# Patent

## Title
Radiation sensitization agents for prostate cancer

## Abstract

Compositions and methods are provided for sensitizing neoplastic cells to radiotherapy. The invention provides aptamer-inhibitory nucleic acid chimeras that selectively inliibit the expression of radiosensitizing genes in neoplastic cells expressing a cell surface molecule that binds the aptamer.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a 35 U.S.C. §371 U.S. national stage entry of International Application PCT/US2011/044997 (WO 2012/012710) having an International filing date of Jul. 22, 2011 which claims the benefit of the following U.S. Provisional Application No. 61/366,734, filed Jul. 22, 2010, the entire contents of which are incorporated herein by reference.


STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH
This work was supported by the following grant from the National Institutes of Health, Grant No: 5P50CA058236-15. The government has certain rights in the invention.


BACKGROUND OF THE INVENTION
An estimated 1 in 6 men will be diagnosed with prostate cancer (PCa). Although the majority of these men can be successfully treated with surgery or radiation therapy, approximately 20%-40% will biochemically recur within 10 years of treatment. This risk of recurrence is elevated to approximately 50% for men with locally advanced disease, a condition that is primarily managed by radiation therapy. Thus, there is a need for new technologies that improve the therapeutic index of radiation therapy for local disease because these will significantly decrease the morbidity and mortality of PCa.
SUMMARY OF THE INVENTION
As described below, the present invention features aptamer-inhibitory nucleic acid molecules that radiosensitize neoplastic cells expressing tumor antigens that bind the aptamer and methods of using aptamer-inhibitory nucleic acid molecules to radiosensitize neoplastic cells.
In one aspect, the invention generally features a method of sensitizing a neoplastic cell to ionizing radiation, the method involving contacting the neoplastic cell with an effective amount of an aptamer-inhibitory nucleic acid chimera.
In another aspect, the invention generally features a method of inducing cell death or terminal differentiation in a neoplastic cell, the method involving contacting the neoplastic cell with an effective amount of an aptamer-inhibitory nucleic acid chimera, and exposing the neoplastic cell to ionizing radiation.
In another aspect, the invention features a method of reducing the growth, proliferation or survival of a neoplastic cell, the method involving contacting the neoplastic cell with an effective amount of an aptamer-inhibitory nucleic acid chimera, and exposing the neoplastic cell to ionizing radiation.
In yet another aspect, the invention features a method of treating neoplasia in a subject involving administering an aptamer-inhibitory nucleic acid chimera to the subject; and exposing the neoplasia to ionizing radiation, thereby treating neoplasia in the subject.
In yet another aspect, the invention features a method of treating prostate cancer in a subject in need thereof involving administering an aptamer-shRNA chimera to the subject, wherein the aptamer-shRNA chimera specifically binds prostate-specific membrane antigen (PSMA), and wherein the shRNA decreases the expression of ACLY, BRCA2, DNMT1, LDHA, MAD2L2, NBN, NONO, DNAPK, RAD23B, or RAD54L; and exposing the subject to ionizing radiation, thereby treating prostate cancer in the subject.
In yet another aspect, the invention features a method of inhibiting angiogenesis in a neoplasia, the method involving contacting neovascular endothelia cells with an effective amount of an aptamer-inhibitory nucleic acid chimera, and exposing the neovascular endothelia cells to ionizing radiation.
In yet another aspect, the invention generally features an oligonucleotide containing an aptamer covalently linked to an shRNA.
In various embodiments of any of the above aspects or any other aspect of the invention delinated herein, the neoplastic cell is in a subject. In another embodiment the inhibitory nucleic acid is selected from the group consisting of shRNA, siRNA, and ribozyme. In further embodiments the inhibitory nucleic acid is siRNA. In other embodiments the aptamer-inhibitory nucleic acid chimera decreases the expression of a target gene. In another embodiment the target gene encodes a DNA repair protein. In yet another embodiment the target gene is selected from the group consisting of ACLY, BRCA2, DNMT1, LDHA, MAD2L2, NBN, NONO, DNAPK, RAD23B, and RAD54L. In further embodiments decreasing the expression of the target gene sensitizes the neoplastic cell to ionizing radiation. In other embodiments the aptamer-inhibitory nucleic acid chimera specifically binds a cell surface molecule. In another embodiment the cell surface molecule is a tumor antigen. In yet another embodiment the tumor antigen is selected from Muc1, HER2, TGFbeta-receptor, Guanylyl Cyclase C (GC-C), PCSA, or prostate-specific membrane antigen (PSMA). In further embodiments the tumor antigen is prostate-specific membrane antigen (PSMA). In other embodiments the aptamer-inhibitory nucleic acid chimera comprises A10-3. In another embodiment the aptamer-inhibitory nucleic acid chimera comprises modified nucleotides. In further embodiments the modified nucleotides are selected from 2′-fluoro-modified pyrimidines, locked-nucleic acids (LNAs), 2′-O-methyl-modified nucleotides, and 2′-amino-modified nucleotides. In other embodiments the modified nucleotides comprise 2′-fluoro-modified pyrimidines. In another embodiment the method is carried out in vivo. In yet another embodiment the aptamer-inhibitory nucleic acid chimera is selected from any of the aptamer-inhibitory nucleic acid chimeras of Table 4. In further embodiments the neoplastic cell is in a subject diagnosed as having a neoplasia selected from the group consisting of prostate cancer, breast cancer, colon cancer, pancreatic cancer, and lung cancer. In other embodiments the method sensitizes the neoplasia to ionizing radiation. In another embodiment the subject is a mammal. In another embodiment the subject is a human.
Compositions and articles defined by the invention were isolated or otherwise manufactured in connection with the examples provided below. Other features and advantages of the invention will be apparent from the detailed description, and from the claims.
Definitions
By “aptamer” is meant an oligonucleotide that is capable of forming a complex with an intended target substance. The complexation is target-specific in the sense that other materials which may accompany the target do not complex to the aptamer. It is recognized that complexation and affinity are a matter of degree; however, in this context, “target-specific” means that the aptamer binds to target with a much higher degree of affinity than it binds to contaminating materials. The meaning of specificity in this context is thus similar to the meaning of specificity as applied to antibodies, for example.
By “small hairpin RNA” or “shRNA” is meant an oligonucleotide that consists of a stem-loop structure with optional 3′ UU-overhangs. While there may be variation, stems can range from 19 to 31 bp (desirably 25 to 29 bp), and the loops can range from 4 to 30 bp (desirably 4 to 23 bp).
By “aptamer-shRNA chimera” is meant an oligonucleotide that comprises an aptamer covalently linked to an shRNA such that the aptamer retains its ability to bind to its cognate target molecule, and the shRNA is properly processed by the cell to act as an siRNA that inhibits the expression of a target protein.
By “ACLY” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—001096 or NM—198830. An exemplary ACLY sequence is provided below:








(SEQ ID NO: 1) 



   1 agccgatggg ggcggggaaa agtccggctg ggccgggaca aaagccggat cccgggaagc



 


  61 taccggctgc tggggtgctc cggattttgc ggggttcgtc gggcctgtgg aagaagcgcc


 


 121 gcgcacggac ttcggcagag gtagagcagg tctctctgca gccatgtcgg ccaaggcaat


 


 181 ttcagagcag acgggcaaag aactccttta caagttcatc tgtaccacct cagccatcca


 


 241 gaatcggttc aagtatgctc gggtcactcc tgacacagac tgggcccgct tgctgcagga


 


 301 ccacccctgg ctgctcagcc agaacttggt agtcaagcca gaccagctga tcaaacgtcg


 


 361 tggaaaactt ggtctcgttg gggtcaacct cactctggat ggggtcaagt cctggctgaa


 


 421 gccacggctg ggacaggaag ccacagttgg caaggccaca ggcttcctca agaacttggt


 


 481 gatcgagccc ttcgtccccc acagtcaggc tgaggagttc tatgtctgca tctatgccac


 


 541 ccgagaaggg gactacgtcc tgttccacca cgaggggggt gtggacgtgg gtgatgtgga


 


 601 cgccaaggcc cagaagctgc ttgttggcgt ggatgagaaa ctgaatcctg aggacatcaa


 


 661 aaaacacctg ttggtccacg cccctgaaga caagaaagaa attctggcca gttttatctc


 


 721 cggcctcttc aatttctacg aggacttgta cttcacctac ctcgagatca atccccttgt


 


 781 agtgaccaaa gatggagtct atgtccttga cttggcggcc aaggtggacg ccactgccga


 


 841 ctacatctgc aaagtgaagt ggggtgacat cgagttccct ccccccttcg ggcgggaggc


 


 901 atatccagag gaagcctaca ttgcagacct cgatgccaaa agtggggcaa gcctgaagct


 


 961 gaccttgctg aaccccaaag ggaggatctg gaccatggtg gccgggggtg gcgcctctgt


 


1021 cgtgtacagc gataccatct gtgatctagg gggtgtcaac gagctggcaa actatgggga


 


1081 gtactcaggc gcccccagcg agcagcagac ctatgactat gccaagacta tcctctccct


 


1141 catgacccga gagaagcacc cagatggcaa gatcctcatc attggaggca gcatcgcaaa


 


1201 cttcaccaac gtggctgcca cgttcaaggg catcgtgaga gcaattcgag attaccaggg


 


1261 ccccctgaag gagcacgaag tcacaatctt tgtccgaaga ggtggcccca actatcagga


 


1321 gggcttacgg gtgatgggag aagtcgggaa gaccactggg atccccatcc atgtctttgg


 


1381 cacagagact cacatgacgg ccattgtggg catggccctg ggccaccggc ccatccccaa


 


1441 ccagccaccc acagcggccc acactgcaaa cttcctcctc aacgccagcg ggagcacatc


 


1501 gacgccagcc cccagcagga cagcatcttt ttctgagtcc agggccgatg aggtggcgcc


 


1561 tgcaaagaag gccaagcctg ccatgccaca agattcagtc ccaagtccaa gatccctgca


 


1621 aggaaagagc accaccctct tcagccgcca caccaaggcc attgtgtggg gcatgcagac


 


1681 ccgggccgtg caaggcatgc tggactttga ctatgtctgc tcccgagacg agccctcagt


 


1741 ggctgccatg gtctaccctt tcactgggga ccacaagcag aagttttact gggggcacaa


 


1801 agagatcctg atccctgtct tcaagaacat ggctgatgcc atgaggaagc atccggaggt


 


1861 agatgtgctc atcaactttg cctctctccg ctctgcctat gacagcacca tggagaccat


 


1921 gaactatgcc cagatccgga ccatcgccat catagctgaa ggcatccctg aggccctcac


 


1981 gagaaagctg atcaagaagg cggaccagaa gggagtgacc atcatcggac ctgccactgt


 


2041 tggaggcatc aagcctgggt gctttaagat tggcaacaca ggtgggatgc tggacaacat


 


2101 cctggcctcc aaactgtacc gcccaggcag cgtggcctat gtctcacgtt ccggaggcat


 


2161 gtccaacgag ctcaacaata tcatctctcg gaccacggat ggcgtctatg agggcgtggc


 


2221 cattggtggg gacaggtacc cgggctccac attcatggat catgtgttac gctatcagga


 


2281 cactccagga gtcaaaatga ttgtggttct tggagagatt gggggcactg aggaatataa


 


2341 gatttgccgg ggcatcaagg agggccgcct cactaagccc atcgtctgct ggtgcatcgg


 


2401 gacgtgtgcc accatgttct cctctgaggt ccagtttggc catgctggag cttgtgccaa


 


2461 ccaggcttct gaaactgcag tagccaagaa ccaggctttg aaggaagcag gagtgtttgt


 


2521 gccccggagc tttgatgagc ttggagagat catccagtct gtatacgaag atctcgtggc


 


2581 caatggagtc attgtacctg cccaggaggt gccgccccca accgtgccca tggactactc


 


2641 ctgggccagg gagcttggtt tgatccgcaa acctgcctcg ttcatgacca gcatctgcga


 


2701 tgagcgagga caggagctca tctacgcggg catgcccatc actgaggtct tcaaggaaga


 


2761 gatgggcatt ggcggggtcc tcggcctcct ctggttccag aaaaggttgc ctaagtactc


 


2821 ttgccagttc attgagatgt gtctgatggt gacagctgat cacgggccag ccgtctctgg


 


2881 agcccacaac accatcattt gtgcgcgagc tgggaaagac ctggtctcca gcctcacctc


 


2941 ggggctgctc accatcgggg atcggtttgg gggtgccttg gatgcagcag ccaagatgtt


 


3001 cagtaaagcc tttgacagtg gcattatccc catggagttt gtgaacaaga tgaagaagga


 


3061 agggaagctg atcatgggca ttggtcaccg agtgaagtcg ataaacaacc cagacatgcg


 


3121 agtgcagatc ctcaaagatt acgtcaggca gcacttccct gccactcctc tgctcgatta


 


3181 tgcactggaa gtagagaaga ttaccacctc gaagaagcca aatcttatcc tgaatgtaga


 


3241 tggtctcatc ggagtcgcat ttgtagacat gcttagaaac tgtgggtcct ttactcggga


 


3301 ggaagctgat gaatatattg acattggagc cctcaatggc atctttgtgc tgggaaggag


 


3361 tatggggttc attggacact atcttgatca gaagaggctg aagcaggggc tgtatcgtca


 


3421 tccgtgggat gatatttcat atgttcttcc ggaacacatg agcatgtaac agagccagga


 


3481 accctactgc agtaaactga agacaagatc tcttccccca agaaaaagtg tacagacagc


 


3541 tggcagtgga gcctgcttta tttagcaggg gcctggaatg taaacagcca ctggggtaca


 


---- ggcaccgaag accaacatcc acaggctaac accccttcag tccacacaaa gaagcttcat


 


3661 atttttttta taagcataga aataaaaacc aagccaatat ttgtgacttt gctctgctac


 


