Treatment of inflammatory diseases

Abstract

The invention described herein relates to methods of screening for pro-inflammatory genes and anti-inflammatory genes which may be useful for treating an inflammatory disease, disorder, or otherwise abnormal condition, such as an inflammatory lung disease. The identified pro-inflammatory genes and anti-inflammatory genes may be used to produce pharmaceutical compositions for use in treating the inflammatory disease, disorder, or otherwise abnormal condition.

1 - 21 . (canceled) 
     
     
         22 . A method of identifying a compound that is potentially useful for treating an inflammatory disease or condition in a subject, the method comprising:
 a) providing a population of test cells, wherein:
 1) the test cells are a clonal expansion of a single epithelial stem cell isolated from said subject, wherein said single epithelial stem cell is capable of propagating for at least about 20 (30, 40, 50, 60, 70, 100, 150, 200, 250, 300, 350, 400 or more) doublings while maintaining a multipotent phenotype; or, 
 2) the test cells are differentiated from said clonal expansion of said single epithelial stem cell; 
   b) contacting the test cells with a pro-inflammatory cytokine associated with the inflammatory disease;   c) contacting the test cells with a candidate compound or a control; and,   d) identifying the candidate compound that antagonizes a function of the pro-inflammatory cytokine;   thereby identifying the compound that is potentially useful for treating the inflammatory disease or condition in the subject.   
     
     
         23 . The method of  claim 22 , wherein the single epithelial stem cell is isolated from a tissue or organ affected by the inflammatory disease or condition, or from a tissue or organ in close proximity to the tissue or organ affected by the inflammatory disease or condition. 
     
     
         24 . The method of  claim 22 , wherein the subject has asthma or COPD, or is predisposed to have asthma or COPD. 
     
     
         25 . The method of  claim 22 , wherein the candidate compound is a small molecule with a molecular weight of less than about 500 Da or 1000 Da, a peptide, a protein, a polynucleotide (antisense, siRNA, miRNA, shRNA, ribozyme, or polynucleotide encoding the same), a lipid, a sterol, or a polysaccharide. 
     
     
         26 . The method of  claim 22 , wherein the candidate compound is a drug known to be effective in treating the inflammatory disease or condition. 
     
     
         27 . The method of  claim 22 , wherein step b) is carried out before step c), and wherein the test cells exhibit a phenotype in response to being contacted by the pro-inflammatory cytokine prior to step c). 
     
     
         28 . The method of  claim 22 , wherein step b) is carried out substantially simultaneously with step c). 
     
     
         29 . The method of  claim 22 , wherein step b) is carried out after step c). 
     
     
         30 . The method of  claim 22 , wherein in step d), the candidate compound antagonizes the function of the pro-inflammatory cytokine by alleviating a phenotype of the test cells in response to being contacted by the pro-inflammatory cytokine. 
     
     
         31 . The method of  claim 30 , wherein the phenotype is increased expression of a pro-inflammatory gene (such as any one listed in Tables 3 and 4), or decreased expression of an anti-inflammatory gene (such as any one listed in Tables 1 and 2). 
     
     
         32 . A pharmaceutical composition for treating an inflammatory disease (e.g., an inflammatory lung disease), comprising:
 a) a protein or a polypeptide or a functional portion thereof encoded by an anti-inflammatory gene selected from ABI3BP, AMTN, APOD, BMP8A, C3, CP, GLIPR1, FN1 IGFBP3, IGFBP6, LGALS1, LTBP1, MSMB, OLFM4, PLUNC, PPBP, SERPINA3, and TNFSF15, or   b) an antagonist of a pro-inflammatory gene selected from: AGR2, ANG, C20orf114, CA2, CCL26, CD200R1, CST1, CST2, DEFB118, DPP4, EPGN, FETUB, GGH, ITLN1, KITLG, PDCD1LG2, PLA2G7, POSTN, PTHLH, SAA4, SERPINB2, SMPDL3B, SPINK5, ST6GAL1, STATH, SULF1, TCN1, TFF1, TIMP1, TMPRSS2, TNFSF10, CCL2, and IL-1A, and,   one or more pharmaceutically acceptable excipients, stabilizers or preservatives.   
     
     
         33 . The pharmaceutical composition of  claim 32 , wherein the antagonist comprises an RNAi agent (siRNA, miRNA, shRNA), an antisense sequence, a ribozyme, or a polynucleotide encoding said RNAi agent, said antisense sequence, or said ribozyme. 
     
     
         34 . The pharmaceutical composition of  claim 32 , wherein the antagonist comprises an antibody specific for a protein or polypeptide encoded by said pro-inflammatory gene. 
     
     
         35 . A pharmaceutical composition for treating an inflammatory disease (e.g., an inflammatory lung disease), comprising an agent which induces the expression of the anti-inflammatory gene of  claim 32 , or which mimics the activity of the gene product of the anti-inflammatory gene of  claim 32 , further comprising one or more pharmaceutically acceptable excipients, stabilizers or preservatives. 
     
     
         36 - 46 . (canceled) 
     
     
         47 . A method of screening for a compound that may be useful for treating an inflammatory disease, disorder, or otherwise abnormal condition in a subject, the method comprising:
 (1) providing a first population of test cells, wherein:
 a) the first population of test cells are a clonal expansion of a first single epithelial stem cell isolated from a diseased tissue of the subject, wherein said first single epithelial stem cell is capable of propagating for at least about 20 (30, 40, 50, 60, 70, 100, 150, 200, 250, 300, 350, 400 or more) doublings while maintaining a multipotent phenotype; or, 
 b) the first population of test cells are differentiated from said clonal expansion of said first single epithelial stem cell; 
   (2) providing a second population of test cells, wherein:
 a) the second population of test cells are a clonal expansion of a second single epithelial stem cell isolated from a matching normal tissue of the subject, wherein said second single epithelial stem cell is capable of propagating for at least about 20 (30, 40, 50, 60, 70, 100, 150, 200, 250, 300, 350, 400 or more) doublings while maintaining a multipotent phenotype; or, 
 b) the second population of test cells are differentiated from said clonal expansion of said second single epithelial stem cell; 
   (3) contacting the first and the second populations of test cells with a candidate therapeutic agent;   (4) determining and comparing the effects of the candidate therapeutic agent on the first and second population of test cells;   wherein the candidate therapeutic agent is identified as the compound that may be useful for treating the inflammatory disease, disorder, or otherwise abnormal condition, if the candidate therapeutic agent alleviates at least one symptom of the first population of test cells, and does not produce an undesirable effect on the second population of test cells.