WO2000059924A1 - Methods and reagents for modulating caspase-mediated apoptosis - Google Patents

Abstract

The invention features caspase-12 polypeptides that modulate apoptosis. The invention also features methods for identifying compounds useful in modulating apoptosis. One method inlcudes: (a) providing a cell having a caspase-12; (b) administering to the cell a candidate compound; and (c) monitoring a biological activity of caspase-12, wherein a change in the biological activity of caspase-12 in the cell relative to the activity in a control cell not administered the candidate compound identifies the candidate compound as a compound useful in modulating apoptosis.

Description

METHODS AND REAGENTS FOR MODULATING CASPASE-MEDTATED APOPTOSTS

The invention relates to cellular apoptosis. Apoptosis, also referred to as programmed cell death, is a form of cell death characterized by membrane blebbing and nuclear DNA fragmentation. Apoptotic cell death is morphologically distinct from necrotic cell death and is important in embryonic development, viral pathogenesis, cancer, autoimmune disorders, and neurodegenerative disease. For example, inappropriate apoptosis may cause or contribute to AIDS, 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, including alcoholism, and ischemic injury (e.g. myocardial infarction, stroke, and reperfusion injury). Conversely, the failure of an apoptotic response has been implicated in the development of cancer, particularly follicular lymphoma, p53 -mediated carcinomas, and hormone-dependent tumors, in autoimmune disorders, such as lupus erythematosis and multiple sclerosis, and in viral infections, including those associated with herpes virus, poxvirus, and adenovirus.

Caspases

Although apoptotic cell death is initially triggered by a specific death signal received, for example, by ligation of the Fas cell surface molecule, execution of the apoptotic pathway occurs only upon the activation of members of the Ced-3/ICE (caspase) family of cysteine proteases. There are at least fourteen known members of the caspase family whose activities lead to site- specific cleavage and consequent activation/inactivation of various target molecules. FLICE and related caspases may initiate apoptosis by activating a downstream caspase cascade, including CPP32 (caspase-3).

The decision to engage the apoptotic execution pathway in response to specific death signals depends on the status of various cellular regulators of apoptosis, including p53 and the Bcl-2/Bax family of proteins. The ratio of heterodimerization between the Bcl-2/Bcl-xL and Bax/Bak family of suppressors and promoters, respectively, determines the outcome— cell death or cell survival— in response to various death signals. Caspase proteins act at a critical point in the cascade of apoptosis induction. For example, caspase-3, caspase-9, and Apaf-1 are critical for developmental neuronal cell death; caspase-2 is essential for doxorubicin- induced egg cell death; and caspase- 1 and caspase- 11 are involved in inflammation and ischemic cell death in the brain. Despite the extensive efforts of researchers in the field of apoptosis, the cellular localization and mechanism of action of most caspases is poorly understood. A better understanding of the signaling cascades that regulate (and are regulated by) caspases would allow for the design of drugs that specifically prevent or trigger apoptosis. Compounds that are negative and positive regulators of apoptosis would have uses in the treatment of apoptosis-mediated disorders (e.g., stroke, neurodegeneration, ischemia, etc.) and proliferative disorders (e.g., cancer), respectively.

Presenilins

One disorder believed to be associated with neurodegeneration is Alzheimer's Disease (AD). The majority (70-80%) of heritable, early-onset AD maps to chromosome 14 and appears to result from one of more than 20 different amino-acid substitutions within presenilin-1, the product of the recently-identified SI 82 gene. Presenilin-2 is a similar, although less common, AD-associated risk locus on chromosome 1. Two missense mutations have been identified within presenilin-2 that appear to be causative for early-onset AD. Based upon mRNA detection, the presenilins appear to be ubiquitously expressed, suggesting that they are housekeeping proteins required by many cell types.

The two mammalian presenilins share 67% amino-acid identity and apparently belong to a larger gene-family of membrane spanning proteins that includes the C. elegans spe-4 and sel-12 genes. Mutations in the spe-4 gene disrupt the formation of a Golgi-derived storage and delivery organelle required for spermatogenesis in the nematode. SEL-12 has been shown to facilitate signaling by LIN- 12, a member of the Notch family of transmembrane receptors critical for cell surface to nucleus signaling during development. A possible ER and or Golgi localization of epitope-tagged constructs overexpressed in cultured cells and a similar immunolabeling pattern reported in mouse pyramidal neurons are consistent with the presenilins being integral membrane proteins found within compartments of the secretory pathway. This, in conjunction with the spe-4 phenotype and the known importance of membrane proteins and their compartmentalization in AD, has led to the conjecture that the presenilins function in membrane protein trafficking and/or processing along the secretory pathway.

Calpains

Calpains are calcium-dependent proteases with isozymes, (e.g., μ- calpain and m-calpain) that are ubiquitously expressed. Like caspases, calpains cleave many proteins. For example, protein kinase C isozymes are converted to active form by a calpain. Calpains are believed to be activated in ischemic brain, in myelin protein degradation (such as multiple sclerosis), and in the brain in AD patients.

An understanding of the signaling cascades that are controlled by calpains would provide new methods, compounds, and drug targets for intervention in disease states, such as those described above.

In a first aspect, the invention features a method for identifying a compound useful in treating an apoptotic condition. The method includes: a) providing a caspase-12; b) contacting the caspase-12 with a candidate compound; and c) monitoring a biological activity of the caspase-12, wherein a decrease in the biological activity of caspase-12, relative to the activity in a control cell not administered the candidate compound, identifies the candidate compound as a compound useful in treating an apoptotic condition. The method may be performed in a cell-free system or in a cell.

In a second aspect, the invention features a method for identifying a compound useful in treating an apoptotic condition. The method includes: a) providing a cell having a caspase and a calpain; b) administering to the cell a candidate compound; and c) monitoring calpain-dependent proteolytic cleavage of the caspase, wherein a decrease in the cleavage of the caspase in the cell, relative to the cleavage in a control cell not administered the candidate compound, identifies the candidate compound as a compound useful in treating an apoptotic condition.

In preferred embodiments of the first or second aspect, the apoptotic condition is stroke, neurodegeneration, ischemia, Alzheimer's disease, or muscular dystrophy, or includes an ER stress-mediated apoptotic condition. Preferably, the cell is a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, or a fibroblast; the cell is in vitro or is in an animal, such as an animal that has an apoptotic condition. In a third aspect, the invention features a method for identifying a compound useful in treating proliferative disease. The method includes: a) providing a caspase-12; b) contacting the caspase-12 with a candidate compound; and c) monitoring a biological activity of caspase-12, wherein an increase in the biological activity of caspase-12, relative to the activity in a control cell not administered the candidate compound, identifies the candidate compound as a compound useful in treating a proliferative disease.

In various embodiments of the first or third aspect, the biological activity is proteolytic cleavage, induction of apoptosis, or binding to p28Bap31, presenilin-1, presenilin-2, or Bcl-xL. In other embodiments, the cell expresses a calpain or a presenilin. Preferably, the caspase-12 is the endogenous caspase- 12, is expressed from a transgene, or is expressed from an extrachromosomal vector. The cell is preferably a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, or a fibroblast; the cell can be in vitro or in an animal, such as an animal that has an apoptotic condition.

In a fourth aspect, the invention features a method for identifying a compound useful in treating a proliferative disease. The method includes: a) providing a cell having a caspase and a calpain; b) administering to the cell a candidate compound; and c) monitoring calpain-dependent proteolytic cleavage of the caspase, wherein an increase in the cleavage of the caspase in the cell, relative to the cleavage in a control cell not administered the candidate compound, identifies the candidate compound as a compound useful in treating a proliferative disease.

In preferred embodiments of the third or fourth aspect, the proliferative disease is cancer, an autoimmune disorder, or a viral infection.

In various embodiments of the second or fourth aspect, the caspase is caspase-7, caspase-8, caspase-9, caspase-11, caspase-12, or Bcl-xL; the caspase is an endogenous caspase, or is expressed from a transgene or an extrachromosomal vector; and the calpain is an endogenous calpain, or is expressed from a transgene or an extrachromosomal vector. In other embodiments, the cell is a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, or a fibroblast. In a fifth aspect, the invention features a transgenic animal expressing transgenic DNA encoding a caspase-12 polypeptide having biological activity.

