Compositions and methods relating to the peroxisomal proliferator activated receptor-alpha mediated pathway

Abstract

The present invention describes polynucleotides and polypeptides associated with PPARα-mediated pathways that are useful as therapeutic compositions in method for the treatment of peroxisomal disorders. These polynucleotides and polypeptides were identified through the use of differential gene expression analysis. In particular, the present invention discloses eleven novel gene fragments, and numerous single nucleotide polymorphisms, located in previously disclosed genes, all of which have been discovered to be associated with PPARα-mediated pathways.

What is claimed is:  
     
         1 . A method of identifying a candidate therapeutic agent for a pathophysiology associated with a PPARα-mediated pathway, the method comprising: 
 (a) providing a cell comprising one or more genes encoding a polypeptide selected from the group consisting of Carnitine/acyl carnitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; delta-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit;  
 (b) contacting the cell with a test agent; and  
 (c) measuring expression of one or more of the genes expressing said polypeptides in said cell,  
 wherein an alteration in expression of said one or more of the genes in the presence of said test agent compared to expression of said genes in a control cell not exposed to said test agent indicates the test agent is a candidate therapeutic agent for a pathophysiology associated with a PPARα-mediated pathway.  
 
     
     
         2 . The method of  claim 1 , wherein said method comprises measuring expression of two or more of said genes.  
     
     
         3 . The method of  claim 1 , wherein said method comprises measuring expression of five or more of said genes.  
     
     
         4 . The method of  claim 1 , wherein said method comprises measuring expression of 10 or more of said genes.  
     
     
         5 . The method of  claim 1 , wherein said method comprises measuring expression of 15 or more of said genes.  
     
     
         6 . The method of  claim 1 , wherein the expression of said gene is increased in the presence of the test agent compared to the absence of the test agent.  
     
     
         7 . The method of  claim 6 , wherein said gene is selected from the group consisting of SEQ ID NOS: 1-11; Camitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; and Heat shock protein 60.  
     
     
         8 . The method of  claim 1 , wherein the expression of said gene is decreased in the presence of the test agent compared to the absence of the test agent.  
     
     
         9 . The method of  claim 8 , wherein said gene is selected from the group consisting of Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit.  
     
     
         10 . The method of  claim 1 , further comprising measuring expression of one or more genes encoding a polypeptide selected from the group consisting of: phenobarbital inducible Cytochrome P450; long chain acyl CoA synthase; fatty acid transport protein; medium chain acyl-CoA dehydrogenase; HMG-CoA synthase; acyl-CoA oxidase; peroxisomal enoyl-CoA hydratase/3-hydroxyacyl CoA dehydrogenase; peroxisomal 3-ketoacyl-CoA thiolase; acyl-CoA hydrolase; acyl-CoA thioesterase; cytochrome p450 4A1; cytochrome p450 4A2; cytochrome p450 4A3; cytochrome p450 4A6; delta-3-delta-2 enoyl-CoA isomerase; acetyl CoA carboxylase; ATP citrate lyase; fatty acid synthase; glucose 6-phosphate dehydrogenase; glycerophosphate acyltransferase; malic enzyme; stearyl-CoA desaturase; hydroxysteroid dehydrogenase IV/bifunctional enzyme II; steroid 3a dehydrogenase; liver fatty acid binding protein; lipoprotein lipase; apolipoprotein A1; apolipoprotein A2; apolipoprotein C3; 1-acylglycerophosphocholine acyltransferase; carnitine palmitoyl transferase-1; and heat shock protein GRP78,  
       wherein an alteration in expression of said genes in the presence of said test agent indicates said test agent is a candidate therapeutic agent for a pathophysiology associated with a PPARα-mediated pathway.  
     
     
         11 . The method of  claim 1 , wherein said cell is provided in vitro.  
     
     
         12 . The method of  claim 1 , wherein said cell is provided ex vivo from a mammalian subject.  
     
     
         13 . The method of  claim 12 , wherein said subject is a human or rodent subject.  
     
     
         14 . The method of  claim 1 , wherein said cell is provided in vivo in a mammalian subject.  
     
     
         15 . The method of  claim 14 , wherein said subject is a human or rodent subject.  
     
     
         16 . The method of  claim 1 , wherein said cell is a liver cell.  
     
     
         17 . The method of  claim 1 , wherein said cell is a human cell.  
     
     
         18 . A method of identifying a ligand for a PPARα-mediated pathway, said method comprising: 
 (a) providing a cell comprising one or more genes encoding a polypeptide selected from the group consisting of Camitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Camitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit;  
 (b) contacting said cell with a test agent; and  
 (c) measuring expression of one or more genes expressing said polypeptide in said cell,  
 wherein an alteration in expression of said polypeptide in the presence of said test agent compared to expression of said genes in a control cell not exposed to said test agent indicates said test agent is a ligand for PPARα.  
 
