Protein and gene biomarkers for rejection of organ transplants

Abstract

Aspects of the present invention include methods for determining a transplant category of a subject having a transplant. Common mechanisms of rejection injury are uncovered across different tissue transplants, and provide a means to understand rational drug design. Various sources of tissues are examined form the patient for understanding AR mechanism (graft biopsy), as well as monitoring by minimal invasive means (blood) or non-invasive means (urine for the kidney allograft). For biomarker discovery different categories of markers are examined such as genes, proteins, peptides and antibodies. These biomarkers can help determine the subject's transplant category (e.g., acute allograft rejection (AR), stable allograft (STA), BK viremia, BK nephritis, drug toxicity or chronic allograft injury (CAI), and the like). Also provided are compositions, systems, kits and computer program products that find use in practicing the subject methods. The methods and compositions find use in a variety of applications.

1 - 33 . (canceled) 
     
     
         34 . A method comprising:
 evaluating the expression level of three or more genes in a sample from a subject who has received an organ allograft, wherein the three or more genes are selected from the group consisting of DUSP1, NAMPT, PSEN1, MAPK9, NKTR, RYBP, RNF130, IFNGR1, ITGAX and CFLAR.   
     
     
         35 . The method according to  claim 34 , wherein the evaluating comprises:
 contacting the sample with a collection of primers or probes for selectively amplifying an expression product of each of the three or more genes; and   assessing, using the collection of primers or probes, an amount of each of the expression products in said sample.   
     
     
         36 . The method according to  claim 35 , wherein the assessing is quantitative. 
     
     
         37 . The method according to  claim 35 , wherein the primers or probes are labelled. 
     
     
         38 . The method according to  claim 35 , wherein the collection comprises primers or probes for selectively amplifying 3 to 100 different genes. 
     
     
         39 . The method according to  claim 34 , wherein the expression level of 5 or more genes is measured. 
     
     
         40 . The method according to  claim 39 , wherein the expression level of 10 or more genes is measured. 
     
     
         41 . The method according to  claim 40 , wherein the expression level of 20 or more genes is measured. 
     
     
         42 . The method according to  claim 34 , wherein the evaluating comprises determining protein levels. 
     
     
         43 . The method according to  claim 34 , wherein the organ allograft is a kidney allograft, a heart allograft, a liver allograft, or a lung allograft. 
     
     
         44 . The method according to  claim 34 , wherein the sample is blood. 
     
     
         45 . A method of determining whether a subject who has received an organ allograft has a graft tolerant or a graft intolerant phenotype, the method comprising:
 (a) obtaining a peripheral blood sample from a subject;   (b) evaluating the level of expression of at least one gene in said peripheral blood sample to obtain a gene expression result, wherein said at least one gene is selected from the group consisting of: DUSP1, NAMPT, PSEN1, MAPK9, NKTR, RYBP, RNF130, IFNGR1, ITGAX and CFLAR;   (c) comparing the gene expression result to at least one reference gene expression profile, wherein the reference gene expression profile is selected from: an acute rejection phenotype gene expression profile and a control phenotype gene expression profile; and   (d) determining that:
 (i) the subject is undergoing an AR response based on the comparing when the gene expression result is similar to the acute rejection phenotype gene expression profile and/or is dissimilar to the control phenotype gene expression profile; or 
 (ii) the subject is not undergoing an AR response based on the comparing when the gene expression result is dissimilar to the acute rejection phenotype gene expression profile and/or is similar to the control phenotype gene expression profile. 
   
     
     
         46 . The method according to  claim 45 , wherein the evaluating comprises:
 extracting mRNA from the sample;   contacting the extracted mRNA with a reagent for assaying the mRNA from the at least one gene;   assessing, using the reagent, the amount of the mRNA from the at least one gene in the sample.   
     
     
         47 . The method according to  claim 45 , wherein the method has a p value that is less than 0.05. 
     
     
         48 . The method according to  claim 45 , wherein the method has a specificity that is higher than 80%. 
     
     
         49 . The method according to  claim 45 , wherein the method has a sensitivity that is higher than 80%. 
     
     
         50 . The method according to  claim 45 , wherein the method has a ROC that is higher than 70%. 
     
     
         51 . The method according to  claim 45 , wherein the method has an AUC that is higher than 70%. 
     
     
         52 . The method according to  claim 45 , wherein the method has a positive predictive value that is higher than 70%. 
     
     
         53 . The method according to  claim 45 , wherein the method has a negative predictive value that is higher than 70%. 
     
     
         54 . The method according to  claim 45 , wherein said reference gene expression profile is from a subject having a stable graft. 
     
     
         55 . The method according to  claim 45 , wherein the comparing step comprises at least one of: comparing digital images of the expression profiles and comparing databases of expression data. 
     
     
         56 . The method according to  claim 45 , wherein the organ is a kidney allograft, a heart allograft, a liver allograft, or a lung allograft. 
     
     
         57 . A method of treating an organ transplant recipient, said method comprising:
 (a) evaluating whether the transplant recipient has an acute rejection phenotype or a non-acute-rejection phenotype by using a gene expression result that was previously obtained from a quantitative determination of the nucleic acid expression levels of three or more genes selected from the group consisting of DUSP1, NAMPT, PSEN1, MAPK9, NKTR, RYBP, RNF130, IFNGR1, ITGAX and CFLAR;   (b) comparing the previously obtained gene expression result to at least one reference gene expression profile, wherein the reference gene expression profile is selected from: an acute rejection phenotype gene expression profile and a control phenotype gene expression profile;   (c) determining that:
 (i) the transplant recipient has an acute rejection phenotype based on the comparing when the gene expression result is similar to the acute rejection phenotype gene expression profile and/or is dissimilar to the control phenotype gene expression profile; or 
 (ii) the transplant recipient has a non-acute-rejection phenotype based on the comparing when the gene expression result is dissimilar to the acute rejection gene expression profile and/or is similar to the control phenotype gene expression profile; and 
   (d) treating the transplant recipient by increasing immunosuppressive therapy if the transplant recipient is determined to have an acute rejection phenotype and decreasing immunosuppressive therapy if the transplant receipt is determined to have a non-acute-rejection phenotype.   
     
     
         58 . The method according to  claim 57 , wherein the organ transplant is a kidney allograft, a heart allograft, a liver allograft, or a lung allograft.