WO2008052115A1

WO2008052115A1 - Materials and methods for predicting physiological responses to cardiovascular drugs

Info

Publication number: WO2008052115A1
Application number: PCT/US2007/082527
Authority: WO
Inventors: Issam Zineh
Original assignee: University Of Florida Research Foundation, Inc.
Priority date: 2006-10-25
Filing date: 2007-10-25
Publication date: 2008-05-02

Abstract

The subject invention provides materials and methods for predicting a patient's physiological response to treatment with a statin. In one embodiment, the subject invention provides diagnostic assays that predict whether an individual's C-reactive protein (CRP) is likely to increase or decrease as a result of treatment with a statin.

Description

DESCRIPTION

MATERIALS AND METHODS FOR PREDICTING PHYSIOLOGICAL RESPONSES TO CARDIOVASCULAR DRUGS

BACKGROUND OF INVENTION

Cardiovascular disease refers to the class of diseases that involve the heart or blood vessels (arteries and veins). Each year, heart disease kills more Americans than cancer. Diseases of the heart alone cause 30% of all deaths, with other diseases of the cardiovascular system causing substantial further death and disability.

Medications, such as blood pressure reducing medications, aspirin and the statin-cholesterol-lowering drugs may be helpful in treating cardiovascular disease; however, the success of treatment with drugs varies widely. This variation from individual to individual frustrates treatment and, heretofore, has been largely unpredictable.

The statins (or HMG-CoA reductase inhibitors) form a class of hypolipidemic agents, used, among things, to lower cholesterol levels in people at risk for cardiovascular disease. Statins work, at least in part, by inhibiting the enzyme HMG- CoA reductase, the enzyme that determines the speed of cholesterol synthesis. Inhibition of this enzyme in the liver stimulates the low density lipoprotein (LDL) receptors, which results in an increased clearance of LDL from the bloodstream and a decrease in blood cholesterol levels.

Statins exhibit action beyond lipid-lowering activity in the prevention of atherosclerosis. Thus, the indications for the prescription of statins have broadened over the years. Initial studies supported the use of statins in secondary prevention for cardiovascular disease, or as primary prevention only when the risk for cardiovascular disease was significantly raised. Indications were broadened considerably by studies such as the heart protection study (HPS), which showed preventative effects of statin use in specific risk groups, such as diabetics.

Statins are currently primarily used for preventing and treating atherosclerosis that causes chest pain, heart attacks, strokes, and intermittent claudication in individuals who have or are at risk for atherosclerosis. Although the important role of cholesterol in atherosclerosis is widely accepted, research also shows that atherosclerosis is a complex process that involves more than just cholesterol. For example, scientists have discovered that inflammation in the walls of the arteries may be an important factor in atherosclerosis. New research shows that, at least on some individuals, statins can reduce inflammation, which could be another mechanism by which statins beneficially affect atherosclerosis. This reduction of inflammation does not appear to depend on statins' ability to reduce cholesterol.

Currently-available statins include, in alphabetical order (brand names vary in different countries):

• Atorvastatin (Lipitor, Torvast)

• Cerivastatin (Lipobay, Baycol)

• Fluvastatin (Lescol)

• Lovastatin (Mevacor, Altocor) • Mevastatin - naturally-occurring compound, found in red yeast rice.

• Pravastatin (Livalo, Pitava)

• Pravastatin (Pravachol, Selektine, Lipostat)

• Rosuvastatin (Crestor)

• Simvastatin (Zocor, Lipex)

LDL-lowering potency varies between the statins. Cerivastatin is the most potent, followed by (in order of decreasing potency) rosuvastatin, atorvastatin, simvastatin, lovastatin, pravastatin, and fluvastatin. The relative potency of pitavastatin has not yet been fully established. Intensive lipid lowering with high dosages of statins is a preferred treatment strategy in certain patient populations. The benefit of high dose treatment is thought to be due to both greater low-density lipoprotein (LDL) reduction as well as a reduction in C-reactive protein (CRP). However, variablility in LDL and CRP responses exist between different individuals, and genetic factors may contribute to these differences.

C-reactive protein (CRP) is a protein produced by the liver. It is a member of the pentraxin family of proteins. It is thought to assist in complement binding to foreign and damaged cells and affect the humoral response to disease. It is also believed to play an important role in innate immunity, as an early defense system against infections.