In a preferred embodiment of the fifth aspect, the transgenic DNA is operably linked to a tightly regulated promoter. In a sixth aspect, the invention features a non-human animal wherein one or both genetic alleles encoding a caspase-12 polypeptide are mutated. In a preferred embodiment, one or both genetic alleles encoding the caspase-12 polypeptide are disrupted, deleted, or otherwise rendered nonfunctional.

In a seventh aspect, the invention features cells from the animal of the fifth or sixth aspect. In a preferred embodiment, the animal is a mouse. In an eighth aspect, the invention features a substantially pure antibody that specifically binds to caspase-12. In various preferred embodiments, the antibody is a monoclonal antibody or is a polyclonal antibody; the antibody does not bind to other caspases; or the antibody is a neutralizing antibody.

The antibodies of the invention may be prepared by a variety of methods. For example, a caspase-12 polypeptide, or antigenic fragments thereof, can be administered to an animal in order to induce the production of polyclonal antibodies. Alternatively, antibodies used as described herein may be monoclonal antibodies, which are prepared using 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 Hyhridomas, Elsevier, NY, 1981). The invention features antibodies that specifically bind human or murine caspase-12 polypeptides, or fragments thereof. In particular the invention features "neutralizing" antibodies. By "neutralizing" antibodies is meant antibodies that interfere with any of the biological activities of caspase-12 polypeptides, particularly the ability of caspase-12 to induce apoptosis. The neutralizing antibody may reduce the ability of caspase-12 polypeptides to induce apoptosis by, preferably 50%, more preferably by 70%, and most preferably by 90% or more. Any standard assay of apoptosis, including those described herein, may be used to assess neutralizing antibodies. In a ninth aspect, the invention features a method for preventing apoptosis, the method including administering an apoptosis-inhibiting amount of an antibody that binds to caspase-12. In a preferred embodiment, the antibody blocks a biological activity of caspase-12. Preferred biological activities include proteolytic cleavage, induction of apoptosis, and binding to p28Bap31 , a presenilin, or Bcl-xL. A preferred presenilin is presenilin-2. In a tenth aspect, the invention features a method for preventing apoptosis in a cell, including administering an inhibitor of the caspase-cleaving activity of a calpain to the cell. Preferably, the cell is a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, or a fibroblast; the cell is in vitro or is in an animal, such as an animal that has an apoptotic condition.

In an eleventh aspect, the invention features a method for increasing apoptosis in a cell, including administering to the cell a caspase-cleaving amount of a calpain protein or a polypeptide fragment thereof. Preferably, the cell is a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, or a fibroblast; the cell is in vitro or is in an animal, such as an animal that has an apoptotic condition.

In a twelfth aspect, the invention features a method for modulating caspase-mediated apoptosis in a cell, the method including administering to the cell a compound identified as modulating cleavage of the caspase by a calpain, the administration at a level sufficient to modulate the cleavage and modulate apoptosis. Preferred compounds include one selected from the group consisting of a chemical, a drug, or an antibody that specifically binds to the calpain. A preferred compound is a caspase-12 polypeptide lacking either apoptosis inducing activity or the ability to be cleaved by a calpain A preferred antibody is a neutralizing antibody. Preferably, the cell is a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, or a fibroblast; the cell is in vitro or is in an animal, such as an animal that has an apoptotic condition or a proliferative disease.

In a thirteenth aspect, the invention features a method for diagnosing a mammal for the presence of a disease involving altered apoptosis or an increased likelihood of developing the disease, including measuring the level of caspase-cleaving activity of a calpain in a sample from the mammal, a change in the level of caspase-cleaving activity of the calpain in the sample, relative to a level of the activity of the calpain in a sample from an unaffected mammal, indicative that the mammal has the disease or has an increased likelihood of developing the disease.

In various embodiments of the thirteenth aspect, the caspase-cleaving activity is measured by measuring cleavage of caspase-12 polypeptide to produce a p35 product, by measuring cleavage of Bcl-xL polypeptide to produce a p25 product, or by measuring in an enzymatic assay.

In a fourteenth aspect, the invention features a method for diagnosing a patient with an apoptotic condition, including measuring the level of caspase- 12 biological activity in a biological sample from the patient, wherein increased amounts of caspase-12 biological activity, relative to a person who does not have an apoptotic disease, indicates the person has an apoptotic condition. In various preferred embodiments of the fourteenth aspect, the apoptotic condition is stroke, neurodegeneration, ischemia, Alzheimer's disease, or muscular dystrophy, or includes an ER stress-mediated apoptotic condition; the biological activity is proteolytic cleavage, induction of apoptosis, or binding to p28Bap31 , presenilin- 1 , presenilin-2, or Bcl-xL.

In a fifteenth aspect, the invention features a substantially pure caspase-12 polypeptide, the polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and 132 of SEQ ID NO: 1. In a sixteenth aspect, the invention features a substantially pure nucleic acid sequence encoding a caspase-12 polypeptide, the polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and 132 of SEQ ID NO: 1.

In a seventeenth aspect, the invention features a substantially pure polypeptide caspase-12 polypeptide, the polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and l58 of SEQ ID NO: 1.

In an eighteenth aspect, the invention features a substantially pure nucleic acid sequence encoding a caspase-12 polypeptide, the polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and 158 of SEQ ID NO: 1.

In a nineteenth aspect, the invention features a kit for diagnosing a mammal for the presence of an apoptotic condition or an increased likelihood of developing an apoptotic condition, the kit including a substantially pure antibody that specifically binds a caspase-12 polypeptide. In a preferred embodiment, the kit further includes a means for detecting binding of the antibody to the caspase-12 polypeptide. In a twentieth aspect, the invention features a method for inducing apoptosis in a cell, the cell in a mammal diagnosed with a proliferative disease, the method including administering to the cell a positive regulator of the caspase- 12-dependent apoptotic pathway. In a preferred embodiment, the positive regulator includes a caspase-12 polypeptide, the polypeptide having a caspase-12 biological activity and lacking five amino acids between amino acids 2 and 158 of SEQ ID NO: 1.

In a twenty- first aspect, the invention features a method of inducing apoptosis in a cell, the cell in a mammal diagnosed with a proliferative disease, the method including administering to the cell a nucleic acid sequence encoding a caspase-12 polypeptide, the polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and 158 of SEQ ID NO: 1, the nucleic acid sequence positioned for expression in the cell. In a twenty-second aspect, the invention features a method of inducing apoptosis in a cell in a mammal diagnosed with a proliferative disease. The method includes administering to the cell a nucleic acid sequence encoding a caspase-12 polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and 158 of SEQ ID NO: 1.

In preferred embodiments, the polypeptide is substantially identical to a polypeptide consisting of amino acids 159 to 419 of SEQ ID NO: 1 or to a polypeptide consisting of amino acids 133 to 419 of SEQ ID NO: 1. In another preferred embodiment, the nucleic acid is operably linked to a promoter (e.g., a heterologous promoter that is inducible, constitutive, or cell-type specific). In still another preferred embodiment, the nucleic acid is in a recombinant viral vector. By a "caspase-cleaving amount" of a calpain is meant an amount of a calpain that cleaves a caspase in an in vitro cleavage assay such as the one described herein. Preferably, the amount of the caspase that is cleaved is at least 5%, more preferably the amount is 25%, and most preferably the amount is at least 50%. Preferably, the caspase is a caspase known to be cleaved by the calpain in vivo.

By a "caspase-12" is meant a polypeptide is substantially identical to the polypeptide of SEQ ID NO: 1 and that binds to an antibody that specifically binds to the polypeptide having the amino acid sequence of SEQ ID NO: 1. By "caspase-12 biological activity" is meant an activity associated with caspase-12 function, including proteotytic cleavage, activation of protease activity, binding to presenilins, p28Bap31, or Bcl-xL, and induction of cell death.

By "modulating apoptosis" or "altering apoptosis" is meant increasing or decreasing the number of cells that would otherwise 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. It will be appreciated that the degree of modulation provided by caspase-12 or a 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 that identifies a compound as one that modulates caspase- 12-mediated apoptosis.

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 10%, more preferably the decrease is 25%, and most preferably the decrease is 50% or at least one-fold.

By "enhancing apoptosis" is meant any increase in the number of cells that apoptose in a given cell population. Preferably, the cell population is selected from a group including ovarian cancer cells, breast cancer cells, pancreatic cancer cells, T cells, neuronal cells, fibroblasts, or any cell line known to proliferate in a laboratory setting. It will be appreciated that the degree of apoptosis enhancement provided by an apoptosis enhancing 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 a compound which enhances. Preferably, "enhancing apoptosis" means that the increase in the number of cells undergoing apoptosis is at least 10%, more preferably the increase is 25%, and most preferably the increase is 50% or at least one-fold. Preferably, the sample monitored is a sample of cells which normally undergo insufficient apoptosis (i.e., cancer cells).

