Patent Publication Number: US-7910299-B2

Title: Methods for diagnosing systemic lupus erythematosus

Description:
CLAIM OF PRIORITY TO RELATED APPLICATIONS 
     This application is a continuation of U.S. patent application Ser. No. 10/222,202, filed on Aug. 16, 2002, now U.S. Pat. No. 7,118,865, the entire contents of which are hereby incorporated by reference. 
    
    
     STATEMENT AS TO FEDERALLY SPONSORED RESEARCH 
     Funding for the work described herein was provided in part by the National Institute of Arthritis and Musculoskeletal Diseases (grant no. NIH N01-AR-1-2256). The federal government may have certain rights in the invention. 
    
    
     BACKGROUND 
     1. Technical Field 
     The invention relates to methods and materials involved in diagnosing systemic lupus erythematosus (SLE). More particularly, the invention relates to methods and materials involved in diagnosing SLE, diagnosing severe SLE, and assessing a mammal&#39;s susceptibility to develop severe SLE. 
     2. Background Information 
     SLE is a chronic, inflammatory autoimmune disease characterized by the production of autoantibodies having specificity for a wide range of self-antigens. SLE autoantibodies mediate organ damage by directly binding to host tissues and by forming immune complexes that deposit in vascular tissues and activate immune cells. Organs targeted in SLE include the skin, kidneys, vasculature, joints, various blood elements, and the central nervous system (CNS). The severity of disease, the spectrum of clinical involvement, and the response to therapy vary widely among patients. This clinical heterogeneity makes it challenging to diagnose and manage lupus. 
     SUMMARY 
     The invention relates to methods and materials involved in diagnosing SLE. More particularly, the invention relates to methods and materials involved in diagnosing SLE, diagnosing severe SLE, and assessing a mammal&#39;s susceptibility to develop severe SLE. For example, the invention provides nucleic acid arrays that can be used to diagnose SLE in a mammal. Such arrays can allow clinicians to diagnose SLE based on a determination of the expression levels of many genes that are differentially expressed in SLE patients as compared to healthy controls. 
     In addition, the invention provides methods and materials involved in diagnosing SLE conditions that are accompanied by activation of an interferon pathway. For the purpose of this invention, the term “SLE accompanied by activation of an interferon pathway” (abbreviated “SLE-AIP”) refers to any SLE condition that coexists with or is caused by activation of an interferon pathway. Activation of an interferon pathway refers to a state where interferon-regulated genes that are up-regulated in response to interferon are up-regulated and where interferon-regulated genes that are down-regulated in response to interferon are down-regulated. Typically, activation of an interferon pathway results in the presence of a gene expression profile that is similar to the gene expression profile observed in cells that were treated with interferon. An interferon pathway can be activated regardless of the presence or absence of detectable levels of interferon. For example, an SLE patient can have low levels of detectable interferon while exhibiting a gene expression profile characteristic of an activated interferon pathway. Such an SLE patient can be diagnosed as having SLE-AIP. 
     Diagnosing patients as having SLE-AIP can help clinicians determine appropriate treatments for those patients. For example, a clinician who diagnoses a patient as having SLE-AIP can treat that patient with medication that improves both the patient&#39;s SLE symptoms and aberrant activation of an interferon pathway. In some cases, a single medication can be used to reverse a patient&#39;s activation of an interferon pathway such that the patient&#39;s SLE symptoms are reduced or relieved. Thus, treating a patient having SLE-AIP by modulating the level of interferon pathway activation can improve that patient&#39;s health and quality of life by, for example, reducing the symptoms associated with SLE. 
     Typically, a diagnosis of SLE can be made on the basis of 11 criteria defined by the American College of Rheumatology (ACR). These criteria include malar rash, discoid rash, photosensitivity, oral ulcers, arthritis, serositis, renal disorder, neurologic disorder, hematologic disorder, immunologic disorder, and antinuclear antibody (Tan et al. (1982)  Arthritis Rheum.  25:1271-1277). A mammal (e.g., a human) can be clinically diagnosed with SLE if be or she meets at least four of the eleven criteria. The term “severe SLE” as used herein refers to an SLE condition where the patient has one or more of the following: renal, central nervous system, or hematologic involvement. 
     The invention is based on the discovery of genes that are differentially expressed between SLE patients and healthy controls. The invention also is based on the discovery that the expression levels of these genes can be used to distinguish mammals with SLE from healthy mammals. For example, the expression levels for the genes listed in Table I can be assessed to diagnose SLE. In addition, the invention is based on the discovery that a portion of SLE patients can have SLE associated with or caused by activation of an interferon pathway. For example, SLE patients having severe SLE can be, at least partially, dependent upon the presence of an activated interferon pathway. Further, the invention is based on the discovery of genes that are differentially expressed between SLE-AIP patients and SLE patients not associated with an activated interferon pathway. For example, the expression levels for the genes listed in Table IV can be assessed to diagnose SLE-AIP. 
     In one aspect, the invention provides a method for diagnosing severe systemic lupus erythematosus. The method can involve determining whether or not a mammal contains cells that express at least 2 of the genes listed in Table 4 to an extent greater than or less than the average level of expression exhibited in control cells from one or more control mammals, wherein the mammal and the one or more control mammals are from the same species, and diagnosing the mammal as having severe systemic lupus erythematosus if the mammal contains the cells and diagnosing the mammal as not having severe systemic lupus erythematosus if the mammal does not contain the cells. The mammal can be a human. The control mammals can be healthy humans or humans with mild systemic lupus erythematosus. The cells and the control cells can be peripheral blood mononuclear cells. The method can involve determining whether or not the mammal contains cells that express at least 5 or at least 10 of the genes to an extent greater than or less than the level of expression exhibited in the control cells. The extent can be less than the average level of expression exhibited in control cells from at least 10 or at least 20 control mammals. The determining step can involve measuring the level of mRNA expressed from the at least 2 of the genes. 
     In another aspect, the invention provides a method for assessing the predisposition of a mammal to develop severe systemic lupus erythematosus. The method can involve determining whether or not the mammal contains cells that express at least 2 of the genes listed in Table 4 to an extent greater than or less than the average level of expression exhibited in control cells from one or more control mammals, wherein the mammal and the one or more control mammals are from the same species, and classifying the mammal as being susceptible to develop severe systemic lupus erythematosus if the mammal contains the cells and classifying the mammal as not being susceptible to develop severe systemic lupus erythematosus if the mammal does not contain the cells. The mammal can be a human. The control mammals can be healthy humans. The cells and the control cells can be peripheral blood mononuclear cells. The method also can involve determining whether or not the mammal contains cells that express at least 5 or at least 10 of the genes to an extent greater than or less than the level of expression exhibited in the control cells. The method can involve determining whether or not the mammal contains cells that express at least 10 of the genes to an extent greater than or less than the level of expression exhibited in the control cells. The extent can be greater than or less than the average level of expression exhibited in control cells from at least 10 or at least 20 control mammals. The determining step can involve measuring the level of mRNA expressed from said at least 5 of the genes. 
     In another aspect, the invention provides a method for diagnosing systemic lupus erythematosus in a mammal. The method can involve determining whether or not the mammal contains cells that express at least 10 of the genes listed in Table 1 to an extent greater than or less than the average level of expression exhibited in control cells from one or more control mammals, wherein the mammal and the one or more control mammals are from the same species, and diagnosing the mammal as having systemic lupus erythematosus if the mammal contains the cells and diagnosing the mammal as not having systemic lupus erythematosus if the mammal does not contain the cells. 
     In yet another aspect, the invention provides a method for diagnosing systemic lupus erythematosus in a mammal. The method can involve determining whether or not the mammal contains cells that express at least 5 of the genes listed in Table 2 to an extent greater than the average level of expression exhibited in control cells from one or more control mammals, wherein the mammal and the one or more control mammals are from the same species, and diagnosing the mammal as having systemic lupus erythematosus if the mammal contains the cells and diagnosing said mammal as not having systemic lupus erythematosus if the mammal does not contain the cells. 
     The invention also provides a method for diagnosing systemic lupus erythematosus in a mammal. The method can involve determining whether or not the mammal contains cells that express at least 5 of the genes listed in Table 3 to an extent less than the average level of expression exhibited in control cells from one or more control mammals, wherein the mammal and the one or more control mammals are from the same species, and diagnosing the mammal as having systemic lupus erythematosus if the mammal contains the cells and diagnosing the mammal as not having systemic lupus erythematosus if the mammal does not contain the cells. 
     In another aspect, the invention provides a nucleic acid array containing at least 20 nucleic acid molecules. Each of the at least 20 nucleic acid molecules can have a different nucleic acid sequence, and at least 50 percent of the nucleic acid molecules of the array can contain a sequence from a gene selected from the group consisting of the genes listed in Table 1. The array can contain at least 50 nucleic acid molecules, and each of the at least 50 nucleic acid molecules can have a different nucleic acid sequence. The array can contain at least 100 nucleic acid molecules, and each of the at least 100 nucleic acid molecules can have a different nucleic acid sequence. Each of the nucleic acid molecules that contain a sequence from a gene selected from the group can contain no more than three mismatches. At least 75 percent or at least 95 percent of the nucleic acid molecules of the array can contain a sequence from a gene selected from the group. The array can contain glass. 
     In yet another aspect, the invention provides a nucleic acid array containing at least 5 nucleic acid molecules. Each of the at least 5 nucleic acid molecules can have a different nucleic acid sequence, and at least 50 percent of the nucleic acid molecules of the array can contain a sequence from a gene selected from the group consisting of the genes listed in Table 4. The array can contain at least 10 nucleic acid molecules, and each of the at least 10 nucleic acid molecules can have a different nucleic acid sequence. The array can contain at least 20 nucleic acid molecules, and each of the at least 20 nucleic acid molecules can have a different nucleic acid sequence. Each of the nucleic acid molecules that contain a sequence from a gene selected from the group can contain no more than three mismatches. At least 75 percent or at least 95 percent of the nucleic acid molecules of the array can contain a sequence from a gene selected from the group. The array can contain glass. 
     Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. 
     Other features and advantages of the invention will be apparent from the following detailed description, and from the claims. 
    
