WO2000022109A1

WO2000022109A1 - Molecular markers for determining a patient's risk of developing agranulocytosis

Info

Publication number: WO2000022109A1
Application number: PCT/US1999/023638
Authority: WO
Inventors: John Lee; Michael Kauffman
Original assignee: Millennium Predictive Medicine, Inc.
Priority date: 1998-10-13
Filing date: 1999-10-13
Publication date: 2000-04-20
Also published as: AU6425499A

Abstract

The invention features methods for determining whether a patient is likely to develop agranulocytosis, for example, as a result of treatment with pharmaceutical agents that adversely affect leukocytes or their progenitors in the bone marrow. Further, it encompasses methods for screening compounds to find those useful in treating or preventing agranulocytosis, as well as methods for treating a patient who is at risk of developing, or who has developed, agranulocytosis. The invention is based, in part, on the identification of differentially expressed genes, i.e., genes that are either overexpressed or underexpressed in bone marrow cells treated with clozapine, the expression being relative to that in untreated bone marrow cells or in bone marrow cells that have been treated with a compound that does not alter expression of the differentially expressed genes of the invention (i.e., olanzapine).

Description

MOLECULAR MARKERS FOR DETERMINING A PATIENT'S RISK OF DEVELOPING AGRANULOCYTOSIS

BACKGROUND OF THE INVENTION Idiosyncratic reactions to drugs represent a difficult problem because they are virtually unforeseeable and can be life-threatening (Uetracht, Drug Safety 2= 51-56 , 1992) . Moreover, very little is known about the mechanism of these reactions. It is unlikely that they are caused by direct cytotoxicity because most patients (or animals that receive a given compound in the course of drug development) do not experience the adverse reaction, even at high doses (Uetrecht, Crit. .Rev. in Toxicol . 2_0:213-235, 1990) . Idiosyncratic reactions are not rare; they are estimated to account for as many as 10% of all adverse drug reactions (Uetrecht, Drug Metabol . Rev. 24.: 299-366, 1992) .

A common type of idiosyncratic reaction is agranulocytosis, a condition in which granulocytic leukocytes are essentially lacking from the circulation (i.e., the normal count of 5,000-10,000 cells/μl of blood falls to less than 500 cells/μl) . The granulocytic leukocytes are neutrophils, eosinophils, and basophils, the predominate cell of the series being the neutrophil (neutropenia is typically defined as a neutrophil count of less than 1500-2000 cells/μl of blood) . Although drug- induced agranulocytosis is usually reversible, the patient can, in the meanwhile, contract an infection that proves fatal even with appropriate antibiotic therapy. The mortality rate from drug-induced agranulocytosis is about 10% (Uetrecht, 1992, supra) . For further review of agranulocytosis see, for example, Vincent (Drugs, 31 : 52 , 1986 or Claas ( Psychopharmacol . 99:S113, 1989). SUMMARY OF THE INVENTION The invention features methods for determining whether a patient is likely to develop agranulocytosis, for example, as a result of treatment with pharmaceutical agents that adversely affect leukocytes or their precursors in the bone marrow. Further, it encompasses methods for screening compounds to find those useful in treating or preventing agranulocytosis, as well as methods for treating a patient who is at risk of developing, or who has developed, agranulocytosis.

The invention is based, in part, on the identification of differentially expressed genes, i.e., genes that are either overexpressed or underexpressed in bone marrow cells treated with clozapine, a drug associated with idiosyncratic occurrences of agranulocytosis, the expression being relative to that in untreated bone marrow cells or in bone marrow cells that have been treated with olanzapine, a compound that is related to clozapine, and like clozapine is used for treatment of schizophrenia, but is not associated with idiosyncratic occurrences of agranulocytosis .

As described further below, idiosyncratic reactions that manifest as agranulocytosis may be caused by differential gene expression or activity that is driven by variations in the sequence of the gene (including the exons that encode protein and the introns) or the gene's regulatory region (i.e., the region found 5' or 3 ' to the coding sequence that regulates gene transcription, e. g. , the promoter) . These variations may differ from one individual to another. Indeed, individual variations are thought to underlie idiosyncratic reactions. Thus, discovering such variations helps to explain why one individual or a small number of individuals may suffer a particular undesirable reaction while the majority of others will not.

Unless otherwise specified, the term "variation (s) in gene sequence" is meant to encompass variation (s) in either the coding or regulatory regions of a gene, the variations being evident as a mutation (i.e., a deletion, insertion, or substitution) of one or more nucleotides. Genes that have a variation in their coding or regulatory regions may be referred to herein as "sequence-variant genes." These genes will be recognizable in that they will retain their ability to hybridize under stringent conditions with either strand of the corresponding wild-type genes described in the Tables presented herein, or the human homologues thereof, yet their sequence will clearly differ from that of the corresponding wild-type genes.

Accordingly, the methods of the present invention, which are directed toward assessing and treating agranulocytosis, encompass sequence analysis of genes and their regulatory regions ( e . g. , the human genes or the human homologues of one or more of the genes defined in the

Tables presented herein) as well as analysis of expression at the mRNA or protein level. As an alternative to assessing the level of gene or protein expression, one can assess the activity of the encoded protein. An advantage of the methods of the invention is that they can be used to determine, before a compound is administered, whether that compound is likely to cause agranulocytosis. That is, they are predictive. As used herein, the term "compound" is meant to encompass any drug or pharmaceutical agent. The methods of the invention can be carried out, for example, by determining whether a patient has a variation in the sequence of a gene that is differentially expressed in cells treated with clozapine. If so, that patient is more likely to be at risk of developing agranulocytosis when treated with a compound (e.g., a compound such as one of those described herein, which are associated with idiosyncratic occurrences of agranulocytosis) .

There are two types of differentially expressed genes: those that are overexpressed in clozapine-treated cells, i.e., are expressed at a higher level in clozapine- treated cells than in untreated or olanzapine-treated, but otherwise comparable, cells) and those that are underexpressed in clozapine-treated cells, i.e., are expressed at a lower level in clozapine-treated cells than in untreated or olanzapine-treated, but otherwise comparable, cells) . Genes found to be overexpressed in clozapine-treated bone marrow cells include GDP-dissociation inhibitor (specific to hematopoietic cells) , argininosuccinate synthetase, glucocorticoid-attenuated response gene 16 (GARG-16) , glucocorticoid-attenuated response gene 39 (GARG-39) , glucocorticoid-attenuated response gene 49 (GARG-49/IRG2) , interferon-induced gene

(ISG15) , tumor-induced 32 kDa protein (p32) , and thymidylate kinase homologue . Genes found to be underexpressed in these cells include 14-3-3 protein (tau isoform) , translation initiation factor (Suil) , ATP synthase A chain, ubiquitin- like protein (x3 ; NEDD8) , growth factor inducible immediate early gene cyr61, and calcium transporting ATPase. Additional differentially regulated genes, discovered by examining clozapine-treated HL-60 cells are disclosed below. All differentially regulated genes may have a mutation. Methods for discovering these mutations, and thereby identifying patients at risk of developing agranulocytosis are described below. By examining either the sequence, level of expression, or activity of one or more of the differentially expressed genes described herein in a biological sample obtained from a patient, e.g., a sample of bone marrow, one can determine whether that patient is likely to develop agranulocytosis if a selected compound, e.g., a dibenzodiazapine such as clozapine, or any other compound known or suspected of causing agranulocytosis, is administered. For example, if, in a biological sample obtained from a patient, the human sequence of one or more of the genes listed in the Tables presented herein (or their regulatory regions) differs from that of the wild-type sequence or that of patients not suffering from agranulocytosis (by, e.g., the insertion, deletion, or substitution of one or more nucleotides) , one can conclude that the patient may have an increased risk of developing agranulocytosis if treated with a compound, particularly clozapine or a related agent. Alternatively, if one or more of the genes listed in the Tables presented herein are overexpressed or underexpressed in cells that are obtained from a patient and treated at some point thereafter with a compound (such as clozapine) and if overexpression or underexpression is generally associated with agranulocytosis rather than, or in addition to, therapeutic benefit, one can again conclude that the patient may have an increased risk of developing agranulocytosis if treated with that compound. Altered levels of activity may also be evaluated as predictors of risk. Importantly, risk can be analyzed on a patient-by-patient basis, which makes it possible to determine whether or not a particular treatment regime is advisable for a particular patient. Accordingly, the invention features a method of monitoring a therapeutic regime by periodically assessing the level of expression of one or more of the genes identified herein, i . e . , of the genes described in the Tables presented herein in a biological sample obtained from the patient.

The invention also features methods of analyzing therapeutic compounds to determine whether or not they are likely to cause idiosyncratic occurrences of agranulocytosis. Presently, such reactions are difficult to detect during drug development because animal testing is usually carried out with inbred strains, and the number of human patients enrolled in clinical trials is not usually large enough to allow detection. However, by applying the therapeutic compound in culture to a large number of samples obtained from different individuals, e. g. , samples obtained from a blood bank, and assessing the cultures for signs of agranulocytosis (e.g., cell death, or a failure to differentiate along the hematopoietic pathway) , one can determine whether or not drug development should be reevaluated (and possibly ended) because it appears likely that the drug will cause an idiosyncratic reaction. At the very least, physicians and patients could be made aware of the risk, which would allow them to make a more informed decision and to monitor the treatment (by, e.g., blood cell counts) more diligently.

Moreover, one can determine whether there are variations in the sequence, level of expression, or activity of differentially expressed genes (including those described herein, which were discovered to be overexpressed or underexpressed in clozapine-treated cells) in cell cultures where signs of agranulocytosis are present (relative to cells in cultures where drug application had little or no effect on cell number or cell type) . It is well within the abilities of ordinarily skilled artisans to design appropriate controls for this and other novel methods described herein.

In addition, the present invention includes methods that make it possible to determine which genes must contain sequence variations or which must be differentially expressed in order for the applied therapeutic agent to exert its effect (e.g., for clozapine to diminish the symptoms of schizophrenia) as well as to determine which contribute instead to the idiosyncratic reactions one aims to avoid. For example, one could examine the time course of gene expression in relation to the onset of agranulocytosis. If the level of expression of genes "A" and "B" changes as the symptoms of the disease or disorder improve but prior to the onset of agranulocytosis, genes "A" and "B" are more likely to mediate the positive aspects of the treatment rather than to contribute to agranulocytosis. In contrast, if the level of expression of genes "A" and "B" remains constant as the symptoms of the disease or disorder improve but changes coincident with the onset of agranulocytosis, genes "A" and "B" are likely to mediate or contribute to agranulocytosis rather than to the positive aspects of the treatment .

It is known in the art that agranulocytosis commonly appears one to three months after drug therapy has begun (Uetrecht, 1992, supra) . This enhances the feasibility of the method suggested here (for determining which differentially expressed, or sequence-variant , gene contributes to, if not causes, agranulocytosis) , as it makes it unlikely that an improvement in the symptoms of the disorder being treated and agranulocytosis will occur at the same time. Accordingly, the invention features a method of determining whether differential expression of any given gene contributes to agranulocytosis. The method can be carried out, for example, by determining whether the level of expression of that gene changes at around the same time as a sign or symptom of agranulocytosis appears.

Alternatively, or in addition, one can determine whether a differentially expressed gene contributes to agranulocytosis by purposely altering its expression and examining the effect of that alteration. Techniques to alter the level of gene expression or the activity of the encoded polypeptide in a cell are now well known in the art. For example, a cell can be transduced (i.e., transfected or transformed) with a gene-bearing construct that is transcribed within the cell, in which case the gene will be overexpressed. In the event the construct is transcribed into a sequence that is antisense to the gene one wishes to affect, or antisense oligonucleotides are otherwise applied, expression of the target gene will be lowered. Similarly, applying antibodies that specifically bind the gene product can alter the activity of the encoded protein. Accordingly, if one suspected that overexpression of gene "A" was necessary and sufficient for agranulocytosis to develop, one could overexpress gene "A" in the absence of any other treatment (e.g., clozapine treatment). If this overexpression triggered agranulocytosis, either in vivo or in culture, one could conclude that overexpression of gene "A" is necessary and sufficient for agranulocytosis to develop. To test further the contribution of any overexpressed gene to agranulocytosis, one could determine whether agranulocytosis is prevented by underexpression of gene "A" . This information is useful in developing animal models of agranulocytosis. As described further herein, once a gene is known to be necessary and sufficient for agranulocytosis, it can be spatially or temporally expressed to produce animals (e.g., transgenic mice) that develop the signs or symptoms of agranulocytosis.

While not wishing to be bound by any theory regarding the mechanisms underlying differential gene expression or activity, it is entirely plausible that these differences result from the aforementioned variations in gene sequence. For example, variations in the sequence of the gene's regulatory region could result in overexpression or underexpression, while variations in the sequence of the gene's coding region could result in an overactive or underactive gene product.

In view of the foregoing, it is clear that the sequence-variant or differentially expressed genes identified herein are potential targets for the development of therapeutic compounds. Accordingly, the invention features a method of developing new therapeutic agents that alter the expression of a gene that is normally misexpressed in the event of agranulocytosis. Alternatively, the method may be used to develop new therapeutic agents that alter the activity of the protein encoded by that gene. Once developed, the new therapeutic agents can be used to reduce the risk of developing agranulocytosis or to reduce its severity should it occur. Accordingly, the invention provides methods for identifying compounds that modulate the expression of genes or the activity of gene products involved in agranulocytosis as well as methods for the treatment of agranulocytosis. Such methods can involve the administration of these modulatory compounds to individuals exhibiting symptoms of agranulocytosis or that are otherwise identified as having or being at risk of developing agranulocytosis .

The data presented below were collected, in part, by coupling systematic search strategies with sensitive and high throughput gene expression assays to identify genes differentially expressed in bone marrow cells treated with clozapine. This approach permits the identification of all genes, whether known or novel, that are differentially expressed in the event of agranulocytosis, particularly that induced by clozapine. The approach is advantageous in that it can be used not only to identify genes and gene products whose expression is associated with agranulocytosis but, further, to identify genes and gene products that can serve as targets for rationale drug design. Therefore, the invention feature methods for the prognosis, diagnosis, monitoring, treatment, and prevention of agranulocytosis.

"Differential expression, " as used herein, refers to either a quantitative or qualitative difference in the expression pattern of a gene, the difference being apparent when expression in a cell treated with a given compound is compared with expression in an untreated cell or a cell treated with a different compound. Genes that are differentially expressed may be referred to herein as genes that are "misexpressed. " As described below, expression may be assessed either by studying expression per se or activity of the encoded gene product .

Any differentially expressed gene can be referred to as a "fingerprint gene," all of which or, more likely, some of which, will also be "target genes" (defined below) . That is, not all fingerprint genes may be target genes, but all target genes will be fingerprint genes. A target gene is a gene that can be used as part of a prognostic or diagnostic assay for agranulocytosis; or for identifying compounds useful for treating agranulocytosis; or for evaluating the efficacy of a treatment for agranulocytosis. For example, if a test compound affects the expression of a fingerprint gene pattern, the affect the compound has on target gene expression (i.e., on quantitative or qualitative expression) can be used to evaluate the efficacy of the compound as a treatment for agranulocytosis or can, additionally, be used to monitor patients undergoing clinical evaluation for the treatment of agranulocytosis .

A "fingerprint pattern" is the pattern generated when the expression pattern of a series of fingerprint genes (which can range from two up to all the fingerprint genes which exist for a given state) is determined. A fingerprint pattern can be analyzed in the same manner one would analyze a single fingerprint gene.

As described above, differentially expressed genes also represent "fingerprint genes" and may represent "target genes." Modulating the expression of one or more target genes (or modulating the levels of activity of the polypeptides they encode) can provide the means to prevent or ameliorate the symptoms of agranulocytosis. Compounds that modulate the expression of the target gene or the activity of the target gene product can be used to treat agranulocytosis. Further, compounds that modulate the expression of a target gene or the activity of a target gene product can be used to deter the onset of agranulocytosis. Optimally, compounds that modulate the expression of a target gene or the activity of a target gene product will be administered prophylactically to reduce or prevent agranulocytosis from developing, particularly in individuals at high risk.

The term "idiosyncratic drug reaction" is used herein in a manner consistent with its commonly ascribed meaning in the art, i.e., to refer to a reaction that does not occur in most patients, even at high doses, and that does not represent an extension of the known pharmacological effects of the drug. Such reactions are also referred to as hypersensitivity reactions or type B reactions, although, to an immunologist, a hypersensitivity reaction implies a reaction involving the immune system (Uetrecht, 1992, supra) and this may or may not be the case with agranulocytosis.

