Methods for identifying therapeutic targets involved in glucose and lipid metabolism
AssigneeRibonomics, Inc.
InventorsRichard Cheatham, Barry Henderson, William Phelps
Life of this patent
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Abstract
The identification and evaluation of mRNA and protein targets associated with RNA binding proteins or mRNP complexes is described. In particular, the invention provides methods for identifying RNA binding proteins associated with physiological pathways that participate in glucose and lipid metabolism and mRNAs that exhibit coordinated gene regulation across those M pathways. Candidate targets are provided that are useful for the diagnosis or treatment of diseases related to diseases, such as disease related to aberrant glucose and lipid metabolism, such as, for example, obesity, diabetes, and hypoglycemia.
Claims37
A method of identifying a therapeutic target, the method comprising the steps of:
- (a) measuring protein or RNA levels of at least one component of an isolated mRNA ribonucleoprotein (mRNP) complex in a first sample enriched for a cell comprising a first phenotype;
- and
- (b) comparing the levels determined in step (a) to the levels of the protein or RNA levels of the component in a second sample enriched for a cell comprising a second phenotype,
- wherein if the levels of the component in the first sample are different from the levels of the component in the second sample, the component, a nucleic acid that encodes the component, or a protein encoded by the component is a potential therapeutic target for the treatment of a disease.
A method for identifying a therapeutic target for the treatment of aberrant glucose metabolism or lipid metabolism, the method comprising the steps of:
- (a) measuring RNA or protein levels of at least one component of an isolated mRNP complex in a first cell sample;
- and
- (b) comparing RNA or protein levels determined in step (a) to the RNA or protein levels of the component from a second cell sample,
- wherein if the levels of the component in the first sample are different from the levels of the component in the second sample, the component, a nucleic acid that encodes the component, or a protein encoded by the component is a potential therapeutic target for the treatment of the disease.
A method for identifying a therapeutic target related to the treatment of a disease, the method comprising the steps of:
- (a) measuring RNA or protein levels of at least one component of an isolated mRNP complex in a sample that has been treated with an agent that alters the expression of a component of a glucose metabolic or lipid metabolic pathway;
- and
- (b) comparing RNA or protein levels determined in step (a) to the RNA or protein levels of the component in an untreated control sample,
- wherein if the levels of the component in the first sample are different from the levels of the component in the second sample, the component, a nucleic acid that encodes the component, or a protein encoded by the component is a potential therapeutic target for the treatment of the disease.
A method for identifying a gene or gene product involved in a physiological pathway in a cell, the method comprising the steps of:
- a. isolating an mRNP complex comprising at least one component that participates in a physiological pathway;
- b. identifying at least one additional component of the isolated mRNP complex,
- wherein the additional component is also involved in a physiological pathway.
A method for identifying an agent that alters a physiological pathway, the method comprising the steps of:
- a. subjecting a cell sample to an agent;
- b. isolating an mRNP complex comprising at least one component that participates in a physiological pathway from the sample;
- c. measuring the RNA or protein levels of at least one component of the isolated mRNP complex,
- d. comparing the RNA or protein levels of step (c) to the RNA or protein levels of the component isolated from an untreated control sample,
- wherein differential expression of the component in the agent-treated sample compared to the untreated control sample is indicative that the agent regulates the physiological pathway.
A method for identifying a protein that regulates glucose metabolism, the method comprising the steps of:
- a. measuring the expression in an isolated mRNP complex of at least one gene product of a cell involved in glucose metabolism, wherein the gene product is selected from the group consisting of an RNA binding protein, an mRNA associated with said RNA binding protein, or an mRNP complex-associated protein;
- b. treating the cell with an agent selected from the group consisting of insulin, glucose, insulin-like growth factor-1 (IGF-1), a β-adrenergic agonist, glucose, glucagon-like peptide-1 (GLP-1), fatty acid, a peroxisome proliferator activated receptor (PPAR) ligand, and insulin-like growth factor 2 (IGF-2);
- and
- c. measuring the expression of the gene product after treatment, wherein a difference in expression of the gene product after treatment compared to expression of the gene product before treatment is indicative that the protein regulates glucose metabolism.
A method for identifying an agent that regulates insulin production, the method comprising the steps of:
- a. contacting a cell involves in insulin production with a nucleic acid capable of binding to at least one protein, wherein the protein is capable of binding to a 3′ untranslated region or a 5′ untranslated region of a preproinsulin mRNA;
- b. separating the nucleic acid from the protein;
- and
- c. identifying the protein.
An mRNP complex-associated with at least one of glucose or lipid metabolism, wherein the mRNP complex comprises a polypyrimidine tract binding (PTB) protein, and at least one mRNA associated with the polypyrimidine tract binding protein.
A method for identifying a component of an mRNP complex, the method comprising the steps of:
- (a) transfecting a cell sample with a nucleic acid that inhibits the expression of an RNA binding protein;
- (b) isolating total RNA from the cell sample and from a control sample;
- (c) identifying RNAs that have altered expression in the nucleic acid-transfected sample compared to the control sample.
Dependencies are inferred from the claim text.