    
     
       DESCRIPTION OF DRAWINGS 
         FIG. 1  is a graph plotting the IFN scores that were calculated for SLE patients and control subjects using the normalized expression levels of the 14 IFN-regulated genes that comprise the IFN signature; p=2.8×10 −7 . 
         FIG. 2  is a graph plotting the number of SLE criteria observed in the 24 SLE patients with the highest IFN scores and in the 24 SLE patients with the lowest IFN scores; p=0.002. 
         FIG. 3  is a graph plotting the number of SLE criteria met by each patient against the IFN score of each patient. 
         FIG. 4  is a bar graph showing the percent of patients in the IFN-high and IFN-low groups with ACR-defined criteria for renal and/or CNS disease (p=7.7×10 −6 ) or hematologic involvement (p=6.1×10 −9 ). 
     
    
    
     DETAILED DESCRIPTION 
     The invention provides to methods and materials involved in diagnosing SLE. More particularly, the invention relates to methods and materials involved in diagnosing SLE, diagnosing severe SLE, and assessing a mammal&#39;s susceptibility to develop severe SLE. For example, the invention provides nucleic acid arrays that can be used to diagnose SLE, severe SLE, and/or SLE-AIP in a mammal. Such arrays can allow clinicians to diagnose SLE, severe SLE, and/or SLE-AIP based on a determination of the expression levels of many genes that are differentially expressed. 
     1. Diagnosing SLE 
     The invention provides methods for diagnosing a mammal (e.g., a human) as having SLE. In one embodiment, a mammal can be diagnosed as having SLE if it is determined that the mammal contains cells that express one or more of the genes listed in Table 1 at a level that is greater or less than the average level of expression of the same one or more genes observed in control cells obtained from control mammals. In another embodiment, a mammal can be diagnosed as having SLE if it is determined that the mammal contains cells that express one or more of the genes listed in Table 2 at a level that is greater than the average level of expression of the same one or more genes observed in control cells obtained from control mammals. In yet another embodiment, a mammal can be diagnosed as having SLE if it is determined that the mammal contains cells that express one or more of the genes listed in Table 3 at a level that is less than the average level of expression of the same one or more genes observed in control cells obtained from control mammals. 
     The mammal can be any mammal such as a human, dog, mouse, or rat. Any cell type can be isolated and evaluated. For example, peripheral blood mononuclear cells (PBMC), total white blood cells, lymph node cells, spleen cells, or tonsil cells can be isolated from a human patient and evaluated to determine if that patient contains cells that (1) express one or more of the genes listed in Table 1 at a level that is greater or less than the average level of expression observed in control cells, (2) express one or more of the genes listed in Table 2 at a level that is greater than the average level of expression observed in control cells, or (3) express one or more of the genes listed in Table 3 at a level that is less than the average level of expression observed in control cells. The expression of any number of the genes listed in Tables 1, 2, or 3 can be evaluated to diagnose SLE. For example, the expression of one or more than one (e.g., two, three, four, five, six, seven, eight, nine, ten, 15, 20, 25, 30, or more than 30) of the genes listed in Table 1, 2, or 3 can be used. 
     The expression level can be greater than or less than the average level observed in control cells obtained from control mammals. Typically, a gene can be classified as being expressed at a level that is greater than or less than the average level observed in control cells if the expression levels differ by at least 1-fold (e.g., 1.5-fold, 2-fold, 3-fold, or more than 3-fold). In addition, the control cells typically are the same type of cells as those isolated from the mammal being evaluated. In some cases, the control cells can be isolated from one or more mammals that are from the same species as the mammal being evaluated. When diagnosing SLE, the control cells can be isolated from healthy mammals such as healthy humans who do not have SLE. Any number of control mammals can be used to obtain the control cells. For example, control cells can be obtained from one or more healthy mammals (e.g., at least 5, at least 10, at least 15, at least 20, or more than 20 control mammals). 
     Any method can be used to determine whether or not a specific gene is expressed at a level that is greater or less than the average level of expression observed in control cells. For example, the level of expression from a particular gene can be measured by assessing the level of mRNA expression from the gene. Levels of mRNA expression can be evaluated using, without limitation, northern blotting, slot blotting, quantitative reverse transcriptase polymerase chain reaction (RT-PCR), or chip hybridization techniques. Methods for chip hybridization assays include, without limitation, those described herein. Such methods can be used to determine simultaneously the relative expression levels of multiple mRNAs. Alternatively, the level of expression from a particular gene can be measured by assessing polypeptide levels. Polypeptide levels can be measured using any method such as immuno-based assays (e.g., ELISA), western blotting, or silver staining. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Genes with expression levels that differ between SLE patients and normal controls 
               
            
           
           
               
               
            
               
                 Accession No. 
                 Gene 
               
               
                   
               
               
                 U60060 
                 fasciculation and elongation protein zeta 1 (zygin I) 
               
               
                 AF057036 
                 collagen-like tail subunit (single strand of homotrimer) of asymmetric 
               
               
                   
                 acetylcholinesterase 
               
               
                 M93107 
                 3-hydroxybutyrate dehydrogenase (heart, mitochondrial) 
               
               
                 U14575 
                 protein phosphatase 1, regulatory (inhibitor) subunit 8 
               
               
                 X15882 
                 collagen VI alpha-2 C-terminal globular domain 
               
               
                 S68805 
                 glycine amidinotransferase (L-arginine:glycine amidinotransferase) 
               
               
                 U75744 
                 deoxyribonuclease I-like 3 
               
               
                 AF091071 
                 similar to  S. cerevisiae  RER1 
               
               
                 AI651806 
                 cysteine-rich motor neuron 1 
               
               
                 AB028994 
                 KIAA1071 protein 
               
               
                 S75168 
                 megakaryocyte-associated tyrosine kinase 
               
               
                 X73617 
                 T cell receptor delta locus 
               
               
                 X07730 
                 kallikrein 3, (prostate specific antigen) 
               
               
                 AF009787 
                 T cell receptor beta locus 
               
               
                 M21624 
                 T cell receptor delta locus 
               
               
                 AB009598 
                 beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I) 
               
               
                 AL021154 
                 E2F transcription factor 2 
               
               
                 L25444 
                 TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated 
               
               
                   
                 factor, 80 kD 
               
               
                 AJ001383 
                 lymphocyte antigen 94 homolog, activating NK-receptor; NK-p46 
               
               
                   
