Tumor tissue microarrays for rapid molecular profiling

Abstract

An array-based technology facilitates rapid correlated gene copy number and expression profiling of a very large numbers of human tumors. Hundreds of cylindrical tissue biopsies (diameter 0.6 mm) from morphologically representative regions of individual tumors can be arrayed in a single paraffin block. Consecutive sections from such arrays provide targets for parrallel in situ visualization and quantitation of DNA, RNA or protein targets. For example, amplifications of six loci (mybL2, erbB2, Cyclin-D1, myc, 17q23 and 20q13) were rapidly determined by fluorescence in situ hybridization from 372 ethanol-fixed breast cancers. Stratification of tumors by estrogen receptor and p53 expression data revealed dictinct patterns of gene amplification in the various subgroups of breast cancer that may have prognostic utility. The tissue array technology is useful in the rapid molecular profiling of hundreds of normal and pathological tissue specimens or cultured cells.

We claim:  
     
         1 . A method of parallel analysis of tissue specimens, comprising: 
 obtaining a plurality of donor specimens;    placing each donor specimen in an assigned location in a recipient array;    obtaining a plurality of sections from the recipient array in a manner that each section contains a plurality of donor specimens that maintain their assigned locations;    performing a different histological analysis of each section; and    comparing the results of the different histological analyses in corresponding assigned locations of different sections to determine if there are correlations between the results of the different histological analyses at each assigned location.    
     
     
         2 . The method of  claim 1 , wherein the donor specimen is obtained by boring an elongated sample from the donor specimen, which is placed in the assigned location in the recipient array.  
     
     
         3 . The method of  claim 2 , wherein placing the donor specimen in an assigned location in the recipient array comprises forming an elongated receptacle in a donor block, and placing the elongated sample in the elongated receptacle of the recipient block.  
     
     
         4 . The method of  claim 3 , wherein the elongated sample is placed in a receptacle having a cross-sectional size and shape complementary to a cross-sectional size and shape of the elongated sample.  
     
     
         5 . The method of  claim 4 , wherein forming the elongated receptacle comprises forming a cylindrical bore in the recipient block, and the sample is obtained by boring a cylindrical tissue specimen from the donor block, wherein a diameter of the elongated receptacle is substantially the same as a diameter of the sample.  
     
     
         6 . The method of  claim 1 , further comprising associating a clinical parameter with each assigned location in the recipient array.  
     
     
         7 . The method of  claim 1  wherein performing the different histological analysis on each slide comprises performing different tests selected from the group of an immunological analysis and a nucleic acid hybridization.  
     
     
         8 . The method of  claim 6 , further comprising determining whether there are correlations between clinical parameters, immunologic analysis and nucleid acid hybridization.  
     
     
         9 . The method of  claim 1 , wherein the biological sample is a tissue specimen or cellular preparation.  
     
     
         10 . A method of parallel analysis of identical arrays of tissue specimens, comprising: 
 forming a donor block comprising a biological specimen embedded in embedding medium;    obtaining a plurality of cylindrical donor sample cores from the biological specimen;    boring receptacle cores from a recipient embedding medium to form an array of cylindrical receptacles;    placing the donor sample cores in the cylindrical receptacles at assigned locations in the array;    sectioning the recipient embedding medium to obtain a cross-section of the donor sample cores in the array, while maintaining the assigned locations in the array in consecutive cross-sections;    performing a different histological analysis of each cross-section; and    comparing a result of each histological analysis in corresponding assigned locations of different sections to determine if there are correlations between the results of the different histological analyses at each assigned location.    
     
     
         11 . The method of  claim 10 , further comprising comparing the results of the different histological analyses at each assigned location to clinical information about the biological specimen at the assigned location.  
     
     
         12 . The method of  claim 11 , wherein the biological specimen is a tissue specimen from a tumor.  
     
     
         13 . The method of  claim 12 , wherein the histological analyses comprise immunologic analysis and nucleic acid hybridization analysis.  
     
