Mammalian IAP gene family, primers, probes, and detection methods
Disclosed is substantially pure DNA encoding mammalian IAP polypeptides; substantially pure polypeptides; and methods of using such DNA to express the IAP polypeptides in cells and animals to inhibit apoptosis. Also disclosed are conserved regions characteristic of the IAP family and primers and probes for the identification and isolation of additional IAP genes. In addition, methods for treating diseases and disorders involving apoptosis are provided.
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There are two general ways by which cells die. An easily recognized pathway is necrosis, a process of cell death usually resulting from severe and sudden injury. In necrosis, changes in cellular homeostasis occur with loss of membrane integrity. Dysregulation of osmotic pressure results and, as a consequence, the cells swell and finally rupture. The cellular contents are then spilled into the surrounding tissue space and, usually, an inflammation response ensues. A second form of cell death is apoptosis. This cell “suicide” pathway or programmed cell death often occurs so rapidly that in some biological systems the apoptotic process is difficult to ascertain. Indeed, it has been only in the past few years that the involvement of apoptosis in a wide spectrum of biological processes has become recognized. Apoptosis is a fundamental physiological pathway of cell death, highly conserved throughout evolution, and playing a major role in development, viral pathogenesis, cancer, autoimmune diseases and neurodegenerative disorders.
Inappropriate increases in apoptosis may cause or contribute to a variety of diseases, including AIDS, neurodegenerative diseases (e.g. Alzheimer's Disease, Parkinson's Disease, Amyotrophic Lateral Sclerosis (ALS), retinitis pigmentosa and other diseases of the retina, myelodysplastic syndrome (e.g., aplastic anemia), toxin-induced liver disease (e.g., alcoholism) and ischemic injury (e.g., myocardial infarction, stroke, and reperfusion injury). In addition, disruption of normally occurring apoptosis has been implicated in the development of some cancers (e.g. follicular lymphoma, p53 carcinomas, and hormone dependent tumors), autoimmune disorders (e.g., lupus erythematosis and multiple sclerosis) and viral infections (e.g., herpes virus, poxvirus, and adenovirus infections).
Mature CD4+ T-lymphocytes in patients with HIV-1 have been observed to respond to stimulation with mitogens or super-antigens by undergoing increased apoptosis. The great majority of these cells are not infected and similar inappropriate antigen-induced apoptosis could be very important in the destruction of this vital part of the immune system early in HIV infection.
Baculoviruses encode inhibitors of apoptosis proteins (IAPs). These proteins inhibit the apoptosis which otherwise occurs when insect cells are infected by the virus. Baculovirus IAP proteins work in a manner which is thought to be independent of other viral proteins. The baculovirus IAP genes include sequences encoding a ring zinc finger-like motif which is presumed to be involved in the direct binding of DNA.
SUMMARY OF THE INVENTIONIn general, the invention features substantially pure DNA (for example, genomic DNA, cDNA, or synthetic DNA) encoding a mammalian IAP polypeptide as defined below. In related aspects, the invention also features a vector, a cell (e.g., a mammalian, yeast or bacterial cell), and a transgenic animal or embryo thereof which includes such a substantially pure DNA encoding an IAP polypeptide.
In preferred embodiments, an IAP gene is the xiap (including human xiap and its murine homolog, m-xiap), hiap1 (including human hiap1 and m-hiap1), or the hiap2 gene (including human hiap2 and m-hiap2). In most preferred embodiments the IAP gene is a human IAP gene. In other various preferred embodiments, the cell is a transformed cell. In related aspects, the invention features a transgenic animal containing a transgene which encodes an IAP polypeptide that is expressed in or delivered to tissue normally susceptible to apoptosis.
In yet another aspect, the invention features DNA encoding fragments of IAP polypeptides including the BIR domains and the RZF domains provided herein.
In specific embodiments, the invention features DNA sequences substantially identical to the DNA sequences shown in
In another aspect, the invention also features RNA which is encoded by the DNA described herein. Preferably, the RNA is mRNA. In another embodiment the RNA is antisense RNA.
In another aspect, the invention features a substantially pure polypeptide having a sequence substantially identical to one of the IAP amino acid sequences shown in
In a second aspect, the invention features a substantially pure DNA which includes a promoter capable of expressing the IAP gene in a cell susceptible to apoptosis. In preferred embodiments, the IAP gene is xiap (including the human or murine xiap), hiap1 (preferably the human or murine hiap1), or hiap2 (preferably the human or murine hiap2). hiap2 may be the full length gene, as shown in
In preferred embodiments, the promoter is the promoter native to an IAP gene. Additionally, transcriptional and translational regulatory regions are preferably native to an IAP gene.
In another aspect, the invention provides transgenic cell lines and transgenic animals. The transgenic cells of the invention are preferably cells which are susceptible to apoptosis. In preferred embodiments, the transgenic cell is a fibroblast, neuronal cell, a lymphocyte cell, or an insect cell. Most preferably, the neuron is a motor neuron and the lymphocyte is a CD4+ T-cell.
In another aspect, the invention features a method of inhibiting apoptosis which involves producing a transgenic cell having a transgene encoding an IAP polypeptide wherein the transgene is integrated into the genome of the cell and is positioned for expression in the cell and wherein the IAP transgene is expressed in the cell at a level sufficient to inhibit apoptosis.
In a related aspect, the invention features a transgenic animal, preferably a mammal, more preferably a rodent, and most preferably a mouse, having either increased copies of IAP genes inserted into the genome or a knockout of an IAP gene in the genome. The transgenic animals may express an increased amount of IAP polypeptide or may express a decreased amount of an IAP polypeptide, respectively. In related embodiments, the invention provides a method of utilizing the IAP nucleic acid to engineer a knockout mutation in an IAP gene and a method of making an animal with increased expression by insertion of IAP gene into the genome.
In another aspect, the invention features a method of detecting an IAP in a cell involving: (a) contacting the IAP gene or a portion thereof greater than 9 nucleic acids, preferably greater than 18 nucleic acids in length with a preparation of genomic DNA from the cell under hybridization conditions providing detection of DNA sequences having about 50% or greater nucleotide sequence identity to the amino acid encoding DNA sequences of hiap1, hiap2, or xiap IAP polypeptides.
In another aspect, the invention features a method of producing an IAP polypeptide which involves: (a) providing a cell transformed with DNA encoding an IAP polypeptide positioned for expression in the cell; (b) culturing the cell under conditions for expressing the DNA; and (c) isolating the IAP polypeptide. In preferred embodiments the IAP polypeptide is expressed by DNA which has a constituative or inducible promotor. In our embodiment, the promotor is a heterologous promotor.
In another aspect, the invention features substantially pure mammalian IAP polypeptide. Preferably, the polypeptide includes a greater than 50 amino acid sequence substantially identical to a greater than 50 amino acid sequence shown in any one of
In another aspect, the invention features a recombinant mammalian polypeptide capable of modulating apoptosis wherein the polypeptide includes at least a ring zinc finger domain and a BIR domain as defined herein. In preferred embodiments, the invention features a substantially pure polypeptide and an oligonucleotide encoding said polypeptide, the polypeptide including a ring zinc finger (RZF) having the sequence:
Glu Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa2 Xaa1 Xaa1 Xaa1 Cys Lys Xaa3 Cys Met Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa3 Xaa1 Phe Xaa1 Pro Cys Gly His Xaa1 Xaa1 Xaa1 Cys Xaa1 Xaa1 Cys Ala Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Cys Pro Xaa1 Cys, wherein Xaa1 is any amino acid, Xaa2 is Glu or Asp, Xaa3 is Val or Ile (SEQ ID NO:1); and at least one BIR domain having the sequence: Xaa1 Xaa1 Xaa1 Arg Leu Xaa1 Thr Phe Xaa1 Xaa1 Trp Pro Xaa2 Xaa1 Xaa1 Xaa2 Xaa2 Xaa1 Xaa1 Xaa1 Xaa1 Leu Ala Xaa1 Ala Gly Phe Tyr Tyr Xaa1 Gly Xaa1 Xaa1 Asp Xaa1 Val Xaa1 Cys Phe Xaa1 Cys Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Trp Xaa1 Xaa1 Xaa1 Asp Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 His Xaa1 Xaa1 Xaa1 Xaa1 Pro Xaa1 Cys Xaa1 Phe Val, wherein Xaa1 may be any amino acid and Xaa2 may be any amino acid or may be absent (SEQ ID NO:2).