The liver X receptors (LXRs) are nuclear receptors that play central roles in the transcriptional control of lipid metabolism. LXRs function as nuclear cholesterol sensors that are activated in response to elevated intracellular cholesterol levels in multiple cell types. Once activated, LXRs induce the expression of an array of genes involved in cholesterol absorption, efflux, transport, and excretion. In addition to their function in lipid metabolism, LXRs have also been found to modulate immune and inflammatory responses in macrophages. Liver X receptor-α (LXRα) and LXRβ (also known as NR1H3 and NR1H2, respectively) were cloned more than a decade ago. LXRs were originally considered "orphan" nuclear receptors, because their natural ligands were unknown (Apfel, R. et al. 1994 "A novel orphan receptor specific for a subset of thyroid hormone-responsive elements and its interaction with the retinoid/thyroid hormone receptor subfamily" MoI. Cell. Biol. 14:7025-7035; Willy, P.J. et al. 1995 "LXR, a nuclear receptor that defines a distinct retinoid response pathway" Genes Dev. 9::1033-1045); however, it was subsequently determined that metabolites of cholesterol — oxysterols — bind to and activate these receptors at physiological concentrations (Willy, PJ. et al, 1995 "LXR, a nuclear receptor that defines a distinct retinoid response pathway" Genes Dev. 9:1033-1045; Lehmann, J.M. et al. 1997, "Activation of the nuclear receptor

LXR by oxysterols defines a new hormone response pathway" J. Biol. Chem. 272:3137-3140).

In addition to their ability to modulate cholesterol metabolism, LXRs are also key regulators of hepatic lipogenesis. Glucose metabolism is also impacted by LXR activity.

Liver receptor X-α (LXRA) is a nuclear receptor that, once activated, induces genes important in metabolic processes (such as cholesterol homeostasis) and inflammation. The gene that encodes LXRA (NR1H3) has been shown to be polymorphic in nature. Currently, CRP and LDL are readily available clinical laboratory tests used in cardiovascular risk stratification. In addition, the statin (and other cardiovascular drugs) mediated changes in both LDL and CRP are thought to be important monitoring parameters for drug response. However, there is no test available currently to help predict an individual^'s likely changes in CRP resulting from treatment with a statin.

BRIEF SUMMARY

The subject invention provides materials and methods that can be used to predict a patient^'s physiological response to treatment with a cardiovascular disease drug. In one embodiment, the subject invention provides diagnostic assays that predict whether an individual's C-reactive protein (CRP) is likely to increase or decrease as a result of treatment with a statin.

Specifically exemplified herein are assays that detect a single nucleotide polymorphism (SNP) on the gene encoding liver X receptor - α (LXRA). In a specific embodiment, as described herein, a G — > A mutation (NRl H3 rs 12221497 G → A) has been found to be associated with a significant increase in CRP after treatment with statins whereas, for wild-type homozygotes (G/G), a reduction in CRP is observed.

CRP is a marker of inflammation and has been implicated in a variety of immunological processes, and statins are being increasingly used, including for conditions other than cardiovascular disease. Therefore, the ability to predict CRP response to statins according to the subject invention provides valuable information that can then be used in the course of formulating and implementing treatments.

For example, the diagnostic assays of the subject invention can be used to identify subsets of the patient population that may have enhanced inflammatory or anti-inflammatory responses resulting from statin treatment. Enhanced antiinflammatory responses may be beneficial in the treatment of a variety of conditions including, but not limited to, rheumatoid arthritis, multiple sclerosis, lupus, vasulitis, and inflammatory bowel disease. Conversely, enhanced inflammatory responses would be expected to be contraindicated in patients being treating for cardiovascular disease and/or having a pathological inflammatory condition.

Further specific aspects of the invention provide methods in which the adenine/guanine substitution is identified by analysis of DNA or mRNA (or other nucleic acid sequences, such as cDNA, developed therefrom) in tissue, blood or other biological samples taken from a patient. Such analysis can include sequencing, probing, and/or amplification of those sequences using otherwise known techniques adapted to identify the aforementioned polymorphism.

In one preferred aspect of the invention, the nucleotide sequences in the samples are amplified, e.g., via polymerase chain reaction (PCR), and the amplified product is analyzed for evidence of the substitution. Such amplification can be performed, for example, using conventional PCR, or single-strand conformation polymorphism (SSCP), and/or amplification refractory mutation system (ARMS) techniques, though other amplification techniques known in the art can be used as well.

