Method and kits for prediction of acute rejection and renal allograft loss using pre-transplant transcriptomic signatures in recipient blood

Abstract

Disclosed herein are gene signature sets expressed by kidney allograft recipients prior to transplant that determine the risk for acute rejection (AR) post-transplant and methods of using the gene signature sets for identifying renal allograft recipients at risk for acute rejection. Also disclosed herein are kits for use in the invention which comprise primer pairs for the gene signature sets.

What is claimed is: 
     
         1 . A method for identifying a renal allograft recipient at risk of developing acute rejection comprising the steps of
 (a) determining the expression levels of a gene signature set in a pre-transplant blood specimen from the renal allograft recipient;   (b) comparing the expression levels of the gene signature set with the expression levels of a gene signature set in a control, and   (c) determining the recipient will be at risk for allograft rejection if the expression level of one or more genes in the gene signature set in the specimen is altered from the expression level of the same one or more genes in the gene signature set in the control.   
     
     
         2 . The method of  claim 1  wherein the alteration comprises an increase or a decrease in the expression level of one or more genes in the gene signature set in the specimen compared to the same one or more genes in the gene signature set in the control. 
     
     
         3 . The method of  claims 1  or  2  wherein the alteration comprises an increase and a decrease in the expression level of one or more genes in the gene signature set in the specimen compared to the same one or more genes in the gene signature set in the control. 
     
     
         4 . The method of any one of  claims 1 ,  2  or  3  wherein the gene signature set is selected from the group consisting of: GZMH, ADGRG1, S1PR5, FGFBP2, NKG7, PRF1, KIAA1671, LAG3, TARP, FCRL6, FASLG, TBX21, TOX, ZNF831, CD8A, C1orf21, CCR5, LDOC1L, CCDC102A, HOPX, PRKCH, SLC25A34 and F12. 
     
     
         5 . The method of any one of  claims 1-3  or  4  wherein the determining step comprises applying the expression levels determined in the patient’s sample to a weighted cumulative risk score r = -(log 10 (p 1 )*g 1 + log 10 (p 2 )*g 2 +... +log 10 (p 1 )*g 1 +... + log 10 (p 23 )*g 23 ), where p i  is the significance p value of t-test on expression values for gene i (i=1...23) between the EAR vs the non-EAR groups in the training set, g i  is a logic number for gene i (i=1...23), 1 (if the expression value of gene i is greater than the median expression value of the EAR group of the training set for an upregulated gene or if the expression value of gene i is less than the median expression value of the EAR group of the training set for a downregulated gene), or -1 (if the expression value of gene i is less than the median value of the non-EAR group of the training set for an upregulated gene or if the expression value of gene i is greater than the median value of the non-EAR group of the training set for a downregulated gene), or 0 (if the expression value of gene i is between the median values of the EAR and the non-EAR groups of the training set) that can be used as a risk score for acute rejection for each patient. 
     
     
         6 . The method of any one of  claim 1-4  or  5  wherein the expression levels are determined by a method selected from the group consisting of Nanostring, TREx and quantitative polymerase chain reaction (qPCR). 
     
     
         7 . A method for identifying a renal allograft recipient at risk of acute rejection of the allograft before transplantation comprising the steps of
 (a) obtaining a blood specimen from the renal allograft recipient;   (b) isolating mRNA from the blood specimen;   (c) synthesizing cDNA from the mRNA;   (d) determining the expression levels of a gene signature set in said recipient’s blood;   (e) diagnosing the allograft recipient as being at risk for acute rejection and allograft loss if the expression level of one or more genes in the gene signature set in the allograft recipient’s blood specimen is altered compared to the expression level of the same one or more genes in the control blood specimen, and treating the recipient identified as being at risk for acute rejection or allograft loss with induction therapy.   
     
     
         8 . The method of  claim 7  wherein said induction therapy comprises administering a therapeutically effective amount of anti-thymocyte globulin or Campath-1H. 
     
