Assay for pre-operative prediction of organ function recovery

Patent metadata

Field	Value
Publication number	US-10704093-B2
Application number	US-201816028369-A
Country	US
Kind code	B2
Filing date	Jul 5, 2018
Priority date	Jul 5, 2017
Publication date	Jul 7, 2020
Grant date	Jul 7, 2020

Abstract

Gene expression is measured in a sample of peripheral blood mononuclear cells (PBMCs) obtained from a subject and used to predict organ function recovery. A Function Recovery Potential (FRP) score is assigned to a sample that reflects the measured expression level of the genes identified herein in a direction associated with recovery from organ failure. Treatment of the subject with optimal medical management (OMM) and/or palliative care (PC) is advised when the FRP score is lower than the reference value, and referring the subject for treatment with therapies including—but not limited to—mechanical circulatory support (MCS) surgery, heart transplant (HTx) surgery, or other intervention for advanced heart failure is advised when the FRP score is greater than the reference value. A method for developing an FRP scoring algorithm that predicts a subject's ability to recover from medical intervention for organ failure is also described.

First claim

What is claimed is:

1. A method for treating an individual suffering from heart failure, comprising:
(i) receiving a sample from the individual;
(ii) determining gene expression levels in the sample for DNM1P46 and at least one additional gene comprising RSG1, TPRA1, SAP25, MFSD3, SPTBN5, CEMP1, ASPSCR1, NAPSB, NAPSA, NLRP2, RHBDD3, FRMD6, TIMP3, ACVR1C, KIR2DL4, USP9Y, ANKRD22, BCORP1, HMCN1, GPR63, BATF2, SLC22A1, AGRN, CKAP2L, IGSF10, HEXA-AS1, LOC728431, PDZK1IP1, NEGRI, KCNH8, CCR8, MME, ETV5, CXCL9, HBEGF, RANBP17, DDX43, C6orf164, C7orf50, NEFL, CDCA2, ALDH1A1, OLFM1, FADS3, SAC3D1, FZD4, RBPMS2, C15orf38, ST6GALNAC1, CHMP6, SKA1, CD209, SNAPC2, AXL, KIR2DL1, NTSR1, SEPT5, KALI, PRRG1, XIST, RPS4Y1, ZFY, PRKY, TTTY15, DDX3Y, UTY, TXLNG2P, KDM5D, EIFIAY, or FITM1; and
(iii) providing a treatment to the individual based on the gene expression levels relative to reference values; wherein the treatment is one of the following:
(a) optimal medical management (OMM), palliative care (PC), or a combination thereof when the gene expression level of DNM1P46 is upregulated relative to a first reference value, or
(b) a surgical therapy, an interventional therapy, or a combination thereof when a gene expression level of DNM1P46 is equal or downregulated relative to the first reference value and
(1) a gene expression level of at least one of RSG1, TPRA1, SAP25, MFSD3, SPTBN5, CEMP1, ASPSCR1, NAPSB, NAPSA, NLRP2, RHBDD3, TIMP3, SLC22A1, HEXA-AS1, LOC728431, PDZK1 IP1, ETV5, RANBP17, C6orf164, C7orf50, FADS3, SAC3D1, RBPMS2, CHMP6, SNAPC2, NTSR1, SEPT5, XIST, or FITM1 is upregulated relative to a second reference value, or
(2) a gene expression level of at least one of FRMD6, ACVR1C, KIR2DL4, USP9Y, ANKRD22, BCORP1, HMCN1, GPR63, BATF2, AGRN, CKAP2L, IGSF10, NEGRI, KCNH8, CCR8, MME, CXCL9, HBEGF, DDX43, NEFL, CDCA2, ALDH1A1, OLFM1, FZD4, C15orf38, ST6GALNAC1, SKA1, CD209, AXL, KIR2DL1, KALI, PRRG1, RPS4Y1, ZFY, PRKY, TTTY15, DDX3Y, UTY, TXLNG2P, KDM5D, or EIFIAY is downregulated relative to a third reference value.

2. The method of claim 1 , wherein the sample comprises blood, urine, sputum, hair, or skin.

3. The method of claim 1 , wherein each reference value is an expected expression level value.

4. The method of claim 1 , wherein gene expression levels in the sample are determined for at least 8 genes selected from the group consisting of RSG1, TPRA1, SAP25, MFSD3, SPTBN5, CEMP1, ASPSCR1, NAPSB, NAPSA, NLRP2, RHBDD3, FRMD6, TIMP3, ACVR1C, DNM1P46, KIR2DL4, USP9Y, ANKRD22, BCORP1, HMCN1, GPR63, BATF2, SLC22A1, AGRN, CKAP2L, IGSF10, HEXA-AS1, LOC728431, PDZK1IP1, NEGRI, KCNH8, CCR8, ME, ETV5, CXCL9, HBEGF, RANBP17, DDX43, C6orf164, C7orf50, NEFL, CDCA2, ALDH1A1, OLFM1, FADS3, SAC3D1, FZD4, RBPMS2, C15orf38, ST6GALNAC1, CHMP6, SKA1, CD209, SNAPC2, AXL, KIR2DL1, NTSR1, SEPT5, KALI, PRRG1, XIST, RPS4Y1, ZFY, PRKY, TTTY15, DDX3Y, UTY, TXLNG2P, KDM5D, EIFIAY, and FITM1, wherein the at least 8 genes includes DNM1P46.

5. The method of claim 4 , wherein the gene expression levels are assigned a score that corresponds to the determined expression level of each of the at least 8 genes, and wherein the treatment is determined based on the score.

6. The method of claim 5 , wherein the score comprises a Function Recovery Potential (FRP) score.

7. The method of claim 6 , wherein the score is determined based on a linear discriminant analysis of data comprising known gene expression levels and known FRP scores of a plurality of individuals.

8. The method of claim 1 , wherein the treatment is a surgical and/or interventional therapy selected from mechanical circulatory support (MCS) surgery, heart transplant (HTx) surgery, coronary artery bypass graft (CABG) surgery, percutaneous coronary interventions (PCI), aortic valve replacement (AVR) surgery, mitral valve replacement (MVR) surgery, trans-catheter aortic valve replacement (TAVR), transcatheter mitral clip, ventricular tachycardia ablation, or stellate gangliectomy.

9. The method of claim 1 , wherein the gene expression levels are levels determined by polymerase chain reaction (PCR), next generation sequencing (NGS), or other gene expression assay platform.

10. The method of claim 1 , wherein gene expression levels in the sample are determined for DNM1P46, BCORP1, HEXA-AS1, BATF2, AGRN, ANKRD22, FRMD6, KIR2DL4, SAP25, NAPSA, TIMP3, and RHBDD3.

11. The method of claim 1 , wherein the reference values are expression levels of normalization genes or expression levels known to be representative of healthy individuals and/or individuals known to recover from heart failure.

Assignees

• Univ California
• The Regents Of The Universtiy Of California

Inventors

• Deng Mario
• Bondar Galyna

Classifications

• C12Q2600/158

  Expression markers · CPC title

• C12Q2600/106

  Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism · CPC title

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• C12Q1/6876 Primary

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title