Classifications

• • 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
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
  • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/158—Expression markers

Definitions

• This invention relates to nucleic acids and encoded polypeptides of human vasa, and diagnostics and therapeutics related to medical conditions associated with such genes and polypeptides, including cancers.
• Germ cells are cells that are specialized to produce haploid gametes in multicellular organisms. Germ cell tumors represent a diverse family of neoplasms affecting a wide range of patients. The great majority of testicular tumors (the most common malignancy in young men) are malignant germ cell tumors. The most common ovarian tumor, the benign or "mature" teratoma, is also of germ cell origin. Additionally, malignant ovarian germ cell tumors and germ cell tumors of various subtypes are of relatively common occurrence in children. Interestingly, benign and malignant germ cell tumors also arise in extragonadal locations (the mediastinum and central nervous system).
• clear cell carcinoma of the ovary can histologically resemble dysgerminoma (the ovarian counterparts of seminoma); mediastinal thymomas can be difficult to distinguish from germ cell tumors, and testicular lymphoma can mimic seminoma (Scully et al, 1998, Armed Forces Institute of Pathology, Washington, D.C.; Suster et al, Seminars in Diagnostic Pathology, 1995, 12(1):98-104).
• metastases in patients with unsuspected primary germ cell tumors can be initially misdiagnosed, resulting in treatment delays.
• Tumor-specific markers have been clinically useful for a variety of reasons, including accurate tissue-based diagnosis by immunohistochemistry, population-based screening, confirmation of a clinical diagnosis prior to surgery, and monitoring of patients in remission.
• the clinical utility of a marker is directly proportional to its specificity.
• ⁇ -hCG a highly sensitive and specific marker for trophoblast
• AFP ⁇ -fetoprotein
• Serum assays for both AFP and ⁇ -hCG are routinely employed in the diagnosis of patients with suspected germ cell tumors to determine if non-seminomatous components are present (which would alter patient management) (Harrison' s).
• Commercially-available AFP and ⁇ -hCG antibodies are also routinely employed in immunohistochemical assays performed by hospital laboratories on paraffin-embedde formalin-fixed tissue.
• vasa gene was originally described in Drosophila, where various studies including whole-mount in situ staining have, reportedly, shown that vasa is expressed only in germ cells (of both sexes) at all stages of development, from the preblastoderm stage to primitive germ cells to gametogenesis in adults. A number of investigations have, reportedly- shown that vasa is not only germ-cell specific in its expression, it is absolutely required for germ cell development, and in Drosophila, vasa mutants fail to develop germ cells (Lasko et al, Nature, 1988, 335:611-617, and SEQ ID NO:7). Subsequently, vasa homologues were .5 identified in mouse, zebrafish, and Xenopus.
• the invention provides isolated nucleic acid molecules, unique fragments of those molecules, expression vectors containing the foregoing, and host cells transfected with those molecules.
• the invention also provides isolated binding polypeptides and binding agents which bind such polypeptides, including antibodies.
• the foregoing can be used, inter alia, in the diagnosis or treatment of conditions characterized by the aberrant expression and/or the
• the invention also provides methods for identifying pharmacological agents useful in the diagnosis or treatment of such conditions.
• isolated nucleic acid molecules that code for a human vasa polypeptide include: (a) nucleic acid molecules which hybridize under stringent conditions to a molecule consisting of a nucleic acid of SEQ ID NO:l and which code for a human vasa polypeptide, (b) deletions, additions and substitutions of (a) which code for a respective human vasa polypeptide, (c) nucleic acid molecules that differ from the nucleic acid molecules of (a) or (b) in codon sequence due to the degeneracy of the genetic code, and (d) complements of (a), (b) or (c).
• the isolated nucleic acid molecule comprises nucleotides 1-2224 of SEQ ID NO:l. In some embodiments the isolated nucleic acid molecules are those comprising the human vasa cDNA corresponding to SEQ ID NO: 15. The isolated nucleic acid molecule also can comprise a molecule which encodes the polypeptide of SEQ ID NO:2 and has human vasa specific s expression.
• nucleic acids of the invention exclude nucleic acids completely composed of the nucleotide sequences of any of GenBank accession numbers listed in Table I (S75275, D 14859, AB005147, Y 12007, AF046043, Z81449.1, X81823, P09052, Q64060, Q61496, Q62167, 000571, P24346, P16381, O15523, AL042306, AA39961 1, AA398976, AA383535, AI217144, AI953070, AI025074, AI654417, AI337133, o AA758412, AI969018, AA400066, AA862553, AA401568, AA316798, T85890, and T82153), or other previously published sequences as of the filing date of this application.
• the invention in another aspect provides an isolated nucleic acid molecule selected from the group consisting of (a) a unique fragment of nucleic acid molecule of SEQ ID NO:l (of sufficient length to represent a sequence unique within the human genome), (b) s complements of (a), provided that the fragment includes a sequence of contiguous nucleotides which is not identical to a sequence selected from the sequence group consisting of: (1) sequences having the database accession numbers of Table I, or sequences encoding a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, and SEQ ID NO:7, (2) complements of o ( 1 ), and (3) fragments of ( 1 ) and (2).
• the sequence of contiguous nucleotides is selected from the group consisting of (1) at least two contiguous nucleotides nonidentical to the sequence group, (2) at least three contiguous nucleotides nonidentical to the sequence group, (3) at least four contiguous nucleotides nonidentical to the sequence group, (4) at least five contiguous 5 nucleotides nonidentical to the sequence group, (5) at least six contiguous nucleotides nonidentical to the sequence group, (6) at least seven contiguous nucleotides nonidentical to the sequence group.
• the fragment has a size selected from the group consisting of at least: 8 nucleotides, 10 nucleotides, 12 nucleotides, 14 nucleotides, 16 nucleotides, 18 nucleotides, 20, nucleotides, 22 nucleotides, 24 nucleotides, 26 nucleotides. 28 nucleotides, 30 nucleotides, 40 nucleotides, 50 nucleotides, 75 nucleotides, 100 nucleotides, 200 nucleotides, 1000 nucleotides and every integer length therebetween.
• the invention provides expression vectors, and host cells transformed or transfected with such expression vectors, comprising the nucleic acid molecules described above.
• an isolated polypeptide is provided.
• the isolated polypeptide is encoded by the foregoing isolated nucleic acid molecules of the invention.
• the isolated polypeptide is encoded by the nucleic acid of SEQ ID NO:l , giving rise to a polypeptide having the sequence of SEQ ID NO:2 that has germ cell specific expression.
• the isolated polypeptide may be a fragment or variant of the foregoing of sufficient length to represent a sequence unique within the human genome, and identifying with a polypeptide that has germ cell specific expression, provided that the fragment excludes: (i) a sequence of contiguous amino acids selected from the group consisting of SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, and SEQ ID NO:7, and (ii) a sequence of contiguous amino acids encoded by an isolated nucleic acid having a nucleotide sequence with a GenBank database accession number selected from the group consisting of S75275, D14859, AB005147, Y12007, AF046043, Z81449.1, X81823, P09052, Q64060, Q61496, Q62167, O00571, P24346, P16381, 015523, AL0423O6, AA399611, AA398976, AA383535, AI217144, AI95
• isolated binding polypeptides which selectively bind a polypeptide encoded by the foregoing isolated nucleic acid molecules of the invention are provided.
• the isolated binding polypeptides selectively bind a polypeptide which comprises the sequence of SEQ ID NO:2, SEQ ID NO:9, SEQ ID NO:l O, or fragments thereof.
• the isolated binding polypeptides include antibodies and fragments of antibodies (e.g., Fab, F(ab') 2 , Fd and antibody fragments which include a CDR3 region which binds selectively to the human vasa polypeptide).
• the antibodies are human.
• kits comprising a package including assays for human vasa epitopes, human vasa nucleic acids, and instructions, and optionally related materials such as controls, for example, a number, color chart, or an epitope of the expression product of the foregoing isolated nucleic acid molecules of the invention, for comparing the level of human vasa polypeptides or human vasa nucleic acids in a test sample to the level in a control sample. This comparison can be used to assess in a subject the presence of a tumor of germ cell origin.
• kits may also include assays for other known genes, and expression products thereof, associated with cancers (e.g., ⁇ -hCG, ⁇ -fetoprotein, placental-type alkaline phosphatase, prostate specific antigen, carcinoembryonic antigen, inhibin, epithelial membrane antigen, desmin, vimentin, GFAP -glial fibrillary acidic protein, synaptophysin, chromogranin, cytokeratin isoforms such as 7 and 20, anti-keratin markers such as AE1/AE3 and CAM5.2, etc.).
• cancers e.g., ⁇ -hCG, ⁇ -fetoprotein, placental-type alkaline phosphatase, prostate specific antigen, carcinoembryonic antigen, inhibin, epithelial membrane antigen, desmin, vimentin, GFAP -glial fibrillary acidic protein, synaptophysin, chromogranin, cytokeratin is
• Another aspect of the invention is a method for determining the level of vasa expression in a subject.
• Expression is defined either as vasa mRNA expression or vasa polypeptide expression.
• Various methods can be used to measure expression.
• Preferred embodiments of the invention include PCR and northern blotting for measuring mRNA. expression, and monoclonal vasa antibodies or polyclonal vasa antisera as reagents to measure (or characterize) vasa polypeptide expression.
• test samples such as tissue (e.g., biopsy) samples, and biological fluids such as blood, are used as test samples.
