WO2003016476A2 - Gene expression profiles in glomerular diseases - Google Patents

Abstract

The present invention is based on the elucidation of the global changes in gene expression in PBL of the patients with glomerular diseases exhibiting different types of clinical and pathological features of glomerular nephropathy as compared to normal PBL as well as the identification of individual genes that are differently expressed in PBL of patients with glomerular diseases.

Description

GENE EXPRESSION PROFILES IN GLOMERULAR DISEASES

INVENTORS: WILLIAM MUNGER, RONALD FAULK, HONGWEI SUN, HITOSHI SASAI, IWAO WAGA, AND JUN YAMAMOTO

FIELD OF THE INVENTION

The invention relates generally to differences in gene expression in tissue from humans with diseased and normal kidneys. The invention relates specifically to representative gene expression profiles comprising panels of genes that are differentially expressed or regulated in renal biopsy samples (Peripheral Blood Leukocyte) from patients with kidney diseases such as, IgA nephropathy (IgAN), antineutrophil cytoplasmic antibody-associated glomerulonephritis (ANCA), Focal Segmental Glomeruloscrelosis (FSGS), lupus nephritis and Minimal Change Disease.

BACKGROUND OF THE INVENTION Abnormal renal function is among the most common ailments requiring intensive medical care. In addition, the incidence and prevalence rates of end-stage renal disease (ESRD) in the United States continue to increase. In 1995, the incidence rate was 262 per million population, with a point prevalence rate of 975 per million population. The exact number of individuals with abnormal renal function but who have not yet progressed to ESRD is difficult to assess. The incidence rate per million population of treated end-stage renal disease (ESRD) has been increasing at similar rates in most countries that record counts of new ESRD patients per year. Data from the United States Renal Data System (USRDS) suggest an exponential growth for both incidence rates and prevalence rates (Port FK, Dis Mon (1998) May; 44(5): 214-234). IgA nephropathy (IgAN) is the most common type of immunologically mediated glomerulonephritis (GN) and is characterized by deposition in the glomerular mesangium of IgA together with C3, C5b-9, and properdin. The co-deposition of IgA together with IgG and/or IgM can lead to a more progressive course of disease in afflicted patients. Fifteen to forty percent of primary glomerulonephritis in parts of Europe, Asia and Japan has been linked to IgAN and it is well accepted that IgAN can lead to ESRD. IgAN often presents either as asymptomatic microscopic hematuria and/or proteinuria

(most common in adults), or episodic gross hematuria following upper respiratory and other infections or exercise. The course of IgAN is variable, with some patients showing no decline in glomerular filtration rate (GFR) over decades and others developing the nephrotic syndrome, hypertension and renal failure. Minimal Change Disease (Min. Ch.), also known as Minimal Change Nephrotic syndrome, a type of glomerulonephritis common in younger and in older adults, may be induced by non-complement fixing antibodies binding to glomerular epithelial cell membrane antigens. The resulting non-inflammatory lesions may be caused by proteases or oxidants or detachment of the glomerular epithelial cells from the underlying basement membrane (Couser W.G.,

Kidney Int Suppl 42 :S 19-26, 1993). Morphological changes of Min. Ch. include thinning of the glomerular basement membrane, as well as moderately increased glomerular area, total glomerular cells per total glomerular area and relative interstitial volume. Min. Ch. can be misdiagnosed, e.g. , as focal segmental glomerulosclerosis, but can be most accurately diagnosed by imrnuno fluorescence microscopy of renal biopsies, as opposed to light or electron microscopy (Danilewicz et al, PolJPathol 47(4): 209-214, 1996).

In necrotizing crescentic glomerulonephritis (NCGN) the internal renal structures, particularly the glomeruli, are damaged and there is a rapid loss of kidney function. The glomeruli are the portions of the internal kidney structures where the blood flows through very small capillaries and is filtered through membranes to form urine. Rapidly progressive glomerulonephritis (inflammation of the glomerulus) includes any type of glomerulonephritis in which progressive loss of kidney function occurs over days to weeks rather than months to years, and in which a kidney biopsy shows crescents in at least 75% of the glomeruli. Morphologically, crescent ("new-moon") -shaped abnormalities are observed upon biopsy of the kidney. It may manifest itself as an acute nephritic syndrome or unexplained renal failure and often rapidly progresses to renal failure and end-stage renal disease.

NCGN occurs in about 1 out of 10,000 people. While it is most common in people 40 to 60 years old, and slightly more common in men, it may occur in either sex and at any age, depending on the cause. It is unusual in preschool children, and slightly more common in later childhood.

Many conditions are known to cause or increase the risk for development of this syndrome. These include vascular diseases such as vasculitis or polyarteritis, abscess of any internal organ, collagen vascular diseases such as lupus nephritis and Henoch-Schonlein purpura, Goodpasture's syndrome, IgA nephropathy, membranoproliferative GN, anti- glomerular basement membrane antibody disease, a history of malignant tumors or blood or lymphatic system disorders, and exposure to hydrocarbon solvents. The symptoms are similar regardless of the cause.

Common symptoms include edema (swelling of the face, eyes, ankles, feet, extremities, abdomen, or generalized swelling). In addition, urine can be dark or smoke colored. There can also be blood in the urine and decreased urine volume. Symptoms that may also appear include the following: fever, myalgia (muscle aches), arthralgia (joint aches), shortness of breath, cough, malaise (general ill feeling), abdominal pain, loss of appetite, and diarrhea.

Signs and tests include an examination that reveals edema. Also, circulatory overload, with associated abnormal heart and lung sounds, may be present and the blood pressure may be elevated. Rapid, progressive loss of kidney function may be present. Urinalysis may be abnormal, showing blood in the urine, urine protein, white blood cells, casts, or other abnormalities. The BUN and creatinine may rise rapidly and the creatinine clearance decreases. Anti-glomerular basement membrane antibody tests may be positive in some cases. Complement levels may be decreased in some cases. Other tests for suspected causes may be performed; however, a kidney biopsy confirms crescentic glomerulonephritis.

Treatment for NCGN varies with the suspected cause. Treatment goals may be a cure of the causative disorder, the control of symptoms, or the treatment of renal failure. Corticosteroids may relieve symptoms in some cases. Other medications may include immunosuppressive agents including cyclophosphamide and azathioprine, anticoagulant (prevent the blood from clotting) or thrombolytic (clot-dissolving) medications, and others depending on the cause of the disorder. Plasmapheresis may relieve the symptoms in some cases where blood plasma (the fluid portion of blood) containing antibodies is removed and replaced with intravenous fluids or donated plasma (without antibodies). Dialysis or a kidney transplant, however, may ultimately be necessary. Without treatment, NCGN may progress to renal failure and end-stage renal disease in 6 months or less, although a few cases may resolve spontaneously. The probable outcome improves with treatment, with as many as 75% of the cases showing attenuation of the symptoms, although the disorder may recur. If the disease occurs in childhood, it is likely that renal failure will eventually develop. Complications of NCGN include congestive heart failure, pulmonary edema, hyperkalemia, acute renal failure, chronic renal failure, and end-stage renal disease.