In various preferred embodiments the protein has at least two or, more preferably at least three BIR domains, the RZF domain has one of the IAP sequences shown in
In another aspect, the invention features an IAP gene isolated according to the method involving: (a) providing a sample of DNA; (b) providing a pair of oligonucleotides having sequence homology to a conserved region of an IAP disease-resistance gene; (c) combining the pair of oligonucleotides with the cell DNA sample under conditions suitable for polymerase chain reaction-mediated DNA amplification; and (d) isolating the amplified IAP gene or fragment thereof.
In preferred embodiments, the amplification is carried out using a reverse-transcription polymerase chain reaction, for example, the RACE method.
In another aspect, the invention features an IAP gene isolated according to the method involving: (a) providing a preparation of DNA; (b) providing a detectably-labelled DNA sequence having homology to a conserved region of an IAP gene; (c) contacting the preparation of DNA with the detectably-labelled DNA sequence under hybridization conditions providing detection of genes having 50% or greater nucleotide sequence identity; and (d) identifying an IAP gene by its association with the detectable label.
In another aspect, the invention features an IAP gene isolated according to the method involving: (a) providing a cell sample; (b) introducing by transformation into the cell sample a candidate IAP gene; (c) expressing the candidate IAP gene within the cell sample; and (d) determining whether the cell sample exhibits an altered apoptotic response, whereby a response identifies an IAP gene.
In another aspect, the invention features a method of identifying an IAP gene in a cell, involving: (a) providing a preparation of cellular DNA (for example, from the human genome or a cDNA library (such as a cDNA library isolated from a cell type which undergoes apoptosis); (b) providing a detectably-labelled DNA sequence (for example, prepared by the methods of the invention) having homology to a conserved region of an IAP gene; (c) contacting the preparation of cellular DNA with the detectably-labelled DNA sequence under hybridization conditions providing detection of genes having 50% nucleotide or greater sequence identity; and (d) identifying an IAP gene by its association with the detectable label.
In another aspect, the invention features a method of isolating an IAP gene from a recombinant library, involving: (a) providing a recombinant library; (b) contacting the library with a detectably-labelled gene fragment produced according to the PCR method of the invention under hybridization conditions providing detection of genes having 50% or greater nucleotide sequence identity; and (c) isolating an IAP gene by its association with the detectable label.
In another aspect, the invention features a method of identifying an IAP gene involving: (a) providing a cell tissue sample; (b) introducing by transformation into the cell sample a candidate IAP gene; (c) expressing the candidate IAP gene within the cell sample; and (d) determining whether the cell sample exhibits inhibition of apoptosis, whereby a change in (i.e. modulation of) apoptosis identifies an IAP gene.
Preferably, the cell sample is a cell type which may be assayed for apoptosis (e.g., lymphocytes, T-cells and B-cells, neuronal cells, baculovirus infected insect cells and fibroblast cells); the candidate IAP gene is obtained from a cDNA expression library; and the apoptosis response is the inhibition of apoptosis.
In another aspect, the invention features a method of inhibiting apoptosis in a mammal wherein the method includes: (a) providing DNA encoding at least one IAP polypeptide to a cell which is susceptible to apoptosis; wherein the DNA is integrated into the genome of the cell and is positioned for expression in the cell; and the IAP gene is under the control of regulatory sequences suitable for controlled expression of the gene(s); wherein the IAP transgene is expressed at a level sufficient to inhibit apoptosis relative to a cell lacking the IAP transgene. It will be appreciated that IAP polypeptides also may be administered directly to inhibit any undesirable apoptosis.
In a related aspect, the invention features a method of inhibiting apoptosis wherein the method involves: (a) producing a cell having integrated in the genome a transgene containing the IAP gene under the control of a promoter providing constitutive expression of the IAP gene.
In yet another related aspect, the invention features a method of inhibiting apoptosis wherein the method involves: (a) producing a cell having integrated in the genome a transgene containing the IAP gene under the control of a promoter providing controllable expression of the IAP gene; and (b) regulating the environment of the cell so that the IAP transgene is controllably expressed in the cell. In preferred embodiments, the IAP gene is expressed using a tissue-specific or cell type-specific promoter, or by a promoter that is activated by the introduction of an external signal or agent, such as a chemical signal or agent. In preferred embodiments the cell is a lymphocyte or B-cell, a neuronal cell, or a fibroblast. In other embodiments the cell is a cell in an HIV infected human, or a mammal with a neurodegenerative disease, ischemia, toxin induced liver disease, or a myelodysplastic syndrome.
In a related aspect, the invention provides a method of inhibiting apoptosis in a mammal by providing an apoptosis-inhibiting amount of IAP polypeptide.
In another aspect, the invention features a purified antibody which binds specifically to an IAP family protein. Such an antibody may be used in any standard immunodetection method for the identification of an IAP polypeptide. Preferably, the antibody binds specifically to xiap, hiap1 or hiap2. In various embodiments the antibody may react with other IAP polypeptides or may be specific for one or a few IAP polypeptides. The antibody may be a monoclonal polyclonal antibody. Preferably, the antibody reacts specifically with only one of the IAP polypeptides, for example, reacts with murine and human xiap, but not with hiap1 or hiap2 from mammalian species.
In another aspect, the invention features a method of identifying a compound which modulates apoptosis. The method includes (a) providing a cell expressing an IAP polypeptide; and (b) contracting the cell with a candidate compound, and monitoring the expression of an IAP gene. An alteration in the level of expression of the IAP gene indicates the presence of a compound which modulates apoptosis. The compound may be an inhibitor or an enhancer of apoptosis. In various preferred embodiments, the cell is a fibroblast, a neuronal cell, a lymphocyte (T-cell or B-cell), or an insect cell; the polypeptide expression being monitored is XIAP, HIAP1, or HIAP2 (e.g., human or murine).
In a related aspect, the invention features methods of detecting compounds which modulate apoptosis using the interaction trap technology and IAP polypeptides or fragments thereof as a component of the bait. In preferred embodiments, the compound being tested as a modulator of apoptosis is also a polypeptide.
In another aspect, the invention features a method for diagnosing a cell proliferation disease, or an increased liklihood of such a disease, using an IAP nucleic acid probe or antibody. Preferably, the disease is a cancer. Most preferably, the disease is selected from the group consisting of promyelocytic leukemia, a Hela-type carcinoma, chronic myelogenous leukemia (preferably using xiap or hiap2 related probes), lymphoblastic leukemia (preferably using a xiap related probe), Burkitt's lymphoma (preferably using an hiap1 related probe), colorectal adenocarcinoma, lung carcinoma, and melanoma (preferably using a xiap probe). Preferably, a diagnosis is indicated by a 2-fold increase in expression or activity, more preferably, at least a 10-fold increase in expression or activity.
By “IAP gene” is meant a gene encoding a polypeptide having at least one BIR domain and a ring zinc finger domain which is capable of modulating (inhibiting or enhancing) apoptosis in a cell or tissue when provided by other intracellular or extracellular delivery methods. In preferred embodiments the IAP gene is a gene having about 50% or greater nucleotide sequence identity to at least one of the IAP amino acid encoding sequences of
By an “IAP gene” is also meant any member of the family of apoptosis inhibitory genes characterized by their ability to modulate apoptosis and having at least 20%, preferably 30%, and most preferably 50% amino acid sequence identity to at least one of the conserved regions of one of the IAP members described herein (i.e., either the BIR or ring zinc finger domains from the human or murine xiap, hiap1 and hiap2). Representative members of the IAP gene family include, without limitation, the human and murine xiap, hiap1, and hiap2 genes. By “IAP protein” is meant a polypeptide encoded by an IAP gene.
By “BIR domain” is meant a domain having the amino acid sequence of the consensus sequence: Xaa1 Xaa1 Xaa1 Arg Leu Xaa1 Thr Phe Xaa1 Xaa1 Trp Pro Xaa2 Xaa1 Xaa1 Xaa2 Xaa2 Xaa1 Xaa1 Xaa1 Xaa1 Leu Ala Xaa1 Ala Gly Phe Tyr Tyr Xaa1 Gly Xaa1 Xaa1 Asp Xaa1 Val Xaa1 Cys Phe Xaa1 Cys Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Trp Xaa1 Xaa1 Xaa1 Asp Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 His Xaa1 Xaa1 Xaa1 Xaa1 Pro Xaa1 Cys Xaa1 Phe Val, wherein Xaa1 is any amino acid and Xaa2 is any amino acid or is absent (SEQ ID NO:2). Preferably, the sequence is substantially identical to one of the BIR domain sequences provided for xiap, hiap1, hiap2 herein.