A further embodiment of the subject invention pertains to the determination that genetic markers associated with the NRl H3 locus are correlated with varying outcomes in individuals with CV disease. Thus, these markers can be used according to the subject invention in diagnostic procedures. In one embodiment, these diagnostic procedures can be used to identify people with a poor disease prognosis such that treatment can be designed accordingly. This treatment may be, for example, more aggressive than the treatment might be if the genetic diagnosis suggested the likelihood of a more favorable outcome.

DETAILED DISCLOSURE

The subject invention provides materials and methods for predicting a patient's physiological response to treatment with a cardiovascular (CV) drug. In one embodiment, the subject invention provides diagnostic assays that predict whether an individual's C-reactive protein (CRP) is likely to increase or decrease as a result of treatment with a CV drug. Specifically exemplified herein are methods and assays relating to statins. Advantageously, the methods of the subject invention facilitate the selection of preferred drugs for the treatment of cardiovascular disease in particular patients. The subject invention provides methods for diagnostic testing of a person's genotype (genetic fingerprint) at the NR1H3 locus. As described herein, the methods of the subject invention are particularly useful for NR1H3 genotype testing to indicate the likely nature of the CRP response in patients treated with a CV drug and, ultimately, to guide drug treatment decisions. Specifically exemplified herein are methods of assessing the likely response to statins. Other CV drugs to which the methods of the subject invention can be applied include, but are not limited to fibrates and cholesterol lowering drugs in general. In specific embodiments, the subject invention provides methods for genotype determination of the NR1H3 rs 12221497 G → A single nucleotide polymorphism (SNP) and for utilizing this information in formulating and implementing an appropriate treatment plan for a particular patient. In specific embodiments, this polymorphism is detected using polymerase chain reaction (PCR) and G → A pyrosequencing.

Advantageously, the methods of the subject invention can be used to identify patients that are likely to experience a significant anti-inflammatory (or inflammatory) response resulting from treatment with a CV drug, such as a statin. As described herein, the methods of the subject invention are particularly useful for NR1H3 genotype testing to indicate the likelihood for CRP response in statin-treated patients and, ultimately, guide cardiovascular drug treatment decisions, as well as treatments for other conditions.

As used herein, the term "nucleic acid" refers to polynucleotides, or oligonucleotides such as deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid (RNA). The term should also be understood to include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs (e.g. peptide nucleic acids) and as applicable to the embodiment being described, single (sense or antisense) and double-stranded polynucleotides.

The term "polymorphism" refers to the coexistence of more than one form of a gene or portion of a gene of which there are at least two different forms, i.e., two different nucleotide sequences. A specific genetic sequence at a polymorphic region of a gene is an allele. A polymorphic region can be a single nucleotide, the identity of which differs in different alleles. A polymorphic region can also be several nucleotides long. As used herein, the term "specifically hybridizes" or "specifically detects" refers to the ability of a nucleic acid molecule to hybridize to at least approximately 6 consecutive nucleotides of a sample nucleic acid. The term "wild-type allele'^" refers to an allele of a gene which, when present in two copies in a subject results in a wild-type phenotype.

Types of cardiovascular diseases include aneurysms, angina, arrhythmia, atherosclerosis, cardiomyopathy, cerebrovascular disease, congenital heart disease, congestive heart failure, myocarditis, valve disease, coronary artery disease, dilated cardiomyopathy, diastolic dysfunction, endocarditis, high blood pressure (hypertension), hypertrophic cardiomyopathy, mitral valve prolapse, heart attack, venous thromboembolism.

Detecting Polymorphisms

A variety of methods are available for detecting the presence of a particular single nucleotide polymorphic allele in an individual.

Applicable diagnostic techniques include, but are not limited to, DNA sequencing including mini-sequencing, primer extension, hybridization with allele- specific oligonucleotides (ASO), oligonucleotide ligation assays (OLA), PCR using allele-specific primers (ARMS), dot blot analysis, flap probe cleavage approaches, restriction fragment length polymorphism (RFLP), kinetic PCR, and PCR-SSCP, fluorescent in situ hybridisation (FISH), pulsed field gel electrophoresis (PFGE) analysis, Southern blot analysis, single stranded conformation analysis (SSCA), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), denaturing HPLC (DHPLC), and RNAse protection assays, all of which are presently known to the person skilled in the art.

