • the frozen tissue was homogenized and lysed in TRIZOL reagent (0.8 g tissue/12 ml; Life Technologies) using a POLYTRON homogenizer (Brinkmann Instruments, Westbury NJ).
  • the lysate was centrifuged over a 5.7 M CsCl cushion using an SW28 rotor in an L8-70M ultracentrifuge (Beckman Coulter, Fullerton CA) for 18 hours at 25,000 rpm at ambient temperature.
  • the mRNA was handled according to the recommended protocols in the SUPERSCRIPT plasmid system (Life Technologies) which contains a Notl primer-adaptor designed to prime the first strand cDNA synthesis at the poly(A) tail of mRNAs. Double stranded cDNA was blunted, ligated to EcoRI adaptors and digested with Notl (New England Biolabs, Beverly MA). The cDNAs were fractionated on a SEPHAROSE CL4B column (APB), and those cDNAs exceeding 400 bp were ligated into pcDNA2.1 plasmid (Invitrogen, Carlsbad CA). The plasmid pcDNA2.1 was subsequently transformed into DH5 ⁇ competent cells (Life Technologies).
  • Plasmid DNA was released from the cells and purified using either the MINIPREP kit (Edge Biosystems, Gaithersburg MD) or the REAL PREP 96 plasmid kit (Qiagen). This kit consists of a 96-well block with reagents for 960 purifications.
  • the recommended protocol was employed except for the following changes: 1) the bacteria were cultured in 1 ml of sterile TERRIFIC BROTH (BD Biosciences, Sparks MD) with carbeniciUin at 25 mg/1 and glycerol at 0.4%; 2) after inoculation, the cells were cultured for 19 hours and then lysed with 0.3 ml of lysis buffer; and 3) following isopropanol precipitation, the plasmid DNA pellet was resuspended in 0.1 ml of distilled water. After the last step in the protocol, samples were transferred to a 96-well block for storage at 4C.
  • the cDNAs were prepared for sequencing using the MICROLAB 2200 system (Hamilton) in combination with the DNA ENGINE thermal cyclers (MJ Research).
  • the cDNAs were sequenced by the method of Sanger and Coulson (1975; J Mol Biol 94:441-448) using an ABI PRISM 377 sequencing system (Applied Biosystems) or the MEGABACE 1000 DNA sequencing system (APB). Most of the isolates were sequenced according to standard ABI protocols and kits (Applied Biosystems) with solution volumes of 0.25x-1.0x concentrations. In the alternative, cDNAs were sequenced using solutions and dyes from APB. Ill Extension of cDNA Sequences
  • the cDNAs were extended using the cDNA clone and oligonucleotide primers.
  • One primer was synthesized to initiate 5' extension of the known fragment, and the other, to initiate 3' extension of the known fragment.
  • the initial primers were designed using OLIGO primer analysis software (Molecular Biology Insights), 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 68C to about 72C. Any stretch of nucleotides that would result in hairpin structures and primer-primer dimerizations was avoided.
  • Selected cDNA libraries were used as templates to extend the sequence. If more than one extension was necessary, additional or nested sets of primers were designed.
  • Preferred libraries have been size-selected to include larger cDNAs and random primed to contain more sequences with 5' or upstream regions of genes.
  • Genomic libraries are used to obtain regulatory elements, especially extension into the 5 'promoter binding region. High fidelity amplification was obtained by PCR using methods such as that taught in
  • PCR was performed in 96-well plates using the DNA ENGINE thermal cycler (MJ Research).
  • the reaction mix contained DNA template, 200 nmol of each primer, reaction buffer containing Mg 2+ , (NH 4 ) 2 SO 4 , and ⁇ -mercaptoethanol, Taq DNA polymerase (APB), ELONGASE enzyme (Life Technologies), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair PCI A and PCI B (Incyte Genomics): Step 1: 94C, three min; Step 2: 94C, 15 sec; Step 3: 60C, one min; Step 4: 68C, two min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68C, five min; Step 7: storage at 4C.
  • the parameters for primer pair T7 and SK+ were as follows: Step 1: 94C, three min; Step 2: 94C, 15 sec; Step 3: 57C, one min; Step 4: 68C, two min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68C, five min; Step 7: storage at 4C.
  • the concentration of DNA in each well was determined by dispensing 100 ⁇ l PICOGREEN quantitation reagent (0.25% reagent in lx TE, v/v; Molecular Probes) and 0.5 ⁇ l of undiluted PCR product into each well of an opaque fluorimeter plate (Corning, Acton MA) and allowing the DNA to bind to the reagent.