                 (mouse) 
               
               
                 U75370 
                 polymerase (RNA) mitochondrial (DNA directed) 
               
               
                 AL049365 
                 DKFZp586A0618 
               
               
                 M16801 
                 nuclear receptor subfamily 3, group C, member 2 
               
               
                 M28827 
                 CD1C antigen, c polypeptide 
               
               
                 U51712 
                 hypothetical protein SMAP31 
               
               
                 X66079 
                 Spi-B transcription factor (Spi-1/PU.1 related) 
               
               
                 U11276 
                 killer cell lectin-like receptor subfamily B, member 1 
               
               
                 M36881 
                 lymphocyte-specific protein tyrosine kinase 
               
               
                 M31523 
                 transcription factor 3 (E2A immunoglobulin enhancer binding factors 
               
               
                   
                 E12/E47) 
               
               
                 M26062 
                 interleukin 2 receptor, beta 
               
               
                 AF026031 
                 putative mitochondrial outer membrane protein import receptor 
               
               
                 AB011115 
                 KIAA0543 protein 
               
               
                 AF041261 
                 leukocyte immunoglobulin-like receptor, subfamily A (without TM 
               
               
                   
                 domain), member 4 
               
               
                 D55716 
                 MCM7 minichromosome maintenance deficient 7 ( S. cerevisiae ) 
               
               
                 L04282 
                 zinc finger protein 148 (pHZ-52) 
               
               
                 AJ001687 
                 DNA segment on chromosome 12 (unique) 2489 expressed sequence 
               
               
                 AI524873 
                 like mouse brain protein E46 
               
               
                 U76421 
                 adenosine deaminase, RNA-specific, B1 (homolog of rat RED1) 
               
               
                 AF031137 
                 lymphocyte antigen 117 
               
               
                 X59871 
                 transcription factor 7 (T-cell specific, HMG-box) 
               
               
                 U43408 
                 tyrosine kinase, non-receptor, 1 
               
               
                 AB018289 
                 KIAA0746 protein 
               
               
                 AI761647 
                 IMAGE-2370113 
               
               
                 M18737 
                 granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine 
               
               
                   
                 esterase 3) 
               
               
                 AB023220 
                 ubiquitin specific protease 20 
               
               
                 W26633 
                 melanoma antigen, family D, 1 
               
               
                 M68892 
                 integrin, beta 7 
               
               
                 AJ236885 
                 zinc finger protein 148 (pHZ-52) 
               
               
                 L13858 
                 son of sevenless ( Drosophila ) homolog 2 
               
               
                 AF094481 
                 CGG triplet repeat binding protein 1 
               
               
                 M28215 
                 RAB5A, member RAS oncogene family 
               
               
                 U43083 
                 guanine nucleotide binding protein (G protein), q polypeptide 
               
               
                 X02344 
                 tubulin, beta, 2 
               
               
                 M22324 
                 alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase 
               
               
                   
                 M, microsomal aminopeptidase, CD13, p150) 
               
               
                 Y07566 
                 Ric-like, expressed in many tissues ( Drosophila ) 
               
               
                 U50553 
                 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3 
               
               
                 X54134 
                 protein tyrosine phosphatase, receptor type, E 
               
               
                 L40388 
                 thyroid receptor interacting protein 15 
               
               
                 L19872 
                 aryl hydrocarbon receptor 
               
               
                 U78107 
                 N-ethylmaleimide-sensitive factor attachment protein, gamma 
               
               
                 AL050272 
                 DKFZP566B183 protein 
               
               
                 U56998 
                 cytokine-inducible kinase 
               
               
                 AI189226 
                 RAB31, member RAS oncogene family 
               
               
                 Z50781 
                 delta sleep inducing peptide, immunoreactor 
               
               
                 S87759 
                 protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha 
               
               
                   
                 isoform 
               
               
                 U88629 
                 ELL-RELATED RNA POLYMERASE II, ELONGATION FACTOR 
               
               
                 AF006513 
                 chromodomain helicase DNA binding protein 1 
               
               
                 AI138605 
                 hypothetical protein DKFZp566A1524 
               
               
                 L16794 
                 MADS box transcription enhancer factor 2, polypeptide D (myocyte 
               
               
                   
                 enhancer factor 2D) 
               
               
                 AL080235 
                 Ras-induced senescence 1 
               
               
                 L17418 
                 complement component (3b/4b) receptor 1, including Knops blood 
               
               
                   
                 group system 
               
               
                 Y00816 
                 complement component (3b/4b) receptor 1, including Knops blood 
               
               
                   
                 group system 
               
               
                 M63835 
                 Fc fragment of IgG, high affinity Ia, receptor for (CD64) 
               
               
                 L13943 
                 glycerol kinase 
               
               
                 U89278 
                 early development regulator 2 (homolog of polyhomeotic 2) 
               
               
                 U58334 
                 tumor protein p53 binding protein, 2 
               
               
                 X54134 
                 protein tyrosine phosphatase, receptor type, E 
               
               
                 X59834 
                 glutamate-ammonia ligase (glutamine synthase) 
               
               
                 AL047596 
                 capicua homolog ( Drosophila ) 
               
               
                 AB023211 
                 peptidyl arginine deiminase, type II 
               
               
                 D43945 
                 transcription factor EC 
               
               
                 U79273 
                 clone 23933 
               
               
                 Z18956 
                 solute carrier family 6 (neurotransmitter transporter, taurine), member 6 
               
               
                 Y10313 
                 interferon-related developmental regulator 1 
               
               
                 AF004849 
                 homeodomain interacting protein kinase 3 
               
               
                 AI808958 
                 KIAA0870 protein 
               
               
                 U47634 
                 tubulin, beta, 4 
               
               
                 X55988 
                 ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin) 
               
               
                 W29030 
                 CGI-49 protein 
               
               
                 U12471 
                 thrombospondin-1 
               
               
                 AF013591 
                 sudD (suppressor of bimD6,  Aspergillus nidulans ) homolog 
               
               
                 X52015 
                 interleukin 1 receptor antagonist 
               
               
                 M16967 
                 coagulation factor V (proaccelerin, labile factor) 
               
               
                 U57094 
                 RAB27A, member RAS oncogene family 
               
               
                 U66711 
                 lymphocyte antigen 6 complex, locus E 
               
               
                 AA521060 
                 IMAGE-826408 
               
               
                 X68090 
                 IgG Fc receptor class IIA 
               
               
                 Y08136 
                 acid sphingomyelinase-like phosphodiesterase 
               
               
                 AL049685 
                 hypothetical protein similar to small G proteins, especially RAP-2A 
               
               
                 L28957 
                 phosphate cytidylyltransferase 1, choline, alpha isoform 
               
               
                 Z22576 
                 CD69 antigen (p60, early T-cell activation antigen) 
               
               
                 U41766 
                 a disintegrin and metalloproteinase domain 9 (meltrin gamma) 
               
               
                 M57230 
                 interleukin 6 signal transducer (gp130, oncostatin M receptor) 
               
               
                 X17094 
                 paired basic amino acid cleaving enzyme (furin, membrane associated 
               
               
                   
                 receptor protein) 
               
               
                 AC005192 
                 interferon-related developmental regulator 1 
               
               
                 AI547258 
                 metallothionein 2A 
               
               
                 L22075 
                 guanine nucleotide binding protein (G protein), alpha 13 
               
               
                 U22431 
                 hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix 
               
               
                   
                 transcription factor) 
               
               
                 AB006746 
                 phospholipid scramblase 1 
               
               
                 AF030196 
                 stannin 
               
               
                 AA010078 
                 H4 histone family, member D 
               
               
                 X56807 
                 desmocollin 2 
               
               
                 AL080156 
                 DKFZP434J214 protein 
               
               
                 AF017257 
                 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) 
               
               
                 AL049340 
                 DKFZp564P056 
               
               
                 M24283 
                 intercellular adhesion molecule 1 (CD54), human rhinovirus receptor 
               
               
                 D49817 
                 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 
               
               
                 AF016903 
                 agrin 
               
               
                 U77914 
                 jagged 1 (Alagille syndrome) 
               
               
                 M33882 
                 myxovirus (influenza) resistance 1, homolog of murine (interferon- 
               
               
                   
                 inducible protein p78) 
               