• fine-needle aspirates can also be used as sources of a test sample.
• Vasa expression in a test sample of a subject is compared to vasa expression in. control sample to, e.g., assess the presence or absence, or stage of a tumor of germ cell origin in a subject.
• a method of detecting a tumor of germ cell origin involves detecting vasa expression in an extragonadal test sample obtained from a subject.
• Vasa expression in the extragonadal test sample is indicative of the presence of a tumor of germ cell origin in the subject.
• Vasa expression and methods of measuring vasa expression are as described in any of the foregoing embodiments.
• the subject has not previously been diagnosed as having a tumor of germ cell origin or a predisposition thereto [e.g., to detect a metastasis in a subject of previously undiagnosed cancer].
• the subject has a clinical diagnosis of a tumor of germ cell origin and the method is to confirm the clinical diagnosis, monitor remission of the tumor, or stage the tumor.
• a method of detecting a tumor of germ cell origin involves detecting vasa overexpression in a test sample obtained from a subject.
• Vasa overexpression in the test sample as compared to a control is indicative of a tumor of germ cell origin in the subject.
• Vasa expression and methods of measuring vasa expression are as described in any of the foregoing embodiments.
• the tumor can be a testicular tumor (e.g., a seminoma), an ovarian tumor (e.g., a dysgerminoma or a teratoma), or a tumor of an extragonadal tissue(e.g., a mediastinal tumor or an intracranial tumor).
• the method can further comprise detecting expression of a tumor-specific agent other than a vasa molecule (nucleic acid or polypeptide) in the test sample.
• Tumor-specific agents other than a vasa molecule include, but are not limited to, ⁇ -hCG, ⁇ -fetoprotein, placental-type alkaline phosphatase, prostate specific antigen, carcinoembryonic antigen, inhibin, epithelial membrane antigen, desmin, vimentin, GFAP -glial fibrillary acidic protein, synaptophysin.
• Preferred subjects are as described in any of the foregoing embodiments.
• a method of subtyping tumors of germ cell origin involves detecting vasa expression in a test sample of a known or suspected germ cell origin tumor obtained from a subject.
• Vasa overexpression in the test sample as compared to a control is indicative of a seminoma in the subject, whereas absence of vasa expression in the test sample as compared to a control is indicative of a nonseminoma in the subject.
• Vasa expression, methods of measuring vasa expression, tumor types, and subjects, are as described in any of the foregoing embodiments.
• Nonseminomas include embryonal carcinoma, teratoma, choriocarcinoma, yolk sac tumor, or combinations of the foregoing.
• the subject has a clinical diagnosis of a tumor of mixed histologic appearance.
• the method can further comprise detecting expression of a tumor-specific agent other than a vasa molecule in the test sample.
• Tumor-specific agents other than a vasa molecule are as described in any of the foregoing embodiments.
• a method of distinguishing a tumor of germ cell origin from a non-germ cell tumor involves detecting expression of a vasa molecule in a test sample, wherein expression of the vasa molecule is indicative of a tumor of a germ cell origin and absence of expression of the vasa molecule is indicative of a non-gerrn cell tumor.
• the non-germ cell tumor resembles histologically a tumor of germ cell origin.
• Non-germ cell tumors include, but are not limited to, clear cell carcinoma of the ovary (can resemble dysgerminoma), a mediastinal thymoma, and a testicular lymphoma.
• a method for treating a tumor of germ cell origin in a subject involves administering to a subject in need of such treatment an agent that inhibits vasa expression in a germ cell of the subject in an effective amount to inhibit vasa expression and inhibit the growth and/or proliferation of the tumor of germ cell origin in the subject.
• the agent is a vasa antisense nucleic acid.
• the method further comprises co-administering an anti- cancer agent.
• the present invention thus involves, in several aspects, human vasa polypeptides, isolated nucleic acids encoding those polypeptides, functional modifications and variants of the foregoing, useful fragments of the foregoing, as well as therapeutics and diagnostics relating thereto.
• Figure 1 depicts a kit comprising an agent of the invention (e.g., anti-human vasa Abs, human vasa epitopes, etc.), a control agent, and instructions for utilizing such agents in diagnostic or therapeutic applications.
• an agent of the invention e.g., anti-human vasa Abs, human vasa epitopes, etc.
• SEQ ID NO: l is the nucleotide sequence of the human vasa cDNA.
• SEQ ID NO:2 is the predicted amino acid sequence of the translation product of human vasa cDNA (SEQ ID NO:l).
• SEQ ID NO:3 is the amino acid sequence of the Mus Musculus vasa cDNA.
• SEQ ID NO:4 is the amino acid sequence of the Rattus Norvegicus vasa cDNA.
• SEQ ID NO:5 is the amino acid sequence of the Xenopus Laevis vasa cDNA.
• SEQ ID NO:6 is the amino acid sequence of the Danio Reio vasa cDNA.
• SEQ ID NO: 7 is the amino acid sequence of the Drosophila Melanogaster vasa cDNA.
• SEQ ID NO: 8 is the nucleotide sequence of a synthetic oligonucleotide primer used in the cloning of the human vasa cDNA.
• SEQ ID NO: 9 is the amino acid sequence of a human-specific vasa epitope used in the generation of anti-human vasa antibodies.
• SEQ ID NO: 10 is the amino acid sequence of a human-specific vasa epitope used in the generation of anti-human vasa antibodies.
• SEQ ID NO: l 1 is the nucleotide sequence of a synthetic human vasa oligonucleotide.
• SEQ ID NO: 12 is the nucleotide sequence of a synthetic human vasa oligonucleotide.
• SEQ ID NO: 13 is the nucleotide sequence of a synthetic oligonucleotide primer used in the detection of human vasa expression using PCR in combination with the synthetic oligonucleotide primer of SEQ ID NO: 14.
• SEQ ID NO: 14 is the nucleotide sequence of a synthetic oligonucleotide primer used in the detection of human vasa expression using PCR in combination with the synthetic oligonucleotide primer of SEQ ID NO: 13.
• SEQ ID NO: 15 is the nucleotide sequence of the largest open reading frame of the human vasa cDNA of SEQ ID NO: l , encoding for the polypeptide of SEQ ID NO:2.
• Human vasa is an isolated nucleic acid molecule that comprises a nucleic acid molecule of SEQ ID NO: l, and codes for a protein that is specifically expressed in the gonads and is believed to play an essential role in gonad development.
• aberrant expression of human vasa has been found in patients with tumors of germ cell origin, making human vasa a specific marker for tumors of such origin.
• the sequence of the human vasa cDNA is presented as SEQ ID NO: l
• the predicted amino acid sequence of this cDNA's encoded protein product is presented as SEQ ID NO:2.
• a subject is a human, non-human primate, cow, horse, pig, sheep, goat, dog, cat or rodent. In all embodiments human vasa and human subjects are preferred.
• the invention thus involves in one aspect an isolated human vasa polypeptide, the cDNA encoding this polypeptide, functional modifications and variants of the foregoing, useful fragments of the foregoing, as well as diagnostics and therapeutics relating thereto.
• isolated means: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) recombinantly produced by cloning; (iii) purified, as by cleavage and gel separation; or (iv) synthesized by, for example, chemical synthesis.
• An isolated nucleic acid is one which is readily manipulable by recombinant DNA techniques well known in the art.
• nucleotide sequence contained in a vector in which 5' and 3' restriction sites are known or for which polymerase chain reaction (PCR) primer sequences have been disclosed is considered isolated but a nucleic acid sequence existing in its native state in its natural host is not.
• An isolated nucleic acid may be substantially purified, but need not be.
• a nucleic acid that is isolated within a cloning or expression vector is not pure in that it may comprise only a tiny percentage of the material in the cell in which it resides. Such a nucleic acid is isolated, however, as the term is used herein because it is readily manipulable by standard techniques known to those of ordinary skill in the art.
• isolated means separated from its native environment in sufficiently pure form so that it can be manipulated or used for any one of the purposes of the invention.
• isolated means sufficiently pure to be used (i) to raise and/or isolate antibodies, (ii) as a reagent in an assay, or (iii) for sequencing, etc.
• isolated nucleic acid molecules that code for a human vasa polypeptide include: (a) nucleic acid molecules which hybridize under stringent conditions to a molecule consisting of a nucleic acid of SEQ ID NO: l and which code for a human vasa polypeptide, (b) deletions, additions and substitutions of (a) which code for a respective human vasa polypeptide, (c) nucleic acid molecules that differ from the nucleic acid molecules of (a) or (b) in codon sequence due to the degeneracy of the genetic code, and (d) complements of (a), (b) or (c).
• nucleic acids of the invention exclude nucleic acids completely composed of the nucleotide sequences of any of GenBank accession numbers listed in Table I (S75275, D14859, AB005147, Y12007, AF046043, Z81449.1 , X81823, P09052, Q64060, Q61496, Q62167, O00571 , P24346, P16381 , 015523, AL042306, AA39961 1, AA398976, AA383535, AI217144, AI953070, AI025074, AI654417, AI337133 , AA758412, AI969018, AA400066, AA862553, AA401568, AA316798, T85890, and T82153), or other previously published sequences as of the filing date of this application.
• an aspect of the invention is those nucleic acid sequences which code for human vasa polypeptides and which hybridize to a nucleic acid molecule consisting of the coding region of SEQ ID NO: l, under stringent conditions.
• stringent conditions refers to parameters with which the art is familiar. Nucleic acid hybridization parameters may be found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989, or Current Protocols in Molecular Biology, F.M.