  • the plate was scanned in a Fluoroskan U (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 clones were desalted, concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and sonicated or sheared prior to religation into pUC18 vector (APB).
  • CviJI cholera virus endonuclease Molecular Biology Research, Madison WI
  • APIB pUC18 vector
  • the digested nucleotide sequences were separated on low concentration (0.6 to 0.8%) agarose gels, fragments were excised, and the agar was digested with AGARACE enzyme (Promega).
  • Extended clones were religated using T4 DNA ligase (New England Biolabs) into pUC18 vector (APB), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into E. coli competent cells. Transformed cells were selected on antibiotic-containing media, and individual colonies were picked and cultured overnight at 37C in 384-well plates in LB/2x carbeniciUin liquid media.
  • the cells were lysed, and DNA was amplified using primers, Taq DNA polymerase (APB) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94C, three min; Step 2: 94C, 15 sec; Step 3: 60C, one min; Step 4: 72C, two min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72C, five min; Step 7: storage at 4C.
  • DNA was quantified using PICOGREEN quantitative reagent (Molecular Probes) as described above. Samples with low DNA recoveries were reamplified using the conditions described above.
  • the cDNAs of the Sequence Listing or their deduced amino acid sequences were used to query databases such as GenBank, SwissProt, BLOCKS, and the like. These databases that contain previously identified and annotated sequences or domains were searched using BLAST or BLAST 2 (Altschul et al. supra: Altschul, supra) to produce alignments and to determine which sequences were exact matches or homologs. The alignments were to sequences of prokaryotic (bacterial) or eukaryotic (animal, fungal, or plant) origin. Alternatively, algorithms such as the one described in Smith and Smith (1992, Protein Engineering 5:35-51) could have been used to ⁇ deal with primary sequence patterns and secondary structure gap penalties. All of the sequences disclosed in this application have lengths of at least 49 nucleotides, and no more than 12% uncalled bases (where N is recorded rather than A, C, G, or T).
  • BLAST matches between a query sequence and a database sequence were evaluated statistically and only reported when they satisfied the threshold of 10 "25 for nucleotides and 10 "14 for peptides. Homology was also evaluated by product score calculated as follows: the % nucleotide or amino acid identity [between the query and reference sequences] in BLAST is multiplied by the % maximum possible BLAST score [based on the lengths of query and reference sequences] and then divided by 100. In comparison with hybridization procedures used in the laboratory, the electronic stringency for an exact match was set at 70, and the conservative lower limit for an exact match was set at approximately 40 (with 1-2% error due to uncalled bases).
  • BLAST software suite includes various sequence analysis programs including "blastn” that is used to align nucleic acid molecules and BLAST 2 that is used for direct pairwise comparison of either nucleic or amino acid molecules.
  • BLAST programs are commonly used with gap and other parameters set to default settings, e.g.: Matrix: BLOSUM62; Reward for match: 1; Penalty for mismatch: -2; Open Gap: 5 and Extension Gap: 2 penalties; Gap x drop-off: 50; Expect: 10; Word Size: 11; and Filter: on.
  • the mammalian cDNAs of this application were compared with assembled consensus sequences or templates found in the LIFESEQ GOLD database.
  • Component sequences from cDNA, extension, full length, and shotgun sequencing projects were subjected to PHRED analysis and assigned a quality score. All sequences with an acceptable quality score were subjected to various pre-processing and editing pathways to remove low quality 3' ends, vector and linker sequences, polyA tails, Alu repeats, mitochondrial and ribosomal sequences, and bacterial contamination sequences. Edited sequences had to be at least 50 bp in length, and low- information sequences and repetitive elements such as dinucleotide repeats, Alu repeats, and the like, were replaced by "Ns" or masked.
  • Edited sequences were subjected to assembly procedures in which the sequences were assigned to gene bins. Each sequence could only belong to one bin, and sequences in each bin were assembled to produce a template. Newly sequenced components were added to existing bins using BLAST and CROSSMATCH. To be added to a bin, the component sequences had to have a BLAST quality score greater than or equal to 150 and an alignment of at least 82% local identity. The sequences in each bin were assembled using PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP. The orientation of each template was determined based on the number and orientation of its component sequences. Bins were compared to one another and those having local similarity of at least 82% were combined and reassembled.
