Methods and compositions related to adenoassociated virus-phage particles

Abstract

Embodiments of the invention are generally directed to compositions and methods of delivering one or more transgene to a target cell, such as a tumor cell, in a site-specific manner to achieve enhanced expression and to constructs and compositions useful in such applications. In certain aspects, expression from a therapeutic nucleic acid may be assessed prior to administration of a treatment or diagnostic procedure to or on a subject.

1 . A method of treating a subject comprising: 
 (a) administering a therapeutic AAVP encoding a reporter to a subject having, suspected of having or at risk of developing a pathologic or disease condition; and    (b) evaluating in situ expression of the therapeutic AAVP in a tissue or cell targeted for treatment by detecting the encoded reporter or reporter activity.    
   
   
       2 . The method of  claim 1 , further comprising administering a cancer treatment to the subject based on expression of a therapeutically sufficient level of a therapeutic gene expressed by the AAVP nucleic acid in the target organ, tissue or cell.  
   
   
       3 . The method of  claim 2 , wherein a second therapeutic AAVP is administered if the expression of the first therapeutic AAVP is not expressed at a therapeutically effective level.  
   
   
       4 . The method of  claim 1 , wherein evaluation of AAVP expression is by non-invasive detection of the reporter or an activity of the reporter.  
   
   
       5 . The method of  claim 1 , wherein the reporter is a therapeutic protein.  
   
   
       6 . The method of  claim 5 , wherein the therapeutic protein is a prodrug converting enzyme.  
   
   
       7 . The method of  claim 4 , wherein the reporter is an enzyme.  
   
   
       8 . The method of  claim 7 , wherein the enzyme is a kinase.  
   
   
       9 . The method of  claim 8 , wherein the kinase is thymidine kinase.  
   
   
       10 . The method of  claim 8 , wherein the kinase modifies a detectably labeled compound.  
   
   
       11 . The method of  claim 10 , wherein the detectable label is detectable by fluorescence, chemiluminescence, surface enhanced raman spectroscopy (SERS), magnetic resonance imaging (MRI), computer tomography (CT), or positron emission tomography (PET) imaging.  
   
   
       12 . The method of  claim 10 , wherein the detectably labeled compound is a nucleoside analog.  
   
   
       13 . The method of  claim 10 , wherein the detectably label compound is fluorodeoxyglucose (FDG); 2′-fluoro-2′deoxy-1beta-D-arabionofuranosyl-5-ethyl-uracil (FEAU); 5 [ 123 I]-2′-fluoro-5-iodo-1β-D-arabinofuranosyl-uracil; 5-[ 124 I]-2′-fluoro-5-iodo-1β-D-arabinofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodo-1β-D-arabinofuranosyl-uracil, 5-[ 18 F]-2′-fluoro-5-fluoro-1-β-D-arabinofuranosyl-uracil; 2-[ 11 I]- and 5-([ 11 C]-methyl)-2′-fluoro-5-methyl-1-β-D-arabinofuranosyl-uracil; 2-[ 11 C]-2′-fluoro-5-ethyl-1-β-D-arabinofuranosyl-uracil; 5-([ 11 C]-ethyl)-2′-fluoro-5-ethyl-1-β-D-arabinofuranosyl-uracil; 5-(2-[ 18 F]-ethyl)-2′-fluoro-5-(2-fluoro-ethyl)-1-β-D-arabinofuranosyl-uracil, 5 [ 123 I]-2′-fluoro-5-iodovinyl-1-β-D-arabinofuranosyl-uracil; 5-[ 124 I]-2′-fluoro-5-iodovinyl-1-β-D-arabinofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodovinyl-1-β-D-arabinofuranosyl-uracil; 5-[ 123 I]-2′-fluoro-5-iodo-1-β-D-ribofuranosyl-uracil; 5-[ 124 I]-2′-fluoro-5-iodo-1-β-D-ribofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodo-1-β-D-ribofuranosyl-uracil; 5 [ 123 I]-2′-fluoro-5-iodovinyl-1-β-D-ribofuranosyl-uracil; 5 [ 124 I]-2′-fluoro-5-iodovinyl-1-β-D-ribofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodovinyl-1-β-D-ribofuranosyl-uracil; or 9-4-[ 18 F]fluoro-3-(hydroxymethyl)butyl]guanine.  
   