• stringent conditions refers, for example, to hybridization at 65°C in hybridization buffer (3.5 x SSC, 0.02% Ficoll, 0.02% polyvinyl pyrolidone, 0.02% Bovine Serum Albumin, 2.5mM NaH 2 PO 4 (pH7), 0.5% SDS, 2miVI
• SSC 0.15M sodium chloride/0.15M sodium citrate, pH7; SDS is sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid.
• SSC 0.15M sodium chloride/0.15M sodium citrate, pH7; SDS is sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid.
• homologs and alleles typically will share at least 75% nucleotide identity and/or at least 90% amino acid identity to SEQ ID NO: l and SEQ ID NO:2, respectively. In some instances homologs and alleles will share at least 90% nucleotide identity and/or at least 95% amino acid identity and in still other instances will share at least 95% nucleotide identity and/or at least 99% amino acid identity.
• Complements of the foregoing nucleic acids also are embraced by the invention.
• the homology can be calculated using various, publicly available software tools developed by NCBI (Bethesda, Maryland).
• Exemplary tools include the heuristic algorithm of Altschul SF, et al., (J Mol Biol, 1990, 215:403-410), also known as BLAST. Pairwise and ClustalW alignments (BLOSUM30 matrix setting) as well as Kyte-Doolittle hydropathic analysis can be obtained using public (EMBL, Heidelberg, Germany) and commercial (e.g., the MacVector sequence analysis software from Oxford Molecular Group/Genetics Computer Group, Madison, WI). Watson-Crick complements of the foregoing nucleic acids also are embraced by the invention.
• a Southern blot may be performed using the foregoing conditions, together with a radioactive probe. After washing the membrane to which the DNA is finally transferred, the membrane can be placed against X-ray film or a phosphoimager plate to detect the radioactive signal.
• allelic human vasa sequences can be isolated from cDNA. libraries prepared from one or more of the tissues in which human vasa expression is abundant (i.e., in the gonads), using standard colony hybridization techniques.
• the invention also includes degenerate nucleic acids which include alternative codons to those present in the native materials. For example, serine residues are encoded by the codons TCA, AGT, TCC, TCG, TCT and AGC. Each of the six codons is equivalent for the purposes of encoding a serine residue.
• any of the serine-encoding nucleotide triplets may be employed to direct the protein synthesis apparatus, in vitro or in vivo, to incorporate a serine residue into an elongating human vasa polypeptide.
• nucleotide sequence triplets which encode other amino acid residues include, but are not limited to: CCA, CCC, CCG and CCT (proline codons); CGA, CGC, CGG, CGT, AGA and AGG (arginine codons); ACA, ACC, ACG and ACT (threonine codons); AAC and AAT (asparagine codons); and ATA, ATC and ATT (isoleucine codons).
• Other amino acid residues may be encoded similarly by multiple nucleotide sequences.
• the invention embraces degenerate nucleic acids that differ from the biologically isolated nucleic acids in codon sequence due to the degeneracy of the genetic code.
• the invention also provides isolated unique fragments of SEQ ID NO:l or SEQ IE>
• a unique fragment is one that is a 'signature' for the larger nucleic acid.
• the unique fragment is long enough to assure that its precise sequence is not found in molecules within the human genome outside of the human vasa nucleic acids defined above. Those of ordinary skill in the art may apply no more than routine procedures to determine if a fragment is unique within the human genome.
• a fragment which is completely composed of the sequence described in the foregoing GenBank deposits is one which does not include any of the nucleotides unique to the sequences of the invention.
• a unique fragment must contain a nucleotide sequence other than the exact sequence of those in GenBank or fragments thereof. The difference may be an addition, deletion or substitution with respect to the GenBank sequence or it may be a sequence wholly separate from the GenBank sequence.
• Unique fragments can be used as probes in Southern and Northern blot assays to identify such nucleic acids, or can be used in amplification assays such as those employing PCR.
• unique fragments also can be used to produce fusion proteins for generating antibodies or determining binding of the polypeptide fragments, as demonstrated in the Examples, or for generating immunoassay components. Likewise, unique fragments can be employed to produce nonfused fragments of the human vasa polypeptides, useful, for example, in the preparation of antibodies, immunoassays or therapeutic applications. Unique fragments further can be used as antisense molecules to inhibit the expression of human vasa nucleic acids and polypeptides respectively.
• the size of the unique fragment will depend upon its conservancy in the genetic code. Thus, some regions of SEQ ID NO: 1 or SEQ ID NO: 15 and complements will require longer segments to be unique while others will require only short segments, typically between 12 and 32 nucleotides long (e.g. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 and 32 bases) or more, up to the entire length of the disclosed sequence.
• this disclosure intends to embrace each and every fragment of each sequence, beginning at the first nucleotide, the second nucleotide and so on, up to 8 nucleotides short of the end, and ending anywhere from nucleotide number 8, 9, 10 and so on for each sequence, up to the very last nucleotide, (provided the sequence is unique as described above).
• Virtually any segment of the region of SEQ ID NO:l beginning at nucleotide 1 and ending at nucleotide 2224, or SEQ ID NO: 15 beginning at nucleotide 1 and ending at nucleotide 2172, or complements thereof, that is 20 or more nucleotides in length will be unique.
• the invention embraces antisense oligonucleotides that selectively bind to a nucleic acid molecule encoding a human vasa polypeptide, to decrease human vasa activity.
• antisense preparations of the invention slow intravenous administration is preferred.
• antisense oligonucleotide or “antisense” describes an oligonucleotide that is an oligoribonucleotide, oligodeoxyribonucleotide, modified oligoribonucleotide, or modified oligodeoxyribonucleotide which hybridizes under physiological conditions to DNA comprising a particular gene or to an mRNA transcript of that gene and, thereby, inhibits the transcription of that gene and/or the translation of that mRNA.
• the antisense molecules are designed so as to interfere with transcription or translation of a target gene upon hybridization with the target gene or transcript.
• the exact length of the antisense oligonucleotide and its degree of complementarity with its target will depend upon the specific target selected, including the sequence of the target and the particular bases which comprise that sequence. It is preferred that the antisense oligonucleotide be constructed and arranged so as to bind selectively with the target under physiological conditions, i.e.. to hybridize substantially more to the target sequence than to any other sequence in the target cell under physiological conditions. Based upon SEQ ID NO: l or upon allelic or homologous genomic and/or cDNA sequences, one of skill in the art can easily choose and synthesize any of a number of appropriate antisense molecules for use in accordance with the present invention.
• antisense oligonucleotides should comprise at least 10 and, more preferably, at least 15 consecutive bases which are complementary to the target, although in certain cases modified oligonucleotides as short as 7 bases in length have been used successfully as antisense oligonucleotides (Wagner et al., Nat. Med. 1(1 1 ): 1 1 16-1 1 18, 1995). Most preferably, the antisense oligonucleotides comprise a complementary sequence of 20-30 bases.
• oligonucleotides may be chosen which are antisense to any region of the gene or mRNA transcripts, in preferred embodiments the antisense oligonucleotides correspond to N-terminal or 5' upstream sites such as translation initiation, transcription initiation or promoter sites. In addition, 3 '-untranslated regions may be targeted by antisense oligonucleotides. Targeting to mRNA splicing sites has also been used in the art but may be less preferred if alternative mRNA splicing occurs. In addition, the antisense is targeted, preferably, to sites in which mRNA secondary structure is not expected (see, e.g., Sainio et al., Cell Mol. Neurobiol.
• SEQ ID No: l discloses a cDNA sequence
• the present invention also provides for antisense oligonucleotides which are complementary to the genomic DNA corresponding to SEQ ID NO: 1.
• antisense to allelic or homologous human vasa cDNAs and genomic DNAs are enabled without undue experimentation.
• the antisense oligonucleotides of the invention may be composed of "natural" deoxyribonucleotides, ribonucleotides, or any combination thereof.
• oligonucleotides may be prepared by art recognized methods which may be carried out manually or by an automated synthesizer. They also may be produced recombinantly by vectors.
• the antisense oligonucleotides of the invention also may include "modified" oligonucleotides. That is, the oligonucleotides may be modified in a number of ways which do not prevent them from hybridizing to their target but which enhance their stability or targeting or which otherwise enhance their therapeutic effectiveness.
• modified oligonucleotide as used herein describes an oligonucleotide in which (1) at least two of its nucleotides are covalently linked via a synthetic internucleoside linkage (i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide) and/or (2) a chemical group not normally associated with nucleic acids has been covalently attached to the oligonucleotide.
• a synthetic internucleoside linkage i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide
• Preferred synthetic internucleoside linkages are phosphorothioates, alkylphosphonates, phosphorodithioates, phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates, carbonates, phosphate triesters, acetamidates, carboxymethyl esters and peptides.
• modified oligonucleotide also encompasses oligonucleotides with a covalently modified base and/or sugar.
• modified oligonucleotides include oligonucleotides having backbone sugars which are covalently attached to low molecular weight organic groups other than a hydroxy 1 group at the 3' position and other than a phosphate group at the 5' position.
• modified oligonucleotides may include a 2'-O-alkylated ribose group.
• modified oligonucleotides may include sugars such as arabinose instead of ribose.
• the present invention contemplates pharmaceutical preparations containing modified antisense molecules that are complementary to and hybridizable with, under physiological conditions, nucleic acids encoding human vasa polypeptides, together with pharmaceutically acceptable carriers.