Other common glomerular disorders include antineutrophil cytoplasmic antibody- associated glomerulonephritis (ANCA), focal segmental glomerulosclerosis (FSGS) and lupus nephritis. In ANCA, patients have circulating antibodies against components of neutrophil primary granules. Several types of ANCA have been characterized, in which patients produce antibodies directed against different granulocytic enzymes. ANCA occur in patients with certain forms of necrotizing vasculitis. The major ANCA-associated vasculitides are Wegener's granulomatosis (WG), microscopic polyangiitis (MPA), and Churg-Strauss syndrome (CSS) (Jennette and Falk, 1995). These account for 40-80% of necrotizing crescentic glomerulonephritis, exhibit no immune deposits, and have been designated as pauci-immune necrotizing vasculitis. Treatment typically involves a combination of steroids (such as corticosteroids) and cytotoxic agents. A diagnosis of FSGS is made in about 15-20% of adults with idiopathic nephrotic syndrome and may be primary or secondary to a number of different disease causes (heroin abuse, HIV, sickle cell disease, obesity or other kidney diseases). Symptoms may include proteinuria, reduced glomerular filtration rate, edema and hypertension. Although the therapy of FSGS is controversial, immunosuppressive treatments with steroids (cylcosporin) and cytotoxics are commonly used (Appel, G.B., Cecil Textbook of Medicine, Chap. 79, pp. 572-578, Bennett et al, eds., W.B. Saunders Co., Philadelphia, 1996.) Lupus nephritis is an inflammation of the kidney caused by systemic lupus erythematosus (SLE), a disease of the immune system. SLE causes harm to the skin, joints, kidneys, and brain. It is related to the autoimmune process of lupus, where the immune system produces antibodies (antinuclear antibody and others) against body components. Complexes of these antibodies and complement accumulate in the kidneys and ignite an inflammatory response. Lupus causes various disorders of the internal structures of the kidney, including interstitial nephritis, mesangial GN, membranous GN, membranoproliferative GN, diffuse proliferative GN, and others. Diagnosis may require urine and blood tests and x-rays of the kidneys. Treatment depends on the symptoms. Medicines can decrease swelling, lower blood pressure, and decrease inflammation by suppressing the immune system. The patient may need to limit protein, sodium, and potassium intake.

If intervention is expected to be successful in halting or slowing down renal disease progression, means of accurately assessing the early manifestations of renal disease need to be established. One way to accurately assess the early manifestations of renal disease is to identify markers that are uniquely associated with disease progression. Likewise, the development of therapeutics to prevent or repair kidney damage relies on the identification of kidney genes responsible for kidney disease induction disease progression and/or cell growth.

SUMMARY OF THE INVENTION

The present invention is based on the elucidation of the global changes in gene expression in PBL of patients with glomerular diseases exhibiting different clinical and pathological features as compared to normal tissue as well as the identification of individual genes that are differentially expressed in PBL of patients with glomerular disease.

The invention includes methods of screening for an agent that modulates glomerular diseases, comprising: preparing a first gene expression profile of a PBL population; exposing the cell population to the agent; preparing second gene expression profile of the agent exposed cell population; and comparing the first and second gene expression profiles.

The invention also includes methods of treating a patient with glomerular disease, comprising administering a pharmaceutical composition to the patient; preparing a gene expression profile from a PBL of the patient; and comparing the patient gene expression profile to a gene expression from a normal PBL.

The invention includes methods of diagnosing glomerular diseases in a patient comprising the step of detecting the level of expression in PBL of two or more genes from Tables 1-31; wherein differential expression of the genes in Tables 1-31 is indicative of glomerular diseases.

The invention further includes methods of diagnosing the subtype of glomerular disease in a patient comprising the step of detecting the level of expression in a PBL sample of two or more genes from Tables 1-31; wherein differential expression of the genes in Tables 1-31 is indicative of the subtype of glomerular disease. The subtypes of GN can be selected from the group consisting of: IgAN, Minimal Change Disease, FSGS, ANCA, and Lupus nephritis.

All of these methods may include the step of detecting the expression levels of at least about 3, 4, 5, 6, 7, 8, 9, 10 or more genes in Tables 1-31. Preferably, expression of all of the genes or nearly all of the genes in Tables 1-31 may be detected.

The invention further includes sets of at least two or more probes, wherein each of the probes comprises a sequence that specifically hybridizes to a gene in Tables 1-31 as well as solid supports comprising at least two or more probes, wherein each of the probes comprises a sequence that specifically hybridizes to a gene in Tables 1-31.

The invention also includes computer systems comprising a database containing information identifying the expression level of a set of genes in PBL from patients with a glomerular disease comprising at least two genes in Tables 1-31; and a user interface to view the information. The database may further comprise sequence information for the genes as well as information identifying the expression level for the set of genes in PBL from normal control populations. The database may further contain or be linked to descriptive information from an external database, which information correlates said genes to records in the external database. Lastly the invention includes methods of using the disclosed computer systems to present information identifying the expression level in a tissue or cell of a set of genes comprising at least two of the genes in Tables 1-31, comprising the step of comparing the expression level of at least one gene in Tables 1-31 in the tissue or cell to the level of expression of the gene in the database. DETAILED DESCRIPTION

Many biological functions are accomplished by altering the expression of various genes through transcriptional (e.g., through control of initiation, provision of RNA precursors, RNA processing, etc.) and/or translational control. For example, fundamental biological processes such as cell cycle, cell differentiation and cell death, are often characterized by the variations in the expression levels of groups of genes.

Changes in gene expression also are associated with pathogenesis. For example, the lack of sufficient expression of functional tumor suppressor genes and/or the over expression of oncogene/protooncogenes may lead to tumorgenesis or hyperplastic growth of cells (Marshall, Cell, 64: 313-326 (1991); Weinberg, Science, 254:1138-1146 (1991). Thus, changes in the expression levels of particular genes (e.g., oncogenes or tumor suppressors) serve as signposts for the presence and progression of various diseases.

Monitoring changes in gene expression may also provide certain advantages during drug screening development. Often drugs are screened for the ability to interact with a major target without regard to other effects the drugs have on cells. Often such effects cause toxicity in the whole animal, which prevent the development and use of the potential drug.

The present invention is based on the investigation of the differences in the global changes in gene expression in the PBLs of patients with diseased and normal kidneys. The present inventors screened PBLs from patients with several types of glomerular disease: IgA nephropathy, ANCA, FSGS, minimal change nephrotic syndrome and lupus nephritis (systemic lupus erythematosus with nephropathy).

The etiology of many glomerular diseases is thought to be caused by circulating cells. It is highly probable that the cause of IgA nephropathy and FSGS, for example, exists in circulating blood cells due to the fact that kidneys transplanted from normal donors often manifest IgA nephropathy pathology in the recipient with diagnosed IgA nephropathy or FSGS. It is also well known that level of serum IgA in patients with IgA nephropathy is significantly higher than normal, suggesting the involvement of humoral factors in the etiology of IgA nephropathy.

In the present study, gene expression profiles were prepared from peripheral blood leukocytes from 8 patients with IgA nephropathy, 5 patients with ANCA, 5 patients with FSGS, 7 patients with minimal change nephrotic syndrome, 8 patients with lupus nephritis (systemic lupus erythematosus with nephropathy) and 11 normal controls.

The expression profiles of each subtype of glomerular disease were then compared with the other glomerular disease subtypes. As a result, the present inventors identified altered gene expression profiles specific to each subtype of glomerular disease. The gene expression profile specific to each subtype of glomerular disease can be used for the differential diagnosis of glomerular disease and the development of new classes of drugs specific for each subtype of glomerular disease. Such new classes of drugs would be capable of treating the disease state with fewer side effects, unlike conventional drugs such as steroids and immunosuppressants that are widely used against chronic inflammatory diseases.

Assay Formats

The genes identified as being differentially expressed in glomerular diseases (Tables 1- 31) may be used in a variety of nucleic acid detection assays to detect or quantitate the expression level of a gene or multiple genes in a given sample. For example, traditional

Northern blotting, nuclease protection, RT- PCR and differential display methods may be used for detecting gene expression levels. Those methods are useful for some embodiments of the invention, in particular when expression levels for a few genes, for instance 50 or less, are assayed. PCR-based assays may be formatted for high through-put screening. Methods and assays of the invention, however, are most efficiently designed with hybridization-based methods for detecting the expression of a large number of genes.

Any hybridization assay format may be used, including solution-based and solid support- based assay formats. Solid supports containing oligonucleotide probes for differentially expressed genes of the invention can be filters, polyvinyl chloride dishes, silicon or glass based chips, etc. Such supports and hybridization methods are widely available, for example, those disclosed by Beattie (WO 95/11755). Any solid surface to which oligonucleotides can be bound, either directly or indirectly, either covalently or non-covalently, can be used.

