Cell preparations and cell supports and their use in theranosis

Abstract

A method of preparing cells from a patient specimen comprising a tissue or a clump of cells; a method of in situ hybridization (ISH) or immunohistochemistry (IHC); a method of theranosing a patient's response to an active agent that targets the tyrosine kinase pathway; an improvement of a method of theranosis comprising the method of ISH or IHC; a cell support on the surface of which are cells, which have been contacted with detectably labeled probes with the method of ISH or IHC; and a kit comprising (a) a cell support and/or at least one probe for ISH or IHC, and (b) instructions for carrying out the method of ISH or IHC on a cell support.

1 .- 23 . (canceled) 
     
     
         24 . A cell support comprising a tissue or clump of cells prepared from a patient specimen by a method comprising:
 (i) soaking a patient specimen in a pre-warmed, balanced salt solution comprising a reducing agent and a chelating agent;   (ii) transferring the patient specimen to a fresh, balanced salt solution comprising a reducing agent, a source of calcium ions, and a polar aprotic solvent and mixing;   (iii) removing the patient specimen from the fresh, balanced salt solution and either (a) centrifuging the solution to pellet disaggregated cells or (b) straining the solution to collect disaggregated cells; and   (iv) after (iii)(a), discarding the supernatant, re-suspending the pelleted cells in residual supernatant, and placing the re-suspended cells in a fixative or, after (iii)(b), placing the strained cells in a fixative.   
     
     
         25 . A cell support for performing in situ hybridization (ISH) or immunohistochemistry (IHC) on a patient specimen with a detectably labeled probe in less than about 14 hours of removal of the specimen from the patient, wherein the cell support comprises cells, which have been disaggregated from a specimen selected from the group consisting of a fine needle aspiration, a core needle biopsy, an excisional biopsy, and a resection. 
     
     
         26 . A kit for performing in situ hybridization (ISH) or immunohistochemistry (IHC) comprising:
 (a) the cell support of  claim 24 ,   (b) at least one probe for performing ISH or IHC, and   (c) instructions for performing ISH or IHC.   
     
     
         27 . A kit for performing in situ hybridization (ISH) or immunohistochemistry (IHC) comprising:
 (a) the cell support of  claim 25 ,   (b) at least one probe for performing ISH or IHC, and   (c) instructions for performing ISH or IHC.   
     
     
         28 .- 29 . (canceled) 
     
     
         30 . The cell support of  claim 24 , wherein the patient specimen is (a) a fresh specimen, (b) a thawed, freshly frozen specimen, or (c) a partially fixed specimen. 
     
     
         31 . The cell support of  claim 24 , wherein the patient specimen is rinsed in a balanced salt solution prior to step (i). 
     
     
         32 . The cell support of  claim 24 , which comprises at least two discrete areas and the cells have been applied to the discrete areas, wherein each area is contacted with at least one detectably labeled probe and, if an area is contacted with two or more detectably labeled probes, the detectably labeled probes can be distinguished. 
     
     
         33 . The cell support of  claim 32 , wherein each discrete area is separately contacted with a mixture of detectably labeled probes, wherein the mixture comprises:
 a two-color break-apart probe for ALK and a two-color break-apart probe for ROSI,
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a probe for c-MET, 
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a two-color break-apart probe for RET, 
 a two-color break-apart probe for RET and a two-color break-apart probe for NTRK1, 
 a two-color break-apart probe for RET and a probe for KIF5B, 
 a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for AURKA, a locus-specific probe for 9p21, a CEP for chromosome 3, a CEP for chromosome 6, and a CEP for chromosome 7, 
 a probe for MYC, a probe for EGFR, a probe for DCC, a locus-specific probe for 13q14, and a CEP for chromosome 18, 
 a probe for MYC, a probe for TERC, and a CEP for chromosome 7, 
 a probe for MYC, a probe for HER2, a probe for ZNF217, and a locus-specific probe for 9p21, 
 a probe for MCL1, a probe for FGFR2, a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for FGFR2, a probe for PIK3CA, a CEP for chromosome 3, and a CEP for chromosome 10, 
 a probe for PTEN, a probe for ERG, and a CEP for chromosome 10, 
 a probe for FGFR1, a probe for FGFR2, a two-color break-away probe for FGFR2, a CEP for chromosome 8, and a CEP for chromosome 10, or 
 a probe for MET, a probe for PIK3CA, a probe for EGFR, a CEP for chromosome 7, and a CEP for chromosome 3. 
   
     
     
         34 . The cell support of  claim 25 , which comprises at least two discrete areas and the cells have been applied to the discrete areas, wherein each area is contacted with at least one detectably labeled probe and, if an area is contacted with two or more detectably labeled probes, the detectably labeled probes can be distinguished. 
     