3721 ctgctgtatt tattatatgg aagcatctaa gtactgtcag gatggggtct tcctcattgt


 


3781 agggcgttag gatgttgctt tctttttcca ttagttaaac atttttttct cctttggagg


 


3841 aagggaatga aacatttatg gcctcaagat actatacatt taaagcaccc caatgtctct


 


3901 cttttttttt ttttacttcc ctttcttctt ccttatataa catgaagaac attgtattaa


 


3961 tctgattttt aaagatcttt ttgtatgtta cgtgttaagg gcttgtttgg tatcccactg


 


4021 aaatgttctg tgttgcagac cagagtctgt ttatgtcagg gggatggggc cattgcatcc


 


4081 ttagccattg tcacaaaata tgtggagtag taacttaata tgtaaagttg taacatacat


 


4141 acatttaaaa tggaaatgca gaaagctgtg aaatgtcttg tgtcttatgt tctctgtatt


 


4201 tatgcagctg atttgtctgt ctgtaactga agtgtgggtc caaggactcc taactacttt


 


4261 gcatctgtaa tccacaaaga ttctgggcag ctgccacctc agtctcttct ctgtattatc


 


4321 atagtctggt ttaaataaac tatatagtaa caaaaaaaaa






By “BRCA2” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—000059. An exemplary BRCA2 sequence is provided below:








(SEQ ID NO: 2)



    1 gtggcgcgag cttctgaaac taggcggcag aggcggagcc gctgtggcac tgctgcgcct



 


   61 ctgctgcgcc tcgggtgtct tttgcggcgg tgggtcgccg ccgggagaag cgtgagggga


 


  121 cagatttgtg accggcgcgg tttttgtcag cttactccgg ccaaaaaaga actgcacctc


 


  181 tggagcggac ttatttacca agcattggag gaatatcgta ggtaaaaatg cctattggat


 


  241 ccaaagagag gccaacattt tttgaaattt ttaagacacg ctgcaacaaa gcagatttag


 


  301 gaccaataag tcttaattgg tctgaagaac tttcttcaga agctccaccc tataattctg


 


  361 aacctgcaga agaatctgaa cataaaaaca acaattacga accaaaccta tttaaaactc


 


  421 cacaaaggaa accatcttat aatcagctgg cttcaactcc aataatattc aaagagcaag


 


  481 ggctgactct gccgctgtac caatctcctg taaaagaatt agataaattc aaattagact


 


  541 taggaaggaa tgttcccaat agtagacata aaagtcttcg cacagtgaaa actaaaatgg


 


  601 atcaagcaga tgatgtttcc tgtccacttc taaattcttg tcttagtgaa agtcctgttg


 


  661 ttctacaatg tacacatgta acaccacaaa gagataagtc agtggtatgt gggagtttgt


 


  721 ttcatacacc aaagtttgtg aagggtcgtc agacaccaaa acatatttct gaaagtctag


 


  781 gagctgaggt ggatcctgat atgtcttggt caagttcttt agctacacca cccaccctta


 


  841 gttctactgt gctcatagtc agaaatgaag aagcatctga aactgtattt cctcatgata


 


  901 ctactgctaa tgtgaaaagc tatttttcca atcatgatga aagtctgaag aaaaatgata


 


  961 gatttatcgc ttctgtgaca gacagtgaaa acacaaatca aagagaagct gcaagtcatg


 


 1021 gatttggaaa aacatcaggg aattcattta aagtaaatag ctgcaaagac cacattggaa


 


 1081 agtcaatgcc aaatgtccta gaagatgaag tatatgaaac agttgtagat acctctgaag


 


 1141 aagatagttt ttcattatgt ttttctaaat gtagaacaaa aaatctacaa aaagtaagaa


 


 1201 ctagcaagac taggaaaaaa attttccatg aagcaaacgc tgatgaatgt gaaaaatcta


 


 1261 aaaaccaagt gaaagaaaaa tactcatttg tatctgaagt ggaaccaaat gatactgatc


 


 1321 cattagattc aaatgtagca aatcagaagc cctttgagag tggaagtgac aaaatctcca


 


 1381 aggaagttgt accgtctttg gcctgtgaat ggtctcaact aaccctttca ggtctaaatg


 


 1441 gagcccagat ggagaaaata cccctattgc atatttcttc atgtgaccaa aatatttcag


 


 1501 aaaaagacct attagacaca gagaacaaaa gaaagaaaga ttttcttact tcagagaatt


 


 1561 ctttgccacg tatttctagc ctaccaaaat cagagaagcc attaaatgag gaaacagtgg


 


 1621 taaataagag agatgaagag cagcatcttg aatctcatac agactgcatt cttgcagtaa


 


 1681 agcaggcaat atctggaact tctccagtgg cttcttcatt tcagggtatc aaaaagtcta


 


 1741 tattcagaat aagagaatca cctaaagaga ctttcaatgc aagtttttca ggtcatatga


 


 1801 ctgatccaaa ctttaaaaaa gaaactgaag cctctgaaag tggactggaa atacatactg


 


 1861 tttgctcaca gaaggaggac tccttatgtc caaatttaat tgataatgga agctggccag


 


 1921 ccaccaccac acagaattct gtagctttga agaatgcagg tttaatatcc actttgaaaa


 


 1981 agaaaacaaa taagtttatt tatgctatac atgatgaaac atcttataaa ggaaaaaaaa


 


 2041 taccgaaaga ccaaaaatca gaactaatta actgttcagc ccagtttgaa gcaaatgctt


 


 2101 ttgaagcacc acttacattt gcaaatgctg attcaggttt attgcattct tctgtgaaaa


 


 2161 gaagctgttc acagaatgat tctgaagaac caactttgtc cttaactagc tcttttggga


 


 2221 caattctgag gaaatgttct agaaatgaaa catgttctaa taatacagta atctctcagg


 


 2281 atcttgatta taaagaagca aaatgtaata aggaaaaact acagttattt attaccccag


 


 2341 aagctgattc tctgtcatgc ctgcaggaag gacagtgtga aaatgatcca aaaagcaaaa


 


 2401 aagtttcaga tataaaagaa gaggtcttgg ctgcagcatg tcacccagta caacattcaa


 


 2461 aagtggaata cagtgatact gactttcaat cccagaaaag tcttttatat gatcatgaaa


 


 2521 atgccagcac tcttatttta actcctactt ccaaggatgt tctgtcaaac ctagtcatga


 


 2581 tttctagagg caaagaatca tacaaaatgt cagacaagct caaaggtaac aattatgaat


 


 2641 ctgatgttga attaaccaaa aatattccca tggaaaagaa tcaagatgta tgtgctttaa


 


 2701 atgaaaatta taaaaacgtt gagctgttgc cacctgaaaa atacatgaga gtagcatcac


 


 2761 cttcaagaaa ggtacaattc aaccaaaaca caaatctaag agtaatccaa aaaaatcaag


 


 2821 aagaaactac ttcaatttca aaaataactg tcaatccaga ctctgaagaa cttttctcag


 


 2881 acaatgagaa taattttgtc ttccaagtag ctaatgaaag gaataatctt gctttaggaa


 


 2941 atactaagga acttcatgaa acagacttga cttgtgtaaa cgaacccatt ttcaagaact


 


 3001 ctaccatggt tttatatgga gacacaggtg ataaacaagc aacccaagtg tcaattaaaa


 


 3061 aagatttggt ttatgttctt gcagaggaga acaaaaatag tgtaaagcag catataaaaa


 


 3121 tgactctagg tcaagattta aaatcggaca tctccttgaa tatagataaa ataccagaaa


 


 3181 aaaataatga ttacatgaac aaatgggcag gactcttagg tccaatttca aatcacagtt


 


 3241 ttggaggtag cttcagaaca gcttcaaata aggaaatcaa gctctctgaa cataacatta


 


 3301 agaagagcaa aatgttcttc aaagatattg aagaacaata tcctactagt ttagcttgtg


 


 3361 ttgaaattgt aaataccttg gcattagata atcaaaagaa actgagcaag cctcagtcaa


 


 3421 ttaatactgt atctgcacat ttacagagta gtgtagttgt ttctgattgt aaaaatagtc


 


 3481 atataacccc tcagatgtta ttttccaagc aggattttaa ttcaaaccat aatttaacac


 


 3541 ctagccaaaa ggcagaaatt acagaacttt ctactatatt agaagaatca ggaagtcagt


 


 3601 ttgaatttac tcagtttaga aaaccaagct acatattgca gaagagtaca tttgaagtgc


 


 3661 ctgaaaacca gatgactatc ttaaagacca cttctgagga atgcagagat gctgatcttc


 


 3721 atgtcataat gaatgcccca tcgattggtc aggtagacag cagcaagcaa tttgaaggta


 


 3781 cagttgaaat taaacggaag tttgctggcc tgttgaaaaa tgactgtaac aaaagtgctt


 


 3841 ctggttattt aacagatgaa aatgaagtgg ggtttagggg cttttattct gctcatggca


 


 3901 caaaactgaa tgtttctact gaagctctgc aaaaagctgt gaaactgttt agtgatattg


 


 3961 agaatattag tgaggaaact tctgcagagg tacatccaat aagtttatct tcaagtaaat


 


 4021 gtcatgattc tgttgtttca atgtttaaga tagaaaatca taatgataaa actgtaagtg


 


 4081 aaaaaaataa taaatgccaa ctgatattac aaaataatat tgaaatgact actggcactt


 


 4141 ttgttgaaga aattactgaa aattacaaga gaaatactga aaatgaagat aacaaatata


 


 4201 ctgctgccag tagaaattct cataacttag aatttgatgg cagtgattca agtaaaaatg


 


 4261 atactgtttg tattcataaa gatgaaacgg acttgctatt tactgatcag cacaacatat


 


 4321 gtcttaaatt atctggccag tttatgaagg agggaaacac tcagattaaa gaagatttgt


 


 4381 cagatttaac ttttttggaa gttgcgaaag ctcaagaagc atgtcatggt aatacttcaa


 


 4441 ataaagaaca gttaactgct actaaaacgg agcaaaatat aaaagatttt gagacttctg


 


 4501 atacattttt tcagactgca agtgggaaaa atattagtgt cgccaaagag tcatttaata


 


 4561 aaattgtaaa tttctttgat cagaaaccag aagaattgca taacttttcc ttaaattctg


 


 4621 aattacattc tgacataaga aagaacaaaa tagaaattct aagttatgag gaaacagaca


 


 4681 tagttaaaca caaaatactg aaagaaagtg tcccagttgg tactggaaat caactagtga


 


 4741 ccttccaggg acaacccgaa cgtgatgaaa agatcaaaga acctactcta ttgggttttc


 


 4801 atacagctag cgggaaaaaa gttaaaattg caaaggaatc tttggacaaa gtgaaaaacc


 


 4861 tttttgatga aaaagagcaa ggtactagtg aaatcaccag ttttagccat caatgggcaa


 


 4921 agaccctaaa gtacagagag gcctgtaaag accttgaatt agcatgtgag accattgaga


 


 4981 tcacagctgc cccaaagtgt aaagaaatgc agaattctct caataatgat aaaaaccttg


 


 5041 tttctattga gactgtggtg ccacctaagc tcttaagtga taatttatgt agacaaactg


 


 5101 aaaatctcaa aacatcaaaa agtatctttt tgaaagttaa agtacatgaa aatgtagaaa


 


 5161 aagaaacagc aaaaagtcct gcaacttgtt acacaaatca gtccccttat tcagtcattg


 


 5221 aaaattcagc cttagctttt tacacaagtt gtagtagaaa aacttctgtg agtcagactt


 


 5281 cattacttga agcaaaaaaa tggcttagag aaggaatatt tgatggtcaa ccagaaagaa


 


 5341 taaatactgc agattatgta ggaaattatt tgtatgaaaa taattcaaac agtactatag


 


 5401 ctgaaaatga caaaaatcat ctctccgaaa aacaagatac ttatttaagt aacagtagca


 


 5461 tgtctaacag ctattcctac cattctgatg aggtatataa tgattcagga tatctctcaa


 


 5521 aaaataaact tgattctggt attgagccag tattgaagaa tgttgaagat caaaaaaaca


 


 5581 ctagtttttc caaagtaata tccaatgtaa aagatgcaaa tgcataccca caaactgtaa


 


 5641 atgaagatat ttgcgttgag gaacttgtga ctagctcttc accctgcaaa aataaaaatg


 


 5701 cagccattaa attgtccata tctaatagta ataattttga ggtagggcca cctgcattta


 


 5761 ggatagccag tggtaaaatc gtttgtgttt cacatgaaac aattaaaaaa gtgaaagaca


 


 5821 tatttacaga cagtttcagt aaagtaatta aggaaaacaa cgagaataaa tcaaaaattt


 


 5881 gccaaacgaa aattatggca ggttgttacg aggcattgga tgattcagag gatattcttc


 


 5941 ataactctct agataatgat gaatgtagca cgcattcaca taaggttttt gctgacattc


 


 6001 agagtgaaga aattttacaa cataaccaaa atatgtctgg attggagaaa gtttctaaaa


 


 6061 tatcaccttg tgatgttagt ttggaaactt cagatatatg taaatgtagt atagggaagc


 


 6121 ttcataagtc agtctcatct gcaaatactt gtgggatttt tagcacagca agtggaaaat


 


 ---- ctgtccaggt atcagatgct tcattacaaa acgcaagaca agtgttttct gaaatagaag


 


 6241 atagtaccaa gcaagtcttt tccaaagtat tgtttaaaag taacgaacat tcagaccagc


 


 6301 tcacaagaga agaaaatact gctatacgta ctccagaaca tttaatatcc caaaaaggct


 


 6361 tttcatataa tgtggtaaat tcatctgctt tctctggatt tagtacagca agtggaaagc


 