               
                 U68385 
                 Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse) 
               
               
                 L05515 
                 cAMP response element-binding protein CRE-BPa 
               
               
                 U15555 
                 serine palmitoyltransferase, long chain base subunit 2 
               
               
                 L42025 
                 HIV-1 Rev binding protein 
               
               
                 X07834 
                 superoxide dismutase 2, mitochondrial 
               
               
                 D90144 
                 small inducible cytokine A3 
               
               
                 M13755 
                 interferon-stimulated protein, 15 kDa 
               
               
                 M83670 
                 carbonic anhydrase IV 
               
               
                 M55047 
                 synaptotagmin I 
               
               
                 U91512 
                 ninjurin 1 
               
               
                 AB008775 
                 aquaporin 9 
               
               
                 X79535 
                 tubulin, beta polypeptide 
               
               
                 J04102 
                 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) 
               
               
                 D10040 
                 fatty-acid-Coenzyme A ligase, long-chain 2 
               
               
                 AW044649 
                 sin3-associated polypeptide, 30 kD 
               
               
                 X03473 
                 H1 histone family, member 0 
               
               
                 AB007448 
                 solute carrier family 22 (organic cation transporter), member 4 
               
               
                 Z14138 
                 mitogen-activated protein kinase kinase kinase 8 
               
               
                 X02419 
                 uPA 
               
               
                 U10473 
                 UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 1 
               
               
                 AI679353 
                 solute carrier family 11 (proton-coupled divalent metal ion transporters), 
               
               
                   
                 member 1 
               
               
                 AA203213 
                 interferon-stimulated protein, 15 kDa 
               
               
                 AB018259 
                 KIAA0716 gene product 
               
               
                 AF055993 
                 sin3-associated polypeptide, 30 kD 
               
               
                 X54486 
                 serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1 
               
               
                 AJ225089 
                 2′-5′-oligoadenylate synthetase-like 
               
               
                 AL022318 
                 similar to APOBEC1 
               
               
                 S59049 
                 regulator of G-protein signaling 1 
               
               
                 Y10032 
                 serum/glucocorticoid regulated kinase 
               
               
                 AI924594 
                 tetraspan 2 
               
               
                 D21205 
                 zinc finger protein 147 (estrogen-responsive finger protein) 
               
               
                 U37707 
                 membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3) 
               
               
                 L40387 
                 2′-5′-oligoadenylate synthetase-like 
               
               
                 X78711 
                 glycerol kinase 
               
               
                 D10923 
                 putative chemokine receptor; GTP-binding protein 
               
               
                 AW006742 
                 IMAGE-2489058 
               
               
                 AL109730 
                 EUROIMAGE 68600 
               
               
                 X99699 
                 XIAP associated factor-1 
               
               
                 AB000115 
                 hypothetical protein, expressed in osteoblast 
               
               
                 L13210 
                 lectin, galactoside-binding, soluble, 3 binding protein 
               
               
                 U22970 
                 interferon, alpha-inducible protein (clone IFI-6-16) 
               
               
                 U96721 
                 Hermansky-Pudlak syndrome 
               
               
                 L10126 
                 activin A receptor, type IB 
               
               
                 S62138 
                 TLS/CHOP 
               
               
                 M33684 
                 protein tyrosine phosphatase, non-receptor type 1 
               
               
                 M63978 
                 vascular endothelial growth factor 
               
               
                 X89101 
                 tumor necrosis factor receptor superfamily, member 6 
               
               
                 M60278 
                 diphtheria toxin receptor (heparin-binding epidermal growth factor-like 
               
               
                   
                 growth factor) 
               
               
                 X59770 
                 interleukin 1 receptor, type II 
               
               
                 X04500 
                 interleukin 1, beta 
               
               
                 D30783 
                 epiregulin 
               
               
                 U43774 
                 Fc fragment of IgA, receptor for 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Genes from Table 1 that are higher in SLE patients as compared to controls 
               
            
           
           
               
               
            
               
                 Accession No. 
                 Gene 
               
               
                   
               
               
                 L13858 
                 son of sevenless ( Drosophila ) homolog 2 
               
               
                 AF094481 
                 CGG triplet repeat binding protein 1 
               
               
                 M28215 
                 RAB5A, member RAS oncogene family 
               
               
                 U43083 
                 guanine nucleotide binding protein (G protein), q polypeptide 
               
               
                 X02344 
                 tubulin, beta, 2 
               
               
                 M22324 
                 alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase 
               
               
                   
                 M, microsomal aminopeptidase, CD13, p150) 
               
               
                 Y07566 
                 Ric-like, expressed in many tissues ( Drosophila ) 
               
               
                 U50553 
                 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3 
               
               
                 X54134 
                 protein tyrosine phosphatase, receptor type, E 
               
               
                 L40388 
                 thyroid receptor interacting protein 15 
               
               
                 L19872 
                 aryl hydrocarbon receptor 
               
               
                 U78107 
                 N-ethylmaleimide-sensitive factor attachment protein, gamma 
               
               
                 AL050272 
                 DKFZP566B183 protein 
               
               
                 U56998 
                 cytokine-inducible kinase 
               
               
                 AI189226 
                 RAB31, member RAS oncogene family 
               
               
                 Z50781 
                 delta sleep inducing peptide, immunoreactor 
               
               
                 S87759 
                 protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha 
               
               
                   
                 isoform 
               
               
                 U88629 
                 ELL-RELATED RNA POLYMERASE II, ELONGATION FACTOR 
               
               
                 AF006513 
                 chromodomain helicase DNA binding protein 1 
               
               
                 AI138605 
                 hypothetical protein DKFZp566A1524 
               
               
                 L16794 
                 MADS box transcription enhancer factor 2, polypeptide D (myocyte 
               
               
                   
                 enhancer factor 2D) 
               
               
                 AL080235 
                 Ras-induced senescence 1 
               
               
                 L17418 
                 complement component (3b/4b) receptor 1, including Knops blood 
               
               
                   
                 group system 
               
               
                 Y00816 
                 complement component (3b/4b) receptor 1, including Knops blood 
               
               
                   
                 group system 
               
               
                 M63835 
                 Fc fragment of IgG, high affinity Ia, receptor for (CD64) 
               
               
                 L13943 
                 glycerol kinase 
               
               
                 U89278 
                 early development regulator 2 (homolog of polyhomeotic 2) 
               
               
                 U58334 
                 tumor protein p53 binding protein, 2 
               
               
                 X54134 
                 protein tyrosine phosphatase, receptor type, E 
               
               
                 X59834 
                 glutamate-ammonia ligase (glutamine synthase) 
               
               
                 AL047596 
                 capicua homolog ( Drosophila ) 
               
               
                 AB023211 
                 peptidyl arginine deiminase, type II 
               
               
                 D43945 
                 transcription factor EC 
               
               
                 U79273 
                 clone 23933 
               
               
                 Z18956 
                 solute carrier family 6 (neurotransmitter transporter, taurine), member 6 
               
               
                 Y10313 
                 interferon-related developmental regulator 1 
               
               
                 AF004849 
                 homeodomain interacting protein kinase 3 
               
               
                 AI808958 
                 KIAA0870 protein 
               
               
                 U47634 
                 tubulin, beta, 4 
               
               
                 X55988 
                 ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin) 
               
               
                 W29030 
                 CGI-49 protein 
               
               
                 U12471 
                 thrombospondin-1 
               
               
                 AF013591 
                 sudD (suppressor of bimD6,  Aspergillus nidulans ) homolog 
               
               
                 X52015 
                 interleukin 1 receptor antagonist 
               
               
                 M16967 
                 coagulation factor V (proaccelerin, labile factor) 
               
               
                 U57094 
                 RAB27A, member RAS oncogene family 
               
               
                 U66711 
                 lymphocyte antigen 6 complex, locus E 
               
               
                 AA521060 
                 IMAGE-826408 
               
               
                 X68090 
                 IgG Fc receptor class IIA 
               
               
                 Y08136 
                 acid sphingomyelinase-like phosphodiesterase 
               
               
                 AL049685 
                 hypothetical protein similar to small G proteins, especially RAP-2A 
               
               
                 L28957 
                 phosphate cytidylyltransferase 1, choline, alpha isoform 
               
               
                 Z22576 
                 CD69 antigen (p60, early T-cell activation antigen) 
               