     
         35 . The cell support of  claim 34 , wherein each discrete area is separately contacted with a mixture of detectably labeled probes, wherein the mixture comprises:
 a two-color break-apart probe for ALK and a two-color break-apart probe for ROSI,
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a probe for c-MET, 
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a two-color break-apart probe for RET, 
 a two-color break-apart probe for RET and a two-color break-apart probe for NTRK1, 
 a two-color break-apart probe for RET and a probe for KIF5B, 
 a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for AURKA, a locus-specific probe for 9p21, a CEP for chromosome 3, a CEP for chromosome 6, and a CEP for chromosome 7, 
 a probe for MYC, a probe for EGFR, a probe for DCC, a locus-specific probe for 13q14, and a CEP for chromosome 18, 
 a probe for MYC, a probe for TERC, and a CEP for chromosome 7, 
 a probe for MYC, a probe for HER2, a probe for ZNF217, and a locus-specific probe for 9p21, 
 a probe for MCL1, a probe for FGFR2, a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for FGFR2, a probe for PIK3CA, a CEP for chromosome 3, and a CEP for chromosome 10, 
 a probe for PTEN, a probe for ERG, and a CEP for chromosome 10, 
 a probe for FGFR1, a probe for FGFR2, a two-color break-away probe for FGFR2, a CEP for chromosome 8, and a CEP for chromosome 10, or 
 a probe for MET, a probe for PIK3CA, a probe for EGFR, a CEP for chromosome 7, and a CEP for chromosome 3. 
   
     
     
         36 . The kit of  claim 26 , wherein the cell support comprises at least two discrete areas and the cells have been applied to the discrete areas, wherein each area is contacted with at least one detectably labeled probe and, if an area is contacted with two or more detectably labeled probes, the detectably labeled probes can be distinguished. 
     
     
         37 . The kit of  claim 36 , wherein each discrete area is separately contacted with a mixture of detectably labeled probes, wherein the mixture comprises:
 a two-color break-apart probe for ALK and a two-color break-apart probe for ROSI,
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a probe for c-MET, 
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a two-color break-apart probe for RET, 
 a two-color break-apart probe for RET and a two-color break-apart probe for NTRK1, 
 a two-color break-apart probe for RET and a probe for KIF5B, 
 a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for AURKA, a locus-specific probe for 9p21, a CEP for chromosome 3, a CEP for chromosome 6, and a CEP for chromosome 7, 
 a probe for MYC, a probe for EGFR, a probe for DCC, a locus-specific probe for 13q14, and a CEP for chromosome 18, 
 a probe for MYC, a probe for TERC, and a CEP for chromosome 7, 
 a probe for MYC, a probe for HER2, a probe for ZNF217, and a locus-specific probe for 9p21, 
 a probe for MCL1, a probe for FGFR2, a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for FGFR2, a probe for PIK3CA, a CEP for chromosome 3, and a CEP for chromosome 10, 
 a probe for PTEN, a probe for ERG, and a CEP for chromosome 10, 
 a probe for FGFR1, a probe for FGFR2, a two-color break-away probe for FGFR2, a CEP for chromosome 8, and a CEP for chromosome 10, or 
 a probe for MET, a probe for PIK3CA, a probe for EGFR, a CEP for chromosome 7, and a CEP for chromosome 3. 
   
     
     
         38 . The kit of  claim 27 , wherein the cell support comprises at least two discrete areas and the cells have been applied to the discrete areas, wherein each area is contacted with at least one detectably labeled probe and, if an area is contacted with two or more detectably labeled probes, the detectably labeled probes can be distinguished. 
     
     
         39 . The kit of  claim 38 , wherein each discrete area is separately contacted with a mixture of detectably labeled probes, wherein the mixture comprises:
 a two-color break-apart probe for ALK and a two-color break-apart probe for ROSI,
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a probe for c-MET, 
 a two-color break-apart probe for ALK, a two-color break-apart probe for ROS1, and a two-color break-apart probe for RET, 
 a two-color break-apart probe for RET and a two-color break-apart probe for NTRK1, 
 a two-color break-apart probe for RET and a probe for KIF5B, 
 a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for AURKA, a locus-specific probe for 9p21, a CEP for chromosome 3, a CEP for chromosome 6, and a CEP for chromosome 7, 
 a probe for MYC, a probe for EGFR, a probe for DCC, a locus-specific probe for 13q14, and a CEP for chromosome 18, 
 a probe for MYC, a probe for TERC, and a CEP for chromosome 7, 
 a probe for MYC, a probe for HER2, a probe for ZNF217, and a locus-specific probe for 9p21, 
 a probe for MCL1, a probe for FGFR2, a probe for MET, a probe for EGFR, and a CEP for chromosome 7, 
 a probe for FGFR2, a probe for PIK3CA, a CEP for chromosome 3, and a CEP for chromosome 10, 
 a probe for PTEN, a probe for ERG, and a CEP for chromosome 10, 
 a probe for FGFR1, a probe for FGFR2, a two-color break-away probe for FGFR2, a CEP for chromosome 8, and a CEP for chromosome 10, or 
 a probe for MET, a probe for PIK3CA, a probe for EGFR, a CEP for chromosome 7, and a CEP for chromosome 3.