DETAILED DESCRIPTION OF THE INVENTION

The invention is based, in part, on the identification of genes that are differentially expressed i.e., genes that are either overexpressed or underexpressed in bone marrow cells treated with clozapine. Because clozapine is associated with idiosyncratic occurrences of agranulocytosis, genes differentially expressed in its presence are likely to be differentially expressed in leukocytes or their precursors when a patient develops agranulocytosis. For the same reason, these genes may be differentially expressed in leukocytes whenever they are exposed to a compound associated with agranulocytosis. Some of the instances in which idiosyncratic occurrences of agranulocytosis have been observed are described below. For example, agranulocytosis has been observed following treatment of thyroid disorders with propylthiouracil or methimazole; following prophylactic treatment of malaria with dapsone; and following treatment of congestive heart failure with vesnarinone. A wealth of information regarding the selection of appropriate pharmaceutical agents (to treat these and similar conditions) is available to those of ordinary skill in the art.

By evaluating the expression of a large number of genes in the presence and absence of a selected compound (most preferably a compound known to cause agranulocytosis) , one can create a profile of the response of affected cells (i.e., leukocytes and their precursors) to the selected compound. I. Predictive Medicine

The nucleic acid molecules described herein and the polypeptides they encode can be used in the area of predictive medicine. For example, they can be used in diagnostic and prognostic (predictive) assays, to monitor clinical trials, and in pharmacogenomics (described further below) .

Agents, or modulators that have a stimulatory or inhibitory effect on gene expression or activity can be administered to individuals to treat agranulocytosis

(prophylactically or therapeutically) . In conjunction with such treatment, the pharmacogenomics (i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug) of the individual may be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug. Thus, the pharmacogenomics of the individual permits the selection of effective agents (e.g., drugs) for prophylactic or therapeutic treatments based on a consideration of the individual's genotype. Such pharmacogenomics can further be used to determine appropriate dosages and therapeutic regimens. Accordingly, the activity of protein, expression of nucleic acid, or mutation content of genes (e.g. , those described in the Tables presented herein) in an individual can be determined to thereby select appropriate agent (s) for therapeutic or prophylactic treatment of the individual. Accordingly, one aspect of the present invention relates to identifying a genetic lesion in one or more of the genes that are differentially expressed in clozapine- treated cells. A lesion may be a mutation (evident as an insertion, deletion, or substitution of one or more of the nucleotides in the coding or non-coding region (including a regulatory region) of the gene) . As described further below, patients identified as having such a lesion (i.e., as having a sequence-variant gene) are considered to have a greater risk of developing agranulocytosis.

Another aspect of the present invention relates to an assay in which the expression of one or more of the genes described in the Tables presented herein (or the activity of the polypeptides they encode) is determined in the context of a biological sample (e.g., a sample of leukocytes or their precursors) . This, in turn, allows one to determine whether an individual may be at risk of developing agranulocytosis. The genes described in the Tables presented herein are therefore useful in that one can detect and, when necessary, quantitate their mRNA expression (e.g., in a biological sample) . Quantitation may be necessary where it is not clear that there is a significant change in gene expression (for example, where the expression level does not appear to have increased or decreased more than two-fold over the level in non-treated (e.g., non-clozapine treated) cells or where investigation has revealed that a certain level (e.g., a three-fold, five-fold, or ten-fold) of expression is required before the signs or symptoms of agranulocytosis will appear) . Of course, not all differentially expressed genes are associated with agranulocytosis. In many cases the overexpression or underexpression is associated primarily with beneficial therapeutic effects.

Given the knowledge that an individual may be at greater risk of developing agranulocytosis, appropriate therapeutic or prophylactic agents can be selected (a process referred to herein as "pharmacogenomics"). Pharmacogenomics allows for the selection of agents (e.g., drugs) for therapeutic or prophylactic treatment of an individual based on the genotype of the individual (i.e., the genotype of an individual is examined to determine the ability of that individual to respond to a particular agent) .

Yet another aspect of the invention pertains to monitoring the influence of agents (e.g., drugs or other compounds) on the expression or activity of one or more of the genes described in the Tables presented herein, or their human homologues, in clinical trials. A. Diagnostic Assays

An exemplary method for detecting the presence or absence of a nucleic acid molecule or polypeptide described herein in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting the protein or the nucleic acid molecule (e.g., mRNA or genomic DNA) that encodes it. A preferred agent for detecting mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to mRNA or genomic DNA. The nucleic acid probe can be, for example, a full-length nucleic acid molecule, such as those described in the Tables presented herein, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length. Alternatively, the probe can be a human homologue of one or more of the genes described in the Tables presented herein. The sequence of the probe should be sufficiently specific to hybridize under stringent conditions to mRNA or genomic DNA corresponding to the naturally-occurring genes represented in the Tables presented herein.

A preferred agent for detecting protein is an antibody capable of specifically binding to that protein. In the context of the present invention, the protein would be one that is over- or underactive due to over- or underexpression, or to a mutation that affects activity. Preferably, the antibody will include a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab')₂) can be used. The term "labeled", used with regard to a probe or antibody, encompasses direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by way of a reaction with another reagent that is itself either directly or indirectly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end- labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin.

The term "biological sample" is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect genomic DNA, mRNA, or protein in a biological sample in vi tro as well as in vivo. For example, in vi tro techniques for detecting genomic DNA include Southern blot analyses, while in vi tro techniques for detecting mRNA include Northern blot analysis and in si tu hybridization. In vi tro techniques for detecting protein include enzyme linked immunosorbent assays (ELISAs) , Western blot analyses, immunoprecipitations, and immunofluorescence. In vivo techniques for detecting protein include introducing into a subject a labeled antibody that specifically binds the targeted protein. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques .

In one embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject.

In another embodiment, the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting protein, mRNA, or genomic DNA (the nucleic acids being represented by those described in the Tables presented herein or the human homologues thereof) , such that the presence of protein, rtiRNA, or genomic DNA can be detected in the biological sample . Routinely, one would compare the presence of a given protein, mRNA or genomic DNA molecule in the control sample with its presence in a test sample. The invention also encompasses kits for detecting the presence of the gene or protein products described in the Tables presented herein, or the human homologues thereof, in biological samples (i.e., control samples and test samples) . Such kits can be used to determine if a subject is suffering from or is at increased risk of developing agranulocytosis, a disorder described herein, which is, by the present study, now associated with aberrant (i.e., differential) expression of one or more of the genes or gene products (i.e., proteins) disclosed in the Tables presented herein or the human homologues thereof. For example, the kit can comprise a labeled compound or agent capable of detecting a protein or mRNA described in the Tables presented herein or the human homologues thereof in a biological sample and means for determining the amount of that protein or mRNA in the sample (e.g., an anti-eIF-4A antibody or an oligonucleotide probe which binds to DNA encoding eIF-4A) . Kits may also include instructions for use. These instructions can, for example, describe how to observe that the test subject is suffering from or is at risk of developing agranulocytosis by describing how to observe one or more of the sequence-variant or differentially expressed genes disclosed herein. Antibody-based kits can include, for example: (1) a first antibody (e.g., attached to a solid support) that specifically binds a protein encoded by a gene disclosed in the Tables presented herein or the human homologue thereof (the target protein); and, optionally, (2) a second (i.e., a different) antibody that specifically binds to either the target protein or to the first antibody. Preferably, the second antibody is conjugated to a detectable marker.

Oligonucleotide-based kits can include, for example: (1) an oligonucleotide, e.g., a detectably labelled oligonucleotide, which hybridizes to a nucleic acid sequence described in the Tables presented herein or a human homologue thereof or (2) a pair of primers that can be used to amplifying one of those nucleic acid molecules.

The kit may also include, e.g., a buffering agent; a preservative; a protein stabilizing agent; components necessary for detecting the detectable agent (e.g., an enzyme or a substrate) . The kit may further include a control sample or a series of control samples that can be assayed and compared to the test sample. Typically, each component of the kit is enclosed within an individual container and all of the various containers are within a single package together with instructions for observing whether the tested subject is suffering from or is at risk of developing agranulocytosis. B. Prognostic Assays

The methods described herein can be used as diagnostic or prognostic assays to identify subjects (i.e., human or other animal patients) that have or who are at risk of developing agranulocytosis. For example, the assays described herein (including the preceding diagnostic assays) can be used to identify a subject that has or is at risk of developing agranulocytosis by virtue of having a mutant

(i.e. sequence-variant) gene, such as one or more of those disclosed in the Tables presented herein or the human homologue (s) thereof. The assays described herein can also be used to evaluate the level of nucleic acid expression or protein activity. Altered expression or activity may be, but is not always necessarily, a direct reflection of the sequence variations described. Thus, the present invention provides a method in which a given protein or nucleic acid molecule (i.e., a nucleic acid molecule described in the Tables presented herein or the human homologue thereof) is detected in a test sample obtained from a subject. The presence of a mutation or an indication of differential expression or activity can be diagnostic for a subject who has or who is at risk of developing agranulocytosis. Furthermore, the prognostic assays described herein can be used to determine whether a subject can be treated with virtually any agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) . For example, such methods can be used to determine whether a subject can be effectively treated with a clozapine. Thus, the present invention provides methods for determining whether a subject is at risk of developing agranulocytosis when treated with a given agent. The method can be carried out, for example, by determining, prior to treatment, whether the patient has either a mutation in one or more of the genes described in the Tables presented herein (or the human homologue thereof), or in their regulatory regions, or whether, in that patient, one or more of those genes for which differential expression is associated with agranulocytosis rather than, or in addition to, therapeutic benefit is differentially expressed. As described above, the methods of the invention can also be used to detect genetic lesions or mutations in one or more of the genes described in the Tables presented herein or the human homologues thereof, thereby determining if a subject with the lesioned gene is at risk of agranulocytosis. In preferred embodiments, the methods include detecting, in a sample of cells (e.g., a sample of blood cells) from the subject, a genetic lesion or mutation characterized by at least one alteration that affects the integrity or expression of a gene described in the Tables presented herein or a human homologue thereof. For example, genetic lesions or mutations can be detected by detecting: (1) a deletion of one or more nucleotides; (2) an addition of one or more nucleotides; (3) a substitution of one or more nucleotides; (4) a chromosomal rearrangement; (5) an alteration in the level of a messenger RNA transcript; (6) an aberrant modification, such as of the methylation pattern of the genomic DΝA; (7) the presence of a non-wild type splicing pattern of a messenger RΝA transcript; (8) a non-wild type level of the encoded protein; (9) an allelic loss of the gene; and (10) an inappropriate post-translational modification. As described herein, there are a large number of assay techniques known in the art which can be used for detecting genetic lesions, mutations, or sequence variations. A preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject.

In certain embodiments, detection of the lesion involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al . Science 24.1:1077-1080 (1988); and Nakazawa eϋ ai . Proc . Natl . Acad. Sci . USA 91:360-364

(1994)), the latter of which can be particularly useful for detecting point mutations ( see, e. g. , Abravaya et al . Nucleic Acids Res . 23_:675-682 (1995)). This method can include the steps of collecting a sample of cells from a patient, isolating nucleic acid (e.g., genomic DNA, mRNA, or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a gene described in the Tables presented herein or a human homologue thereof under conditions such that hybridization and amplification of the gene (if present) occurs . One can then detect the presence or absence of an amplification product, or the size of the amplification product and compare the length to that of a control sample. It is anticipated that PCR and/or LCR may will be used as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.

Alternative amplification methods include: self sustained sequence replication (Guatelli et al . Proc . Natl . Acad . Sci . USA 87 : 1874-1878 (1990)), transcriptional amplification system (Kwoh et al . Proc . Natl . Acad. Sci . USA 86:1173-1177 (1989)), Q-Beta Replicase (Lizardi et al . Bio /Technology 6 : 1197 (1988)), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of ordinary skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. In an alternative embodiment, mutations in a gene (i.e., a gene described in the Tables presented herein or a human homologue thereof) from a sample cell can be identified by alterations in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally) , digested with one or more restriction endonucleases, and fragment length sizes compared following gel electrophoresis. Differences in fragment lengths between sample and control DNA indicate mutations in the sample DNA. Moreover, the use of sequence specific ribozymes ( see, e. g. , U.S. Patent No. 5,498,531) can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.

In other embodiments, genetic mutations can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotides probes (Cronin et al . , Human Mutation 7:244-255 (1996); Kozal et al . , Nature Medicine 2:753-759 (1996)). For example, genetic mutations can be identified in two-dimensional arrays containing light-generated DΝA probes as described in Cronin et ai . ( supra) . Briefly, a first hybridization array of probes is used to scan through long stretches of DΝA in a test sample and in a control sample to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations, and is followed by a second hybridization array that allows characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected. Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene .

In yet another embodiment, any of a variety of sequencing reactions known in the art can be used to directly sequence any of the genes described in the Tables presented herein or a human homologue thereof and to detect mutations by comparing the sequence of the test sample with the corresponding wild-type (control) sequence. Examples of sequencing reactions include those based on techniques developed by Maxim and Gilbert ( Proc. Natl . Acad . Sci . USA 74:560 (1977)) or Sanger (Proc. Natl . Acad. Sci . USA 74:5463 (1977)) . In addition, any of a variety of automated sequencing procedures can be used when performing the diagnostic assays (Bio/Techniques _.19:448 (1995)), including sequencing by mass spectrometry ( see, e . g. , PCT Publication o. WO 94/16101; Cohen et al . , Adv. Chro atogr. 36.: 127-162 (1996); and Griffin et al . , Appl . Biochem. Biotechnol . 3j3:147-159 (1993)).

Other methods for detecting mutations include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al . , Science 23_0: 1242 (1985)). In general, the technique of "mismatch cleavage" entails providing heteroduplexes formed by hybridizing (labeled) RNA or DNA containing a wild-type sequence with potentially mutant RNA or DNA obtained from a tissue sample. The double-stranded duplexes are treated with an agent that cleaves single- stranded regions of the duplex, such as which will exist due to basepair mismatches between the control and sample strands . RNA/DNA duplexes can be treated with RNase to digest mismatched regions , and DNA/DNA hybrids can be treated with SI nuclease to digest mismatched regions. In other embodiments, either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions . After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, e. g. , Cotton et al . , Proc . Natl . Acad . Sci . USA 85:4397 (1988); Saleeba et al . , Methods Enzymol . 217 :286-295 (1992). In a preferred embodiment, the control DNA or RNA can be labeled for detection.

In still another embodiment, the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA mismatch repair" enzymes) in defined systems for detecting and mapping point mutations in cDNAs obtained from samples of cells. For example, the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al . ,

Carcinogenesis 15.: 1657-1662 (1994)). According to an exemplary embodiment, a probe based on a wild-type sequence described in the Tables presented herein or a human homologue thereof is hybridized to a cDNA or other DNA product from a test cell (s) . The duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, e.g., U.S. Patent No. 5,459,039.

In other embodiments, alterations in electrophoretic mobility will be used to identify mutations in genes. For example, single strand conformation polymorphism (SSCP) may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids (Orita et al . , Proc. Natl . Acad. Sci . USA 86.:2766 (1989); see also Cotton Λfutat. Res . 285:125-144 (1993); Hayashi Genet. Anal. Tech . Appl . 9:73-79 (1992)). Single-stranded DΝA fragments of sample and control nucleic acids will be denatured and allowed to renature. The secondary structure of single- stranded nucleic acids varies according to sequence, and the resulting alteration in electrophoretic mobility enables the detection of even a single base change. The DΝA fragments may be labeled or detected with labeled probes. The sensitivity of the assay may be enhanced by using RΝA

(rather than DΝA) , in which the secondary structure is more sensitive to a change in sequence. In a preferred embodiment, the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al . , Trends Genet . 7:5 (1991)).

In yet another embodiment, the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE) (Myers et al . , Nature 313 :495

(1985)) . When DGGE is used as the method of analysis, DΝA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC-rich DΝA by PCR. In a further embodiment, a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DΝA (Rosenbaum and Reissner Biophys . Chem . 265:12753 (1987)).

Examples of other techniques for detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al . , Nature 324 : 163 (1986)); Saiki et al . , Proc . Natl . Acad . Sci . USA 86:6230 (1989)). Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.

Alternatively, allele specific amplification technology that depends on selective PCR amplification may be used in conjunction with the instant invention. Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al . , Nucleic Acids Res . 17:2437- 2448 (1989)) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent or reduce polymerase extension (Prossner, TiJbtech 11:238 (1993)). In addition, it may be desirable to introduce a novel restriction site in the region of the mutation to create cleavage-based detection (Gasparini et al . , Mol . Cell Probes 6.:1 (1992)). It is anticipated that in certain embodiments, amplification may also be performed using Taq ligase for amplification (Barany, Proc. Natl . Acad . Sci . USA 88:189 (1991)). In such cases, ligation will occur only if there is a perfect match at the 3' end of the 5' sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification. The methods described herein may be performed, for example, by utilizing pre-packaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of agranulocytosis.