By “ring zinc finger” or “RZF” is meant a domain having the amino acid sequence of the consensus sequence: Glu Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa2 Xaa1 Xaa1 Xaa1 Cys Lys Xaa3 Cys Met Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Xaa3 Xaa1 Phe Xaa1 Pro Cys Gly His Xaa1 Xaa1 Xaa1 Cys Xaa1 Xaa1 Cys Ala Xaa1 Xaa1 Xaa1 Xaa1 Xaa1 Cys Pro Xaa1 Cys, wherein Xaa1 is any amino acid, Xaa2 is Glu or Asp, and Xaa3 is Val or Ile (SEQ ID NO:1). Preferably, the sequence is substantially identical to the RZF domains provided herein for the human or murine xiap, hiap1, or hiap2.
By “modulating apoptosis” or “altering apoptosis” is meant increasing or decreasing the number of cells which undergo apoptosis in a given cell population. Preferably, the cell population is selected from a group including T-cells, neuronal cells, fibroblasts, or any other cell line known to undergo apoptosis in a laboratory setting (e.g., the baculovirus infected insect cells). It will be appreciated that the degree of modulation provided by an IAP or modulating compound in a given assay will vary, but that one skilled in the art can determine the statistically significant change in the level of apoptosis which identifies an IAP or a compound which modulates an IAP.
By “inhibiting apoptosis” is meant any decrease in the number of cells which undergo apoptosis relative to an untreated control. Preferably, the decrease is at least 25%, more preferably the decrease is 50%, and most preferably the decrease is at least one-fold.
By “polypeptide” is meant any chain of amino acids, regardless of length or post-translational modification (e.g., glycosylation or phosphorylation).
By “substantially identical” is meant a polypeptide or nucleic acid exhibiting at least 50%, preferably 85%, more preferably 90%, and most preferably 95% homology to a reference amino acid or nucleic acid sequence. For polypeptides, the length of comparison sequences will generally be at least 16 amino acids, preferably at least 20 amino acids, more preferably at least 25 amino acids, and most preferably 35 amino acids. For nucleic acids, the length of comparison sequences will generally be at least 50 nucleotides, preferably at least 60 nucleotides, more preferably at least 75 nucleotides, and most preferably 110 nucleotides.
Sequence identity is typically measured using sequence analysis software (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705). Such software matches similar sequences by assigning degrees of homology to various substitutions, deletions, and other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine, valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.
By a “substantially pure polypeptide” is meant an IAP polypeptide which has been separated from components which naturally accompany it. Typically, the polypeptide is substantially pure when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, IAP polypeptide. A substantially pure IAP polypeptide may be obtained, for example, by extraction from a natural source (e.g., a fibroblast, neuronal cell, or lymphocyte cell); by expression of a recombinant nucleic acid encoding an IAP polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, e.g., those described in column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.
A protein is substantially free of naturally associated components when it is separated from those contaminants which accompany it in its natural state. Thus, a protein which is chemically synthesized or produced in a cellular system different from the cell from which it naturally originates will be substantially free from its naturally associated components. Accordingly, substantially pure polypeptides include those derived from eukaryotic organisms but synthesized in E. coli or other prokaryotes.
By “substantially pure DNA” is meant DNA that is free of the genes which, in the naturally-occurring genome of the organism from which the DNA of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or which exists as a separate molecule (e.g., a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. It also includes a recombinant DNA which is part of a hybrid gene encoding additional polypeptide sequence.
By “transformed cell” is meant a cell into which (or into an ancestor of which) has been introduced, by means of recombinant DNA techniques, a DNA molecule encoding (as used herein) an IAP polypeptide.
By “transgene” is meant any piece of DNA which is inserted by artifice into a cell, and becomes part of the genome of the organism which develops from that cell. Such a transgene may include a gene which is partly or entirely heterologous (i.e., foreign) to the transgenic organism, or may represent a gene homologous to an endogenous gene of the organism.
By “transgenic” is meant any cell which includes a DNA sequence which is inserted by artifice into a cell and becomes part of the genome of the organism which develops from that cell. As used herein, the transgenic organisms are generally transgenic mammalian (e.g., rodents such as rats or mice) and the DNA (transgene) is inserted by artifice into the nuclear genome.
By “transformation” is meant any method for introducing foreign molecules into a cell. Lipofection, calcium phosphate precipitation, retroviral deliver, electroporation and biolistic transformation are just a few of the teachings which may be used. For example, Biolistic transformation is a method for introducing foreign molecules into a cell using velocity driven microprojectiles such as tungsten or gold particles. Such velocity-driven methods originate from pressure bursts which include, but are not limited to, helium-driven, air-driven, and gunpowder-driven techniques. Biolistic transformation may be applied to the transformation or transfection of a wide variety of cell types and intact tissues including, without limitation, intracellular organelles (e.g., and mitochondria and chloroplasts), bacteria, yeast, fungi, algae, animal tissue, and cultured cells.
By “positioned for expression” is meant that the DNA molecule is positioned adjacent to a DNA sequence which directs transcription and translation of the sequence (i.e., facilitates the production of, e.g., an IAP polypeptide, a recombinant protein or a RNA molecule).
By “reporter gene” is meant a gene whose expression may be assayed; such genes include, without limitation, β-glucuronidase (GUS), luciferase, chloramphenicol transacetylase (CAT), and β-galactosidase.
By “promoter” is meant minimal sequence sufficient to direct transcription. Also included in the invention are those promoter elements which are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue-specific or inducible by external signals or agents; such elements may be located in the 5′ or 3′ regions of the native gene.
By “operably linked” is meant that a gene and a regulatory sequence(s) are connected in such a way as to permit gene expression when the appropriate molecules (e.g., transcriptional activator proteins) are bound to the regulatory sequence(s).
By “conserved region” is meant any stretch of six or more contiguous amino acids exhibiting at least 30%, preferably 50%, and most preferably 70% amino acid sequence identity between two or more of the IAP family members, (e.g., between human HIAP1, HIAP2, and XIAP). Examples of preferred conserved regions are shown (as boxed or designated sequences) in
By “detectably-labelled” is meant any means for marking and identifying the presence of a molecule, e.g., an oligonucleotide probe or primer, a gene or fragment thereof, or a cDNA molecule. Methods for detectably-labelling a molecule are well known in the art and include, without limitation, radioactive labelling (e.g., with an isotope such as 32P or 35S) and nonradioactive labelling (e.g., chemiluminescent labelling, e.g., fluorescein labelling).
By “purified antibody” is meant antibody which is at least 60%, by weight, free from proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably 90%, and most preferably at least 99%, by weight, antibody, e.g., an IAP specific antibody. A purified antibody may be obtained, for example, by affinity chromatography using recombinantly-produced protein or conserved motif peptides and standard techniques.
By “specifically binds” is meant an antibody which recognizes and binds a protein but which does not substantially recognize and bind other molecules in a sample, e.g., a biological sample, which naturally includes protein.
Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.
DETAILED DESCRIPTIONThe drawings will first be described.
Drawings
We have discovered a new class of mammalian proteins which modulate apoptosis (IAPs) and the genes which encode these proteins. The IAP proteins are characterized by the presence of a ring zinc finger (RZF) domain (
This application is related to U.S. Ser. No. 08/511,485, filed Aug. 4, 1995. U.S. Ser. No. 08/511,485 is hereby incorporated by reference.
*Positions indicate correspond to those shown in FIGS. 1-4.
*Positions indicate correspond to those shown in FIGS. 1-4.
Recognition of this mammalian IAP family has provided emergent patterns of protein structure. Recognition of these patterns has also allowed us assign the function of a modulator of apoptosis to a drosophila gene product of previously unknown function (Genbank Accession Number M96581). The amino acid sequence of this protein, termed diap, is shown in
The IAP proteins may be used to inhibit the apoptosis which occurs as part of disease or disorder processes. For example, IAP polypeptides or nucleic acid encoding IAP polypeptides may be administered for the treatment of or prevention of apoptosis which occurs as a part of AIDS, neurodegenerative diseases, ischemic injury, toxin-induced liver disease and myelodysplastic syndromes. Nucleic acid encoding the IAP polypeptide may also be provided to inhibit apoptosis.