• Antisense oligonucleotides may be administered as part of a pharmaceutical composition.
• a pharmaceutical composition may include the antisense oligonucleotides in combination with any standard physiologically and/or pharmaceutically acceptable carriers which are known in the art.
• the compositions should be sterile and contain a therapeutically effective amount of the antisense oligonucleotides in a unit of weight or volume suitable for administration to a patient.
• pharmaceutically acceptable means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients.
• physiologically acceptable refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics of the carrier will depend on the route of administration.
• Physiologically and pharmaceutically acceptable carriers include diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art.
• the invention also involves expression vectors coding for human vasa proteins and fragments and variants thereof and host cells containing those expression vectors.
• Examples include bacterial cells such as E.coli and mammalian cells such as mouse, hamster, pig, goat, primate, etc. They may be of a wide variety of tissue types, including mast cells, fibroblasts, oocytes and lymphocytes, and they may be primary cells or cell lines. Specific examples include CHO cells and COS cells. Cell-free transcription systems also may be used in lieu of cells.
• a "vector" may be any of a number of nucleic acids into which a desired sequence may be inserted by restriction and ligation for transport between different genetic environments or for expression in a host cell.
• Vectors are typically composed of DNA although RNA vectors are also available.
• Vectors include, but are not limited to, plasmids, phagemids and virus genomes.
• a cloning vector is one which is able to replicate in a host cell, and which is further characterized by one or more endonuclease restriction sites at which the vector may be cut in a determinable fashion and into which a desired DNA sequence may be ligated such that the new recombinant vector retains its ability to replicate in the host cell.
• replication of the desired sequence may occur many times as the plasmid increases in copy number within the host bacterium or just a single time per host before the host reproduces by mitosis. In the case of phage, replication may occur actively during a lytic phase or passively during a lysogenic phase.
• An expression vector is one into which a desired DNA sequence may be inserted by restriction and ligation such that it is operably joined to regulatory sequences and may be expressed as an RNA transcript. Vectors may further contain one or more marker sequences suitable for use in the identification of cells which have or have not been transformed or transfected with the vector.
• Markers include, for example, genes encoding proteins which increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose activities are detectable by standard assays known in the art (e.g., ⁇ -galactosidase or alkaline phosphatase), and genes which visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques (e.g., green fluorescent protein).
• Preferred vectors are those capable of autonomous replication and expression of the structural gene products present in the DNA segments to which they are operably joined.
• a coding sequence and regulatory sequences are said to be "operably” joined when they are covalently linked in such a way as to place the expression or transcription of the coding sequence under the influence or control of the regulatory sequences.
• two DNA sequences are said to be operably joined if induction of a promoter in the 5 ' regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein.
• a promoter region would be operably joined to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript might be translated into the desired protein or polypeptide.
• regulatory sequences needed for gene expression may vary between species or cell types, but shall in general include, as necessary, 5 ' non-transcribed and 5' non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like.
• 5' non-transcribed regulatory sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined gene.
• Regulatory sequences may also include enhancer sequences or upstream activator sequences as desired.
• the vectors of the invention may optionally include 5' leader or signal sequences. The choice and design of an appropriate vector is within the ability and discretion of one of ordinary skill in the art.
• RNA heterologous DNA
• RNA heterologous DNA
• That heterologous DNA (RNA) is placed under operable control of transcriptional elements to permit the expression of the heterologous DNA in the host cell.
• Preferred systems for mRNA expression in mammalian cells are those such as pRc/CMV and pcDNA3.1 (available from Invitrogen, Carlsbad, CA) that contain a selectable marker such as a gene that confers G418 resistance (which facilitates the selection of stably transfected cell lines) and the human cytomegalovirus (CMV) enhancer-promoter sequences.
• a selectable marker such as a gene that confers G418 resistance (which facilitates the selection of stably transfected cell lines) and the human cytomegalovirus (CMV) enhancer-promoter sequences.
• CMV cytomegalovirus
• suitable for expression in primate or canine cell lines is the pCEP4 vector (Invitrogen, Carlsbad, CA), which contains an Epstein Barr virus (EBV) origin of replication, facilitating the maintenance of plasmid as a multicopy extrachromosomal element.
• EBV Epstein Barr virus
• Another expression vector is the pEF-BOS plasmid containing the promoter of polypeptide Elongation Factor let, which stimulates efficiently transcription in vitro.
• the plasmid is described by Mishizuma and Nagata (Nuc. Acids Res. 18:5322, 1990), and its use in transfection experiments is disclosed by, for example, Demoulin (Mol. Cell. Biol. 16:4710-4716, 1996).
• Still another preferred expression vector is an adenovirus, described by Stratford-Perricaudet, which is defective for El and E3 proteins (J. Clin. Invest. 90:626-630, 1992).
• adenovirus as an Adeno.PlA recombinant is disclosed by Warnier et al., in intradermal injection in mice for immunization against P1A (Int. J. Cancer, 67:303-310, 1996).
• the invention also embraces so-called expression kits, which allow the artisan to prepare a desired expression vector or vectors.
• expression kits include at least separate portions of each of the previously discussed coding sequences. Other components may be added, as desired, as long as the previously mentioned sequences, which are required, are included.
• the invention embraces the use of the above described, human vasa cDNA sequence containing expression vectors, to transfect host cells and cell lines, be these prokaryotic (e.g., E. coli), or eukaryotic (e.g., CHO cells, COS cells, yeast expression systems and recombinant baculovirus expression in insect cells).
• prokaryotic e.g., E. coli
• eukaryotic e.g., CHO cells, COS cells, yeast expression systems and recombinant baculovirus expression in insect cells.
• mammalian cells such as mouse, hamster, pig, goat, primate, etc. They may be of a wide variety of tissue types, and include primary cells and cell lines. Specific examples include dendritic cells, U293 cells, peripheral blood leukocytes, bone marrow stem cells and embryonic stem cells.
• the invention also permits the construction of human vasa gene "knock-outs" in cells and in animals, providing materials for
• the invention also provides isolated polypeptides (including whole proteins and partial proteins), encoded by the foregoing human vasa nucleic acids, and include the polypeptide of SEQ ID NO:2 and unique fragments thereof. Such polypeptides are useful, for example to generate antibodies, as components of an immunoassay, etc. Polypeptides can be isolated from biological samples including tissue or cell homogenates, and can also be expressed recombinantly in a variety of prokaryotic and eukaryotic expression systems by constructing an expression vector appropriate to the expression system, introducing the expression vector into the expression system, and isolating the recombinantly expressed protein.
• Short polypeptides including antigenic peptides (such as are presented by MHC molecules on the surface of a cell for immune recognition) also can be synthesized chemically using well-established methods of peptide synthesis.
• a unique fragment of an human vasa polypeptide in general, has the features and characteristics of unique fragments as discussed above in connection with nucleic acids. As will be recognized by those skilled in the art, the size of the unique fragment will depend upon factors such as whether the fragment constitutes a portion of a conserved protein domain. Thus, some regions of SEQ ID NO:2 will require longer segments to be unique while others will require only short segments, typically between 5 and 12 amino acids (e.g.
• any segment of SEQ ID NO:2, excluding the ones that share identity with it (the polypeptides having amino acid sequences as set forth in SEQ ID NOs: 3, 4, 5, 6, and 7) that is 9 or more amino acids in length will be unique.
• Unique fragments of a polypeptide preferably are those fragments which retain a distinct functional capability of the polypeptide. Functional capabilities which can be retained in a unique fragment of a polypeptide include interaction with antibodies, interaction with other polypeptides or fragments thereof, selective binding to receptors, tissue specific expression, etc. One important activity is the ability to act as a signature for identifying the polypeptide.
• Those skilled in the art are well versed in methods for selecting unique amino acid sequences, typically on the basis of the ability of the unique fragment to selectively distinguish the sequence of interest from non-family members or from family members of other species. A comparison of the sequence of the fragment to those on known databases typically is all that is necessary.
• a "variant" of a human vasa polypeptide is a polypeptide which contains one or more modification to the primary amino acid sequence of a human vasa polypeptide.
• Modifications which create a human vasa polypeptide variant are typically made to the nucleic acid which encodes the human vasa polypeptide, and can include deletions, point mutations, truncations, amino acid substitutions and addition of amino acids or non-amino acid moieties to: 1) reduce or eliminate an activity of a human vasa polypeptide; 2) enhance a property of a human vasa polypeptide, such as protein stability in an expression system or the stability of protein-protein binding; 3) provide a novel activity or property to a human vasa polypeptide, such as addition of an antigenic epitope or addition of a detectable moiety; or 4) to provide equivalent or better binding to a human vasa polypeptide receptor or other molecule (e.g., heparin).
• heparin e.g., heparin
• modifications can be made directly to the polypeptide, such as by cleavage, addition of a linker molecule, addition of a detectable moiety, such as biotin, addition of a fatty acid, and the like.
• Modifications also embrace fusion proteins comprising all or part of the human vasa amino acid sequence.
• One of skill in the art will be familiar with methods for predicting the effect on protein conformation of a change in protein sequence, and can thus "design" a variant human vasa polypeptide according to known methods.
• One example of such a method is described by Dahiyat and Mayo in Science 278:82-87, 1997, whereby proteins can be designed de novo.
• the method can be applied to a known protein to vary a only a portion of the polypeptide sequence.