               
                 U41766 
                 a disintegrin and metalloproteinase domain 9 (meltrin gamma) 
               
               
                 M57230 
                 interleukin 6 signal transducer (gp130, oncostatin M receptor) 
               
               
                 X17094 
                 paired basic amino acid cleaving enzyme (furin, membrane associated 
               
               
                   
                 receptor protein) 
               
               
                 AC005192 
                 interferon-related developmental regulator 1 
               
               
                 AI547258 
                 metallothionein 2A 
               
               
                 L22075 
                 guanine nucleotide binding protein (G protein), alpha 13 
               
               
                 U22431 
                 hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix 
               
               
                   
                 transcription factor) 
               
               
                 AB006746 
                 phospholipid scramblase 1 
               
               
                 AF030196 
                 stannin 
               
               
                 AA010078 
                 H4 histone family, member D 
               
               
                 X56807 
                 desmocollin 2 
               
               
                 AL080156 
                 DKFZP434J214 protein 
               
               
                 AF017257 
                 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) 
               
               
                 AL049340 
                 DKFZp564P056 
               
               
                 M24283 
                 intercellular adhesion molecule 1 (CD54), human rhinovirus receptor 
               
               
                 D49817 
                 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 
               
               
                 AF016903 
                 agrin 
               
               
                 U77914 
                 jagged 1 (Alagille syndrome) 
               
               
                 M33882 
                 myxovirus (influenza) resistance 1, homolog of murine (interferon- 
               
               
                   
                 inducible protein p78) 
               
               
                 U68385 
                 Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse) 
               
               
                 L05515 
                 cAMP response element-binding protein CRE-BPa 
               
               
                 U15555 
                 serine palmitoyltransferase, long chain base subunit 2 
               
               
                 L42025 
                 HIV-1 Rev binding protein 
               
               
                 X07834 
                 superoxide dismutase 2, mitochondrial 
               
               
                 D90144 
                 small inducible cytokine A3 
               
               
                 M13755 
                 interferon-stimulated protein, 15 kDa 
               
               
                 M83670 
                 carbonic anhydrase IV 
               
               
                 M55047 
                 synaptotagmin I 
               
               
                 U91512 
                 ninjurin 1 
               
               
                 AB008775 
                 aquaporin 9 
               
               
                 X79535 
                 tubulin, beta polypeptide 
               
               
                 J04102 
                 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) 
               
               
                 D10040 
                 fatty-acid-Coenzyme A ligase, long-chain 2 
               
               
                 AW044649 
                 sin3-associated polypeptide, 30 kD 
               
               
                 X03473 
                 H1 histone family, member 0 
               
               
                 AB007448 
                 solute carrier family 22 (organic cation transporter), member 4 
               
               
                 Z14138 
                 mitogen-activated protein kinase kinase kinase 8 
               
               
                 X02419 
                 uPA 
               
               
                 U10473 
                 UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 1 
               
               
                 AI679353 
                 solute carrier family 11 (proton-coupled divalent metal ion transporters), 
               
               
                   
                 member 1 
               
               
                 AA203213 
                 interferon-stimulated protein, 15 kDa 
               
               
                 AB018259 
                 KIAA0716 gene product 
               
               
                 AF055993 
                 sin3-associated polypeptide, 30 kD 
               
               
                 X54486 
                 serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1 
               
               
                 AJ225089 
                 2′-5′-oligoadenylate synthetase-like 
               
               
                 AL022318 
                 similar to APOBEC1 
               
               
                 S59049 
                 regulator of G-protein signalling 1 
               
               
                 Y10032 
                 serum/glucocorticoid regulated kinase 
               
               
                 AI924594 
                 tetraspan 2 
               
               
                 D21205 
                 zinc finger protein 147 (estrogen-responsive finger protein) 
               
               
                 U37707 
                 membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3) 
               
               
                 L40387 
                 2′-5′-oligoadenylate synthetase-like 
               
               
                 X78711 
                 glycerol kinase 
               
               
                 D10923 
                 putative chemokine receptor; GTP-binding protein 
               
               
                 AW006742 
                 IMAGE-2489058 
               
               
                 AL109730 
                 EUROIMAGE 68600 
               
               
                 X99699 
                 XIAP associated factor-1 
               
               
                 AB000115 
                 hypothetical protein, expressed in osteoblast 
               
               
                 L13210 
                 lectin, galactoside-binding, soluble, 3 binding protein 
               
               
                 U22970 
                 interferon, alpha-inducible protein (clone IFI-6-16) 
               
               
                 U96721 
                 Hermansky-Pudlak syndrome 
               
               
                 L10126 
                 activin A receptor, type IB 
               
               
                 S62138 
                 TLS/CHOP 
               
               
                 M33684 
                 protein tyrosine phosphatase, non-receptor type 1 
               
               
                 M63978 
                 vascular endothelial growth factor 
               
               
                 X89101 
                 tumor necrosis factor receptor superfamily, member 6 
               
               
                 M60278 
                 diphtheria toxin receptor (heparin-binding epidermal growth factor-like 
               
               
                   
                 growth factor) 
               
               
                 X59770 
                 interleukin 1 receptor, type II 
               
               
                 X04500 
                 interleukin 1, beta 
               
               
                 D30783 
                 epiregulin 
               
               
                 U43774 
                 Fc fragment of IgA, receptor for 
               
               
                   
               
            
           
         
       
     
                     TABLE 3                  Genes from Table 1 that are lower in SLE patients as compared to controls                     Accession No.   Gene               U60060   fasciculation and elongation protein zeta 1 (zygin I)       AF057036   collagen-like tail subunit (single strand of homotrimer) of asymmetric           acetylcholinesterase       M93107   3-hydroxybutyrate dehydrogenase (heart, mitochondrial)       U14575   protein phosphatase 1, regulatory (inhibitor) subunit 8       X15882   collagen VI alpha-2 C-terminal globular domain       S68805   glycine amidinotransferase (L-arginine:glycine amidinotransferase)       U75744   deoxyribonuclease I-like 3       AF091071   similar to  S. cerevisiae  RER1       AI651806   cysteine-rich motor neuron 1       AB028994   KIAA1071 protein       S75168   megakaryocyte-associated tyrosine kinase       X73617   T cell receptor delta locus       X07730   kallikrein 3, (prostate specific antigen)       AF009787   T cell receptor beta locus       M21624   T cell receptor delta locus       AB009598   beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I)       AL021154   E2F transcription factor 2       L25444   TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated           factor, 80 kD       AJ001383   lymphocyte antigen 94 homolog, activating NK-receptor; NK-p46,           (mouse)       U75370   polymerase (RNA) mitochondrial (DNA directed)       AL049365   DKFZp586A0618       M16801   nuclear receptor subfamily 3, group C, member 2       M28827   CD1C antigen, c polypeptide       U51712   hypothetical protein SMAP31       X66079   Spi-B transcription factor (Spi-1/PU.1 related)       U11276   killer cell lectin-like receptor subfamily B, member 1       M36881   lymphocyte-specific protein tyrosine kinase       M31523   transcription factor 3 (E2A immunoglobulin enhancer binding factors           E12/E47)       M26062   interleukin 2 receptor, beta       AF026031   putative mitochondrial outer membrane protein import receptor       AB011115   KIAA0543 protein       AF041261   leukocyte immunoglobulin-like receptor, subfamily A (without TM           domain), member 4       D55716   MCM7 minichromosome maintenance deficient 7 ( S. cerevisiae )       L04282   zinc finger protein 148 (pHZ-52)       AJ001687   DNA segment on chromosome 12 (unique) 2489 expressed sequence       AI524873   like mouse brain protein E46       U76421   adenosine deaminase, RNA-specific, B1 (homolog of rat RED1)       AF031137   lymphocyte antigen 117       X59871   transcription factor 7 (T-cell specific, HMG-box)       U43408   tyrosine kinase, non-receptor, 1       AB018289   KIAA0746 protein       AI761647   IMAGE-2370113       M18737   granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine           esterase 3)       AB023220   ubiquitin specific protease 20       W26633   melanoma antigen, family D, 1       M68892   integrin, beta 7       AJ236885   zinc finger protein 148 (pHZ-52)                    
2. Diagnosing Severe SLE and SLE-AIP
 
