Protein and gene biomarkers for rejection of organ transplants

Patent metadata

Field	Value
Publication number	US-9535075-B2
Application number	US-201113635667-A
Country	US
Kind code	B2
Filing date	Mar 25, 2011
Priority date	Mar 25, 2010
Publication date	Jan 3, 2017
Grant date	Jan 3, 2017

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.

First claim

What is claimed is:

1. A method of 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 comprise GZMK, NKTR, and SLC25A37, wherein said evaluating comprises:
contacting said sample with a collection of primers or probes for selectively amplifying an expression product of each of said three or more genes, wherein the primers or probes are labelled and the collection comprises primers or probes for selectively amplifying 3 to 100 different genes; and
assessing, using the collection of primers or probes, an amount of each of said expression products in said sample.

2. The method of claim 1 , wherein said organ allograft is a kidney allograft, a heart allograft, a liver allograft, or a lung allograft.

3. The method of claim 1 , wherein said evaluating further comprises evaluating the expression level of one or more genes of ABTB, ANK1, B2M, CFLAR, CHST11, DUSP1, EPOR, GBP2, IFNGR1, ITGAX, LYST, MAP2K3, MAPK9, NAMPT, PCTP, PSEN1, RNF130, RYBP, RARA, RXRA, and TNFRSF1A.

4. The method of claim 1 , wherein said evaluating further comprises evaluating the expression level of one or more genes of ADAMS, ADAM19, ADAMTS3, AIF1, AIM2, ARHGAP4, ARHGDIB, ARPC1B, ATF5, BASP1, BATF, BBC3, BIRC5, BTN3A2, Clorf38, CASP4, CCL13, CD2, CD3D, CD6, CD7, CD8A, CD14, CD44, CD48, CD53, CDC20, CORO1A, CXCL10, CXCL9, DDB2, DDX11, DDX23, F13A1, FCER1G, FOXM1, FZD2, GZMA, HCP5, HLA-A, HLA-DMA, HLA-DQB1, HLA-E, HLA-F, HLA-G, IFITM3, IKBKE, IL2RB, IL10RA, IL15RA, INPP5D, IRF1, IRF3, IRF4, IRF5, ISG20, ITGB2, ITGB7, KRT17, LCK, LEF1, LGALS9, MAN2B1, MAP3K11, MAP4K1, MARCKS, MCM5, MDK, MMP9, NELL2, NKG7, NNMT, NUP210, PLCB2, PLEK, PML, POLR2A, PRKD2, PSMB9, PSME1, PTPRC, PTPRCAP, RAB27A, RGS10, RUNX3, SERPINH1, SH2D2A, STAB1, STAT1, STK10, TAP1, TNF, TNFAIP2, TNFRSF1B, TNFRSF9, TNFRSF14, UCP2, VAMP5, and ZAP70.

5. The method of claim 1 wherein said three or more genes are differentially expressed in monocytes.

6. The method of claim 3 , wherein said evaluating further comprises evaluating the expression level of DUSP1, PSEN1, ITGAX and CFLAR.

7. The method of claim 1 , wherein the expression level of 5 or more genes is measured.

8. The method of claim 1 , wherein the expression level of 10 or more genes is measured.

9. The method of claim 1 , wherein said evaluating further comprises evaluating the expression level of CFLAR, DUSP1, EPOR, PSEN1, RARA, EPOR and RYBP.

10. The method of claim 1 , wherein the expression level of 20 or more genes is measured.

11. The method of claim 1 , wherein the sample is blood.

12. The method according to claim 1 , wherein said assessing is quantitative.

13. A method of determining whether a subject who has received an organ allograft has a graft tolerant or a graft intolerant phenotype comprising:
(a) obtaining a peripheral blood sample comprising a peripheral blood monocyte 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: GZMK, NKTR, and SLC25A37, and wherein said evaluating comprises:
extracting mRNA from said sample; contacting said mRNA with a reagent for assaying said mRNA from said at least one gene;
assessing, using said reagent, the amount of said mRNA from said at least one gene in said sample;

(c) comparing said gene expression result to at least one reference gene expression profile, wherein said 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 said subject is undergoing an AR response based on said comparing when said gene expression result of said three or more genes is similar to said acute rejection phenotype gene expression profile and/or is dissimilar to said control phenotype gene expression profile; or determining that said subject is not undergoing an AR response based on said comparing when said gene expression result is dissimilar to said acute rejection phenotype gene expression profile and/or is similar to said control phenotype gene expression profile.

14. A method of treating a transplant recipient, said method comprising:
(a) evaluating whether said 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 comprising GZMK, NKTR, and SLC25A37;
(b) comparing said previously obtained gene expression result to at least one reference gene expression profile, wherein said reference gene expression profile is selected from: an acute rejection phenotype gene expression profile and a control phenotype gene expression profile;
(c) determining that said transplant recipient has an acute rejection phenotype based on said comparing when said gene expression result is similar to said acute rejection phenotype gene expression profile and/or is dissimilar to said control phenotype gene expression profile; and determining that said transplant recipient has a non-acute-rejection phenotype based on said comparing when said gene expression result is dissimilar to said acute rejection gene expression profile and/or is similar to said control phenotype gene expression profile; and
(d) treating said transplant recipient by increasing immunosuppressive therapy if said transplant recipient is determined to have an acute rejection phenotype and decreasing immunosuppressive therapy if said transplant receipt is determined to have a non-acute-rejection phenotype.

15. The method of claim 13 , wherein the method has a p value that is less than 0.05.

16. The method of claim 13 , wherein the method has a specificity that is higher than 80%.

17. The method of claim 13 , wherein the method has a sensitivity that is higher than 80%.

18. The method of claim 13 , wherein the method has a ROC that is higher than 70%.

19. The method of claim 13 , wherein the method has an AUC that is higher than 70%.

20. The method of claim 13 , wherein the method has a positive predictive value that is higher than 70%.

21. The method of claim 13 , wherein the method has a negative predictive value that is higher than 70%.

22. The method according to claim 13 , wherein said reference gene expression profile is from a subject having a stable graft.

23. The method according to claim 13 , wherein said comparing step comprises at least one of: comparing digital images of the expression profiles and comparing databases of expression data.

Assignees

• Sarwal Minnie M
• Sigdel Tara
• Kaushal Amit
• Li Li
• Xiao Wenzhong
• Butte Atul J
• Khatri Purvesh
• Univ Leland Stanford Junior

Inventors

• Sarwal Minnie M
• Sigdel Tara
• Kaushal Amit
• Li Li
• Xiao Wenzhong
• Butte Atul J
• Khatri Purvesh

Classifications

• C12Q2600/158

  Expression markers · CPC title

• G01N2800/245

  Transplantation related diseases, e.g. graft versus host disease · CPC title

• C12Q1/6809

  Methods for determination or identification of nucleic acids involving differential detection · CPC title

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• G01N33/6893 Primary

  related to diseases not provided for elsewhere · CPC title