   
       14 . The method of  claim 10 , wherein the detectable label comprises a  18 F,  277 Ac,  211 At,  128 Ba,  131 Ba,  7 Be,  204 Bi,  205 Bi,  206 Bi,  76 Br,  77 Br,  82 Br,  109 Cd,  47 Ca,  11 C,  14 C,  36 Cl,  48 Cr,  51 Cr,  62 Cu,  64 Cu,  67 Cu,  165 Dy,  155 Eu,  153 Gd,  66 Ga,  67 Ga,  68 Ga,  72 Ga,  198 Au,  3 H,  166 Ho,  111 In,  113 In,  115 In,  123 I,  125 I,  131 I,  189 Ir,  191 Ir,  192 Ir,  194 Ir,  52 Fe,  55 Fe,  59 Fe,  177 Lu,  15 O,  191 Os,  109 Pd,  32 P,  33 P,  42 K,  226 Ra,  186 Re,  188 Re,  82 Rb,  153 Sm,  46 Sc,  47 Sc,  72 Se,  75 Se,  105 Ag,  22 Na,  24 Na,  89 Sr,  35 S,  38 S,  177 Ta,  96 Tc,  99m Tc,  201 Tl,  202 Tl,  113 Sn,  117m Sn,  121 Sn,  166 Yb,  169 Yb,  175 Yb,  88 Y,  90 Y,  62 Zn, or  65 Zn.  
   
   
       15 . The method of  claim 14 , wherein the detectable label is  131 I,  125 I,  123 I,  111 I,  99m Tc,  90 Y,  186 Re,  188 Re,  32 P,  153 Sm,  67 Ga,  201 Tl,  77 Br, or  18 F label.  
   
   
       16 . The method of  claim 1 , wherein the AAVP comprises a moiety that selectively targets a tissue or cell targeted for treatment.  
   
   
       17 . The method of  claim 16 , wherein the moiety is encoded by a capsid protein of the AAVP.  
   
   
       18 . The method of  claim 17 , wherein the surface protein is recombinant capsid protein.  
   
   
       19 . The method of  claim 18 , wherein the recombinant capsid protein comprises a targeting peptide.  
   
   
       20 . The method of  claim 19 , wherein the targeting peptide is a cyclic peptide.  
   
   
       21 . The method of  claim 19 , wherein the targeting peptide is a linear peptide.  
   
   
       22 . The method of  claim 19 , wherein the targeting peptide selectively binds a cell expressing an integrin on the cell surface.  
   
   
       23 . The method of  claim 20 , wherein the integrin is αvβ3 or αvβ5 integrin.  
   
   
       24 . The method of  claim 22 , wherein the peptide comprises an RGD motif.  
   
   
       25 . The method of  claim 19 , wherein the peptide selectively binds a cell expressing a transferrin receptor.  
   
   
       26 . The method of  claim 25 , wherein the peptide comprises an amino acid sequence comprising CRTIGPSVC.  
   
   
       27 . The method of  claim 1 , wherein the subject is has, is suspected of having, or at risk of developing a hyperproliferative disease.  
   
   
       28 . The method of  claim 27 , wherein the hyperproliferative disease is fibrosarcoma, myosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, gastric cancer, esophageal cancer, rectal cancer, pancreatic cancer, ovarian cancer, prostate cancer, uterine cancer, cancer of the head and neck, skin cancer, brain cancer, squamous cell carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinoma, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, testicular cancer, small cell lung carcinoma, non-small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, retinoblastoma, leukemia, lymphoma, or Kaposi sarcoma  
   
   
       29 . The method of  claim 1 , wherein the reporter gene is operatively coupled to a tissue or cell selective promoter, or a tissue or cell specific promoter.  
   
   
       30 . The method of  claim 1 , wherein evaluating expression comprises administering a label that is selectively metabolized by a cell expressing the AAVP nucleic acid.  
   
   
       31 . The method of  claim 1 , wherein the therapeutic AAVP encodes a second therapeutic gene.  
   
   
       32 . The method of  claim 31 , wherein the second therapeutic gene is tumor suppressor, inhibitory RNA, inhibitory DNA, or prodrug converting enzyme.  
   
   
       33 . A therapeutic AAVP nucleic acid comprising a nucleic acid segment comprising an inhibitory RNA or inhibitory DNA.  
   
   
       34 . The nucleic acid of  claim 33 , wherein the inhibitory RNA is a siRNA, miRNA, or antisense RNA.  
   
   
       35 . A phage particle comprising the AAVP nucleic acid of  claim 33 .  
   
   
       36 . The phage particle of  claim 35 , further comprising a targeting ligand.  
   
   
       37 . A method for modulating the expression of a gene comprising administering an AAVP nucleic acid of  claim 26 .  
   