     The invention also provides methods for diagnosing a mammal (e.g., a human) as having severe SLE or SLE-AIP. In one embodiment, a mammal can be diagnosed as having severe SLE or SLE-AIP if it is determined that the mammal contains cells that express one or more of the genes listed in Table 4 at a level that is greater than the average level of expression of the same one or more genes observed in control cells obtained from control mammals. 
     As described above, the mammal can be any mammal such as a human, dog, mouse, or rat. Any cell type can be isolated and evaluated. For example, peripheral blood mononuclear cells (PBMC), total white blood cells, lymph node cells, spleen cells, or tonsil cells can be isolated from a human patient and evaluated to determine if that patient contains cells that express one or more of the genes listed in Table 4 at a level that is greater than the average level of expression observed in control cells. The expression of any number of the genes listed in Table 4 can be evaluated to diagnose severe SLE or SLE-AIP. For example, the expression of one or more than one (e.g., two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, or all 14) of the genes listed in Table 4 can be used. 
     The expression level can be greater than or less than the average level observed in control cells obtained from control mammals. Typically, a gene can be classified as being expressed at a level that is greater than or less than the average level observed in control cells if the expression levels differ by at least 1-fold (e.g., 1.5-fold, 2-fold, 3-fold, or more than 3-fold). In addition, the control cells typically are the same type of cells as those isolated from the mammal being evaluated. In some cases, the control cells can be isolated from one or more mammals that are from the same species as the mammal being evaluated. When diagnosing severe SLE or SLE-AIP, the control cells can be isolated from mammals having mild SLE or from healthy mammals such as healthy humans who do not have SLE. Any number of control mammals can be used to obtain the control cells. For example, control cells can be obtained from one or more healthy mammals (e.g., at least 5, at least 10, at least 15, at least 20, or more than 20 control mammals). 
     Any method can be used to determine whether or not a specific gene is expressed at a level that is greater or less than the average level of expression observed in control cells. For example, the level of expression from a particular gene can be measured by assessing the level of mRNA expression from the gene. Levels of mRNA expression can be evaluated using, without limitation, northern blotting, slot blotting, quantitative reverse transcriptase polymerase chain reaction (RT-PCR), or chip hybridization techniques. Methods for chip hybridization assays include, without limitation, those described herein. Such methods can be used to determine simultaneously the relative expression levels of multiple mRNAs. Alternatively, the level of expression from a particular gene can be measured by assessing polypeptide levels. Polypeptide levels can be measured using any method such as immuno-based assays (e.g., ELISA), western blotting, or silver staining. 
                     TABLE 4                  Genes with expression levels that differ between SLE patients having low and high IFN       scores                     Accession No.   Gene               M63835   Fc fragment of IgG, high affinity Ia, receptor for (CD64)       X54486   serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1       L13210   lectin, galactoside-binding, soluble, 3 binding protein       M33882   myxovirus (influenza) resistance 1, homolog of murine (interferon-           inducible protein p78)       AA203213   interferon-stimulated protein, 15 kDa       X99699   XIAP associated factor-1       AJ225089   2′-5′-oligoadenylate synthetase-like       U22970   interferon, alpha-inducible protein (clone IFI-6-16)       AB000115   hypothetical protein, expressed in osteoblast       AL047596   capicua homolog ( Drosophila )       AB006746   phospholipid scramblase 1       AL022318   similar to APOBEC1       U66711   lymphocyte antigen 6 complex, locus E       X55988   ribonuclease, RNase A family, 2 (liver, eosinophil-derived neurotoxin)                    
3. Identifying Mammals Predisposed to Develop Severe SLE and SLE-AIP
 
