Automated analysis of circulating tumor cells

Abstract

The disclosure provides methods for automated characterization of circulating tumor cells (CTCs), for example using automated tissue strainers. In specific examples, such methods permit characterizing a prostate cancer sample by simultaneously or contemporaneously detecting ERG rearrangements and PTEN deletions in the same CTC. Also provided are kits that can be used with such methods.

1 . A method of analyzing a sample containing circulating tumor cells (CTCs) using an automated instrument, comprising:
 obtaining the sample from a subject,   depositing the sample on a substrate configured for use with the automated instrument,   placing the substrate within the automated instrument,   retrieving targets on the sample using the automated instrument,   contacting the sample with CTC identification reagents using the automated instrument,   contacting the sample with CTC characterization reagents using the automated instrument,   imaging the sample,   locating the CTCs by locating the CTC identification reagents,   spectral imaging the CTCs by location, and   analyzing the sample by analyzing the spectral imaging.   
     
     
         2 . The method of  claim 1 , further comprising enriching the CTC content of the sample using a capture antibody specific for an ETS related gene (ERG) protein, a prostate specific membrane antigen (PSMA) protein, or an epithelial cell adhesion molecule (EpCAM), protein, wherein enriching the CTC content of the sample occurs prior to depositing the sample on the substrate. 
     
     
         3 . The method of  claim 1 , wherein the CTC characterization reagents comprise nucleic acid probes directed to four genomic markers. 
     
     
         4 . The method of  claim 3 , wherein the four genomic markers are analyzed for gene expression and/or genetic rearrangements/deletions. 
     
     
         5 . The method of  claim 3 , wherein the four genomic markers comprise a gene expression probe and a rearrangement/deletion probe combination. 
     
     
         6 . The method of  claim 1 , wherein the subject has prostate cancer. 
     
     
         7 . The method of  claim 6 , wherein the prostate cancer is a castrate-resistant prostate cancer (CRPC). 
     
     
         8 . The method of  claim 7 , wherein the CRPC is a metastatic CRPC (mCRPC). 
     
     
         9 . The method of  claim 3 , wherein the four genomic markers comprise ETS related gene (ERG), phosphatase and tensin homolog (PTEN), and centromere 10 (CEN-10). 
     
     
         10 . The method of  claim 3 , wherein the nucleic acid probes are a 5′ ERG probe, a 3′ ERG probe, a PTEN probe, and a CEN-10 probe. 
     
     
         11 . The method of  claim 1 , wherein the CTC identification reagents comprise immunohistochemical reagents directed to CTC protein markers. 
     
     
         12 . The method of  claim 11 , wherein the CTC protein markers comprise a CD45 protein, a cytokeratin (CK) protein, an ERG protein, an androgen receptor (AR), a PSMA protein, or combinations thereof. 
     
     
         13 . The method of  claim 1 , wherein the CTC characterization reagents comprise nucleic acid probes directed to four genomic markers and the CTC identification reagents comprise immunohistochemical reagents directed to CTC protein markers. 
     
     
         14 . The method of  claim 13 , wherein the four genomic markers comprise ETS related gene (ERG), phosphatase and tensin homolog (PTEN), and centromere 10 (CEN-10) and the CTC protein markers comprise a CD45 protein, a CK protein, an ERG protein, an AR, a PSMA protein, or combinations thereof. 
     
     
         15 . The method of  claim 1 , wherein imaging the sample comprises imaging immunofluorescence of the CTC identification reagents. 
     
     
         16 . The method of  claim 15 , wherein imaging the sample comprises using multi-spectral bandpass filters. 
     
     
         17 . The method of  claim 15 , wherein the immunofluorescence emanates from antibodies directly labeled with fluorophores. 
     
     
         18 . The method of  claim 17 , wherein the immunofluorescence results from exciting the fluorophores with spectrally filtered visible light. 
     
     
         19 . The method of  claim 18 , wherein the spectrally filtered visible light includes a first selected range to excite a first fluorophore and a second selected range to excite a second fluorophore, wherein the first selected range does not significantly excite the second fluorophore and the second selected range does not significantly excite the first fluorophore. 
     