• specific variants of a polypeptide can be proposed and tested to determine whether the variant retains a desired conformation.
• Variants can include human vasa polypeptides which are modified specifically to alter a feature of the polypeptide unrelated to its physiological activity. For example, cysteine residues can be substituted or deleted to prevent unwanted disulfide linkages. Similarly, certain amino acids can be changed to enhance expression of a human vasa polypeptide by eliminating proteolysis by proteases in an expression system (e.g., dibasic amino acid residues in yeast expression systems in which KEX2 protease activity is present).
• an expression system e.g., dibasic amino acid residues in yeast expression systems in which KEX2 protease activity is present.
• Mutations of a nucleic acid which encodes a human vasa polypeptide preferably preserve the amino acid reading frame of the coding sequence, and preferably do not create regions in the nucleic acid which are likely to hybridize to form secondary structures, such a hairpins or loops, which can be deleterious to expression of the variant polypeptide.
• Mutations can be made by selecting an amino acid substitution, or by random mutagenesis of a selected site in a nucleic acid which encodes the polypeptide. Variant polypeptides are then expressed and tested for one or more activities to determine which mutation provides a variant polypeptide with the desired properties. Further mutations can be made to variants (or to non-variant human vasa polypeptides) which are silent as to the amino acid sequence of the polypeptide, but which provide preferred codons for translation in a particular host. The preferred codons for translation of a nucleic acid in, e.g., E. coli, are well known to those of ordinary skill in the art. Still other mutations can be made to the noncoding sequences of a human vasa gene or cDNA clone to enhance expression of the polypeptide.
• conservative amino acid substitutions may be made in human vasa polypeptides to provide functionally equivalent variants of the foregoing polypeptides, i.e, the variants retain the functional capabilities of the human vasa polypeptides.
• a "conservative amino acid substitution” refers to an amino acid substitution which does not alter the relative charge or size characteristics of the protein in which the amino acid substitution is made.
• Variants can be prepared according to methods for altering polypeptide sequence known to one of ordinary skill in the art such as are found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J .
• Exemplary functionally equivalent variants of the human vasa polypeptides include conservative amino acid substitutions of SEQ ID N0:_2.
• Conservative substitutions of amino acids include substitutions made amongst amino acids within the following groups: (a) M, I, L, V; (b) F, Y, W; (c) K, R, H; (d) A, G; (e) S, T; (f) Q, N; and (g) E, D.
• variants of human vasa polypeptides i.e., variants of human vasa polypeptides which retain the function of the natural human vasa polypeptides
• amino acid sequence of human vasa polypeptides to produce functionally equivalent variants of human vasa polypeptides typically are made by alteration of a nucleic acid encoding human vasa polypeptides (SEQ ID NOs:l, 15).
• substitutions can be made by a variety of methods known to one of ordinary skill in the art.
• amino acid substitutions may be made by PCR-directed mutation, site-directed mutagenesis according to the method of Kunkel (Kunkel, Proc. Nat.
• the invention permits isolation of human vasa polypeptides.
• the polypeptide may be purified from cells which naturally produce the polypeptide by chromatographic means or immunological recognition.
• an expression vector may be introduced into cells to cause production of the polypeptide.
• mRNA transcripts may be microinjected or otherwise introduced into cells to cause production of the encoded polypeptide.
• Translation of human vasa mRNA in cell-free extracts such as the reticulocyte lysate system also may be used to produce human vasa polypeptides.
• Those skilled in the art also can readily follow known methods for isolating human vasa polypeptides. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography and immune-affinity chromatography.
• the invention also provides, in certain embodiments, "dominant negative" polypeptides derived from human vasa polypeptides.
• a dominant negative polypeptide is an inactive variant of a protein, which, by interacting with the cellular machinery, displaces an active protein from its interaction with the cellular machinery or competes with the active protein, thereby reducing the effect of the active protein.
• a dominant negative receptor which binds a ligand but does not transmit a signal in response to binding of the ligand can reduce the biological effect of expression of the ligand.
• a dominant negative catalytically-inactive kinase which interacts normally v/ith target proteins but does not phosphorylate the target proteins can reduce phosphorylation of the target proteins in response to a cellular signal.
• a dominant negative transcription factor which binds to a promoter site in the control region of a gene but does not increase gene transcription can reduce the effect of a normal transcription factor by occupying promoter binding sites without increasing transcription.
• the end result of the expression of a dominant negative polypeptide in a cell is a reduction in function of active proteins.
• One of ordinary skill in the art can assess the potential for a dominant negative variant of a protein, and using standard mutagenesis techniques to create one or more dominant negative variant polypeptides. See, e.g., U.S . Patent No. 5,580,723 and Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. The skilled artisan then can test the population of mutagenized polypeptides for diminution in a selected and/or for retention of such an activity. Other similar methods for creating and testing dominant negative variants of a protein will be apparent to one of ordinary skill in the art.
• the isolation of the human vasa cDNA also makes it possible for the artisan to diagnose a disorder characterized by an abenant expression of human vasa.
• These methods involve determining expression of the human vasa gene, and or human vasa polypeptides derived therefrom. In the former situation, such determinations can be carried out via any standard nucleic acid determination assay, including the polymerase chain reaction, or assaying with labeled hybridization probes as exemplified below. In the latter situation, such determination can be earned out via any standard immunological assay using, for example, antibodies which bind to the secreted human vasa protein.
• the invention also embraces isolated peptide binding agents which, for example, can be antibodies or fragments of antibodies ("binding polypeptides"), having the ability to selectively bind to human vasa polypeptides.
• binding polypeptides include polyclonal and monoclonal antibodies, prepared according to conventional methodology.
• the invention excludes binding agents (e.g., antibodies) that bind to the polypeptides encoded by the nucleic acids of SEQ ID NOs: 3, 4, 5, 6, and 7, and or the nucleic acids having nucleotide sequences with GenBank accession numbers as those described in Table I, and/or polypeptides having amino acid sequences with GenBank accession numbers as those described in Table I..
• an antibody from which the pFc' region has been enzymatically cleaved, or which has been produced without the pFc' region designated an F(ab') 2 fragment
• an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region designated an Fab fragment
• Fab fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain denoted Fd .
• the Fd fragments are the major determinant of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity) and Fd fragments retain epitope-binding ability in isolation.
• CDRs complementarity determining regions
• FRs framework regions
• CDRl through CDR3 complementarity determining regions
• the present invention also provides for F(ab') 2 , Fab, Fv and Fd fragments; chimeric antibodies in which the Fc and/or FR. and or CDRl and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric F(ab') 2 fragment antibodies in which the FR and/or CDRl and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric Fab fragment antibodies in which the FR and/or CDRl and or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; and chimeric Fd fragment antibodies in which the FR and/or CDRl and/or CDR2 regions have been replaced by homologous human or non-human sequences.
• the present invention also includes so-called single chain antibodies.
• polypeptides of numerous size and type that bind specifically to human vasa polypeptides, and complexes of both human vasa polypeptides and their binding partners.
• polypeptide binding agents can be provided by degenerate peptide libraries which can be readily prepared in solution, in immobilized form, as bacterial flagella peptide display libraries or as phage display libraries.
• Combinatorial libraries also can be synthesized of peptides containing one or more amino acids. Libraries further can be synthesized of peptides and non-peptide synthetic moieties.
• Phage display can be particularly effective in identifying binding peptides useful according to the invention. Briefly, one prepares a phage library (using e.g. ml3, fd, or lambda phage), displaying inserts from 4 to about 80 amino acid residues using conventional procedures.
• the inserts may represent, for example, a completely degenerate or biased array.
• DNA sequence analysis can be conducted to identify the sequences of the expressed polypeptides.
• the minimal linear portion of the sequence that binds to the human vasa polypeptide or complex can be determined.
• Yeast two-hybrid screening methods also may be used to identify polypeptides that bind to the human vasa polypeptides.
• the human vasa polypeptides of the invention or a fragment thereof, or complexes of human vasa and a binding partner can be used to screen peptide libraries, including phage display libraries, to identify and select peptide binding partners of the human vasa polypeptides of the invention.
• Such molecules can be used, as described, for screening assays, for purification protocols, for interfering directly with the functioning of human vasa and for other purposes that will be apparent to those of ordinary skill in the art.
• a human vasa polypeptide, or a fragment thereof, also can be used to isolate their native binding partners. Isolation of binding partners may be performed according to well-known methods. For example, isolated human vasa polypeptides (that include human vasa phosporylated polypeptides) can be attached to a substrate, and then a solution suspected of containing an human vasa binding partner may be applied to the substrate. If the binding partner for human vasa polypeptides is present in the solution, then it will bind to the substrate-bound human vasa polypeptide. The binding partner then may be isolated. Other proteins which are binding partners for human vasa, may be isolated by similar methods without undue experimentation.
• the invention also provides novel kits which could be used to measure the levels of the nucleic acids of the invention, expression products of the invention or anti-human vasa antibodies.
• pairs of primers for amplifying human vasa nucleic acids can be included.
• the preferred kits would include controls such as known amounts of nucleic acid probes, human vasa epitopes (such as human vasa expression products) or anti-human vasa antibodies, as well as instructions or other printed material.
• the printed material can characterize the presence of a tumor based upon the outcome of the assay.
• kits may include standard materials such as labeled immunological reagents (such as labeled anti-IgG antibodies) and the like.