II. CLONING OF IAP GENESA. XIAP
Our search for human genes potentially involved in apoptosis has resulted in the identification of an x-linked sequence tag site (STS) in the GenBank which demonstrated strong homology with the conserved RZF domain of CpIAP and OpIAP, the two baculovirus genes known to inhibit apoptosis (Clem et al., Mol. Cell Biol., 14:5212-5222, (1994); and Birnbaum et al, J. Virol. 68:2521-8, (1994)). Screening a human fetal brain ZapII cDNA library (Stratagene, La Jolla, Calif.) with this STS resulted in the identification and cloning of xiap (for X-linked Inhibitor of apoptosis Protein gene). The human gene has a 1.7 kb coding sequence that includes three BIR (baculovirus inhibitor of apoptosis repeat (Crook et al., J. Virol. 67:2168-74, (1993), Clem et al., Science 254:1388-90, (1991); and Birnbaum et al., J. Virol., 68:2521-8, (1994)) domains and a zinc finger. Northern analysis with xiap reveals a greater than 7 kb message expressed in different tissues particularly liver and kidney (
B. Human HIAP1 and HIAP2
The hiap1 and hiap2 genes were cloned by screening a human liver library (Stratagene) with a probe including the whole xiap coding region at low stringency (40° C. wash, 2×ssc, 10% SDS) (
C. M-XIAP
Screening of a mouse embryo λgt11 cDNA library (Clonetech, Palo Alto, Calif.) and a mouse FIX II genomic library with a xiap cDNA clones probe has resulted in the identification of 14 positive cDNA and two hybridizing genomic clones. A cDNA contig spanning 8.0 kb was constructed using 12 overlapping mouse clones. DNA sequencing revealed a coding sequence of about 1.7 kb. The mouse gene called m-xiap (for mouse x-linked inhibitor of apoptosis protein gene) shows striking amino acid homology with xiap at and around the initiation methionine, the stop codon, the three BIR domains and the zinc finger domain. As with the human gene, the mouse homologue contains large 5′ and 3′ UTRs predicted to result in a transcript as large as 7-8 kb.
Sequencing and restriction mapping of m-xiap can be used to further delineate the structure and genomic organization of m-xiap. Southern blot analysis and inverse PCR technique (Groden et al., Cell 66:589-600 (1991) can be employed to map exons and sequence exon-intron boundaries.
Antisera can be raised against a m-xiap fusion protein expressed in Escherichia coli using a bacterial expression system. The resulting antisera can be used along with Northern blot analysis to analyze the spatial and temporal expression of m-xiap in the mouse.
D. M-HIAP1 and M-HIAP2
The murine homologs to hiap1 and hiap2 were cloned and sequenced in the same general manner as m-xiap using the human hiap1 and hiap2 sequences as probes. Cloning of m-hiap1 and m-hiap2 provide further demonstrations of the case with which homologs from different species may be detected and obtained using the techniques provided herein and those generally known to one skilled in the art of molecular biology.
III. CLONING OF ADDITIONAL IAP GENESLow stringency Southern blot hybridization of human genomic DNA using probes specific for xiap, hiap1 and hiap2 show bands which correspond to the other known human IAP sequences. In addition, these probes detect sequences which do not correspond to known IAP sequences. This result indicates that additional IAP sequences may be readily identified using low stringency hybridization. Examples of murine and human xiap, hiap1, and hiap2 specific primers which may be used to clone additional genes by RT PCR are shown in Table 5. Standard techniques including PCR and hybridization may be used to clone homologs and additional genes.
IV. CHARACTERIZATION OF IAP APOPTOSIS MODULATING ACTIVITYThe apoptosis inhibiting capability of IAPs can be defined in an in vitro system know to detect alterations in apoptosis. Mammalian expression constructs carrying IAPs and their truncated forms can be introduced into various cell lines such as CHO, HIH 3T3, HL60, Rat-1, or Jurkart cells, for example. In addition, SF21 insect cells may be used in which case the IAP gene is preferentially expressed using an insect heat shock promotor. Apoptosis will then be induced in transfected cells and controls employing standard methodologies (e.g. serum withdrawal and staurosporine). A survival index (ratio of surviving transfected cells to surviving control cells) will indicate the strength of each IAP construct in inhibiting apoptosis. These experiments can confirm the presence of apoptosis inhibiting or enhancing activity and, can help to determine the minimal functional region of an IAP. These methods may also be used in combination with compounds to identify compounds which modulate apoptosis via their effect on IAP expression.
Specific examples of apoptosis assays are also provided in the following references:
Lymphocyte: C. J. Li et al., “Induction of apoptosis in uninfected lymphocytes by HIV-1 Tat protein”, Science, 268:429-431 (1995); D. Gibellini et al., “Tat-expressing Jurkat cells show an increased resistance to different apoptotic stimuli, including acute human immunodeficiency virus-type 1 (HIV-1) infection”, Br. J. Haematol. 89:24-33, (1995); S. J. Martin et al., “HIV-1 infection of human CD4+ T cells in vitro. Differential induction of apoptosis in these cells.” J. Immunol. 152:330-42, (1994); C. Terai et al., “Apoptosis as a mechanism of cell death in cultured T lymphoblasts acutely infected with HIV-1”, J. Clin Invest., 87:1710-5, (1991); J. Dhein et al., “Autocrine T-cell suicide mediated by APO-1/(Fas/CD95)”, Nature 373:438-441, (1995); P. D. Katsikis et al., “Fas antigen stimulation induces marked apoptosis of T lymphocytes in human immunodeficiency virus-infected individuals”, J. Exp. Med. 1815:2029-2036, (1995); Michael O. Westendorp et al., Sensitization of T cells to CD95-mediated apoptosis by HIV-1 Tat and gp120″, Nature, 375:497, (1995); DeRossi et al., Virology 198:234-44, (1994).
Fibroblasts: H. Vossbeck et al., “Direct transforming activity of TGF-beta on rat fibroblasts”, Int. J. Cancer, 61:92-97, (1995); S. Goruppi et al., “Dissection of c-myc domains involved in S phase induction of NIH3T3 fibroblasts”, Oncogene, 9:1537-44, (1994); A. Fernandez et al., “Differential sensitivity of normal and Ha-ras-transformed C3H mouse embryo fibroblasts to tumor necrosis factor: induction of bcl-2, c-myc, and manganese superoxide dismutase in resistant cells”, Oncogene, 9:2009-17, (1994); E. A. Harrington et al., “c-Myc-induced apoptosis in fibroblasts in inhibited by specific cytokines”, Embo J., 13:3286-3295, (1994); N. Itoh et al., “A novel protein domain required for apoptosis. Mutational analysis of human Fas antigen”, J. Biol. Chem., 268:10932-7, (1993).
Neuronal Cells: G. Melino et al., “Tissue transglutaminase and apoptosis: sense and antisense transfection studies with human neuroblastoma cells”, Mol. Cell. Biol., 14:6584-6596, (1994); D. M. Rosenbaum et al., “Evidence for hypoxia-induced, programmed cell death of cultured neurons”, Ann. Neurol., 36:864-870, (1994); N. Sato et al., “Neuronal differentiation of PC12 cells as a result of prevention of cell death by bcl-2”, J. Neurobiol, 25:1227-1234, (1994); G. Ferrari et al., “N-acetylcysteine (D- and L-stereoisomers) prevents apoptotic death of neuronal cells”, J. Neurosci., 1516:2857-2866, (1995); A. K. Talley et al., “Tumor necrosis factor alpha-induced apoptosis in human neuronal cells: protection by the antioxidant N-acetylcysteine and the genes bcl-2 and crmA”, Mol. Cell Biol., 1585:2359-2366, (1995); A. K. Talley et al., “Tumor Necrosis Factor Alpha-Induced Apoptosis in Human Neuronal Cells: Protection by the Antioxidant N-Acetylcysteine and the Genes bcl-2 and crmA”, Mol. and Cell. Biol., 15:2359-2366, (1995); G. Walkinshaw et al., “Induction of apoptosis in catecholaminergic PC12 cells by L-DOPA. Implications for the treatment of Parkinson's disease.”, J. Clin. Invest. 95:2458-2464, (1995).
