# US 9,752,191 B2 · Gene expression profiles associated with chronic allograft nephropathy

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- Number: US 9,752,191 B2
- Document ID: US9752191B2
- Status: Granted
- Kind: B2
- Application number: 13/261,130
- Filed: 2010-07-09
- Published: 2012-07-12
- Granted: 2017-09-05
- Earliest claimed: 2009-07-09
- Assignees: The Scripps Research Institute
- Applicants: Daniel Salomon; Sunil M. Kurian; Steven R. Head
- Inventors: Daniel Salomon; Sunil M. Kurian; Steven R. Head
- Web page: https://patentgrep.com/patent/US9752191B2

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/112: Disease subtyping, staging or classification
- C12Q 2600/136: Screening for pharmacological compounds
- C12Q 2600/158: Expression markers
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

By a genome-wide gene analysis of expression profiles of over 50,000 known or putative gene sequences in peripheral blood, the present inventors have identified a consensus set of gene expression-based molecular biomarkers associated with chronic allograft nephropathy and/or interstitial fibrosis and tubular atrophy CAN/IFTA and subtypes thereof. These genes sets are useful for diagnosis, prognosis, monitoring and/or subtyping of CAN/IFTA.

## Claims

### Claim 1

A method of prognosing, diagnosing or monitoring CAN/IFTA (chronic allograft nephropathy, interstitial fibrosis and tubular atrophy, or chronic allograft nephropathy and interstitial fibrosis and tubular atrophy), comprising
(a) obtaining target nucleic acids, wherein the target nucleic acids comprise mRNA from a blood sample from a human subject or nucleic acids derived from the mRNA from the blood sample from the human subject, wherein the human subject is a recipient of a transplanted kidney and has received an immunosuppressant drug;
(b) contacting the target nucleic acids with at least ten probes, wherein the at least ten probes are specific for genes associated with the presence or absence of CAN/IFTA and are specific for at least genes ANTXR2, SYNPO, VSIG4, GFI1B, SPTLC2, RNF175, and EST56;
(c) detecting expression levels in the human subject of the at least genes ANTXR2, SYNPO, VSIG4, GFI1B, SPTLC2, RNF175, and EST56;
(d) prognosing, diagnosing or monitoring CAN/IFTA in the transplanted kidney of the human subject when the expression levels of SYNPO and GFI1B detected in step (c) have a statistically significant negative-fold change relative to a kidney transplant patient without CAN/IFTA and the expression levels of ANXR2, VSIG4, SPTLC2, RNF17S, and EST56 detected in step (c) have a statistically significant positive-fold change relative to a kidney transplant patient without CAN/IFTA; and
(e) administering an increased dose of the immunosuppressant drug to the human subject in order to treat or prevent the CAN/IFTA prognosed, diagnosed or monitored in the transplanted kidney of the human subject in step (d) or administering a new immunosuppressant drug to the human subject in order to treat or prevent the CAN/IFTA prognosed, diagnosed or monitored in the transplanted kidney of the human subject in step (d).

### Claim 2 (depends on 1)

The method of claim 1, wherein step (c) further comprises for each of the at least genes ANTXR2, SYNPO, VSIG4, GFI1B, SPTLC2, RNF175, and EST56 assigning the expression level of the gene in the human subject a value or other designation providing an indication whether the human subject has or is at risk of CAN/IFTA.

### Claim 3 (depends on 2)

The method of claim 2, wherein the expression level of each of the at least genes ANTXR2, SYNPO, VSIG4, GFI1B, SPTLC2, RNF175, and EST56 is assigned a value on a normalized scale of values associated with a range of expression levels in kidney transplant patients with and without CAN/IFTA.

### Claim 4 (depends on 2)

The method of claim 2, wherein the expression level of each of the at least genes ANTXR2, SYNPO, VSIG4, GFI1B, SPTLC2, RNF175, and BST56 is assigned a value or other designation providing an indication that the human subject has or is at risk of CAN/IFTA, lacks and is not at risk of CAN/IFTA, or that the expression level is uninformative.

### Claim 5 (depends on 2)

The method of claim 2, wherein (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 human subject has or is at risk of CAN/IFTA.

### Claim 6 (depends on 5)

The method of claim 5, wherein the method is repeated at different times on the human subject.

### Claim 7 (depends on 5)

The method of claim 5, wherein a change in the combined value or designation over time provides an indication of the effectiveness of the immunosuppressant drug received by the human subject.

### Claim 8 (depends on 1)

The method of claim 1, wherein the human subject has undergone a kidney transplant within 1-10 years of performing step (a).

### Claim 9 (depends on 1)

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

### Claim 10 (depends on 9)

The method of claim 9, wherein the peripheral blood sample is a peripheral blood lymphocyte sample.

### Claim 11 (depends on 1)

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

### Claim 12 (depends on 1)

The method of claim 1, wherein the target nucleic acids are mRNA extracted from the blood sample from the human subject.

### Claim 13 (depends on 12)

The method of claim 12, wherein the target nucleic acids are nucleic acids derived from the mRNA extracted from the blood sample from the human subject.

### Claim 14 (depends on 13)

The method of claim 13, wherein the target nucleic acids are DNA derived from the mRNA extracted from the blood sample from the human subject.