• labeled immunological reagents such as labeled anti-IgG antibodies
• One kit is a packaged polystyrene microtiter plate coated with human vasa protein and a container containing labeled anti-human IgG antibodies. A well of the plate is contacted with, for example, serum, washed and then contacted with the anti-IgG antibody. The label is then detected.
• a kit embodying features of the present invention, generally designated by the numeral 1 1, is illustrated in Figure 1.
• Kit 1 1 is comprised of the following major elements : packaging 15, an agent of the invention 17 (e.g., an anti-human vasa antibody), a control agent 19 (e.g., a human vasa epitope), and instructions 21.
• Packaging 15 is a box-like structure for holding a vial (or number of vials) containing an agent of the invention 17, a vial (or number of vials) containing a control agent 19, and instructions 21. Individuals skilled in the art can readily modify packaging 15 to suit individual needs.
• the invention also provides methods to measure the level of human vasa expression in a subject. This can be performed by first obtaining a test sample from the subject.
• the test sample can be tissue, biological fluid, or both (as, for example, in a fine needle aspirate). Tissues include brain, heart, serum, breast, colon, bladder, uterus, prostate, stomach, testis, ovary, pancreas, pituitary gland, adrenal gland, thyroid gland, salivary gland, mammary gland, kidney, liver, intestine, spleen, thymus, bone marrow, trachea, and lung.
• test samples originate from brain, testis, breast and prostate tissues, and biological fluids include blood, saliva, semen, fellopian fluid, and urine.
• vasa expression is used interchangeably with “vasa molecule expression,” and refers to a vasa nucleic acid or a vasa peptide (including polypeptide and protein) expression.
• PCR and Northern blotting can be used to determine the level of human vasa mRNA using products of this invention described earlier, and protocols well known in the art that are found in references which compile such methods.
• human vasa expression can be determined using either polyclonal anti-human vasa sera or monoclonal antibodies in combination with standard immunological assays.
• the preferred methods of the invention compare the measured level of human vasa expression of the test sample to a control having a known human vasa expression (e.g., to assess the presence or absence, or stage of a tumor of germ cell origin in a subject).
• a control human vasa expression can include a known amount of a nucleic acid probe, a human vasa epitope (such as a human vasa expression product), or a sample from the same tissue (fluid or aspirate) of a subject with a 'normal' (control) level of human vasa expression.
• the test sample can be of extragonadal (nongonadal) or gonadal tissue origin.
• the method involves detecting vasa expression in a test sample obtained from an extragonadal tissue of a subject.
• Vasa expression in the extragonadal test sample is indicative of the presence of a tumor of germ cell origin in the subject.
• the preferred methods of the invention compare the measured level of human vasa expression in the extragonadal test sample to the level of vasa expression in a control sample, preferably from the same extragonadal tissue of a 'normal' (control) subject.
• extragonadal test samples from 'normal' subjects contain undetectable expression levels of a vasa molecules; test samples having detectable vasa expression levels are indicative of the presence of a tumor of germ cell origin in the subject.
• the method involves detecting vasa overexpression in the test sample, since vasa molecules are typically expressed at a baseline level conesponding to a 'normal' level in control gonadal tissues.
• Examination of gonadal tissue test samples typically involves examination of histologic samples (e.g., biopsy tissue slides). Histologic samples are commonly stained with agents that reveal tissue/cell morphology.
• histologic samples e.g., from a gonadal tissue biopsy
• histologic samples are commonly stained with agents that reveal tissue/cell morphology.
• the skilled artisan selects histologic samples (e.g., from a gonadal tissue biopsy) that include tissue areas depicting both 'abnormal' and 'normal' morphologic appearance.
• the tissue areas with 'normal' appearance serve as an internal negative control (a preferred control).
• gonadal tissues from 'normal' subjects can be used as a negative control.
• the test samples are compared to the control samples (e.g., negative controls as discussed above or positive controls, i.e., samples of gonadal tissue having tumors of known germ cell origin) and vasa overexpression is determined.
• control samples e.g., negative controls as discussed above or positive controls, i.e., samples of gonadal tissue having tumors of known germ cell origin
• vasa overexpression in the gonadal test sample as compared to a negative control sample is indicative of the presence of a tumor of germ cell origin in the subject.
• the subject has not previously been diagnosed as having a tumor of germ cell origin or a predisposition thereto (e.g., to detect a metastasis in a subject of previously undiagnosed cancer).
• the subject has a clinical diagnosis of a tumor of germ cell origin and the method is to confirm the clinical diagnosis, monitor remission of the tumor, or stage the tumor.
• the tumor can be a testicular tumor (e.g., a seminoma), an ovarian tumor (e.g., a dysgerminoma or a teratoma), or a tumor of an extragonadal tissue (e.g., a rnediastinal tumor or an intracranial tumor).
• the method when the test sample examined is of gonadal origin, can further comprise detecting expression of a tumor-specific agent other than a vasa molecule (nucleic acid or polypeptide) in the test sample.
• Tumor- specific agents other than a vasa molecule include, but are not limited to, ⁇ -hCG, ⁇ - fetoprotein, placental-type alkaline phosphatase. prostate specific antigen, carcinoembryonic antigen, inhibin, epithelial membrane antigen, desmin, vimentin, GFAP -glial fibrillary acidic protein, synaptophysin, chromogranin, cytokeratin isoforms such as 7 and 20, and anti-keratin markers such as AE1/AE3 and CAM5.2.
• a method of subtyping tumors of germ cell origin is provided.
• the method involves detecting vasa expression in a test sample of a known or suspected germ cell origin tumor obtained from a subject.
• Vasa overexpression in the test sample as compared to a control is indicative of a seminoma in the subject, whereas absence of vasa expression in the test sample as compared to a control can be indicative of a nonseminoma in the subject.
• Nonseminomas include embryonal carcinoma, teratoma, choriocarcinoma, yolk sac tumor, or combinations of the foregoing.
• the subject has a tumor of mixed histologic appearance.
• the method can further comprise detecting expression of a tumor-specific agent other than a vasa molecule in the test sample.
• Tumor-specific agents other than a vasa molecule are as described elsewhere herein.
• a method of distinguishing a tumor of germ cell origin from a non-germ cell tumor involves detecting expression of a vasa molecule in a test sample, wherein expression of the vasa molecule is indicative of a tumor of a germ cell origin, and absence of expression of the vasa molecule is indicative of a non-germ cell tumor.
• the non-germ cell tumor resembles histo logically a tumor of germ cell origin.
• Non-germ cell tumors include, but are not limited to, clear cell carcinoma of the ovary (can resemble dysgerminoma), a rnediastinal thymoma, and a testicular lymphoma.
• tumors aberrantly expressing human vasa can include: biliary tract cancer; brain cancer, including glioblastomas and medulloblastomas; breast cancer; cervical cancer; choriocarcinoma; colon cancer; endometrial cancer; esophageal cancer; gastric cancer; hematological neoplasms, including acute lymphocytic and myelogenous leukemia; multiple myeloma; AIDS associated leukemias and adult T-cell leukemia lymphoma; intraepithelial neoplasms, including Bowen's disease and Paget's disease; liver cancer; lung cancer; lymphomas, including Hodgkin's disease and lymphocytic lymphomas; neuroblastomas; oral cancer, including squamous cell carcinoma; ovarian cancer, including those arising from epithelial cells, stromal cells, germ cells and mesenchymal cells; pancreas cancer; prostate cancer; colorectal cancer;
• choriocarcinomas stromal tumors and germ cell tumors; thyroid cancer, including thyroid adenocarcinoma and medullar carcinoma; and renal cancer including adenocarcinoma and Wilms tumor.
• Aberrant expression of a vasa molecule in all of the foregoing tumors is indicative that such tumors originated from cells of germ cell origin, which cells either through development or metastases became part of the tissue presently characterized as tumorous.
• aberrant expression is overexpression of a human vasa molecule.
• Human vasa polypeptides preferably are produced recombinantly, although such polypeptides may be isolated from biological extracts.
• Recombinantly produced human vasa polypeptides include chimeric proteins comprising a fusion of a human vasa protein with another polypeptide, e.g., a polypeptide capable of providing or enhancing protein-protein binding, sequence specific nucleic acid binding (such as GAL4), enhancing stability of the human vasa polypeptide under assay conditions, or providing a detectable moiety, such as green fluorescent protein.
• a polypeptide fused to a human vasa polypeptide or fragment may also provide means of readily detecting the fusion protein, e.g., by immunological recognition or by fluorescent labeling.
• Detection may be effected in any convenient way for cell-based assays such as two- or three-hybrid screens.
• the transcript resulting from a reporter gene transcription assay of human vasa polypeptide interacting with a target molecule typically encodes a directly or indirectly detectable product, e.g., ⁇ -galactosidase activity, luciferase activity, and the like.
• one of the components usually comprises, or is coupled to. a detectable label.
• labels can be used, such as those that provide direct detection (e.g., radioactivity, luminescence, optical or electron density, etc), or indirect detection (e.g., epitope tag such as the FLAG epitope, enzyme tag such as horseseradish peroxidase, etc.).
• the label may be bound to a human vasa binding partner, or incorporated into the structure of the binding partner.
• a variety of methods may be used to detect the label, depending on the nature of the label and other assay components. For example, the label may be detected while bound to the solid substrate or subsequent to separation from the solid substrate. Labels may be directly detected through optical or electron density, radioactive emissions, nonradiative energy transfers, etc. or indirectly detected with antibody conjugates, strepavidin-biotin conjugates, etc. Methods for detecting the labels are well known in the art.