By "proliferative disease" is meant a disease which is caused by or results in inappropriately high levels of cell division, inappropriately low levels of apoptosis, or both. For example, cancers such as lymphoma, leukemia, melanoma, ovarian cancer, breast cancer, pancreatic cancer, and lung cancer are all examples of proliferative disease.

By "polypeptide" is meant any chain of more than two amino acids, regardless of post-translational modification such as glycosylation or phosphorylation. By "substantially pure polypeptide" is meant a polypeptide that has been separated from the components that 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 polypeptide is a caspase-12 polypeptide that is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, pure. A substantially pure caspase-12 polypeptide may be obtained, for example, by extraction from a natural source (e.g. a fibroblast, neuronal cell, or lymphocyte) by expression of a recombinant nucleic acid encoding a caspase-12 polypeptide, or by chemically synthesizing the protein. Purity can be measured by any appropriate method, e.g., by column chromatography, polyacrylamide gel electrophoresis, or 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. co li or other prokaryotes.

By "substantially pure nucleic acid" 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 "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 "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., a caspase-12 polypeptide, a recombinant protein or a RNA molecule). By "operably linked" is meant that a gene and one or more regulatory sequences 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 sequences). 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., a caspase- 12-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 "substantially identical" is meant that 30 or more consecutive amino acids exhibit at least 50%, preferably 85%, more preferably 90%, and most preferably 95% identity to a reference amino acid sequence. The length of substantial identity will generally be at least 30 amino acids, preferably at least 50 amino acids, more preferably at least 100 amino acids, and most preferably 200 amino acids. One sequence may include additions or deletions (i.e., gaps) of 20% or less when compared to the second sequence.

By "specifically binds" is meant an antibody that recognizes and binds a protein but that does not substantially recognize and bind other molecules in a sample, e.g., a biological sample, that naturally includes protein.

By a "p28Bap31" is meant a polypeptide substantially identical to human p28Bap31 (GenBank accession no. S71117) and that binds to an antibody that specifically binds to human p28Bap31. By an "m-calpain" is meant a polypeptide substantially identical to mouse m-calpain (GenBank accession no. CAA71227) and that binds to an antibody that specifically binds to mouse m-calpain. By a "caspase" is meant a polypeptide substantially identical to a member of the Ced-3 family of proteases. Preferably, the caspase is substantially identical to caspase-7 (GenBank accession no. NP_001218), caspase-8 (GenBank accession no. NP_001219), caspase-9 (GenBank accession no. NP_001220), caspase-11 (GenBank accession no. NP_031635), caspase-12, OR Bcl-xL (GenBank accession no. Q07817) and that binds to an antibody that specifically binds to one of the foregoing caspases.

Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.

Fig. IA is a series of photographs of western blots showing immunodetection of caspase-12, Bcl-xL, Bcl-2, caspase-3, cytochrome C, and TRAPα in fractionated mouse cerebral cortex and kidney ly sates. Fig. IB is a photograph showing immunohistochemistry of caspase-12 in mouse brain.

Figs. 2A-2L are a series of photographs showing endogenous expression of caspase-12 (Fig. 2A), caspase-3 (Fig. 2C), caspase-1 (Fig. 2D), TRAPα (Fig. 2E) and BiP (Fig. 2F) in L929 cells and caspase-8 (Fig. 2B) in HeLa cells. Fig. 2G is a negative control using supernatant of hybrydoma, which does not produce specific antibody, as first antibody. Fig. 2H and 21 are confocal image of caspase-12 and TRAPα (Fig. 2H) or BiP (Fig. 21) in L929 cells. Localization of GFP-fusion constructs transfected into COS cells is shown for caspase- 12-EGFP (Fig. 2J), EGFP-p28BAP31 (Fig. 2K), and EGFP-presenilin- 2 (Fig. 2L).

Fig. 3 A is a series of photographs showing co-immunoprecipitation of caspase-12, p28Bap31, and Bcl-xL in 293T cells. Western blotting (upper panel) shows the expression of the transfected proteins. Western blotting following immunoprecipitation is shown in the lower panel. Antibodies were as follows: mcaspl2Ab~monoclonal antibody to caspase-12; pl2~polyclonal antibody to caspase-12; mGFP— monoclonal antibody to GFP (Clontech, Palo Alto, CA); pGFP-polyclonal antibody to GFP (Chemicon, Temecula, CA); mHA~monoclonal antibody to HA (Covance, Richmond, CA).

Fig. 3B is a series of photographs of western blots showing that caspase- 12 and presenilin-2 form a complex. The upper panel shows an in vitro binding assay using ³⁵S-presenilin-2, GST-Bcl-xL, GST-p28Bap31, and GST-caspase- 12. The lower panel shows a western blot.

Fig. 4A is a series of photographs of western blots of caspase-12, Bcl- xL, BiP, and tubulin proteins in lysates from mixed glial cells following 15 hours of oxygen and glucose deprivation (OGD), or oxygen deprivation (OD), or untreated (UT). Figs. 4B and 4C are each a series of photographs of western blots showing that tunicamycin (TUN), thapsigargin (TH), and A23187 induce ER stress in embryonic fibroblast (EF) cells (Fig. 4B) and glial cells (Fig. 4C).

Fig. 5 is a schematic illustration showing the resistance of caspase-12 -/- mice to tunicamycin-induced lethality. Fig. 6A is a photograph of caspase-12 +/+ and caspase-12 -/- kidneys after tunicamycin injection.

Figs. 6B and 6C are photographs of kidney sections processed for immunohistochemistry with anti-caspase-12 antibodies. Caspase-12 is mainly expressed in renal tubular cells (Fig. 6B). No caspase-12 expression was detected in caspase-12 -/- mice (Fig. 6C).

Figs. 6D-6G are photographs of hematoxylin and eosin stained samples of wild-type mice (Figs. 6D and 6F) and caspase-12 -/- mice (Figs. 6E and 6G) either untreated (Figs. 6D and 6E) or treated with 1 mg/kg tunicamycin injection (Figs. 6F and 6G).

Figs. 6H and 61 are photographs of TUNEL staining performed on day 4 kidney following injection of 0.25mg/kg tunicamycin into caspase-12 +/- (Fig. 6H) or caspase-12 -/- mice (Fig. 61).

Fig. 7 is a series of photographs of western blots of caspase-12, BiP, and tubulin proteins in lysates from kidney.

Fig. 8 A is a schematic illustration showing analysis of DNA content by FACS of propidium iodide-stained EF cells with caspase- 12+/- and caspase-12- /- genotype in two days after treatment of tunicamycin or thapsigargin for six hours or in one day after treatment of staurosporine.

Fig. 8B is a schematic illustration showing viability in tunicamycin or thapsigargin treated EF cells with indicated genotypes.

Figs. 9A and 9B are a series of photographs of western blots showing calpain inhibitors are protective for caspase-12 and Bcl-xL cleavages.

Fig. 9C is a series of schematic illustrations showing that viability in tunicamycin or thapsigargin treated EF cells was increased by calpain inhibitor MDL28170 or the cell permeable calcium chelator BAPTA-AM.

Fig. 10 is a photograph of a western blot showing caspase-12 is cleaved by cerebral cortex soluble protein in a calcium dependent manner.

Fig. 11 is a series of photographs of western blots showing that caspase- 12 and Bcl-xL are cleaved by purified m-calpain.

Fig. 12 is a photograph of a western blot showing the cleavage of caspase-12 is inhibited by peptide 174-187. Fig. 13 is a schematic illustration showing that caspase-12 is cleaved by m-calpain in vitro at T132/A133 and K158/T159. We have discovered that caspase-12, a caspase-1 subfamily member, is predominantly localized to the endoplasmic reticulum (ER), is activated through ER stress, and induces apoptosis. Our protein binding studies revealed that caspase-12 interacts with at least three other proteins in cells, Bcl-xL, presenilin-2, and p28Bap31. We also find that embryonic fibroblasts from caspase-12 knockout mice are resistant to ER stress-mediated death and presenilin-2-mediated death. Caspase-12 is cleaved by calpain in vitro between the prodomain and the large subunit, while caspase-12 activation is inhibited by calpain inhibitors in vivo. Similarly, Bcl-xL is cleaved and inactivated by calpains; this cleavage is also inhibited by calpain inhibitors. These data indicate that caspase-12 is part of a calpain-mediated apoptotic pathway in the ER.