Insect Cells: R. J. Clem et al., “Prevention of apoptosis by a baculovirus gene during infection of insect cells”, Science, 254:1388-90, (1991); N. E. Crook et al., “An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif”, J. Virol., 67:2168-74, (1993); S. Rabizadeh et al., “Expression of the baculovirus p35 gene inhibits mammalian neural cell death”, J. Neurochem., 61:2318-21, (1993); M. J. Birnbaum et al., “An apoptosis-inhibiting gene from a nuclear polyhidrosis virus encoding a polypeptide with Cys/His sequence motifs”, J. Virol, 68:2521-8, (1994); R. J. Clem et al., “Control of programmed cell death by the baculovirus genes p35 and iap”, Mol. Cell. Biol., 14:5212-5222, (1994).
V. CONSTRUCTION OF A TRANSGENIC ANIMALCharacterization of IAPs can provide information that allows for the development of an IAP knockout animal model, preferably mammal, most preferably a mouse, by homologous recombination. Similarily, an IAP overproducing animal may be produced by means of DNA sequence integration into the genome.
A replacement type targeting vector to create a knockout can be constructed using an isogenic genomic clone from a mouse strain, e.g. 129/Sv (Strategene LaJolla, Calif.). The targeting vector will be introduced into a J1 line of embryonic stem (ES) cells by electroporation to generate ES cell lines that carry a profoundly truncated form of an IAP. To generate chimeric founder mice, the targeted cell lines will be injected into a mouse blastula stage embryo. Heterozygote offspring will be interbred to homozygosity. Knockout mice may be constructed as a means of screening in vivo for therapeutic compounds which modulate apoptosis.
Animals having enhanced IAP expression may also be constructed using standard transgenic technologies.
VI. IAP PROTEIN EXPRESSIONIAP genes may be expressed in both prokaryotic and eukaryotic cell types. For those IAP's which increase apoptosis it may be desirable to express the protein under control of an inducible promotor for the purposes of protein production.
In general, IAP proteins according to the invention may be produced by transformation of a suitable host cell with all or part of a IAP-encoding cDNA fragment (e.g., the cDNA described above) in a suitable expression vehicle.
Those skilled in the field of molecular biology will understand that any of a wide variety of expression systems may be used to provide the recombinant protein. The precise host cell used is not critical to the invention. The IAP protein may be produced in a prokaryotic host (e.g., E. coli) or in a eukaryotic host (e.g., Saccharomyces cerevisiae, insect cells, e.g., Sf21 cells, or mammalian cells, e.g., COS 1, NIH 3T3, or HeLa cells). Such cells are available from a wide range of sources (e.g., the American Type Culture Collection, Rockland, Md.; also, see, e.g., Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1994). The method of transformation or transfection and the choice of expression vehicle will depend on the host system selected. Transformation and transfection methods are described, e.g., in Ausubel et al., (supra); expression vehicles may be chosen from those provided, e.g., in Cloning Vectors: A Laboratory Manual (P. H. Pouwels et al., 1985, Supp. 1987).
One preferred expression system is the baculovirus system (using, for example, the vector pBacPAK9) available from Clontech (Palo Alto, Calif.). If desired, this system may be used in conjunction with other protein expression techniques, for example, the myc tag approach described by Evan et al. (Mol. Cell Biol. 5:3610-3616, 1985).
Alternatively, a IAP protein is produced by a stably-transfected mammalian cell line. A number of vectors suitable for stable transfection of mammalian cells are available to the public, e.g., see Pouwels et al. (supra); methods for constructing such cell lines are also publicly available, e.g., in Ausubel et al. (supra). In one example, cDNA encoding the IAP protein is cloned into an expression vector which includes the dihydrofolate reductase (DHFR) gene. Integration of the plasmid and, therefore, the IAP protein-encoding gene into the host cell chromosome is selected for by inclusion of 0.01-300 μM methotrexate in the cell culture medium (as described in Ausubel et al., supra). This dominant selection can be accomplished in most cell types. Recombinant protein expression can be increased by DHFR-mediated amplification of the transfected gene. Methods for selecting cell lines bearing gene amplifications are described in Ausubel et al. (supra); such methods generally involve extended culture in medium containing gradually increasing levels of methotrexate. DHFR-containing expression vectors commonly used for this purpose include pCVSEII-DHFR and pAdD26SV(A) (described in Ausubel et al., supra). Any of the host cells described above or, preferably, a DHFR-deficient CHO cell line (e.g., CHO DHFR− cells, ATCC Accession No. CRL 9096) are among the host cells preferred for DHFR selection of a stably-transfected cell line or DHFR-mediated gene amplification.
Once the recombinant IAP protein is expressed, it is isolated, e.g., using affinity chromatography. In one example, an anti-IAP protein antibody (e.g., produced as described herein) may be attached to a column and used to isolate the IAP protein. Lysis and fractionation of IAP protein-harboring cells prior to affinity chromatography may be performed by standard methods (see, e.g., Ausubel et al., supra).
Once isolated, the recombinant protein can, if desired, be further purified, e.g., by high performance liquid chromatography (see, e.g., Fisher, Laboratory Techniques In Biochemistry And Molecular Biology, eds., Work and Burdon, Elsevier, 1980).
Polypeptides of the invention, particularly short IAP protein fragments, can also be produced by chemical synthesis (e.g., by the methods described in Solid Phase Peptide Synthesis, 2nd ed., 1984 The Pierce Chemical Co., Rockford, Ill.).
These general techniques of polypeptide expression and purification can also be used to produce and isolate useful IAP fragments or analogs (described herein).
VI. ANTI-IAP ANTIBODIESTo generate IAP-specific antibodies, a IAP coding sequence (i.e., amino acids 180-276) can be expressed as a C-terminal fusion with glutathione S-transferase (GST) (Smith et al., Gene 67:31-40, 1988). The fusion protein can be purified on glutathione-Sepharose beads, eluted with glutathione cleaved with thrombin (at the engineered cleavage site), and purified to the degree necessary for immunization of rabbits. Primary immunizations can be carried out with Freund's complete adjuvant and subsequent immunizations with Freund's incomplete adjuvant. Antibody titres are monitored by Western blot and immunoprecipitation analyses using the thrombin-cleaved IAP protein fragment of the GST-IAP fusion protein. Immune sera are affinity purified using CNBr-Sepharose-coupled IAP protein. Antiserum specificity is determined using a panel of unrelated GST proteins (including GSTp53, Rb, HPV-16 E6, and E6-AP) and GST-trypsin (which was generated by PCR using known sequences).
As an alternate or adjunct immunogen to GST fusion proteins, peptides corresponding to relatively unique hydrophilic regions of IAP may be generated and coupled to keyhole limpet hemocyanin (KLH) through an introduced C-terminal lysine. Antiserum to each of these peptides is similarly affinity purified on peptides conjugated to BSA, and specificity tested in ELISA and Western blots using peptide conjugates, and by Western blot and immunoprecipitation using IAP expressed as a GST fusion protein.
Alternatively, monoclonal antibodies may be prepared using the IAP proteins described above and standard hybridoma technology (see, e.g., Kohler et al., Nature 256:495, 1975; Kohler et al., Eur. J. Immunol. 6:511, 1976; Kohler et al., Eur. J. Immunol. 6:292, 1976; Hammerling et al., In Monoclonal Antibodies and T Cell Hybridomas, Elsevier, N.Y., 1981; Ausubel et al., supra). Once produced, monoclonal antibodies are also tested for specific IAP recognition by Western blot or immunoprecipitation analysis (by the methods described in Ausubel et al., supra). Antibodies which specifically recognize IAP are considered to be useful in the invention; such antibodies may be used, e.g., in an immunoassay to monitor the level of IAP produced by a mammal (for example, to determine the amount or subcellular location of IAP).
Preferably, antibodies of the invention are produced using fragments of the IAP protein which lie outside highly conserved regions and appear likely to be antigenic, by criteria such as those provided by the Peptidestructure program of the Genetics Computer Group Sequence Analysis Package (Program Manual for the GCG Package, Version 7, 1991) using the algorithm of Jameson and Wolf (CABIOS 4:181 1988)). Specifically these regions, which are found between BIR1 and BIR2 of all the IAP proteins, are in hiap1 from amino acid 99 to 170, hiap2 from amino acid 123 to 184, xiap from 116 to 133 and m-xiap from 116 to 133. In one specific example, such fragments are generated by standard techniques of PCR and cloned into the pGEX expression vector (Ausubel et al., supra). Fusion proteins are expressed in E. coli and purified using a glutathione agarose affinity matrix as described in Ausubel et al. (supra). To attempt to minimize the potential problems of low affinity or specificity of antisera, two or three such fusions are generated for each protein, and each fusion is injected into at least two rabbits. Antisera are raised by injections in a series, preferably including at least three booster injections.