     
         14 . The method of  claim 10 , further comprising aligning a thin tissue section above the donor block to identify an area of interest from which the donor sample core is taken.  
     
     
         15 . The method of  claim 10 , wherein the cylindrical donor sample core has a diameter that is less than about 1 mm.  
     
     
         16 . A cross-section of the donor sample cores obtained by the method of  claim 10 .  
     
     
         17 . An apparatus for preparing specimens for parallel analysis of sections of biological material arrays, comprising: 
 a holder that can be positioned to maintain a tissue donor block in a donor position; and    a reciprocal punch positioned in relation to the holder to punch a tissue specimen from the donor block in the donor position, wherein the holder is also capable of holding a recipient block in a recipient position, and the recipient block comprises an array of receptacles, each of which can be positioned in a preselected position in relation to the reciprocal punch to deliver a tissue specimen from the reciprocal punch into a receptacle in the preselected position.    
     
     
         18 . The apparatus of  claim 17 , wherein the holder comprises an x-y positioning device that can be incrementally positioned to align sequential receptacles with the reciprocal punch.  
     
     
         19 . The apparatus of  claim 17 , further comprising a stylet positioned for introduction into the reciprocal punch to expel the tissue specimen from the punch into one of the receptacles aligned with the punch.  
     
     
         20 . The apparatus of  claim 17 , further comprising a positioner that positions a thin section slide over the donor block, to align structures of interest in the thin section slide with corresponding tissue specimen regions in the donor block.  
     
     
         21 . The apparatus of  claim 17 , further comprising a separate reciprocal punch capable of being positioned in a fixed position relative to the recipient block for forming the array of receptacles in the recipient block.  
     
     
         22 . The apparatus of  claim 21 , further comprising a recorder for recording the positions of the receptacles in the recipient block.  
     
     
         23 . The apparatus of  claim 22 , wherein the recorder is a computer implemented system for recording the positions of the receptacles, and an identification of the tissue specimen that is placed in each receptacle.  
     
     
         24 . A computer implemented system for parallel analysis of consecutive sections of tissue arrays, comprising: 
 an x-y positioning platform for moving a tray to a plurality of coordinates that correspond to positions in a recipient block array;    a receptacle punch positioned in punching relationship with respect to the positioning platform, such that the receptacle punch can punch a receptacle core from a recipient block on the positioning platform,    a donor punch positioned in a punching relationship with respect to the positioning platform, such that the donor punch can punch a donor specimen from a donor block on the positioning platform, wherein the receptacle core has a diameter that is substantially the same as the diameter of the donor specimen;    a stylet that is selectively alternatively aligned with the donor punch and the recipient punch, for displacing contents of the receptacle punch after a receptacle core is punched from the recipient block, and for displacing contents of the donor punch into receptacles of the recipient block array after a donor specimen is punched from the donor block; and    wherein the system records an identification of tissue in the receptacles of the recipient array.    
     
     
         25 . The computer implemented system of  claim 24 , further comprising a microscope for viewing the donor block, and locating a structure of interest in a reference slide aligned with the donor block.  
     
     
         26 . The computer implemented system of  claim 24 , wherein the system punches a receptacle core from the recipient block and displaces the receptacle core from the receptacle punch with the stylet, then punches a donor specimen from the donor block, aligns the donor punch with a selected receptacle in the recipient block, and displaces the donor specimen into the selected receptacle.  
     
     
         27 . A method of analyzing ex vivo tissue specimens, comprising punching an elongated tissue sample from the ex vivo tissue specimen, and subjecting the sample to a biological analysis.  
     
     
         28 . The method of  claim 27 , wherein punching the elongated tissue sample from the tissue specimen comprises placing the tissue specimen in a holder below a reciprocal punch, and advancing the reciprocal punch into a predetermined location of the tissue specimen.  
     
     
         29 . The method of  claim 28 , further comprising placing the tissue specimen in an embedding medium prior to punching.  
     
     
         30 . The method of  claim 29 , wherein the predetermined location of the tissue specimen is determined by examining a thin section cut from the embedding medium.