 6421 aagtttccat tttagaaagt tccttacaca aagttaaggg agtgttagag gaatttgatt


 


 6481 taatcagaac tgagcatagt cttcactatt cacctacgtc tagacaaaat gtatcaaaaa


 


 6541 tacttcctcg tgttgataag agaaacccag agcactgtgt aaactcagaa atggaaaaaa


 


 6601 cctgcagtaa agaatttaaa ttatcaaata acttaaatgt tgaaggtggt tcttcagaaa


 


 6661 ataatcactc tattaaagtt tctccatatc tctctcaatt tcaacaagac aaacaacagt


 


 6721 tggtattagg aaccaaagtg tcacttgttg agaacattca tgttttggga aaagaacagg


 


 6781 cttcacctaa aaacgtaaaa atggaaattg gtaaaactga aactttttct gatgttcctg


 


 6841 tgaaaacaaa tatagaagtt tgttctactt actccaaaga ttcagaaaac tactttgaaa


 


 6901 cagaagcagt agaaattgct aaagctttta tggaagatga tgaactgaca gattctaaac


 


 6961 tgccaagtca tgccacacat tctcttttta catgtcccga aaatgaggaa atggttttgt


 


 7021 caaattcaag aattggaaaa agaagaggag agccccttat cttagtggga gaaccctcaa


 


 7081 tcaaaagaaa cttattaaat gaatttgaca ggataataga aaatcaagaa aaatccttaa


 


 7141 aggcttcaaa aagcactcca gatggcacaa taaaagatcg aagattgttt atgcatcatg


 


 7201 tttctttaga gccgattacc tgtgtaccct ttcgcacaac taaggaacgt caagagatac


 


 7261 agaatccaaa ttttaccgca cctggtcaag aatttctgtc taaatctcat ttgtatgaac


 


 7321 atctgacttt ggaaaaatct tcaagcaatt tagcagtttc aggacatcca ttttatcaag


 


 7381 tttctgctac aagaaatgaa aaaatgagac acttgattac tacaggcaga ccaaccaaag


 


 7441 tctttgttcc accttttaaa actaaatcac attttcacag agttgaacag tgtgttagga


 


 7501 atattaactt ggaggaaaac agacaaaagc aaaacattga tggacatggc tctgatgata


 


 7561 gtaaaaataa gattaatgac aatgagattc atcagtttaa caaaaacaac tccaatcaag


 


 7621 cagcagctgt aactttcaca aagtgtgaag aagaaccttt agatttaatt acaagtcttc


 


 7681 agaatgccag agatatacag gatatgcgaa ttaagaagaa acaaaggcaa cgcgtctttc


 


 7741 cacagccagg cagtctgtat cttgcaaaaa catccactct gcctcgaatc tctctgaaag


 


 7801 cagcagtagg aggccaagtt ccctctgcgt gttctcataa acagctgtat acgtatggcg


 


 7861 tttctaaaca ttgcataaaa attaacagca aaaatgcaga gtcttttcag tttcacactg


 


 7921 aagattattt tggtaaggaa agtttatgga ctggaaaagg aatacagttg gctgatggtg


 


 7981 gatggctcat accctccaat gatggaaagg ctggaaaaga agaattttat agggctctgt


 


 8041 gtgacactcc aggtgtggat ccaaagctta tttctagaat ttgggtttat aatcactata


 


 8101 gatggatcat atggaaactg gcagctatgg aatgtgcctt tcctaaggaa tttgctaata


 


 8161 gatgcctaag cccagaaagg gtgcttcttc aactaaaata cagatatgat acggaaattg


 


 8221 atagaagcag aagatcggct ataaaaaaga taatggaaag ggatgacaca gctgcaaaaa


 


 8281 cacttgttct ctgtgtttct gacataattt cattgagcgc aaatatatct gaaacttcta


 


 8341 gcaataaaac tagtagtgca gatacccaaa aagtttccat tattgaactt acagatgggt


 


 8401 ggtatgctgt taaggcccag ttagatcctc ccctcttagc tgtcttaaag aatggcagac


 


 8461 tgacagttgg tcagaagatt attcttcatg gagcagaact ggtgggctct cctgatgcct


 


 8521 gtacacctct tgaagcccca gaatctctta tgttaaagat ttctgctaac agtactcggc


 


 8581 ctgctcgctg gtataccaaa cttggattct ttcctgaccc tagacctttt cctctgccct


 


 8641 tatcatcgct tttcagtgat ggaggaaatg ttggttgtgt tgatgtaatt attcaaagag


 


 8701 cataccctat acagtggatg gagaagacat catctggatt atacatattt cgcaatgaaa


 


 8761 gagaggaaga aaaggaagca gcaaaatatg tggaggccca acaaaagaga ctagaagcct


 


 8821 tattcactaa aattcaggag gaatttgaag aacatgaaga aaacacaaca aaaccatatt


 


 8881 taccatcacg tgcactaaca agacagcaag ttcgtgcttt gcaagatggt gcagagcttt


 


 8941 atgaagcagt gaagaatgca gcagacccag cttaccttga gggttatttc agttaagagc


 


 9001 agttaagagc cttgaataat cacaggcaaa tgttgaatga taagaaacaa gctcagatcc


 


 9061 agttggaaat taggaaggcc atggaatctg ctgaacaaaa ggaacaaggt ttatcaaggg


 


 9121 atgtcacaac cgtgtggaag ttgcgtattg taagctattc aaaaaaagaa aaagattcag


 


 9181 ttatactgag tatttggcgt ccatcatcag atttatattc tctgttaaca gaaggaaaga


 


 9241 gatacagaat ttatcatctt gcaacttcaa aatctaaaag taaatctgaa agagctaaca


 


 9301 tacagttagc agcgacaaaa aaaactcagt atcaacaact accggtttca gatgaaattt


 


 9361 tatttcagat ttaccagcca cgggagcccc ttcacttcag caaattttta gatccagact


 


 9421 ttcagccatc ttgttctgag gtggacctaa taggatttgt cgtttctgtt gtgaaaaaaa


 


 9481 caggacttgc ccctttcgtc tatttgtcag acgaatgtta caatttactg gcaataaagt


 


 9541 tttggataga ccttaatgag gacattatta agcctcatat gttaattgct gcaagcaacc


 


 9601 tccagtggcg accagaatcc aaatcaggcc ttcgtgcttt atttgctgga gatttttctg


 


 9661 tgttttctgc tagtccaaaa gagggccact ttcaagagac attcaacaaa atgaaaaata


 


 9721 ctgttgagaa tattgacata ctttgcaatg aagcagaaaa caagcttatg catatactgc


 


 9781 atgcaaatga tcccaagtgg tccaccccaa ctaaagactg tacttcaggg ccgtacactg


 


 ---- ctcaaatcat tcctggtaca ggaaacaagc ttctgatgtc ttctcctaat tgtgagatat


 


 9901 attatcaaag tcctttatca ctttgtatgg ccaaaaggaa gtctgtttcc acacctgtct


 


 9961 cagcccagat gacttcaaag tcttgtaaag gggagaaaga gattgatgac caaaagaact


 


10021 gcaaaaagag aagagccttg gatttcttga gtagactgcc tttacctcca cctgttagtc


 


10081 ccatttgtac atttgtttct ccggctgcac agaaggcatt tcagccacca aggagttgtg


 


10141 gcaccaaata cgaaacaccc ataaagaaaa aagaactgaa ttctcctcag atgactccat


 


10201 ttaaaaaatt caatgaaatt tctcttttgg aaagtaattc aatagctgac gaagaacttg


 


10261 cattgataaa tacccaagct cttttgtctg gttcaacagg agaaaaacaa tttatatctg


 


10321 tcagtgaatc cactaggact gctcccacca gttcagaaga ttatctcaga ctgaaacgac


 


10381 gttgtactac atctctgatc aaagaacagg agagttccca ggccagtacg gaagaatgtg


 


10441 agaaaaataa gcaggacaca attacaacta aaaaatatat ctaagcattt gcaaaggcga


 


10501 caataaatta ttgacgctta acctttccag tttataagac tggaatataa tttcaaacca


 


10561 cacattagta cttatgttgc acaatgagaa aagaaattag tttcaaattt acctcagcgt


 


10621 ttgtgtatcg ggcaaaaatc gttttgcccg attccgtatt ggtatacttt tgcttcagtt


 


10681 gcatatctta aaactaaatg taatttatta actaatcaag aaaaacatct ttggctgagc


 


10741 tcggtggctc atgcctgtaa tcccaacact ttgagaagct gaggtgggag gagtgcttga


 


10801 ggccaggagt tcaagaccag cctgggcaac atagggagac ccccatcttt acaaagaaaa


 


10861 aaaaaagggg aaaagaaaat cttttaaatc tttggatttg atcactacaa gtattatttt


 


10921 acaagtgaaa taaacatacc attttctttt agattgtgtc attaaatgga atgaggtctc


 


10981 ttagtacagt tattttgatg cagataattc cttttagttt agctactatt ttaggggatt


 


11041 ttttttagag gtaactcact atgaaatagt tctccttaat gcaaatatgt tggttctgct


 


11101 atagttccat cctgttcaaa agtcaggatg aatatgaaga gtggtgtttc cttttgagca


 


11161 attcttcatc cttaagtcag catgattata agaaaaatag aaccctcagt gtaactctaa


 


11221 ttccttttta ctattccagt gtgatctctg aaattaaatt acttcaacta aaaattcaaa


 


11281 tactttaaat cagaagattt catagttaat ttattttttt tttcaacaaa atggtcatcc


 


11341 aaactcaaac ttgagaaaat atcttgcttt caaattggca ctgatt






By “DNMT1” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—001130823 NM—001379. An exemplary DNMT1 sequence is provided below:










(SEQ ID NO: 3)



   1
ggctccgttc catccttctg cacagggtat cgcctctctc cgtttggtac atcccctcct



 


  61
cccccacgcc cggactgggg tggtagacgc cgcctccgct catcgcccct ccccatcggt


 


 121
ttccgcgcga aaagccgggg cgcctgcgct gccgccgccg cgtctgctga agcctccgag


 


 181
atgccggcgc gtaccgcccc agcccgggtg cccacactgg ccgtcccggc catctcgctg


 


 241
cccgacgatg tccgcaggcg gctcaaagat ttggaaagag acagcttaac agaaaaggaa


 


 301
tgtgtgaagg agaaattgaa tctcttgcac gaatttctgc aaacagaaat aaagaatcag


 


 361
ttatgtgact tggaaaccaa attacgtaaa gaagaattat ccgaggaggg ctacctggct


 


 421
aaagtcaaat cccttttaaa taaagatttg tccttggaga acggtgctca tgcttacaac


 


 481
cgggaagtga atggacgtct agaaaacggg aaccaagcaa gaagtgaagc ccgtagagtg


 


 541
ggaatggcag atgccaacag cccccccaaa cccctttcca aacctcgcac gcccaggagg


 


 601
agcaagtccg atggagaggc taagcgttca agagaccctc ctgcctcagc ctcccaagta


 


 661
actgggatta gagctgaacc ttcacctagc cccaggatta caaggaaaag caccaggcaa


 


 721
accaccatca catctcattt tgcaaagggc cctgccaaac ggaaacctca ggaagagtct


 


 781
gaaagagcca aatcggatga gtccatcaag gaagaagaca aagaccagga tgagaagaga


 


 841
cgtagagtta catccagaga acgagttgct agaccgcttc ctgcagaaga acctgaaaga


 


 901
gcaaaatcag gaacgcgcac tgaaaaggaa gaagaaagag atgaaaaaga agaaaagaga


 


 961
ctccgaagtc aaaccaaaga accaacaccc aaacagaaac tgaaggagga gccggacaga


 


1021
gaagccaggg caggcgtgca ggctgacgag gacgaagatg gagacgagaa agatgagaag


 


1081
aagcacagaa gtcaacccaa agatctagct gccaaacgga ggcccgaaga aaaagaacct


 


1141
gaaaaagtaa atccacagat ttctgatgaa aaagacgagg atgaaaagga ggagaagaga


 


1201
cgcaaaacga cccccaaaga accaacggag aaaaaaatgg ctcgcgccaa aacagtcatg


 


1261
aactccaaga cccaccctcc caagtgcatt cagtgcgggc agtacctgga cgaccctgac


 


1321
ctcaaatatg ggcagcaccc accagacgcg gtggatgagc cacagatgct gacaaatgag


 


1381
aagctgtcca tctttgatgc caacgagtct ggctttgaga gttatgaggc gcttccccag


 


1441
cacaaactga cctgcttcag tgtgtactgt aagcacggtc acctgtgtcc catcgacacc


 


1501
ggcctcatcg agaagaatat cgaactcttc ttttctggtt cagcaaaacc aatctatgat


 


1561
gatgacccat ctcttgaagg tggtgttaat ggcaaaaatc ttggccccat aaatgaatgg


 


1621
tggatcactg gctttgatgg aggtgaaaag gccctcatcg gcttcagcac ctcatttgcc


 


1681
gaatacattc tgatggatcc cagtcccgag tatgcgccca tatttgggct gatgcaggag


 


1741
aagatctaca tcagcaagat tgtggtggag ttcctgcaga gcaattccga ctcgacctat


 


1801
gaggacctga tcaacaagat cgagaccacg gttcctcctt ctggcctcaa cttgaaccgc


 


1861
ttcacagagg actccctcct gcgacacgcg cagtttgtgg tggagcaggt ggagagttat


 


1921
gacgaggccg gggacagtga tgagcagccc atcttcctga caccctgcat gcgggacctg


 


1981
atcaagctgg ctggggtcac gctgggacag aggcgagccc aggcgaggcg gcagaccatc


 


2041
aggcattcta ccagggagaa ggacagggga cccacgaaag ccaccaccac caagctggtc


 