     The invention also provides methods for diagnosing a mammal (e.g., a human) as being predisposed to develop severe SLE or SLE-AIP. In one embodiment, a mammal can be diagnosed as being predisposed to develop severe SLE or SLE-AIP if it is determined that the mammal contains cells that express one or more of the genes listed in Table 4 at a level that is greater than the average level of expression of the same one or more genes observed in control cells obtained from control mammals. 
     As described above, the mammal can be any mammal such as a human, dog, mouse, or rat. Any cell type can be isolated and evaluated. For example, peripheral blood mononuclear cells (PBMC), total white blood cells, lymph node cells, spleen cells, or tonsil cells can be isolated from a human patient and evaluated to determine if that patient contains cells that express one or more of the genes listed in Table 4 at a level that is greater than the average level of expression observed in control cells. The expression of any number of the genes listed in Table 4 can be evaluated to diagnose a mammal as being predisposed to develop severe SLE or SLE-AIP. For example, the expression of one or more than one (e.g., two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, or all 14) of the genes listed in Table 4 can be used. 
     The expression level can be greater than or less than the average level observed in control cells obtained from control mammals. Typically, a gene can be classified as being expressed at a level that is greater than or less than the average level observed in control cells if the expression levels differ by at least 1-fold (e.g., 1.5-fold, 2-fold, 3-fold, or more than 3-fold). In addition, the control cells typically are the same type of cells as those isolated from the mammal being evaluated. In some cases, the control cells can be isolated from one or more mammals that are from the same species as the mammal being evaluated. When determining a mammal&#39;s susceptibility to develop severe SLE or SLE-AIP, the control cells can be isolated from mammals having mild SLE or from healthy mammals such as healthy humans who do not have SLE. Any number of control mammals can be used to obtain the control cells. For example, control cells can be obtained from one or more healthy mammals (e.g., at least 5, at least 10, at least 15, at least 20, or more than 20 control mammals). 
     Any method can be used to determine whether or not a specific gene is expressed at a level that is greater or less than the average level of expression observed in control cells. For example, the level of expression from a particular gene can be measured by assessing the level of mRNA expression from the gene. Levels of mRNA expression can be evaluated using, without limitation, northern blotting, slot blotting, quantitative reverse transcriptase polymerase chain reaction (RT-PCR), or chip hybridization techniques. Methods for chip hybridization assays include, without limitation, those described herein. Such methods can be used to determine simultaneously the relative expression levels of multiple mRNAs. Alternatively, the level of expression from a particular gene can be measured by assessing polypeptide levels. Polypeptide levels can be measured using any method such as immuno-based assays (e.g., ELISA), western blotting, or silver staining. 
     4. Arrays 
     The invention also provides nucleic acid arrays. The arrays provided herein can be two-dimensional arrays, and can contain at least 10 different nucleic acid molecules (e.g., at least 20, at least 30, at least 50, at least 100, or at least 200 different nucleic acid molecules). Each nucleic acid molecule can have any length. For example, each nucleic acid molecule can be between 10 and 250 nucleotides (e.g., between 12 and 200, 14 and 175, 15 and 150, 16 and 125, 18 and 100, 20 and 75, or 25 and 50 nucleotides) in length. In addition, each nucleic acid molecule can have any sequence. For example, the nucleic acid molecules of the arrays provided herein can contain sequences that are present within the genes listed in Tables 1, 2, 3, and/or 4. 
     Typically, at least 25% (e.g., at least 30%, at least 40%, at least 50%, at least 60%, at least 75%, at least 80%, at least 90%, at least 95%, or 100%) of the nucleic acid molecules of an array provided herein contain a sequence that is (1) at least 10 nucleotides (e.g., at least 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, or more nucleotides) in length and (2) at least about 95 percent (e.g., at least about 96, 97, 98, 99, or 100) percent identical, over that length, to a sequence present within a gene listed in Tables 1, 2, 3, and/or 4. For example, an array can contain 100 nucleic acid molecules located in known positions, where each of the 100 nucleic acid molecules is 100 nucleotides in length while containing a sequence that is (1) 30 nucleotides is length, and (2) 100 percent identical, over that 30 nucleotide length, to a sequence of one of the genes listed in Table 4. Thus, a nucleic acid molecule of an array provided herein can contain a sequence present within a gene listed in Tables 1, 2, 3, and/or 4, where that sequence contains one or more (e.g., one, two, three, four, or more) mismatches. 
     The nucleic acid arrays provided herein can contain nucleic acid molecules attached to any suitable surface (e.g., plastic or glass). In addition, any method can be use to make a nucleic acid array. For example, spotting techniques and in situ synthesis techniques can be used to make nucleic acid arrays. Further, the methods disclosed in U.S. Pat. Nos. 5,744,305 and 5,143,854 can be used to make nucleic acid arrays. 
     The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims. 
     EXAMPLES 
     Example 1 
     Identifying Genes that can be Used to Diagnose SLE 
     PBMCs were collected from 48 SLE patients and 42 healthy, age- and gender-matched control individuals. All patients had physician-verified SLE and met at least four of the eleven ACR criteria for lupus. The average, age of SLE patients was 45±11 years, and the average age of controls was 34±13 years. Each PBMC sample contained monocytes/macrophages, B and T lymphocytes, and natural killer cells. 
     For the first 11 patients and 11 controls, poly A +  mRNA was extracted from the collected PBMC samples. Briefly, 60 mL of peripheral blood was drawn into a heparinized syringe. Whole blood was layered over an equal volume of Histopaque and centrifuged at 400×g for 30 minutes at 25° C. Plasma was harvested and stored at −80° C. PBMCs were harvested and washed twice in 1×PBS, and the mRNA was isolated using a FastTrack mRNA isolation kit (Invitrogen, Carlsbad, Calif.). 
     For the next 37 patients and 31 controls, total RNA was extracted from the collected PBMC samples. Briefly, peripheral blood was drawn into CPT tubes (Becton-Dickinson, Franklin Lakes, N.J.), and plasma and PBMCs were collected according to manufacturer&#39;s protocol. Plasma was stored at −80° C., and total RNA was isolated from PBMCs using Trizol (Gibco-BRL, Invitrogen, Carlsbad, Calif.) followed by an RNeasy cleanup (Qiagen, Valencia, Calif.). 
     About 5 to 10 μg of total RNA or about 100-200 ng of poly A +  RNA was used to prepare biotinylated cRNA for hybridization using the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix, Inc., 2000). Briefly, RNA was converted to first strand cDNA using a T7-linked oligo(dT) primer (Genset, La Jolla, Calif.) followed by second strand synthesis (Gibco-BRL). The dscDNA was then used as template for labeled in vitro transcription reactions using biotinylated ribonucleotides (Enzo, Farmingdale, N.Y.). Fifteen μg of each labeled cRNA was hybridized to Affymetrix U95A GeneChips (Affymetrix, Santa Clara, Calif.) using standard conditions in an Affymetrix fluidics station. 
     After chip hybridization and initial data analysis, the expression values for 10,260 genes represented on the chip were compared between SLE patients and controls using a non-paired Student&#39;s T-test. 
     Affymetrix Microarray Suite (MAS) 4.0 software was used to generate expression values (referred to as an “average difference;” AD) for each gene. Each chip was scaled to an overall intensity of 1500 to correct for minor differences in overall chip hybridization intensity and to allow comparison between chips. A threshold of 20 AD units was assigned to any gene that was called “Absent” by MAS. In addition, any gene with an AD less than 20 was assigned this threshold. Data from U95Av1 and U95Av2 chips were aligned by discarding the 51 probe sets that were not present on both chips. The analysis identified 161 unique genes that were differentially expressed using the following criteria: p&lt;0.001, fold-change &gt;1.5, mean expression value difference &gt;100 units. 
     Despite the use of the same oligo(dT) primer for cDNA synthesis, consistent differences between the raw AD values obtained from polyA +  RNA and total RNA samples were noted that were not corrected by chip scaling. Furthermore, each dataset (i.e., polyA +  RNA and total RNA) showed similar differential gene expression between the respective groups of patients and controls. For example, the initial 11/11 dataset identified a larger than expected number of interferon-regulated genes. A gene-by-gene scaling approach thus was employed so that the two datasets could be combined and examined together. The scaling strategy was based on the assumption that the mean expression level (mean AD) of genes between the two control groups (total vs. polyA +  RNA) should be equal. For each gene, the mean of the two control groups was compared to generate the gene-specific scaling factor. The polyA +  samples were corrected by the scaling factor so that the means of the two control groups (total and polyA + ) were identical. This scaled dataset then was used for all subsequent analysis. 
     Identification of stress response genes: During the course of collecting and analyzing the various samples, it was determined that many genes in peripheral blood cells undergo striking stress responses following incubation ex vivo, even during somewhat limited periods of time (i.e., less than 1 hour). A formal experiment was designed and performed to identify those genes that were regulated by incubation of cells ex vivo. Changes in global gene expression were examined using whole blood after overnight shipment by a commercial carrier. This study utilized samples from eight healthy control individuals. Approximately 30 mL of blood was drawn into four CPT tubes. PBMCs were isolated from two tubes and resuspended in RNAlater (Ambion, Austin, Tex.). RNAlater immediately lyses the cells and protects the RNA from degradation, thus providing an accurate profile of gene expression immediately ex vivo. The RNA preserved in RNAlater and the two CPT tubes with whole blood were shipped by overnight carrier. Total RNA was extracted and prepared for hybridization as described above. Thus, global gene expression profiles were obtained from both a fresh blood sample and from blood shipped overnight, with both samples coming from the same blood draw. 
     Data were analyzed using MAS 4.0 and each chip was scaled to 1500. Absent and low expression values were assigned a threshold of 20 AD units as described above. A paired T-Test was used to compare the gene expression profiles of fresh blood vs. blood shipped by overnight carrier. Based on this experiment, 2076 genes were identified that displayed significant changes in expression under these environmental stresses (p&lt;0.01). These genes, many of which are involved in various cell stress pathways, were excluded from further analysis due to the high level of variability that they exhibited. 