A preferred solid support is a high density array or DNA chip. These contain a particular oligonucleotide probe in a predetermined location on the array. Each predetermined location may contain more than one molecule of the probe, but each molecule within the predetermined location has an identical sequence. Such predetermined locations are termed features. There may be, for example, from 2, 10, 100, 1000 to 10,000, 100,000 or 400,000 of such features on a single solid support. The solid support, or the area within which the probes are attached, may be on the order of about a square centimeter. Oligonucleotide probe arrays for expression monitoring can be made and used according to any technique known in the art (see for example, Lockhart et al, Nat. Biotechnol. (1996) 14, 1675-1680; McGall et al, Proc. Nat. Acad. Sci. USA (1996) 93, 13555-13460). Such probe arrays may contain at least two or more oligonucleotides that are complementary to or hybridize to two or more of the genes described in Tables 1-31. For instance, such arrays may also contain oligonucleotides that are complementary or hybridize to at least about 2, 3, 4, 5, 6, 7, 8, 9, 10,

20, 30, 50, 70, 100 or more of the genes described herein.

The genes that are assayed according to the present invention are typically in the form of mRNA or reverse transcribed mRNA. The genes may be cloned or not. The genes also may be amplified or not. The cloning or amplification does not appear to bias the representation of genes within a population. It may be preferable, however, to use polyA+ RNA as a source as it can be used with less processing steps.

The sequences of the expression marker genes of the invention are in the public databases. Tables 1-31 provide the GenBank Accession under the column labeled "Affy Name." The sequences of the genes in GenBank are publicly available (see www.ncbi.nlm.nih.gov) and are herein expressly incorporated by reference as of the filing date of this application as are all related sequences such as shorter fragments, sequence variants, etc.

Probes based on the sequences of the genes described above may be prepared by any commonly available method. Oligonucleotide probes for interrogating the tissue or cell sample are preferably of sufficient length to specifically hybridize only to appropriate, complementary genes or transcripts. Typically the oligonucleotide probes will be at least about 10, 12, 14, 16,

18, 20 or 25 nucleotides in length. In some cases longer probes of at least about 30, 40, or 50 nucleotides will be desirable.

As used herein, oligonucleotide sequences that are complementary to one or more of the genes described in Tables 1-31, refer to oligonucleotides that are capable of hybridizing under stringent conditions to at least part of the nucleotide sequences of said genes. Such hybridizable oligonucleotides will typically exhibit at least about 75 % sequence identity at the nucleotide level to said genes, preferably at least about 80% or 85% sequence identity or more preferably at least about 90% or 95% or more sequence identity to said genes. As used herein, the term "bind(s) substantially" refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target polynucleotide sequence.

As used herein, the terms "background" or "background signal intensity" refer to hybridization signals resulting from non-specific binding, or other interactions, between the labeled target nucleic acids and components of the oligonucleotide array (e.g., the oligonucleotide probes, control probes, the array substrate, etc). Background signals may also be produced by intrinsic fluorescence of the array components themselves. A single background signal can be calculated for the entire array, or a different background signal may be calculated for each target nucleic acid. In a preferred embodiment, background is calculated as the average hybridization signal intensity for the lowest 5% to 10% of the probes in the array, or, where a different background signal is calculated for each target gene, for the lowest 5% to 10% of the probes for each gene. Of course, one of skill in the art will appreciate that where the probes to a particular gene hybridize well and thus appear to be specifically binding to a target sequence, they should not be used in a background signal calculation. Alternatively, background may be calculated as the average hybridization signal intensity produced by hybridization to probes that are not complementary to any sequence found in the sample (e.g., probes directed to nucleic acids of the opposite sense or to genes not found in the sample such as bacterial genes where the sample is mammalian nucleic acids). Background can also be calculated as the average signal intensity produced by regions of the array that lack any probes at all.

As used herein, the phrase "hybridizing specifically to" refers to the binding, duplexing, or hybridizing of a molecule substantially to or only to a particular nucleotide sequence or sequences under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. Assays and methods of the invention may utilize available formats to simultaneously screen at least about 100, preferably at least about 1000, more preferably at least about 10,000 and most preferably at least about 100,000-1,000,000 different nucleic acid hybridizations.

As used herein, the term "probe" is defined as a nucleic acid, capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. As used herein, a probe may include natural (i.e., A, G, U, C, or T) or modified bases (7- deazaguanosine, inosine, etc.). In addition, the bases in probes may be joined by a linkage other than a phosphodiester bond, so long as it does not interfere with hybridization. Thus, probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages.

As used herein, the terms "mismatch control" or "mismatch probe" refer to a probe whose sequence is deliberately selected not to be perfectly complementary to a particular target sequence. For each mismatch (MM) control in a high-density array there typically exists a corresponding perfect match (PM) probe that is perfectly complementary to the same particular target sequence. The mismatch may comprise one or more bases.

While the mismatch(s) may be located anywhere in the mismatch probe, terminal mismatches are less desirable as a terminal mismatch is less likely to prevent hybridization of the target sequence. In a particularly preferred embodiment, the mismatch is located at or near the center of the probe such that the mismatch is most likely to destabilize the duplex with the target sequence under the test hybridization conditions. As used herein, the term "perfect match probe" refers to a probe that has a sequence that is perfectly complementary to a particular target sequence. The test probe is typically perfectly complementary to a portion (subsequence) of the target sequence. The perfect match (PM) probe can be a "test probe", a "normalization control" probe, an expression level control probe and the like. A perfect match control or perfect match probe is, however, distinguished from a "mismatch control" or "mismatch probe."

As used herein, the term "stringent conditions" refers to conditions under which a probe will hybridize to its target subsequence, but with only insubstantial hybridization to other sequences or to other sequences such that the difference may be identified. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH.

Typically, stringent conditions will be those in which the salt concentration is at least about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C for short probes (e.g. 10 to 50 nucleotide). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.

As used herein, "highly stringent conditions" include those that (1) employ low ionic strength and high temperature for washing, for example, 0.015 M NaCl/0.0015 M sodium citrate/0.1% SDS at 50°C, or (2) employ during hybridization a denaturing agent such as formamide, for example, 50% (vol vol) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrate at 42°C. Another example is hybridization in 50% formamide, 5x SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1 % SDS, and 10%) dextran sulfate at 42°C, with washes at 42°C in 0.2x SSC and 0.1% SDS. A skilled artisan can readily determine and vary the stringency conditions appropriately to obtain a clear and detectable hybridization signal.

The "percentage of sequence identity" or "sequence identity" is determined by comparing two optimally aligned sequences or subsequences over a comparison window or span, wherein the portion of the polynucleotide sequence in the comparison window may optionally comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical submit (e.g., nucleic acid base or amino acid residue) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Percentage sequence identity when calculated using the programs GAP or BESTFIT (see below) is calculated using default gap weights.

Probe design

One of skill in the art will appreciate that an enormous number of array designs are suitable for the practice of this invention. The high density array will typically include a number of probes that specifically hybridize to the sequences of interest. See WO 99/32660 for methods of producing probes for a given gene or genes. In addition, in a preferred embodiment, the array will include one or more control probes.

High density array chips of the invention include "test probes." Test probes could be oligonucleotides that range from about 5 to about 500 nucleotides, more preferably from about 10 to about 40 nucleotides and most preferably from about 15 to about 40 nucleotides in length. In other particularly preferred embodiments the probes are about 20 or 25 nucleotides in length. In another preferred embodiment, test probes are double or single strand DNA sequences. DNA sequences are isolated or cloned from natural sources or amplified from natural sources using native nucleic acid as templates. These probes have sequences complementary to particular subsequences of the genes whose expression they are designed to detect. Thus, the test probes are capable of specifically hybridizing to the target nucleic acid they are to detect.

In addition to test probes that bind the target nucleic acid(s) of interest, the high density array can contain a number of control probes. The control probes fall into three categories referred to herein as 1) normalization controls; 2) expression level controls; and 3) mismatch controls. Normalization controls are oligonucleotide or other nucleic acid probes that are complementary to labeled reference oligonucleotides or other nucleic acid sequences that are added to the nucleic acid sample to be screened. The signals obtained from the normalization controls after hybridization provide a control for variations in hybridization conditions, label intensity, "reading" efficiency and other factors that may cause the signal of a perfect hybridization to vary between arrays. In a preferred embodiment, signals (e.g., fluorescence intensity) read from all other probes in the array are divided by the signal (e.g., fluorescence intensity) from the control probes thereby normalizing the measurements.