2101
taccagatct tcgatacttt cttcgcagag caaattgaaa aggatgacag agaagacaag


 


2161
gagaacgcct ttaagcgccg gcgatgtggc gttggtgatg tgtgtcagca gcctgagtgt


 


2221
gggaaatgta aagcctgcaa ggacatggtt aaatttggtg gcagtggacg gagcaagcag


 


2281
gcttgccaag agcggaggtg tcccaatatg gccatgaagg aggcagatga cgatgaggaa


 


2341
gtcgatgata acatcccaga gatgccgtca cccaaaaaaa tgcaccaggg gaagaagaag


 


2401
aaacagaaca agaatcgcat ctcttgggtc ggagaagccg tcaagactga tgggaagaag


 


2461
agttactata agaaggtgtg cattgatgcg gaaaccctgg aagtggggga ctgtgtctct


 


2521
gttattccag atgattcctc aaaaccgctg tatctagcaa gggtcacggc gctgtgggag


 


2581
gacagcagca acgggcagat gtttcacgcc cactggttct gcgctgggac agacacagtc


 


2641
ctcggggcca cgtcggaccc tctggagctg ttcttggtgg atgaatgtga ggacatgcag


 


2701
ctttcatata tccacagcaa agtgaaagtc atctacaaag ccccctccga aaactgggcc


 


2761
atggagggag gcatggatcc cgagtccctg ctggaggggg acgacgggaa gacctacttc


 


2821
taccagctgt ggtatgatca agactacgcg agattcgagt cccctccaaa aacccagcca


 


2881
acagaggaca acaagttcaa attctgtgtg agctgtgccc gtctggctga gatgaggcaa


 


2941
aaagaaatcc ccagggtcct ggagcagctc gaggacctgg atagccgggt cctctactac


 


3001
tcagccacca agaacggcat cctgtaccga gttggtgatg gtgtgtacct gccccctgag


 


3061
gccttcacgt tcaacatcaa gctgtccagt cccgtgaaac gcccacggaa ggagcccgtg


 


3121
gatgaggacc tgtacccaga gcactaccgg aaatactccg actacatcaa aggcagcaac


 


3181
ctggatgccc ctgagcccta ccgaattggc cggatcaaag agatcttctg tcccaagaag


 


3241
agcaacggca ggcccaatga gactgacatc aaaatccggg tcaacaagtt ctacaggcct


 


3301
gagaacaccc acaagtccac tccagcgagc taccacgcag acatcaacct gctctactgg


 


3361
agcgacgagg aggccgtggt ggacttcaag gctgtgcagg gccgctgcac cgtggagtat


 


3421
ggggaggacc tgcccgagtg cgtccaggtg tactccatgg gcggccccaa ccgcttctac


 


3481
ttcctcgagg cctataatgc aaagagcaaa agctttgaag atcctcccaa ccatgcccgt


 


3541
agccctggaa acaaagggaa gggcaaggga aaagggaagg gcaagcccaa gtcccaagcc


 


3601
tgtgagccga gcgagccaga gatagagatc aagctgccca agctgcggac cctggatgtg


 


3661
ttttctggct gcggggggtt gtcggaggga ttccaccaag caggcatctc tgacacgctg


 


3721
tgggccatcg agatgtggga ccctgcggcc caggcgttcc ggctgaacaa ccccggctcc


 


3781
acagtgttca cagaggactg caacatcctg ctgaagctgg tcatggctgg ggagaccacc


 


3841
aactcccgcg gccagcggct gccccagaag ggagacgtgg agatgctgtg cggcgggccg


 


3901
ccctgccagg gcttcagcgg cttgaaccgc ttcaattcgc gcacctactc caagttcaaa


 


3961
aactctctgg tggtttcctt cctcagctac tgcgactact accggccccg gttcttcctc


 


4021
ctggagaatg tcaggaactt tgtctccttc aagcgctcca tggtcctgaa gctcaccctc


 


4081
cgctgcctgg tccgcatggg ctatcagtgc accttcggcg tgctgcaggc cggtcagtac


 


4141
ggcgtggccc agactaggag gcgggccatc atcctggccg cggcccctgg agagaagctc


 


4201
cctctgttcc cggagccact gcacgtgttt gctccccggg cctgccagct gagcgtggtg


 


4261
gtggatgaca agaagtttgt gagcaacata accaggttga gctcgggtcc tttccggacc


 


4321
atcacggtgc gagacacgat gtccgacctg ccggaggtgc ggaatggagc ctcggcactg


 


4381
gagatctcct acaacgggga gcctcagtcc tggttccaga ggcagctccg gggcgcacag


 


4441
taccagccca tcctcaggga ccacatctgt aaggacatga gtgcattggt ggctgcccgc


 


4501
atgcggcaca tccccttggc cccagggtca gactggcgcg atctgcccaa catcgaggtg


 


4561
cggctctcag acggcaccat ggccaggaag ctgcggtata cccaccatga caggaagaac


 


4621
ggccgcagca gctctggggc cctccgtggg gtctgctcct gcgtggaagc cggcaaagcc


 


4681
tgcgaccccg cagccaggca gttcaacacc ctcatcccct ggtgcctgcc ccacaccggg


 


4741
aaccggcaca accactgggc tggcctctat ggaaggctcg agtgggacgg cttcttcagc


 


4801
acaaccgtca ccaaccccga gcccatgggc aagcagggcc gcgtgctcca cccagagcag


 


4861
caccgtgtgg tgagcgtgcg ggagtgtgcc cgctcccagg gcttccctga cacctaccgg


 


4921
ctcttcggca acatcctgga caagcaccgg caggtgggca atgccgtgcc accgcccctg


 


4981
gccaaagcca ttggcttgga gatcaagctt tgtatgttgg ccaaagcccg agagagtgcc


 


5041
tcagctaaaa taaaggagga ggaagctgct aaggactagt tctgccctcc cgtcacccct


 


5101
gtttctggca ccaggaatcc ccaacatgca ctgatgttgt gtttttaaca tgtcaatctg


 


5161
tccgttcaca tgtgtggtac atggtgtttg tggccttggc tgacatgaag ctgttgtgtg


 


5221
aggttcgctt atcaactaat gatttagtga tcaaattgtg cagtactttg tgcattctgg


 


5281
attttaaaag ttttttatta tgcattatat caaatctacc actgtatgag tggaaattaa


 


5341
gactttatgt agtttttata tgttgtaata tttcttcaaa taaatctctc ctataaacca


 


5401
aaaaaaaaaa aaaaaaaaaa aaaaa






By “LDHA” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—005566, NM—001135239, NM—001165414, NM—001165415, NM—001165416, or NR—028500. An exemplary LDHA sequence is provided below:










(SEQ ID NO: 4)



   1
gtctgccggt cggttgtctg gctgcgcgcg ccacccgggc ctctccagtg ccccgcctgg



 


  61
ctcggcatcc acccccagcc cgactcacac gtgggttccc gcacgtccgc cggccccccc


 


 121
cgctgacgtc agcatagctg ttccacttaa ggcccctccc gcgcccagct cagagtgctg


 


 181
cagccgctgc cgccgattcc ggatctcatt gccacgcgcc cccgacgacc gcccgacgtg


 


 241
cattcccgat tccttttggt tccaagtcca atatggcaac tctaaaggat cagctgattt


 


 301
ataatcttct aaaggaagaa cagacccccc agaataagat tacagttgtt ggggttggtg


 


 361
ctgttggcat ggcctgtgcc atcagtatct taatgaagga cttggcagat gaacttgctc


 


 421
ttgttgatgt catcgaagac aaattgaagg gagagatgat ggatctccaa catggcagcc


 


 481
ttttccttag aacaccaaag attgtctctg gcaaagacta taatgtaact gcaaactcca


 


 541
agctggtcat tatcacggct ggggcacgtc agcaagaggg agaaagccgt cttaatttgg


 


 601
tccagcgtaa cgtgaacatc tttaaattca tcattcctaa tgttgtaaaa tacagcccga


 


 661
actgcaagtt gcttattgtt tcaaatccag tggatatctt gacctacgtg gcttggaaga


 


 721
taagtggttt tcccaaaaac cgtgttattg gaagcggttg caatctggat tcagcccgat


 


 781
tccgttacct aatgggggaa aggctgggag ttcacccatt aagctgtcat gggtgggtcc


 


 841
ttggggaaca tggagattcc agtgtgcctg tatggagtgg aatgaatgtt gctggtgtct


 


 901
ctctgaagac tctgcaccca gatttaggga ctgataaaga taaggaacag tggaaagagg


 


 961
ttcacaagca ggtggttgag agtgcttatg aggtgatcaa actcaaaggc tacacatcct


 


1021
gggctattgg actctctgta gcagatttgg cagagagtat aatgaagaat cttaggcggg


 


1081
tgcacccagt ttccaccatg attaagggtc tttacggaat aaaggatgat gtcttcctta


 


1141
gtgttccttg cattttggga cagaatggaa tctcagacct tgtgaaggtg actctgactt


 


1201
ctgaggaaga ggcccgtttg aagaagagtg cagatacact ttgggggatc caaaaggagc


 


1261
tgcaatttta aagtcttctg atgtcatatc atttcactgt ctaggctaca acaggattct


 


1321
aggtggaggt tgtgcatgtt gtccttttta tctgatctgt gattaaagca gtaatatttt


 


1381
aagatggact gggaaaaaca tcaactcctg aagttagaaa taagaatggt ttgtaaaatc


 


1441
cacagctata tcctgatgct ggatggtatt aatcttgtgt agtcttcaac tggttagtgt


 


1501
gaaatagttc tgccacctct gacgcaccac tgccaatgct gtacgtactg catttgcccc


 


1561
ttgagccagg tggatgttta ccgtgtgtta tataacttcc tggctccttc actgaacatg


 


1621
cctagtccaa cattttttcc cagtgagtca catcctggga tccagtgtat aaatccaata


 


1681
tcatgtcttg tgcataattc ttccaaagga tcttattttg tgaactatat cagtagtgta


 


1741
cattaccata taatgtaaaa agatctacat acaaacaatg caaccaacta tccaagtgtt


 


1801
ataccaacta aaacccccaa taaaccttga acagtgacta ctttggttaa ttcattatat


 


1861
taagatataa agtcataaag ctgctagtta ttatattaat ttggaaatat taggctattc


 


1921
ttgggcaacc ctgcaacgat tttttctaac agggatatta ttgactaata gcagaggatg


 


1981
taatagtcaa ctgagttgta ttggtaccac ttccattgta agtcccaaag tattatatat


 


2041
ttgataataa tgctaatcat aattggaaag taacattcta tatgtaaatg taaaatttat


 


2101
ttgccaactg aatataggca atgatagtgt gtcactatag ggaacacaga tttttgagat


 


2161
cttgtcctct ggaagctggt aacaattaaa aacaatctta aggcagggaa aaaaaaaaaa


 


2221
aaaaaa






By “MAD2L2” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—001127325, NM—006341, or BC015244.










(SEQ ID NO: 5)



   1
tgcccccagc cgaggggcag ccccggggcc gggcccggcg cgcacccggc cagcgcgccc



 


  61
tcgccagctg cgctctgagt tctgggccag ctccccagag gcctaggcgc cgccgccgcg


 


 121
agggcgcggg gcagacaaag gaggcagaca aaggcgggcg cagcccagca gccgtgcggg


 


 181
caccgggcga ggcaggccca ctcctcccgg tagcgggaag gatgaccacg ctcacacgac


 


 241
aagacctcaa ctttggccaa gtggtggccg atgtgctctg cgagttcctg gaggtggctg


 


 301
tgcatctcat cctctacgtg cgcgaggtct accccgtggg catcttccag aaacgcaaga


 


 361
agtacaacgt gccggtccag atgtcctgcc acccggagct gaatcagtat atccaggaca


 


 421
cgctgcactg cgtcaagcca ctcctggaga agaatgatgt ggagaaagtg gtggtggtga


 


 481
ttttggataa agagcaccgc ccagtggaga aattcgtctt tgagatcacc cagcctccac


 


 541
tgctgtccat cagctcagac tcgctgttgt ctcatgtgga gcagctgctc cgggccttca


 


 601
tcctgaagat cagcgtgtgc gatgccgtcc tggaccacaa ccccccaggc tgtaccttca


 


 661
cagtcctggt gcacacgaga gaagccgcca ctcgcaacat ggagaagatc caggtcatca


 


 721
aggatttccc ctggatcctg gcggatgagc aggatgtcca catgcatgac ccccggctga


 


 781
taccactaaa aaccatgacg tcggacattt taaagatgca gctttacgtg gaagagcgcg


 


 841
ctcataaagg cagctgaggg ggcacctgcc accccactga tgcccaaact gtcagacttt


 


 901
gggggatccc cgcctagggc agtgctgcat ggctgccctg attccaagtg ctcttatcgc


 


 961
ctctgtgtgt ggatcgcccg ccccagcccg gggccgctca ggtctgcttg gaggatgcct


 


1021
cccccaggag ggcagtgagg gatgccgcaa cctcgacttc tcagcctcct ggggttccgc


 


1081
cggccaacac tgtctgtctc aaatactgtg ctgtgagttg tttcaataaa ggggccccaa


 


1141
gggctgggct gaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaa






By “NBN” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—002485. An exemplary NBN sequence is provided below:










(SEQ ID NO: 6)



   1
gagcgcgcac gtcccggagc ccatgccgac cgcaggcgcc gtatccgcgc tcgtctagca



 


  61
gccccggtta cgcggttgca cgtcggcccc agccctgagg agccggaccg atgtggaaac


 


 121
tgctgcccgc cgcgggcccg gcaggaggag aaccatacag acttttgact ggcgttgagt


 


 181
acgttgttgg aaggaaaaac tgtgccattc tgattgaaaa tgatcagtcg atcagccgaa


 