Furthermore, any cell type or tissue, preferably peripheral blood leukocytes, in which one or more of the genes described in the Tables presented herein is expressed may be utilized in the prognostic assays described herein. C. Monitoring of Effects During Clinical Trials Determining whether patients in clinical trials have a mutation that is associated with agranulocytosis in one or more of the genes described in the Tables presented herein or whether the expression or activity of one or more of those genes varies is useful for a number of reasons. For example, patients with such mutant genes can be excluded from the trial altogether, thereby reducing the risk of participating in the study. In addition, should a drug that is on trial cause differential expression of one or more of those genes in which altered expression or activity is associated with agranulocytosis rather than, or in addition to, beneficial therapeutic effects, it can be re-engineered or dropped from the trial at an early stage. This analysis will help prevent a drug that is likely to cause agranulocytosis from reaching the market and will save deve1opment costs.

More specifically, but not by way of limitation, genes, including those described in the Tables presented herein, that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) can be identified. Thus, to study the effect of agents on the development of agranulocytosis, for example, in a clinical trial, cells can be isolated and RNA prepared and analyzed for the levels of expression. The levels of gene expression (i.e., a gene expression pattern) can be quantified by Northern blot analysis or RT-PCR, as described herein, or alternatively, by measuring the amount of protein produced, by one of the methods as described herein, or by measuring the levels of activity of one or more of the genes described in the Tables presented herein. In this way, the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during, treatment of the individual with the agent. In a preferred embodiment, the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) comprising the steps of d) detecting the level of expression of a protein, mRNA, or genomic DNA described in the Tables presented herein (or their human homologues) in a "pre-administration" sample obtained from the patient ( i . e . , a sample obtained before any treatment is begun) ; (ii) obtaining one or more post- administration samples from the subject; (in) detecting the level of expression or activity of the protein, mRNA, or genomic DNA in the post-administration samples (that protein being encoded by a gene described in the Tables presented herein, or a human homologue thereof) ; (iv) comparing the level of expression or activity of the protein, mRNA, or genomic DNA m the pre-administration sample with that of the protein, mRNA, or genomic DNA in the post-administration sample or samples; and (v) altering the administration of the agent to the subject accordingly. For example, one would consider ceasing administration of the agent when the expression or activity of a gene that is up-regulated (e.g., that is more highly expressed) in bone marrow cells treated with clozapine is up-regulated in a post-administration sample provided that up-regulation is associated with agranulocytosis rather than, or in addition to, beneficial therapeutic effects.

II. The Use of Sequence-variant or Differentially

Expressed Genes in Selecting and Monitoring Drug Therapies

The sequence or expression levels of the differentially expressed genes identified herein (see the Tables presented herein) may be used to select a course of drug treatment for patients suffering from a variety of disorders (including, but not limited to, schizophrenia) and to assess the risk that those patients will develop agranulocytosis as a result of the selected treatment. Moreover, should a patient elect to take a drug that may cause agranulocytosis, one can monitor the drug therapy by periodically assessing the differentially expressed genes of the invention as the therapy progresses; a change in gene expression providing an early warning that agranulocytosis might be developing. The drug therapy can then be altered

(for example by altering gene expression or activity, as described below) or discontinued. The mutation or alteration in expression or activity is most useful in the selection and monitoring of therapies when it is associated with agranulocytosis rather than with beneficial therapeutic effects .

A. Drugs that are Known to Cause Agranulocytosis

1. Aminopyrine One of the first drugs to become associated with a high incidence (0.1-1.0%) of agranulocytosis was aminopyrine

(also known as aminphenazone) , a pyrazolne derivative (Madison and Squier, J. Am. Med. Assoc. 102 :755, 1934) . In some reports, the delay between administration of the drug and the onset of agranulocytosis was short (see, e.g., Hartl, Semin . Hematol . 2.:313, 1965). However, it is likely that patients experiencing such a rapid onset had been exposed to the drug ("sensitized") previously (aminopyrine was initially readily available and was a component of several different mixtures) (Uetrecht, Drug Metabol . Rev. 24:299-366, 1992) . In other reports, the delay between aminopyrine administration and the development of agranulocytosis was around one month, which is typical for other drug- induced agranulocytosis (Uetrecht, 1992, supra) . Regardless of the length of the delay, patients invariably had a rapid onset of symptoms with fever, chills, and a decline in peripheral neutrophils within a few hours. The rapid appearance of symptoms underscores the need for a better means to detect agranulocytosis before its onset .

2. Procainamide

Procainamide is associated with a relatively high but variable incidence of agranulocytosis. Ellrodt et al . (Ann. Intern. Med. 100:197, 1987) found agranulocytosis and severe neutropenia in 4.4% of patients who received procainamide after open heart surgery while Meyers et al . (Am. Heart . J. 109 :1393, 1985) found a lower incidence, 0.55%, in other groups of patients. Studies have suggested that an antibody that recognizes antigens present only on immature cells of the granulocytic series was responsible for agranulocytosis in these patients (Uetrecht, 1992, supra) .

3. Dapsone During the war in Vietnam, dapsone was administered as a prophylactic treatment for malaria. Sixteen cases of agranulocytosis and eight deaths were reported in connection with its administration (Ognibene, Ann. Intern. Med . 72 : 521, 1970) . Although the incidence is difficult to determine, dapsone was estimated to cause approximately one case of agranulocytosis for every 10,000 soldiers treated. A higher incidence was subsequently reported when Swedish patients were treated for dermatitis herpetiformis (Hornsten and Wiholm, Arch . Der atol . 126:919, 1990). The mechanism of dapsone-induced agranulocytosis is unknown, although it does seem clear that the hydroxylamme metabolite of dapsone, but not dapsone itself, inhibits granulocytopoiesis (Weetman et al . , Br. J. Haematol . 45:361, 1980).

4. Sulfonamides , Sulfasalazme, and

Trimethoprim

Sulfonamides were also among the first drugs to be associated with agranulocytosis (Rmkoff and Spring, Ann. Intern . Med. 15.: 89, 1941) and are currently associated with possibly the largest number of cases of agranulocytosis. Sulfonamides are frequently administered together with trimethoprim, which can also cause neutropenia (Uetrecht, 1992, supra). Similarly, sulfasalazine is associated with a high incidence of agranulocytosis.

5. Other Arylammes

Primary arylammes are not found in many commonly administered drugs, possibly because this functional group is associated with a relatively high incidence of adverse reactions, including agranulocytosis. Metoclopramide, a derivative of procainamide, reportedly causes agranulocytosis even though it is usually given at l/50th the dose of procainamide (Uetrecht, 1992, supra) . Para- am osalicylic acid, which is also associated with agranulocytosis, is an isomer of 5-amιnosalιcylιc acid and is released when sulfasalazme is reduced.

Ammoglutethimide is associated with a high incidence of idiosyncratic reactions including agranulocytosis (see, e . g. , Gez and Sulkes, Oncology 41:399, 1984) .

Even though it is a tertiary, rather than a primary, arylamine, aprindine is associated with a high incidence of agranulocytosis, and this has severely limited its use as an antiarrhythmic agent ( see, e . g. , Opie, Lancet 2 : 689 , 1980).

Diclofenac is a secondary arylamine that has been reported to cause agranulocytosis and aplastic anemia (Salama et al . , Br. J. Haematol . 72:127, 1989). 6__^_ Chloramphenicol

Chloramphenicol is the classic drug associated with aplastic anemia, albeit of a low incidence, and to an even lesser extent, with agranulocytosis. Analogues of chloramphenicol, such as thiamphenicol , are also associated with agranulocytosis.

7. Chlorpromazine Chlorpromazine is a significant cause of agranulocytosis (Uetrecht, 1992, supra) and may exert its action via direct toxicity to bone marrow. 8^. Amodiaσuine and Acetaminophen

Amodiaquine is an antimalarial drug associated with a relatively high incidence of agranulocytosis. In one case study (Lind et al . , Br. Med . J. 1:458, 1973), examination of a sample of the patient's bone marrow revealed a lack of all neutrophil precursors. Related drugs - chloroquine and sulfadoxine (but not proguanil, pyrimethamine, and quinine) were found to have a similar effect.

Acetaminophen is considered to be associated with a low incidence of idiosyncratic drug reactions (Dukes et al . Meyler' s Side Effects of Drugs, Elsevier Press, Amsterdam,

1988) . Its oxidation by the yeloperoxidase system is similar to that of amodiaquine, and it has been estimated to be responsible for 10% of drug- induced agranulocytosis (Uetrecht, 1992, supra) .

9. Vesnarinone

Vesnarinone is an ionotropic agent developed for the treatment of severe congestive heart failure. Although no toxicity was observed in clinical studies in Japan, in early trials in the United States, four of the first 28 patients treated developed agranulocytosis (possibly due to concomitant administration of an influenza vaccine) . Bone marrow of affected patients lack more mature cells such as myelocytes and promyelocytes .

10. Mianserin

About one in every 2000 patients given mianserin develop agranulocytosis, usually, between the fourth and sixth week of therapy (Coulter and Edwards, Lancet 336 : 785 , 1990) . Case studies show a depression of all granulocyte precursors in the bone marrow (Page, Br. Med . J. 287 : 1912 , 1982) .

11. Clozapine Clozapine is an antipsychotic agent that has proven effective in treating patients who suffer, for example, from schizophrenia that is refractory to treatment with other agents . Clozapine was withdrawn from the market in Finland when, within six months of being released, it caused 17 cases of neutropenia and 9 deaths (approximately 3000 patients were treated) .

12. Propylthiouracil and Methimazole The most common serious adverse reaction to antithyroid medication is agranulocytosis, with an incidence of about 0.4% (Uetrecht, 1992, supra ; Cooper et al . , Ann . Intern . Med. 98 : 26 , 1983) . Most patients who develop agranulocytosis as a result of this type of therapy are female or elderly. 13. Captopril and Penicillamine

Captopril and penicillamine are both associated with bone marrow toxicity (agranulocytosis and pancytopenia) and may be the only two such associated drugs that are thiols. Both drugs are able to suppress agranulocytopoiesis in vi tro (Hammond et al . , Exp. Hematol . 16:674, 1988).

14. Carbamazepine

Although carbamazepine is associated with a low incidence of agranulocytosis, it can be difficult to determine when its use should be discontinued because transient neutropenia is common, with an incidence of 10% and persistent leukopenia has an incidence of about 2% (Hart and Easton, Ann. Neuroi . 11:309, 1982).

15. Phenylbutazone Phenylbutazone is related to aminopyrine and is seldom prescribed; it is associated with a high incidence of agranulocytosis and aplastic anemia (Uetrecht, 1992, supra).

16. Benzene

Benezene has long been associated with bone marrow toxicity, and it is known that the drug must be metabolized by the liver for this toxicity to ensue. Most of the toxicity of benzene involving bone marrow can be reproduced in animals; therefore, it is not really an idiosyncratic reaction and probably involves direct toxicity of reactive metabolites (Uetrecht, 1992, supra) .

17. Interferon

The possibility that interferon (IFΝ) caused maturational arrest of myeloid progenitor cells was considered when agranulocytosis was observed 13 days after IFΝ-alpha 2b (6 MU/day) therapy was begun for chronic active hepatitis C (Higashi et al . , J. Gastroenterol . Hepatol . 11:1012-1015, 1996) . In a more extensive study, the adverse effects of interferon therapy were monitored in 38 patients affected with type II essential mixed cryoglobul emia. Patients were treated either with 3 million units (MU) of recombinant terferon-alpha 2a daily, or on alternate days

(35 patients) , or with natural interferon-beta (3 patients) . The treatment lasted between 6 and 15 months, and patients were followed from 8 to 93 months. None of the patients treated with interferon alone developed significant hematologic alterations. Similarly, none of 7 patients treated with angiotens -converting enzyme (ACE) inhibitors alone showed hematologic toxicity. However, three patients treated with a combination of interferon and ACE inhibitors developed severe granulocytopenia a few days after starting treatment. (Casato et al . , Am. J. Med . 99:386-391, 1995).

B. Reactive Intermediates

Many types of adverse drug reactions appear to involve reactive metabolites. It has been proposed that reactive metabolites formed by neutrophils, or neutrophil precursors in the bone marrow, are responsible for drug- induced agranulocytosis (Uetrecht, 1992, supra) . More specifically, experiments with clozapine led Uetrecht to propose that such a metabolite, a nitrenium on, was responsible for clozapme-induced agranulocytosis, either by direct toxicity or through an immune-mediated mechanism

(Drug Safety 7:51-56, 1992). It is certainly reasonable to expect that the formation of a reactive metabolite on the surface of neutrophils, or neutrophil precursors in the bone marrow, would be more likely to result in agranulocytosis than if those same metabolites were formed in the liver.

Only activated neutrophils metabolize drugs. Therefore, infections or other inflammatory conditions in which the cells are activated may be additional risk factors for drug-induced agranulocytosis. The incidence of agranulocytosis associated with vesnarinone, a drug used to treat heart failure, was increased in patients who also received an influenza vaccine. Reportedly, the influenza vaccine, which had been opsonised by incubation with serum, activated neutrophils so that they metabolised vesnarinone to a metabolite that covalently bound to the neutrophils (Uetrecht, 1992, supra) .

C. Cell Types Amenable to Testing In Culture Stem cells within the human hematopoietic system can be identified by the expression of CD34 on their surface (Civin and Shaper, J. Immunol . 133 : 157 , 1984), which declines as the cells transition to late progenitors and mature blood cells. CD34^*/CD38^" cells constitute from 1 to 5% of the total CD34* population of cells and are highly enriched in pluripotent hematopoietic progenitors with self- renewal potential or stem cell activity ( see, e . g. , Reems et al . , Blood 8.5:1480, 1995). CD38 is upregulated during the differentiation of CD34⁺/CD38^" cells into committed progenitors, with simultaneous acquisition of various other lineage-specific markers (Terstappen et al . , Blood 77 : 1218 , 1991) .

While it has been difficult to establish human stromal cell clones, immortalization in vi tro with SV40 large-T antigen has recently permitted the establishment of stable stromal cell lines capable of maintaining hematopoiesis (Cicuttini et al . , Blood 80:102, 1992; Thalmeier et al . , Blood 83.: 1799, 1994; Aizawa et al . , Exp . Hematol . 2_2:482, 1994), each of which is hereby incorporated by reference) .

In addition, transgenic mice bearing a temperature- sensitive SV40 large T-antigen have been used to establish immortalized cell clones from various tissues (Jat et al . , Proc. Natl . Acad . Sci . USA 88.:5096, 1991), clones that phenotypically and functionally resemble their in vivo counterparts ( see, e . g. , Mehler et al . , Nature 262 : 62 , 1993) . Aiuti et al . recently generated a panel of conditionally immortalized stromal cell clones from the bone marrow of these transgenic mice, and characterized them for their ability to maintain and expand mouse myeloid and lymphoid progenitor cells (Exp . Hematol . 2j5: 143-157, 1998), hereby incorporated by reference) . Immortalized stromal cell clones such as these can be used in the methods described herein, including methods for determining whether a compound can be used to prevent or reduce the signs or symptoms of agranulocytosis in a patient, particularly when it results from a given drug therapy. Dj. Assessing Agranulocytosis by Conventional Means

The criterion for agranulocytosis is a blood granulocyte count below 0.5 x 10⁹/L and, most commonly, total blood granulocyte absence with normal erythrocyte and platelet levels (Ruvidic, Biomed . & Pharmacother. 50 :275- 278, 1996) . To confirm that a patient is suffering from agranulocytosis, one can obtain a sample of serum and apply it to normal neutrophils. For example, serum from patients with acute aminophenazone-induced agranulocytosis causes complement -dependent agglutination of normal neutrophils (Uetrecht, Drug Safety 7: 51-56, 1992).

E. Methods for Selecting and Monitoring Drug

Treatment with Differentially Expressed Genes or their Products

The sequence-variant or differentially expressed genes identified herein (or those identified subsequently by the same or similar methods) can be used to select an appropriate therapy for an individual or to monitor an ongoing therapy. They may also serve as markers to monitor patients for agranulocytosis in clinical trials of various drugs being tested for safety or efficacy.

One can determine whether a given patient will benefit from a given drug ("the test drug") without a significant risk of developing agranulocytosis by examining the sequence or expression of one or more of the differentially expressed genes identified herein. For example, if one or more of the genes found to be overexpressed in clozapine-treated cells are also overexpressed in the patient's neutrophils or bone marrow stem cells when those cells are exposed to the test drug, and if overexpression is associated with agranulocytosis rather than, or in addition to, beneficial therapeutic effects, there is a higher probability that the patient will develop agranulocytosis.