In pyrosequencing, a short oligonucleotide (sequencing primer) binds at the single strand DNA close to the mutation and is elongated by dispensing deoxynucleotide triphosphates (dNTP). If the dispensed dNTP matches the next nucleotide of the DNA sequence, it is incorporated into the oligonucleotide and pyrophosphate (PPi) is released (DNAn+ dNTP + DNAn+ 1 + PPi). The PPi is used together with adenosine 5-phosphosulfate (APS) as a substrate for ATP sulfurylase. The resulting ATP triggers the luciferase catalyzed conversion of luciferin to oxiluciferin, emitting light of intensity proportional to the number of added nucleotides. It is visualized as a peak in the so-called programs, whereas no peak is observed in case of non-incorporation. In a merely illustrative embodiment, the method of the subject invention can include the steps of (i) collecting a sample of cells from a patient, (ii) isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, (iii) contacting the nucleic acid sample with one or more primers that specifically hybridize 5^" and 3^" to an appropriate allele under conditions such that hybridization and amplification of the allele occurs, and (iv) detecting the amplification product. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.

In one embodiment, the single base polymorphism can be detected by using a specialized exonuclease-resistant nucleotide, as disclosed, e.g., in Mundy, CR. (U.S.

Pat. No. 4,656,127). In another embodiment of the invention, a solution-based method is used for determining the identity of the nucleotide of a polymorphic site. Cohen, D. et al (French Patent 2,650,840; PCT Appln. No. WO 91/02087). The method determines the identity of the nucleotide of that site using labeled dideoxynucleotide derivatives, which, if complementary to the nucleotide of the polymorphic site will become incorporated onto the terminus of the primer. An alternative method, known as Genetic Bit Analysis or GBA™ is described by Goelet, P. et al. (PCT Appln. No. 92/15712).

In other embodiments, any of a variety of sequencing reactions known in the art can be used to directly sequence the allele. These are described in, for example,

U.S. Pat. No. 6,746,839, which is incorporated herein, in its entirety, by reference.

Several primer-guided nucleotide incorporation procedures for assaying polymorphic sites in DNA have been described (Komher, J. S. et al, Nucl. Acids. Res. 17:7779-7784 (1989); Sokolov, B.P., Nucl. Acids Res. 18:3671 (1990); Syvanen, A. - C, et al, Genomics 8:684-692 (1990); Kuppuswamy, M.N. et al. Proc. Natl. Acad.

Sci. (U.S.A.) 88:1143-1 147 (1991); Prezant, T.R. et al, Hum. Mutat. 1 :159-164 (1992); Ugozzoli, L. et al, GATA 9:107-112 (1992); Nyren, P. et al Anal. Biochem. 208: 171-175 (1993)).

Another detection method is allele specific hybridization using probe overlapping a region of an allele and having about 5, 10, 20, 25, or 30 nucleotides around the mutation or polymorphic region. Oligonucleotides can be bound to a solid support by a variety of processes, including lithography. Mutation detection analysis using these chips comprising oligonucleotides, also termed ''DNA probe arrays^"' is described e.g. in Cronin et al. (1996) Human Mutation 7:244.

Amplification techniques are known to those of skill in the art and include, but are not limited to cloning, polymerase chain reaction (PCR), polymerase chain reaction of specific alleles (ASA), ligase chain reaction (LCR), nested polymerase chain reaction, self sustained sequence replication (Guatelli, J. C. et al, 1990, Proc. Natl. Acad. Sci. USA 87: 1874-1878), transcriptional amplification system (Kwoh, D.Y. et al, 1989, Proc. Natl. Acad. Sci. USA 86:1173-1177), and Q-Beta Replicase (Lizardi, P.M. et al. 1988, Bio/Technology 6:1197). Amplification products may be assayed in a variety of ways, including size analysis, restriction digestion followed by size analysis, detecting specific tagged oligonucleotide primers in the reaction products, allele-specific oligonucleotide (ASO) hybridization, allele specific 5' exonuclease detection, sequencing, hybridization, and the like. For a known polymorphism, direct determination of the respective genotype is often the method of choice. State of the art approaches for industrial high-throughput genotyping typically rely on one of four different mechanisms: allele-specific primer extension, allele-specific hybridization, allele-specific oligonucleotide ligation and allele-specific cleavage of a flap probe (Kwok, Pharmacogenomics 1, 95 (2000)). Sequencing or mini-sequencing protocols are part of the primer extension methods, e.g. genomic DNA sequencing, either manual or by automated means. Minisequencing (primer extension) technology is based on determining the sequence at a specific base by allowing the elongation of a primer by one base directly at the variant site (Landegren et al., Genome Res. 8: 769-76 (1998)). Short sequence reactions coupled with an alternative detection method are the nature of real time pyrophosphate sequencing (Nyren et al., Science 281 :363 (1998)).

