Methods for identifying and using organ-specific proteins in blood

• US 9,002,652 B1
• Filed: 01/27/2006
• Issued: 04/07/2015
• Est. Priority Date: 01/27/2005
• Status: Active Grant

• Current Assignee: Institute for System Biology
• Original Assignee: Institute for System Biology
• Inventors: Hood, Leroy, Lin, Biaoyang
• Primary Examiner(s): Skibinsky, Anna
• Application Number:
  US11/342,366
• Time in Patent Office: 3,357 Days
• US Class Current: 702/19
• CPC Class Codes: G01N 33/68 involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: G01N 33/6893 related to diseases not provided for elsewhere
• CPC Class Codes: G06V 20/69 Microscopic objects, e.g. biological cells or cellular parts
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The present invention relates generally to methods for identifying organ-specific secreted proteins and for identifying organ-specific molecular blood fingerprints therefrom. As such, the present invention provides compositions comprising such proteins, detection reagents for detecting such proteins, and panels, and arrays for determining organ-specific molecular blood fingerprints.

Claims

1. A method for identifying a set of at least 5 organ-specific proteins that are specifically produced in a preselected organ and are shed into the blood comprising,

(a) determining, using mRNA transcripts, the sequences of sequences 17-20 nucleotides long that have been identified as signature sequences characteristic of mRNA transcripts that encode proteins from substantially all mRNA transcripts isolated from a sample of said preselected organ;

(b) comparing, using a computer, the signature sequences to a database of known RNA transcripts to identify the mRNA transcripts that encode proteins to obtain a preliminary set of mRNA transcripts;

(c) comparing, using a computer, the identified mRNA transcripts to mRNA transcripts known to be expressed in other organs;

(d) removing, using a computer, from said preliminary set any mRNA transcripts that are known to be substantially expressed in other organs thus obtaining an intermediate set of mRNA transcripts;

(e) identifying, using a computer, from the remaining mRNA transcripts in the intermediate set those mRNA transcripts that include a sequence encoding a signal peptide, thereby identifying transcripts that encode organ-specific secreted proteins from said preselected organ; and

(f) confirming, using a blood sample, the presence of the organ-specific secreted proteins by assessing the blood sample, thereby identifying a set of at least 5 organ-specific proteins from said preselected organ that are shed into blood.

2. The method of claim 1 wherein one of said at least 5 organ-specific proteins identified is carboxypeptidase E precursor (CPE) having SEQ ID NO:

1520 or olfactory receptor, family 51, subfamily E, member 2 (OR51e2) having SEQ ID NO;

1740.

3. A method for identifying a set of at least 5 organ-specific proteins that are specifically produced in a preselected organ and are shed into the blood comprising,

(a) determining, using mRNA transcripts, the sequences of sequences 17-20 nucleotides long that have been identified as signature sequences characteristic of mRNA transcripts that encode proteins from substantially all mRNA transcripts isolated from a sample of said preselected organ;

(b) comparing, using a computer, the signature sequences to a database of known RNA transcripts to identify the mRNA transcripts that encode proteins to obtain a preliminary set of mRNA transcripts;

(c) identifying, using a computer, from among the mRNA transcripts identified in (b) as encoding proteins, those mRNA transcripts that are expressed in the preselected organ at a level at least 2.5 times the level of expression of the same mRNA transcripts observed in other organs;

(d) identifying, using a computer, from the transcripts in (c) those transcripts that include a sequence encoding a signal peptide, thereby identifying transcripts that encode organ-specific proteins secreted or shed into the blood; and

(e) confirming, using a blood sample, the presence of the organ-specific secreted proteins by assessing the blood sample thereby identifying a set of at least 5 organ-specific proteins shed into blood.

4. The method of claim 3 wherein an identified organ-specific protein is carboxypeptidase E precursor (CPE) having SEQ ID NO:

1520 or olfactory receptor, family 51, subfamily E, member 2 (OR51e2) having SEQ ID NO;

1740.