  • Bins having templates with less than 95% local identity were split. Templates were subjected to analysis by STLTCHER/EXON MAPPER algorithms that analyze the probabilities of the presence of splice variants, alternatively spliced exons, splice junctions, differential expression of alternative spliced genes across tissue types or disease states, and the like. Assembly procedures were repeated periodically, and templates were annotated using
  • templates were subjected to BLAST, motif, and other functional analyses and categorized in protein hierarchies using methods described in USSN 08/812,290 and USSN 08/811,758, both filed March 6, 1997; in USSN 08/947,845, filed October 9, 1997; and in USSN 09/034,807, filed March 4, 1998. Then templates were analyzed by translating each template in all three forward reading frames and searching each translation against the PFAM database of hidden Markov model-based protein families and domains using the HMMER software package (Washington University School of Medicine, St. Louis MO; http://pfam.wustl.edu/).
  • the cDNA was further analyzed using MACDNASIS PRO software (Hitachi Software Engineering), and LASERGENE software (DNASTAR) and queried against public databases such as the GenBank rodent, mammalian, vertebrate, prokaryote, and eukaryote databases, SwissProt, BLOCKS, PRINTS, PFAM, and Prosite.
  • the procedure for identifying known genes that exhibited a statistically significant coexpression pattern with NRP is as follows. First, the presence or absence of a gene sequence in a cDNA library was defined: a gene was present in a cDNA library when at least one cDNA fragment corresponding to that gene was detected in a cDNA sample taken from the library, and a gene was absent from a library when no corresponding cDNA fragment was detected in the sample.
  • the probability method can be the Fisher exact test, the chi-squared test, or the kappa test. These tests and examples of their applications are well known in the art and can be found in standard statistics texts (Agresti (1990) Categorical Data Analysis, John Wiley & Sons, New York NY; Rice (1988) Mathematical Statistics and Data Analysis, Duxbury Press, Pacific Grove CA).
  • a Bonferroni correction (Rice, supra, p. 384) can also be applied in combination with one of the probability methods for correcting statistical results of one gene versus multiple other genes.
  • the due-to-chance probability was measured by a Fisher exact test, and the threshold of the due-to- chance probability was set preferably to less than 0.001, more preferably to less than 0.00001.
  • occurrence data vectors can be generated as illustrated in Table 4. The presence of a gene occurring at least once in a library was indicated by a one, and its absence from the library, by a zero.
  • Table 5 For a given pair of genes, the occurrence data in Table 4 can be summarized in a 2 x 2 contingency table (Table 5).
  • Table 5 presents co-occurrence data for gene A and gene B in a total of 30 libraries. Both gene A and gene B occur 10 times in the libraries. Table 5 summarizes and presents: 1) the number of times gene A and B are both present in a library; 2) the number of times gene A and B are both absent in a library; 3) the number of times gene A is present, and gene B is absent; and 4) the number of times gene B is present, and gene A is absent.
  • the upper left entry is the number of times the two genes co-occur in a library, and the middle right entry is the number of times neither gene occurs in a library.
  • the off diagonal entries are the number of times one gene occurs, and the other does not. Both A and B are present 8 times and absent 18 times.
  • Gene A is present, and gene B is absent, two times; and gene B is present, and gene A is absent, two times.
  • the probability (“p-value”) that the above association occurs due to chance as calculated using a Fisher exact test is 0.0003. Associations are generally considered significant if ap-value is less than 0.01 (Agresti, supra; Rice, supra).
  • the cDNAs are applied to a substrate by one of the following methods.
  • a mixture of cDNAs is fractionated by gel electrophoresis and transferred to a nylon membrane by capillary transfer.
  • the cDNAs are individually ligated to a vector and inserted into bacterial host cells to form a library.
  • the cDNAs are then arranged on a substrate by one of the following methods, the first method, bacterial cells containing individual clones are robotically picked and arranged on a nylon membrane.
  • the membrane is placed on LB agar containing selective agent (carbeniciUin, kanamycin, ampicillin, or chloramphenicol depending on the vector used) and incubated at 37C for 16 hr.
  • the membrane is removed from the agar and consecutively placed colony side up in 10% SDS, denaturing solution (1.5 M NaCl, 0.5 M NaOH), neutralizing solution (1.5 M NaCl, 1 M Tris, pH 8.0), and twice in 2xSSC for 10 min each.
  • the membrane is then UV irradiated in a STRATALINKER UV-crosslinker (Stratagene).