 241
atcatgctgt gttaactgct aacttttctg taaccaacct gagtcaaaca gatgaaatcc


 


 301
ctgtattgac attaaaagat aattctaagt atggtacctt tgttaatgag gaaaaaatgc


 


 361
agaatggctt ttcccgaact ttgaagtcgg gggatggtat tacttttgga gtgtttggaa


 


 421
gtaaattcag aatagagtat gagcctttgg ttgcatgctc ttcttgttta gatgtctctg


 


 481
ggaaaactgc tttaaatcaa gctatattgc aacttggagg atttactgta aacaattgga


 


 541
cagaagaatg cactcacctt gtcatggtat cagtgaaagt taccattaaa acaatatgtg


 


 601
cactcatttg tggacgtcca attgtaaagc cagaatattt tactgaattc ctgaaagcag


 


 661
ttgagtccaa gaagcagcct ccacaaattg aaagttttta cccacctctt gatgaaccat


 


 721
ctattggaag taaaaatgtt gatctgtcag gacggcagga aagaaaacaa atcttcaaag


 


 781
ggaaaacatt tatatttttg aatgccaaac agcataagaa attgagttcc gcagttgtct


 


 841
ttggaggtgg ggaagctagg ttgataacag aagagaatga agaagaacat aatttctttt


 


 901
tggctccggg aacgtgtgtt gttgatacag gaataacaaa ctcacagacc ttaattcctg


 


 961
actgtcagaa gaaatggatt cagtcaataa tggatatgct ccaaaggcaa ggtcttagac


 


1021
ctattcctga agcagaaatt ggattggcgg tgattttcat gactacaaag aattactgtg


 


1081
atcctcaggg ccatcccagt acaggattaa agacaacaac tccaggacca agcctttcac


 


1141
aaggcgtgtc agttgatgaa aaactaatgc caagcgcccc agtgaacact acaacatacg


 


1201
tagctgacac agaatcagag caagcagata catgggattt gagtgaaagg ccaaaagaaa


 


1261
tcaaagtctc caaaatggaa caaaaattca gaatgctttc acaagatgca cccactgtaa


 


1321
aggagtcctg caaaacaagc tctaataata atagtatggt atcaaatact ttggctaaga


 


1381
tgagaatccc aaactatcag ctttcaccaa ctaaattgcc aagtataaat aaaagtaaag


 


1441
atagggcttc tcagcagcag cagaccaact ccatcagaaa ctactttcag ccgtctacca


 


1501
aaaaaaggga aagggatgaa gaaaatcaag aaatgtcttc atgcaaatca gcaagaatag


 


1561
aaacgtcttg ttctctttta gaacaaacac aacctgctac accctcattg tggaaaaata


 


1621
aggagcagca tctatctgag aatgagcctg tggacacaaa ctcagacaat aacttattta


 


1681
cagatacaga tttaaaatct attgtgaaaa attctgccag taaatctcat gctgcagaaa


 


1741
agctaagatc aaataaaaaa agggaaatgg atgatgtggc catagaagat gaagtattgg


 


1801
aacagttatt caaggacaca aaaccagagt tagaaattga tgtgaaagtt caaaaacagg


 


1861
aggaagatgt caatgttaga aaaaggccaa ggatggatat agaaacaaat gacactttca


 


1921
gtgatgaagc agtaccagaa agtagcaaaa tatctcaaga aaatgaaatt gggaagaaac


 


1981
gtgaactcaa ggaagactca ctatggtcag ctaaagaaat atctaacaat gacaaacttc


 


2041
aggatgatag tgagatgctt ccaaaaaagc tgttattgac tgaatttaga tcactggtga


 


2101
ttaaaaactc tacttccaga aatccatctg gcataaatga tgattatggt caactaaaaa


 


2161
atttcaagaa attcaaaaag gtcacatatc ctggagcagg aaaacttcca cacatcattg


 


2221
gaggatcaga tctaatagct catcatgctc gaaagaatac agaactagaa gagtggctaa


 


2281
ggcaggaaat ggaggtacaa aatcaacatg caaaagaaga gtctcttgct gatgatcttt


 


2341
ttagatacaa tccttattta aaaaggagaa gataactgag gattttaaaa agaagccatg


 


2401
gaaaaacttc ctagtaagca tctacttcag gccaacaagg ttatatgaat atatagtgta


 


2461
tagaagcgat ttaagttaca atgttttatg gcctaaattt attaaataaa atgcacaaaa


 


2521
ctttgattct tttgtatgta acaattgttt gttctgtttt caggctttgt cattgcatct


 


2581
ttttttcatt tttaaatgtg ttttgtttat taaatagtta atatagtcac agttcaaaat


 


2641
tctaaatgta cgtaaggtaa agactaaagt cacccttcca ccattgtcct agctacttgg


 


2701
ttcccctcag aaaaaaattc atgatactca tttcttatga atctttccag ggatttttga


 


2761
gtcctattca aattcctatt tttaaataat ttcctacaca aatgatagca taacatatgc


 


2821
agtgttctac accttgcttt tttacttagt agattaaaaa ttataggaat atcaatataa


 


2881
tgtttttaat attttttctt ttccattatg ctgtagtctt acctaaactc tggtgatcca


 


2941
aacaaaatgg cttcagtggt gcagatgtca cctacatgtt attctagtac tagaaactga


 


3001
agaccatgtg gagacttcat caaacatggg tttagttttc accagaatgg aaagacctgt


 


3061
accccttttt ggtggtctta ctgagctggg tgggtgtctg ttttgagctt atttagagtc


 


3121
ctagttttcc tacttataaa gtagaaatgg tgagattgtt ttctttttct accttaaagg


 


3181
gagatggtaa gaaacaatga atgtcttttt tcaaacttta ttgacaagtg attttcaagt


 


3241
ctgtgttcaa aaatatattc atgtacctgt gatccagcaa gaagggagtt ccagtcaaga


 


3301
gtcactacaa ctgattagtt gtttagagaa tgagaaatgg aacagtgagg aatggaggcc


 


3361
atatttccat gacttccctt gtaaacagaa gcaacagaag ggacaagagg ctggcctcta


 


3421
catcactctc accttccaaa tcttgtggaa gtgcatctac ttgccagaac caaattaact


 


3481
tacttccaag ttctggctgc ttgcaggtgg aactccagct gcaagggagt tagggaaatg


 


3541
aaggtctttt tttaaaagct tctcagcctt cctagggaac agaaattggg tgagccaatc


 


3601
tgcaatttct actacaggca ttgagaccag ttagattatt gaaatattat agagagttat


 


3661
gaacacttaa attatgatag tggtatgaca ttggatagaa catgggatac tttagaagta


 


3721
gaattgacag ggcatattag ttgatgaaat ggagtcattt gagtctctta atagccatgt


 


3781
atcataatta ccaagtgaag ctggtggaac atatggtctc cattttacag ttaaggaata


 


3841
taatggacag attaatattg ttctctgtca tgcccacaat ccctttctaa ggaagactgc


 


3901
cctactatag cagtttttat atttgtcaat ttatgaatat aatgaatgag agttctggta


 


3961
cctcctgtct ttacaaatat tggtgttgtc agtatttttc ctttttaacc attccaatcg


 


4021
gtgtgtagtg atgtttcatt ttggttttaa tttgtatatc cctgatagct ataattgggt


 


4081
catagaaatt ctttatacat tctagatgca agtctcttgt cggatatatg tattgagata


 


4141
ttacacctag tctgtggctt gactgttttc tttatgtctt ttgatgaata gaagttttaa


 


4201
attttgacaa ggtcaaattt atttttttct tttgtttgat attttttctc tccaatttaa


 


4261
ccccaagatt tcagatattc tgctctatta tataaacttt atatttttat atttgtgatc


 


4321
taccttgaat tgatatgtat gttgtgaatt atggatcagg gttctttttt tcccccatac


 


4381
aagtatccag tcattgtaac actgtttatt gaaagaatta tcctttcctc attaaattac


 


4441
cttgccaatt agtaaaaaat caattaacca taatggtgga tctgtttctg gactttctgt


 


4501
ttggttacac tgaaatgttt gtccatcctt gcactcactc ataccatact gccttgaatt


 


4561
actgtagctg catagatgct ccttaagttg ggattacatt gtaataaacg caatgtaagt


 


4621
taaaaaaaaa aaaaaaaaa






By “NONO” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—001145408, NM—007363, NM—001145409, or NM—001145410. An exemplary NONO sequence is provided below:










(SEQ ID NO: 7)



   1
caggcgcagt gcaggactgc tccgagcacg cctacgcgcg cattttctcc ccttcctctc



 


  61
cctctttcca ctttcctctc cctttttctc ctctcctttc cccctcccac cacttggtct


 


 121
ttcagtcttt cagtcagttc gtttaggtct ctccttccga cccccacccc cagctcctct


 


 181
ccctttcctt ttccccctcc ccctttcctt tcccgtctca cgcgccaggc cgcttgcaca


 


 241
tgcgcattag gtacaaagcc tcgctctttg tccccatctg tcgttcacac gaactcaagc


 


 301
ctttggcatt cggcagccaa tagaatctaa gaaatggcgg aaaaatgatt ccgcctcggg


 


 361
agctaaacct tgattggcag tttagctaac caatcgagaa cgccattttg taccccttgg


 


 421
caggcaccga gctccgtcgt ctcgtttccg gcggtcgcgc gctcttttct cgggacggga


 


 481
gaggccgtgt agcgtcgccg ttactccgag gagataccag tcggtagagg agaagtcgag


 


 541
gttagaggga actgggaggc actttgctgt ctgcaatcga agttgagagg cccagtattt


 


 601
aggcgacagt gaatttatta ctctgaagag ggttctgcac atatttccaa attatattgg


 


 661
tggtcatcag aagtaggtga taggaagaaa tacttctcaa gggtgcaaaa atgcagagta


 


 721
ataaaacttt taacttggag aagcaaaacc atactccaag aaagcatcat caacatcacc


 


 781
accagcagca gcaccaccag cagcaacagc agcagccgcc accaccgcca atacctgcaa


 


 841
atgggcaaca ggccagcagc caaaatgaag gcttgactat tgacctgaag aattttagaa


 


 901
aaccaggaga gaagaccttc acccaacgaa gccgtctttt tgtgggaaat cttcctcccg


 


 961
acatcactga ggaagaaatg aggaaactat ttgagaaata tggaaaggca ggcgaagtct


 


1021
tcattcataa ggataaagga tttggcttta tccgcttgga aacccgaacc ctagcggaga


 


1081
ttgccaaagt ggagctggac aatatgccac tccgtggaaa gcagctgcgt gtgcgctttg


 


1141
cctgccatag tgcatccctt acagttcgaa accttcctca gtatgtgtcc aacgaactgc


 


1201
tggaagaagc cttttctgtg tttggccagg tagagagggc tgtagtcatt gtggatgatc


 


1261
gaggaaggcc ctcaggaaaa ggcattgttg agttctcagg gaagccagct gctcggaaag


 


1321
ctctggacag atgcagtgaa ggctccttcc tgctaaccac atttcctcgt cctgtgactg


 


1381
tggagcccat ggaccagtta gatgatgaag agggacttcc agagaagctg gttataaaaa


 


1441
accagcaatt tcacaaggaa cgagagcagc cacccagatt tgcacagcct ggctcctttg


 


1501
agtatgaata tgccatgcgc tggaaggcac tcattgagat ggagaagcag cagcaggacc


 


1561
aagtggaccg caacatcaag gaggctcgtg agaagctgga gatggagatg gaagctgcac


 


1621
gccatgagca ccaggtcatg ctaatgagac aggatttgat gaggcgccaa gaagaacttc


 


1681
ggaggatgga agagctgcac aaccaagagg tgcaaaaacg aaagcaactg gagctcaggc


 


1741
aggaggaaga gcgcaggcgc cgtgaagaag agatgcggcg gcagcaagaa gaaatgatgc


 


1801
ggcgacagca ggaaggattc aagggaacct tccctgatgc gagagagcag gagattcgga


 


1861
tgggtcagat ggctatggga ggtgctatgg gcataaacaa cagaggtgcc atgccccctg


 


1921
ctcctgtgcc agctggtacc ccagctcctc caggacctgc cactatgatg ccggatggaa


 


1981
ctttgggatt gaccccacca acaactgaac gctttggtca ggctgctaca atggaaggaa


 


2041
ttggggcaat tggtggaact cctcctgcat tcaaccgtgc agctcctgga gctgaatttg


 


2101
ccccaaacaa acgtcgccga tactaataag ttgcagtgtc tagtttctca aaacccttaa


 


2161
aagaaggacc ctttttggac tagccagaat tctaccctgg aaaagtgtta gggattcctt


 


2221
ccaatagtta gatctaccct gcctgtacta ctctagggag tatgctggag gcagagggca


 


2281
agggaggggt ggtattaaac aagtcaattc tgtgtggtat attgtttaat cagttctgtg


 


2341
tggtgcattc ctgaagtctc taatgtgact gttgagggcc tggggaaacc atggcaaagt


 


2401
ggatccagtt agagcccatt aatcttgatc attccggttt tttttttttt tgtccaggtt


 


2461
gtttcatttg cttgccccgc ccccgagacg gagtcttact ctgtcgccca ggctggagtg


 


2521
tagtggcatg atctcggctc actgcaatct ctgcctcccg ggttcaagct tgtccaggtt


 


2581
gatcttgaac tcctgacctc gtgatctacc cacctcggcc tcccaaaatg ctgggattac


 


2641
aggggtgagc caccgtgccc aacctcactt gcttcttatc cttacactcc cccagcccca


 


2701
gagaaactgc cacatacacc acaaaaacca aacatccccc aatgacctta gccccattgc


 


2761
tccattcact cccaggtgag aattcaggca aacgtccaca aaggtcacag gcagcgtaca


 