     
         9 . The method of  claims 7  or  8  wherein the gene signature set is selected from the group consisting of GZMH, ADGRG1, S1PR5, FGFBP2, NKG7, PRF1, KIAA1671, LAG3, TARP, FCRL6, FASLG, TBX21, TOX, ZNF831, CD8A, C1orf21, CCR5, LDOC1L, CCDC102A, HOPX, PRKCH, SLC25A34, and F12. 
     
     
         10 . The method of any one of  claims 7-8  or  9  wherein the expression levels are determined by a method selected from the group consisting of Nanostring, TREx, and quantitative polymerase chain reaction (qPCR). 
     
     
         11 . A kit for identifying renal allograft recipients at risk for acute rejection and allograft loss comprising in one or more separate containers primer pairs for the gene signature set: GZMH, ADGRG1, S1PR5, FGFBP2, NKG7, PRF1, KIAA1671, LAG3, TARP, FCRL6, FASLG, TBX21, TOX, ZNF831, CD8A, C1orf21, CCR5, LDOC1L, CCDC102A, HOPX, PRKCH, SLC25A34, F12, buffers, positive and negative controls and instructions for use. 
     
     
         12 . The kit of  claim 11  further comprising a housekeeping gene panel and primers for the housekeeping gene panel. 
     
     
         13 . The kit of any one of  claims 11  or  12  wherein the genes in said housekeeping gene panel is selected from the group consisting of CHTOP, YKT6, RER1, PI4KB, ZDHHC5, TMEM248, C6orf89, SMU1, SHC1, DLST, UBE2Q1, FBXO18 and SLC35E1. 
     
     
         14 . The method of  claims 7  or  8  further comprising calculating a weighted cumulative score (r = -(log 10 (p 1 )*g 1 + log 10 (p 2 )*g 2 +... +log 10 (p i )*g i +... + log 10 (p 23 )*g 23 ), where p i  is the significance p value of t-test on expression values for gene i (i=1...23) between the EAR vs the non-EAR groups in the training set, g i  is a logic number for gene i (i=1...23), 1 (if the expression value of gene i is greater than the median expression value of the EAR group of the training set for an upregulated gene or if the expression value of gene i is less than the median expression value of the EAR group of the training set for a downregulated gene), or -1 (if the expression value of gene i is less than the median value of the non-EAR group of the training set for an upregulated gene or if the expression value of gene i is greater than the median value of the non-EAR group of the training set for a downregulated gene), or 0 (if the expression value of gene i is between the median values of the EAR and the non-EAR groups of the training set) that can be used as a risk score for acute rejection for each patient. 
     
     
         15 . The method of  claim 14  wherein the probability score is determined using a computer based system. 
     
     
         16 . The method of any one of  claims 14  or  15  wherein the probability score is used to determine the cutoff value. 
     
     
         17 . A method for selecting a renal allograft patient for induction therapy prior to transplantation to reduce the risk of renal acute rejection or allograft loss which comprises
 comparing the expression level of a gene signature set obtained from the patient with the expression level of a gene signature set in a control sample obtained from an allograft recipient that did not suffer acute rejection, and selecting the patient for treatment with induction therapy if the expression level of one or more genes in the gene signature set from the patient is altered compared to the expression level of one or more of the genes in the gene signature set in the control, and   administering induction therapy to said patient.   
     
     
         18 . The method of  claim 17  wherein said Induction therapy comprises administering a therapeutically effective amount of anti-thymocyte globulin or Campath-1H. 
     
     
         19 . The method of any one of  claims 17  or  18  wherein the gene signature set comprises at least the genes GZMH, ADGRG1, S1PR5, FGFBP2, NKG7, PRF1, KIAA1671, LAG3, TARP, FCRL6, FASLG, TBX21, TOX, ZNF831, CD8A, C1orf21, CCR5, LDOC1L, CCDC102A, HOPX, PRKCH, SLC25A34, and F12.