Accordingly, the invention features a method for determining whether a compound can be administered to a patient without significant risk that the patient will develop agranulocytosis. The method can be carried out, for example, by determining the expression level of one or more of the genes described in the Tables presented herein, or a human homologue thereof, in a biological sample obtained from the patient and comparing that level with the expression level of the same gene(s) in the same (or an equivalent) biological sample that has been treated with the test (e.g., clozapine) compound. If treatment with the test compound elevates the level of expression of the gene(s) examined and if overexpression is associated with agranulocytosis rather than, or in addition to, beneficial therapeutic effects, there is a significant risk that the patient will develop agranulocytosis if treated with the test compound. Alternatively, or in addition, the method can be carried out by determining the expression level of one or more of the genes represented in the Tables presented herein or a human homologue thereof in a biological sample obtained from the patient and comparing that level with the expression level of the same gene(s) in the same (or an equivalent) biological sample that has been treated with the test compound. If treatment with the test compound reduces the level of expression of the gene(s) examined and if underexpression is associated with agranulocytosis rather than or in addition to beneficial therapeutic effects, there is a significant risk that the patient will develop agranulocytosis if treated with the test compound.

The biological sample used in this method, or in any method described herein, may be a sample of cells obtained from the bone marrow (i.e., hematopoietic stem cells) or from peripheral blood (i.e., granulocytes). In some instances, for example, in the event gene expression is examined in the course of testing a new drug for safety, cells from cell lines derived from bone marrow or peripheral blood can also be examined. It is preferable to assess the expression of a panel of differentially expressed genes (i.e., two or more of the genes represented in the Tables presented herein) .

If desired, in the assay described above (and others) , one may compare expression levels (in treated and non-treated samples) that have been "normalized."

Normalization refers to correcting the expression level of a differentially expressed gene by comparing its expression to the expression of a gene that is not differentially expressed in response to the test compound, e.g., a gene that is not differentially expressed in bone marrow cells in response to clozapine. Suitable genes for normalization include "housekeeping" genes, such as the actin gene. As described above, expression levels can be assessed in a number of ways, including measuring: the mRNA encoded by each of the selected genes; the amount of protein encoded by each of the selected genes; and the activity of the protein encoded by each of the selected genes.

The identified genes can also be used as markers to monitor a course of drug treatment. Samples obtained periodically (e.g., daily) from a patient undergoing drug treatment can be assessed to determine whether the level of expression of one or more of the genes represented in the

Tables presented herein or the human homologue (s) thereof is progressively increasing (i.e., whether the level of expression is higher in a sample obtained, for example, 30 days after drug treatment was begun than the level of expression in a sample obtained 29 days after drug treatment was begun) . For genes whose overexpression is associated with agranulocytosis rather than, or in addition to, beneficial therapeutic effects, an increase in gene expression reflects an increase in the risk that the patient will develop agranulocytosis. Alternatively, or in addition, samples obtained periodically (e.g., daily) from a patient undergoing drug treatment can be assessed to determine whether the level of expression of one or more of the genes represented in the Tables presented herein or a human homologue thereof is progressively decreasing ( i . e. , whether the level of expression is lower in a sample obtained, for example, 30 days after drug treatment was begun than the level of expression in a sample obtained 29 days after drug treatment was begun) . For genes whose underexpression is associated with agranulocytosis rather than or in addition to beneficial therapeutic effects, a decrease in gene expression reflects an increase in the risk that the patient will develop agranulocytosis. Should the respective increase or decrease in gene expression occur, the drug treatment can be modified or discontinued to prevent agranulocytosis. Should the respective increase or decrease in gene expression fail to occur, the drug treatment can be continued without fear that the patient is on the verge of developing agranulocytosis.

III. The Use of Sequence-variant or Differentially Expressed Genes in Diagnosing Agranulocytosis

A variety of methods can be employed for the early diagnosis of agranulocytosis. These methods can be carried out using the fingerprint gene nucleotide sequences disclosed herein and antibodies directed against differentially expressed fingerprint gene products. Specifically, these reagents can be used to detect either overexpression or underexpression of certain differentially expressed genes or the presence of a mutation in the regulatory sequence of certain differentially expressed genes .

A differentially expressed gene (e.g., a gene that is overexpressed or underexpressed in drug-treated cells of a patient who consequently develops agranulocytosis) can be used as diagnostic markers. For example, samples obtained periodically (e.g., daily) from a patient undergoing drug treatment can be assessed to determine whether the level of expression of one or more of the genes represented in the Tables as "upregulated" is progressively increasing (i.e., whether the level of expression is higher in a sample obtained, for example, 30 days after drug treatment was begun than the level of expression in a sample obtained 29 days after drug treatment was begun) . For genes whose overexpression is associated with agranulocytosis rather than, or in addition to, beneficial therapeutic effects, such an increase in gene expression reflects an increase in the risk that the patient will develop agranulocytosis. Alternatively, or in addition, samples obtained periodically (e.g., daily) from a patient undergoing drug treatment can be assessed to determine whether the level of expression of one or more of the genes represented in the Tables in which gene expression is "downregulated" is progressively decreasing (i.e., whether the level of expression is lower in a sample obtained, for example, 30 days after drug treatment was begun than the level of expression in a sample obtained 29 days after drug treatment was begun) . For genes whose underexpression is associated with agranulocytosis rather than, or in addition to, beneficial therapeutic effects, such a decrease in gene expression reflects an increase in the risk that the patient will develop agranulocytosis .

Should the respective increase or decrease in gene expression occur, the drug treatment can be modified or discontinued to prevent agranulocytosis. Should the respective increase or decrease in gene expression fail to occur, the drug treatment can be continued without fear that the patient is on the verge of developing agranulocytosis.

The diagnostic methods described above (and the methods of the invention generally) can be performed with pre-packaged diagnostic kits comprising at least one specific fingerprint gene nucleic acid or anti-fingerprint gene antibody reagent (such as one of those described below) , which can be conveniently used, for example, in clinical settings, to diagnose patients, preferably even before symptoms of agranulocytosis appear. A. Detection of Fingerprint Gene Expression DNA or RNA from the cell type or tissue to be analyzed can be isolated using procedures that are well known to those of ordinary skill in the art. Diagnostic procedures can also be performed in si tu on fixed or frozen cells obtained from the patient by, for example, aspirating bone marrow or collecting peripheral blood. In the event that whole cells are analyzed, no nucleic acid purification is necessary. Nucleic acid reagents such as those described above can be used as probes or primers for in si tu procedures (see, for example, Nuovo, 1992, PCR in si tu Hybridization: Protocols and Applications, Raven Press, NY) .

Fingerprint gene nucleotide sequences consisting of either RNA or DNA, can be used in hybridization or amplification assays to detect genes and expression patterns associated with agranulocytosis. The assays can include, but are not limited to, Southern blot analyses, Northern blot analyses, single stranded conformational polymorphism analyses, in si tu hybridization assays, and polymerase chain reaction (PCR) analyses. These analyses can reveal both quantitative and qualitative features of the expression pattern of the fingerprint gene or feature's of the genes' composition. That is, such techniques can reveal, for example, point mutations, insertions, deletions, chromosomal rearrangements, and activation or inactivation of gene expression.

Preferably, diagnostic methods in which one detects fingerprint gene-specific RNA molecules (a reflection of the level of gene expression) can involve contacting and incubating nucleic acid molecules derived from the cell type or tissue being analyzed with one or more labeled nucleic acid reagents ("probes") under conditions in which they can specifically anneal to complementary sequences withm the nucleic acid molecule of interest. Preferably, these probes are at least 15 to 30 nucleotides long. Following incubation, essentially all non-annealed nucleic acid molecules are removed from the hybrid molecule (nucleic acid probe : fingerprint RNA). The presence of nucleic acids from the target tissue that have hybridized with the probe is then determined. Using this scheme, the nucleic acid molecules from the tissue or cell type of interest can be immobilized, for example, to a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads. In this case, after incubation, non-annealed, labeled fingerprint nucleic acid reagents are easily removed. Detection of the remaining, annealed, labeled nucleic acid reagents is accomplished using standard techniques well-known to those of ordinary skill m the art.

Alternatively, diagnostic methods can be performed by detecting fingerprint gene-specific nucleic acid molecules that have been amplified by the PCR (Mullis, 1987, U.S. Patent No. 4,683,202), ligase chain reaction (Barany,

Proc. Natl. Acad. Sci . USA 8_8:189-193 , 1991), self sustained sequence replication (Guatelli et al . , Proc . Natl . Acad . Sci . USA 87 : 1874-1878, 1990), transcriptional amplification system (Kwoh et al . , Proc . Natl . Acad . Sci . USA 86 :1173- 1177, 1989), Q-Beta Replicase (Lizardi et al . ,

Bio /Technology 6 : 1197 , 1988), or any other nucleic acid amplification method. The amplified molecules are then detected using techniques well known to those of ordinary skill in the art (see below) . Detection schemes in which nucleic acid molecules are amplified are especially useful for detecting nucleic acid molecules that are present in a biological cell or sample m very low numbers. In one embodiment, the detection methods include obtaining a cDNA molecule from an RNA molecule of interest (e.g., by reverse transcription of the RNA molecule into cDNA) . Cell types or tissues from which such RNA can be isolated include any cell type of tissue in which a wild type fingerprint gene is known to be expressed. A sequence withm the cDNA is then used as the template for a nucleic acid amplification reaction, such as PCR amplification, or the like. The nucleic acid sequences used to initiate synthesis (i.e., nucleic acid primers) in the reverse transcription and nucleic acid amplification steps of this method are chosen from among the fingerprint gene nucleic acid sequences. The preferred lengths of nucleic acid sequences to be used as reagents are at least 19-30 nucleotides.

To detect the amplified product, the nucleic acid amplification can be performed using nucleotides that are labeled, for example, with a radioisotope, a fluorophore, or any other detectable marker. Alternatively, the nucleic acid molecule can be amplified to the point where the product can be visualized by standard ethidium bromide staining (or any other suitable nucleic acid stain) .

In addition to methods that focus primarily on the detection of a single nucleic acid sequence, detection schemes can be used to produce fingerprint profiles by, for example, utilizing a differential display procedure, as described above, Northern blot analysis, or RT-PCR. Any of the fingerprint gene sequences described above can be used as probes and/or PCR primers for the generation and corroboration of such fingerprint profiles. B . Detection of Fingerprint Gene Products Antibodies directed against wild-type or mutant fingerprint gene products can also be used in diagnostic, prognostic, and treatment methods for agranulocytosis. These methods, can be used to detect abnormalities in: the level of expression of fingerprint gene products; the temporal or spatial pattern of expression of fingerprint gene products (i.e., expression in a different cellular or subcellular location or a expression at a different time) ; or the structure of fingerprint gene products. Structural differences can include, for example, differences in the size, electronegativity, or antigenicity of the mutant fingerprint gene product relative to the normal fingerprint gene product . Protein from the tissue or cell type to be analyzed can be isolated using techniques that are well known to those of ordinary skill in the art, such as those described in Harlow and Lane (1988, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York) , which is incorporated herein by reference in its entirety) .

Preferably, methods to detect wild-type or mutant fingerprint gene products will involve an immunoassay in which a fingerprint gene product is detected by its interaction with an anti-fingerprint gene-specific antibody. For example, antibodies, or fragments of antibodies, useful in the present invention can be used to quantitatively or qualitatively detect the presence of wild-type or mutant fingerprint gene products. This can be accomplished, for example, by immunofluorescence techniques employing a fluorescently labeled antibody (see below) coupled with light microscopic, flow cytometric, or fluorimetric detection. Such techniques are especially preferred when the fingerprint gene products are expressed on the cell surface.

In addition, antibodies (or fragments thereof) useful in the present invention can be applied to cells for in si tu detection of target gene products. Tn situ detection can be accomplished by removing a histological specimen from a patient, and applying thereto a labeled antibody of the present invention. Preferably, the antibody (or fragment) is applied by overlaying the labeled antibody (or fragment) onto the biological specimen. This procedure makes it possible to determine not only whether the fingerprint gene product is present, but how it is distributed. Those of ordinary skill in the art will readily perceive that any of a wide variety of histological methods (such as staining procedures) can be modified in order to detect a fingerprint gene product in si tu .

Immunoassays for wild-type or mutant fingerprint gene products typically include incubating a biological sample, such as a biological fluid, tissue extract, freshly harvested cells, or cells that have been incubated in tissue culture with a detectably labeled antibody that is capable of specifically binding the fingerprint gene product, and then detecting the bound antibody by any of a number of techniques well-known in the art. The biological sample can be brought in contact with and immobilized onto a solid phase support or carrier such as nitrocellulose, or other solid support which is capable of immobilizing cells, cell particles, or soluble proteins. The support can then be washed with suitable buffers followed by application of the detectably labeled fingerprint gene product -specific antibody. The solid phase support can then be washed with the buffer a second time to remove unbound antibody. The amount of bound label on the solid support can then be detected by conventional means. Suitable solid phase supports or carriers include any support capable of binding an antigen or an antibody. Well-known supports or carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite. The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present invention. The support material can have virtually any possible structural configuration so long as the coupled molecule is capable of binding to an antigen or antibody. Thus, the support configuration can be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface can be flat such as a sheet or test strip. Preferred supports include polystyrene beads . Those of ordinary skill in the art will know of many other suitable carriers for binding antibody or antigen, or will be able to ascertain the same by use of routine experimentation. The binding activity of a given lot of anti- fingerprint gene product-specific antibody (whether generated against a wild type or mutant gene product) can be determined according to well-known methods. Those of ordinary skill in the art are able to determine operative and optimal assay conditions for each determination by employing routine experimentation.

One of the ways in which the fingerprint gene product-specific antibody can be detectably labeled is by linking it to an enzyme for use in an enzyme immunoassay

(EIA) . The enzyme that is bound to the antibody will react with an appropriate substrate, preferably a chromogenic substrate, to produce a chemical moiety that can be detected, for example, by spectrophotometric, fluorimetric or visual means. Enzymes that can be used to detectably label the antibody include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta-5-steroid isomerase, yeast alcohol dehydrogenase, α-glycerophosphate, dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-6-phosphate dehydrogenase, glucoamylase and acetylcholinesterase. Detection can be accomplished by colorimetric methods that employ a chromogenic substrate for the enzyme. Detection can also be accomplished visually comparing the extent of enzymatic reaction of a substrate with similarly prepared standards. Detection can also be accomplished using any of a variety of other immunoassays. For example, by radioactively labeling the antibodies or antibody fragments, it is possible to detect fingerprint gene products (wild type or mutant) by radioimmunoassay (RIA) . The radioactive isotope can be detected by autoradiography or by using a gamma counter or scintillation counter.

It is also possible to label the antibody with a fluorescent compound. When the fluorescently labeled antibody is exposed to light of the proper wave length, its presence can be detected due to fluorescence. Among the most commonly used fluorescent labeling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine . The antibody can also be detectably labeled using fluorescence emitting metals such as ¹⁵²Eu, or others of the lanthanide series. These metals can be attached to the antibody using such metal chelating groups as diethylenetri- aminepentacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA) .

The antibody also can be detectably labeled by coupling it to a chemiluminescent compound. The tagged antibody can be detected by detecting the luminescence that arises during the course of a chemical reaction. Examples of particularly useful chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester. Likewise, a bioluminescent compound can be used to label the antibody of the present invention. Biolumi- nescence is a type of chemiluminescence found in biological systems in which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence. Important bioluminescent compounds for purposes of labeling are luciferin, luciferase and aequorin.

IV. Characterization of Differentially Expressed Genes Differentially expressed genes can be further characterized, primarily to determine their biological function, by using techniques known to those of ordinary skill in the art. Assessing the biological functions of the differentially expressed genes, in addition, will allow their designation as fingerprint genes to include (or not, depending on the result) the designation of "target genes."

Specifically, any of the differentially expressed genes whose further characterization indicates that a modulation of the gene's expression or a modulation of the gene product's activity can reduce symptoms of agranulocytosis are designated "target genes, " which can, in turn, be used to identify therapeutic agents. When further characterization of a differentially expressed gene product indicates that that gene product is not necessary for an administered drug to exert its therapeutic effect but, instead, contributes to the adverse side effect of agranulocytosis, the fingerprint gene is designated a "target gene" and the polypeptide it encodes as a "target gene product." Such genes and their products can be used, as described above, as diagnostic markers and to select and monitor a drug-based treatment regime, the goal being to prevent or detect agranulocytosis as soon as possible. In addition, and as described further below, a subset of fingerprint genes can be designated target genes because their products can serve as targets for therapies aimed at preventing the development of agranulocytosis. While the differentially expressed genes disclosed herein (see the Tables presented herein) are known, analysis may reveal that these genes (or their products) have previously unidentified functions. Moreover, those of ordinary skill in the art can readily identify additional genes and analyze their function. In either case (whether examining a previously unknown function of a known gene or determining the function of a newly discovered gene) , a variety of techniques can be utilized to determine whether the genes can be classified as target genes. One way to further characterize these genes is to obtain their sequence, which can be readily obtained using standard techniques well known to those of ordinary skill in the art. By analyzing the sequence obtained, one may discover homologies with one or more known sequence motifs which can, in turn, yield information regarding the biological function of the identified gene product.