The invention described herein provides new screens for compounds useful in the treatment of cell death resulting, for example, from stroke, myocardial infarction, muscular dystrophy, and neurodegeneration. Based on the discovery that calpains regulate caspase-12 cleavage and activation, as well as Bcl-xL cleavage and inactivation, the invention also provides new uses for inhibitors of calpain activity as inhibitors of ER stress-mediated apoptosis.

Subcellular distribution of caspase-12

To determine the subcellular distribution of caspase-12, lysates from brain cortices or kidneys of newborn mice were fractionated into nuclear, mitochondrial, microsomal, and soluble fractions, and analyzed by western blotting. The fractionation of lysates was confirmed by western blotting using compartment-specific protein (cytochrome C: mitochondria; TRAPα: endoplasmic reticulum). Procaspase-12, the inactive form of caspase-12, was associated with the microsomal fraction (Fig. 1 A). Cleaved caspase-12, most likely produced during the fractionation procedure, was associated with the soluble fraction.

We examined subcellular distribution by immunohistochemistry and immunocytochemistry. In brain sections, caspase-12 is localized to the cytoplasm, cell body, and dendrites of neurons (Fig. IB). In culture, caspase- 12 is predominantly localized around the nucleus of L929 cells. This is in stark contrast to caspase-1, caspase-3, and caspase-8, which were each detected as being diffusely localized in the cytoplasm of L929 or Hela cells (Figs. 2B-2D). The expression pattern of caspase-12 was similar to that of TRAPα and BiP, both of which specifically localize to the endoplasmic reticulum (Figs. 2E and 2F). Co-localization of caspase-12 with TRAPα or BiP in L929 cells in the endoplasmic reticulum was confirmed using confocal microscopy. In addition, subcellular distribution of transfected caspase-12 in COS cells was found to be similar to that of both presenilin-2 and p28Bap31 (Figs. 2H-2K), two additional ER membrane proteins. Together, these data established that caspase-12 was specifically localized to the endoplasmic reticulum.

Caspase-12 is localized on the cytoplasmic side of. the ER

To further understand the mechanism of caspase-12 activation, we determined whether caspase-12 is localized on the lumenal or cytoplasmic side of the ER. We prepared mouse kidney microsomal fraction and analyzed the orientation of caspase-12 by limited trypsin digestion. We found that caspase-12, like the IP3 receptor, an ER resident protein facing the cytoplasmic side, was quickly digested by trypsin treatment. In contrast, grp78 (BiP), grp94, and calreticulin, which are each localized on the lumenal side of ER, are protected from trypsin digestion. These data indicates that caspase-12 is localized on the cytoplasmic side of the ER. Caspase-12 binds to presenilin- 1. presenilin-2, and p28Bap31

Based on the observation that caspase-12 had an expression pattern similar to that of both presenilin-2 and p28Bap31, we hypothesized that these three proteins might form part of a signaling unit. To further examine this possibility, we tested whether caspase-12 could directly bind to either presenilin-2 or p28Bap31.

293T cells were co-transfected with caspase-12 and p28Bap31-GFP, and then lysed. Immunoprecipitation was performed with either an anti-caspase-12 antibody, followed by western blotting using an anti-GFP monoclonal antibody. Caspase-12 and p28Bap31 were detected in the immunoprecipitated complex. These data show that caspase-12 and p28Bap31 are capable of forming part of a complex in the ER of cultured cells.

Using similar techniques, we also found that caspase-12 and Bcl-xL could also be co-immunoprecipitated. This was consistent with previous observations that p28Bap31 interacts with Bcl-xL (Ng. et al., J. Biol. Chem. 273:3140-3143, 1998).

Caspase-12 also bound presenilin-2. This was determined using two different approaches. First, ³⁵S-presenilin-2, produced by in vitro translation, was capable of binding to GST-caspase-12, but not to the GST control (Fig. 3B). Presenilin-2 also bound to GST-Bcl-xL and GST-p28Bap31, suggesting that these four proteins form a complex in vitro. Interestingly, presenilin-2 could interact with caspase-12, Bcl-xL, or p28Bap31 without all four members being present.

Using methods similar to those described above, we also found that caspase- 12 bound presenilin- 1. Cleavage of caspase-12 following ER stress-inducing treatment

We examined the caspase-12 activating cascade using primary culture (glial cells, EF cells) or W4 cells. Caspase-12 was specifically cleaved to produce a 35 kDa product following a treatment that induces ER stress (Fig. 4A-4C). Other treatments that can induce apoptosis, including low serum, Fas activation, TNF plus cyclohexamide, and aposide, did not result in caspase-12 cleavage. ER stress response was indicated by the induction of BiP protein, a chaperone protein found specifically in the ER. After staurosporine treatment, a small amount of caspase-12 was cleaved. It is likely that staurosporine partially activated caspase-12 because intracellular calcium increased following staurosporine treatment. The amount of cleavage of caspase-12 was enhanced by administration of thapsigargin (which inhibits calcium- ATPase and, as a result, increases cytoplasmic calcium) or calcium ionophore (A23187) (Fig. 4C). We conclude from these data that the caspase-12 activating pathway is specifically dependent upon ER stress response, and, furthermore, that caspase- 12 is activated through the elevation of intracellular calcium.

Bcl-xL was also cleaved to produce a 25 kDa proteolytic fragment in glial cells lysate after oxygen and glucose deprivation (OGD) treatment (Fig. 4A). This 25 kDa protein was not Bcl-xS because the short form of mRNA was not detected by RT-PCR.

We generated caspase-12 mutant mice. Mice homozygous for the germline caspase-12 mutation (caspase-12-/-) were indistinguishable in appearance from wild-type littermates. Tunicamycin (an inhibitor of protein glycosylation) induces programmed cell death in renal epithelial cells. Sublethal doses of tunicamycin (0.25-1 mg/kg body weight) were intrapenitorially injected into wild-type and caspase-12-/- mice. Two of five wild-type mice died by four days after injection, whereas all six caspase-12-/- mice lived (Fig. 5).

Because caspase-12 is specifically expressed in renal proximal tubular epithelial cells, and not the glomerulus (Fig. 6B), we examined the involvement of caspase-12 in renal tubular epithelial cell death after tunicamycin treatment. After tunicamycin treatment, kidneys from wild-type mice were congestive (Fig. 6A). The histological alteration was restricted to the tubular epithelium, whereas the glomeruli were spared. The renal tubular epithelium from caspase- 12 +/+ mice was completely destroyed after high dose tunicamycin injection (1 mg/kg). In contrast, in caspase-12 -/-mice, renal tubular epithelial cells were preserved (Figs. 6F and 6G).

Programmed cell death was specifically examined in sections. TUNEL staining of kidneys four days after tunicamycin treatment (0.25mg/kg) showed fewer TUNEL-positive cells in kidney from caspase-12 -/- mice (149 +/- 41 in caspase-12 +/+ or +/- (n=4), compared with 27 +/- 20 in caspase-12-/- kidney (n=4)) (Figs. 6H and 61). In support, western blotting indicated that ER stress occurred in kidney cells four days after tunicamycin treatment and that caspase- 12 was activated (Fig. 7).

We performed FACS analysis of DNA content and Thiazolyl Blue (MTT) assay of tunicamycin, thapsigargin, or staurosporine-treated EF cells (Figs. 8A and 8B). The typical subdiploid DNA of apoptotic cells was evident in the caspase- 12+/- but not caspase-12-/- EF cells after treatment with tunicamycin or thapsigargin (Fig. 8A). In contrast, EF cells from either genotype were equally susceptible to staurosporine (Fig. 8 A). We suggest, then, that the cell death signaling pathway through the ER is different from that induced by staurosporine.

The MTT assay showed greater cell death in caspase-12 +/- EF cells after treatment of tunicamycin or thapsigargin than in caspase-12 -/- EF cells. These data indicate that tunicamycin-induced renal tubular epithelial cell death was mediated by caspase-12, and that caspase-12 is required in ER stress induced cell death.

