Profiling microvesicle nucleic acids and uses thereof as signatures in diagnosis of renal transplant rejection

Abstract

The invention relates generally to the use of microvesicle RNA signatures for diagnosis, predicting, and/or to monitor treatment efficacy, including patients who are candidates for renal transplant and/or who have received a renal transplant.

What is claimed is: 
     
         1 . A method for characterizing kidney transplant subjects for the diagnosis, prognosis, monitoring or therapy selection for kidney transplant rejection in a subject in need thereof, the method comprising the steps of:
 (a) providing a biological sample from a subject;   (b) isolating a microvesicle fraction from the biological sample;   (c) extracting one or more nucleic acids from the microvesicle fraction;   (d) detecting a level of expression of at least one biomarker in the extracted nucleic acids from step (c), and   (e) comparing the level of expression of the at least one biomarker from step (d) with a control level of expression of the at least one biomarker to determine and/or to predict kidney transplant rejection in the subject, wherein the control level of expression of the at least one biomarker is from a patient who has experienced kidney transplant rejection or wherein the control level of expression of the at least one biomarker is from a patient who has not experienced any symptom of kidney transplant rejection.   
     
     
         2 . The method of  claim 1 , wherein a difference in the level of expression of the at least one biomarker from step (d) and the control level of expression for the at least one biomarker indicates that the subject is likely to experience kidney transplant rejection. 
     
     
         3 . The method of  claim 1 , wherein a difference in the level of expression of the at least one biomarker from step (d) and the control level of expression for the at least one biomarker indicates that the subject is not likely to experience kidney transplant rejection. 
     
     
         4 . The method of  claim 1 , wherein the at least one biomarker is selected from the group consisting of CXCL9, IFNGR1, CXCL10, PXMP2, TNFRSF19, IL32, AGTR1, EPHX2, PDE4A, IRAK2, IL22RA1, IL1RAP, CXCL13, CXCL6, PTGES, STAT1, TSLP, BMP7, IL15RA, CCL8, PYCARD, C3, ZMYND15, and combinations thereof. 
     
     
         5 . The method of  claim 4 , wherein the at least one biomarker is a panel of biomarkers comprising CXCL9, IFNGR1, CXCL10, PXMP2, TNFRSF19, IL32, AGTR1, EPHX2, PDE4A, IRAK2, IL22RA1, IL1RAP, CXCL13, CXCL6, PTGES, STAT1, TSLP, BMP7, IL15RA, CCL8, PYCARD, C3, and ZMYND15. 
     
     
         6 . The method of  claim 4 , wherein the at least one biomarker is a panel of biomarkers consisting of CXCL9, IFNGR1, CXCL10, PXMP2, TNFRSF19, IL32, AGTR1, EPHX2, PDE4A, IRAK2, IL22RA1, IL1RAP, CXCL13, CXCL6, PTGES, STAT1, TSLP, BMP7, IL15RA, CCL8, PYCARD, C3, and ZMYND15. 
     
     
         7 . The method of  claim 1 , wherein the at least one biomarker is selected from the group consisting of IL32, IL15RA, CXCL9, PXMP2, CXCL10, C1R, TNFRSF19, CXCL14, C3, PYCARD, IL1F5, LEP, C7, FABP4, CXCL6, CD55, KRT1, BMP7, INHBA, IL1F8, PTGES, EREG, IL12A, and combinations thereof. 
     
     
         8 . The method of  claim 7 , wherein the at least one biomarker is a panel of biomarkers comprising IL32, IL15RA, CXCL9, PXMP2, CXCL10, C1R, TNFRSF19, CXCL14, C3, PYCARD, IL1F5, LEP, C7, FABP4, CXCL6, CD55, KRT1, BMP7, INHBA, IL1F8, PTGES, EREG, and IL12A. 
     
     
         9 . The method of  claim 7 , wherein the at least one biomarker is a panel of biomarkers consisting of IL32, IL15RA, CXCL9, PXMP2, CXCL10, C1R, TNFRSF19, CXCL14, C3, PYCARD, IL1F5, LEP, C7, FABP4, CXCL6, CD55, KRT1, BMP7, INHBA, IL1F8, PTGES, EREG, and IL12A. 
     
     
         10 . The method of any one of  claims 1 - 9 , wherein the biological sample is urine. 
     
     
         11 . The method of any one of  claims 1 - 10 , wherein the extracted nucleic acid is RNA. 
     
     
         12 . The method of any one of  claims 1 - 11 , wherein step (a) comprises (i) processing microvesicles to exclude proteins, lipids, debris from dead cells, and other contaminants; (ii) purifying microvesicles using ultracentrifugation or a nanomembrane ultrafiltration concentrator; and (iii) washing the microvesicles.