  • cDNAs are amplified from bacterial vectors by thirty cycles of PCR using primers complementary to vector sequences flanking the insert. PCR amplification increases a starting concentration of 1-2 ng nucleic acid to a final quantity greater than 5 ⁇ g.
  • Amplified nucleic acids from about 400 bp to about 5000 bp in length are purified using SEPHACRYL-400 beads (APB). Purified nucleic acids are arranged on a nylon membrane manually or using a dot/slot blotting manifold and suction device and are immobilized by denaturation, neutralization, and UV irradiation as described above.
  • nucleic acids are robotically arranged and immobilized on polymer-coated glass slides using the procedure described in USPN 5,807,522.
  • Polymer-coated slides are prepared by cleaning glass microscope slides (Corning, Acton MA) by ultrasound in 0.1% SDS and acetone, etching in 4% hydrofluoric acid (VWR Scientific Products, West Chester PA), coating with 0.05% aminopropyl silane (Sigma Aldrich) in 95% ethanol, and curing in a HOC oven. The slides are washed extensively with distilled water between and after treatments.
  • the nucleic acids are arranged on the slide and then immobilized by exposing the array to UV irradiation using a STRATALINKER UV-crosslinker (Stratagene).
  • Arrays are then washed at room temperature in 0.2% SDS and rinsed three times in distilled water. Non-specific'binding sites are blocked by incubation of arrays in 0.2% casein in phosphate buffered saline (PBS; Tropix, Bedford MA) for 30 min at 60C; then the arrays are washed in 0.2% SDS and rinsed in distilled water as before.
  • Probe Preparation for Membrane Hybridization PBS; Tropix, Bedford MA
  • Hybridization probes derived from the cDNAs of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA in membrane-based hybridizations. Probes are prepared by diluting the cDNAs to a concentration of 40-50 ng in 45 ⁇ l TE buffer, denaturing by heating to 100C for five min, and briefly centrifuging. The denatured cDNA is then added to a REDIPRIME tube (APB), gently mixed until blue color is evenly distributed, and briefly centrifuged. Five ⁇ l of [ 32 P]dCTP is added to the tube, and the contents are incubated at 37C for 10 min.
  • APB REDIPRIME tube
  • probe is purified from unincorporated nucleotides using a PROBEQUANT G-50 microcolumn (APB).
  • APB PROBEQUANT G-50 microcolumn
  • the purified probe is heated to 100C for five min, snap cooled for two min on ice, and used in membrane-based hybridizations as described below.
  • Hybridization probes derived from mRNA isolated from samples are employed for screening cDNAs of the Sequence Listing in array-based hybridizations.
  • Probe is prepared using the GEMbright kit (Incyte Genomics) by diluting mRNA to a concentration of 200 ng in 9 ⁇ l TE buffer and adding 5 ⁇ l 5x buffer, 1 ⁇ l 0.1 M DTT, 3 ⁇ l Cy3 or Cy5 labeling mix, 1 ⁇ l RNase inhibitor, 1 ⁇ l reverse transcriptase, and 5 ⁇ l lx yeast control mRNAs.
  • Yeast control mRNAs are synthesized by in vitro transcription from noncoding yeast genomic DNA (W. Lei, unpublished).
  • one set of control mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse transcription reaction mixture at ratios of 1:100,000, 1:10,000, 1:1000, and 1: 100 (w/w) to sample mRNA respectively.
  • a second set of control mRNAs are diluted into reverse transcription reaction mixture at ratios of 1:3, 3:1, 1: 10, 10: 1, 1:25, and 25: 1 (w/w).
  • the reaction mixture is mixed and incubated at 37C for two hr.
  • the reaction mixture is then incubated for 20 min at 85C, and probes are purified using two successive CHROMA SPIN+TE 30 columns (Clontech, Palo Alto CA).
  • Purified probe is ethanol precipitated by diluting probe to 90 ⁇ l in DEPC-treated water, adding 2 ⁇ l lmg/ml glycogen, 60 ⁇ l 5 M sodium acetate, and 300 ⁇ l 100% ethanol.
  • the probe is centrifuged for 20 min at 20,800xg, and the pellet is resuspended in 12 ⁇ l resuspension buffer, heated to 65C for five min, and mixed thoroughly. The probe is heated and mixed as before and then stored on ice. Probe is used in high density array-based hybridizations as described below.
  • Membrane-based Hybridization as described below.