Virtually any probe may serve as a normalization control. However, it is recognized that hybridization efficiency varies with base composition and probe length. Preferred normalization probes are selected to reflect the average length of the other probes present in the array, however, they can be selected to cover a range of lengths. The normalization control(s) can also be selected to reflect the (average) base composition of the other probes in the array, however in a preferred embodiment, only one or a few probes are used and they are selected such that they hybridize well (i.e., no secondary structure) and do not match any target-specific probes. Expression level controls are probes that hybridize specifically with constitutively expressed genes in the biological sample. Virtually any constitutively expressed gene provides a suitable target for expression level controls. Typically expression level control probes have sequences complementary to subsequences of constitutively expressed "housekeeping genes" including, but not limited to an actin gene, the transferrin receptor gene, the GAPDH gene, and the like.

Mismatch controls may also be provided for the probes to the target genes, for expression level controls or for normalization controls. Mismatch controls are oligonucleotide probes or other nucleic acid probes identical to their corresponding test or control probes except for the presence of one or more mismatched bases. A mismatched base is a base selected so that it is not complementary to the corresponding base in the target sequence to which the probe would otherwise specifically hybridize. One or more mismatches are selected such that under appropriate hybridization conditions (e.g., stringent conditions) the test or control probe would be expected to hybridize with its target sequence, but the mismatch probe would not hybridize (or would hybridize to a significantly lesser extent). Preferred mismatch probes contain a central mismatch. Thus, for example, where a probe is a 20 mer, a corresponding mismatch probe will have the identical sequence except for a single base mismatch (e.g., substituting a G, a C or a T for an A) at any of positions 6 through 14 (the central mismatch).

Mismatch probes thus provide a control for non-specific binding or cross hybridization to a nucleic acid in the sample other than the target to which the probe is directed. Mismatch probes also indicate whether a hybridization is specific or not. For example, if the target is present the perfect match probes should be consistently brighter than the mismatch probes. In addition, if all central mismatches are present, the mismatch probes can be used to detect a mutation. The difference in intensity between the perfect match and the mismatch probe provides a good measure of the concentration of the hybridized material.

Nucleic Acid Samples

As is apparent to one of ordinary skill in the art, nucleic acid samples used in the methods and assays of the invention may be prepared by any available method or process. Methods of isolating total mRNA are well known to those of skill in the art. For example, methods of isolation and purification of nucleic acids are described in detail in Chapter 3 of Laboratory Techniques in Biochemistry and Molecular Biology: Hybridization With Nucleic

Acid Probes, Part I Theory and Nucleic Acid Preparation, P. Tijssen, Ed., Elsevier, N.Y.

(1993). Such samples include RNA samples, but also include cDNA synthesized from a mRNA sample isolated from a cell or tissue of interest. Such samples also include DNA amplified from the cDNA, and RNA transcribed from the amplified DNA. One of skill in the art would appreciate that it is desirable to inhibit or destroy RNase present in homogenates before homogenates can be used.

Biological samples may be of any biological tissue or fluid or cells from any organism as well as cells raised in vitro, such as cell lines and tissue culture cells. Frequently the sample will be a "clinical sample" which is a sample derived from a patient. Typical clinical samples include, but are not limited to PBLs, sputum, blood, blood-cells (e.g., white cells), tissue or fine needle biopsy samples, urine, peritoneal fluid, and pleural fluid, or cells therefrom. Biological samples may also include sections of tissues, such as frozen sections or formalin fixed sections taken for histological purposes. When PBLs are used in the assays of the invention, PBL samples from multiple patients with a given GN may be collected and pooled. Alternatively, standard leucopheresis techniques may be used to collect large numbers (8 10⁸ cells) from a single patient. See De Fliedner et al,

Blut (1974) Oct; 29(4): 265-76.

As used herein, "PBL" refers to peripheral blood leukocytes, or white blood cells. The term "PBL" includes any white blood cell population, regardless of whether the population has been purified or separated from other cell types.

Forming High Density Arrays.

Methods of forming high density arrays of oligonucleotides with a minimal number of synthetic steps are known. The oligonucleotide analogue array can be synthesized on a solid substrate by a variety of methods, including, but not limited to, light-directed chemical coupling, and mechanically directed coupling. See Pirrung et al, U.S. Patent No. 5,143, 854.

In brief, the light-directed combinatorial synthesis of oligonucleotide arrays on a glass surface proceeds using automated phosphoramidite chemistry and chip masking techniques. In one specific implementation, a glass surface is derivatized with a silane reagent containing a functional group, e.g., a hydroxyl or amine group blocked by a photolabile protecting group. Photolysis through a photolithographic mask is used selectively to expose functional groups that are then ready to react with incoming 5' photoprotected nucleoside phosphoramidites. The phosphoramidites react only with those sites which are illuminated (and thus exposed by removal of the photolabile blocking group). Thus, the phosphoramidites only add to those areas selectively exposed from the preceding step. These steps are repeated until the desired array of sequences has been synthesized on the solid surface. Combinatorial synthesis of different oligonucleotide analogues at different locations on the array is determined by the pattern of illumination during synthesis and the order of addition of coupling reagents. In addition to the foregoing, additional methods that can be used to generate an array of oligonucleotides on a single substrate are described WO 93/09668. High density nucleic acid arrays can also be fabricated by depositing premade or natural nucleic acids in predetermined positions. Synthesized or natural nucleic acids are deposited on specific locations of a substrate by light directed targeting and oligonucleotide directed targeting. Another embodiment uses a dispenser that moves from region to region to deposit nucleic acids in specific spots.

Hybridization

Nucleic acid hybridization simply involves contacting a probe and target nucleic acid under conditions where the probe and its complementary target can form stable hybrid duplexes through complementary base pairing. See WO 99/32660. The nucleic acids that do not form hybrid duplexes are then washed away leaving the hybridized nucleic acids to be detected, typically through detection of an attached detectable label. It is generally recognized that nucleic acids are denatured by increasing the temperature or decreasing the salt concentration of the buffer containing the nucleic acids. Under low stringency conditions (e.g., low temperature and or high salt) hybrid duplexes (e.g. , DNA:DNA, RNA:RNA, or RNA:DNA) will form even where the annealed sequences are not perfectly complementary.

In assays of the invention, specificity of hybridization is reduced at lower stringency. Conversely, at higher stringency (e.g., higher temperature or lower salt) successful hybridization tolerates fewer mismatches. One of skill in the art will appreciate that hybridization conditions may be selected to provide any degree of stringency. In a preferred embodiment, hybridization is performed at low stringency in this case in 6X SSPE-T at 37°C (0.005% Triton X-100) to ensure hybridization and then subsequent washes are performed at higher stringency (e.g., I X SSPE-T at 37°C) to eliminate mismatched hybrid duplexes. Successive washes may be performed at increasingly higher stringency (e.g., down to as low as 0.25 X SSPET at 37°C to 50°C) until a desired level of hybridization specificity is obtained. Stringency can also be increased by addition of agents such as formamide. Hybridization specificity may be evaluated by comparison of hybridization to the test probes with hybridization to the various controls that can be present (e.g., expression level control, normalization control, mismatch controls, etc.). In general, there is a tradeoff between hybridization specificity (stringency) and signal intensity. Thus, in a preferred embodiment, the wash is performed at the highest stringency that produces consistent results and that provides a signal intensity greater than approximately 10% of the background intensity. Thus, in a preferred embodiment, the hybridized array may be washed at successively higher stringency solutions and read between each wash. Analysis of the data sets thus produced will reveal a wash stringency above which the hybridization pattern is not appreciably altered and which provides adequate signal for the particular oligonucleotide probes of interest.

Signal Detection

The hybridized nucleic acids are typically detected by detecting one or more labels attached to the sample nucleic acids. The labels may be incorporated by any of a number of means well known to those of skill in the art. See WO 99/32660.

Databases

The present invention includes relational databases containing sequence information, for instance, for the genes of Tables 1-31 as well as gene expression information in various tissue or cell samples. Databases may also contain information associated with a given sequence or tissue sample such as descriptive information about the gene associated with the sequence information, or descriptive information concerning the clinical status of the tissue sample, or the patient from which the sample was derived. The database may be designed to include different parts, for instance a sequence database and a gene expression database. Methods for the configuration and construction of such databases are widely available, for instance, see U.S. Patent 5,953,727, which is herein incorporated by reference in its entirety.