VII. IDENTIFICATION OF MOLECULES THAT MODULATE IAP PROTEIN EXPRESSIONIsolation of the IAP cDNAs also facilitates the identification of molecules which increase or decrease IAP expression. According to one approach, candidate molecules are added at varying concentrations to the culture medium of cells expressing IAP mRNA. IAP expression is then measured, for example, by standard Northern blot analysis (Ausubel et al., supra) using a IAP cDNA (or cDNA fragment) as a hybridization probe (see also Table 5). The level of IAP expression in the presence of the candidate molecule is compared to the level measured for the same cells in the same culture medium but in the absence of the candidate molecule.
If desired, the effect of candidate modulators on expression may, in the alternative, be measured at the level of IAP protein production using the same general approach and standard immunological detection techniques, such as Western blotting or immunoprecipitation with a IAP-specific antibody (for example, the IAP antibody described herein).
Candidate modulators may be purified (or substantially purified) molecules or may be one component of a mixture of compounds (e.g., an extract or supernatant obtained from cells; Ausubel et al., supra). In a mixed compound assay, IAP expression is tested against progressively smaller subsets of the candidate compound pool (e.g., produced by standard purification techniques, e.g., HPLC or FPLC) until a single compound or minimal compound mixture is demonstrated to modulate IAP expression.
Alternatively, or in addition, candidate compounds may be screened for those which modulate IAP apoptosis inhibiting activity. In this approach, the degree of apoptosis in the presence of a candidate compound is compared to the degree of apoptosis in its absence, under equivalent conditions. Again, such a screen may begin with a pool of candidate compounds, from which one or more useful modulator compounds are isolated in a step-wise fashion. Apoptosis activity may be measured by any standard assay, for example, those described herein.
Another method for detecting compounds which modulate IAP polypeptide activity is to screen for compounds which physically interact with a given IAP polypeptide. Such compounds may be detected using adaptations of the interaction trap expression systems known in the art. Such systems detect protein interactions using a transcriptional activation assay and are generally described in Gyuris et al., Cell 75:791-803 (1993), and Field and Song, Nature 340:245-246, (1989), and are commercially available from Clonetech (Palo Alto, Calif.). In addition, PCT Publication WO 95/28497 (hereby incorporated by reference) describe a method for detecting proteins involved in apoptosis by virtue of their interaction with Bcl-2 using such an interaction trap assay. A similar method may be exploited to identify proteins and other compounds which interact with the IAP polypeptides.
Candidate IAP modulators include peptide as well as non-peptide molecules (e.g., peptide or non-peptide molecules found, e.g., in a cell extract, mammalian serum, or growth medium on which mammalian cells have been cultured).
A molecule which promotes an increase in IAP expression or IAP activity is considered particularly useful in the invention; such a molecule may be used, for example, as a therapeutic to increase cellular levels of IAP and thereby exploit the effect of IAP polypeptides for the inhibition of apoptosis.
A molecule which decreases IAP activity (e.g., by decreasing gene expression or polypeptide activity) may be useful for decreasing cell proliferation. Such uses include treatment of neoplasms (see Table 3, below) or other cell proliferative diseases.
Modulators found to be effective at the level of IAP expression or activity may be confirmed as useful in animal models and, if successful, may be used as anti-cancer therapeutics for either the inhibition or the enhancement of apoptosis, as appropriate.
IX. IAP THERAPYBecause expression levels of IAP genes correlates with the levels of apoptosis, the IAP gene also finds use in anti-apoptosis gene therapy. In particular, to sustain neuronal cells, lymphocytes (T-cells and B-cells), or cells exposed to ischemic injury, a functional IAP gene may be introduced into cells at the sites predicted to undergo undesirable apoptosis.
Retroviral vectors, adenoviral vectors, adeno-associated viral vectors, or other viral vectors with the appropriate tropism for cells likely to be involved in apoptosis (for example, epithelial cells) may be used as a gene transfer delivery system for a therapeutic IAP gene construct. Numerous vectors useful for this purpose are generally known (Miller, Human Gene Therapy 15-14, 1990; Friedman, Science 244:1275-1281, 1989; Eglitis and Anderson, BioTechniques 6:608-614, 1988; Tolstoshev and Anderson, Current Opinion in Biotechnology 1:55-61, 1990; Sharp, The Lancet 337:1277-1278, 1991; Cornetta et al., Nucleic Acid Research and Molecular Biology 36:311-322, 1987; Anderson, Science 226:401-409, 1984; Moen, Blood Cells 17:407-416, 1991; and Miller and Rosman, Biotechniques 7:980-990, 1989; Le Gal La Salle et al., Science 259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995). Retroviral vectors are particularly well developed and have been used in clinical settings (Rosenberg et al., N. Engl. J. Med 323:370, 1990; Anderson et al., U.S. Pat. No. 5,399,346).
Non-viral approaches may also be employed for the introduction of therapeutic DNA into cells otherwise predicted to undergo apoptosis. For example, IAP may be introduced into a neuronal cell or a T-cell by the techniques of lipofection (Felgner et al., Proc. Natl. Acad. Sci. USA 84:7413, 1987; Ono et al., Neuroscience Lett 117:259, 1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubinger and Papahadjopoulos, Meth. Enz. 101:512, 1983); asialorosonucoid-polylysine conjugation (Wu and Wu, J. Biol. Chem. 263:14621, 1988; Wu et al., J. Biol. Chem. 264:16985, 1989); or, less preferably, microinjection under surgical conditions (Wolff et al., Science 247:1465, 1990).
For any of the above approaches, the therapeutic IAP DNA construct is preferably applied to the site of the predicted apoptosis event (for example, by injection), but may also be applied to tissue in the vicinity of the predicted apoptosis event or even to a blood vessel supplying the cells predicted to undergo apoptosis.
In the gene therapy constructs, IAP cDNA expression is directed from any suitable promoter (e.g., the human cytomegalovirus, simian virus 40, or metallothionein promoters), and its production is regulated by any desired mammalian regulatory element. For example, if desired, enhancers known to direct preferential gene expression in neural cells or T-cells may be used to direct IAP expression. Such enhancers include, without limitation, those enhancers which are characterized as tissue or cell specific in their expression.
Alternatively, if a IAP genomic clone is utilized as a therapeutic construct (for example, following its isolation by hybridization with the IAP cDNA described above), IAP expression is regulated by its cognate regulatory sequences or, if desired, by regulatory sequences derived from a heterologous source, e.g., any of the promoters or regulatory elements described above.
Less preferably, IAP gene therapy is accomplished by direct administration of the IAP mRNA to a cell predicted to undergo apoptosis. This mRNA may be produced and isolated by any standard technique, but is most readily produced by in vitro transcription using a IAP cDNA under the control of a high efficiency promoter (e.g., the T7 promoter). Administration of IAP mRNA to malignant cells is carried out by any of the methods for direct nucleic acid administration described above.
Ideally, the production of IAP protein by any gene therapy approach described above results in a cellular level of IAP that is at least equivalent to the normal, cellular level of IAP in an unaffected individual. Treatment by any IAP-mediated gene therapy approach may be combined with more traditional therapies.
Another therapeutic approach included within the invention involves direct administration of recombinant IAP protein, either to the site of a predicted apoptosis event (for example, by injection) or systemically by any conventional recombinant protein administration technique. The actual dosage of IAP depends on a number of factors, including the size and health of the individual patient, but, generally, between 0.1 mg and 100 mg inclusive are administered per day to an adult in any pharmaceutically-acceptable formulation.
X. ADMINISTRATION OF IAP POLYPEPTIDES, IAP GENES, OR MODULATORS OF IAP SYNTHESIS OR FUNCTIONA IAP protein, gene, or modulator may be administered with a pharmaceutically-acceptable diluent, carrier, or excipient, in unit dosage form. Conventional pharmaceutical practice may be employed to provide suitable formulations or compositions to administer IAP to patients suffering from or presymptomatic for a IAP-associated carcinoma. Any appropriate route of administration may be employed, for example, parenteral, intravenous, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intracisternal, intraperitoneal, intranasal, aerosol, or oral administration. Therapeutic formulations may be in the form of liquid solutions or suspensions; for oral administration, formulations may be in the form of tablets or capsules; and for intranasal formulations, in the form of powders, nasal drops, or aerosols.