Second, one can analyze the distribution of the mRNA produced by the identified genes is cell types and tissues (again, by standard techniques well known to those of ordinary skill in the art (e.g., Northern blot analyses, RT-coupled PCR, and RNAase protection assays) ) . This analysis will reveal whether the identified genes are expressed in tissues affected by agranulocytosis or in tissues targeted by the therapeutic agent being administered. If the identified genes are expressed in tissues affected by agranulocytosis (i.e., bone marrow stem cells and their progeny) but not in the tissues targeted by the therapeutic agent (e.g., the nervous system), the identified genes are likely to serve well as fingerprint genes. Such analyses can also provide quantitative information regarding steady state mRNA regulation. In addition, standard in si tu hybridization techniques can be utilized to obtain information regarding which cells within a given tissue express the identified gene. This analysis can provide information regarding the biological function of an identified gene in instances wherein only a subset of the cells within the tissue is thought to be relevant, either to the development of agranulocytosis or to the action of the administered therapeutic agent (i.e., the agent suspected of causing the adverse agranulocytic condition) .

Third, the sequences of the identified genes can be used, according to standard techniques, to place the genes onto genetic maps, e.g., murine (Copeland and Jenkins,

Trends in Genetics 1:113-118, 1991) or human genetic maps (Cohen et al . , Na ture 366:698-701, 1993). Mapping the genetic loci can provide information regarding the genes' importance to human disease by, for example, identifying genes that map within genetic regions to which a possible predisposition to agranulocytosis also maps.

Fourth, the biological function of the identified genes can be more directly assessed by utilizing relevant in vivo and in vi tro systems. In vivo systems can include, but are not limited to, animal systems that naturally exhibit symptoms of agranulocytosis or that have been engineered to exhibit such symptoms. For example, genes identified by the methods described herein as having a mutation or as being differentially expressed in the event of agranulocytosis may be appropriately expressed in an animal model, such as a transgenic mouse. For example, a gene that is overexpressed (possibly due to a mutation) when an animal develops agranulocytosis in response to, e.g., clozapine treatment can be overexpressed in a transgenic animal (those of ordinary skill in the art are well able to overexpress a given gene in a transgenic animal) . Conversely, a gene that is underexpressed when an animal develops agranulocytosis, as described above, can be

"knocked out", again using techniques known and practiced by those of ordinary skill in the art.

Those of ordinary skill in the art will be well aware of other techniques to modulate the expression or activity of a gene that causes or substantially contributes to the development of agranulocytosis (e.g., the genes described in the Tables presented herein) . For example, one can modulate the expression or activity of a gene described in the Tables presented herein by contacting a cell with an agent that modulates (inhibits or stimulates) its expression or activity. In one embodiment, the agent is an antibody that specifically binds to the corresponding, encoded protein. In another embodiment, the agent modulates gene expression by modulating transcription, splicing, or translation of an mRNA of a gene described in the Tables presented herein. In yet another embodiment, the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of the an mRNA or gene described in the Tables presented herein in which gene expression is "upregulated" .

The role of identified gene products can be determined by transfecting cDNAs encoding these gene products into appropriate cell lines, such as, for example, an HL-60 cell line and analyzing the effect of the gene product on cell growth.

To further characterize the biological function of the identified genes (i.e., the sequence-variant or differentially expressed genes) , their expression can be modulated within in vivo or in vi tro systems, i.e., either overexpressed or underexpressed, and the subsequent effect on the system then assayed. Alternatively, the activity of gene's product can be modulated by either increasing or decreasing the level of activity in the in vivo or in vi tro system of interest, and assessing the effect of such modulation.

The information obtained by modulating the level of gene expression or activity can suggest methods for treating agranulocytosis. For example, treatment can include modulating the expression of a fingerprint gene or the activity of a fingerprint gene product. Characterizing expression or activity levels, or other features of the gene, as described herein, provide an indication as to whether the modulation should involve an increase or a decrease in the expression of the gene or the activity of the gene product of interest .

A. Expression of Polypeptides Encoded by Differentially Expressed Genes A variety of host-expression vector systems can be used to express the differentially expressed gene coding sequences of the invention. These systems represent vehicles by which coding sequences of interest can be produced and subsequently purified, as well as cells that can, when transformed or transfected with the appropriate nucleotide coding sequences, exhibit the differentially expressed gene protein in si tu . The systems include, but are not limited to, microorganisms such as bacteria (e.g., E. coli and B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA, or cosmid DNA expression vectors containing differentially expressed gene protein coding sequences; yeast (e.g., Saccharomyces and Pichia) transformed with recombinant yeast expression vectors containing the differentially expressed gene protein coding sequences; insect cell systems infected with recombinant virus expression vectors ( e . g. , baculovirus) containing the differentially expressed gene protein coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing differentially expressed gene protein coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter) .

In bacterial systems, a number of expression vectors can be advantageously selected depending upon the use intended for the differentially expressed gene product being expressed. For example, when a large quantity of such a protein is to be produced (for the generation of antibodies or to screen peptide libraries, for example), vectors that direct the expression of high levels of fusion protein products that are readily purified can be desirable. These vectors include, but are not limited to, the E. coli expression vector pUR278 (Ruther et al . , EMBO J. 2:1791, 1983) , in which the differentially expressed gene product coding sequence can be ligated individually into the vector in frame with the lacZ coding region so that a fusion protein is produced; pIN vectors (Inouye and Inouye Nucleic Acids Res . 13.: 3101-3109, 1985; Van Heeke and Schuster, J^". Biol . Chem. 264:5503-5509, 1989; and the like. pGEX vectors can also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST) . In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione- agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.

In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The differentially expressed gene coding sequence can be cloned individually into non-essential regions (e.g., the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (e.g., the polyhedrin promoter) . Successful insertion of differentially expressed gene coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene) . These recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed (e.g., see Smith et al . , J. Viol . 46_.: 584, 1983; Smith, U.S. Patent No. 4,215,051). In mammalian host cells, a number of viral-based expression systems can be used. In cases where an adenovirus is used as an expression vector, the differentially expressed gene coding sequence of interest can be ligated to an adenovirus transcription/translation control complex, for example, the late promoter and tripartite leader sequence. This chimeric gene can then be inserted in the adenovirus genome by in vi tro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region El or E3) will result in a recombinant virus that is viable and capable of expressing differentially expressed gene protein in infected hosts (e.g., see Logan & Shenk, Proc . Natl . Acad . Sci . USA 81 :3655-3659, 1984) . Specific initiation signals can also be required for efficient translation of inserted differentially expressed gene coding sequences. These signals include the ATG initiation codon and adjacent sequences. In cases where an entire identified gene, including its own initiation codon and adjacent sequences, is inserted into the appropriate expression vector, no additional translational control signals can be needed. However, in cases where only a portion of the identified coding sequence is inserted, exogenous translational control signals, including, perhaps, the ATG initiation codon, must be provided. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc., ( see Bittner et al . , Methods in Enzymol . 153:516-544, 1987) . In addition, a host cell strain can be chosen that modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products can be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, eukaryotic host cells that possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product can be used. Useful mammalian host cells include, but are not limited to, CHO, VERO, BHK, HeLa, COS, MDCK, 293, 3T3 , WI38, etc.

For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines that stably express the differentially expressed gene protein can be engineered. Rather than using expression vectors that contain viral origins of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter or enhancer sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells can be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. This method can advantageously be used to engineer cell lines that express the identified gene protein. Cell lines engineered in this way can be particularly useful in screening and evaluating compounds that affect the endogenous activity of the differentially expressed gene product. A number of selection systems can be used. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler et al . , Cell 11:223, 1977), hypoxanthine-guanine phosphoribosyltransferase (Szybalska and Szybalski, Proc. Natl . Acad. Sci . USA 18:2026, 1962), and adenine phosphoribosyltransferase (Lowy et al . , Cell 2_2:817, 1980) genes in tk^" , hgprt^" or aprt^" cells, respectively. Also, antimetabolite resistance can be used as the basis of selection for dhfr, which confers resistance to methotrexate (Wigler et al . , Proc . Natl . Acad . Sci . USA 77:3567, 1980; O'Hare et al . , Proc . Natl . Acad . Sci . USA 2.8:1527, 1981); gpt , which confers resistance to mycophenolic acid (Mulligan and Berg, Proc . Natl . Acad. Sci . USA 78.:2072, 1981); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin et al . , J. Mol . Biol . 150 : 1 , 1981); and hygro, which confers resistance to hygromycin (Santerre et al . , Gene 3_0:147, 1984) genes.

An alternative fusion protein system allows for the ready purification of non-denatured fusion proteins expressed in human cell lines (Janknecht et al . , Proc. Natl . Acad. Sci . USA 88_.: 8972-8976, 1991) . In this system, the gene of interest is subcloned into a vaccinia recombination plasmid such that the gene's open reading frame is translationally fused to an amino-terminal tag consisting of six histidine residues. Extracts from cells infected with recombinant vaccinia virus are loaded onto Ni²⁺ nitriloacetic acid-agarose columns and histidine-tagged proteins are selectively eluted with imidazole-containing buffers . When used as a component in assay systems such as that described herein, the differentially expressed gene product can be labeled, either directly or indirectly, to facilitate detection of a complex formed between the differentially expressed gene product and a test substance. Any of a variety of suitable labeling systems can be used including but not limited to radioisotopes such as ¹²⁵I ; enzyme labeling systems that generate a detectable colorimetric signal or light when exposed to substrate; and fluorescent labels.

Where recombinant DNA technology is used to produce the differentially expressed gene protein for such assay systems, it can be advantageous to engineer fusion proteins that can facilitate labeling, solubility, immobilization and/or detection.

Indirect labeling involves the use of a third protein, such as a labeled antibody, which specifically binds to either a differentially expressed gene product. Such antibodies include but are not limited to polyclonal, monoclonal, chimeric, single chain, Fab fragments and fragments produced by a Fab expression library.

B. Antibodies Specific for Differentially Expressed Gene Products

Described below are methods to produce antibodies capable of specifically recognizing one or more differentially expressed gene products. These antibodies can include, but are not limited to, polyclonal antibodies, monoclonal antibodies (mAbs) , humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab')₂ fragments, fragments produced by an Fab expression library, anti-idiotypic (anti-Id) antibodies, and epitope-binding fragments of any of the above. The antibodies can be used, for example, to detect a fingerprint or target gene product in a biological sample, or, alternatively, to inhibit abnormal target gene activity. Thus, such antibodies can be used in treatment methods or as part of diagnostic techniques whereby patients can be tested for abnormal levels of fingerprint or target gene proteins, or for the presence of abnormal forms of the such proteins .

To produce antibodies to a differentially expressed gene, various host animals can be immunized by injection with a differentially expressed gene protein, or a portion thereof. Suitable host animals include, but are not limited to, rabbits, mice, and rats. Various adjuvants can be used to increase the immunological response, depending on the host species. These include, but are not limited to, Freund's (complete or incomplete) adjuvant, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (Bacilli Calmette-Guerin) and Corynebacterium parvum. Polyclonal antibodies are heterogeneous populations of antibody molecules derived from the sera of animals immunized with an antigen, such as a target gene product, or an antigenically functional derivative thereof. For the production of polyclonal antibodies, host animals such as those described above, can be immunized by injection with a differentially expressed gene product supplemented with adjuvants (also described above) .

Monoclonal antibodies, which are homogeneous populations of antibodies to a particular antigen, can be obtained by any technique that provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique of Kohler and Milstein, (Nature 256:495-497, 1975; and U.S. Patent No. 4,376,110), the human B-cell hybridoma technique (Kosbor et al . , Immunology Today 4:72, 1983; Cole et al . , Proc . Natl . Acad . Sci . USA 80 -. 2026 -2030 , 1983), and the BV-hybridoma technique (Cole et al . , Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., pp. 77- 96, 1985) . Antibodies useful in the methods of the invention can be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD, and any subclass thereof. The hybridoma producing a mAb of the invention can be cultivated in vi tro or in vivo . Production of high titers of mAbs in vivo makes this the presently preferred method of production.

In addition, techniques developed for the production of "chimeric antibodies" (Morrison et al . , Proc . Natl . Acad. Sci . USA 81:6851-6855, 1984; Neuberger et al . , Nature 3_12:604-608, 1984; Takeda et al . , Nature 314 : 452-454 , 1985; U.S. Patent No. 4,816,567) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region.

Alternatively, techniques described for the production of single chain antibodies (U.S. Patent

4,946,778; Bird, Science 242:423-426, 1988; Huston et al . , Proc . Natl . Acad. Sci . USA 85: 5879-5883 , 1988; and Ward et al . , Nature 334.: 544-546, 1989) and for making humanized monoclonal antibodies (U.S. Patent No. 5,225,539, which is incorporated herein by reference in its entirety) can be utilized to produce anti-differentially expressed gene product antibodies. Antibody fragments that recognize specific epitopes can be generated by known techniques. For example, such fragments include, but are not limited to: the F(ab')₂ fragments, which can be produced by pepsin digestion of the antibody molecule, and the Fab fragments, which can be generated by reducing the disulfide bridges of the F(ab')₂ fragments. Alternatively, Fab expression libraries can be constructed (Huse et al . , Science 246:1275-1281, 1989) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.

C. In vi tro and In vivo Systems for Gene Characterization

Described below are in vi tro and in vivo systems that can be used to further characterize differentially expressed genes. These systems can also be used as part of a screening strategy to identify compounds that are capable of preventing or ameliorating symptoms of agranulocytosis.

Thus, these systems can be used to identify drugs, pharmaceutical agents, therapies, and interventions that can effectively treat agranulocytosis and to determine the in vivo efficacy of drugs, pharmaceutical agents, therapies, interventions, and the like.

1. In Vi tro Systems Cells that contain and express target gene sequences and exhibit cellular phenotypes associated with bone marrow stem cells or their progeny (particularly granulocytes) , can be used to identify compounds useful in treating or preventing agranulocytosis.

Further, the fingerprint gene expression pattern in cells affected by agranulocytosis can be analyzed and compared with that in "normal" (or unaffected) cells such as healthy bone marrow stem cells or neutrophils. Compounds that cause cells to exhibit the cellular phenotype of, for example, a neutrophil by producing a fingerprint pattern that more closely resembles that of a normal neutrophil are candidate therapeutic compounds and should be tested further for an ability to ameliorate the symptoms of agranulocytosis.

Cells that will be utilized for such assays can, for example, include HL-60 cells. Alternatively, bone marrow stem cells or their progeny derived from either transgenic or non- ransgenic animals can be used, as can recombinant cells or cells derived from transgenic cell lines. For examples of techniques that can be used to derive a continuous cell line from a transgenic animal, see Small et al . (Mol . Cell Biol . 5:642-648, 1985).

Alternatively, cells affected by agranulocytosis can be transfected with sequences capable of increasing or decreasing the amount of target gene expression within the cell. For example, target gene sequences can be introduced into, and overexpressed in, the genome of the cell of interest, or, if endogenous target gene sequences are present, they can either be overexpressed or, alternatively, be disrupted in order to underexpress or inactivate target gene expression.

To overexpress a target gene sequence, the coding portion of the target gene sequence can be ligated to a regulatory sequence that is capable of driving gene expression in the cell type of interest. Regulatory regions will be well known to those of ordinary skill in the art.

For underexpression of an endogenous target gene sequence, the sequence can be isolated and engineered such that, when reintroduced into the genome of the cell type of interest, the endogenous target gene alleles will be inactivated. Preferably, the engineered target gene sequence is introduced via gene targeting so that the endogenous target sequence is disrupted when the engineered target gene sequence is integrated into the cell's genome.

Transfection of a nucleic acid sequence that represents a target gene can be accomplished using standard techniques ( see, e . g. , Ausubel, supra) . Transfected cells should be evaluated for the presence of the recombinant target gene sequences; for expression and accumulation of target gene mRNA; and for the presence of recombinant target gene protein production. In the event a decrease in target gene expression is desired, standard techniques can be used to demonstrate that a decrease in endogenous target gene expression (or in target gene product) has indeed occurred. 2. Jn Vivo Systems In vivo systems of agranulocytosis can include recombinantly engineered transgenic animals. Recombinant animal models can be engineered by utilizing, for example, one or more target gene sequences such as those described herein in conjunction with techniques for producing transgenic animals that are well known to those of ordinary skill in the art. For example, target gene sequences can be introduced into, and overexpressed in, the genome of the animal of interest, or, alternatively, can be disrupted in order to underexpress or inactivate target gene expression. To overexpress a target gene sequence, the coding portion of the target gene sequence can be ligated to a regulatory sequence that is capable of driving gene expression in the animal and cell type of interest. Such regulatory regions will be well known to those of ordinary skill in the art. To obtain underexpression of an endogenous target gene sequence, such a sequence can be introduced into the genome of the animal of interest such that the endogenous target gene alleles will be inactivated. Preferably, an engineered sequence containing at least part of the target gene sequence is utilized and is introduced, via gene targeting, such that the endogenous target sequence is disrupted upon integration of the engineered target gene sequence into the animal's genome.