The databases of the invention may be linked to an outside or external database. In a preferred embodiment, as described in Tables 1-31, the external database is GenBank and the associated databases maintained by the National Center for Biotechnology Information (NCBI). Any appropriate computer platform may be used to perform the necessary comparisons between sequence information, gene expression information and any other information in the database or provided as an input. For example, a large number of computer workstations are available from a variety of manufacturers, such has those available from Silicon Graphics. Client/server environments, database servers and networks are also widely available and appropriate platforms for the databases of the invention.

The databases of the invention may be used to produce, among other things, electronic Northerns that allow the user to determine the cell type or tissue in which a given gene is expressed and to allow determination of the abundance or expression level of a given gene in a particular tissue or cell. The databases of the invention may also be used to present information identifying the expression level in a tissue or cell of a set of genes comprising at least two of the genes in Tables 1-31, comprising the step of comparing the expression level of at least one gene in Tables 1-31 in the tissue to the level of expression of the gene in the database. Such methods may be used to predict the physiological or disease state of a given tissue by comparing the level of expression of a gene or genes in Tables 1-31 from a sample, to the expression levels found in PBL from normal controls and/or patients with glomerulonephritis as contained in the database. Such methods may also be used in the drug or agent screening assays as described below.

Diagnostic Uses for the Glomerular Diseases Markers

As described above, the genes and gene expression information provided in Tables 1-31 may be used as diagnostic markers for the prediction or identification of glomerular diseases. For instance, a patient's PBL sample may be assayed by any of the methods described above, and the expression levels from a gene or genes from Tables 1-31 may be compared to the expression levels found in PBL of normal controls and/or patients with glomerular diseases or with the expression levels found in the databases of the invention. The comparison of expression data, as well as available sequence or other information may be done by researcher or diagnostician or may be done with the aid of a computer and databases as described above.

Use of the Glomerular disease Markers for Diagnosis of Subtype of Glomerular Disease

As described above, the genes and gene expression information provided in Tables 1-31 may also be used as markers for the diagnosis of disease subtype, such as IgA nephropathy, Minimal Change Disease, ANCA, FSGS and lupus nephritis. For instance, a PBL sample may be assayed by any of the methods described above, and the expression levels from a gene or genes from Tables 1-31 may be compared to the expression levels found in PBL of normal controls and patients with glomerular diseases or with the expression levels found in the databases of the invention. The comparison of the expression data, as well as available sequence or other information may be done by researcher or diagnostician or may be done with the aid of a computer and databases as described above. The glomerular disease markers of the invention may also be used to track or predict the progress or efficacy of a treatment regime in a patient. For instance, a patient's progress or response to a given drug may be monitored by creating a gene expression profile, for instance, using the genes of Tables 1-31, from a tissue or cell sample after treatment or administration of the drug. The gene expression profile may also be compared to a gene expression profile prepared from PBL of normal controls and patients with glomerular diseases before and or after treatment. The gene expression profile may be made from at least one gene, preferably more than one gene, and in some assays all or nearly all of the genes in Tables 1-31.

Use of the GN Markers for Drug Screening According to the present invention, the genes identified in Tables 1-31 may be used as markers to evaluate the effects of a candidate drug or agent on tissues or cells, including PBLs, particularly PBLs undergoing activation or PBLs from a patient with glomerular disease. A candidate drug or agent can be screened for the ability to stimulate the transcription or expression of a given marker or markers or to down-regulate or counteract the transcription or expression of a marker or markers. In a particular embodiment, expression levels of genes in cells exposed to the agent can be compared to the mean levels or fold-change data of expression of the diseased and control sample sets in Tables 1-30 to determine the effects of the agent on the gene expression profile of the cells. According to the present invention one can also compare the specificity of a drug's effects by looking at the number of markers which the drug induces and comparing them to the unexposed cell. More specific drugs will have less transcriptional targets. Similar sets of markers identified for two drugs indicate a potential similarity of effects.

Assays to monitor the expression of a marker or markers as defined in Tables 1-31 may utilize any available means of monitoring for changes in the expression level of the nucleic acids of the invention. As used herein, an agent is said to modulate the expression of a nucleic acid of the invention if it is capable of up- or down-regulating expression of the nucleic acid in a cell. In one assay format, gene chips containing probes to at least 2 genes from Tables 1-31 may be used to directly monitor or detect changes in gene expression in the treated or exposed cell as described in more detail above. In another format, cell lines that contain reporter gene fusions between the open reading frame and/or 5' or 3' regulatory regions of a gene in Tables 1- 31 and any assayable fusion partner may be prepared. Numerous assayable fusion partners are known and readily available including the firefly luciferase gene and the gene encoding chloramphenicol acetyltransferase (Alam et al. (1990) Anal. Biochem. 188:245-254). Cell lines containing the reporter gene fusions are then exposed to the agent to be tested under appropriate conditions and time. Differential expression of the reporter gene between samples exposed to the agent and control samples identifies agents that modulate the expression of the nucleic acid.

Additional assay formats may be used to monitor the ability of the agent to modulate the expression of a gene identified in Tables 1-31. For instance, as described above, mRNA expression may be monitored directly by hybridization of probes to the nucleic acids of the invention. Cell lines are exposed to the agent to be tested under appropriate conditions and time and total RNA or mRNA is isolated by standard procedures such those disclosed in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Ed. Cold Spring Harbor Laboratory Press, 1989). In another assay format, cells or cell lines are first identified which express the gene products of the invention physiologically. Cells and/or cell lines so identified would be expected to comprise the necessary cellular machinery such that the fidelity of modulation of the transcriptional apparatus is maintained with regard to exogenous contact of agent with appropriate surface transduction mechanisms and/or the cytosolic cascades. Such cell lines may be, but are not required to be, PBL derived. Further, such cells or cell lines may be transduced or transfected with an expression vehicle (e.g., a plasmid or viral vector) construct comprising an operable non-translated 5 '-promoter containing end of the structural gene encoding the instant gene products fused to one or more antigenic fragments which are peculiar to the instant gene products, wherein said fragments are under the transcriptional control of said promoter and are expressed as polypeptides whose molecular weight can be distinguished from the naturally occurring polypeptides or may further comprise an immunologically distinct tag or some other detectable marker or tag. Such a process is well known in the art.

Cells or cell lines transduced or transfected as outlined above are then contacted with agents under appropriate conditions; for example, the agent comprises a pharmaceutically acceptable excipient and is contacted with cells comprised in an aqueous physiological buffer such as phosphate buffered saline (PBS) at physiological pH, Eagles balanced salt solution (BSS) at physiological pH, PBS or BSS comprising serum or conditioned media comprising PBS or BSS and/or serum incubated at 37°C . Said conditions may be modulated as deemed necessary by one of skill in the art. Subsequent to contacting the cells with the agent, said cells are disrupted and the polypeptides of the lysate are fractionated such that a polypeptide fraction is pooled and contacted with an antibody to be further processed by immunological assay (e.g. , ELISA, immunoprecipitation or Western blot). The pool of proteins isolated from the "agent- contacted" sample is then compared with a control sample where only the excipient is contacted with the cells and an increase or decrease in the immunologically generated signal from the "agent-contacted" sample compared to the control is used to distinguish the effectiveness of the agent.

Another embodiment of the present invention provides methods for identifying agents that modulate at least one activity of a protein(s) encoded by the genes in Tables 1-31. Such methods or assays may utilize any means of monitoring or detecting the desired activity. In one format, the relative amounts of a protein of the invention between a cell population that has been exposed to the agent to be tested compared to an un-exposed control cell population may be assayed. In this format, probes such as specific antibodies are used to monitor the differential expression of the protein in the different cell populations. Cell lines or populations are exposed to the agent to be tested under appropriate conditions and time. Cellular lysates may be prepared from the exposed cell line or population and a control, unexposed cell line or population. The cellular lysates are then analyzed with the probe, such as a specific antibody.