  • Membranes are pre-hybridized in hybridization solution containing 1% Sarkosyl and lx high phosphate buffer (0.5 M NaCl, 0.1 M Na 2 HPO 4 , 5 mM EDTA, pH 7) at 55C for two hr.
  • the probe diluted in 15 ml fresh hybridization solution, is then added to the membrane.
  • the membrane is hybridized with the probe at 55C for 16 hr.
  • the membrane is washed for 15 min at 25C in ImM Tris (pH 8.0), 1% Sarkosyl, and four times for 15 min each at 25C in ImM Tris (pH 8.0).
  • XOMAT-AR film Eastman Kodak, Rochester NY is exposed to the membrane overnight at -70C, developed, and examined visually.
  • Probe is heated to 65C for five min, centrifuged five min at 9400 rpm in a 5415C microcentrifuge (Eppendorf Scientific, Westbury NY), and then 18 ⁇ l is aliquoted onto the array surface and covered with a coverslip.
  • the arrays are transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide.
  • the chamber is kept at 100% humidity internally by the addition of 140 ⁇ l of 5xSSC in a corner of the chamber.
  • the chamber containing the arrays is incubated for about 6.5 hr at 60C.
  • the arrays are washed for 10 min at 45C in lxSSC, 0.1% SDS, and three times for 10 min each at 45C in O.lxSSC, and dried.
  • Hybridization reactions are performed in absolute or differential hybridization formats.
  • absolute hybridization format probe from one sample is hybridized to array elements, and signals are detected after hybridization complexes form. Signal strength correlates with probe mRNA levels in the sample.
  • differential hybridization format differential expression of a set of genes in two biological samples is analyzed. Probes from the two samples are prepared and labeled with different labeling moieties. A mixture of the two labeled probes is hybridized to the array elements, and signals are examined under conditions in which the emissions from the two different labels are individually detectable. Elements on the array that are hybridized to substantially equal numbers of probes derived from both biological samples give a distinct combined fluorescence (Shalon WO95/35505).
  • Hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Santa Clara CA) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5.
  • the excitation laser light is focused on the array using a 20X microscope objective (Nikon, Melville NY).
  • the slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster-scanned past the objective with a resolution of 20 micrometers.
  • the two fluorophores are sequentially excited by the laser.
  • Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater NJ) corresponding to the two fluorophores.
  • Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals.
  • the emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5.
  • the sensitivity of the scans is calibrated using the signal intensity generated by the yeast control mRNAs added to the probe mix.
  • a specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1:100,000.
  • the output of the photomultiplier tube is digitized using a 12-bit RTI-835H analog-to- digital (AID) conversion board (Analog Devices, Norwood MA) installed in an IBM-compatible PC computer.
  • the digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal).
  • the data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using the emission spectrum for each fluorophore.
  • a grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid.
  • the fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal.
  • the software used for signal analysis is the GEMTOOLS program (Incyte Genomics).
  • BLAST Human and rat sequences were calculated as follows: the BLAST score is multiplied by the % nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences), such that a 100% alignment over the length of the shorter sequence gives a product score of 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 at least 70, the match will be exact. Similar or related molecules are usually identified by selecting those which show product scores between 8 and 40.
  • Molecules complementary to the cDNA from about 5 (PNA) to about 5000 bp (complement of a cDNA insert), are used to detect or inhibit gene expression. These molecules are selected using OLIGO primer analysis software (Molecular Biology Insights). Detection is described in Example VII.
  • the complementary molecule is designed to bind to the most unique 5' sequence and includes nucleotides of the 5' UTR upstream of the initiation codon of the open reading frame.
  • Complementary molecules include genomic sequences (such as enhancers or infrons) and are used in "triple helix" base pairing to compromise the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules.
  • a complementary molecule is designed to prevent ribosomal binding to the mRNA encoding the mammalian protein.
  • Complementary molecules are placed in expression vectors and used to transform a cell line to test efficacy; into an organ, tumor, synovial cavity, or the vascular system for transient or short term therapy; or into a stem cell, zygote, or other reproducing lineage for long term or stable gene therapy. Transient expression lasts for a month or more with a non-replicating vector and for three months or more if appropriate elements for inducing vector replication are used in the transformation/expression system.
  • the pUB6/V5-His vector system (Invitrogen, Carlsbad CA) is used to express NRP in CHO cells.