2821
tacggttctg ttatacccca tatattaccc cttcatgtcc taaagaagac attttctctt


 


2881
agagattttc attttagtgt atctttaaaa aaaaatcttg tgttaacttg cctccatctt


 


2941
tttcttgggt gaggacaccc aggaatgacc cttttgtgtc tatgatgttg ctgttcacag


 


3001
cttttcttga taggcctagt acaatcttgg gaacagggtt actgtatact gaaggtctga


 


3061
cagtagctct tagactcgcc tatcttaggt agtcatgctg tgcatttttt ttttcattgg


 


3121
tgtactgtgt ttgatttgtc tcatatattt ggagtttttc tgaaaaatgg agcagtaatg


 


3181
cagcatcaac ctattaaaat acattttaag ccttttaaaa aaaaaaaa






By “DNAPK” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—006904 or NM—001081640. DNAPK is also refered to as PRKDC. An exemplary DNAPK sequence is provided below:










(SEQ ID NO: 8)



    1
ggggcatttc cgggtccggg ccgagcgggc gcacgcgcgg gagcgggact cggcggcatg



 


   61
gcgggctccg gagccggtgt gcgttgctcc ctgctgcggc tgcaggagac cttgtccgct


 


  121
gcggaccgct gcggtgctgc cctggccggt catcaactga tccgcggcct ggggcaggaa


 


  181
tgcgtcctga gcagcagccc cgcggtgctg gcattacaga catctttagt tttttccaga


 


  241
gatttcggtt tgcttgtatt tgtccggaag tcactcaaca gtattgaatt tcgtgaatgt


 


  301
agagaagaaa tcctaaagtt tttatgtatt ttcttagaaa aaatgggcca gaagatcgca


 


  361
ccttactctg ttgaaattaa gaacacttgt accagtgttt atacaaaaga tagagctgct


 


  421
aaatgtaaaa ttccagccct ggaccttctt attaagttac ttcagacttt tagaagttct


 


  481
agactcatgg atgaatttaa aattggagaa ttatttagta aattctatgg agaacttgca


 


  541
ttgaaaaaaa aaataccaga tacagtttta gaaaaagtat atgagctcct aggattattg


 


  601
ggtgaagttc atcctagtga gatgataaat aatgcagaaa acctgttccg cgcttttctg


 


  661
ggtgaactta agacccagat gacatcagca gtaagagagc ccaaactacc tgttctggca


 


  721
ggatgtctga aggggttgtc ctcacttctg tgcaacttca ctaagtccat ggaagaagat


 


  781
ccccagactt caagggagat ttttaatttt gtactaaagg caattcgtcc tcagattgat


 


  841
ctgaagagat atgctgtgcc ctcagctggc ttgcgcctat ttgccctgca tgcatctcag


 


  901
tttagcacct gccttctgga caactacgtg tctctatttg aagtcttgtt aaagtggtgt


 


  961
gcccacacaa atgtagaatt gaaaaaagct gcactttcag ccctggaatc ctttctgaaa


 


 1021
caggtttcta atatggtggc gaaaaatgca gaaatgcata aaaataaact gcagtacttt


 


 1081
atggagcagt tttatggaat catcagaaat gtggattcga acaacaagga gttatctatt


 


 1141
gctatccgtg gatatggact ttttgcagga ccgtgcaagg ttataaacgc aaaagatgtt


 


 1201
gacttcatgt acgttgagct cattcagcgc tgcaagcaga tgttcctcac ccagacagac


 


 1261
actggtgacg accgtgttta tcagatgcca agcttcctcc agtctgttgc aagcgtcttg


 


 1321
ctgtaccttg acacagttcc tgaggtgtat actccagttc tggagcacct cgtggtgatg


 


 1381
cagatagaca gtttcccaca gtacagtcca aaaatgcagc tggtgtgttg cagagccata


 


 1441
gtgaaggtgt tcctagcttt ggcagcaaaa gggccagttc tcaggaattg cattagtact


 


 1501
gtggtgcatc agggtttaat cagaatatgt tctaaaccag tggtccttcc aaagggccct


 


 1561
gagtctgaat ctgaagacca ccgtgcttca ggggaagtca gaactggcaa atggaaggtg


 


 1621
cccacataca aagactacgt ggatctcttc agacatctcc tgagctctga ccagatgatg


 


 1681
gattctattt tagcagatga agcatttttc tctgtgaatt cctccagtga aagtctgaat


 


 1741
catttacttt atgatgaatt tgtaaaatcc gttttgaaga ttgttgagaa attggatctt


 


 1801
acacttgaaa tacagactgt tggggaacaa gagaatggag atgaggcgcc tggtgtttgg


 


 1861
atgatcccaa cttcagatcc agcggctaac ttgcatccag ctaaacctaa agatttttcg


 


 1921
gctttcatta acctggtgga attttgcaga gagattctcc ctgagaaaca agcagaattt


 


 1981
tttgaaccat gggtgtactc attttcatat gaattaattt tgcaatctac aaggttgccc


 


 2041
ctcatcagtg gtttctacaa attgctttct attacagtaa gaaatgccaa gaaaataaaa


 


 2101
tatttcgagg gagttagtcc aaagagtctg aaacactctc ctgaagaccc agaaaagtat


 


 2161
tcttgctttg ctttatttgt gaaatttggc aaagaggtgg cagttaaaat gaagcagtac


 


 2221
aaagatgaac ttttggcctc ttgtttgacc tttcttctgt ccttgccaca caacatcatt


 


 2281
gaactcgatg ttagagccta cgttcctgca ctgcagatgg ctttcaaact gggcctgagc


 


 2341
tataccccct tggcagaagt aggcctgaat gctctagaag aatggtcaat ttatattgac


 


 2401
agacatgtaa tgcagcctta ttacaaagac attctcccct gcctggatgg atacctgaag


 


 2461
acttcagcct tgtcagatga gaccaagaat aactgggaag tgtcagctct ttctcgggct


 


 2521
gcccagaaag gatttaataa agtggtgtta aagcatctga agaagacaaa gaacctttca


 


 2581
tcaaacgaag caatatcctt agaagaaata agaattagag tagtacaaat gcttggatct


 


 2641
ctaggaggac aaataaacaa aaatcttctg acagtcacgt cctcagatga gatgatgaag


 


 2701
agctatgtgg cctgggacag agagaagcgg ctgagctttg cagtgccctt tagagagatg


 


 2761
aaacctgtca ttttcctgga tgtgttcctg cctcgagtca cagaattagc gctcacagcc


 


 2821
agtgacagac aaactaaagt tgcagcctgt gaacttttac atagcatggt tatgtttatg


 


 2881
ttgggcaaag ccacgcagat gccagaaggg ggacagggag ccccacccat gtaccagctc


 


 2941
tataagcgga cgtttcctgt gctgcttcga cttgcgtgtg atgttgatca ggtgacaagg


 


 3001
caactgtatg agccactagt tatgcagctg attcactggt tcactaacaa caagaaattt


 


 3061
gaaagtcagg atactgttgc cttactagaa gctatattgg atggaattgt ggaccctgtt


 


 3121
gacagtactt taagagattt ttgtggtcgg tgtattcgag aattccttaa atggtccatt


 


 3181
aagcaaataa caccacagca gcaggagaag agtccagtaa acaccaaatc gcttttcaag


 


 3241
cgactttata gccttgcgct tcaccccaat gctttcaaga ggctgggagc atcacttgcc


 


 3301
tttaataata tctacaggga attcagggaa gaagagtctc tggtggaaca gtttgtgttt


 


 3361
gaagccttgg tgatatacat ggagagtctg gccttagcac atgcagatga gaagtcctta


 


 3421
ggtacaattc aacagtgttg tgatgccatt gatcacctat gccgcatcat tgaaaagaag


 


 3481
catgtttctt taaataaagc aaagaaacga cgtttgccgc gaggatttcc accttccgca


 


 3541
tcattgtgtt tattggatct ggtcaagtgg cttttagctc attgtgggag gccccagaca


 


 3601
gaatgtcgac acaaatccat tgaactcttt tataaattcg ttcctttatt gccaggcaac


 


 3661
agatccccta atttgtggct gaaagatgtt ctcaaggaag aaggtgtctc ttttctcatc


 


 3721
aacacctttg aggggggtgg ctgtggccag ccctcgggca tcctggccca gcccaccctc


 


 3781
ttgtaccttc gggggccatt cagcctgcag gccacgctat gctggctgga cctgctcctg


 


 3841
gccgcgttgg agtgctacaa cacgttcatt ggcgagagaa ctgtaggagc gctccaggtc


 


 3901
ctaggtactg aagcccagtc ttcacttttg aaagcagtgg ctttcttctt agaaagcatt


 


 3961
gccatgcatg acattatagc agcagaaaag tgctttggca ctggggcagc aggtaacaga


 


 4021
acaagcccac aagagggaga aaggtacaac tacagcaaat gcaccgttgt ggtccggatt


 


 4081
atggagttta ccacgactct gctaaacacc tccccggaag gatggaagct cctgaagaag


 


 4141
gacttgtgta atacacacct gatgagagtc ctggtgcaga cgctgtgtga gcccgcaagc


 


 4201
ataggtttca acatcggaga cgtccaggtt atggctcatc ttcctgatgt ttgtgtgaat


 


 4261
ctgatgaaag ctctaaagat gtccccatac aaagatatcc tagagaccca tctgagagag


 


 4321
aaaataacag cacagagcat tgaggagctt tgtgccgtca acttgtatgg ccctgacgcg


 


 4381
caagtggaca ggagcaggct ggctgctgtt gtgtctgcct gtaaacagct tcacagagct


 


 4441
gggcttctgc ataatatatt accgtctcag tccacagatt tgcatcattc tgttggcaca


 


 4501
gaacttcttt ccctggttta taaaggcatt gcccctggag atgagagaca gtgtctgcct


 


 4561
tctctagacc tcagttgtaa gcagctggcc agcggacttc tggagttagc ctttgctttt


 


 4621
ggaggactgt gtqaqcqcct tqtqaqtctt ctcctgaacc cagcggtgct gtccacggcg


 


 4681
tccttgggca gctcacaggg cagcgtcatc cacttctccc atggggagta tttctatagc


 


 4741
ttgttctcag aaacgatcaa cacggaatta ttgaaaaatc tggatcttgc tgtattggag


 


 4801
ctcatgcagt cttcagtgga taataccaaa atggtgagtg ccgttttgaa cggcatgtta


 


 4861
gaccagagct tcagggagcg agcaaaccag aaacaccaag gactgaaact tgcgactaca


 


 4921
attctgcaac actggaagaa gtgtgattca tggtgggcca aagattcccc tctcgaaact


 


 4981
aaaatggcag tgctggcctt actggcaaaa attttacaga ttgattcatc tgtatctttt


 


 5041
aatacaagtc atggttcatt ccctgaagtc tttacaacat atattagtct acttgctgac


 


 5101
acaaagctgg atctacattt aaagggccaa gctgtcactc ttcttccatt cttcaccagc


 


 5161
ctcactggag gcagtctgga ggaacttaga cgtgttctgg agcagctcat cgttgctcac


 


 5221
ttccccatgc agtccaggga atttcctcca ggaactccgc ggttcaataa ttatgtggac


 


 5281
tgcatgaaaa agtttctaga tgcattggaa ttatctcaaa gccctatgtt gttggaattg


 


 5341
atgacagaag ttctttgtcg ggaacagcag catgtcatgg aagaattatt tcaatccagt


 


 5401
ttcaggagga ttgccagaag gggttcatgt gtcacacaag taggccttct ggaaagcgtg


 


 5461
tatgaaatgt tcaggaagga tgacccccgc ctaagtttca cacgccagtc ctttgtggac


 


 5521
cgctccctcc tcactctgct gtggcactgt agcctggatg ctttgagaga attcttcagc


 


 5581
acaattgtgg tggatgccat tgatgtgttg aagtccaggt ttacaaagct aaatgaatct


 


 5641
acctttgata ctcaaatcac caagaagatg ggctactata agattctaga cgtgatgtat


 


 5701
tctcgccttc ccaaagatga tgttcatgct aaggaatcaa aaattaatca agttttccat


 


 5761
ggctcgtgta ttacagaagg aaatgaactt acaaagacat tgattaaatt gtgctacgat


 


 5821
gcatttacag agaacatggc aggagagaat cagctgctgg agaggagaag actttaccat


 


 5881
tgtgcagcat acaactgcgc catatctgtc atctgctgtg tcttcaatga gttaaaattt


 


 5941
taccaaggtt ttctgtttag tgaaaaacca gaaaagaact tgcttatttt tgaaaatctg


 


 6001
atcgacctga agcgccgcta taattttcct gtagaagttg aggttcctat ggaaagaaag


 


 6061
aaaaagtaca ttgaaattag gaaagaagcc agagaagcag caaatgggga ttcagatggt


 


 6121
ccttectata tgtcttccct gtcatatttg gcagacagta ccctgagtga ggaaatgagt


 


 6181
caatttgatt tctcaaccgg agttcagagc tattcataca gctcccaaga ccctagacct


 


 6241
gccactggtc gttttcggag acgggagcag cgggacccca cggtgcatga tgatgtgctg


 


 6301
gagctggaga tggacgagct caatcggcat gagtgcatgg cgcccctgac ggccctggtc


 


 6361
aagcacatgc acagaagcct gggcccgcct caaggagaag aggattcagt gccaagagat


 


 6421
cttccttctt ggatgaaatt cctccatggc aaactgggaa atccaatagt accattaaat


 


 6481
atccgtctct tcttagccaa gcttgttatt aatacagaag aggtctttcg cccttacgcg


 


 6541
aagcactggc ttagcccctt gctgcagctg gctgcttctg aaaacaatgg aggagaagga


 


 6601
attcactaca tggtggttga gatagtggcc actattcttt catggacagg cttggccact


 