     Comparison analyses: The individual gene expression levels of SLE patients and controls were compared using an unpaired Student&#39;s T-test. Genes selected for further analysis met the following three criteria: 
     (i) p&lt;0.001 by unpaired T-test, 
     (ii) change in expression of at least 1.5-fold when comparing the means of the two groups, and 
     (iii) difference in expression of at least 100 when comparing the means of the two groups. 
     Overall, 484 genes were differentially expressed at the p&lt;0.001 level, while 178 genes were both differentially expressed at the p&lt;0.001 level and showed mean AD values that differed by more than 1.5-fold. The final dataset of 161 individual genes (represented by 171 Genbank accession numbers) met all three criteria. These genes, which demonstrated differential expression between SLE patients and normal controls, are listed in Table 1. 
     Expression values for each of the 161 genes were converted to “fold-differences” by dividing each value by the mean of the control expression values. Unsupervised hierarchical clustering then was applied to the dataset. Hierarchical clustering was performed using Cluster and visualized using TreeView (M. Eisen, Stanford; available on the internet at rana.lbl.gov). This analysis identified gene expression patterns that differentiated most SLE patients from healthy controls. Thirty-seven of the 48 SLE patients clustered tightly together, while 11 of the patients co-clustered with controls. Six of the 42 control subjects clustered together with the large group of patients. 
     Most (124 of 161, 77%) of the genes that best distinguished SLE from control PBMCs were expressed at higher levels in SLE patients than in normal subjects. These are presented in Table 2. A number of these genes have known or suspected roles in the immune system. For example, many SLE patients were found to overexpress mRNA for the following cell surface markers: TNFR6 (Fas/CD95), a death receptor; ICAM-1 (CD54), an adhesion molecule; CD69, an activation antigen; and complement receptor 1. Of interest, three different Fc receptors were expressed at elevated levels: the Fe receptor for IgA (FCAR, CD89), and the IgG receptors FcRγIIA (CD32) and FcRγI (CD64). Three molecules in the inflammatory IL-1 cytokine pathway—IL-1β, the IL-1 receptor II (IL-1RII), and the IL-1 receptor antagonist—also were generally overexpressed. Interestingly, Jagged 1, a ligand for Notch 1 located in the SLE susceptibility interval on chromosome 20p, also was overexpressed in some patients. Other notable genes that were overexpressed in SLE patients include the signaling molecules MAP3K-8, RAB27, interleukin-6 signal transducer, the transcription factors v-ets 2, MADS box transcription factor 2, and the estrogen responsive zinc finger protein 147. 
     A number of genes were expressed at lower levels in patients than controls. These are presented in Table 3, and included T cell genes such as Lck, TCR delta, and TCR beta. Flow cytometry of freshly stained PBMCs was used to confirm that there was a T cell lymphopenia in many of the patients (i.e., about a 20% decrease, on average, in percentage of CD3 +  T cells). The patients also demonstrated a significant increase in the percentage of monocytes, as compared to the percentage of monocytes in controls. Specifically, PBMC populations from SLE patients (n=18) contained 52% T cells, 5% B cells, 28% monocytes/macrophages, and 15% NK cells. PMBC populations from control subjects (n=28) contained 65% T cells, 6% B cells, 13% monocytes/macrophages, and 16% NK cells. The percentages of T cells (p=0.014) and monocytes (p=0.00001) thus differed between SLE and controls. These differences in baseline cell populations clearly contribute to some of the differences in gene expression observed, and highlight the importance of documenting cell percentages in mixed cell populations. 
     Identification of IFN-regulated genes: One of the most striking mRNA clusters contained several genes previously identified as being interferon-regulated (Der et al. (1998)  Proc. Natl. Acad. Sci. U.S.A.  95:15623). Interferons are highly active cytokines important for maintaining viral immunity (IFN-α and IFN-β) and for mediating TH1 immune responses (IFN-γ). Genes in this cluster were up-regulated in about half of the SLE patients, and were expressed at low levels in most of the control subjects. 
     Experiments were conducted to examine the extent to which the genes in this cluster could be regulated in PBMCs by IFN treatment in vitro. Peripheral blood was drawn from each of four healthy control individuals. PBMCs were isolated over Lymphocyte Separation Medium (Mediatech Cellgro, Herndon, Va.) according to the manufacturer&#39;s protocol. After the last wash, cells were resuspended in complete media (RPMI1640, 10% heat inactivated FBS, 2 mM L-glutamine, pen/strep) at a final concentration of 2×10 6  cells/mL. PBMCs were cultured for six hours at 37° C. with the following additions: 
     (i) PBS+0.1% BSA control, 
     (ii) IFN-α and IFN-β (R&amp;D Systems, Minneapolis, Minn.), each at 1000 U/mL in PBS+0.1% BSA, and 
     (iii) IFN-γ (R&amp;D Systems, Minneapolis, Minn.), 1000 U/mL in PBS+0.1%. 
     Following the incubation, total RNA was isolated, and cRNA probes were prepared for chip hybridization. Data were analyzed in MAS 4.0, and all chips were scaled to 1500. Absent and low expression values were assigned a threshold of 20 AD units as described above. Genes that met both of the criteria below in all four experiments were identified as IFN-regulated: 
     (i) change in expression of at least 2-fold when compared to untreated control, and 
     (ii) difference in expression of at least 500 AD units when compared to untreated control. 
     Changes in gene expression following IFN treatment were assessed relative to a six-hour control culture. This analysis identified 286 genes that demonstrated more than a 2-fold change in expression from baseline, and an absolute mean difference in the level of expression of greater than 500 units. The induction of many known IFN-regulated genes, such as Stat1, myxovirus resistance 1 (Mx-1), and ISGF-3, validated the approach. Using this list of IFN-regulated genes, 13 of 14 unique genes in the cluster were identified as bona fide IFN-regulated transcripts. Overall, 23 of the 161 genes (14.3%) were found to be IFN-regulated, compared with 7 genes (4.3%) that would have been expected by chance alone. The overrepresentation of interferon-regulated genes in the list of transcripts that best discriminated SLE patients from controls was consistently observed when a variety of different filters were used to define both IFN-regulated and SLE genes. 
     The mRNA levels of the IFNs themselves were not significantly different between patients and controls. Plasma/serum IFN-γ and IFN-α proteins were measured by ELISA (Pierce Endogen, Rockford, Ill.). IFN-γ was undetectable in all samples (less than 25 pg/mL). IFN-α was detectable in only two patients (26 and 29 pg/mL) and one control subject (56 pg/mL). 
     An IFN “score” was calculated for each patient and control, based on expression of genes in the IFN cluster. Scores were calculated by first normalizing the expression values within each row of genes so that the maximum value in any row was 1.0. Then the columns (samples) were summed to obtain the score. The IFN score (mean±SD) for patients was 3.7±2.6, compared to controls 1.5±0.5, p=4.2×10 −7 . Approximately half of the SLE patients exhibited an elevated IFN score, while the others had scores indistinguishable from controls ( FIG. 1 ). 
     The lupus patient population was divided into two groups, with the IFN-high group containing the 24 patients with the highest IFN scores, and the IFN-low group containing the 24 patients with the lowest scores. Differences in gene expression were examined. Table 4 contains a list of the genes that displayed differential expression between the IFN-high and IFN-low groups. All of the genes listed in Table 4 were expressed at a greater level in the IFN-high group that in the IFN-low group. 
     Studies then were conducted to determine whether the IFN gene expression signature correlated with clinical features of SLE. SLE typically is diagnosed using eleven criteria developed by the ACR (Hochberg (1997)  Arthritis Rheum.  40:1725). These criteria span the clinical spectrum of SLE and include skin criteria (malar rash, oral ulcers, photosensitivity, and discoid rash), systemic criteria (pleuritis or pericarditis, arthritis, renal disease, or CNS involvement), and laboratory criteria (cytopenias, anti-dsDNA or anti-phospholipid Abs, and antinuclear antibodies). A patient must meet four of these criteria to be classified as having definite SLE. The number of SLE criteria met by each patient was plotted against his or her IFN score ( FIG. 2 ). This analysis revealed that the IFN score was correlated with the number of SLE criteria displayed in each patient. 
     In a similar analysis, the clinical features of the 24 SLE patients with the highest IFN scores (IFN-high) were compared to the clinical features of the 24 SLE patients with the lowest scores (IFN-low). As depicted in  FIG. 3 , patients in the IFN-high group had a significantly higher number of SLE criteria (6.8±1.3) than those in the IFN-low group (5.7±1.1; p=0.004). Patients in the IFN-high group also showed a trend towards being diagnosed with SLE at an earlier age (25±12 compared with 30±13 years; p=0.192). Importantly, 15 of 24 patients (63%) in the IFN-high group fulfilled the ACR criteria for involvement of kidneys and/or the CNS, the most serious complications of lupus, compared with 5 of 24 patients (21%) in the IFN-low group ( FIG. 4 ). In addition, 18 of 24 IFN-high patients (75%) showed hematologic involvement in their disease (severe leukopenia, hemolytic anemia or thrombocytopenia), compared with only 5 of 24 IFN-low patients (21%). An elevated interferon score thus correlated with the more severe manifestations of SLE. 
     The hypothesis that IFNs are important in the pathogenesis of lupus is supported by a number of observations. Mice transgenic for IFN-γ develop lupus-like autoimmunity (Seery et al. (1997)  J. Exp. Med.  186:1451), and lupus-prone NZB/NZW F1 mice treated with anti-IFN-γ Abs or bred onto the IFN-γ −/−  background show amelioration of disease (Jacob et al. (1987)  J. Exp. Med.  166:798; and Balomenos et al. (1998)  J. Clin. Invest.  101:364). The interferon-inducible gene IFI-202 has been identified as an SLE gene within the Nba2 SLE locus on mouse chromosome 1, NZB mice, the parental strain for this locus, show constitutively high expression of this transcription factor (Rozzo et al. (2001)  Immunity  15:435). In humans, elevated levels of IFN-α have been reported in the sera of some SLE patients (for review see Ronnblom and Alm (2001)  J. Exp. Med.  194:59), and a significant percentage of individuals treated with IFN-α for viral hepatitis develop lupus-related autoantibodies (Fukuyama et al. (2000)  Am. J. Gastroenterol.  95:310). Finally, IFN-α in the sera of some pediatric SLE patients induces maturation of monocytes into highly active antigen-presenting plasmacytoid dendritic cells (Blanco et al. (2001)  Science  294:1540). 
     While genes in IFN-signaling pathways exhibited dysregulated expression in some lupus patients, the mRNA levels of the IFNs themselves were not significantly different between patients and controls. IFN-γ protein was not detectable by ELISA in any patient or control sample, and IFN-α was detectable in only 2 of 48 patients and 1 of 42 controls. Thus, other cytokines that utilize Jak/Stat signaling pathways downstream of their receptors, such as IL-4, IL-13, or IL-2 (Hirano et al. (2000)  Oncogene  19:2548), could contribute to the gene expression patterns observed. 
     OTHER EMBODIMENTS 
     It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.