  • the vector contains the selectable bsd gene, multiple cloning sites, the promoter/enhancer sequence from the human ubiquitin C gene, a C-terminal V5 epitope for antibody detection with anti-V5 antibodies, and a C- terminal polyhistidine (6xHis) sequence for rapid purification on PROBOND resin (Invitrogen).
  • Transformed cells are selected on media containing blasticidin.
  • Spodoptera frugiperda (Sf9) insect cells are infected with recombinant Autographica califomica nuclear polyhedrosis virus (baculovirus).
  • the polyhedrin gene is replaced with the mammalian cDNA by homologous recombination and the polyhedrin promoter drives cDNA transcription.
  • the protein is synthesized as a fusion protein with 6xhis which enables purification as described above. Purified protein is used in the following activity and to make antibodies
  • NRP is purified using polyacrylamide gel electrophoresis and used to immunize mice or rabbits. Antibodies are produced using the protocols below. Alternatively, the amino acid sequence of NRP is analyzed using LASERGENE software (DNASTAR) to determine regions of high antigenicity. An antigenic epitope, usually found near the C-terminus or in a hydrophilic region is selected, synthesized, and used to raise antibodies.
  • epitopes of about 15 residues in length are produced using an ABI 431 A peptide synthesizer (Applied Biosystems) using Fmoc-chemistry and coupled to KLH (Sigma-Aldrich) by reaction with N- maleimidobenzoyl-N-hydroxysuccinimide ester to increase antigenicity.
  • Rabbits are immunized with the epitope-KLH complex in complete Freund's adjuvant. Immunizations are repeated at intervals thereafter in incomplete Freund's adjuvant. After a minimum of seven weeks for mouse or twelve weeks for rabbit, antisera are drawn and tested for antipeptide activity. Testing involves binding the peptide to plastic, blocking with 1% bovine serum albumin, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti- rabbit IgG. Methods well known in the art are used to determine antibody titer and the amount of complex formation. XII Purification of Naturally Occurring Protein Using Specific Antibodies
  • Naturally occurring or recombinant protein is purified by immunoaffinity chromatography using antibodies which specifically bind the protein.
  • An immunoaffinity column is constructed by covalently coupling the antibody to CNBr-activated SEPHAROSE resin (APB). Media containing the protein is passed over the immunoaffinity column, and the column is washed using high ionic strength buffers in the presence of detergent to allow preferential absorbance of the protein. After coupling, the protein is eluted from the column using a buffer of pH 2-3 or a high concentration of urea or thiocyanate ion to disrupt antibody/protein binding, and the protein is collected.
  • APB CNBr-activated SEPHAROSE resin
  • the cDNA, or fragments thereof, or the protein, or portions thereof, are labeled with 32 P- dCTP, Cy3-dCTP, or Cy5-dCTP (APB), or with BIODIPY or FITC (Molecular Probes, Eugene OR), respectively.
  • Libraries of candidate molecules or compounds previously arranged on a substrate are incubated in the presence of labeled cDNA or protein. After incubation under conditions for either a nucleic acid or amino acid sequence, the substrate is washed, and any position on the substrate retaining label, which indicates specific binding or complex formation, is assayed, and the ligand is identified. Data obtained using different concentrations of the nucleic acid or protein are used to calculate affinity between the labeled nucleic acid or protein and the bound molecule.
  • a yeast two-hybrid system MATCHMAKER LexA Two-Hybrid system (Clontech Laboratories, Palo Alto CA), is used to screen for peptides that bind the mammalian protein of the invention.
  • a cDNA encoding the protein is inserted into the multiple cloning site of a pLexA vector, ligated, and transformed into E. coli.
  • cDNA, prepared from mRNA is inserted into the multiple cloning site of a pB42AD vector, ligated, and transformed into E. coli to construct a cDNA library.
  • the pLexA plasmid and pB42AD-cDNA library constructs are isolated fromE.
  • Transformed yeast cells are plated on synthetic dropout (SD) media lacking histidine (-His), tryptophan (-Trp), and uracil (-Ura), and incubated at 30C until the colonies have grown up and are counted.
  • SD synthetic dropout
  • the colonies are pooled in a minimal volume of lx TE (pH 7.5), replated on SD/-His/-Leu/-Trp/-Ura media supplemented with 2% galactose (Gal), 1% raffinose (Raf), and 80 mg/ml 5-bromo-4-chloro-3-indolyl ⁇ -d- galactopyranoside (X-Gal), and subsequently examined for growth of blue colonies.