Agents that are assayed in the above methods can be randomly selected or rationally selected or designed. As used herein, an agent is said to be randomly selected when the agent is chosen randomly without considering the specific sequences involved in the association of the a protein of the invention alone or with its associated substrates, binding partners, etc. An example of randomly selected agents is the use a chemical library or a peptide combinatorial library, or a growth broth of an organism. As used herein, an agent is said to be rationally selected or designed when the agent is chosen on a nonrandom basis which takes into account the sequence of the target site and/or its conformation in connection with the agent's action. Agents can be rationally selected or rationally designed by utilizing the peptide sequences that make up these sites. For example, a rationally selected peptide agent can be a peptide whose amino acid sequence is identical to or a derivative of any functional consensus site.

The agents of the present invention can be, as examples, peptides, small molecules, vitamin derivatives, as well as carbohydrates. Dominant negative proteins, DNAs encoding these proteins, antibodies to these proteins, peptide fragments of these proteins or mimics of these proteins may be introduced into cells to affect function. "Mimic" used herein refers to the modification of a region or several regions of a peptide molecule to provide a structure chemically different from the parent peptide but topographically and functionally similar to the parent peptide (see Grant GA. in: Meyers (ed.) Molecular Biology and Biotechnology (New York, VCH Publishers, 1995), pp. 659-664). A skilled artisan can readily recognize that there is no limit as to the structural nature of the agents of the present invention.

Kits

The invention further includes kits combining, in different combinations, high-density oligonucleotide arrays, reagents for use with the arrays, signal detection and array-processing instruments, gene expression databases and analysis and database management software described above. The kits may be used, for example, to track or predict the progress or efficacy of a treatment regime in a patient, to monitor the progression of glomerular disease states, to identify genes that show promise as new drug targets and to screen known and newly designed drugs as discussed above.

The databases packaged with the kits are a compilation of expression patterns from human and/or laboratory animal genes and gene fragments (corresponding to the genes of Tables 1-31). Data is collected from a repository of both normal and diseased human and animal tissues and provides reproducible, quantitative results, i.e., the degree to which a gene is up- regulated or down-regulated upon exposure to a therapeutic agent. In particular, the database software and packaged information include the expression results of Tables 1-31 that can be used to assay a patient's PBL sample by comparing the expression levels of a gene or set of genes from Tables 1-31 to the expression levels found in PBL of normal controls and/or patients with glomerular diseases or with expression levels found in the databases of the invention.

The kits may used in the pharmaceutical industry, where the need for early drug testing is strong due to the high costs associated with drug development, but where bioinformatics, in particular gene expression informatics, is still lacking. These kits will reduce the costs, time and risks associated with traditional new drug screening using cell cultures and laboratory animals. The results of large-scale drug screening of pre-grouped patient populations, pharmacogenomics testing, can also be applied to select drugs with greater efficacy and fewer side-effects. The kits may also be used by smaller biotechnology companies and research institutes who do not have the facilities for performing such large-scale testing themselves.

Databases and software designed for use with use with microarrays is discussed in Balaban et al, U.S. Patent Nos. 6,229,911, a computer-implemented method for managing information, stored as indexed tables, collected from small or large numbers of microarrays, and 6,185,561, a computer-based method with data mining capability for collecting gene expression level data, adding additional attributes and reformatting the data to produce answers to various queries. Chee et al, U.S. Patent No. 5,974,164, disclose a software-based method for identifying mutations in a nucleic acid sequence based on differences in probe fluorescence intensities between wild type and mutant sequences that hybridize to reference sequences.

Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the compounds of the present invention and practice the claimed methods. The following working examples therefore, specifically point out the preferred embodiments of the present invention, and are not to be construed as limiting in any way the remainder of the disclosure.

EXAMPLES Example 1: Gene chip expression analysis

Peripheral Blood Leukocytes (PBL) were obtained from normal volunteers and patients with IgA nephropathy, ANCA nephritis, FSGS, Minimal Change Nephrotic Syndrome and Lupus nephritis. Microarray sample preparation was conducted with minor modifications, following the protocols set forth in the Affymetrix GeneChip Expression Analysis Manual.

Blood was drawn from IgA nephropathy patients and retrieved in four 7.0 ml purple top EDTA Vacutainer tubes per patient sample. Five ml of blood were transferred into 50 ml polypropylene conical tubes then lysed with 45 ml NH C1. Red blood cells were completely lysed by inverting tube 10 times, and then incubating at room temp for 11 min followed by inverting several times at 5 min. The tube was centrifuged for 10 min at 1200 RPM (200 G) at room temp. The supernatant was discarded by aspiration. One ml of HBSS (room temp) was added and the pellet was re-suspended and transferred into a 15 ml polypropylene conical tube. HBSS was added to bring the volume in the 15 ml tube up to 14 ml. The tube was inverted five times to mix then spun down for 6 min at 1200 RPM (200 G) at room temperature. After discarding the supernatant by aspiration, the pellet was resuspend with 2.0 ml RNA Stat 60 and lml aliquots was transferred into 1.5 ml microfuge tubes. The tubes were incubated at room temp for -5-10 min.

Two hundred 71 of chloroform per 1.0 ml aliquot was added then mixed by vigorous inversion for ~15 sec. The tube was incubated at room temp for 3 min, then spun down at

10,500 RPM (no more than 12,000 G) at 4 degrees for 15 min. The tubes were set in a water bath at 67°C. The aqueous (top) layer was transferred to clean microfuge tube, being careful not to extract the white protein interface. 0.5 ml of isopropanol was added and mixed by pipetting. The tube was incubated at room temp for 5-10 min, then spun down at 10,500 RPM (No more than 12,000 G) at 4 degrees for 10 min. The supernatant was poured off then tube was blotted on a towel. One ml of 75 % EtOH was added to each microfuge tube then vortexed for approximately 5 sec per tube. The tube was spun down at 10,500 RPM at 4 degrees for 5 min. The supernatant was poured off and the tube was blotted on a towel. The tube was spun at 10,500 RPM at 4 degrees for 1 min and placed in hood with cap open for -15 min to evaporate EtOH. The pellet was resuspend in 50-100 μl nuclease free water. The samples were diluted to final concentration of 0.5 μg/μl.

Double stranded cDNA was generated from mRNA using the Superscript Choice system (GibcoBRL). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. The cDNA was phenol-chloroform extracted and ethanol precipitated to a final concentration of 1 μg/ml. From 2 μg of cDNA, cRNA was synthesized using Ambion's T7 MegaScript in vitro Transcription Kit.

To biotin label the cRNA, nucleotides Bio-11-CTP and Bio-16-UTP (Enzo Diagnostics) were added to the reaction. Following a 37°C incubation for six hours, impurities were removed from the labeled cRNA following the RNeasy Mini kit protocol (Qiagen). cRNA was fragmented (fragmentation buffer consisting of 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc) for thirty- five minutes at 94°C. Following the Affymetrix protocol, 55 μg of fragmented cRNA was hybridized on the Affymetrix Human 42K array set for twenty-four hours at 60 rpm in a 45 °C hybridization oven. The chips were washed and stained with Streptavidin Phycoerythrin (SAPE) (Molecular Probes) in Affymetrix fluidics stations. To amplify staining, SAPE solution was added twice with an anti-streptavidin biotinylated antibody (Vector Laboratories) staining step in between. Hybridization to the probe arrays was detected by fluorometric scanning (Hewlett Packard Gene Array Scanner). Data was analyzed using Affymetrix GeneChip® version 3.0 and Expression Data Mining Tool (EDMT) software (version 1.0).

Differential expression of genes between PBLs from patients with glomerular disease and normal PBL samples was determined using the Affymetrix 42K human gene chip set by the following criteria:

For each gene, Affymetrix GeneChip average difference values were calculated by using proprietary Affymetrix EDMT software algorithms. All negative average difference values were floored to +20 so that fold change calculations could be made where values were not already greater than or equal to +20. Median levels of expression were compared between the normal control group and the GN disease group and filtered for those genes showing a fold-change greater than or equal 2 fold up or down. The median value for the higher expressing group needed to be greater than or equal to 200 average difference units in order to be considered for statistical significance. Genes passing all previous criteria were analyzed for statistical significance using a two-tailed t-test at a significance level of 0.05. The following formula was used to compute the fold change:

FoldChange = β^Λ[^ln £>^{~ ln}(_N) The following formula was used to compute the t-statistic:

Where μ denotes mean values, 'n' denotes sample size values and V denotes 'variance', which is: ∑(x- Ϋ

Variance = n - \

Where μ denotes the mean of the population. The square root of variance is the standard deviation. All these things would be known to one of ordinary skill in the art.

