Tissue molecular signatures of kidney transplant rejection

Abstract

By a genome-wide gene analysis of expression profiles of known or putative gene sequences in kidney biopsy samples, the present inventors have identified a consensus set of gene expression-based molecular biomarkers for distinguishing kidney transplantation patients who have Acute Rejection (AR), Acute Dysfunction No Rejection (ADNR), Chronic Allograft Nephropathy(CAN), or Transplant Excellent/Normal (TX). These molecular biomarkers are useful for diagnosis, prognosis and monitoring of transplantation patients.

We claim: 
     
         1 . A method of prognosing, detecting, diagnosing or monitoring a kidney transplant rejection or injury, or lack thereof in a subject, comprising:
 (a) obtaining nucleic acids of interest, wherein the nucleic acids of interest comprise mRNA extracted from a sample from a subject or nucleic acids derived from the mRNA extracted from the sample from the subject;   (b) detecting expression levels in the subject of the at least five genes selected from the at least one of Tables 7, 8, 9, 10, and 11, using the nucleic acids of interest obtained in step (a); and   (c) prognosing, detecting, diagnosing or monitoring the kidney transplant rejection or injury, or lack thereof in the subject from the expression levels detected in step (c).   
     
     
         2 . The method of  claim 1 , further comprising contacting the nucleic acids of interest with probes, wherein the probes are specific for the at least five genes selected in step (b). 
     
     
         3 . The method of  claim 1 , wherein the sample from the subject is a biopsy sample. 
     
     
         4 . The method of  claim 1 , wherein the subject has acute rejection (AR), acute dysfunction no rejection (ADNR), chronic allograft nephropathy (CAN), or well-functioning normal transplant (TX). 
     
     
         5 . The method of  claim 1 , wherein for each of the at least five genes, step (c) comprises comparing the expression level of the gene in the subject to one or more reference expression levels of the gene associated with AR, ADNR, CAN, or TX. 
     
     
         6 . The method of  claim 5 , wherein step (c) further comprises for each of the at least five genes assigning the expression level of the gene in the subject a value or other designation providing an indication whether the subject has AR, ADNR, CAN, or TX. 
     
     
         7 . The method of  claim 6 , wherein the expression level of each of the at least five genes is assigned a value on a normalized scale of values associated with a range of expression levels in kidney transplant patients with AR, ADNR, CAN, or TX. 
     
     
         8 . The method of  claim 7 , wherein the expression level of each of the at least five genes is assigned a value or other designation providing an indication that the subject has or is at risk of AR, ADNR, CAN, has well-functioning normal transplant, or that the expression level is uninformative. 
     
     
         9 . The method of  claim 6 , wherein step (c) further comprises combining the values or designations for each of the genes to provide a combined value or designation providing an indication whether the subject has or is at risk of AR, ADNR, CAN, or has TX. 
     
     
         10 . The method of  claim 9 , wherein the method is repeated at different times on the subject. 
     
     
         11 . The method of  claim 9 , wherein the subject is receiving a drug, and a change in the combined value or designation over time provides an indication of the effectiveness of the drug. 
     
     
         12 . The method of  claim 1 , wherein the subject has undergone a kidney transplant within 1 month, 3 months, 1 year, 2 years, 3 years or 5 years of performing step (a). 
     
     
         13 . The method of  claim 1 , wherein step (b) is performed on at least 10, 20, 40, or 100 genes. 
     
     
         14 . The method of  claim 1 , further comprising changing the treatment regime of the subject responsive to the prognosing, detecting, diagnosing or monitoring step. 
     
     
         15 . The method of  claim 14 , wherein the subject has received a drug before performing the methods, and the changing the treatment regime comprises administering an additional drug, administering a higher dose of the same drug, administering a lower dose of the same drug or stopping administering the same drug. 
     
     
         16 . The method of  claim 1 , wherein the subject is prognosed or diagnosed to have AR, have ADNR, have CAN, or have TX, and wherein the at least five genes are selected from the at least one of Tables 7, 8, 9, 10, and 11. 
     
     
         17 . The method of  claim 1 , wherein expression levels are determined at the mRNA level or at the protein level. 
     
     
         18 . The method of  claim 1 , wherein step (c) is performed by a computer. 
     
     
         19 . An array, comprising a support or supports bearing a plurality of nucleic acid probes complementary to a plurality of mRNAs fewer than 5000 in number, wherein the plurality of mRNAs includes mRNAs expressed by at least five genes selected from the at least one of Tables 7, 8, 9, 10 and 11. 
     
     
         20 . The array of  claim 19 , wherein the plurality of mRNAs are fewer than 1000 or fewer than 100 in number. 
     
     
         21 . The array of  claim 19 , wherein the plurality of nucleic acid probes are attached to a planar support or to beads. 
     
     
         22 . An array, comprising a support or supports bearing a plurality of ligands that specifically bind to a plurality of proteins fewer than 5000 in number, wherein the plurality of proteins includes at least five proteins encoded by genes selected from the at least one of Tables 7, 8, 9, 10, and 11. 
     
     
         23 . The array of  claim 22 , wherein the plurality of proteins are fewer than 1000 or fewer than 100 in number. 
     
     
         24 . The array of  claim 22 , wherein the plurality of ligands are attached to a planar support or to beads. 
     
     
         25 . The array of  claim 22 , wherein the ligands are different antibodies, wherein the different antibodies bind to different proteins of the plurality of proteins. 
     
     
         26 . A method of expression analysis, comprising determining expression levels of up to 5000 genes in a sample from a subject having a kidney transplant, wherein the genes include at least five genes selected from the at least one of Tables 7, 8, 9, 10, and 11. 
     
     
         27 . The method of  claim 26 , wherein the expression levels of up to 100 or 1000 genes are determined. 
     
     
         28 . The method of  claim 26 , wherein the expression levels are determined at the mRNA level or at the protein level. 
     
     
         29 . The method of  claim 26 , wherein the expression levels are determined by quantitative PCR, hybridization to an array or RNA sequencing. 
     
     
         30 . A method of screening a compound for activity in inhibiting or treating a kidney transplant rejection or injury, comprising:
 (a) administering the compound to a subject having or at risk of developing a kidney transplant rejection;   (b) determining expression levels of at least five genes in the subject selected from the at least one of Tables 7, 8, 9, 10, and 11, and species variants thereof before and after administering the compound to the subject; and   (c) determining whether the compound has activity in inhibiting or treating the kidney transplant rejection from a change in expression levels of the genes after administering the compound.   
     
     
         31 . The method of  claim 30 , wherein the kidney transplant rejection or injury is AR, ADNR, or CAN. 
     
     
         32 . The method of  claim 30 , wherein step (c) comprising for each of the at least five changes assigning a value or designation depending on whether the change in the expression level of the gene relative to one or more reference levels indicating presence or absence of the kidney transplant rejection. 
     
     
         33 . The method of  claim 30 , further comprising determining a combined value or designation for the at least five genes from the values or designations determined for each gene. 
     
     
         34 . The method of  claim 30 , wherein the subject is human or a nonhuman animal model of the kidney transplant rejection.