 6661
ccaacagggg tccctaaaga tgaagtgtta gcaaatcgat tgcttaattt cctaatgaaa


 


 6721
catgtctttc atccaaaaag agctgtgttt agacacaacc ttgaaattat aaagaccctt


 


 6781
gtcgagtgct ggaaggattg tttatccatc ccttataggt taatatttga aaagttttcc


 


 6841
ggtaaagatc ctaattctaa agacaactca gtagggattc aattgctagg catcgtgatg


 


 6901
gccaatgacc tgcctcccta tgacccacag tgtggcatcc agagtagcga atacttccag


 


 6961
gctttggtga ataatatgtc ctttgtaaga tataaagaag tgtatgccgc tgcagcagaa


 


 7021
gttctaggac ttatacttcg atatgttatg gagagaaaaa acatactgga ggagtctctg


 


 7081
tgtgaactgg ttgcgaaaca attgaagcaa catcagaata ctatggagga caagtttatt


 


 7141
gtgtgcttga acaaagtgac caagagcttc cctcctcttg cagacaggtt catgaatgct


 


 7201
gtgttctttc tgctgccaaa atttcatgga gtgttgaaaa cactctgtct ggaggtggta


 


 7261
ctttgtcgtg tggagggaat gacagagctg tacttccagt taaagagcaa ggacttcgtt


 


 7321
caagtcatga gacatagaga tgatgaaaga caaaaagtat gtttggacat aatttataag


 


 7381
atgatgccaa agttaaaacc agtagaactc cgagaacttc tgaaccccgt tgtggaattc


 


 7441
gtttcccatc cttctacaac atgtagggaa caaatgtata atattctcat gtggattcat


 


 7501
gataattaca gagatccaga aagtgagaca gataatgact cccaggaaat atttaagttg


 


 7561
gcaaaagatg tgctgattca aggattgatc gatgagaacc ctggacttca attaattatt


 


 7621
cgaaatttct ggagccatga aactaggtta ccttcaaata ccttggaccg gttgctggca


 


 7681
ctaaattcct tatattctcc taagatagaa gtgcactttt taagtttagc aacaaatttt


 


 7741
ctgctcgaaa tgaccagcat gagcccagat tatccaaacc ccatgttcga gcatcctctg


 


 7801
tcagaatgcg aatttcagga atataccatt gattctgatt ggcgtttccg aagtactgtt


 


 7861
ctcactccga tgtttgtgga gacccaggcc tcccagggca ctctccagac ccgtacccag


 


 7921
gaagggtccc tctcagctcg ctggccagtg gcagggcaga taagggccac ccagcagcag


 


 7981
catgacttca cactgacaca gactgcagat ggaagaagct catttgattg gctgaccggg


 


 8041
agcagcactg acccgctggt cgaccacacc agtccctcat ctgactcctt gctgtttgcc


 


 8101
cacaagagga gtgaaaggtt acagagagca cccttgaagt cagtggggcc tgattttggg


 


 8161
aaaaaaaggc tgggccttcc aggggacgag gtggataaca aagtgaaagg tgcggccggc


 


 8221
cggacggacc tactacgact gcgcagacgg tttatgaggg accaggagaa gctcagtttg


 


 8281
atgtatgcca gaaaaggcgt tgctgagcaa aaacgagaga aggaaatcaa gagtgagtta


 


 8341
aaaatgaagc aggatgccca ggtcgttctg tacagaagct accggcacgg agaccttcct


 


 8401
gacattcaga tcaagcacag cagcctcatc accccgttac aggccgtggc ccagagggac


 


 8461
ccaataattg caaaacagct ctttagcagc ttgttttctg gaattttgaa agagatggat


 


 8521
aaatttaaga cactgtctga aaaaaacaac atcactcaaa agttgcttca agacttcaat


 


 8581
cgttttctta ataccacctt ctctttcttt ccaccctttg tctcttgtat tcaggacatt


 


 8641
agctgtgggc acgcagccct gctgagcctc gacccagcgg ctgttagcgc tggttgcctg


 


 8701
gccagcctac agcagcccgt gggcatccgc ctgctagagg aggctctgct ccgcctgctg


 


 8761
cctgctgagc tgcctgccaa gcgagtccgt gggaaggccc gcctccctcc tgatgtcctc


 


 8821
agatgggtgg agcttgctaa gctgtataga tcaattggag aatacgacgt cctccgtggg


 


 8881
atttttacca gtgagatagg aacaaagcaa atcactcaga gtgcattatt agcagaagcc


 


 8941
agaagtgatt attctgaagc tgctaagcag tatgatgagg ctctcaataa acaagactgg


 


 9001
gtagatggtg agcccacaga agccgagaag gatttttggg aacttgcatc ccttgactgt


 


 9061
tacaaccacc ttgctgagtg gaaatcactt gaatactgtt ctacagccag tatagacagt


 


 9121
gagaaccccc cagacctaaa taaaatctgg agtgaaccat tttatcagga aacatatcta


 


 9181
ccttacatga tccgcagcaa gctgaagctg ctgctccagg gagaggctga ccagtccctg


 


 9241
ctgacattta ttgacaaagc tatgcacggg gagctccaga aggcgattct agagcttcat


 


 9301
tacagtcaag agctgagtct gctttacctc ctgcaagatg atgttgacag agccaaatat


 


 9361
tacattcaaa atggcattca gagttttatg cagaattatt ctagtattga tgtcctctta


 


 9421
caccaaagta gactcaccaa attgcagtct gtacaggctt taacagaaat tcaggagttc


 


 9481
atcagcttta taagcaaaca aggcaattta tcatctcaag ttccccttaa gagacttctg


 


 9541
aacacctgga caaacagata tccagatgct aaaatggacc caatgaacat ctgggatgac


 


 9601
atcatcacaa atcgatgttt ctttctcagc aaaatagagg agaagcttac ccctcttcca


 


 9661
gaagataata gtatgaatgt ggatcaagat ggagacccca gtgacaggat ggaagtgcaa


 


 9721
gagcaggaag aagatatcag ctccctgatc aggagttgca agttttccat gaaaatgaag


 


 9781
atgatagaca gtgcccggaa gcagaacaat ttctcacttg ctatgaaact actgaaggag


 


 9841
ctgcataaag agtcaaaaac cagagacgat tggctggtga gctgggtgca gagctactgc


 


 9901
cgcctgagcc actgccggag ccggtcccag ggctgctctg agcaggtgct cactgtgctg


 


 9961
aaaacagtct ctttgttgga tgagaacaac gtgtcaagct acttaagcaa aaatattctg


 


10021
gctttccgtg accagaacat tctcttgggt acaacttaca ggatcatagc gaatgctctc


 


10081
agcagtgagc cagcctgcct tgctgaaatc gaggaggaca aggctagaag aatcttagag


 


10141
ctttctggat ccagttcaga ggattcagag aaggtgatcg cgggtctgta ccagagagca


 


10201
ttccagcacc tctctgaggc tgtgcaggcg gctgaggagg aggcccagcc tccctcctgg


 


10261
agctgtgggc ctgcagctgg ggtgattgat gcttacatga cgctggcaga tttctgtgac


 


10321
caacagctgc gcaaggagga agagaatgca tcagttattg attctgcaga actgcaggcg


 


10381
tatccagcac ttgtggtgga gaaaatgttg aaagctttaa aattaaattc caatgaagcc


 


10441
agattgaagt ttcctagatt acttcagatt atagaacggt atccagagga gactttgagc


 


10501
ctcatgacaa aagagatctc ttccgttccc tgctggcagt tcatcagctg gatcagccac


 


10561
atggtggcct tactggacaa agaccaagcc gttgctgttc agcactctgt ggaagaaatc


 


10621
actgataact acccgcaggc tattgtttat cccttcatca taagcagcga aagctattcc


 


10681
ttcaaggata cttctactgg tcataagaat aaggagtttg tggcaaggat taaaagtaag


 


10741
ttggatcaag gaggagtgat tcaagatttt attaatgcct tagatcagct ctctaatcct


 


10801
gaactgctct ttaaggattg gagcaatgat gtaagagctg aactagcaaa aacccctgta


 


10861
aataaaaaaa acattgaaaa aatgtatgaa agaatgtatg cagccttggg tgacccaaag


 


10921
gctccaggcc tgggggcctt tagaaggaag tttattcaga cttttggaaa agaatttgat


 


10981
aaacattttg ggaaaggagg ttctaaacta ctgagaatga agctcagtga cttcaacgac


 


11041
attaccaaca tgctactttt aaaaatgaac aaagactcaa agccccctgg gaatctgaaa


 


11101
gaatgttcac cctggatgag cgacttcaaa gtggagttcc tgagaaatga gctggagatt


 


11161
cccggtcagt atgacggtag gggaaagcca ttgccagagt accacgtgcg aatcgccggg


 


11221
tttgatgagc gggtgacagt catggcgtct ctgcgaaggc ccaagcgcat catcatccgt


 


11281
ggccatgacg agagggaaca ccctttcctg gtgaagggtg gcgaggacct gcggcaggac


 


11341
cagcgcgtgg agcagctctt ccaggtcatg aatgggatcc tggcccaaga ctccgcctgc


 


11401
agccagaggg ccctgcagct gaggacctat agcgttgtgc ccatgacctc caggttagga


 


11461
ttaattgagt ggcttgaaaa tactgttacc ttgaaggacc ttcttttgaa caccatgtcc


 


11521
caagaggaga aggcggctta cctgagtgat cccagggcac cgccgtgtga atataaagat


 


11581
tggctgacaa aaatgtcagg aaaacatgat gttggagctt acatgctaat gtataagggc


 


11641
gctaatcgta ctgaaacagt cacgtctttt agaaaacgag aaagtaaagt gcctgctgat


 


11701
ctcttaaagc gggccttcgt gaggatgagt acaagccctg aggctttcct ggcgctccgc


 


11761
tcccacttcg ccagctctca cgctctgata tgcatcagcc actggatcct cgggattgga


 


11821
gacagacatc tgaacaactt tatggtggcc atggagactg gcggcgtgat cgggatcgac


 


11881
tttgggcatg cgtttggatc cgctacacag tttctgccag tccctgagtt gatgcctttt


 


11941
cggctaactc gccagtttat caatctgatg ttaccaatga aagaaacggg ccttatgtac


 


12001
agcatcatgg tacacgcact ccgggccttc cgctcagacc ctggcctgct caccaacacc


 


12061
atggatgtgt ttgtcaagga gccctccttt gattggaaaa attttgaaca gaaaatgctg


 


12121
acaaaagtgg ggtcatggat tcaagaaata aatgttgctg aaaaaaattg gtacccccga


 


12181
cagaaaatat gttacgctaa gagaaagtta gcaggtgcca atccagcagt cattacttgt


 


12241
gatgagctac tcctgggtca tgagaaggcc cctgccttca gagactatgt ggctgtggca


 


12301
cgaggaagca aagatcacaa cattcgtgcc caagaaccag agagtgggct ttcagaagag


 


12361
actcaagtga agtgcctgat ggaccaggca acagacccca acatccttgg cagaacctgg


 


12421
gaaggatggg agccctggat gtgaggtctg tgggagtctg cagatagaaa gcattacatt


 


12481
gtttaaagaa tctactatac tttggttggc agcattccat gagctgattt tcctgaaaca


 


12541
ctaaagagaa atgtcttttg tgctacagtt tcgtagcatg agtttaaatc aagattatga


 


12601
tgagtaaatg tgtatgggtt aaatcaaaga taaggttata gtaacatcaa agattaggtg


 


12661
aggtttatag aaagatagat atccaggctt accaaagtat taagtcaaga atataatatg


 


12721
tgatcagctt tcaaagcatt tacaagtgct gcaagttagt gaaacagctg tctccgtaaa


 


12781
tggaggaaat gtggggaagc cttggaatgc ccttctggtt ctggcacatt ggaaagcaca


 


12841
ctcagaaggc ttcatcacca agattttggg agagtaaagc taagtatagt tgatgtaaca


 


12901
ttgtagaagc agcataggaa caataagaac aataggtaaa gctataatta tggcttatat


 


12961
ttagaaatga ctgcatttga tattttagga tatttttcta ggttttttcc tttcatttta


 


13021
ttctcttcta gttttgacat tttatgatag atttgctctc tagaaggaaa cgtctttatt


 


13081
taggagggca aaaattttgg tcatagcatt cacttttgct attccaatct acaactggaa


 


13141
gatacataaa agtgctttgc attgaatttg ggataacttc aaaaatccca tggttgttgt


 


13201
tagggatagt actaagcatt tcagttccag gagaataaaa gaaattccta tttgaaatga


 


13261
attcctcatt tggaggaaaa aaagcatgca ttctagcaca acaagatgaa attatggaat


 


13321
acaaaagtgg ctccttccca tgtgcagtcc ctgtcccccc ccgccagtcc tccacaccca


 


13381
aactgtttct gattggcttt tagctttttg ttgttttttt ttttccttct aacacttgta


 


13441
tttggaggct cttctgtgat tttgagaagt atactcttga gtgtttaata aagttttttt


 


13501
ccaaaagta






By “RAD23B” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—002874. An exemplary RAD23B sequence is provided below:










(SEQ ID NO: 9)



   1
gggggcacgt ctcggcgagt cacgatgatg gcggccacca tcctgtggtg agctagcgga



 


  61
ttccctgctt gtctcgccga ccccctcgcg ccttctgcag actccgtggc tggcgctcgg


 


 121
cgcgtgagga agcacggcgg cccgagttcg cggggaaggc cgcagtcgcg gaggcagcgg


 


 181
cgcggtccgg ggcacgggct gggggagagg ccgctccgct gggcgaatgt gacaagcccc


 


 241
cacccccacc gccttcctcc ccagagcgcg aggagcgcgg gcgaccccgg ggccccgcca


 