• the invention provides human rasa-specific binding agents, methods of identifying and making such agents, and their use in diagnosis, therapy and pharmaceutical development .
• human v ⁇ y ⁇ -specific pharmacological agents are useful in a variety of diagnostic and therapeutic applications, especially where disease or disease prognosis is associated with altered human vasa binding characteristics.
• Novel human rasa-specific binding agents include human v ⁇ s ⁇ -specific antibodies, cell surface receptors, and other natural intracellular and extracellular binding agents identified with assays such as two hybrid screens, and non-natural intracellular and extracellular binding agents identified in screens of chemical libraries and the like.
• the specificity of human vasa binding to a specific molecule is determined by binding equilibrium constants.
• Targets which are capable of selectively binding a human vasa polypeptide preferably have binding equilibrium constants of at least about 10 M " ' ,
• cell based and cell free assays may be used to demonstrate human v ⁇ ra-specific binding.
• Cell based assays include one, two and three hybrid screens, assays in which human ras ⁇ -mediated transcription is inhibited or increased, etc.
• Cell free assays include human v ⁇ s ⁇ -protein binding assays, immunoassays, etc.
• Other assays useful for screening agents which bind human vasa polypeptides include fluorescence resonance energy transfer (FRET) , and electrophoretic mobility shift analysis (EMSA).
• FRET fluorescence resonance energy transfer
• EMSA electrophoretic mobility shift analysis
• the method involves administering to a subject in need of such treatment an agent that inhibits vasa expression in a germ cell of the subject in an effective amount to inhibit vasa expression and inhibit the growth and/or proliferation of the tumor of germ cell origin in the subject.
• the agent is a vasa antisense nucleic acid.
• the method further comrises co-administering an anti- cancer agent.
• Anti-cancer agents include, but are not limited to: Acivicin; Aclarubicin; Acodazole
• Carmustine Carubicin Hydrochloride; Carzelesin; Cedefingol; Chlorambucil; Cirolemycin; Cisplatin; Cladribine; Crisnatol Mesylate; Cyclophosphamide; Cytarabine; dacarbazine;
• Droloxifene Droloxifene Citrate; Dromostanolone Propionate; Duazomycin; Edatrexate;
• Eflomithine Hydrochloride Elsamitmcin; Enloplatin; Enpromate; Epipropidine; Epirubicin Hydrochloride; Erbulozole; Esorubicin Hydrochloride; Estramustine; Estramustine Phosphate
• Fazarabine Fenretinide; Floxuridine; Fludarabine Phosphate; Fluorouracil; Flurocitabine ;
• Idarubicin Hydrochloride Ifosfamide; Ilmofosine; Interferon Alfa-2a; Interferon Alfa-2b; Interferon Alfa-nl; Interferon Alfa-n3; Interferon Beta-I a; Interferon Gamma-I b; Iproplatin;
• Irinotecan Hydrochloride Lanreotide Acetate; Letrozole; Leuprolide Acetate; Liarozole
• Melphalan Menogaril; Mercaptopurine; Methotrexate; Methotrexate Sodium; Metoprine; Meturedepa; Mitindomide; Mitocarcin; Mitocromin; Mitogillin; Mitomalcin; Mitomycin;
• Mitosper Mitosper; Mitotane; Mitoxantrone Hydrochloride; Mycophenolic Acid; Nocodazole;
• vasa inhibitory agents of the invention are administered in effective amounts.
• An effective amount is a dosage of the vasa inhibitory agent sufficient to provide a medically desirable result.
• the effective amount will vary with the particular condition being treated, the age and physical condition of the subject being treated, the severity of the condition, the duration of the treatment, the nature of the concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. For example, in connection with treating a tumor of germ cell origin in a subject, an effective amount is that amount which inhibits or reduces growth and/or proliferation of the tumor in the subject.
• vasa inhibitory agents of the invention can be used to treat the above- noted conditions according to the preferred modes of administration described below. It is preferred generally that a maximum dose be used, that is, the highest safe dose according to sound medical judgment.
• a subject refers to a human with a tumor of germ cell origin.
• a vasa inhibitory agent of the invention may be administered alone or as part of a pharmaceutical composition.
• a pharmaceutical composition may include the vasa inhibitory agent in combination with any standard physiologically and/or pharmaceutically acceptable carriers which are known in the art.
• the compositions should be sterile and contain a therapeutically effective amount of the vasa inhibitory agent in a unit of weight or volume suitable for administration to a patient.
• pharmaceutically-acceptable earner as used herein means one or more compatible solid or liquid filler, diluents or encapsulating substances which are suitable for administration into a human or other animal.
• carrier denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application.
• compositions also are capable of being co-mingled with the molecules of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy.
• Pharmaceutically acceptable further means a non-toxic material, that is compatible with a biological system such as a cell, cell culture, tissue, or organism.
• the characteristics of the carrier will depend on the route of administration.
• Physiologically and pharmaceutically acceptable carriers include diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art.
• Parenteral vehicles include sodium chloride solution. Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's or fixed oils.
• compositions suitable for parenteral administration conveniently comprise sterile aqueous and non-aqueous preparations of the vasa inhibitory agents of the invention.
• This aqueous preparation may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents.
• Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
• non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate, and including synthetic mono- or di-glycerides.
• the sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butane diol.
• fatty acids such as oleic acid may be used in the preparation of injectables.
• Carrier formulations suitable for oral, subcutaneous, intravenous, intramuscular, etc. administrations can be found in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.
• Parenteral administration routes are preferred according to the present invention. Any local parenteral administration that is medically acceptable, meaning any local administration that produces effective levels of the active compounds without causing clinically unacceptable adverse effects can be used to deliver agents of the invention. Delivery by injection into the affected gonadal tissue is preferred.
• the pharmaceutical preparations are administered in effective amounts.
• the effective amount will depend upon the mode of administration, the particular condition being treated and the desired outcome. It will also depend upon, as discussed above, the stage of the condition, the age and physical condition of the subject, the nature of concurrent therapy, if any, and like factors well known to the medical practitioner. For therapeutic applications, it is that amount sufficient to achieve a medically desirable result. In some cases this is a decrease in germ cell growth and/or proliferation.
• doses of active compounds of the present invention would be from about 0.01 mg/kg per day to 1000 mg/kg per day. It is expected that doses ranging from 50-500 mg/kg will be suitable.
• compositions may conveniently be presented in unit dosage form _> and may be prepared by any of the methods well-known in the art of pharmacy. All methods include the step of bringing the vasa inhibitory agents of the invention into association with a carrier which constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing the vasa inhibitory agents into association with a liquid carrier, a finely divided solid earner, or both, and then, if necessary, shaping the o product.
• compositions suitable for parenteral administration include suspensions in aqueous liquids or non-aqueous liquids such as a syrup, elixir or an emulsion.
• Other delivery systems can include time-release, delayed release or sustained release s delivery systems. Such systems can avoid repeated administrations of the vasa inhibitory agents of the invention, increasing convenience to the subject and the physician.
• Many types of release delivery systems are available and known to those of ordinary skill in the art. They include the above-described polymeric systems, as well as polymer base systems such as poly(lactide-glycolide), copolyoxalates, polycaprolactones, polyesteramides, polyorthoesters, o polyhydroxybutyric acid, and polyanhydrides. Microcapsules of the foregoing polymers containing drugs are described in. for example. U.S. Patent 5,075,109.
• Delivery systems also include non-polymer systems that are: lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono- di- and tri-glycerides; hydrogel release systems; sylastic systems; peptide based systems; wax coatings; compressed tablets using 5 conventional binders and excipients; partially fused implants; and the like.
• lipids including sterols such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono- di- and tri-glycerides
• hydrogel release systems such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono- di- and tri-glycerides
• sylastic systems such as cholesterol, cholesterol esters and fatty acids or neutral fats such as mono- di- and tri-glycerides
• peptide based systems such as fatty acids
• wax coatings such as those described in U.S. Patent Nos.
• Long-term sustained release means that the implant is constructed and arranged to delivery therapeutic levels of the active ingredient for at least 30 days, and preferably 60 days.
• Long-term sustained release implants are well-known to those of ordinary skill in the art and include some of the release systems described above.
• the vasa inhibitory agents of the invention may be administered alone or in combination (co-administered) with the above-described drug therapies by any conventional route, including injection, repeated injection, topical application, etc., over time.
• the administration may, for example, be oral, intraperitoneal, intramuscular, intra-cavity, subcutaneous, intravenous or transdermal for the co-administered anti-cancer agent .
• direct administration to the affected site e.g., ovaries, testis, etc.
• administration by injection is preferred.
• co-administered means administered substantially simultaneously with another anti-cancer agent.
• vasa inhibitory agent of the invention is administered to the subject close enough in time with the administration of the anti-cancer agent.
• the anti-cancer agent may be present in a different formulation than the vasa inhibitory agent of the invention, or it may be part of the same formulation (and therefore be administered locally together with the agent of the invention).
• the co-administered agent can act cooperatively, additively or synergistically with a vasa inhibitory agent of the invention to produce a desired effect, for example, inhibition of the tumor of germ cell origin. Since germ cells are relatively 'dispensible' (i.e., necessary for reproduction but not necessary for survival), as long as the agent is delivered to the gonads, normal (nontumorous) germ cells can also be targeted with the therapeutic agents of the invention.