Tables 1-31 list the genes and their levels of differential expression in PBLs from patients with glomerular disease. The columns of each table are labeled such that "AffyName" refers to the GenBank Accession Number. "Meanl" refers to the Mean for the control sample set. "Stdl" refers to the Standard deviation for the control sample set. "Nl" is the number of samples contained within the control sample set. "Mean2" is the Mean for the experimental

(disease) sample set. "Std2" is the standard deviation for the experimental sample set. N2 is the number of samples in the experimental sample set. "FC" is the calculated control vs. experimental fold-change. The term "t" is the score resulting from a t-test performed on the control vs. experimental sample sets and screened for a significance level of 0.05. The title of each table is the control sample set verses the experimental sample set followed by the regulation pattern. Table 1 lists the genes determined to be up-regulated in Minimal Change Disease as compared to normal PBL samples, while Table 2 lists the genes that were downregulated. Tables 3 and 4 provide the genes shown to be up and down-regulated respectively in lupus nephritis samples as compared to normal PBL samples. Table 5 lists the genes determined to be up-regulated in IgAN as compared to normal PBL samples, while Table 6 lists the genes that were downregulated. Table 7 lists the genes determined to be up-regulated in FSGS as compared to normal PBL samples, while Table 8 lists the genes that were downregulated. Table 9 lists the genes determined to be up-regulated in ANCA samples as compared to normal PBL samples, while Table 10 lists the genes that were downregulated. Table 11 lists the genes determined to be up-regulated in Minimal Change Disease as compared to lupus nephritis samples, while Table 12 lists the genes that were downregulated. Table 13 lists the genes determined to be up-regulated in Minimal Change Disease as compared to IgAN samples, while Table 14 lists the genes that were downregulated. Table 15 lists the genes determined to be up- regulated in lupus nephritis as compared to IgAN samples, while Table 16 lists the genes that were downregulated. Table 17 lists the genes determined to be up-regulated in Minimal Change Disease as compared to FSGS samples, while Table 18 lists the genes that were downregulated. Table 19 lists the genes determined to be up-regulated in lupus nephritis as compared to FSGS samples, while Table 20 lists the genes that were downregulated. Table 21 lists the genes determined to be up-regulated IgAN as compared to FSGS samples, while Table 22 lists the genes that were downregulated. Table 23 lists the genes determined to be up-regulated in FSGS samples as compared to ANCA samples, while Table 24 lists the genes that were downregulated. Table 25 lists the genes determined to be up-regulated in lupus nephritis as compared to ANCA samples, while Table 26 lists the genes that were downregulated. Table 27 lists the genes determined to be up-regulated in IgAN as compared to ANCA samples, while Table 28 lists the genes that were downregulated. Table 29 lists the genes determined to be up- regulated in Minimal Change Disease as compared to ANCA samples, while Table 30 lists the genes that were down-regulated.

Example 2: Drug Screening Assay As expected, complex alterations in the gene expression profiles were manifested in

PBLs of patients compared to the normal PBL samples. These disease specific gene expression profiles can be used for drug screening by measuring the changes of the expression profiles in PBL or cell lines after the treatment with test agents or compounds. The compounds that normalize the abnormal expression profiles (one or more marker genes) may be further screened as candidate therapeutics. The methods used to measure the disease marker genes include any type of technique for detecting mRNA, such as microarray, DNA chip, RT-PCR(TaqMan), RNA, ELIS A, branched RNA methods and so on.

For example, normalized expression levels from cells exposed to the agent are compared to the normalized expression levels in control cells. Expression levels of the genes in the cells exposed to the agent can further be compared to the mean levels or fold-change data of expression of the diseased and control sample sets in Tables 1-30 to determine the effects of the agent on the gene expression profile of the cells. Agents that modulate the expression of one or more the genes may be further tested as drug candidates in appropriate glomerular disease in vitro or in vivo models.

Example 3: Selection of surrogate markers for drug screening by cluster analysis

The changes in gene expression for multiple genes can be determined, for example, by branched DNA (bDNA) technology. The cells are treated with compounds and the level of expression for each disease marker in the treated cells is analyzed. Hit compounds that normalize the disease specific expression profile, are selected for further analysis. In case of a random compound screening, it is desired to screen as many compounds and to monitor as many markers as possible.

In a preferred embodiment, 60 surrogate marker genes may be used that were selected from an original 362 gene fragments altered in IgA nephropathy, as the representative of the group of the genes whose expression is regulated in a same way based on gene clustering analysis (see Table 31). The gene clustering analysis here is based on the assumption that the genes which share the similar promoter or whose expression are regulated by the same molecules or in the same pathway, should show the similar expression patterns. These disease genes were classified into 10 clusters by expression profiles and 5-6 genes were selected from each cluster as surrogate markers.

Example 4: PBL from patients with Glomerular Nephritis for drug screening assay

As described above, PBLs from patients with glomerular diseases were originally analyzed for abnormal gene expression patterns or profiles. Since the disease markers selected here are altered in PBL from patients with glomerular disease, PBLs from these or similar patients constitute a superb cell based drug screening system. The PBLs from patients with glomerular disease can be collected by conventional blood draw. In order to obtain enough PBLs to screen large numbers of compounds, however, it is necessary to recruit several patients, which might cause some degree of variation in gene expression and the artificial activation if the patient PBLs are pooled.

Alternatively, large numbers of PBLs may be obtained by leukopheresis. Leukopheresis is the method of purifying leukocytes from 3-8 litters of whole blood while plasma, red blood cells and platelets are returned to the donor. Using leukopheresis, it is possible to collect 10⁸ of PBLs from one donor, which makes it possible to screen more than 1000 compounds from the PBLs isolated from a single patient. For cell based drug screening, PBL prepared from patients and healthy volunteers by leukopheresis can be used. This method can be applicable to any type of drug screening not only for glomerular diseases but also for any types of disease such as leukemia, autoimmune disease, any inflammatory diseases, infectious diseases, cancers, sepsis, allergies, anemia, rheumatoid arthritis, arteriosclerosis, and so on.

Although the present invention has been described in detail with reference to examples above, it is understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims. All cited patents, applications and publications referred to in this application are herein incorporated by reference in their entirety.

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Table 31

Gene Fragment

Seq ID N Known Gene Name Count ID

1 T52813 9994 putative lymphocyte G0/G1 switch gene

2 M28130 12785 interleukin 8

3 Y09943 11190 BTG family, member 2

4 L49169 2617 FBJ murine osteosarcoma viral oncogene homolog B

5 X52541 8827 early growth response 1 prostaglandin-endoperoxide synthase 2

6 L15326 4721

(prostaglandin G/H synthase and cyclooxygenase)

Gardner-Rasheed feline sarcoma viral (v-fgr)

7 M 19722 13161 oncogene homolog

8 D 10495 12250 protein kinase C, delta

9 X62320 1833 granulin

10 M84332 12222 ADP-ribosylation factor 1 early growth response 2 (Krox-20 (Drosophila)

11 AA446027 8296 homolog)

12 N22822 1377 period (Drosophila) homolog 1

13 W46420 9576 KIAA0805 protein

14 X89109 1609 coronin, actin-binding protein, 1A ubiquitin-activating enzyme E1 (A1S9T and BN75

15 M58028 10974 temperature sensitivity complementing)

16 N58561 5756 natural killer-tumor recognition sequence

17 U05237 1990 fetal Alzheimer antigen

18 T58044 10432 RNB6

19 M20566 1365 interleukin 6 receptor

20 L11672 7149 zinc finger protein 91 (HPF7, HTF10) granzyme A (granzyme 1 , cytotoxic T-lymphocyte-

21 M18737 9591 associated serine esterase 3)

22 L04282 5300 zinc finger protein 148 (pHZ-52)

23 D50840 10118 UDP-glucose ceramide glucosyltransferase killer cell immunoglobulin-like receptor, two domains,

24 X97231 4339 short cytoplasmic tail, 3

25 M29696 7541 interleukin 7 receptor

26 U30610 543 killer cell lectin-like receptor subfamily D, member 1

27 AA449845 12916 candidate mediator of the p53-dependent G2 arrest

HG987-

28 insulin-like growth factor binding protein 7

HT987

29 AA133681 10421 myosin phosphatase, target subunit 1

30 U28686 7101 RNA binding motif protein 3 splicing factor, arginine/serine-rich (transformer 2 U68063 9413

Drosophila homolog) 10 Z26491 3344 catechol-O-methyltransferase

DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 X98743 12841

(Myc-regulated)