     
         20 . The method of  claim 18 , wherein imaging the sample comprises acquiring a first immunofluorescence image of the sample excited by the first selected range and acquiring a second immunofluorescence image of the sample excited by the second selected range and locating the CTCs by locating the CTC identification reagents comprises comparing or overlaying the first immunofluorescence image and the second immunofluorescence image. 
     
     
         21 . The method of  claim 20 , wherein imaging the first immunofluorescence image identifies CK+ cells, the second immunofluorescence image identifies CD45+ cells, wherein comparing or overlaying comprises identifying cells that are CK+ and CD45−. 
     
     
         22 . The method of  claim 20 , wherein locating the CTCs by locating the CTC identification reagents comprises algorithmically analyzing the first immunofluorescence image and the second immunofluorescence image using a computer. 
     
     
         23 . The method of  claim 22 , wherein algorithmically analyzing comprises digitally interrogating the images to measure cell size, cell compartment localization of markers, and/or intensity of marker expression. 
     
     
         24 . The method of  claim 1 , wherein spectral imaging the CTCs comprises spectral imaging luminescence of the CTC characterization reagents, the luminescence emanating from specific binding moieties labeled with quantum dots. 
     
     
         25 . The method of  claim 24 , wherein the specific binding moieties are directly labeled with the quantum dots. 
     
     
         26 . The method of  claim 24 , wherein the specific binding moieties are indirectly labeled with the quantum dots, the luminescence emanating from the quantum dots labeling anti-hapten secondary antibodies, the anti-hapten secondary antibodies being specific to haptens labeling the specific binding moieties. 
     
     
         27 . The method of  claim 24 , wherein the specific binding moieties are nucleic acid probes. 
     
     
         28 . The method of  claim 24 , wherein spectral imaging the CTCs comprises exciting the quantum dots with radiation. 
     
     
         29 . The method of  claim 28 , wherein the radiation is UV or near-UV radiation. 
     
     
         30 . The method of  claim 28 , wherein the radiation has a spectral emission profile with a maximum between 300 and 400 nm. 
     
     
         31 . The method of  claim 24 , wherein spectral imaging the CTCs comprises multispectral imaging. 
     
     
         32 . The method of  claim 24 , wherein spectral imaging the CTCs comprises hyperspectral imaging. 
     
     
         33 . The method of  claim 1 , wherein spectral imaging is guided by the step of locating the CTCs to regions of interest to the exclusion of regions devoid of interest. 
     
     
         34 . The method of  claim 33 , wherein regions of interest comprise CTCs. 
     
     
         35 . The method of  claim 18 , wherein the spectrally filtered visible light does not result in significant quantum dot luminescence. 
     
     
         36 . The method of  claim 1 , wherein imaging the sample comprises multi-spectral imaging immunofluorescence of the CTC identification reagents and spectral imaging the CTCs comprises hyper-spectral imaging the CTC characterization reagents. 
     
     
         37 . The method of  claim 36 , wherein the multi-spectral and hyper-spectral imaging differentiates at least about four CTC identification reagents and/or CTC characterization reagents, at least about five CTC identification reagents and/or CTC characterization reagents, or at least about six CTC identification reagents and/or CTC characterization reagents. 
     
     
         38 . The method of  claim 36 , wherein the multi-spectral imaging differentiates at least about two CTC identification reagents and the hyper-spectral imaging differentiates at least about four CTC characterization reagents. 
     
     
         39 . The method of  claim 1 , wherein retrieving targets comprises contacting the sample with a tris-based buffer having a slightly basic pH and applying heat so that covalent bonds resulting from fixation are broken. 
     
     
         40 . The method of  claim 1 , further comprising contacting the sample with a protease. 
     
     
         41 . The method of  claim 1 , further comprising contacting the sample with a citrate buffer having a slightly acidic pH and applying heat so that covalent bonds resulting from fixation are broken. 
     