  • Interaction between expressed protein and cDNA fusion proteins activates expression of a LEU2 reporter gene in EGY48 and produces colony growth on media lacking leucine (-Leu).
  • Interaction also activates expression of ⁇ -galactosidase from the p8op-lacZ reporter construct that produces blue color in colonies grown on X-Gal.
  • NRP The activity of NRP is determined in ligand-binding assays using candidate ligand molecules, such as other sarcomeric proteins, actin, myosin, calmodulin, tropomyosin, troponin, and ⁇ -actinin.
  • candidate ligand molecules such as other sarcomeric proteins, actin, myosin, calmodulin, tropomyosin, troponin, and ⁇ -actinin.
  • NRP is labeled with 125 I Bolton-Hunter reagent (Bolton and Hunter (1973) Biochem J 133:529-539).
  • Candidate molecules, previously arrayed in wells of a multi-well plate, are incubated with the labeled NRP, washed, and any wells with labeled NRP complex are assayed. Data obtained using different concentrations of NRP are used to calculate values for the number, affinity, and association of NRP with the candidate molecules.
  • HEAADIR01 4405 heart right atrium/muscle wall, Pompe's, 7mM, RP 2 0.0454
  • CARDFEM01 25535 heart fetal, 19w, NORM, CGAP/ M/WN CARDFEP01 1882 heart, fetal, 8-10w, pool, BI CARDFEP02 12375 heart, fetal, 8-10w, pool, BI CARDFEP03 766 heart, fetal, 8-10w, pool, BI HEARFEE03 2817 heart, aw/Patau's syndrome, fetal, 20 M, 5RP HEARFEP02 1749 heart, fetal, TIGR HEARFETOl 3930 heart, fetal, 18wM HEARFET02 6919 heart, hypoplastic left, fetal, 23wM HEARFE 03 3821 heart, fetal, 18wM HEARFET05 2524 heart, fetal, M

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Abstract

La présente invention concerne un ADNc mammifère codant pour une protéine liée à la nébuline. L'invention concerne également l'utilisation de l'ADNc, de fragments, de compléments, et de variants de ceux-ci, ainsi que de la protéine codée, de portions de celle-ci, et d'anticorps dirigés contre elle, pour permettre le diagnostic et le traitement de troubles cardiaques et musculaires, en particulier la myopathie à némaline, et qui sont utilisés comme marqueur de l'ontogénie cardiaque. L'invention concerne également la mise au point de cette protéine, ainsi que des vecteurs d'expression et des cellules hôtes supplémentaires pour la production de la protéine, ainsi qu'un système de modèle transgénique.
PCT/US2001/050876 2000-11-09 2001-10-31 Proteine liee a la nebuline WO2002046420A2 (fr)

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AU2002241748A AU2002241748A1 (en) 2000-11-09 2001-10-31 Nebulin-related protein

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Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
DATABASE EMBL [Online] annotation: similar to Nebulin, 1 January 1997 (1997-01-01) HILLIER ET AL.: "zp36f12.r1 Stratagene muscle 937209 Homo sapiens cDNA clone" Database accession no. AA176595 XP002226566 *
DATABASE EMBL [Online] from "Atrium cDNA library Human Heart", 9 August 1994 (1994-08-09) GENZENTRUM MUENCHEN: "H. sapiens partial cDNA sequence; clone HEA19W" Database accession no. Z36252 XP002226567 *
HOROWITS R ET AL: "Nebulin and nebulin-related proteins in striated muscle." ADVANCES IN BIOPHYSICS. JAPAN 1996, vol. 33, 1996, pages 143-150, XP002226563 ISSN: 0065-227X *
LUO GANG ET AL: "Complete cDNA sequence and tissue localization of N-RAP, a novel nebulin-related protein of striated muscle." CELL MOTILITY AND THE CYTOSKELETON, vol. 38, no. 1, 1997, pages 75-90, XP001121693 ISSN: 0886-1544 -& DATABASE EMBL [Online] 3 September 1997 (1997-09-03) LUO G AT AL.: "Mus musculus N-RAP" Database accession no. U76618 XP002226565 *
WANG KUAN ET AL: "Human skeletal muscle nebulin sequence encodes a blueprint for thin filament architecture: Sequence motifs and affinity profiles of tandem repeats and terminal SH3." JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 271, no. 8, 1996, pages 4304-4314, XP002226564 ISSN: 0021-9258 *

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