Caspase-12 -/- mice were also resistant to presenilin-mediated cell death. Heterozygous and homozygous null EF cells were transfected with GFP-PS2, GFP-PS2^N14H (a mutant presenilin-2 that is found in familial Alzheimer's disease), or a control GFP vector. Following culture for 24 hours, the percent cell death was determined by morphology. In the heterozygous EF cells transfected with either the wild-type or mutant presenilin-2, cell death was 2-3 fold higher than in the control condition (Table 1). Caspase-12 -/- EF cells, however, were partially resistant to death mediated by either wild-type presenilin (43.7 +/- 2.7% compared to 74.0 +/- 4.4%) or mutant presenilin (50.2 +/- 2.1% compared to 66.6 +/- 3.9%). These data show that not only do presenilin-2 and caspase-12 interact in vitro, but that caspase-12 is required in part for presenilin-mediated cell death.

Table 1

Inhibition of caspase-12 and Bc1-xL cleavage by calpain

Because ER stress agents (e.g., tunicamycin, thapsigargin, and A23187) increase calcium concentration in the cytosol and because the spatial expression pattern of caspase-12 in the kidney is same as expression of calpains (Yoshimura et al., J. Biol. Chem. 259:9847-9852, 1984), we examined the involvement of calpains in caspase-12 activation. Calpain inhibitors (calpain inhibitor I and II, E64d) , but not ZVAD (200μM) or proteasome inhibitor I (PSI), inhibited the cleavage of caspase-12 in glial cells after OGD treatment (Figs. 9 A and 9B). These effects were dose-dependent. Cell death was partially prevented by E64d and ZVAD in glial cells after OGD treatment (Fig. 9B), and by MDL28170 (a specific calpain inhibitor), and BAPTA-AM (a cell permeable calcium chelator) in EF cells after ER stress treatment (Fig. 9C). Bcl-xL cleavage was also inhibited by calpain inhibitors (Fig. 9A). Bcl-xL cleavage product was detected in lysate of caspase-12 -/- glial cells after OGD treatment, however, indicating that caspase-12 is not required for cleavage of Bcl-xL. Cerebral cortex soluble fraction (S-100) had a calcium-dependent protease activity for caspase-12 (Fig. 10). These data suggested that a calpain- like protease directly cleaves caspase-12 and Bcl-xL. To confirm these data, we examined in vitro cleavage of ³⁵S-caspase-12 or ³⁵S-Bcl-xL by purified m- calpain (Fig. 11). m-calpain cleaved caspase-12 between the prodomain and the large subunit. Cleaved caspase-12 product most likely autoprocessed to the large subunit and small subunit (Fig. 11), because full length caspase-12 was effectively cleaved to 35kDa by m-calpain and then cleavage products of the large and small subunits appeared in a time dependent manner. To investigate the cleavage site within caspase-12, we examined peptide inhibition of caspase-12 cleavage by S-100 (Fig. 12). Peptide 174-187, as well as neighboring peptides 156-168, and 165-177, inhibited caspase-12 cleavage, suggesting that caspase-12 residues 156-177 may have an important role in recognition of caspase-12 by calpain. These residues are near the cleavage sites present in other caspases (e.g., caspase-2, -3, -8, and -14).

We determined the sites at which caspase-12 was cleaved by m-calpain by direct peptide sequencing of the N-terminal fraction following separation by SDS-PAGE. Two cleavage sites were identified (Fig. 13). The first was at T132/A133 and the second was at K158/T159. Other caspases were also cleaved by calpain, including caspase-7, -8, -9, and -11. Moreover, m-calpain directly cleaved Bcl-xL at one site in the loop domain (A60/D61). Interestingly, this site of cleavage in Bcl-xL by calpain is very close to the reported cleavage site of Bcl-xL by caspase-1 (D61/S62) and caspase-3 (D61/S62 and D76/A77). Since the cleaved products of Bcl-xL by caspase-1 or -3 have proapoptotic activity, the cleaved product of Bcl-xL by m-calpain most likely has similar function. These data suggest that active calpain converts pro-caspase-12 into active caspase-12 and Bcl-xL from an anti-apoptotic protein into a proapoptotic form.

Calcium is required for calpain-mediated caspase-12 cleavage

Since calcium is essential for activation of calpain, we reasoned that calcium should be essential for caspase-12 activation as well. To examine the requirement of calcium for caspase-12 cleavage, we used the S-100 fraction of mouse cerebral cortex as a source of calpain to cleave in vitro translated caspase-12. We found that the cortical S-100 cleaved the full length caspase-12 into fragments around 35 kDa in the presence of millimolar but not micromolar calcium and this cleavage was inhibited by the addition of EGTA and EDTA.

In summary, the cleavage of caspase-12 by m-calpain demonstrates that this specific calcium signaling cascade is important for some types of cell death cascades, most notably ER stress-induced cell death. Caspase-12 is specifically localized in the ER, as demonstrated by immunocytochemistry, and immunoprecipitation indicates that caspase-12 binds to the ER localizing proteins, p28Bap31 and presenilin-2. We propose that the calpain-caspase-12 cascade is activated in pathological condition or diseases such as, for example, ischemia (stroke, myocardial infarction, etc.), neuronal degeneration, and muscular atrophy. Presenilins and ERAB are localized to the ER (Yan et al., Nature 389:689-695 (1997)), and mutations of presenilins have been found in familial Alzheimer Disease. The prion protein isoforms that cause transmissible or heritable prion disease are also synthesized in the ER (Hegde et al., Science 279:827-834, 1998). It is likely that these proteins are inducing cellular apoptosis through interactions that lead to caspase-12 cleavage and activation.

Examples of additional apoptosis assays

Specific examples of apoptosis assays are provided in the following references. Assays for apoptosis in lymphocytes are disclosed by: Li et al., Science 268:429-431, 1995; Gibellini et al, Br. J. Haematol. 89:24-33, 1995;

Martin et al, J. Immunol. 152:330-342, 1994; Terai et al, J. Clin Invest.

87:1710-1715, 1991; Dhein et al. Nature 373:438-441, 1995; Katsikis et al, J.

Exp. Med. 1815:2029-2036, 1995; Westendorp et al. Nature 375:497, 1995;

DeRossi et al. Virology 198:234-244, 1994. Assays for apoptosis in fibroblasts are disclosed by: Vossbeck et al. Int.

J. Cancer 61:92-97, 1995; Goruppi et al, Oncogene 9:1537-1544, 1994;

Fernandez et al, Oncogene 9:2009-2017, 1994; Harrington et al, EMBO J,

13:3286-3295, 1994; Itoh et al, J. Biol. Chem. 268:10932-10937, 1993.

Assays for apoptosis in neuronal cells are disclosed by: Melino et al, Mol. Cell Biol. 14:6584-6596, 1994; Rosenbaum et al, Ann. Neurol. 36:864-

870, 1994; Sato et al, J. Neurobiol 25:1227-1234, 1994; Ferrari et al, J.

Neurosci. 1516:2857-2866, 1995; Talley et al, Mol. Cell Biol. 1585:2359-

2366, 1995; Talley et al, Mol. Cell. Biol. 15:2359-2366, 1995; Walkinshaw et al, J. Clin. Invest. 95:2458-2464, 1995. Assays for apoptosis in insect cells are disclosed by: Clem et al. Science

254:1388-90, 1991; Crook et al, J. Virol. 67:2168-74, 1993; Rabizadeh et al. J. Neurochem. 61 :2318-21, 1993; Birnbaum et al, J. Virol. 68:2521-8, 1994; Clem et al, Mol. Cell. Biol. 14:5212-5222, 1994.

Identification of molecules that modulate caspase-12 biological activity

One assay for the ability of candidate compounds to modulate caspase- 12 mediated apoptosis is to monitor caspase-12 cleavage by using standard protein detection techniques such as those described herein. In general, a compound that decreases caspase-12 cleavage will also decrease caspase-12 mediated cell death, while a compound that increases caspase-12 cleavage will increase caspase-12 mediated cell death. Compounds that decrease caspase-12 cleavage and are described herein include caspase-12 peptide sequences 174- 187, 156-168, and 165-177 of caspase-12 (SEQ ID NO: 1). One skilled in the art will recognize that other peptides can be readily produced that will result in the same decrease in caspase-12 cleavage.

Another compound that is likely to decrease caspase-12 cleavage is a mutated caspase-12 that binds to calpains but is not cleaved by them. Such caspase-12 molecules include those in which amino acid positions 132, 133, 158, and/or 159 are modified to be another amino acid. By binding to calpains, these molecules will reduce the amount of free calpains and, thus, reduce cleavage of endogenous caspase-12 protein. Similarly, a compound that is cleaved by calpains but that does not have apoptosis inducing activity will act as a competitive substrate, reducing the amount of caspase-12 cleaved by calpains.

