Methods for diagnosing risk of renal allograft fibrosis and rejection

Patent metadata

Field	Value
Publication number	US-10787709-B2
Application number	US-201916424014-A
Country	US
Kind code	B2
Filing date	May 28, 2019
Priority date	Jun 26, 2014
Publication date	Sep 29, 2020
Grant date	Sep 29, 2020

Abstract

Disclosed herein is a method for diagnosing a renal allograft recipient's risk for developing fibrosis of the allograft and allograft loss. The method includes determining the expression levels of certain microRNAs, which have been determined to be predictive of an allograft recipient's risk. Also disclosed herein is a method of treating a renal allograft recipient to inhibit fibrosis of the allograft and allograft loss, as well as kits for use in the methods disclosed herein.

First claim

What is claimed is:

1. A method for identifying a renal allograft recipient at risk for developing fibrosis of the allograft the method comprising:
(a) determining the expression levels of four miRNAs in a blood sample from the recipient,
wherein the miRNAs are hsa-mir-128, hsa-mir-29b-3p, hsa-mir-302b-3p, and hsa-mir-192-5p; and
(b) identifying the recipient as being at risk for developing fibrosis of the allograft when the expression levels of said miRNAs hsa-miR-128 and hsa-miR-302b-3p are increased relative to a control level for each miRNA, and the expression levels of hsa-miR-29b-3p and hsa-miR-192-5p miRNAs are decreased relative to the control level for each miRNA.

2. The method of claim 1 , wherein determining the expression levels comprise
synthesizing cDNA from miRNA isolated from said blood sample; and
determining the expression levels of miRNAs hsa-mir-128, hsa-mir-29b-3p, hsa-mir-302b-3p, and hsa-mir-192-5p in said sample.

3. The method of claim 2 , wherein identifying the recipient's risk comprises applying the expression levels determined in the recipient's sample to a penalized logistic regression fitting model.

4. The method of claim 3 , wherein the penalized logistic regression fitting model utilizes the formula:

log
⁢

p
⁡

(
x
)

1
-

p
⁡

(
x
)

=

β

0
+

*

⁢

β
1
*

⁢

g
1

+

β
i
*

⁢

g
i

+
…
+

β
4
*

⁢

g
4

where (p(x) is the probability of developing fibrosis, β* i is penalized coefficiency and g i is the expression value of miRNA i.

5. The method of claim 1 , further comprising administering an anti-rejection drug to the allograft recipient identified as being at high risk for developing fibrosis of the allograft.

6. The method of claim 5 , wherein the anti-rejection drug is cyclosporine.

7. The method of claim 5 , wherein the anti-rejection drug is an immunosuppressive or anti-proliferative agent.

8. The method of claim 7 , wherein the immunosuppressive agent is a member selected from the group consisting of a mycophenolate mofetil (MMF), sirolimus, prednisone, Mycophenolate Sodium and Azathioprine.

9. The method of claim 1 , further comprising administering an anti-fibrosis drug to the allograft recipient identified as being at high risk for developing fibrosis of the allograft.

10. The method of claim 9 , wherein the anti-fibrosis drug is selected from the group consisting of Pirfenidone, relaxin, Bone morphogenetic protein 7 (BMP-7) and Hepatic growth factor (HGF) 6.

11. The method of claim 2 , wherein determining the expression levels of miRNAs hsa-mir-128, hsa-mir-29b-3p, hsa-mir-302b-3p, and hsa-mir-192-5p comprises performing an assay selected from the group consisting of qPCR analysis, microarray, and Nanostring analysis.

12. The method of claim 11 , further comprising modifying the immunosuppression regimen of an allograft recipient identified as being at high risk for fibrosis of the allograft.

13. The method of claim 12 , wherein modifying the immunosuppression regimen comprises administering to the recipient an anti-rejection drug selected from the group consisting of Belatacept, rapamycin and Mycophenolate Mofetil.

14. The method of claim 12 , wherein modifying the immunosuppression regimen comprises administering to the recipient an anti-fibrosis drug selected from the group consisting of Pirfenidone, relaxin, Bone morphogenetic protein 7 (BMP-7) and Hepatic growth factor (HGF) 6.

15. The method of claim 1 further comprising identifying the recipient as being at low risk for developing fibrosis of the allograft when the expression levels of miRNAs hsa-miR-128 and hsa-miR-302b-3p are decreased relative to the control level for each miRNA, and the expression levels of hsa-miR-29b-3p and hsa-miR-192-5p are increased relative to the control level for each miRNA.

16. The method of claim 15 , wherein identifying the recipient comprises calculating the recipient's risk by applying the expression levels determined in the recipient's sample to a penalized logistic regression fitting model.

17. The method of claim 16 , further comprising calculating the probability score of fibrosis risk for said recipient using the equation:
log( p ( x ))/(1− p ( x ))=β*0+β*1 g 1+β* igi+ . . . +β* 4 g 4

where (p(x) is the probability of developing fibrosis, β*i is penalized coefficiency and gi is the expression value of miRNA i.

18. The method of claim 17 wherein determining the expression levels of miRNAs hsa-mir-128, hsa-mir-29b-3p, hsa-mir-302b-3p, and hsa-mir-192-5p comprises performing an assay selected from the group consisting of qPCR analysis, microarray, and Nanostring analysis.

19. The method of claim 18 , further comprising modifying the immunosuppression regimen of the allograft recipient identified as being at low risk for fibrosis of the allograft.

20. The method of claim 19 wherein modifying the immunosuppression regimen comprises administering to the recipient an anti-rejection drug selected from the group consisting of Belatacept, rapamycin and Mycophenolate Mofetil.

21. The method of claim 20 , wherein modifying the immunosuppression regimen comprises administering to the recipient an anti-fibrosis drug selected from the group consisting of Pirfenidone, relaxin, Bone morphogenetic protein 7 (BMP-7) and Hepatic growth factor (HGF) 6.

22. A method for identifying a renal allograft recipient at risk for allograft loss comprising the steps of
determining the expression levels of miRNAs hsa-mir-128, hsa-mir-29b-3p, hsa-mir-302b-3p, and hsa-mir-192-5p in a blood sample obtained from said recipient, and
identifying the recipient as being at risk for allograft loss when the expression levels of said miRNAs are altered relative to a control level for each-miRNA.

23. The method of claim 22 further comprising identifying

Assignees

• Icahn School Med Mount Sinai

Inventors

• Murphy Barbara
• Zhang Weijia

Classifications

• G01N2800/245

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

• A61K38/13

  Cyclosporins · CPC title

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• A61K31/4412

  having oxo groups directly attached to the heterocyclic ring · CPC title

• A61K38/2221

  Relaxins · CPC title