Microarrays and uses therefor

Abstract

Methods of using microarrays to simplify analysis and characterization of genes and their function are provided. Such methods can be used to identify and characterize antibodies having binding affinity for a specific target antigen. A method of determining gene expression at the protein level by contacting an array of characterized or uncharacterized antibodies on a solid surface with one or more proteins and identifying the antibodies to which said protein(s) binds also is provided. This method can be used to compare the protein expression in two different populations of cells, such as normal cells and cancer cells or resting cells and stimulated cells. In addition, a method of determining gene expression at the protein level by contacting a microarray of nucleic acid samples derived from a variety of different sources with one or more nucleic acid probes then identifying the sample or samples to which the probe binds is provided.

That which is claimed is:  
     
         1 . A method of identifying antibodies having binding affinity for an antigen, said method comprising: 
 (a) contacting an array of uncharacterized antibodies on a solid surface with at least one antigen; and    (b) identifying the antibodies to which the antigen binds.    
     
     
         2 . A method according to  claim 1  wherein the antigen is a protein.  
     
     
         3 . A method according to  claim 1  wherein the antigen is an intact cell.  
     
     
         4 . A method according to  claim 1  wherein the antigen is a cell lysate.  
     
     
         5 . A method according to  claim 2  wherein the protein is recombinant.  
     
     
         6 . A method according to  claim 5  wherein the protein is full-length.  
     
     
         7 . A method according to  claim 5  wherein the protein is a protein fragment.  
     
     
         8 . A method according to  claim 7  wherein the protein fragment is encoded by an EST fragment.  
     
     
         9 . A method according to  claim 1  wherein the antibodies are monoclonal antibodies.  
     
     
         10 . A method according to  claim 1  wherein the antibodies are polyclonal antibodies.  
     
     
         11 . A method according to  claim 1  wherein the antibodies are antibody fragments.  
     
     
         12 . A method according to  claim 11  wherein the antibody fragments are single chain antibodies.  
     
     
         13 . A method according to  claim 1  wherein the antibodies are recombinant antibodies.  
     
     
         14 . A method according to  claim 1  wherein the antigen is detectably labeled.  
     
     
         15 . A method according to  claim 14  wherein the detectable label is a fluorescent moiety, avidin, streptavidin, or biotin.  
     
     
         16 . A method according to  claim 1  wherein the antigen is a fusion protein comprised of an epitope tag or a fluorescent protein.  
     
     
         17 . A method according to  claim 1  wherein the binding affinity of said antibody for said antigen is determined by iterative washing of said solid surface with a suitable diluent and detecting when antigen is no longer released therefrom.  
     
     
         18 . A method of comparing protein expression in two or more populations of cells, said method comprising: 
 (a) contacting an array of antibodies on a solid surface with a cell lysate of a first cell population, generating a first binding pattern;    (b) contacting a duplicate array of antibodies on a solid surface with a cell lysate of a second cell population, generating a second binding pattern; and    (c) comparing the binding pattern of the first cell lysate with the binding pattern of the second cell lysate.    
     
     
         19 . A method according to  claim 18  wherein the antibodies are uncharacterized antibodies.  
     
     
         20 . A method according to  claim 18  wherein the antibodies are recombinant antibodies.  
     
     
         21 . A method according to  claim 18  wherein the first cell lysate is derived from normal cells and the second cell lysate is derived from abnormal cells.  
     
     
         22 . A method according to  claim 21  wherein the abnormal cells are cancer cells.  
     
     
         23 . A method according to  claim 18  wherein the first cell lysate is derived from normal cells in a resting state and the second cell lysate is derived from normal cells in a stimulated state.  
     
     
         24 . A method according to  claim 18  wherein the difference between the first and second set of cells is the presence of a different detectable label.  
     
     
         25 . A method for determining the effect of varying binding conditions on the binding affinity of antibodies to a specific antigen, said method comprising: 
 (a) contacting an array of antibodies on a solid surface with at least one antigen under a first set of binding conditions, generating a first binding pattern;    (b) contacting a duplicate array with the antigen under a second set of binding conditions, generating a second binding pattern;    (c) comparing the first and second binding patterns.    
     