We have shown that other caspases are also cleaved by calpains. One skilled in the art will recognize that the strategies outlined for identifying inhibitors of calpain-mediated cleavage of caspase-12 are amenable to these and other caspases. The effect of candidate molecules on caspase- 12-mediated apoptosis can be measured at the level of protein-protein interaction by using the general approach described above with standard protein detection techniques, such as Western blotting or immunoprecipitation with a caspase- 12-specific antibody (for example, the caspase-12 antibodies described herein), a presenilin antibody, a Bcl-xL antibody, or a p28Bap31 antibody.

Compounds may also be screened for their ability to modulate caspase- 12 apoptosis 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, the 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 that modulate the activity of caspase-12 is to screen for compounds that interact physically with caspase-12. These compounds may be detected by adapting interaction trap expression systems known in the art. These systems detect protein interactions using a transcriptional activation assay and are generally described by Gyuris et al. (Cell 75:791-803, 1993) and Field et al. Nature 340:245-246, 1989), and are commercially available from Clontech (Palo Alto, CA). In addition, PCT

Publication WO 95/28497 describes an interaction trap assay in which proteins involved in apoptosis, by virtue of their interaction with Bcl-2, are detected. A similar method may be used to identify proteins and other compounds that interact with caspase-12. Compounds that modulate caspase-12 protein-protein interactions or caspase-12 cleavage or activation may be purified, or substantially purified, or may be one component of a mixture of compounds such as an extract or supernatant obtained from cells (Ausubel et al. Current Protocols in Biology, John Wiley & Sons, New York, NY, 1994). In an assay of a mixture of compounds, a caspase-12 biological activity is tested against progressively smaller subsets of the compound pool (e.g, produced by standard purification techniques such as HPLC or FPLC) until a single compound or minimal number of effective compounds is demonstrated to modulate this biological activity.

Compounds or molecules that function as modulators of caspase- 12- mediated cell death may include peptide and non-peptide molecules such as those present in cell extracts, mammalian serum, or growth medium in which mammalian cells have been cultured.

A molecule that results in a decrease in caspase-12 expression or biological activity is considered particularly useful in the invention; such a molecule may be used, for example, as a therapeutic to decrease the ability of caspase-12 to induce apoptosis. A molecule that increases caspase-12 activity (e.g, by increasing cleavage of caspase-12) may be used to decrease cellular proliferation. This would be advantageous in the treatment of neoplasms or other cell proliferative diseases (including, but not limited to, follicular lymphoma, p53-mediated carcinomas, and hormone-dependent tumors), autoimmune disorders (e.g, lupus erythematosis and multiple sclerosis, and viral infections (including those associated with herpes virus, poxvirus, and adenovirus).

Compounds described herein that are likely to increase caspase-12 biological activity include the carboxy fragments of caspase-12 polypeptides cleaved at T132/A133 or K158/T159 of SEQ ID NO: 1. These polypeptides should be function as activated caspase-12, resulting in decreased proliferation or death. It is understood that these polypeptides can be part of a fusion protein to allow for expression or entry into a cell without losing their biological activity. Similarly, nucleic acid sequences encoding such polypeptides can be operably linked to a suitable promoter (e.g, an inducible or a cell-type specific promoter) and used for gene therapy.

In general, compounds are identified from large libraries of both natural product and synthetic (or semi-synthetic) extracts or chemical libraries according to methods known in the art. Those skilled in the field of drug discovery and development will understand that the precise source of test extracts or compounds is not critical to the screening procedure(s) of the invention. Accordingly, virtually any number of chemical extracts or compounds can be screened using the methods described herein. Examples of such extracts or compounds include, but are not limited to, plant-, fungal-, prokaryotic- or animal-based extracts, fermentation broths, and synthetic compounds, as well as modification of existing compounds. Numerous methods are also available for generating random or directed synthesis (e.g, semi- synthesis or total synthesis) of any number of chemical compounds, including, but not limited to, saccharide-, lipid-, peptide-, and nucleic acid- based compounds. Synthetic compound libraries are commercially available from Brandon Associates (Merrimack, NH) and Aldrich Chemical (Milwaukee, WI). Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant, and animal extracts are commercially available from a number of sources, including Biotics (Sussex, UK), Xenova (Slough, UK), Harbor Branch Oceangraphics Institute (Ft. Pierce, FL), and PharmaMar, U.S.A. (Cambridge, MA). In addition, natural and synthetically produced libraries are produced, if desired, according to methods known in the art, e.g, by standard extraction and fractionation methods. Furthermore, if desired, any library or compound is readily modified using standard chemical, physical, or biochemical methods. In addition, those skilled in the art of drug discovery and development readily understand that methods for dereplication (e.g, taxonomic dereplication, biological dereplication, and chemical dereplication, or any combination thereof) or the elimination of replicates or repeats of materials already known for their anti-pathogenic activity should be employed whenever possible.

When a crude extract is found to have a desired modulating activity, or a binding activity, further fractionation of the positive lead extract is necessary to isolate chemical constituents responsible for the observed effect. Thus, the goal of the extraction, fractionation, and purification process is the careful characterization and identification of a chemical entity within the crude extract having the desired activity. Methods of fractionation and purification of such heterogenous extracts are known in the art. If desired, compounds shown to be useful agents for the treatment of pathogenicity are chemically modified according to methods known in the art.

I Jses

For therapeutic uses, the compounds, compositions, or agents identified using the methods disclosed herein may be administered systemically, for example, formulated in a pharmaceutically-acceptable buffer such as physiological saline. Treatment may be accomplished directly, e.g, by treating the animal with antagonists which disrupt, suppress, attenuate, or neutralize the biological events associated with a disease. Preferable routes of administration include, for example, inhalation or subcutaneous, intravenous, interperitoneally, intramuscular, or intradermal injections which provide continuous, sustained levels of the drug in the patient. Treatment of human patients or other animals will be carried out using a therapeutically effective amount of an anti-apoptotic agent in a physiologically-acceptable carrier. Suitable carriers and their formulation are described, for example, in Remington: The Science and Practice of Pharmacy, (19th ed.) ed. A.R. Gennaro AR, 1995, Mack Publishing Company, Easton, PA. The amount of the anti-apoptotic agent to be administered varies depending upon the manner of administration, the age and body weight of the patient, and with the type of disease and extensiveness of the disease. Generally, amounts will be in the range of those used for other agents used in the treatment of other apoptotic diseases, although in certain instances lower amounts will be needed because of the increased specificity of the compound. A compound is administered at a dosage that inhibits cell death. For example, for systemic administration a compound is administered typically in the range of 0.1 ng - 10 g/kg body weight.

Therapy

Gene therapy is a potential therapeutic approach in which normal copies of the caspase-12 gene or nucleic acid encoding cleaved caspase-12 sense or antisense RNA is introduced into cells. The gene must be delivered to those cells in a form in which it can be taken up and encode for sufficient protein to provide effective function.

Transducing retroviral, adenoviral, and human immunodeficiency viral

(HIV) vectors can be used for somatic cell gene therapy especially because of their high efficiency of infection and stable integration and expression (see, for example, Cayouette and Gravel, Hum. Gene Ther, 8:423-430, 1997; Kido et al.

Curr. Eye Res, 15:833-844, 1996; Bloomer et al, J. Virol, 71:6641-6649,

1997; Naldini et al. Science 272:263-267, 1996; Miyoshi et al, Proc. Natl.

Acad. Sci. USA, 94:10319-10323, 1997). For example, a nucleic acid encoding the carboxy fragment of cleaved caspase-12, or portions thereof, can be cloned into a retroviral vector and driven from its endogenous promoter or from the retroviral long terminal repeat or from a promoter specific for the target cell type of interest. Other viral vectors which can be used include adenovirus, adeno-associated virus, vaccinia virus, bovine papilloma virus, or a herpes virus such as Epstein-Barr virus.

Gene transfer could also be achieved using non- viral means requiring infection in vitro. This would include calcium phosphate, DEAE dextran, electroporation, and protoplast fusion. Liposomes may also be potentially beneficial for delivery of DNA into a cell. Although these methods are available, many of these are of lower efficiency.

Transplantation of normal genes into the affected cells of a patient can also be useful therapy. In this procedure, a nucleic acid encoding a carboxy fragment of cleaved caspase-12 is transferred into a cultivatable cell type, either exogenously or endogenously to the patient. These cells are then injected into the targeted tissue(s).