Several techniques have been developed for detection of an hybridization event. In the 5' nuclease assay and in the molecular beacon assay the hybridization probes are fluorescently labeled and probe binding is detected via changes in the behavior of the fluorescent label (Livak, Genet. Anal. 14, 143 (1999); Tyagi et al.,

Nat. Biotechnol. 16, 49 (1998)). Hybridization events may occur in liquid phase or with either the probe or the target bound to a solid surface. Hybridization is thus also used when arrays (microchips) are used for genotyping purposes. This technique of nucleic acid analysis is also applicable to the present invention. A chip typically consists of thousands of distinct nucleotide probes which are built up in an array on a silicon chip. Nucleic acid to be analyzed is fluorescently labeled, and hybridized to the probes on the chip. This method is one of parallel processing of thousands of probes at once and can tremendously accelerate the analysis. In several publications the use of this method is described (Hacia et al., Nature Genetics 14, 441 (1996); Shoemaker et al., Nature Genetics 14, 450 (1996); Chee et al., Science 274, 610 (1996); DeRisi et al., Nature Genetics 14, 457 (1996), Fan et al., Genome Res, 10, 853 (2000)).

Allele-specific oligonucleotide ligation assays have a high specificity. Oligonucleotides differing in the allele-specific base at the 5'- or 3 '-end are only processed by a ligation reaction if they are perfectly bound to the template at the respective oligonucleotide end. This method has been coupled with fluorescence resonance energy transfer (FRET) labeling 'to create a homogeneous assay system

(Chen et al. Genome Res. 8, 549 (1998)). Allele-specific cleavage of a flap probe use the property of recently discovered flap endonucleases (cleavases) to cleave structures created by two overlapping oligonucleotides. In this approach two overlapping oligonucleotides are bound to the polymorphic site. Which oligo has had a perfect match to the target sequence is then detected by the cleavage reaction (Lyamichev et al., Nat. Biotechnol. 17:292 (1999)).

The use of proteins which recognize nucleotide mismatches, such as the E. coli mutS protein may help in detecting mismatched DNA molecules (Modrich, Ann. Rev. Genetics, 25, 229 (1991)). In the mutS assay, the protein binds only to sequences that contain a nucleotide mismatch in a heteroduplex between mutant and wild-type sequences. RNase protection assays are another option (Finkelstein et al., Genomics 7, 167 (1990)). The RNAse protection assay involves cleavage of the mutant fragment into two or more smaller fragments. Another way is to make use of the single- stranded conformation polymorphism assay (SSCP; Orita et al., Proc Natl Acad Sci USA 86, 2766 (1989)). Variations in the DNA sequence of the gene from the reference sequences will be detected due to a shifted mobility of the corresponding DNA- fragments in SSCP gels. SSCP detects bands which migrate differently because the variation causes a difference in single strand, intra-molecular base pairing.

Alternatively, or in addition, the mutation can be detected by identification of the variant protein in those tissues. For mutations that produce premature termination of protein translation, the protein truncation test (PTT) offers an efficient diagnostic approach (Roest, et ah, (1993) Hum. MoI. Genet. 2: 1719-21 ; van der Luijt, et ah (1994) Genomics 20:1-4. For PTT, RNA is initially isolated from available tissue and reverse-transcribed, and the segment of interest is amplified by PCR. The products of reverse transcription PCR are then used as a template for nested PCR amplification with a primer that contains RNA polymerase promoter and a sequence for initiating eukaryotic translation. After amplification of the region of interest, the unique motifs incorporated into the primer permit sequential in vitro transcription and translation of the PCR products. Upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis of translation products, the appearance of truncated polypeptides signals the presence of a mutation that causes premature termination of translation. In a variation of this technique, DNA (as opposed to RNA) is used as a PCR template when the target region of interest is derived from a single exon.