     
         26 . A method according to  claim 21  wherein said varying binding conditions comprise varying pH, temperature, salt concentration, and/or duration.  
     
     
         27 . A method for characterizing a cell, based on the pattern of protein expression produced thereby, said method comprising: 
 (a) contacting an array of antibodies on a solid surface with a cell lysate; and    (b) identifying the profile of antibodies to which components of the lysate binds.    
     
     
         28 . A method of diagnosing a disorder, said method comprising: 
 (a) contacting an array of antibodies specific for one or more antigens characteristic of a disorder with a biological sample obtained from a subject under conditions suitable for the formation of an antigen:antibody complex, wherein the presence of the antigens in the biological sample would be indicative of the disorder;    and    (b) detecting the formation of any antibody: antigen complexes.    
     
     
         29 . A method according to  claim 28  wherein the biological sample is cerebral spinal fluid, blood, plasma, urine, feces, saliva, tears, or extracted tissue.  
     
     
         30 . A method according to  claim 29  wherein the disorder is stroke, cerebral hemorrhage, myocardial infarction, peripheral blood clots, diabetes, cancer, Alzheimer's disease, and sepsis.  
     
     
         31 . A kit comprising: 
 (a) an array of uncharacterized antibodies on a solid surface; and    (b) instructions for using the array.    
     
     
         32 . A kit according to  claim 31  wherein the instructions are for identifying antibodies to a specific antigen, comparing protein expression in two or more populations of cells, characterizing a cell based on the pattern of protein expression produced thereby, or determining the effect of varying binding conditions on the binding affinity of the antibodies.  
     
     
         33 . A kit according to  claim 31  wherein the antibodies are monoclonal antibodies, polyclonal antibodies or antibody fragments.  
     
     
         34 . A kit according to  claim 33  wherein the antibody fragments are single chain antibodies.  
     
     
         35 . A kit according to  claim 31  wherein the antibodies are recombinant antibodies.  
     
     
         36 . A kit according to  claim 31  further comprising reagents for detecting an antigen and instructions for use thereof.  
     
     
         37 . A kit comprising: 
 (a) an array of antibodies on a solid surface; and    (b) instructions for using the array; wherein the instructions are for diagnosing a disorder, characterizing a cell based on the pattern of protein expression produced thereby, or comparing protein expression in two or more populations of cells.    
     
     
         38 . A kit according to  claim 37  further comprising reagents for detecting an antigen and instructions for use thereof.  
     
     
         39 . A kit according to  claim 37  wherein the antibodies are recombinant antibodies.  
     
     
         40 . A kit according to  claim 37  wherein the antibodies are single chain antibodies.  
     
     
         41 . A method of comparing protein expression patterns, said method comprising: 
 (a) contacting a microarray of nucleic acid samples derived from different sources with one or more nucleic acid probes and    (b) identifying the sample or samples to which the probe(s) binds.    
     
     
         42 . A method according to  claim 41  wherein the microarray comprises nucleic acid samples derived from a single tissue type but from different species.  
     
     
         43 . A method according to  claim 41  wherein the microarray comprises nucleic acid samples derived from a single species but from different tissue types.  
     
     
         44 . A method according to  claim 41  wherein the microarray comprises nucleic acid samples derived from the same tissue type at different developmental stages.  
     
     
         45 . A method according to  claim 41  wherein the nucleic acid samples are comprised of mRNA or cDNA.  
     
     
         46 . A method according to  claim 41  wherein the probe is detectably labeled.  
     
     
         47 . A method according to  claim 46  wherein the detectable label is a fluorescent label.  
     
     
         48 . A method according to  claim 18  wherein the first and second cell lysates are derived from cells from a single tissue type but from different species.  
     
     
         49 . A method according to  claim 18  wherein the first and second cell lysates are derived from cells from a single species but from different tissue types.  
     
     
         50 . A method according to  claim 18  wherein the first and second cell lysates are derived from cells from the same tissue type at different developmental stages.