In the constructs described, caspase-12 cDNA expression can be directed from any suitable promoter (e.g, the human cytomegalovirus (CMV), simian virus 40 (SV40), or metallothionein promoters), and regulated by any appropriate mammalian regulatory element. For example, if desired, enhancers known to preferentially direct gene expression in tumor cells may be used to direct caspase-12 expression. The enhancers used could include, without limitation, those that are characterized as tissue- or cell-specific in their expression. Alternatively, regulation may be mediated by the cognate regulatory sequences or, if desired, by regulatory sequences derived from a heterologous source, including any of the promoters or regulatory elements described above. An alternative strategy for inhibiting caspase-12 function using gene therapy involves intracellular expression of an anti-caspase-12 antibody or a portion of an anti-caspase-12 antibody. For example, a nucleic acid (or fragment thereof) encoding a monoclonal antibody that specifically binds to caspase-12 and inhibits its biological activity may be placed under the transcriptional control of a cell type-specific gene regulatory sequence.

Another therapeutic approach within the invention involves administration of a recombinant cleaved caspase-12 polypeptide (e.g, the ones described herein), either directly to the site of a potential or actual cell proliferation event (for example, by injection) or systemically (for example, by any conventional recombinant protein administration technique). The dosage of caspase-12 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.

Methods

Fractionation experiments

Brain cortices and kidney of newborn mice were lysed and homogenized in buffer A (50 mM Tris HCl pH 8.0, 1 mM 2-mercaptoethanol, 1 mM EDTA, 0.32 M sucrose, 0.1 mM PMSF). The nuclear fraction was the pellet following centrifugation at 900 x g for 10 minutes. The supernatant was re-centrifuged at 5000 x g for 10 minutes, and the resulting pellet was the mitochondrial fraction The second supernatant was centrifuged at 105,000 x g for one hour; the microsomal and soluble fraction were extracted from the pellet and supernatant, respectively. Western blotting was performed using antibodies to: caspase-12; Bcl-xL (M-125, Santa Cruz Immunochemicals, Santa Cruz, CA); Bcl-2 ( 4C11, Santa Cruz); caspase-3 ; cytochrome C ( 7H8.2C12, PharMingen, San Diego, CA); and TRAPα. Immunohistochemistry

Mouse brains were removed, fixed in 4% formaldehyde for two hours on ice, and enbedded in paraffin. Immunostaining was performed using anti- caspase-12 antibody and the VECSTAIN Elite ABC kit following the manufacturer's protocol.

Cell culture, transfection, and immunocytochemistry

Endogenous expression of caspases (caspase-12, -3, and -8), BiP (StressGen, Victoria, British Columbia), and TRAPα in L929 cells or HeLa cells was detected by immunocytochemistry. Cells were fixed in 4% formaldehyde for 15 min at 4°C. Immunostaining was done by using primary antibody followed by FITC-conjugated anti-rat or anti-rabbit or TRITC- conjugated anti-mouse antibodies (Jackson ImmunoResearch Laboratories, West Grove, PA), and nuclear staining (bisbenzimide).

COS cells were maintained in DMEM supplemented with 10% fetal bovine serum. Cells were seeded onto cover glass coated with poly-L-lysine. Expression plasmid DNA (0.8 μg) was transfected with lipofectamine. Cells were fixed in 4% formaldehyde and examined by fluorescence microscopy.

Generation of caspase-12 knockout mice

Gene targeting was performed using standard methods. Briefly, the caspase-12 gene fragments were cloned from a 129/sv mouse genomic library (Stratagene, La Holla, CA). The DT-A fragment was cloned into a pGEM7 vector with a neomycin-resistance gene (PGK-neo). A 2.0 kb Sacl-Stu fragment and a 9.0 kb Nøtl (cloning site from phage

fragment were subcloned into PGK-neo-DT-A vector to generate the targeting construct. The targeting construct was transfected into J-l ES cells by electroporation. G418-resistant transfectants were screened by genomic southern blot analysis with 3' flanking probe. The efficiency of homologous recombination was five in 232 clones. Two of the targeted clones transmitted the mutant allele. Homozygous mice were generated by interbreeding heterozygous mice (129 X C57BL/6J). Histology and TUNEL assay of kidney

Caspase-12 mutant mice and wild-type or heterozygote littermates were injected with tunicamycin (0.25-1.0 μg/g weight) intraperitorially and sacrificed at four days after injection. Kidney tissue was dissected free, fixed in 4% formaldehyde, and embedded in paraffin. Sections of kidney were stained with hematoxylin and eosin. The TUNEL assay was performed as directed by the manufacturer (ApopTag®, Oncor ™).

Glial cell culture

Mixed glial cells cultures were prepared from C57BL/6 mice at approximately embryonic day 18. Briefly, cerebral cortices from mouse brains, were dissected free of meninges and passed through a nylon mesh (200-300 μm). Cells were collected by centrifuge (160 x g for 5 minutes) and resuspended in culture medium containing MEM , 10% fetal bovine serum, 5mg/ml insulin, and 2% glucose. Cells were then plated in an uncoated culture flask.

Embryonic fibroblast cells

Mouse embryonic fibroblast (EF) cells were prepared using standard techniques. Briefly, a homozygous female mated with heterozygous male was sacrificed at day 14.5 of gestation. Embryos were decapitated and eviscerated, then digested in trypsin. Cultured cells were aliquoted and frozen after two passages. Experiments were performed with EF cells of identical passage from sibling embryos. Induction and determination of cell death

Glial cells were washed three times with DMEM without glucose, then transferred to an anaerobic chamber. Viability were determined by propidium iodide staining or with an MTT assay.

Preparation of cell lysates and immunoblotting

Glial cells were collected by scraping, then lysed in 62.5mM Tris-Cl (pH 6.8), 2% SDS, 0.72M β-mercaptoethanol, and 7% glycerol. Lysates were analysed by western blotting with antibodies to Bcl-xL/S(l:1000); caspase-12 (1 :5); Bcl-2(1:250) (SantaCruz Immunochemicals), or tubulin (1:10,000).

In vitro cleavage reaction pcDNA3.1 -Bcl-xL and -caspases were transcribed and translated in vitro using the TNT coupled transcription/translation kit (Promega, Madison, WI) in the presence of [³⁵S] methionine. In vitro cleavage reactions were performed in a buffer containing 150mM NaCl, 20mM Tris-Cl (pH 7.6), ImM DTT, and lOOmg/ml BSA with 5mM calcium and m-calpain (Sigma Chemicals, St. Louis, MO) at 37°C. Reactions were terminated by addition of lysis buffer. Samples were boiled, separated by SDS-PAGE, and detected by autoradiography.

Cerebral cortex S-100 and cleavage assay S-100 was prepared as fractionation in buffer B (20mM Tris HCl pH

7.6, 2 mM EDTA, lOmM EGTA, 0.25M sucrose). 300 mg S-100 protein was used for the cleavage assay in buffer C (12mM Tris HCl pH 8.0, 5mM β- mercaptoethanol, 0.2mM EDTA, ImM EGTA, 25mM sucrose plus calcium) at 30°C. Immunoprecipitation

Following transfection, 293T cells were lysed in buffer A (50mM Hepes pH. 8.0, 150mM NaCl, ImM EDTA, 0.1%NP40, 10% glycerol, and protease inhibitors). Cell lysates were immunoprecipitated by protein A with the indicated antibodies. Precipitates were washed in buffer A, separated by SDS- PAGE, and transferred to a membrane for western blotting.

In vitro binding

GST binding assays were performed in buffer B (50mM Tris-Cl pH. 7.5, 150mM NaCl, 10% glycerol, 1% NP40, O.lmM EDTA, ImM DTT) with the indicated GST fusion proteins and ³⁵S-presenilin-2 protein. Following washing with buffer B, the binding product was separated by SDS-PAGE and detected by autoradiography.

Determination of caspase-12 cleavage sites

Truncated caspase-12 expressed in E. coli was purified by Ni-NTA (Qiagen, Valencia, CA). Purified caspase-12 was cleaved by m-calpain (Sigma Chemicals) in buffer (150mM NaCl, 20mM Tris-Cl pH 7.6, ImM DTT). After separation by SDS-PAGE, proteins were transferred to PVDF membrane (BioRad, Hercules, CA). N-terminal amino acids were determined by direct protein sequencing.

