Blood rna biomarkers of coronary artery disease

Abstract

The present invention discloses a unique panel of gene transcripts down-regulated in patients with coronary artery disease (CAD). Methods and compositions for detecting CAD in patient blood samples are provided.

What is claimed is: 
     
         1 . A method for determining an increased likelihood of having or developing coronary artery disease, the method comprising:
 obtaining a blood sample from a subject;   extracting RNA from the blood sample;   quantitating RNA levels in at least a portion of the extracted RNA;   calculating expression levels for a plurality of RNA transcripts in the extracted RNA;   comparing the expression levels for the plurality of TRAC RNA transcripts to control expression levels for the same RNA transcripts; and   determining whether the expression levels for the plurality of TRAC RNA transcripts in the extracted RNA are, collectively, significantly different from the control expression levels for the same RNA transcripts, wherein a significant difference in expression levels indicates that the subject has an increased likelihood of having or developing coronary artery disease.   
     
     
         2 . The method of  claim 1 , wherein the blood sample comprises whole blood. 
     
     
         3 . The method of  claim 1 , further comprising depleting ribosomal RNA from the extracted RNA prior to quantitating at least the portion of the extracted RNA. 
     
     
         4 . The method of  claim 3 , wherein depleting ribosomal RNA from the extracted RNA comprises treating the extracted RNA with probes that are specific for ribosomal RNA. 
     
     
         5 . The method of  claim 1 , wherein the plurality of RNA transcripts include FOXP3, CD4, CD25, ETS1, and RUNX1, and wherein expression levels for each of FOXP3, CD4, CD25, ETS1, and RUNX1 are down-regulated when there is a significant difference in expression levels. 
     
     
         6 . The method of  claim 5 , wherein the expression levels for each of FOXP3, CD4, CD25, ETS1, and RUNX1 are down-regulated between 1.5-fold and 2-fold when there is a significant difference in expression levels. 
     
     
         7 . The method of  claim 1 , wherein the plurality of RNA transcripts include DGKA, DLG1, ICOSLG, IKZF4/Eos, SMYD3, TCF3 and TRIM28, and wherein expression levels for each of DGK, DLG1, ICOSLG, IKZF4/Eos, SMYD3, TCF3 and TRIM28 are down regulated when there is a significant difference in expression levels. 
     
     
         8 . The method of  claim 7 , wherein the expression levels for each of DGKA, DLG1, ICOSLG, IKZF4/Eos, SMYD3, TCF3 and TRIM28 are down-regulated between 1.5-fold and 2-fold when there is a significant difference in expression levels. 
     
     
         9 . The method of  claim 1 , wherein the subject is human. 
     
     
         10 . The method of  claim 1 , further comprising selecting a subject that has been identified as having one or more risk factors for coronary artery disease prior to obtaining the blood sample from the subject. 
     
     
         11 . The method of  claim 10 , wherein the risk factors are selected from the group consisting of hypertension, advanced age, elevated cholesterol, and a family history of coronary artery disease. 
     
     
         12 . The method of  claim 1 , wherein the method identifies coronary artery disease with a positive predictive value of greater than 80%. 
     
     
         13 . The method of  claim 12 , wherein the method identifies coronary artery disease with a positive predictive value of greater than 90%. 
     
     
         14 . The method of  claim 1 , further comprising treating the subject with one or more of a statin, aspirin, an ACE inhibitor, a diuretic, a glucose control medication, or a beta blocker based on the determination that the subject has an increased likelihood of having or developing coronary artery disease. 
     
     
         15 . The method of  claim 1 , further comprising subjecting the subject to coronary angiography based on the determination that the subject has an increased likelihood of having or developing coronary artery disease. 
     
     
         16 . The method of  claim 1 , wherein the control expression levels are determined based on empirical expression level data from individuals who do not have coronary artery disease. 
     
     
         17 . The method of  claim 16 , wherein the individuals who do not have coronary artery disease have been identified as not having coronary artery disease by coronary catheterization angiography. 
     
     
         18 . A method for determining an increased likelihood of having or developing coronary artery disease, the method comprising:
 obtaining RNA that has been extracted from a blood sample of a subject; determining expression levels for a plurality of biomarkers in the extracted RNA; comparing the expression levels for the plurality of biomarkers in the extracted RNA to the expression levels of the same biomarkers from a control; and   determining whether the expression levels for the plurality of biomarkers in the extracted RNA are, collectively, significantly different from the expression levels for the same biomarkers in the control;   wherein at least 20% of the plurality of biomarkers are selected from the group consisting of, AML1, CD4, CD3E, CD25, CTLA4, DGKA, DLG1, ETS1, FOXP3, ICOSLG, IKZF4/Eos, IL2RA, IL2RB, IL2RG, SMYD3, RUNX1, TCF3, TRIM28, and ZAP70.   
     
     
         19 . The method of  claim 18 , further comprising performing coronary catheterization angiography if the expression levels for the plurality of biomarkers are significantly different from the expression levels for the same biomarkers in the control. 
     
     
         20 . The method of  claim 18 , wherein more than 80% of the biomarkers are, individually, differentially down-regulated more than 1.5-fold. 
     