### Claim 15 (depends on 13)

The method of claim 13, wherein the detecting the expression levels in the human subject comprises one or more of the following: (a) hybridizing the mRNA to an array; (b) nucleic acid amplification; (c) monitoring the formation of an amplification product; or (d) synthesizing a nucleic acid using the mRNA as a template.

### Claim 16 (depends on 1)

The method of claim 1, wherein the prognosing, diagnosing or monitoring CAN/IFTA in the transplanted kidney of the human subject in step (d) further comprises performing an additional procedure to detect CAN/IFTA or risk thereof if the detecting expression levels provides an indication the subject has or is at risk of CAN/IFTA.

### Claim 17 (depends on 16)

The method of claim 16, wherein the additional procedure is a kidney biopsy.

### Claim 18 (depends on 1)

The method of claim 1, further comprising determining baseline values of expression levels in the human subject before a kidney transplant.

### Claim 19 (depends on 18)

The method of claim 18, wherein prognosing, diagnosing or monitoring CAN/IFTA in the human subject comprises comparing the baseline values of expression levels in the human subject before the kidney transplant with the expression levels in the human subject after the kidney transplant.

### Claim 20 (depends on 16)

The method of claim 16, wherein the additional procedure is a creatinine or glomerular filtration rate analysis.

### Claim 21 (depends on 12)

The method of claim 12, wherein the detecting the expression levels in the human subject comprises hybridizing the mRNA to an array.

### Claim 22 (depends on 14)

The method of claim 14, wherein the detecting the expression levels in the human subject comprises hybridizing the DNA to an array.

### Claim 23 (depends on 1)

The method of claim 1, wherein the method comprises diagnosing CAN/IFTA in the human subject from the expression levels detected in step (c).

### Claim 24 (depends on 1)

The method of claim 1, wherein the method comprises prognosing, diagnosing or monitoring CAN/IFTA in the transplanted kidney of the human subject when the expression levels of at least 50 genes exhibit a statistically significant fold change.

### Claim 25 (depends on 1)

The method of claim 1, wherein the method comprises prognosing, diagnosing or monitoring CAN/IFTA in the transplanted kidney of the human subject when the expression levels of at least 100 genes exhibit a statistically significant fold change.

### Claim 26 (depends on 1)

The method of claim 1, wherein the transplanted kidney is a transplanted kidney organ.

### Claim 27 (depends on 1)

The method of claim 1, wherein the transplanted kidney is transplanted kidney tissues or cells.

### Claim 28 (depends on 1)

The method of claim 1, wherein the method comprises administering an increased dose of the immunosuppressant drug to the human subject in order to treat or prevent the CAN/IFTA prognosed, diagnosed or monitored in the transplanted kidney of the human subject in step (d).

### Claim 29 (depends on 1)

The method of claim 1, wherein the method comprises administering a new immunosuppressant drug to the human subject in order to treat or prevent the CAN/IFTA prognosed, diagnosed or monitored in the transplanted kidney of the human subject in step (d).

### Claim 30 (depends on 1)

The method of claim 1, wherein the immunosuppressant drug or the new immunosuppressant drug is a calcineurin inhibitor.

### Claim 31 (depends on 30)

The method of claim 30, wherein the calcineurin inhibitor is cyclosporin or tacrolimus.

### Claim 32 (depends on 1)

The method of claim 1, wherein the immunosuppressant drug or the new immunosuppressant drug is an mTOR inhibitor.

### Claim 33 (depends on 32)

The method of claim 32, wherein the mTOR inhibitor is sirolimus or everolimus.

### Claim 34 (depends on 1)

The method of claim 1, wherein the immunosuppressant drug or new immunosuppressant drug is selected from the group consisting of: azathioprine, mycophenolic acid, prednisolone, hydrocortisone, basiliximab, daclizumab, orthoclone, anti-thymocyte globulin, anti-lymphocyte globulin, an anti-proliferative drug, and an anti-T cell antibody.

### Claim 35 (depends on 1)

The method of claim 1, wherein the method comprises prognosing, diagnosing or monitoring CAN/IFTA in the transplanted kidney of the human subject when the expression levels of at least 20 genes from Table A, B, C, D, E, F, G, H, I and/or J and less than 1000 total genes exhibit a statistically significant fold change.

### Claim 36 (depends on 1)

The method of claim 1, wherein the method comprises prognosing, diagnosing or monitoring CAN/IFTA in the transplanted kidney of the human subject when the expression levels of at least 40 and up to 500 genes exhibit a statistically significant fold change.

### Claim 37 (depends on 1)

The method of claim 1, wherein step (d) of the method comprises diagnosing CAN/IFTA in the transplanted kidney of the human subject.

### Claim 38 (depends on 36)

The method of claim 36, wherein step (e) comprises administering the increased dose of the immunosuppressant drug to the human subject in order to treat the CAN/IFTA diagnosed in the transplanted kidney of the human subject in step (d).

### Claim 39 (depends on 36)

The method of claim 36, wherein step (e) comprises administering the new immunosuppressant drug to the human subject in order to treat the CAN/IFTA diagnosed in the transplanted kidney of the human subject in step (d).