Other Embodiments

All publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent publication was specifically and individually indicated to be incorporated by reference.

While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications. This application is intended to cover any variations, uses, or adaptations following, in general, the principles of the invention and including such departures from the present disclosure within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the appended claims.

What is claimed is:

Claims

1. A substantially pure caspase-12 polypeptide lacking at least five amino acids between amino acids 2 and 132 of SEQ ID NO: 1.

2. The substantially pure caspase-12 polypeptide of claim 1, said polypeptide lacking at least five amino acids between amino acids 2 and 158 of SEQ ID NO: 1.

3. The substantially pure caspase-12 polypeptide of claim 1, wherein said polypeptide is substantially identical to a polypeptide consisting of amino acids 159 to 419 of SEQ ID NO: 1.

4. The substantially pure caspase-12 polypeptide of claim 1, wherein said polypeptide is substantially identical to a polypeptide consisting of amino acids 133 to 419 of SEQ ID NO: 1.

5. A substantially pure nucleic acid sequence encoding a caspase-12 polypeptide, said polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and 158 of SEQ ID NO: 1.

6. The substantially pure nucleic acid sequence of claim 5, wherein said polypeptide has a caspase-12 biological activity and lacks at least five amino acids between amino acids 2 and 132 of SEQ ID NO: 1.

7. A substantially pure caspase-12 polypeptide, wherein said peptide comprises an amino acid change at positions 132, 133, 158, or 159 of SEQ ID NO: 1.

8. The substantially pure caspase-12 polypeptide of claim 7, wherein said caspase-12 cannot be cleaved by m-calpain.

10. A method for identifying a compound useful in modulating apoptosis condition, said method comprising: a) providing a caspase-12; b) contacting said caspase-12 with a candidate compound; and c) monitoring a biological activity of caspase-12, wherein a change in the biological activity of caspase-12 relative to said activity when not contacted with said candidate compound identifies said candidate compound as a compound useful modulating apoptosis.

11. The method of claim 10, wherein said biological activity is proteolytic cleavage.

12. The method of claim 10, wherein said biological activity is caspase- 12 mediated induction of apoptosis.

13. The method of claim 10, wherein said biological activity is binding to p28Bap31 , presenilin- 1 , presenilin-2, or Bcl-xL.

14. The method of claim 10, wherein said caspase-12 is in a cell.

15. The method of claim 14, wherein said cell comprises m-calpain.

16. The method of claim 14, wherein said cell comprises presenilin- 1 or presenilin-2.

17. The method of claim 14, wherein said cell comprises p28Bap31.

18. The method of claim 14, wherein said cell comprises Bcl-xL.

19. The method of claim 14, wherein said caspase-12 is the endogenous caspase-12, is expressed from a transgene, or is expressed from an extrachromosomal vector.

20. The method of claim 14, wherein said cell is selected from the group consisting of a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, and a fibroblast.

21. The method of claim 14, wherein said cell is in vitro.

22. The method of claim 14, wherein said cell is in an animal.

23. The method of claim 22, wherein said animal has an apoptotic condition.

24. A method for identifying a compound useful modulating apoptosis, said method comprising: a) providing a cell comprising a caspase and a calpain; b) administering to said cell a candidate compound; and c) monitoring the proteolytic cleavage of said caspase by said calpain, wherein a change in said cleavage of said caspase in said cell relative to said cleavage in a control cell not administered said candidate compound identifies said candidate compound as a compound useful in treating an apoptotic condition.

25. The method of claim 24, wherein said caspase is selected from the group consisting of caspase-7, caspase-8, caspase-9, caspase-11, caspase-12, and Bcl-xL.

26. The method of claim 25, wherein said caspase is caspase-12.

27. The method of claim 26, wherein said caspase-12 is the endogenous caspase-12, is expressed from a transgene, or is expressed from an extrachromosomal vector.

28. The method of claim 24, wherein said calpain is an endogenous calpain, is from expressed from a transgene, or is expressed from an extrachromosomal vector.

29. The method of claim 24, wherein said cell is selected from the group consisting of a lymphocyte, a neuronal cell, a kidney cell, a muscle cell, and a fibroblast.

30. The method of claim 24, wherein said cell is in vitro.

31. The method of claim 30, wherein said cell is in an animal.

32. The method of claim 31 , wherein said animal has an apoptotic condition.

33. A transgenic non-human animal expressing transgenic DNA encoding a caspase-12 polypeptide polypeptide lacking at least five amino acids between amino acids 2 and 132 of SEQ ID NO: 1.

34. The animal of claim 33, wherein said polypeptide is substantially identical to a polypeptide consisting of amino acids 159 to 419 of SEQ ID NO: 1.

35. The animal of claim 33, wherein said polypeptide is substantially identical to a polypeptide consisting of amino acids 133 to 419 of SEQ ID NO: 1.

36. The transgenic animal of claim 33, wherein said transgenic DNA is operably linked to a tightly regulated promoter.

37. A non-human animal wherein one or both genetic alleles encoding a caspase-12 polypeptide are mutated.

38. The animal of claim 37, wherein one or both genetic alleles encoding a caspase-12 polypeptide are disrupted, deleted, or otherwise rendered nonfunctional.

39. The animal of claim 37, wherein said animal is a mouse.

40. Cells from the animal of claim 37.

41. A substantially pure antibody that specifically binds to a polypeptide encoded by the amino acid sequence of SEQ ID NO: 1.

42. The antibody of claim 41, wherein said antibody is a monoclonal antibody.

43. The antibody of claim 41, wherein said antibody is a polyclonal antibody.

44. The antibody of claim 41, wherein said antibody is a neutralizing antibody.

45. A method for preventing apoptosis, said method comprising administering an apoptosis-mhibiting amount of an antibody that binds to a polypeptide encoded by the amino acid sequence of SEQ ID NO: 1.

46. The method of claim 45, wherein said antibody blocks a biological activity of caspase- 12.

47. The method of claim 46, wherein said biological activity is proteolytic cleavage.

48. The method of claim 46, wherein said biological activity is induction of apoptosis.

49. The method of claim 46, wherein said biological activity is binding to p28Bap31, presenilin- 1 , presenilin-2, or Bcl-xL.

50. A method for preventing apoptosis in a cell, said method comprising administering an inhibitor of the caspase-cleaving activity of a calpain to said cell.

51. A method for increasing apoptosis in a cell, said method comprising administering to said cell a caspase-cleaving amount of a calpain protein or a polypeptide fragment thereof.

52. A method for modulating caspase-mediated apoptosis in a cell, said method comprising administering to said cell a compound that modulates cleavage of said caspase by a calpain.

53. The method of claim 52, wherein said compound is selected from the group consisting of a chemical, a drug, and an antibody that specifically binds to said calpain.

54. The method of claim 53, wherein said antibody is a neutralizing antibody.

55. The method of claim 50, 51 or 52, wherein said cell is in vitro.

56. The method of claim 50, 51, or 52, wherein said cell is in an animal.

57. The method of claim 56, wherein said animal has a proliferative disease.

58. The method of claim 56, wherein said animal has an apoptotic condition.

59. A method of inducing apoptosis in a cell, said cell in a mammal diagnosed with a proliferative disease, said method comprising administering to said cell a positive regulator of the caspase- 12-dependent apoptotic pathway.

60. The method of claim 59, wherein said positive regulator comprises a caspase-12 polypeptide, said polypeptide having a caspase-12 biological activity and lacking five amino acids between amino acids 2 and 158 of SEQ ID NO: 1.

61. A method of inducing apoptosis in a cell, said cell in a mammal diagnosed with a proliferative disease, said method comprising administering to said cell a nucleic acid sequence encoding a caspase-12 polypeptide, said polypeptide having a caspase-12 biological activity and lacking at least five amino acids between amino acids 2 and 158 of SEQ ID NO: 1, said nucleic acid sequence positioned for expression in said cell.

62. The method of claim 60 or 61, wherein said polypeptide is substantially identical to a polypeptide consisting of amino acids 159 to 419 of SEQ ID NO: 1.

63. The method of claim 60 or 61, wherein said polypeptide is substantially identical to a polypeptide consisting of amino acids 133 to 419 of SEQ ID NO: 1.

64. The method of claim 61, wherein said nucleic acid is operably linked to a promoter.

65. The method of claim 64, wherein said promoter is a heterologous promoter.

66. The method of claim 61, wherein said nucleic acid is in a recombinant viral vector.