• the anti-cancer agent is administered in effective amounts. Such amounts maybe less than these sufficient to provide a therapeutic benefit when the agent is administered alone and not in combination with a vasa inhibitory agent of the invention. A person of ordinary skill in the art would be able to determine the effective amounts needed. The invention will be more fully understood by reference to the following examples.
• EST's Expressed sequence tags (EST's) corresponding to the human vasa gene were identified in a publically available database maintained by the National Center for Biotechnology Information (NCBI) using the BLAST program. The DNA sequence corresponding to the mouse vasa cDNA (Genbank accession #2500525) was the query sequence; default search parameters were employed. Several EST's (zt93a07.sl- Genbank_# AA399611; zt93a07.rl - Genbank #AA398976; qf47dll.x - Genbank #AI217144) corresponding to the 3' end of the human vasa gene were identified.
• a 28-mer oligonucleotide corresponding to the 3' untranslated region was designed nad synthesized (5'-CTC TGC ATC AAA ACC ACA GAC TTG AAG G-3', SEQ ID NO:8). This oligonucleotide was then used in a 5' RACE (rapid amplification of cDNA ends) reaction to obtain a human vasa cDNA..
• Example 2 Preparation and Testing of Antibodies Selective for a Vasa Protein. Regions likely to be antigenic were identified by an algorithm for antigencity
• VDTRKGKSTLNTAGFSSSRAPNPVDDESW SEQ ID NO: 10 (amino acids 695-723 of SEQ ID NO:2).
• SEQ ID NO: 10 amino acids 695-723 of SEQ ID NO: 2.
• PCR was performed on pVAS3 with the primers 5' -AAG TCA, CCA TGG GGG ATG AA-3', SEQ ID NO: 11 (designed around a naturally occuring Nc ⁇ J site) and 5'-TTA AGA TCT TTT TTG CAC AGG AGT AAG C-3', SEQ ID NO:12 (which contains an engineering Bglll site).
• the product was digested with the restriction enzymes Ncol and Bglll and ligated in the expression vector PQE-60 (QIAGEN) linearized with Nc ⁇ J and Bglll (directional cloning).
• An -vasa antibodies were prepared and tested for selectivity for the vasa protein using conventional immunohisto- and immunocyto- chemistry methods adapted to include the vasa protein (or fragment thereof) as a positive control and a non-vasa protein (lacking sequence homology to vasa protein) as a negative control. Additional controls (e.g., negative controls containing nongonadal tissue, tumors of non-germ cell origin), can be included in the assay to establish the specificity of the antibodies for detecting tumors of germ cell origin in a complex sample.
• additional controls e.g., negative controls containing nongonadal tissue, tumors of non-germ cell origin
• tissue samples are performed on formalin-fixed, paraffin- embedded tissue following antigen retrieval as routinely done on clinical material in a hospital pathology laboratory setting.
• Exemplary samples include: normal testes and ovaries, other normal tissues, a range of major tumor types (to evaluate specificity) and germ cell tumors of various histologic subtypes and anatomic locations (to establish clinical utility for detecting these tumors).
• Preliminary results confirmed the predicted cytoplasmic immunoreactivity in germ cells with an appropriate negative result obtained for the preimmune control.
• the specificity of anti-human vasa antibodies for testicular germ cell tumors was also confirmed using immunohistochemical stains.
• Granulosa cell tumor non-germ cell tumor of the ovary -negative control
• classic seminoma classic seminoma
• Permatocytic seminoma testis
• sections were incubated with a 1 : 1000 dilution of affinity-purified polyclonal an ⁇ -vasa antibody. Detection was performed as described elsewhere herein using diaminobenzidine as the chromogen. Slides were counterstained with hematoxylin.
• Example 3 Detection of A Vasa Protein By Immunoassay.
• Vasa protein (peptide and/or polypeptide) detection is carried out by the indirect enzyme-linked immunosorbent assay (ELISA).
• ELISA indirect enzyme-linked immunosorbent assay
• assays are well known in the art. Briefly, ninety six-well microtiter plates (Dynatech Laboratories, Alexandria, VA) are coated with, for example, serum, germ cell tumor culture supernatants, germ cell tumor lysates/extracts, etc., and left overnight at 4°C. The plates were then washed 3 times with PBS containing 0.05% Tween-20 and blocked with 5% dry milk for 2 hrs at 37 °C.
• the plates are washed and incubated again overnight at 4°C with polyclonal vasa antisera or vasa monoclonal antibodies as described earlier (diluted 1 : 100 -1 : 10 7 in PBS with 1% dry milk).
• the plates are washed, and lOO ⁇ l of peroxidase-conjugated goat anti-mouse (or anti-anima/ used to generate antibodies/sera) IgG (Kirkegaard & Perry Laboratories, Inc., Gaithersburg, MD) at 1 :2,000 dilution in PBS with 0.05% Tween-20 and 1 % dry milk, are added.
• the plates are incubated for 2 hrs at 37 °C.
• the plates are then washed 3 times with PBS containing 0.05% Tween-20. Then, l OO ⁇ l of O-phenylenediamine (0.4mg/ml in citrate phosphate buffer containing 0.015% hydrogen peroxide; Sigma Chemical Co. St Louis, MO), are added to each well, and the reaction is stopped by the addition of 2.5N HC1. After 15 minutes the optical density at 492nm (OD 492 ) is measured using a EL308 ELISA reader (Bio- Tek Instruments, WinooskiNT). The titer expressed in OD 49 unit is calculated as a multiple of the dilution in the linear portion of a standard plot.
• Example 4 Detection of Vasa Nucleic Acid by PCR amplification.
• Vasa protein expression is detected by determining whether mRNA for the vasa protein is present in a sample.
• the preferred procedure for detecting mRNA for vasa protein is by PCR amplification.
• RT-PCR_ assay of vasa mRNA expression were designed using the Primer3 program (Whitehead Institute for Biomedical Research) for an RT-PCR_ assay of vasa mRNA expression.
• RT-PCR was performed using the Superscript One-Step PCR kit (GIBCO) per the manufacturer ' s instructions.
• GEBCO Superscript One-Step PCR kit
• Example 5 Detection of vasa molecules in Tumor Test Samples
• An exemplary procedure for detecting a tumor marker in a breast tumor tissue sample or extract is provided in U.S. Patent No. 5,723,302, entitled, "Detection of prostrate-specific antigen in breast tumors", issued to E. Diamandis.
• An exemplary procedure for detecting a tumor marker in a blood sample is provided in U.S. Patent No. 5,935,775, entitled, "Whole blood analysis of prostate specific antigen spotted on a solid support", issued to G. Savjani. It is to be understood that these exemplary procedures can be modified by one of ordinary skill in the art using no more that routine experimentation to detect the vasa molecule in any type of sample using the novel reagents disclosed herein.
• Solid tissue/tumor samples A tumor sample or intact tissue is prepared in accordance with standard histological procedures and analyzed by, e.g., in situ immunohistochemistry, enzyme immunoassay (to detect vasa protein), or by, e.g., nucleic acid enrichment (to detect a vasa nucleic acid). Immunoassays are performed as described above (Example 3) using the anti-vasa protein antibodies that selectively bind to the vasa protein or peptides. Nucleic acid assays are performed as described above (Example 4) for detection of a vasa nucleic acid, e.g., by PCR amplification.
• RNA or mRNA is isolated from the tumor samples and cDNA synthesized by reverse transcription. PCR amplification of cDNA is accomplished using vasa specific primers also as described above. A probe is used to detect cDNA for vasa. Other methods for detecting an RNA for vasa may also be used, such as, the northern blot technique.
• Blood samples can be used directly in liquid form, dried onto a solid support (see, e.g., U.S. 5,935,775), or can be further processed in accordance with standard procedures known to those of ordinary skill in the art for use in the assays of the invention. For example, the sera can be separated into fractions prior to analysis for the presence of a vasa molecule. Analysis.
• vasa molecule in a tumor sample of a subject is diagnostic of the presence of a tumor of germ cell origin in the subject.
• samples of known pathology are assayed to determine the presence or absence of a vasa molecule and the presence or absence of the vasa molecule is correlated to the presence or absence of a tumor of germ cell origin in known samples of positive controls (tumor present) and negative controls (tumor absent), respectively.
• Additional internal assay controls can be used to verify assay reproducibility (e.g., analysis of known sample components, such as other known protein or other known nucleic acid components in the tissue from which the sample is derived, e.g., ⁇ -hCG, ⁇ -fetoprotein, placental-type alkaline phosphatase, prostate specific antigen, carcinoembryonic antigen, inhibin, epithelial membrane antigen, desmin, vimentin, GFAP -glial fibrillary acidic protein, synaptophysin, chromogranin, cytokeratin isoforms such as 7 and 20, anti-keratin markers such as AE1/AE3 and CAM5.2, etc.).
• known sample components such as other known protein or other known nucleic acid components in the tissue from which the sample is derived, e.g., ⁇ -hCG, ⁇ -fetoprotein, placental-type alkaline phosphatase, prostate specific antigen, carcinoembryonic anti
• a statistically significant, positive conelation is established between the presence of a vasa molecule and the presence of a tumor of germ cell origin.
• a statistically significnt positive correlation also is established between the relative amount of the vasa molecule present in the sample (e.g., of gonadal origin) of a subject, and the stage and/or size of the subject's tumor, as well as the degree of metastasis in the subject. This correlation is used to evaluate patient response to treatment modalities, monitor tumor regression and/or remission, and/or to predict patient survival.

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