   
       38 . A method of detecting gene transfer to and expression in a target tissue of a host subject comprising: 
 (a) delivering to the target tissue of the host subject an AAVP vector containing a reporter gene not naturally present in the host subject wherein the reporter gene is selected from the group consisting of wild-type, mutant or genetically engineered herpes simplex virus-thymidine kinase gene, or human thymidine kinase type 2, and wherein the transfer vector is introduced to cells of the target tissue, and the reporter gene is expressed in the cells of the target tissue, thereby generating a reporter gene product (protein) which accumulates only in the cells effectively transfected by the AAVP vector;    (b) administering to the host subject a labeled reporter substrate where cells expressing the reporter gene product of step (a) metabolizes the labeled reporter substrate to produce a labeled reporter metabolite wherein the labeled reporter substrate comprises a radiolabeled nucleoside analogue; and    (c) non-invasively imaging the target tissue or cells containing the labeled metabolite of the reporter substrate after clearance of residual reporter substrate not metabolized by the reporter gene product from said host subject thereby detecting gene transfer to and expression in the target tissue.    
   
   
       39 . The method of  claim 1  further comprising waiting a time-period after step (b) sufficient to allow at least 67% of non-specific label derived from residual reporter substrate not metabolized by the reporter gene product to clear from the subject.  
   
   
       40 . The method of  claim 1  further comprising waiting a time-period after step (b) sufficient to allow at least 80% of non-specific label derived from residual reporter substrate not metabolized by the reporter gene product to clear from the subject.  
   
   
       41 . The method of  claim 1  further comprising waiting a time-period after step (b) sufficient to allow at least 90% of non-specific label derived from residual reporter substrate not metabolized by the reporter gene product to clear from the subject.  
   
   
       42 . The method of  claim 1  wherein the AAVP vector is introduced to the cells of the target tissue by in vitro or in vivo transfection (or transduction).  
   
   
       43 . The method of  claim 1  wherein the reporter substrate is labeled with a radioisotope suitable for imaging by positron emission tomography, gamma camera, or single-photon emission computed tomography.  
   
   
       44 . The method of  claim 1  wherein the reporter substrate and metabolite of the reporter substrate are compounds containing a stable-isotope nuclide selected from the group consisting of  2 H,  13 C,  15 N and  19 F.  
   
   
       45 . The method of  claim 1  wherein the labeled reporter substrate metabolite is imaged by positron emission tomography.  
   
   
       46 . The method of  claim 1  wherein the labeled reporter substrate metabolite is imaged by gamma camera or single-photon emission computed tomography.  
   
   
       47 . The method of  claim 1  wherein the labeled reporter substrate metabolite is imaged by magnetic resonance imaging.  
   
   
       48 . The method of  claim 1  wherein the AAVP vector, incorporates the reporter gene and suitable transcription promoter and enhancer elements, ensuring tissue-specific, transcription factor-specific, or signal transduction-specific transcriptional activation of reporter and therapeutic gene co-expression.  
   
   
       49 . The method of  claim 48 , wherein using an AAVP vector the cells (or a cell) is transfected with the reporter gene and suitable transcription promoter and enhancer elements ex vivo (in vitro) prior to administration of the cells (or a cell) to the host subject.  
   
   
       50 . The method of  claim 38 , wherein the labeled 2′-fluoro-nucleoside analogue is 5-[ 123 I]-2′-fluoro-5-iodo-1β-D-arabinofuranosyl-uracil; 5 [ 124 I]-2′-fluoro-5-iodo-1β-D-arabinofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodo-1β-D-arabinofuranosyl-uracil, 5-[ 18 F]-2′-fluoro-5-fluoro-1-β-D-arabinofuranosyl-uracil; 2-[ 11 I]- and 5-([ 11 C]-methyl)-2′-fluoro-5-methyl-1-β-D-arabinofuranosyl-uracil; 2-[ 11 C]-2′-fluoro-5-ethyl-1-β-D-arabinofuranosyl-uracil; 5-([ 11 C]-ethyl)-2′-fluoro-5-ethyl-1-β-D-arabinofuranosyl-uracil; 5-(2-[ 18 F]-ethyl)-2′-fluoro-5-(2-fluoro-ethyl)-1-β-D-arabinofuranosyl-uracil, 5 [ 123 I]-2′-fluoro-5-iodovinyl-1-β-D-arabinofuranosyl-uracil; 5-[ 124 I]-2′-fluoro-5-iodovinyl-1-β-D-arabinofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodovinyl-1-β-D-arabinofuranosyl-uracil; 5-[ 123 I]-2′-fluoro-5-iodo-1-β-D-ribofuranosyl-uracil; 5-[ 124 I]-2′-fluoro-5-iodo-1-β-D-ribofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodo-1-β-D-ribofuranosyl-uracil; 5-[ 123 I]-2′-fluoro-5-iodovinyl-1-β-D-ribofuranosyl-uracil; 5-[ 124 I]-2′-fluoro-5-iodovinyl-1-β-D-ribofuranosyl-uracil; 5-[ 131 I]-2′-fluoro-5-iodovinyl-1-β-D-ribofuranosyl-uracil; or 9-4-[ 18 F]fluoro-3-(hydroxymethyl)butyl]guanine.