ESTs, Moderately similar to ALU1_HUMAN ALU

R40978 846 SUBFAMILY J SEQUENCE CONTAMINATION

WARNING ENTRY [H.sapiens]

N67108 7117 ESTs

Weakly similar to alternatively spliced product using

AA086399 3682 exon 13A small inducible cytokine A4 (homologous to mouse

M69203 11465

Mip-1b)

R62633 9316 ESTs

Homo sapiens mRNA; cDNA DKFZp566F164 (from

T16484 12858 clone DKFZp566F164)

T86914 10713 ESTs

AA196306 2355 ESTs

W93403 1584 ESTs

Homo sapiens cDNA FLJ10457 fis, clone

AA236455 9303

NT2RP1001424

W72798 11120 KIAA1404 protein

AA235289 3715 ESTs (UniGene name may be wrong.)

AA262491 7861 ESTs

AA599267 269 KIAA0697 protein

H00647 6704 ESTs

Homo sapiens mRNA; cDNA DKFZp566J2446 (from

N51488 7219 clone DKFZp566J2446)

AA032081 11113 ESTs

U19247 11776 interferon gamma receptor 1

D10923 2751 putative chemokine receptor; GTP-binding protein

M60922 13210 flotillin 2

X95735 1794 zyxin

U19523 564 GTP cyclohydrolase 1 (dopa-responsive dystonia)

L42324 6865 G protein-coupled receptor 18

U72511 992 B-cell associated protein

N63930 137 ESTs (UniGene name may be wrong.)

R94756 2637 ESTs

AA452855 10390 lectin, mannose-binding, 1

Claims

We claim:

1. A method of screening for an agent that modulates the onset or progression of a glomerulonephritis (GN), comprising:

(a) preparing a first gene expression profile of a blood cell;

(b) exposing the cell population to the agent;

(c) preparing second gene expression profile of the agent exposed cell population; and

(d) comparing the first and second gene expression profiles.

2. The method of claim 1, wherein the gene expression profile comprises the expression levels for a set of genes that are differentially regulated in PBL from patients with a GN compared to normal PBL.

3. The method of claim 1, wherein the agent modulates the level of expression for at least one gene in the PBL of patient with a GN to the expression level found in a normal PBL.

4. The method of any one of claims 1-3, wherein the gene expression profile comprises the expression levels in a cell of at least one gene in Tables 1-31.

5. The method of claim 4, wherein the gene expression profiles comprises the expression levels in a cell of at least two genes in Tables 1-31.

6. A method of diagnosing a glomerulonephritis (GN) in a patient comprising the step of:

(a) detecting the level of expression in a blood cell population of two or more genes from Tables 1-31; wherein differential expression of the genes in Tables 1-31 is indicative of a GN.

7. A method of detecting the progression of a glomerulonephritis (GN) in a patient comprising the step of: (a) detecting the level of expression in a tissue sample of two or more genes from Tables 1-31; wherein differential expression of the genes in Tables 1-31 is indicative of a GN progression.

8. A method of diagnosing a glomerulonephritis (GN) disease subtype in a patient comprising the step of:

(a) detecting the level of expression in a blood cell sample of two or more genes from Tables 1-31; wherein differential expression of the genes in Tables 1-31 is indicative of a GN disease subtype.

9. A method of screening for an agent capable of modulating the onset or progression of a glomerulonephritis (GN), comprising the steps of

(a) exposing a cell to the agent; and

(b) detecting the expression level of two or more genes from Tables 1-31.

10. The method of any one of claims 6-9, wherein the expression levels of at least 3 genes are detected.

11. The method of any one of claims 6-9, wherein the expression levels of at least 4 genes are detected.

12. The method of any one of claims 6-9, wherein the expression levels of at least 5 genes are detected.

13. The method of any one of claims 6-9, wherein the expression levels of at least 6 genes are detected.

14. The method of any one of claims 6-9, wherein the expression levels of at least 7 genes are detected.

15. The method of any one of claims 6-9, wherein the expression levels of at least 8 genes are detected.

16. The method of any one of claims 6-9, wherein the expression levels of at least 9 genes are detected.

17. The method of any one of claims 6-9, wherein the expression levels of at least 10 genes are detected.

18. A set of at least two probes, wherein each of the probes comprises a sequence that specifically hybridizes to a gene in Tables 1-31.

19. The set of probes according to claim 18, wherein the set comprises probes that hybridize to at least 3 genes.

20. The set of probes according to claim 18, wherein the set comprises probes that hybridize to at least 5 genes.

21. The set of probes according to claim 18, wherein the set comprises probes that hybridize to at least 7 genes.

22. The set of probes according to claim 18, wherein the set comprises probes that hybridize to at least 10 genes.

23. The set of probes according to any one of claims 18-22, wherein the probes are attached to a solid support.

24. The set of probes according to claim 23, wherein the solid support is selected from the group consisting of a membrane, a glass support and a silicon support.

25. A solid support comprising at least two probes, wherein each of the probes comprises a sequence that specifically hybridizes to a gene in Tables 1-31.

26. The solid support of claim 25, wherein the solid support is an array comprising at least 10 different oligonucleotides in discrete locations per square centimeter.

27. The solid support of claim 25, wherein the array comprises at least 100 different oligonucleotides in discrete locations per square centimeter.

28. The solid support of claim 25, wherein the array comprises at least 1000 different oligonucleotides in discrete locations per square centimeter.

29. The solid support of claim 25 wherein the array comprises at least 10,000 different oligonucleotides in discrete locations per square centimeter.

30. A computer system comprising:

(a) a database containing information identifying the expression level in glomerulonephritis (GN) tissue of a set of genes comprising at least two genes in Tables 1-31; and

(b) a user interface to view the information.

31. The computer system of claim 30, wherein the database further comprises sequence information for the genes.

32. The computer system of claim 30, wherein the database further comprises information identifying the expression level for the set of genes in normal PBL.

33. The computer system of claim 30, wherein the database further comprises information identifying the expression level of the set of genes in kidney cancer tissue.

34. The computer system of any of claims 30-33, further comprising records including descriptive information from an external database, which information correlates said genes to records in the external database.

35. The computer system of claim 34, wherein the external database is GenBank.

36. A method of using a computer system of any one of claims 30-35 to present information identifying the expression level in a tissue or cell of a set of genes comprising at least two of the genes in Tables 1-31, comprising the step of: (a) comparing the expression level of at least one gene in Tables 1-31 in the tissue or cell to the level of expression of the gene in the database.

37. The method of claim 36, wherein the expression levels of at least two genes are compared.

38. The method of claim 36, wherein the expression levels of at least five genes are compared.

39. The method of claim 36, wherein the expression levels of at least ten genes are compared.

40. The method of claim 36, further comprising the step of displaying the level of expression of at lest one gene in the tissue or cell sample compared to the expression level in

GN.

41. A method of monitoring the treatment of a patient with a glomerulonephritis (GN), comprising:

(a) administering a pharmaceutical composition to the patient;

(b) preparing a gene expression profile from a cell or tissue sample from the patient; and

(c) comparing the patient gene expression profile to a gene expression from a normal cell or GN disease cell sample.

42. The method of any one of claims 1, 6, 7, 8, 9 or 41, wherein the GN is selected from the group consisting of IgAN, ANCA, FSGS, Minimal Change disease, and lupus nephritis.

43. The method of claim 42, wherein the cell population comprises PBLs.