Animals of any species, including, but not limited to, mice, rats, rabbits, guinea pigs, pigs, micro-pigs, goats, and non-human primates, for example, baboons, monkeys, and chimpanzees can be used to generate animal models of agranulocytosis.

Any technique known in the art can be used to introduce a target gene transgene into animals to produce founder lines of transgenic animals. These techniques include, but are not limited to, pronuclear microinjection (Hoppe and Wagner, U.S. Pat. No. 4,873,191, 1989); retrovirus mediated gene transfer into germ lines (Van der Putten et al . , Proc . Natl . Acad . Sci . , USA 82 : 6148-6152, 1985) ; gene targeting in embryonic stem cells (Thompson et al . , Cell 5_6:313-321, 1989); electroporation of embryos (Lo, Mol . Cell . Biol . 2:1803-1814, 1983); and sperm-mediated gene transfer (Lavitrano et al . , Cell 5_7:717-723, 1989).

The present invention provides for transgenic animals that carry the transgene in all their cells, as well as animals which carry the transgene in some, but not all of their cells, i.e., mosaic animals. The transgene can be integrated, either as a single transgene or in concatamers, for example, head-to-head tandems or head-to-tail tandems. The transgene can also be selectively introduced into and activated in a particular cell type using known techniques (Lasko et al . , Proc . Natl . Acad . Sci . USA 89:6232-6236,

1992) . The regulatory sequences required for such a cell- type specific activation will depend upon the particular cell type of interest, and will be apparent to those of ordinary skill in the art.

When it is desired that the target gene transgene be integrated into the chromosomal site of the endogenous target gene, gene targeting is preferred. Briefly, when such a technique is to be utilized, vectors containing some nucleotide sequences homologous to the endogenous target gene of interest are designed for the purpose of integrating, via homologous recombination with chromosomal sequences, into and disrupting the function of, the nucleotide sequence of the endogenous target gene. The transgene can also be selectively introduced into a particular cell type, thus inactivating the endogenous gene of interest in only that cell type, by following, for example, the teaching of Gu et al . ( Science 265 : 103-106 ,

1994) . The regulatory sequences required for such a cell- type specific inactivation will depend upon the particular cell type of interest, and will be apparent to those of ordinary skill in the art. Once transgenic animals have been generated, the expression of the recombinant target gene and protein can be assayed utilizing standard techniques. Initially, Southern blot analysis or PCR techniques can be used to determine whether integration of the transgene has taken place. The level of mRNA expression of the transgene in the tissues of the transgenic animals can also be assessed using techniques that include, but are not limited to, Northern blot analysis of tissue samples obtained from the animal, in si tu hybridization analysis, and RT-coupled PCR. Samples of target gene-expressing tissue, can also be evaluated immunocytochemically using antibodies specific for the transgenic product of interest . The target gene transgenic animals that express target gene mRNA or target gene transgene peptide (detected immunocytochemically, using antibodies directed against target gene product epitopes) at easily detectable levels should then be further evaluated to identify those animals that experience agranulocytosis.

Additionally, specific cell types within the transgenic animals can be analyzed for cellular phenotypes characteristic of agranulocytosis. Such cellular phenotypes can include, for example, differential gene expression characteristic of agranulocytic cells.

Once target gene transgenic founder animals are produced ( i . e . , those animals that express target gene proteins in cells or tissues of interest, and which, preferably, exhibit agranulocytosis when the transgene is expressed or inhibited) , they can be bred, inbred, outbred, or crossbred to produce colonies of the particular animal. Examples of such breeding strategies include, but are not limited to: outbreeding of founder animals with more than one integration site in order to establish separate lines; inbreeding of separate lines in order to produce compound target gene transgenics that express the target gene transgene of interest at higher levels because of the effects of additive expression of each target gene transgene; crossing of heterozygous transgenic animals to produce animals homozygous for a given integration site in order to both augment expression and eliminate the possible need for screening of animals by DNA analysis; crossing of separate homozygous lines to produce compound heterozygous or homozygous lines; breeding animals to different inbred genetic backgrounds to examine effects of modifying alleles on expression of the target gene transgene and the development of symptoms of agranulocytosis. One such approach is to cross the target gene transgenic founder animals with a wild-type strain to produce an FI generation that exhibits symptoms of agranulocytosis. The FI generation can then be inbred in order to develop a homozygous line, if it is found that homozygous target gene transgenic animals are viable.

D. Identification of Compounds that Interact with a Target Gene Product

The following assays are designed to identify compounds that bind to a target gene product; bind to other cellular proteins that interact with a target gene product; or interfere with the interaction between a target gene product and other cellular proteins. These compounds can include, but are not limited to, other cellular proteins. Specifically, the compounds can include, but are not limited to, peptides, such as, for example, soluble peptides, including, but not limited to Ig-tailed fusion peptides that contain extracellular portions of target gene product transmembrane receptors, and members of random peptide libraries ( see, e . g. , Lam et al . , Nature 354 : 82-84, 1991; Houghton et al . , Nature 354:84-86, 1991), made of D- or L-configuration amino acids, phosphopeptides (including, but not limited to, members of random or partially degenerate phosphopeptide libraries; see, e.g., Songyang et al . , Cell 12:767-778, 1993), antibodies (including, but not limited to, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab')₂ and FAb expression library fragments, and epitope-binding fragments thereof) , and small organic or inorganic molecules.

Compounds identified via assays such as those described herein can be used, for example, to elaborate the biological function of a target gene product, and to ameliorate the signs and symptoms of agranulocytosis. For example, in instances in which agranulocytosis is associated with underexpression of a target gene product or lower target gene product activity, compounds that interact with the target gene product can include those that increase the activity of the target gene product. Such compounds would bring about an effective increase in the level of target gene activity, thus ameliorating symptoms of agranulocytosis. Conversely, in instances in which a mutation within a target gene causes aberrant target gene products that have a deleterious effect leading to agranulocytosis to be made, compounds that bind target gene product can be identified that inhibit the activity of the target gene product . i_j_ Screening Assays for Compounds and

Cellular Proteins that Bind to a Target Gene Product

In vi tro systems can be designed to identify compounds capable of binding a target gene product of the invention. The compounds identified can be useful, for example, in modulating the activity of a wild type or, preferably, mutant target gene product; elaborating the biological function of a target gene product; screening for compounds that disrupt normal target gene interactions. Alternatively, the compounds may be useful because they, themselves, disrupt such interactions.

The assays used to identify compounds that bind to a target gene product rest on the principle that one must prepare a reaction mixture of the target gene protein and the test compound under conditions and for a time sufficient to allow the two components to interact and bind, thus forming a complex that can be removed from or detected in the reaction mixture. These assays can be conducted in a variety of ways . One method involves anchoring a target gene product or the test substance onto a solid phase and detecting target gene product/test compound complexes anchored on the solid phase at the end of the reaction. In one embodiment of such a method, the target gene product can be anchored onto a solid surface, and the test compound, which is not anchored, can be labeled, either directly or indirectly.

In practice, microtiter plates can serve conveniently as the solid phase. The anchored component can be immobilized by non-covalent or covalent attachments. Non-covalent attachment can be accomplished simply by coating the solid surface with a solution of the protein and allowing it to dry. Alternatively, an immobilized antibody, preferably a monoclonal antibody that is specific for the protein to be immobilized, can be used to anchor the protein to the solid surface. The surfaces can be prepared in advance and stored.

To conduct the assay, the non-immobilized component is added to the coated surface containing the anchored

(immobilized) component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions that permit any complexes formed to remain immobilized on the solid surface. Complexes anchored to the solid surface can be detected in a number of ways. Where the previously immobilized component is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the previously non-immobilized component is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; for example, using a labeled antibody specific for the immobilized component (the antibody, in turn, can be directly labeled or indirectly labeled with an anti-Ig antibody) . Alternatively, a reaction can be conducted in a liquid phase, the reaction products separated from unreacted components, and complexes detected. For example, one can use an immobilized antibody specific for a target gene or the test compound to anchor any complexes formed in solution, and a labeled antibody specific for the other component of the possible complex to detect anchored complexes .

Any method suitable for detecting protein-protein interactions can be employed for identifying novel target product-cellular or extracellular protein interactions. In such a case, the target gene serves as the known "bait" gene.

2. Assays for Compounds that Interfere with the Binding of a Target Gene

Product to a Second Cellular Protein

The target gene products of the invention can interact with one or more cellular or extracellular macromolecules (referred to herein as "binding partners"), such as proteins, in vivo . Compounds that disrupt such interactions can be used to regulate the activity of the target gene product, especially a mutant target gene product. Useful compounds include, but are not limited to, molecules such as antibodies, peptides, and small molecules. The assay systems used to identify compounds that interfere with the interaction between the target gene product and its cellular or extracellular binding partner (s) rests on the principle that a reaction mixture will contain the target gene product and the binding partner under conditions and for a time sufficient to allow the two products to interact and bind, thus forming a complex. To test a compound for inhibitory activity, the reaction mixture is prepared in the presence and absence of the test compound. The test compound can be initially included in the reaction mixture, or can be added afterward (i.e., after the addition of the target gene product and its cellular or extracellular binding partner) . Control reaction mixtures are incubated without the test compound or with a placebo. Any complexes that form between the target gene product and the cellular or extracellular binding partner are then detected. The formation of a complex in the control reaction, but not in the reaction mixture containing the test compound, indicates that the compound interferes with the interaction of the target gene product and the interactive binding partner. Complexes within reaction mixtures containing the test compound and normal target gene product can also be compared to complexes within reaction mixtures containing the test compound and a mutant target gene product . This comparison can be important in cases where it is desirable to identify compounds that disrupt an interaction of a mutant, but not a normal, target gene product . The assay for compounds that interfere with the interaction of a target gene product and a binding partner can be conducted in a heterogeneous or homogeneous format . Heterogeneous assays involve anchoring either the target gene product or the binding partner onto a solid phase and detecting complexes anchored on the solid phase at the end of the reaction. In homogeneous assays, the entire reaction is carried out in a liquid phase. In either approach, the order of addition of reactants can be varied to obtain different information about the compounds being tested. For example, test compounds that interfere with the interaction between a target gene product and a binding partner, for example, by competition, can be identified by conducting the reaction in the presence of the test substance; i.e., by adding the test substance to the reaction mixture prior to or simultaneously with the target gene product and the interactive cellular or extracellular binding partner. Alternatively, test compounds that disrupt preformed complexes, for example, compounds with higher binding constants that displace one of the components from the complex, can be tested by adding the test compound to the reaction mixture after complexes have been formed. The various formats are described briefly below. In a heterogeneous assay system, either the target gene product or the interactive cellular or extracellular binding partner, is anchored onto a solid surface, while the non-anchored species is labeled, either directly or indirectly. In practice, microtiter plates are conveniently used. The anchored species can be immobilized by non- covalent or covalent attachments. Non-covalent attachment can be accomplished simply by coating the solid surface with a solution of the target gene product or binding partner and drying. Alternatively, an immobilized antibody specific for the species to be anchored can be used to anchor the species to the solid surface. The surfaces can be prepared in advance and stored.

To conduct the assay, the partner of the immobilized species is exposed to the coated surface with or without the test compound. After the reaction is complete, unreacted components are removed ( e . g. , by washing) and any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the non-immobilized species is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the non-immobilized species is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e. g. , using a labeled antibody specific for the initially non- immobilized species (the antibody, in turn, can be directly labeled or indirectly labeled with a labeled anti-Ig antibody) . Depending upon the order of addition of reaction components, test compounds that inhibit complex formation or that disrupt preformed complexes can be detected.

Alternatively, the reaction can be conducted in a liquid phase in the presence or absence of the test compound, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for one of the binding components to anchor any complexes formed in solution, and a labeled antibody specific for the other partner to detect anchored complexes. Again, depending upon the order of addition of reactants to the liquid phase, test compounds which inhibit complex or which disrupt preformed complexes can be identified.

In an alternate embodiment of the invention, a homogeneous assay can be used. In this approach, a preformed complex of target gene product and interactive cellular or extracellular binding partner product is prepared in which either the target gene product or the binding partner is labeled, but the signal generated by the label is quenched due to complex formation (see, e.g., U.S. Patent No. 4,109,496 which utilizes this approach for immunoassays) . The addition of a test substance that competes with and displaces one of the species from the preformed complex will result in the generation of a signal above background. In this way, test substances that disrupt target gene product-cellular or extracellular binding partner interaction can be identified. In a particular embodiment, the target gene product can be prepared for immobilization using recombinant DNA techniques. For example, the target gene coding region can be fused to a glutathione-S-transferase (GST) gene using a fusion vector such as pGEX-5X-l, in such a manner that its binding activity is maintained in the resulting fusion product. The interactive cellular or extracellular product can be purified and used to raise a monoclonal antibody, using methods routinely practiced in the art. This antibody can be labeled with the radioactive isotope ^12SI, for example, by methods routinely practiced in the art. In a heterogeneous assay, for example, the GST-Target gene fusion product can be anchored to glutathione-agarose beads. The interactive cellular or extracellular binding partner product can then be added in the presence or absence of the test compound in a manner that allows interaction and binding to occur. At the end of the reaction period, unbound material can be washed away, and the labeled monoclonal antibody can be added to the system and allowed to bind to the complexed components. The interaction between the target gene product and the interactive cellular or extracellular binding partner can be detected by measuring the amount of radioactivity that remains associated with the glutathione-agarose beads. A successful inhibition of the interaction by the test compound will result in a decrease in measured radioactivity.

Alternatively, the GST-target gene fusion product and the interactive cellular or extracellular binding partner product can be mixed together in liquid in the absence of the solid glutathione-agarose beads. The test compound can be added either during or after the binding partners are allowed to interact. This mixture can then be added to the glutathione-agarose beads and unbound material is washed away. Again the extent of inhibition of the binding partner interaction can be detected by adding the labeled antibody and measuring the radioactivity associated with the beads. These same techniques can be employed using peptide fragments that correspond to the binding domains of the target gene product and the interactive cellular or extracellular binding partner (in case where the binding partner is a product) , in place of one or both of the full length products. Any number of methods routinely practiced in the art can be used to identify and isolate the protein' s binding site. These methods include, but are not limited to, mutagenesis of one of the genes encoding one of the products and screening for disruption of binding in a co- immunoprecipitation assay. Compensating mutations in the gene encoding the second species in the complex can be selected. Sequence analysis of the genes encoding the respective products will reveal the mutations that correspond to the region of the product involved in interactive binding. Alternatively, one product can be anchored to a solid surface using methods described above, and allowed to interact with and bind to its labeled binding partner, which has been treated with a proteolytic enzyme, such as trypsin. After washing, a short, labeled peptide comprising the binding domain can remain associated with the solid material, which can be isolated and identified by amino acid sequencing. Also, once the gene coding for the cellular or extracellular binding partner product is obtained, short gene segments can be engineered to express peptide fragments of the product, which can then be tested for binding activity and purified or synthesized. V. Identification of Differentially Expressed Genes

Expression of the genes described in the Tables presented herein, their human homologues, or additional sequence-variant or differentially expressed genes (the additional genes being identified in the same manner as those described in the Tables presented herein) can be assessed by one or more of the following methods, or by the methods described in the Examples that follow. Differential expression refers to quantitative or qualitative differences in the expression pattern of a gene or a group of genes. Thus, a differentially expressed gene can be a gene whose expression is quantitatively increased or decreased in, for example, clozapine-treated bone marrow cells relative to untreated cells or cells that have been treated with an agent that is similar to clozapine but does not cause agranulocytosis .

In some cases, the difference in expression between treated and untreated (control) cells may be qualitative rather than quantitative. Thus, the expression of a selected gene can be detected using a certain method to assay the activity of the gene product, which may be apparent in the presence of a given drug and undetectable using the same assay in the absence of the drug. Conversely, the activity of the gene product may be undetectable in the presence of a given drug and readily apparent in its absence.