Advancements in this field have provided accurate, easy, and inexpensive large-scale SNP genotyping. For example, several new techniques have been described including dynamic allele-specific hybridization (DASH), microplate array diagonal gel electrophoresis (MADGE), pyrosequencing, oligonucleotide-specific ligation, the TaqMan system as well as various DNA "chip" technologies such as the Affymetrix SNP chips. These methods require amplification of the target genetic region, typically by PCR. Still other newly developed methods, based on the generation of small signal molecules by invasive cleavage followed by mass spectrometry or immobilized padlock probes and rolling-circle amplification, might eventually eliminate the need for PCR. The method of the present invention is understood to include all available methods for identifying SNPs.

Samples to be tested

Detection of polymorphisms/point mutations may be accomplished by amplification, for instance by PCR, from genomic or cDNA and sequencing of the amplified nucleic acid or by molecular cloning of the allele and sequencing the allele using techniques well known in the art.

The nucleic acid that forms part of the method according to the present invention can be DNA, genomic DNA, RNA, cDNA, hnRNA and/or mRNA. The detection can be accomplished by sequencing, mini-sequencing, hybridisation, restriction fragment analysis, oligonucleotide ligation assay or allele specific PCR.

Any cell type or tissue may be utilized to obtain nucleic acid samples for use in the diagnostics described herein. In a preferred embodiment, the DNA sample is obtained from a bodily fluid, e.g., blood, obtained by known techniques (e.g. venipuncture) or saliva. Alternatively, nucleic acid tests can be performed on dry samples (e.g. hair or skin). Diagnostic procedures may also be performed in situ directly upon tissue sections (fixed and/or frozen) of patient tissue obtained from biopsies or resections, such that no nucleic acid purification is necessary.

Although the method of the invention can be performed in mammals in general, it is preferred to perform the method with human samples.

Kits

Another embodiment of the invention is directed to kits. This kit may contain one or more oligonucleotides, including oligonucleotides that hybridize at least one target allele.

For use in a kit, oligonucleotides may be any of a variety of natural and/or synthetic compositions such as synthetic oligonuucleotides, restriction fragments, cDNAs, synthetic peptide nucleic acids (PNAs), and the like. The assay kit and method may also employ labeled oligonucleotides to allow ease of identification in the assays. Examples of labels which may be employed include radio-labels, enzymes, fluorescent compounds, streptavidin, avidin, biotin, magnetic moieties, metal binding moieties, antigen or antibody moieties, and the like.

The kit may, optionally, also include DNA sampling means. DNA sampling means are well known to one of skill in the art and can include, but note be limited to substrates, such as filter papers, the AmpliCard™ (University of Sheffield, Sheffield,

England SlO 2JF; Tarlow, J, W., et al, J. of Invest. Dermatol. 103:387-389 (1994)) and the like; DNA purification reagents such as Nucleon™ kits, lysis buffers, proteinase solutions and the like; PCR reagents, such as lOxreaction buffers, thermostable polymerase, dNTPs, and the like.

The kit can contain other compounds such as enzymes, buffers, and/or dyes for performing the method(s) of the present invention. In another example, the kit according to the invention is suitable to perform a chip-based analysis in at least one

SNP according to the invention. The kit can also include instructions for performing the SNP-analysis and/or the software for a statistical analysis as described herein.

Following is an example that illustrates procedures for practicing the invention. These examples should not be construed as limiting. All percentages are by weight and all solvent mixture proportions are by volume unless otherwise noted.

Example 1 — LXRA genotype association with statin-mediated CRP changes

Materials and Methods

Study Population

Eligible participants had to be at least 18 years of age without known cardiovascular disease (CVD), CVD risk equivalents, or contraindications to statins.

All subjects provided written informed consent that their biological samples and clinical data could be used in genetics research.

Statistical Analyses

Participants received atorvastatin 80 mg daily for eight weeks. Baseline and

8-week lipids and CRP were obtained from the university hospital clinical laboratory. Genotype determination of the LXRA rs 12221497 G/A SNP was performed by pyrosequencing. Biomarker changes were tested by t-test and multivariate analysis.