     
     
         19 . A method of identifying a candidate therapeutic agent for a pathophysiology associated with a PPARα-mediated pathway, the method comprising: 
 (a) contacting a test agent with polypeptide selected from the group consisting of: Camitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase;  
 Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit; and  
 (b) determining whether said test agent binds to said polypeptide,  
 wherein binding of said test agent to said polypeptide indicates that said test agent is a candidate therapeutic agent for a pathophysiology associated with a PPARα-mediated pathway.  
 
     
     
         20 . A method of identifying a candidate therapeutic agent for a pathophysiology associated with a PPARα-mediated pathway, the method comprising: 
 (a) administering the agent to a first mammal;  
 (b) obtaining a first cell sample from said first mammal and a second cell sample from a second mammal, wherein said second mammal has not been administered to said agent; and  
 (c) assessing differential gene expression in said first and second cell samples of one or more genes encoding a polypeptide selected from the group consisting of: Camitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Camitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit,  
 wherein determining that one or more said genes is differentially expressed indicates said agent is a candidate therapeutic agent for a pathophysiology associated with a PPARα-mediated pathway.  
 
     
     
         21 . The method of  claim 20 , further comprising administering a control composition to said second mammal.  
     
     
         22 . The method of  claim 20 , wherein said first and second mammals are rodents.  
     
     
         23 . The method of  claim 20 , wherein said first and second cell samples are liver cell samples.  
     
     
         24 . A method of determining whether a candidate therapeutic agent has PPARα-specific ligand binding activity, the method comprising: 
 (a) administering the agent to a first mammal;  
 (b) obtaining a first cell sample from said first mammal and a second cell sample from a second mammal, wherein said agent has not been administered to said second mammal; and  
 (c) assessing expression in said first and second cell samples of one or more genes encoding a polypeptide selected from the group consisting of: Carnitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Camitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit,  
 wherein determining that one or more of said genes is differentially expressed in said first and second samples indicates said agent has PPARα-specific ligand binding activity.  
 
     
     
         25 . A method of screening a candidate pharmaceutical agent for effector activity for a PPARα-associated gene product, the method comprising: 
 (a) administering the agent to a first mammal;  
 (b) obtaining a cell sample from the first mammal after administering the agent, and a second cell sample from a second mammal; and  
 (c) assessing differential expression of a PPARα-associated gene in said first and second cell samples, wherein said gene is selected from the group consisting of Carnitine/acyl carnitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit,  
 wherein a difference in expression of said PPARα gene in said first and second samples indicates that the agent has an effector activity for said PPARα-associated gene product.  
 
     
     
         26 . The method of  claim 25 , wherein the differential expression pattern of said agent is the same as the differential expression elicited in said cell by the compound GW9578.  
     
     
         27 . A method of screening a candidate pharmaceutical agent as a potential ligand for a PPARα-associated gene product, the method comprising: 
 (a) administering the agent to a first mammal;  
 (b) obtaining a cell sample from the first mammal after administering the agent, and a second cell sample from a second mammal;  
 (c) measuring expression of one or more PPARα-associated genes in said first and second cell samples, wherein said gene is selected from the group consisting of Carnitine/acyl carnitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit; and  
 (d) comparing the expression of said PPARα-associated genes in said first and second samples,  
 wherein a difference in expression in said first and second samples indicates that the agent is a potential ligand for a PPARα-associated gene product.  
 
     
     
         28 . A method of determining whether a candidate pharmaceutical agent has PPARα-specific ligand activity, the method comprising: 
 (a) generating a profile of differential gene expression, wherein the difference is induced by administration of said agent to a mammal, wherein said profile is of a gene selected from the group consisting of Carnitine/acyl carnitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit; and  
 (b) comparing said profile to a differential gene expression profile of a plurality of genes known to be differentially expressed when a PPARα-specific ligand is administered to the same species of mammal;  
 wherein a similarity in the expression profile indicates that the agent has PPARα-specific ligand binding activity.  
 
     
     
         29 . A method of determining the efficacy of an agent as a therapeutic agent in a pathology related to the expression of a PPARα-associated gene product, the method comprising: 
 (a) administering an agent modulating the expression of one or more PPARα-associated gene products to a subject suffering from, or suspected of being prone to develop, a pathology related to the expression of a PPARα-associated gene product;  
 (b) obtaining a cell sample from said subject;  
 (c) assessing expression of one or more PPARα-associated gene products in said sample, wherein said gene product is selected from the group consisting of Camitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Camitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit, thereby generating a gene expression profile in said subject for said agent; and  
 (d) comparing the gene expression profile to a reference gene expression profile previously determined to represent levels characteristic of therapeutic effectiveness, wherein a correspondence in the gene expression profile in said sample to said reference gene expression profile indicates the agent is efficacious in treating a pathology related to the expression of a PPARα-associated gene product.  
 