As an alternative to "all-or-none" differences in gene expression (detectable expression versus undetectable expression) , a differentially expressed gene can exhibit an expression level that simply differs, i.e., is quantitatively increased or decreased in treated cells versus control cells. The degree to which expression differs need only be large enough to be visualized via standard techniques for characterizing gene expression, such as, for example, a differential display technique. Other standard and well-known techniques for assessing differences in gene expression include, but are not limited to, quantitative reverse transcriptase (RT) -coupled PCR,

Northern analyses, RNAse protection analyses, and methods that employ arrays of nucleic acid molecules, e.g., cDNAs linked to a solid support, e.g., a Gene Expression Micro-Array™ (Synteni, Inc.; Fremont, CA) . In addition, gene expression can be assessed using the Perkin-Elmer/ABI 7700 Sequence Detection System, which employs TaqMan™ technology. Briefly, TaqMan technology relies on standard RT-PCR with the addition of a third gene- specific oligonucleotide (referred to as a probe) which has a fluorescent dye coupled to its 5' end (typically, 6-FAM) and a quenching dye at the 3' end (typically, TAMRA) . When the fluorescently tagged oligonucleotide is intact, the fluorescent signal from the 5' dye is quenched. As PCR proceeds, the 5' to 3 ' nucleolytic activity of taq polymerase digests the labeled primer, producing a free nucleotide labeled with 6-FAM, which is now detected as a fluorescent signal. The PCR cycle where fluorescence is first released and detected is directly proportional to the starting amount of the gene of interest in the test sample, thus providing a way of quantitating the initial template concentration. Samples can be internally controlled by the addition of a second set of primers/probe specific for a housekeeping gene such as GADPH, which has been labeled with a different fluorophor on the 5' end (typically, JOE) . A__^ Paradigms to Identify Differentially

Expressed Genes

A variety of paradigms can be used to identify differentially expressed genes. In all of these, drug- treated cells are compared with untreated cells (or cells that have been treated with different drugs, preferably, drugs that are of the same or similar type but that do not affect gene expression) . The paradigms can differ in that the cells being tested or examined can be cells of a cell line, e.g., DI or HL-60 cells (an " in vi tro paradigm"); or cells within or obtained from an animal that has agranulocytosis (an " in vivo paradigm"); or white blood cells or bone marrow cells from human patients that have agranulocytosis (a "clinical paradigm").

Stromal cell clones useful in the invention include those described by Friedrich et al . (Blood 87 : 4596-4606 , 1996; see also Aiuti et al . , Experimental Hematol . 26 : 1-15 , 1998, both of which are hereby incorporated by reference in their entirety) . Those of ordinary skill in the art are well able to culture these and similar cell types. If guidance is required, one may consult, for example, Dexter et al . J. Cell Physiol . 91:335-344, 1976). HL-60 cells are commonly used and can be obtained from the American Type Culture Collection (Manassas, VA; Accession No. CCL-240) .

Once a particular differentially expressed gene has been examined in one paradigm, its sequence or expression pattern can be studied in a different paradigm. A gene may exhibit one pattern of differential expression in a first paradigm, and another pattern of differential expression in a second paradigm. Therefore, using multiple paradigms can help distinguish the roles and relative importance of particular genes in agranulocytosis. For example, if one finds that a given gene is differentially regulated in a consistent manner, whether the cell being examined is a cell of a cell line or obtained from a patient, then that gene is more likely to play an active role in the development of agranulocytosis . In an in vi tro paradigm, differentially expressed genes can be detected by comparing the pattern of gene expression in the experimental (drug-treated) leukocytes (or their precursors) in culture with that in control cells (e.g., leukocytes that are cultured under essentially the same conditions but have not been drug-treated or that have been treated with a different drug, as described above) .

In the in vivo paradigm, laboratory animals can be used to discover differentially expressed genes and to examine their sequence. This paradigm is described further below.

In the clinical paradigm, samples from the bone marrow, liver, or peripheral blood are used. Such specimens can represent normal tissue, or any stage in the development of agranulocytosis (see Uetrecht, supra, for a description of the stages of agranulocytosis). Samples of tissue, e . g. , bone marrow, can be procured by standard techniques and, if necessary, frozen and stored in liquid nitrogen (see, e.g., Basic Cell Culture Protocols, 2nd Ed., Pollard, J. and Walker, J. , Eds., Ch. 16 and 19).

Nucleic acids can be isolated from the samples by routine techniques. For example, RNA can be isolated by differential centrifugation of homogenized tissue, and analyzed for differential expression relative to expression in other samples. Preferably, these other samples will consist of cells obtained from the same patient at a different time, e.g., before drug treatment, during treatment with a different drug, or at an earlier time during treatment with the same drug. B__J_ Methods for Identifying Differentially

Expressed Genes

To identify differentially expressed genes, RNA (either total RNA or mRNA) can be isolated from cells and analyzed in paradigms such as those described above. Any RNA isolation technique that does not select against the isolation of mRNA can be used to purify RNA from a biological sample ( see, e. g. , Ausubel et al . , Eds., 1987- 1997, Current Protocols in Molecular Biology, John Wiley & Sons, Inc., New York). Additionally, large numbers of tissue samples can readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski (U.S. Patent No. 4,843,155).

Transcripts within the collected RNA samples, which represent differentially expressed genes, can be identified using a variety of methods that are well known to those of ordinary skill in the art. These methods include differential screening (Tedder et al . , Proc. Natl . Acad . Sci . USA 85:208-212, 1988), subtractive hybridization (Hedrick et al . , Nature 308.: 149-153 , 1984; Lee et al . , Proc . Na tl . Acad . Sci . USA 88 : 2825 , 1984), and, preferably, differential display (Liang and Pardee, U.S. Patent No. 5,262,311) .

Differential screening involves duplicate screening of a cDNA library: one copy of the library is screened with a total cell cDNA probe corresponding to the mRNA population of a first sample and a second copy of the cDNA library is screened with a total cell cDNA probe corresponding to the mRNA population of a second sample. For example, one cDNA probe can correspond to the total cell cDNA from a cell or tissue that represents the experimental (e.g., drug-treated) sample, while the second cDNA probe can correspond to the total cell cDNA from a cell or tissue that represents the control sample. The clones that hybridize to one probe but not to the other represent, at least potentially, clones derived from genes that are differentially expressed in the cell of interest, relative to control.

Subtractive hybridization techniques generally involve: isolation of mRNA obtained from two different sources, e.g., treated and untreated cells; hybridization of the mRNA or single-stranded cDNA reverse-transcribed from the isolated mRNA; and removal of all hybridized, and therefore double-stranded, sequences. The remaining non- hybridized, single-stranded cDNAs, represent clones derived from genes that are, at least potentially, differentially expressed in the two mRNA sources. The single-stranded cDNAs are then used to construct a library containing clones derived from differentially expressed genes.

Differential display is a procedure that, utilizing the well-known polymerase chain reaction (PCR) , allows one to identify sequences derived from genes that are differentially expressed (the experimental embodiment of PCR is set forth in Mullis, U.S. Patent No. 4,683,202). To begin, isolated RNA is reverse-transcribed into single- stranded cDNA by standard techniques that are well known to those of ordinary skill in the art. Primers for the reverse transcriptase reaction can include, but are not limited to, oligo dT-containing primers, preferably of the 3' primer type of oligonucleotide described below. Next, pairs of PCR primers, as described below, are used to amplify clones representing a random subset of the RNA transcripts present within any given cell. Utilizing different pairs of primers allows each of the mRNA transcripts present in a cell to be amplified. One can then identify, from among the amplified transcripts, those that have been produced from differentially expressed genes.

The 3' oligonucleotide primers of the primer pairs can contain an oligo-dT stretch of 10-13 dT nucleotides (preferably, 11 dT nucleotides) at their 5' ends, which will hybridize to the poly (A) tails of mRNAs or to the complement of cDNAs reverse transcribed from mRNA poly (A) tails. To increase the specificity of the 3' primer, it can contain one or more (preferably, two) additional nucleotides at its 3' end. Because, statistically, only a subset of the mRNA derived sequences present in the sample of interest will hybridize to such primers, the additional nucleotides allow the primers to amplify only a subset of the mRNA derived sequences present in the sample of interest. This is preferable because it allows more accurate characterization of each of the bands representing amplified sequences.

The 5' oligonucleotide primers of the primer pairs can contain nucleotide sequences expected, statistically, to hybridize to cDNA sequences derived from the tissues of interest. The sequences of these primers can be arbitrary, and their length can vary, for example, from about 9 to about 15 nucleotides. Preferably, the primers will contain 13 nucleotides. Due to the arbitrary nature of the 5' primers (which anneal randomly along the target sequence) , the partial cDNAs that are thereby amplified are of variable length and can be separated by standard denaturing sequencing gel electrophoresis. Moreover, the conditions under which the PCR is performed can be selected to optimize the yield of the amplified products and their lengths. The way in which reaction conditions (including the temperature at which primers are allowed to anneal to their targets and the time permitted for elongation of the intervening sequence) are well known to those of ordinary skill in the art.

The clones that result from reverse transcription and amplification of the mRNA of two different cell types can be displayed via sequencing gel electrophoresis and compared. Differences in the two banding patterns represent genes that are potentially differentially expressed. One can then perform further tests to corroborate differential expression. For example, one can perform well known techniques such as Northern blot analysis, quantitative RT- coupled PCR, or RNAase protection assays.

Upon corroboration, differentially expressed genes can be further characterized and referred to as target genes or fingerprint genes with confidence. Once obtained, the sequences of differentially expressed genes can be used to isolate full length clones of the corresponding genes. The full-length coding portion of a gene can be isolated without undue experimentation by molecular biological techniques well known in the art. For example, the amplified fragment representing a differentially expressed gene can be isolated, labeled, and used as a probe to screen either a cDNA library or a genomic library.

PCR technology can also be used to isolate full- length cDNA sequences. Amplified gene fragments that are about at least 10 nucleotides long (and preferably longer, e.g., about 15 nucleotides long), and that were obtained through differential display, have their 5' terminal ends at some random point within the gene and their 3 ' terminal ends at the 3' end of the transcribed portion of the gene. Once nucleotide sequence information is obtained from an amplified fragment, the remainder of the gene (i.e., the 5' end of the gene, when utilizing differential display) can be obtained using, for example, RT-PCR. A reverse transcription reaction can be performed on the RNA using an oligonucleotide primer (complementary to the mRNA that corresponds to the amplified cloned fragment) to prime first strand synthesis. Because the primer is anti-parallel to the mRNA, extension will proceed toward the 5' end of the mRNA. The resulting RNA/DNA hybrid can then be "tailed" with guanines using a standard terminal transferase reaction, the hybrid can be digested with RNAase H, and second strand synthesis can be primed with a poly-C primer. Using the two primers, the 5' portion of the gene is then amplified using PCR. Sequences obtained can then be isolated and recombined with those isolated previously to generate a full-length cDNA of the differentially expressed gene. For a review of cloning strategies and recombinant DNA techniques that can be used in the context of the present invention, see, e . g. , Sambrook et al . , 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; and Ausubel et al . , supra .

VI . Treatment of Agranulocytosis by Modulating

Differentially Expressed Genes or their Products

Agranulocytosis can be treated by modulating the expression of a target gene or the activity of a target gene product. The modulation can be of a positive or negative nature, depending on the specific situation involved, but each modulatory event yields a net result in which the signs and symptoms of agranulocytosis are ameliorated.

"Negative modulation, " refers to a reduction in the level and/or activity of target gene product relative to the level and/or activity of the target gene product in the absence of the modulatory treatment.

"Positive modulation, " refers to an increase in the level and/or activity of target gene product relative to the level and/or activity of target gene product in the absence of modulatory treatment.

It is possible that agranulocytosis can be caused, at least in part, by an abnormal level of a target gene product , or by the presence of a target gene product exhibiting abnormal activity. As such, the reduction in the level and/or activity of the target gene product would bring about the amelioration of the signs and symptoms of agranulocytosis.

Alternatively, it is possible that agranulocytosis can be brought about, at least in part, by the absence or reduction of the level of expression of a target, or a reduction in the level of activity of a target gene product. As such, an increase in the level of target gene expression and/or the activity of target gene product would bring about the amelioration of the signs or symptoms of agranulocytosis .

A. Negative Modulatory Techniques As discussed, above, successful treatment of agranulocytosis can be brought about by techniques that serve to inhibit the expression or activity of target gene products .

For example, compounds such as those identified using an assay described above, which exhibit negative modulatory activity, can be used in accordance with the invention to prevent and/or ameliorate the signs and symptoms of agranulocytosis. These molecules can include, but are not limited to, peptides, phosphopeptides, small organic or inorganic molecules, and antibodies (including, e.g., polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab')₂ and FAb expression library fragments, and epitope-binding fragments thereof) . Further, antisense and ribozyme molecules that inhibit expression of the target gene can also be used in accordance with the invention to reduce the level of target gene expression and, thereby, effectively reduce the level of target gene activity. Still further, triple helix molecules can be utilized to reduce the level of target gene activity.

Among the compounds that can exhibit an ability to prevent and/or ameliorate the signs and symptoms of agranulocytosis are antisense, ribozyme, and triple helix molecules. These molecules can be designed to reduce or inhibit either wild type, or where appropriate, mutant target gene activity. Techniques for the production and use of such molecules are well known to those of ordinary skill in the art .

Antisense RNA and DNA molecules act to directly block the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation. With respect to antisense DNA, oligodeoxyribonucleotides derived from the translation initiation site, for example, between the -10 and +10 regions of the target gene nucleotide sequence of interest, are preferred.

Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. (For a review, see, for example, Rossi, Current Biology 4.:469-471, 1994) . The mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by a endonucleolytic cleavage. The composition of ribozyme molecules must include one or more sequences complementary to the target gene mRNA and must include the well-known catalytic sequence responsible for mRNA cleavage. For this sequence, see U.S. Patent No. 5,093,246, which is incorporated by reference herein in its entirety. As such, within the scope of the invention are engineered hammerhead motif ribozyme molecules that specifically and efficiently catalyze endonucleolytic cleavage of RNA sequences encoding target gene proteins. Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the molecule of interest for ribozyme cleavage sites which include the following sequences, GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target gene containing the cleavage site can be evaluated for predicted structural features, such as secondary structure, which can render the oligonucleotide sequence unsuitable. The suitability of candidate sequences can also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.

Nucleic acid molecules to be used in triplex helix formation (to inhibit transcription) should be single stranded and composed of deoxynucleotides . The base composition of these oligonucleotides must be designed to promote triple helix formation via Hoogsteen base pairing rules, which generally require sizeable stretches of either purines or pyrimidines to be present on one strand of a duplex. Nucleotide sequences can be pyrimidine-based, which will result in TAT and CGC* triplets across the three associated strands of the resulting triple helix. The pyrimidine-rich molecules provide base complementarily to a purine-rich region of a single strand of the duplex in a parallel orientation to that strand. In addition, nucleic acid molecules can be chosen that are purine-rich, for example, contain a stretch of G residues. These molecules will form a triple helix with a DNA duplex that is rich in GC pairs, in which the majority of the purine residues are located on a single strand of the targeted duplex, resulting in GGC triplets across the three strands in the triplex. Alternatively, the potential sequences that can be targeted for triple helix formation can be increased by creating a so called "switchback" nucleic acid molecule. Switchback molecules are synthesized in an alternating 5' -3', 3' -5' manner, such that they base pair with first one strand of a duplex and then the other, eliminating the necessity for a sizeable stretch of either purines or pyrimidines to be present on one strand of a duplex.

In instances where the antisense, ribozyme, or triple helix molecules described herein are utilized to reduce or inhibit mutant gene expression, it is possible that the technique utilized can also efficiently reduce or inhibit the transcription (triple helix) or translation (antisense, ribozyme) of mRNA produced by normal target gene alleles such that the possibility can arise wherein the concentration of normal target gene product present can be lower than is necessary for a normal phenotype. In such cases, to ensure that substantially normal levels of target gene activity are maintained, nucleic acid molecules that encode and express target gene polypeptides exhibiting normal target gene product activity can be introduced into cells via gene therapy method. Alternatively, in instances in which the target gene encodes an extracellular protein, it can be preferable to co-administer normal target gene protein into the cell or tissue in order to maintain the requisite level of cellular or tissue target gene activity.

Anti -sense RNA and DNA, ribozyme and triple helix molecules of the invention can be prepared by any method known in the art for the synthesis of DNA and RNA molecules. These include techniques for chemically synthesizing oligodeoxyribonucleotides and oligoribonucleotides well known in the art such as, for example, solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules can be generated by in vi tro and in vivo transcription of DNA sequences encoding the antisense RNA molecule. Such DNA sequences can be incorporated into a wide variety of vectors which incorporate suitable RNA polymerase promoters such as the T7 or SP6 polymerase promoters. Alternatively, antisense cDNA constructs that synthesize antisense RNA constitutively or inducibly, depending on the promoter used, can be introduced stably into cell lines. Various well-known modifications to the DNA molecules can be introduced as a means of increasing intracellular stability and half-life. Possible modifications include but are not limited to the addition of flanking sequences of ribo- or deoxy- nucleotides to the 5' or 3 ' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the oligodeoxyribonucleotide backbone.

Antibodies can be generated which are both specific for a target gene product and which reduce the activity of the target gene product. Such antibodies may, therefore, by administered in instances whereby negative modulatory techniques are appropriate for the treatment of agranulocytosis. Antibodies can be generated using standard techniques against the proteins themselves or against peptides corresponding to portions of the proteins. The antibodies include but are not limited to polyclonal, monoclonal, Fab fragments, single chain antibodies, chimeric antibodies, and the like.

