Use of micro-ribonucleic acid (mirna) to diagnose transplant rejection and tolerance of immunosuppression therapy

Abstract

The present invention relates to the discovery that the expression levels of some microRNAs (miRNAs) can use a diagnostic signature to predict transplant outcomes in a transplant recipient. Thus, in various embodiments described herein, the methods of the invention relate to methods of diagnosing a transplant subject for acute rejection such as acute cellular rejection (ACR), methods of predicting a subject's risk of having or developing ACR and methods of assessing in a subject the likelihood of a successful or failure minimization of immunosuppression therapy (IST) dosage from standard ranges.

What is claimed is: 
     
         1 . A method for detecting or predicting transplant rejection of a transplanted organ in a subject, the method comprising:
 i. determining a level of at least one miRNA expression in a sample from the subject;   ii. comparing the level of at least one miRNA in the sample from the subject relative to a baseline level in a control wherein a difference in the level of the least one miRNA in the sample from the level of the at least one miRNA in the control is indicative of an acute transplant rejection; and,   iii. wherein when acute transplant rejection is indicated, treatment for the rejection is recommended.   
     
     
         2 . The method of  claim 1 , wherein the acute transplant rejection comprises acute cellular rejection (ACR). 
     
     
         3 . The method of  claim 1 , wherein the at least one miRNA is selected from the group consisting of SEQ ID NOs: 1-3. 
     
     
         4 . The method of  claim 1 , wherein the at least one miRNA is selected from the group consisting of SEQ ID NOs: 4-15. 
     
     
         5 . The method of  claim 1 , wherein the at least one miRNA is selected from the group consisting SEQ ID NOs: 16-23. 
     
     
         6 . The method of  claim 1 , wherein the at least one miRNA is selected from the group consisting of SEQ ID NOs: 1-23. 
     
     
         7 . The method of  claim 1 , wherein the at least one miRNA is selected from the group consisting of SEQ ID NOs: 1-23 and 97-134. 
     
     
         8 . The method of  claim 1 , wherein the subject is a mammal. 
     
     
         9 . The method of  claim 8 , wherein the mammal is a human. 
     
     
         10 . The method of  claim 1 , wherein the level of the at least one miRNA is higher than the level of the at least one miRNA in the control by at least 1 fold. 
     
     
         11 . The method of  claim 1 , wherein determining the level of the at least one miRNA employs at least one technique selected from the group consisting of reverse transcription, PCR, microarray, and Next Generation Sequencing. 
     
     
         12 . The method of  claim 1 , wherein the sample is at least one selected from the group consisting of urine, peripheral blood, serum, bile, bronchoalveolar lavage (BAL) fluid, pericardial fluid, gastrointestinal fluids, stool samples, biological fluid gathered from an anatomic area in proximity to an allograft, and biological fluid from an allograft. 
     
     
         13 . The method of  claim 1 , wherein the transplanted organ is at least one selected from the group consisting of heart, liver, lung, kidney, an intestine, pancreas, pancreatic islet cells, eye, skin, and stem cells. 
     
     
         14 . The method of  claim 1 , wherein the comparison of level of miRNA expression is computed in a regression model to indicate a trajectory of acute rejection of the transplanted organ. 
     
     
         15 . A method for predicting minimization of immunosuppression therapy (IST) in a transplant subject, the method comprising:
 i. determining a level of at least one miRNA expression in a sample from the subject;   ii. comparing the level of at least one miRNA in the sample from the subject relative to a baseline level in a control wherein a difference in the level of the least one miRNA in the sample from the level of the at least one miRNA in the control is indicative of likelihood of success or failure of IST minimization; and,   iii. wherein when failure of IST minimization is indicated, treatment of the subject is recommended.   
     
     
         16 . The method of  claim 15 , wherein the at least one miRNA is selected from the group consisting of SEQ ID NOs: 24-26. 
     
     
         17 . The method of  claim 15 , wherein the at least one miRNA is selected from the group consisting of SEQ ID NOs: 6-8, 22, 27-48. 
     
     
         18 . The method of  claim 15 , wherein the at least one miRNA is selected from the group consisting of SEQ ID NOs: 6-8, 22, 24-48. 
     
     
         19 . The method of  claim 15 , wherein the minimization of IST is lower than the initial dosage by at least 75%. 
     
     
         20 . The method of  claim 15 , wherein the minimization of IST is lower than the initial dosage by at least 25%, by at least 30%, by at least 35%, by at least 40%, by at least 45%, by at least 50%, by at least 55%, by at least 60%, by at least 65%, by at least 70%, by at least 75%, by at least 80%, by at least 85%, by at least 90%, by at least 95%, or by at least 100%. 
     
     
         21 . The method of  claim 15 , wherein the subject is a mammal. 
     
     
         22 . The method of  claim 21 , wherein the mammal is a human. 
     
     
         23 . The method of  claim 15 , wherein the level of the at least one miRNA is higher than the level of the at least one miRNA in the control by at least 1 fold. 
     
     
         24 . The method of  claim 15 , wherein determining the level of the at least one microRNA utilizes at least one technique selected from the group consisting of reverse transcription, PCR, microarray, Next Generation Sequencing. 
     
     
         25 . The method of  claim 15 , wherein the sample is at least one selected from the group consisting of urine, peripheral blood, serum, bile, bronchoalveolar lavage (BAL) fluid, pericardial fluid, gastrointestinal fluids, stool samples, biological fluid gathered from an anatomic area in proximity to an allograft, and biological fluid from an allograft. 
     
     
         26 . The method of  claim 15 , wherein the transplanted organ is at least one selected from the group consisting of heart, liver, lung, kidney, an intestine, pancreas, pancreatic islet cells, eye, skin, and stem cells. 
     
     
         27 . The method of  claim 15 , wherein the comparison of level of miRNA expression is computed in a regression model to predict the likelihood of success or failure of IST minimization. 
     
     
         28 . A composition for detecting or predicting transplant rejection of a transplanted organ in a subject comprising a plurality of miRNAs consisting of SEQ ID NOs: 1-23. 
     
     
         29 . A composition for detecting or predicting transplant rejection of a transplanted organ in a subject comprising a plurality of miRNAs consisting of SEQ ID NOs: 1-23 and 97-134. 
     
     
         30 . A kit comprising:
 a plurality of oligonucleotides that are configured to detect at least one miRNA from selected from the group consisting of SEQ ID NOs: 1-23 and 97-134.   
     
     
         31 . The kit of  claim 30 , wherein the oligonucleotides are configured to detect at least SEQ ID NOs: 1-3. 
     
     
         32 . The kit of  claim 30 , wherein at least one of the oligonucleotides is selected from the group consisting of SEQ ID NOs: 49-71 and 135-172. 
     
     
         33 . A composition for detecting or predicting the ability, or non-ability, of minimizing IST dosage in a subject post-transplantation comprising a plurality of miRNAs consisting of SEQ ID NOs: 6-8, 22, 24-48. 
     
     
         34 . A kit comprising:
 a plurality of oligonucleotides that are configured to detect at least one miRNA from the group consisting of SEQ ID NOs: 6-8, 22, 24-48.   
     
     
         35 . The kit of  claim 34 , wherein the oligonucleotides are configured to detect at least SEQ ID NOs: 24-26. 
     
     
         36 . The kit of  claim 34 , wherein at least one of the oligonucleotides is selected from the group consisting of SEQ ID NOs: 53-55, 70, 72-96.