     
         42 . The method of  claim 1 , wherein
 retrieving targets comprises contacting the sample with a tris-based buffer having a slightly basic pH and applying heat so that covalent bonds resulting from fixation are broken and contacting the sample with a protease prior to contacting the sample with CTC identification reagents, and   the method further comprises contacting the sample with a citrate buffer having a slightly acidic pH and applying heat so that covalent bonds resulting from fixation are broken and contacting the sample with a protease prior to contacting the sample with CTC characterization reagents.   
     
     
         43 . The method of  claim 1 , wherein contacting the sample with the CTC characterization reagent comprises a reagent directed towards one or more housekeeping molecules in the CTCs, wherein analyzing the sample includes comparing expression of the one or more housekeeping molecules in the CTCs to a control representing the one or more housekeeping molecules expected in a normal prostate sample. 
     
     
         44 . The method of  claim 1 , wherein analyzing the sample comprises detecting one or more other prostate cancer-related molecules in the CTCs and comparing expression of the one or more other prostate cancer related molecules in the CTCs to a control the one or more other prostate cancer-related molecules expected in a normal prostate sample. 
     
     
         45 . The method of  claim 6 , further comprising:
 predicting the likelihood that the prostate cancer will respond to a poly-(ADP) ribose polymerase (PARP) inhibitor, radiotherapy, or hormone blocker;   predicting the likelihood of disease recurrence,   predicting the likelihood of prostate cancer progression;   predicting the likelihood of prostate cancer metastasis;   predicting likelihood survival time; or   combinations thereof.   
     
     
         46 . The method of  claim 6 , further comprising:
 predicting that the prostate cancer will respond to PARP inhibitor when the CTCs have an ERG rearrangement and/or a PTEN deletion;   predicting that the prostate cancer will not respond to radiotherapy when the CTCs have an ERG rearrangement and/or a PTEN deletion;   predicting that the prostate cancer will respond to a hormone blocker when the CTCs have an ERG rearrangement and/or a PTEN deletion;   predicting that the prostate cancer has a higher likelihood of recurring when the CTCs have an ERG rearrangement and/or a PTEN deletion;   predicting that the prostate cancer has a higher likelihood of progressing when the CTCs have an ERG rearrangement and/or a PTEN deletion;   predicting that the prostate cancer is more likely to metastasize when the CTCs have an ERG rearrangement and/or a PTEN deletion;   predicting a survival time of less than 5 years when the CTCs have an ERG rearrangement and/or a PTEN deletion; or   combinations thereof.   
     
     
         47 . A kit for characterizing prostate cancer, comprising:
 one or more nucleic acid probes that can specifically detect an ERG genomic rearrangement;   one or more nucleic acid probes that can specifically detect a PTEN genomic deletion; and   one or more nucleic acid probes that can specifically detect CEN-10;   wherein the nucleic acid probes comprise a quantum dot.   
     
     
         48 . The kit of  claim 47 , further comprising:
 one or more antibodies specific for an EpCAM protein;   one or more antibodies specific for a CD45 protein;   one or more antibodies specific for a CK protein;   one or more antibodies specific for an ERG protein;   one or more antibodies specific for AR;   one or more antibodies specific for a PSMA protein;   one or more microscope slides; or   combinations thereof.   
     
     
         49 . The kit of  claim 47 , further comprising:
 one or more nucleic acid probes or antibodies specific for one or more housekeeping genes or proteins;   one or more nucleic acid probes or antibodies specific for one or more prostate cancer-related genes or proteins; or   combinations thereof.   
     
     
         50 . A method of characterizing a prostate cancer, comprising:
 isolating circulating tumor cells (CTCs) from a subject having prostate cancer using anti-ETS related gene (ERG) antibodies;   spreading the isolated CTCs onto a glass slide to form a homogeneous layer;   contacting the CTCs on the glass slide with one or more nucleic acid probes specific for ERG, PTEN, and CEN-10, wherein each probe comprises one or more quantum dots;   detecting signals from the one or more quantum dots on the one or more nucleic acid probes;   determining whether one or more ERGs is rearranged, whether one or more PTEN genes is deleted, and whether CEN-10 is detected; and   characterizing the prostate cancer based on whether one or more ERGs is rearranged, whether one or more PTEN genes is deleted, and whether CEN-10 is detected.