In instances where the target gene protein to which the antibody is directed is intracellular and whole antibodies are used, internalizing antibodies can be preferred. However, lipofectin or liposomes can be used to deliver the antibody or a fragment of the Fab region which binds to the target gene epitope into cells. Where fragments of the antibody are used, the smallest inhibitory fragment which binds to the target protein's binding domain is preferred. For example, peptides having an amino acid sequence corresponding to the domain of the variable region of the antibody that binds to the target gene protein can be used. Such peptides can be synthesized chemically or produced via recombinant DNA technology using methods well known in the art (e.g., see Creighton, 1983, supra; and Sambrook et al . , 1989, supra) . Alternatively, single chain neutralizing antibodies which bind to intracellular target gene product epitopes can also be administered. Such single chain antibodies can be administered, for example, by expressing nucleotide sequences encoding single-chain antibodies within the target cell population by utilizing, for example, techniques such as those described in Marasco et al . ( Proc . Natl . Acad . Sci . USA 90 : 7889-7893 , 1993). B. Positive modulatory techniques As discussed above, successful treatment of the signs and symptoms of agranulocytosis can be brought about by techniques that serve to increase the level of target gene expression or to increase the activity of target gene product .

For example, compounds, e.g., compounds identified through assays described, which prove to exhibit positive modulatory activity can be used in accordance with the invention to ameliorate the signs and symptoms of agranulocytosis. Such molecules can include, but are not limited to, peptides, phosphopeptides, small organic or inorganic molecules, or antibodies (including, for example, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab')₂ and FAb expression library fragments, and epitope-binding fragments thereof) .

For example, a target gene protein, at a level sufficient to ameliorate the signs and symptoms of agranulocytosis can be administered to a patient exhibiting such symptoms. One of skill in the art will readily know how to determine the concentration of effective, non-toxic doses of the normal target gene protein.

In instances wherein the compound to be administered is a peptide compound, DNA sequences encoding the peptide compound can, alternatively, be directly administered to a patient exhibiting the signs and symptoms of agranulocytosis, at a concentration sufficient to generate the production of an amount of target gene product adequate to ameliorate the signs and symptoms of agranulocytosis. The DNA molecules can be produced, for example, by well- known recombinant techniques .

In the case of peptide compounds that act extracellularly, the DNA molecules encoding such peptides can be taken up and expressed by any cell type, so long as a sufficient circulating concentration of peptide results for the elicitation of a reduction in the signs and symptoms of agranulocytosis. In the case of compounds that act intracellularly, the DNA molecules encoding such peptides must be taken up and expressed by cells involved in agranulocytosis at a sufficient level to bring about the reduction of the signs and symptoms of agranulocytosis.

Any technique that serves to selectively administer DNA molecules to any granulocyte affected by agranulocytosis is, therefore, preferred for the DNA molecules encoding intracellularly acting peptides. VII . Therapeutic Treatment

The identified compounds that modify ( i . e. , inhibit or stimulate) target gene expression or target gene product activity can be administered to a patient at therapeutically effective doses to prevent, treat or ameliorate agranulocytosis. A therapeutically effective dose refers to that amount of the compound sufficient to result in amelioration of the symptoms of agranulocytosis. A. Effective Dose Toxicity and therapeutic efficacy of such modulatory compounds can be determined by standard pharmaceutical procedures carried out in cell culture or in experimental animals. For example, it is routine in the art to determine the LD₅₀ (the dose of a compound that is lethal to 50% of the population) and the ED_S0 (the dose of a compound that is therapeutically effective in 50% of the population) . The dose ratio between toxic and therapeutic effects is the therapeutic index, which is expressed as the ratio LD_S0/ED_S0. Compounds that exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects can be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects. The data obtained from cell culture assays and animal studies can be used to formulate a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED_S0 with little or no toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration. For any compound used in a method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays . A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC₅₀ (i.e., the concentration of the test compound that achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma can be measured, for example, by high performance liquid chromatography. B . Formulations and Use Pharmaceutical compositions for use in accordance with the present invention can be formulated in a conventional manner using one or more physiologically acceptable carriers or excipients. Thus, the compounds and their physiologically acceptable salts and solvates can be formulated for administration by inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral, or rectal administration.

For oral administration, the pharmaceutical compositions can take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose) ; fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulphate) . The tablets can be coated by methods well known in the art. Liquid preparations for oral administration can take the form of, for example, solutions, syrups, or suspensions, or they can be presented as a dry product for constitution with water, or any other suitable vehicle, before use. Such liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non- aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetable oils) ; and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations can also contain buffer salts, flavoring, coloring and sweetening agents as appropriate. Preparations for oral administration can be suitably formulated to give controlled release of the active compound .

For buccal administration, the compositions can take the form of tablets or lozenges formulated in conventional manner.

For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or any other suitable gas. In the case of a pressurized aerosol, the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, for example, gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

The compounds can be formulated for parenteral administration by injection, for example, by bolus injection or continuous infusion. Formulations for injection can be presented in unit dosage form, for example, in ampoules or in multi-dose containers, with an added preservative. The compositions can take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles, and can contain formulatory agents such as suspending, stabilizing, or dispersing agents. Alternatively, the active ingredient can be in powder form for constitution with a suitable vehicle, for example, sterile pyrogen-free water, before use.

The compounds can also be formulated in rectal compositions such as suppositories or retention enemas, for example, containing conventional suppository bases such as cocoa butter or other glycerides .

In addition to the formulations described previously, the compounds can also be formulated as a depot preparation. Such long acting formulations can be administered by implantation (e.g., subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds can be formulated with suitable polymeric or hydrophobic materials (e.g., as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

The compositions can, if desired, be presented in a pack or dispenser device that can contain one or more unit dosage forms containing the active ingredient . The pack can, for example, contain metal or plastic foil, such as a blister pack. The pack or dispenser device can be accompanied by instructions for administration.

EXAMPLES Experiments that were performed to detect genes that are differentially expressed in clozapine-treated cells are described below. The experiments were carried out in HL-60 cells and, separately, in DI cells. Cell culture: The HL-60 cells were cultured in RPMI 60 Media with 20% fetal bovine serum (FBS) (available from GibcoBRL #11875 and Sigma Chemical Co. #F-4135, respectively) . The DI cells were cultured in IMDM (Iscove's medium) with 10% FBS, 2 mM L-glutamine, 50 μM

2-mercaptoethanol and 20 U/ml recombinant mouse IFNγ .

Drug preparation: A 100 mg table of clozapine was ground up, and suspended in 100 ml 100% ethanol. The concentration of the stock used for treatment was 100 ng/ml. Olanzapine was also suspended in 100% ethanol, and the concentration of the stock used for treatment was 10 ng/ml.

Drug application: HL-60 cells were harvested, centrifuged to form a pellet, and resuspended in fresh medium with either clozapine or olanzapine to 2 x 10^s cells/ml. The cells were split and fresh, drug-containing medium was applied after 48 hours. The total treatment time was 96 hours. DI cells (murine BMSC) were seeded at 50% confluency (approximately 1.1 x 10⁴ cells/cm²) and allowed to adhere to the culture flask overnight. Drug treatment was then begun and continued for 96 hours. At the conclusion of the treatment period, cells were harvested and pelleted in preparation for RΝA extraction.

Time Course Experiments: In some experiments, cells were harvested after shorter treatment intervals, i.e., after 12, 24, 48, and 72 hours of exposure to clozapine or olanzapine.

A. Example 1: Genes That are Upregulated in the Presence of Clozapine

Table 1 describes genes whose expression was found to be greater in clozapine-treated DI cells than in untreated DI cells, or DI cells treated with olanzapine. TABLE 1

Table 3 describes genes whose expression was found to be greater in clozapine-treated HL-60 cells than in untreated HL-60 cells.

TABLE 3

Appendix A is a list of genes whose expression is higher in clozapine-treated DI cells than in untreated DI cells or olanzapine-treated DI cells (or both) . For each gene, the normalized level of expression in untreated, clozapine-treated, or olanzapine-treated cells is listed along with the Genbank Accession number, an identifier (gene name) and gene description. Also listed is the ratio of expression in cells subjected to various treatments.

The genes in the first group are expressed at a higher level in clozapine-treated cells than olanzapine- treated cells or untreated cells. These genes are potentially associated with agranulocytosis because increased expression is associated with clozapine, a drug associated with agranulocytosis, but not with olanzapine, a drug that is not associated with agranulocytosis, or no treatment .

The genes in the second group are expressed at a higher level in clozapine-treated or olanzapine-treated cells than in untreated cells. These genes are unlikely to be associated with agranulocytosis because increased expression is associated with both clozapine, a drug that is associated with agranulocytosis, and olanzapine, a drug that is not associated with agranulocytosis.

The genes in the third group are expressed at a higher level in clozapine-treated cells than olanzapine- treated cells. These genes are potentially associated with agranulocytosis because increased expression is associated with clozapine, a drug associated with agranulocytosis, but not olanzapine, a drug that is not associated with agranulocytosis.

The genes in the fourth group are expressed at a higher level in clozapine-treated cells than in untreated cells. These genes are potentially associated with agranulocytosis because increased expression is associated with clozapine, a drug associated with agranulocytosis, but not associated with "no treatment."

Whether altered expression or activity of a particular sequence polymorphism in any of the genes listed in Table 1, Table 3, or Appendix A is tightly associated with agranulocytosis, depends on whether altered expression or activity or a particular sequence polymorphism occurs in patients which develop agranulocytosis as compared to those who do not develop agranulocytosis . B. Example 2 : Genes that are Downregulated in the Presence of Clozapine

Table 2 describes genes that are underexpressed in clozapine-treated DI cells relative to untreated or olanzapine-treated DI cells.

TABLE 2

Table 4 describes genes whose expression is lower in clozapine-treated HL-60 cells than in untreated HL-60 cells.

TABLE 4

Appendix B is a list of genes whose expression is lower in clozapine-treated DI cells than in untreated DI cells or olanzapine-treated cells (or both) . The normalized level of expression in untreated, clozapine-treated, and olanzapine-treated cells is listed along with the Genbank Accession number, an identifier (gene name) and gene description. Also listed is the ratio of expression in cells subjected to various treatments.

The genes in the first group are expressed at a lower level in clozapine-treated and olanzapine-treated cells than in untreated cells. These genes are not expected to be associated with agranulocytosis because lower expression is associated with clozapine, a drug associated with agranulocytosis, and olanzapine, a drug that is not associated with agranulocytosis. The genes in the second group are expressed at a lower level in clozapine-treated cells than untreated cells or olanzapine-treated cells. These genes are potentially associated with agranulocytosis because lower expression is associated with clozapine, a drug associated with agranulocytosis, but not with olanzapine, a drug that is not associated with agranulocytosis, or with cells that have not been treated with a drug.

The genes in the third group are expressed at lower levels in clozapine-treated cells than in untreated cells. These genes are potentially associated with agranulocytosis because lower expression is associated with clozapine, a drug associated with agranulocytosis, but not with cells that have not been treated.

The genes in the fourth group are expressed at a lower level in clozapine-treated cells than olanzapine treated cells. These genes are potentially associated with agranulocytosis because lower expression is associated with clozapine, a drug associated with agranulocytosis, but not with olanzapine, a drug that is not associated with agranulocytosis.

Whether altered expression or activity of a particular sequence polymorphism in any of the genes listed in Table 2, Table 4, or Appendix B is tightly associated with agranulocytosis depends on whether altered expression or activity or a particular sequence polymorphism occurs in patients who develop agranulocytosis as compared to patients who do not develop agranulocytosis.

OTHER EMBODIMENTS

The present invention is not to be limited in scope by the specific embodiments described, which are intended as single illustrations of individual aspects of the invention. Functionally equivalent methods and compositions are within the scope of the invention, and will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such functional equivalents are intended to fall within the scope of the appended claims.

What is claimed is:

Claims

1. A method for assessing whether a patient is at risk of developing agranulocytosis when treated with a selected compound, the method comprising determining whether the patient has a mutation in the human homologue of at least one of the genes described in Tables 1-4, the presence of the mutation indicating that the patient is at risk of developing agranulocytosis.

2. The method of claim 1, wherein the gene is described in Table 1.

3. The method of claim 1, wherein the gene is described in Table 2.

4. The method of claim 1, wherein the gene is described in Table 3.

5. The method of claim 1, wherein the gene is described in Table 4.

6. The method of claim 1, wherein the mutation is within the coding region of the gene.

7. The method of claim 1, wherein the mutation is within the regulatory region of the gene.

8. The method of claim 1, wherein the mutation causes an alteration in the level of gene expression or the level of protein activity.

9. A method for assessing whether a patient is at risk of developing agranulocytosis when treated with a selected compound, the method comprising determining the level of expression of at least one of the genes described in Tables 1-4 in a first and a second biological sample obtained from the patient, the first sample being untreated and the second sample being treated with the selected compound, a change in the level of expression of the one or more genes in the second sample, relative to the first sample, indicating that the patient is at risk of developing agranulocytosis.

10. The method of claim 9, wherein the change in expression is an increase in expression and the at least one gene is a gene described in Table 1 or Table 3.

11. The method of claim 9, wherein the change in expression is a decrease in expression and the at least one gene is a gene described in Table 2 or Table 4.

12. A method for determining whether administration of a selected compound to a patient should be modified or discontinued, the method comprising determining the level of expression of at least one of the genes described in Tables 1-4 in a first and a second biological sample obtained from the patient, the first sample being untreated and the second sample being treated with the selected compound, a change in the level of expression of the one or more genes in the second sample, relative to the first sample, indicating that administration of the compound should be modified or discontinued because there is an increased risk that the patient will develop agranulocytosis.

13. The method of claim 12 , wherein the change in expression is an increase in expression and the at least one gene is a gene described in Table 1 or Table 3.

14. The method of claim 12 , wherein the change in expression is a decrease in expression and the at least one gene is a gene described in Table 2 or Table 4.

15. The method of claim 9 or claim 12, wherein the level of expression of the at least one gene is determined by measuring the amount of mRNA encoded by the gene .

16. The method of claim 9 or claim 12, wherein the level of expression of the at least one gene is determined by measuring the amount of protein encoded by the gene.

17. The method of claim 1, claim 9, or claim 12, wherein the selected compound is an antipsychotic, antimalarial, or antithyroid medication.

18. The method of claim 17, wherein the antipsychotic agent is clozapine.

19. The method of claim 9 or claim 12, wherein the first and second biological samples are samples of bone marrow.

20. The method of claim 9 or claim 12, wherein the first and second biological samples are samples of blood.

21. A method for determining whether a compound can be used to treat or prevent agranulocytosis, the method comprising determining the level of expression of at least one of the genes described in Table 1 or Table 3 in a first and second biological sample obtained from a patient, the first sample being treated with clozapine and the second sample being treated with clozapine and the compound, an increase in the level of expression of the at least one gene in the first sample and a lesser increase in the level of expression of the at least one gene in the second sample indicating that the compound can be used to treat or prevent agranulocytosis.

22. A method for determining whether a compound can be used to treat or prevent agranulocytosis, the method comprising determining the level of expression of at least one of the genes described in Table 2 or Table 4 in a first and second biological sample obtained from a patient, the first sample being treated with clozapine and the second sample being treated with clozapine and the compound, a decrease in the level of expression of the at least one gene in the first sample and a lesser decrease in the level of expression of the at least one gene in the second sample indicating that the compound can be used to treat or prevent agranulocytosis.

23. A method for treating agranulocytosis, the method comprising administering to a patient a compound identified by the method of claim 21 or claim 22.

24. A method for assessing whether a patient is at risk of developing agranulocytosis when treated with a selected compound, the method comprising determining the level of activity of at least one protein encoded by a gene described in The Tables presented herein-4 in a first and a second biological sample obtained from the patient, the first sample being untreated and the second sample being treated with the selected compound, a change in the level of activity of the protein in the second sample, relative to that in the first sample, indicating that the patient is at risk of developing agranulocytosis.

25. The method of claim 24, wherein the change in activity in the second sample is an increase in activity and the at least one gene is a gene described in Table 1 or Table 3.

26. The method of claim 24, wherein the change in activity in the second sample is a decrease in activity and the at least one gene is a gene described in Table 2 or Table 4.

27. A method for determining whether administration of a selected compound to a patient should be modified or discontinued, the method comprising determining the level of activity of at least one protein encoded by a gene described in The Tables presented herein-4 in a first and a second biological sample obtained from the patient, the first sample being untreated and the second sample being treated with the selected compound, a change in the level of activity of the protein in the second sample, relative to that in the first sample, indicating that administration of the compound should be modified or discontinued because there is an increased risk that the patient will develop agranulocytosis.

28. The method of claim 27, wherein the change in activity in the second sample is an increase in activity and the gene is a gene described in Table 1 or Table 3.

29. The method of claim 12, wherein the change in activity in the second sample is a decrease in activity and the gene is a gene described in Table 2 or Table 4.