Methods well known in the art for making formulations are found in, for example, “Remington's Pharmaceutical Sciences.” Formulations for parenteral administration may, for example, contain excipients, sterile water, or saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated napthalenes. Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds. Other potentially useful parenteral delivery systems for IAP modulatory compounds include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation may contain excipients, for example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or as a gel.
If desired, treatment with a IAP protein, gene, or modulatory compound may be combined with more traditional therapies for the disease such as surgery, radiation, or chemotherapy for cancers; surgery, steroid therapy, and chemotherapy for autoimmune diseases; antiviral therapies for AIDS; and for example, TPA for ischemic injury.
XI. DETECTION OF A CONDITION INVOLVING ALTERED APOPTOSISIAP polypeptides and nucleic acid sequences find diagnostic use in the detection or monitoring of conditions involving aberrant levels of apoptosis. For example, decrease expression of IAP may be correlated with enhanced apoptosis in humans (see XII, below). Accordingly, a decrease or increase in the level of IAP production may provide an indication of a deleterious condition. Levels of IAP expression may be assayed by any standard technique. For example, its expression in a biological sample (e.g., a biopsy) may be monitored by standard Northern blot analysis or may be aided by PCR (see, e.g., Ausubel et al., supra; PCR Technology: Principles and Applications for DNA Amplification, ed., H. A. Ehrlich, Stockton Press, NY; and Yap and McGee, Nucl. Acids. Res. 19:4294, 1991).
Alternatively, a patient sample may be analyzed for one or more mutations in the IAP sequences using a mismatch detection approach. Generally, these techniques involve PCR amplification of nucleic acid from the patient sample, followed by identification of the mutation (i.e., mismatch) by either altered hybridization, aberrant electrophoretic gel migration, binding or cleavage mediated by mismatch binding proteins, or direct nucleic acid sequencing. Any of these techniques may be used to facilitate mutant IAP detection, and each is well known in the art; examples of particular techniques are described, without limitation, in Orita et al., Proc. Natl. Acad. Sci. USA 86:2766-2770, (1989); and Sheffield et al., Proc. Natl. Acad. Sci. USA 86:232-236, (1989).
In yet another approach, immunoassays are used to detect or monitor IAP protein in a biological sample. IAP-specific polyclonal or monoclonal antibodies (produced as described above) may be used in any standard immunoassay format (e.g., ELISA, Western blot, or RIA assay) to measure IAP polypeptide levels; again comparison is to wild-type IAP levels, and a decrease in IAP production is indicative of a condition involving increased apoptosis. Examples of immunoassays are described, e.g., in Ausubel et al., supra. Immunohistochemical techniques may also be utilized for IAP detection. For example, a tissue sample may be obtained from a patient, and a section stained for the presence of IAP using an anti-IAP antibody and any standard detection system (e.g., one which includes a secondary antibody conjugated to horseradish peroxidase). General guidance regarding such techniques can be found in, e.g., Bancroft and Stevens (Theory and Practice of Histological Techniques, Churchill Livingstone, 1982) and Ausubel et al. (supra).
In one preferred example, a combined diagnostic method may be employed that begins with an evaluation of IAP protein production (for example, by immunological techniques or the protein truncation test (Hogerrorst, F. B. L., et al., Nature Genetics 10:208-212 (1995) and also includes a nucleic acid-based detection technique designed to identify more subtle IAP mutations (for example, point mutations). As described above, a number of mismatch detection assays are available to those skilled in the art, and any preferred technique may be used (see above). By this approach, mutations in IAP may be detected that either result in loss of IAP expression or loss of IAP biological activity. In a variation of this combined diagnostic method, IAP biological activity is measured as protease activity using any appropriate protease assay system (for example, those described above).
Mismatch detection assays also provide the opportunity to diagnose a IAP-mediated predisposition to diseases of apoptosis. For example, a patient heterozygous for an IAP mutation may show no clinical symptoms and yet possess a higher than normal probability of developing one or more types of neurodegenerative, myelodysplastic or ischemic diseases. Given this diagnosis, a patient may take precautions to minimize their exposure to adverse environmental factors (for example, UV exposure or chemical mutagens) and to carefully monitor their medical condition (for example, through frequent physical examinations). This type of IAP diagnostic approach may also be used to detect IAP mutations in prenatal screens.
The IAP diagnostic assays described above may be carried out using any biological sample (for example, any biopsy sample or bodily fluid or tissue) in which IAP is normally expressed (for example, the inhibition of apoptosis). Identification of a mutant IAP gene may also be assayed using these sources for test samples. Alternatively, a IAP mutation, particularly as part of a diagnosis for predisposition to IAP-associated degenerative disease, may be tested using a DNA sample from any cell, for example, by mismatch detection techniques; preferably, the DNA sample is subjected to PCR amplification prior to analysis.
To demonstrate the utility of IAP gene sequences as diagnostics and prognostics for cancer we probed the Clonetech (La Jolla) Human Cancer Cell Line Multiple Tissue Northern Blot (#7757-1). As Table 3 shows, all cancer lines tested showed increased IAP expression relative to samples from non-cancerous control cell lines. xiap expression was particularly high in HeLa (S-3), chronic myelogenous leukemia (K-562), colorectal adenocarcinoma (SW-480) and melanoma (G-361) lines. hiap1 expression was extremely high in Burkitt's lymphoma and was also elevated in colorectal adenocarcinoma. hiap2 expression was particularly high in chronic myelogenous leukemia (K-562) and colorectal adenocarcinoma (SW-480).
In addition, we note that we have mapped hiap1 and hiap2 to human chromosome 11g23. This is a known hotspot for cancer causing mutations.
*Levels are indicated by a (+) and are the approximate increase in RNA levels relative to Northern blots of RNA from non-cancerous control cell lines. A single plus indicates an estimated increase of at least 1-fold
We have found that hiap1 and hiap 2 expression is decreased significantly in HIV infected human cells. This decrease precedes apoptosis. The result indicates that administration of HIAP1, HIAP2, genes encoding these proteins, or compounds which upregulate these genes can be used to prevent T-cell attrition in HIV infected patients. The following assay may also be used to screen for compounds which alter hiap1 and hiap2 expression and which also prevent apoptosis.
The experiments were preformed as follows: Cultured mature lymphocyte CD-4+ T-cell lines (H9 labelled “a”; CEM/CM-3 labelled “b”; 6T-CEM labelled “c”; and Jurkat labelled “d” in
In
For the experiment examining hiap gene expression, total RNA was prepared from the cultured cells and subject to a reverse transcriptase reaction using oligo-dT priming. The RT cDNA products were PCR amplified using specific primers (as shown in Table 5) for the detection of hiap2a, hiap2b and hiap 1. PCR conditions were routine (94° C. melting for 1 minute, 55° C. annealing for 2 minutes and 72° C. extension for 1.5 minutes for 35 cycles) using a Perkin-Elmer 480 thermocycler. The
The data from these experiments is summarized in the accompanying Table 5. The β-action gene expression was consistent in all cell lines tested, indicating that a flow in the RT-PCR assay does not account for the decreases in hiap gene expression.
*Nucleotide position as determined from FIGS. 1-4 for each IAP gene
aPCR product size of hiap2a
bPCR product size of hiap2b
In a patient diagnosed to be heterozygous for an IAP mutation or to be susceptible to IAP mutations (even if those mutations do not yet result in alteration or loss of IAP biological activity), or a patent diagnosed as HIV positive, any of the above therapies may be administered before the occurrence of the disease phenotype. For example, the therapies may be provided to a patient who is HIV positive but does not yet show a diminished T-cell count or other signs of full-blown AIDS. In particular, compounds shown to increase IAP expression or IAP biological activity may be administered by any standard dosage and route of administration (see above). Alternatively, gene therapy using an IAP expression construct may be undertaken to reverse or prevent the cell defect prior to the development of the degenerative disease.
The methods of the instant invention may be used to reduce or diagnose the disorders described herein in any mammal, for example, humans, domestic pets, or livestock. Where a non-human mammal is treated or diagnosed, the IAP polypeptide, nucleic acid, or antibody employed is preferably specific for that species.