     
         21 . The method of  claim 18 , wherein the method identifies coronary artery disease with a positive predictive value of greater than 90%. 
     
     
         22 . The method of  claim 18 , further comprising treating the subject with one or more of a statin, aspirin, an ACE inhibitor, a diuretic, or a beta blocker based on the determination that the subject has an increased likelihood of having or developing coronary artery disease. 
     
     
         23 . The method of  claim 18 , wherein the subject is human. 
     
     
         24 . A method of analyzing an RNA sample from a subject, the method comprising: determining expression levels for a plurality of biomarkers in the RNA sample, wherein the plurality of biomarkers comprises biomarkers for which expression levels in individuals with coronary artery disease differ from expression levels in individuals without coronary artery disease;
 wherein the level of expression of the plurality of biomarkers in comparison to a control indicates that the subject has an increased likelihood of having or developing coronary artery disease.   
     
     
         25 . The method of  claim 24 , wherein the RNA sample is an RNA sample that has been isolated from whole blood. 
     
     
         26 . The method of  claim 24 , wherein the control is a database comprising expression levels of the plurality of biomarkers in individuals without coronary artery disease. 
     
     
         27 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts listed in Table 8. 
     
     
         28 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts of Table 7. 
     
     
         29 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts of Table 6. 
     
     
         30 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts of Table 5. 
     
     
         31 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts of Table 4. 
     
     
         32 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts of Table 3. 
     
     
         33 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts of Table 2. 
     
     
         34 . The method of  claim 24 , wherein the plurality of biomarkers comprises the transcripts of Table 61. 
     
     
         35 . The method of  claim 24 , wherein the plurality of biomarkers comprises at least 50%, 60%, 70%, 80%, 90%, and/or 95% of the transcripts of any of the biomarkers listed in Tables 3-10. 
     
     
         36 . The method of  claim 24 , wherein at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% and/or 95% of the plurality of biomarkers are down-regulated at least 1.5 fold when the subject is determined to have the increase likelihood of having or developing coronary artery disease. 
     
     
         37 . The method of  claim 24 , wherein at least 50%, 60%, 70%, 80%, 90%, and/or 95% of the plurality of biomarkers are selected from any of the biomarkers listed in Tables 3-10. 
     
     
         38 . A method of treating a subject that has been identified as having one or more risk factors for coronary artery disease, the method comprising:
 analyzing an RNA sample using the method of  claim 24 ; and   administering a medicament to or carrying out a medical procedure on the subject on the basis of the determination that the subject has an increased likelihood of having or developing coronary artery disease.   
     
     
         39 . The method of  claim 38 , wherein the risk factors are selected from the group consisting of hypertension, advanced age, elevated cholesterol, and a family history of coronary artery disease. 
     
     
         40 . A method for determining an increased likelihood of having or developing coronary artery disease, the method comprising:
 obtaining a blood sample from a subject;   extracting protein from the blood sample;   quantitating protein levels in at least a portion of the extracted protein;   calculating the concentrations of a plurality of proteins in the extracted protein;   comparing the expression levels for the plurality of proteins to control levels for the same proteins; and   determining whether the levels for the plurality of proteins in the extracted protein sample are, collectively, significantly different from the control levels for the same proteins, wherein a significant difference in protein levels indicates that the subject has an increased likelihood of having or developing coronary artery disease.   
     
     
         41 . The method of  claim 40 , wherein the plurality of proteins include AML1, CD4, CD3E, CD25, CTLA4, DGKA, DLG1, ETS1, FOXP3, ICOSLG, IKZF4/Eos, IL2RA, IL2RB, IL2RG, SMYD3, RUNX1, TCF3, TRIM28, and ZAP70. 
     
     
         42 . A method of analyzing a protein sample from a subject, the method comprising: determining expression levels for a plurality of biomarkers in the protein sample, wherein the plurality of biomarkers comprises biomarkers for which expression levels in individuals with coronary artery disease differ from expression levels in individuals without coronary artery disease;
 wherein the level of expression of the plurality of biomarkers in comparison to a control indicates that the subject has an increased likelihood of having or developing coronary artery disease.   
     
     
         43 . The method of  claim 42 , wherein the plurality of biomarkers comprises at least 50%, 60%, 70%, 80%, 90%, and/or 95% of the proteins encoded by any of the biomarkers listed in Tables 3-10. 
     
     
         44 . The method of  claim 42 , wherein at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% and/or 95% of the plurality of biomarkers are down-regulated at least 1.5 fold when the subject is determined to have the increase likelihood of having or developing coronary artery disease. 
     
     
         45 . The method of  claim 42 , wherein at least 50%, 60%, 70%, 80%, 90%, and/or 95% of the plurality of biomarkers are selected from any of the biomarkers listed in Tables 3-10. 
     
     
         46 . A method of treating a subject that has been identified as having one or more risk factors for coronary artery disease, the method comprising:
 analyzing a protein sample using the method of  claim 42 ; and   administering a medicament to or carrying out a medical procedure on the subject on the basis of the determination that the subject has an increased likelihood of having or developing coronary artery disease.   
     
     
         47 . The method of  claim 46 , wherein the risk factors are selected from the group consisting of hypertension, advanced age, elevated cholesterol, and a family history of coronary artery disease.