Results

A total of 61 subjects (59% women; 79% white) were analyzed. Baseline age, total cholesterol, LDL, HDL, triglycerides, and CRP were 32 ± 13 years, 178 ± 38 mg/dl, 98 ± 31 mg/dl. 62 ± 18 mg/dl, 97 ± 54 mg/dl, and 1.8 ± 2.9 mg/L, respectively.

The variant A allele frequency was 16%. There were no differences in lipid changes by genotype (not shown). However, wild-type homozygotes (G/G) had an 11% reduction in CRP compared with a 25% increase in variant carriers (p=0.047). In multivariate analysis, age (p=0.01), baseline CRP (p=0.02), and LXRA genotype (p=().O4) were significant predictors of CRP response (model p=0.002; r2=0.23).

LXRA genotype did not affect LDL response to eight weeks of high-dose atorvastatin. However, LXRA genotype was associated with atorvastatin-mediated CRP changes. This is the first study to demonstrate a genetic association with the

CRP statin response and should be further evaluated.

Example 2

In one embodiment, the subject invention provides a method of diagnosing in a patient a predisposition for an increase in CRP as a result of treatment of the patient with a statin, wherein said method comprises detecting a polymorphism in a liver X receptor -α (LXRA) gene that is correlated with said predisposition for an increase in

CRP as a result of treatment of the patient with a statin.

Example 3

In one embodiment, the subject invention provides a method for determining the likely effect on a patient's C-reactive protein (CRP) levels that would result from the administration of a statin to that patient, wherein said method comprises determining whether a patient's gene encoding the liver X receptor -α (LXRA) comprises a single nucleotide polymorphism (SNP) such that there is a G → A mutation (DNRl H3 rs 12221497 G → A), wherein the presence of said mutation is indicative of an increased probability of an increase in CRP after treatment of the patient with a statin.

Example 4

In one embodiment, the subject invention provides a method for determining the suitability of a patient for treatment with a statin, wherein the administration of a pro-inflammatory treatment is contraindicated for that patient, and wherein said method comprises determining whether the patient's gene encoding the liver X receptor -α (LXRA) comprises a G → A mutation (DNR1H3 rs 12221497 G → A) and wherein the presence of said SNP is correlated with the patient being less suited for treatment with a statin Example 5

In one embodiment, the subject invention provides a method for treating cardiovascular disease in a patient wherein said method comprises screening the patient for a predisposition to increased C-reactive protein (CRP) levels as a result of administration of a statin; and if such a predisposition exists, reducing or eliminating the use of statins to treat the patient.

Example 6

In one embodiment, the subject invention provides a method for treating a disease wherein said treatment comprises administering to a patient an antiinflammatory agent, wherein said method comprises screening the patient to determine the likely effect on the patient's C-reactive protein (CRP) levels that would result from the administration of a statin to that patient, wherein said screening comprises detecting a polymorphism in a liver X receptor ^a (LXRA) gene that is correlated with a predisposition for an increase in CRP as a result of treatment of the patient with a statin, and wherein said method further comprises administering to the patient a statin only if the results of said screening indicate that the CRP level for said patient will likely decrease as a result of administering said statin.

Example 7

A further embodiment of the subject invention pertains to the determination that genetic markers associated with the NRl H3 locus are correlated with varying outcomes in individuals with CV disease. Thus, these markers can be used according to the subject invention in diagnostic procedures. In a specific embodiment, these diagnostic procedures can be used to identify people with a poor disease prognosis such that treatment can be designed accordingly. This treatment may be, for example, more aggressive than the treatment might be if the genetic diagnosis suggested the likelihood of a more favorable outcome. In accordance with the subject invention, NR1H3 SNPs that are associated with variable CV disease outcome include, but are not limited to: rs2279238 rs326213 rs7120118 rslO5O1321 rsl 1039149 rsl lO39159 rsl 2221497

Thus, diagnostic methods can be used to identify SNPs at these locations and use this information in disease prognosis and or to guide treatment in a patient- specific manner.

' All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.

It should be understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application.

Claims

CLAIMS I claim:

1. A method of diagnosing in a patient a predisposition for an increase in CRP as a result of treatment of the patient with a cardiovascular disease (CV) drug, wherein said method comprises detecting a polymorphism in a liver X receptor -α (LXRA) gene that is correlated with said predisposition for an increase in CRP as a result of treatment of the patient with a CV drug.