     
     
         30 . A method of determining an effective dosing regimen of an agent as a therapeutic agent in a pathology related to the expression of a PPARα-associated gene product, the method comprising: 
 (a) administering the agent to a subject suffering from, or suspected of being prone to develop, a pathology related to the expression of a PPARα-associated gene product;  
 (b) obtaining a cell sample from said subject;  
 (c) assessing gene expression of one or more PPARα-associated gene products in said sample relative to expression products in the absence of said agent, wherein said gene products are selected from the group consisting of: Carnitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit, thereby generating a gene expression profile in said subject for said agent;  
 (d) comparing the gene expression profile to a gene expression profile previously determined to represent levels characteristic of therapeutic effectiveness; and  
 (e) repeating steps (a)-(d) as desired until the gene expression profile generated in step (c) corresponds to said gene expression profile previously determined to represent levels characteristic of therapeutic effectiveness,  
 thereby determining the effective dosing regimen of said agent as a therapeutic agent in a pathology related to the expression of a PPARα-associated gene product.  
 
     
     
         31 . A method of identifying a candidate pharmaceutical agent that selectively induces PPARα-ligand activity, the method comprising: 
 (a) obtaining a first tissue sample from a mammal known to express preferentially PPARα and a second tissue sample from the mammal known not to express preferentially PPARα;  
 (b) contacting the first tissue sample and the second tissue sample with a candidate pharmaceutical agent; and  
 (c) analyzing gene expression in said first and second samples relative to gene expression samples in tissue samples not exposed to said agents, thereby generating differential gene expression patterns for said first and second samples, wherein said gene expression is for a gene selected from the group consisting of Camitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit,  
 wherein a differential gene expression pattern characteristic of a PPARα-ligand in the first sample and a differential gene expression pattern not characteristic of a PPARα ligand in the second sample indicates that the agent selectively induces PPARα ligand activity.  
 
     
     
         32 . A method of diagnosing a pathophysiology associated with a PPARα-mediated pathway in a subject, said method comprising: 
 (a) providing a cell from said subject, wherein said cell comprises one or more genes encoding a polypeptide selected from the group consisting of: Carnitine/acyl carnitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Carnitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit; and  
 (b) measuring expression of one or more genes expressing said polypeptides in said subject, wherein an alteration in expression of said genes as compared to the expression of said genes in a control cell indicates that said subject has a pathophysiology associated with a PPARα-mediated pathway.  
 
     
     
         33 . A method of assessing the efficacy of a treatment for a pathophysiology associated with a PPARα-mediated pathway in a subject, the method comprising: 
 (a) providing a cell from a subject exposed to said treatment, wherein said cell comprises nucleic acid sequences encoding one or more polypeptides selected from the group consisting of: Carnitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Camitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit; and  
 (b) measuring expression of said nucleic acid sequences in said cell, wherein an alteration in expression of said nucleic acid in said cell compared to expression of said polypeptide in a control cell not exposed to said treatment indicates said treatments is efficacious.  
 
     
     
         34 . A method for selecting a therapeutic agent for treatment of a pathophysiology associated with a PPARα-mediated pathway in a subject, the method comprising: 
 (a) providing a cell from said subject, wherein said cell comprises one or more nucleic acid sequences encoding a polypeptide selected from the group consisting of: Camitine/acyl camitine carrier protein; Long chain acyl-CoA dehydrogenase; Short chain acyl CoA dehydrogenase; Long chain enoyl-CoA hydratase; Long chain ketoacyl-CoA thiolase; Propionyl-CoA carboxylase; Camitine octanoyl transferase; Epoxide hydrolase; Acetoacetyl-CoA thiolase; 8-aminolevulinate synthase; Porphobilinogen deaminase; Histidine decarboxylase; Catalase; Dynein-like protein 3; Heat shock protein 60; Hydroxysteroid sulfotransferase; Cytochrome p450 M1; Androgen repressible liver protein SMP-2; UDP-glucosuronyl transferase-21; Metallothionein-1; and Glutathione transferase Ya subunit;  
 (b) contacting said cell with a test agent; and  
 (c) measuring expression of the gene expressing said polypeptide in said subject, 
 wherein an alteration in expression of said nucleic acid sequence in said cell compared to expression of said nucleic acid sequence in a control cell not exposed to said test agent indicates said test agent is a therapeutic agent for treatment of a pathophysiology associated with a PPARα-mediated pathway in said subject.  
 
 
     
     
         35 . A method for selecting a therapeutic agent for treatment of a pathophysiology associated with a PPARα-mediated pathway in a subject, the method comprising: 
 (a) providing a cell from said subject, wherein said cell comprises one or more nucleic acid sequences selected from the group consisting of: Seq. Nos. 1-11;  
 (b) contacting said cell with a test agent, and  
 (c) measuring expression of said nucleic acids in said cell,  
 wherein an alteration in expression of said nucleic acids in said cell compared to expression of said nuclei acid in a control cell not exposed to said test agent indicates that said test agent is a therapeutic agent for treatment of a pathophysiology associated with a PPARα-mediated pathway in said subject.