Other Embodiments In other embodiments, the invention includes any protein which is substantially identical to a mammalian IAP polypeptides (
The invention further includes analogs of any naturally-occurring IAP polypeptide. Analogs can differ from the naturally-occurring IAP protein by amino acid sequence differences, by post-translational modifications, or by both. Analogs of the invention will generally exhibit at least 85%, more preferably 90%, and most preferably 95% or even 99% identity with all or part of a naturally-occurring IAP amino acid sequence. The length of sequence comparison is at least 15 amino acid residues, preferably at least 25 amino acid residues, and more preferably more than 35 amino acid residues. Modifications include in vivo and in vitro chemical derivatization of polypeptides, e.g., acetylation, carboxylation, phosphorylation, or glycosylation; such modifications may occur during polypeptide synthesis or processing or following treatment with isolated modifying enzymes. Analogs can also differ from the naturally-occurring IAP polypeptide by alterations in primary sequence. These include genetic variants, both natural and induced (for example, resulting from random mutagenesis by irradiation or exposure to ethanemethylsulfate or by site-specific mutagenesis as described in Sambrook, Fritsch and Maniatis, Molecular Cloning: A Laboratory Manual (2d ed.), CSH Press, 1989, or Ausubel et al., supra). Also included are cyclized peptides, molecules, and analogs which contain residues other than L-amino acids, e.g., D-amino acids or non-naturally occurring or synthetic amino acids, e.g., β or γ amino acids.
In addition to full-length polypeptides, the invention also includes IAP polypeptide fragments. As used herein, the term “fragment,” means at least 20 contiguous amino acids, preferably at least 30 contiguous amino acids, more preferably at least 50 contiguous amino acids, and most preferably at least 60 to 80 or more contiguous amino acids. Fragments of IAP polypeptides can be generated by methods known to those skilled in the art or may result from normal protein processing (e.g., removal of amino acids from the nascent polypeptide that are not required for biological activity or removal of amino acids by alternative mRNA splicing or alternative protein processing events).
Preferable fragments or analogs according to the invention are those which facilitate specific detection of a IAP nucleic acid or amino acid sequence in a sample to be diagnosed. Particularly useful IAP fragments for this purpose include, without limitation, the amino acid fragments shown in Table 2.
All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.
Claims
1. A substantially pure nucleic acid encoding a mammalian inhibitor of apoptosis: protein (IAP) polypeptide, wherein said inhibitor of apoptosis protein is a protein that modulates apoptosis and comprises a ring zinc finger domain and at least one baculovirus inhibitor of apoptosis repeat (BIR) domain.
2. The nucleic acid of claim 1, wherein said polypeptide has at least two BIR domains.
3. The nucleic acid of claim 2, wherein said polypeptide has at least three BIR domains.
4. The nucleic acid of claim 1, wherein said nucleic acid contains the X-linked inhibitor of apoptosis protein (xiap) gene.
5. The nucleic acid of claim 1, wherein said nucleic acid contains the human inhibitor of apoptosis protein 2 (hiap2) gene.
6. The nucleic acid of claim 1, wherein said nucleic acid contains the human inhibitor of apoptosis protein 1 (hiap1) gene.
7. The nucleic acid of claim 1, wherein said nucleic acid is genomic DNA.
8. The nucleic acid of claim 1, wherein said nucleic acid is cDNA.
9. The nucleic acid of claim 1, wherein said nucleic acid is mammalian DNA.
10. The nucleic acid of claim 9, wherein said mammalian DNA is human DNA.
11. The nucleic acid of claim 11, wherein said mammalian DNA is murine DNA.
12. A substantially pure nucleic acid having the sequence of FIG. 5 (SEQ ID NO: 39), or degenerate variants thereof, and encoding the amino acid sequence of FIG. 5 (SEQ ID NO: 40).
13. A substantially pure nucleic acid having the sequence of FIG. 6 (SEQ ID NO: 41), or degenerate variants thereof, and encoding the amino acid sequence of FIG. 6 (SEQ ID NO: 42).
14. A method of producing a mammalian IAP polypeptide comprising:
- (a) providing a cell transformed with a nucleic acid encoding a mammalian IAP polypeptide positioned for expression in said cell, said polypeptide comprising a ring zinc finger (RZF) domain;
- (b) culturing said transformed cell of step (a) under conditions for expressing said nucleic acid; and
- (c) producing said IAP polypeptide.
15. The method of claim 14, wherein said mammalian IAP polypeptide is murine human inhibitor of apoptosis protein 1 (m-HIAP1).
16. The method of claim 14, wherein said mammalian IAP polypeptide is murine human inhibitor of apoptosis protein 2 (m-HIAP2).
17. A substantially pure nucleic acid that hybridizes to a probe of at least 40 nucleotides in length, said probe derived from the nucleic acid sequence of FIG. 5 (SEQ ID NO: 39), wherein said nucleic acid hybridizes to said probe under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C., and wherein said nucleic acid encodes a mammalian LAP polypeptide, said polypeptide comprising a ring zinc finger domain and at least one BIR domain.
18. A substantially pure nucleic acid that hybridizes to a probe of at least 40 nucleotides in length, said probe derived from the DNA sequence of FIG. 6 (SEQ ID NO: 41), wherein said nucleic acid hybridizes to said probe under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C., and wherein said nucleic acid encodes a mammalian IAP polypeptide, said polypeptide comprising a ring zinc finger domain and at least one BIR domain.
19. A substantially pure nucleic acid encoding a BIR domain, said nucleic acid comprising a sequence selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 66, and SEQ ID NO: 67.
20. A substantially pure nucleic acid encoding a ring zinc finger domain, said nucleic acid comprising a sequence selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 56, SEQ ID NO: 60, SEQ ID NO: 64, and SEQ ID NO: 68.
21. A substantially pure nucleic acid that hybridizes to a probe of at least 40 nucleotides in length, said probe derived from the DNA sequence of FIG. 1 (SEQ ID NO: 3), wherein said nucleic acid hybridizes to said probe under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C., and wherein said nucleic acid encodes a mammalian IAP polypeptide, said polypeptide comprising a ring zinc finger domain and at least one BIR domain.
22. A substantially pure nucleic acid that hybridizes to a probe of at least 40 nucleotides in length, said probe derived from the DNA sequence of FIG. 2 (SEQ ID NO: 5), wherein said nucleic acid hybridizes to said probe under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C., and wherein said nucleic acid encodes a mammalian IAP polypeptide, said polypeptide comprising a ring zinc finger domain and at least one BIR domain.
23. A substantially pure nucleic acid that hybridizes to a probe of at least 40 nucleotides in length, said probe derived from the DNA sequence of FIG. 3 (SEQ ID NO: 7), wherein said nucleic acid hybridizes to said probe under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C., and wherein said nucleic acid encodes a mammalian IAP polypeptide, said polypeptide comprising a ring zinc finger domain and at least one BIR domain.
24. A substantially pure nucleic acid that hybridizes to a probe of at least 40 nucleotides in length, said probe derived from the DNA sequence of FIG. 4 (SEQ ID NO: 9), wherein said nucleic acid hybridizes to said probe under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C., and wherein said nucleic acid encodes a mammalian IAP polypeptide, said polypeptide comprising a ring zinc finger domain and at least one BIR domain.
25. A substantially pure nucleic acid probe of at least 40 nucleotides in length, wherein said probe hybridizes to the DNA sequence of FIG. 1 (SEQ ID NO: 3) under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C.
26. A substantially pure nucleic acid probe of at least 40 nucleotides in length, wherein said probe hybridizes to the DNA sequence of FIG. 2 (SEQ ID NO: 5) under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C.
27. A substantially pure nucleic acid probe of at least 40 nucleotides in length, wherein said probe hybridizes to the DNA sequence of FIG. 3 (SEQ ID NO: 7) under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C.
28. A substantially pure nucleic acid probe of at least 40 nucleotides in length, wherein said probe hybridizes to the DNA sequence of FIG. 4 (SEQ ID NO: 9) under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C.
29. A substantially pure nucleic acid probe of at least 40 nucleotides in length, wherein said probe hybridizes to the DNA sequence of FIG. 6 (SEQ ID NO: 41) under low stringency conditions, said conditions comprising washing with 2×SSC at 40° C.
Type: Application
Filed: Sep 1, 2005
Publication Date: Jun 15, 2006
Applicant: University of Ottawa (Ottawa)
Inventors: Robert Korneluk (Ottawa), Alexander MacKenzie (Ottawa), Stephen Baird (Ottawa), Peter Liston (Ottawa)
Application Number: 11/217,557
International Classification: C12Q 1/68 (20060101); C07H 21/04 (20060101); C12N 9/99 (20060101);