2. The method, according to claim 1, wherein the polymorphism is a single nucleotide polymorphism (SNP).

3. The method, according to claim 2, wherein the SNP is a G → A mutant identified as DNR 1H3 rs 12221497 G → A.

4. The method, according to claim 1, wherein said polymorphism is detected using a method that comprises at least one of the group consisting of sequencing, probing, and amplifying a polynucleotide sequence of said gene.

5. The method, according to claim 1, wherein the CV drug is a cholesterol lowering drug.

6. The method, according to claim 1, wherein the CV drug is a fibrate.

7. The method, according to claim 1 , wherein the CV drug is a statin.

8. The method, according to claim 7, wherein said statin is selected from the group consisting of Atorvastatin, Cerivastatin, Fluvastatin, Lovastatin, Mevastatin, Pravastatin, Pravastatin, Rosuvastatin, and Simvastatin.

9. A method for determining the likely effect on a patient^'s C-reactive protein (CRP) levels that would result from the administration of a CV drug to that patient, wherein said method comprises determining whether a patient^'s gene encoding the liver X receptor -α (LXRA) comprises a single nucleotide polymorphism (SNP) such that there is a G → A mutation (DNRl H3 rs 12221497 G → A), wherein the presence of said mutation is indicative of an increased probability of an increase in CRP after treatment of the patient with a CV drug.

10. The method, according to claim 9, wherein the CV drug is a fibrate.

11. The method, according to claim 9, wherein the CV drug is a cholesterol lowering drug.

12. The method, according to claim 9, wherein the CV drug is a statin.

13. The method, according to claim 12, wherein said statin is selected from the group consisting of Atorvastatin, Cerivastatin, Fluvastatin, Lovastatin, Mevastatin, Pitavastatin, Pravastatin, Rosuvastatin, and Simvastatin.

14. The method, according to claim 9, wherein the determination of whether the SNP is present comprises the use of PCR and/or pyrosequcncing.

15. A method for determining the suitability of a patient for treatment with a CV drug, wherein the administration of a pro-inflammatory treatment is contraindicated for that patient, and wherein said method comprises determining whether the patient's gene encoding the liver X receptor -α (LXRA) comprises a G → A mutation (DNRl H3 rs 12221497 G → A) and wherein the presence of said SNP is correlated with the patient being less suited for treatment with a CV drug.

16. The method, according to claim 15, wherein the patient has a condition selected from the group consisting of rheumatoid arthritis, multiple sclerosis, lupus, vasulitis, and inflammatory bowel disease.

17. A method for treating cardiovascular disease in a patient wherein said method comprises screening the patient for a predisposition to increased C-reactive protein (CRP) levels as a result of administration of a statin; and if such a predisposition exists, reducing or eliminating the use of statins to treat the patient.

18. The method, according to claim 17, wherein said screening comprises detecting a polymorphism in a liver X receptor -α (LXRA) gene that is correlated with said predisposition for an increase in CRP as a result of treatment of the patient with a statin.

19. The method, according to claim 18, wherein the polymorphism is a single nucleotide polymorphism (SNP).

20. The method, according to claim 19. wherein the SNP is a G → A mutant identified as DNR 1H3 rs 12221497 G → A.

21. A method for treating a disease wherein said treatment comprises administering to a patient an anti-inflammatory agent, wherein said method comprises screening the patient to determine the likely effect on the patient's C-reactive protein (CRP) levels that would result from the administration of a statin to that patient, wherein said screening comprises detecting a polymorphism in a liver X receptor -α (LXRA) gene that is correlated with a predisposition for an increase in CRP as a result of treatment of the patient with a statin, and wherein said method further comprises administering to the patient a statin only if the results of said screening indicate that the CRP level for said patient will likely decrease as a result of administering said statin.

22. A method for assessing the prognosis of a patient with a CV disease, wherein said method comprises evaluating the patient to determine the presence of SNPs in the NRl H3 locus.

23. The method, according to claim 22, which comprises determining whether SNPs exist at one or more of the following sites: rs 12221497, rs2279238, rs326213, rs7120118, rslO5O1321, rsl 1039149, rsl 1039159, and rsl 2221497.