 301
ggccacagac cccgcccagc ggccagcacc cggcgcaggc ccggcagccg agctgcgcgg


 


 361
cggcaccatg caggtcaccc tgaagaccct ccagcagcag accttcaaga tagacattga


 


 421
ccccgaggag acggtgaaag cactgaaaga gaagattgaa tctgaaaagg ggaaagatgc


 


 481
ctttccagta gcaggtcaaa aattaattta tgcaggcaaa atcctcaatg atgatactgc


 


 541
tctcaaagaa tataaaattg atgagaaaaa ctttgtggtg gttatggtga ccaaacccaa


 


 601
agcagtgtcc acaccagcac cagctacaac tcagcagtca gctcctgcca gcactacagc


 


 661
agttacttcc tccaccacca caactgtggc tcaggctcca acccctgtcc ctgccttggc


 


 721
ccccacttcc acacctgcat ccatcactcc agcatcagcg acagcatctt ctgaacctgc


 


 781
acctgctagt gcagctaaac aagagaagcc tgcagaaaag ccagcagaga caccagtggc


 


 841
tactagccca acagcaactg acagtacatc gggtgattct tctcggtcaa acctttttga


 


 901
agatgcaacg agtgcacttg tgacgggtca gtcttacgag aatatggtaa ctgagatcat


 


 961
gtcaatgggc tatgaacgag agcaagtaat tgcagccctg agagccagtt tcaacaaccc


 


1021
tgacagagca gtggagtatc ttttaatggg aatccctgga gatagagaaa gtcaggctgt


 


1081
ggttgacccc cctcaagcag ctagtactgg ggctcctcag tcttcagcag tggctgcagc


 


1141
tgcagcaact acgacagcaa caactacaac aacaagttct ggaggacatc cccttgaatt


 


1201
tttacggaat cagcctcagt ttcaacagat gagacaaatt attcagcaga atccttcctt


 


1261
gcttccagcg ttactacagc agataggtcg agagaatcct caattacttc agcaaattag


 


1321
ccaacaccag gagcatttta ttcagatgtt aaatgaacca gttcaagaag ctggtggtca


 


1381
aggaggagga ggtggaggtg gcagtggagg aattgcagaa gctggaagtg gtcatatgaa


 


1441
ctacattcaa gtaacacctc aggaaaaaga agctatagaa aggttaaagg cattaggatt


 


1501
tcctgaagga cttgtgatac aagcgtattt tgcttgtgag aagaatgaga atttggctgc


 


1561
caattttctt ctacagcaga actttgatga agattgaaag ggactttttt atatctcaca


 


1621
cttcacacca gtgcattaca ctaacttgtt cactggattg tctgggatga cttgggctca


 


1681
tatccacaat acttggtata aggtagtaga ttgttggggg tggggaggga gggatctagg


 


1741
atacagggca gggataaata cagtgcatgt ctgcttcaat tagcagatgc cgcaactcca


 


1801
cacagtgtgt aaaatatata caaccaaaaa tcagcttttg caggtcttta tttcttctgt


 


1861
aaaacagtag gtaacttttc ctaggtttca ctctttttag tgtactagat ccagaaactt


 


1921
agtgtaatgc cctgctttat atttctttga cttaacattg gtttcagaaa gaatcttagc


 


1981
tacctagaat ttacagtctc tgtttcatgg caacactgga taatggcttt gtgaaattta


 


2041
aaaaattttt gtagcgactg taaacagaaa tgccaaattg atggttaatt gttgctgctt


 


2101
caaaaataag tataaaatta atatgtaagg aagcccattc tttcatgtta aatacttggg


 


2161
gtgggagggg agaaagggaa ccttttctta aaatgaaaat aattactgct attttaaaat


 


2221
ttcttgatca ttgaatgtga gacccttcta acatgatttg agaagctgta caagtatagg


 


2281
cagagttatt ttcctgttta catttttttt ttgttttggg gaaaaaattg gtaggtgtct


 


2341
aattactgtt tacttcattg ttatattgca gtaaaagttt taaaacaacc attgcatgtt


 


2401
tgcttttgat gtatcccttt gtgaaattag cacttttggg gccaatggag aaatgcagca


 


2461
ttcactctcc ctgtcttttc cccttccctc agcagaaacg tgtttatcag caagtcgtga


 


2521
gtcaaactgc tgccttttaa aaaacccaca aaatgctgat tcagttcaaa attaatgcaa


 


2581
atgtttcaaa actgggtttc tgatatttgt aaatgtgttt ctttattaga taagagtgta


 


2641
ttaccattaa agtcattagt ataatattgc tttcaaaaag aaatggtaga caaaactata


 


2701
atccagcatc ttttattgca ttggaaagac tggcaaagtc ttttggatgg gttgggagat


 


2761
gtggctggaa agtactttgg aaaatataca atcaagatat ctcatggcat attaaaagaa


 


2821
aaatcttaat agcagtgttg gcttttattt ggattttttc atctcagttt tttctgtgga


 


2881
atctccttca ttggcattgt tatttaatca taaacggggc agatgtctac ttgttcagtt


 


2941
tttcaaatct gttttcctga gtataaataa gagtatttaa agaaataatt tggattgctt


 


3001
ttgttttttg tttccttttt tttaaccatc tgatactaag aagatgaatt tgcacagatt


 


3061
tctctgcata atttctcaat atctttagca cagtatggtg atgatgactt ttaagcattt


 


3121
acatcacgta ctcataacct attatgaaaa taaatgaaac tggctgggta tggtggctca


 


3181
tgcctataat cccagcactt tgggaggccg aggtgggcag atcacttgag gccaggagat


 


3241
tgagaccagc ctgaccgtca tggcgaaacc ccgtctatac taaaaataca aaaaatagcc


 


3301
aggcatggtg gcgcacgcct gtggtcccag ctacttggga ggctgaggca tgagaattgc


 


3361
ttgaacccgg gaagtgaagg ttgccgtgag ctgagatcac accactgcca taaacatgac


 


3421
aggcttttgg actttgtatt acctgtatgt tttataatgg atcatgcata atttctcagg


 


3481
agaataaaat gagaattcat atatacgttc atctttcaag tcagagcaat gagttgggaa


 


3541
aagaggtggc atttctgatc ggataatgga atactctcat ttattttatg acattctctg


 


3601
tctactcaga tcatagtgaa aactggaaac aaaaaaaaaa aacagcctct tcttggaaag


 


3661
tgacagcaga aggtggcatg gagcttgtgt ccttggacaa caaatctgga tatactagga


 


3721
ttaattatca gaagacagct caggccaagt tttgatcgtt ccatacagta ccttgtttat


 


3781
ctgcttctta aagaatcagc cgagacacca taaaagaaat aggctttttg tgccttttgc


 


3841
tgttaatgtt taatttacaa actgttttgg taaatctctt aatgtaagta gctafttgac


 


3901
tttggaattt tgcattcgag gtatactgtc atttcttgaa atctttttct cgtttagttg


 


3961
ctctgtggga aatgtgagga agcctaagtt tgtatttgta aatttcttat gccatcctct


 


4021
agtcaaattt tttttcattg tttaaaaata cggaagtgtt ccaatataat tttttcctgt


 


4081
actggatggc taggattcta gagaattgat tataaaatat tttcaataca






By “RAD54L” is meant a gene that transcribes an RNA having at least 85% nucleotide sequence identity to NM—003579 or NM—001142548. An exemplary RAD54L sequence is provided below:










(SEQ ID NO: 10)



   1
gatacgacgg cagcgcggcg ggaggttcga ttgacccggt cttggcgggt cggtgagtct



 


  61
tggcggctgt taacgcgcgc tttgggaaca ggaaggttga gagagaggtg ctggggtctg


 


 121
cgtctatctc tgtcgctctt ttcagcccct cctggtattc ccctcctaac ctgggttttt


 


 181
tacacgcccg cgtggcttcc tgctcgacct ccctgagtct gatcctggtt tccacctcca


 


 241
gccctgggaa atttcctttc tccagactcg ccctccccac ccgggcctcg gactttcacc


 


 301
ccagcttctc tctcctggcc agtgattacc cacccccaat cccaccccgc cccgccgcgc


 


 361
aactacctcc tcccttcacc cggactggga ccatcatccc cactccactc cgcccagtct


 


 421
gggactccac ctgcctcctc cccaatccca cactaatctc tgcttggtct cttcctcttt


 


 481
ggcctaatct ctcgtctcgg cttattgggg acggccactc tcacagtttg gttccaaaca


 


 541
ccagttcctg gatggattcc cgccatccat gccccctctt taattagccg gtcctctcaa


 


 601
taatgtagca gccccctcta cagattagac cctggtccta cactcttagc cgctgcctgc


 


 661
ttttgacctt tggctcatgg gtacttgacg ttttaaactc ctaggcccag gatgaggagg


 


 721
agcttggctc ccagccagct ggccaagaga aaacctgaag gcaggtcctg tgatgatgaa


 


 781
gactggcaac ctggcctagt gactcctagg aaacggaaat ccagcagtga gacccagatc


 


 841
caggagtgtt tcctgtctcc ttttcggaaa cctttgagtc agctaaccaa tcaaccacct


 


 901
tgtctggaca gcagtcagca tgaagcattt attcgaagca ttttgtcaaa gcctttcaaa


 


 961
gtccccattc caaattatca aggtcctctg ggctctcgag cattgggcct gaaaagggct


 


1021
ggggtccgcc gggccctcca tgaccccctg gaaaaagatg ccttggttct gtatgagcct


 


1081
cccccgctga gcgctcatga ccagctgaag cttgacaagg agaaactccc tgtccatgtg


 


1141
gttgttgacc ctattctcag taaggttttg cggcctcatc agagagaggg agtgaaattc


 


1201
ctgtgggagt gtgtcaccag tcggcgcatc cctggcagcc atggctgcat catggctgat


 


1261
gagatgggcc taggaaagac gctgcagtgc atcacattga tgtggacact tttacgccag


 


1321
agtccagagt gcaagccaga aattgacaag gcagtggtgg tgtcgccttc cagcctggtg


 


1381
aagaactggt acaatgaggt tgggaaatgg ctcggaggga ggatccaacc tctggccatc


 


1441
gatggaggat ctaaggatga aatagaccaa aagctggaag gattcatgaa ccagcgtgga


 


1501
gccagggtgt cttctcccat cctcatcatt tcctatgaga ccttccgcct tcatgttgga


 


1561
gtcctccaga aaggaagtgt tggtctggtc atatgtgacg agggacacag gctcaagaac


 


1621
tctgagaatc agacttacca agccctggac agcttgaaca ccagccggcg ggtgctcatc


 


1681
tccggaactc ccatccagaa tgatctgctt gagtatttca gcttggtaca ttttgttaat


 


1741
tccggcatcc tagggactgc ccatgaattc aagaagcatt ttgaattgcc aattttgaag


 


1801
ggtcgagacg ctgctgctag tgaggcagac aggcagctag gagaggagcg gctgcgggag


 


1861
ctcaccagca ttgtgaatag atgcctgata cggaggactt ctgatatcct ttctaaatat


 


1921
ctgcctgtga agattgagca ggtcgtttgt tgtaggctga caccccttca gactgagtta


 


1981
tacaagaggt ttctgagaca agccaaaccg gcagaagaat tgcttgaggg caagatgagt


 


2041
gtgtcttccc tttcttccat cacctcgcta aagaagcttt gtaatcatcc agctctaatc


 


2101
tatgataagt gtgtggaaga ggaggatggc tttgtgggtg ccttggacdt cttccctcct


 


2161
ggttacagct ctaaggccct ggagccccag ctgtcaggta agatgctggt cctggattat


 


2221
attctggcgg tgacccgaag ccgtagcagt gacaaagtag tgctggtgtc gaattacacc


 


2281
cagactttgg atctctttga gaagctgtgc cgtgcccgaa ggtacttata cgtccgcctg


 


2341
gatggcacga tgtccattaa gaagcgagcc aaggttgtag aacgcttcaa tagtccatcg


 


2401
agccctgact ttgtcttcat gctgagcagc aaagctgggg gctgtggcct caatctcatt


 


2461
ggggctaacc ggctggtcat gtttgaccct gactggaacc cagccaatga tgaacaagcc


 


2521
atggcccggg tctggcgaga tggtcaaaag aagacttgct atatctaccg cctgctgtct


 


2581
gcagggacca ttgaggagaa gatcttccag cgtcagagcc acaagaaggc actgagcagc


 


2641
tgtgtggtgg atgaggagca ggatgtagag cgccacttct ctctgggcga gttgaaggag


 


2701
ctgtttatcc tggatgaagc tagectcagt gacacacatg acaggttgca ctgccgacgt


 


2761
tgtgtcaaca gccgtcagat ccggccaccc cctgatggtt ctgactgcac ttcagacctg


 


2821
gcagggtgga accactgcac tgataagtgg gggctccggg atgaggtact ccaggctgcc


 


2881
tgggatgctg cctccactgc catcaccttc gtcttccacc agcgttctca tgaggagcag


 


2941
cggggcctcc gctgataacc agctggtctg ggtgtagctc ttagaggaag gagataggga


 


3001
aaaggggctc cttgctccac agggccctgt tgaattttgt tctctgggag aaaatcatca


 


3061
agaagggctg catgatgttt gcccaaaatt tattttataa gaaaaacttt tttggttaaa


 


3121
aaaaagaata aaggtatgaa agggttaaaa aaaaaaaaaa aaaa






By “PSMA” is meant prostate-specific membrane antigen, a polypeptide having at least 85% amino acid sequence identity to NP—004467, NP00104986, NP—001180400, NP—001180401, or NP—001180402.
By “A10-3” is meant an aptamer as shown in FIG. 13.
By “agent” is meant any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or fragments thereof.
By “ameliorate” is meant to decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.
By “alteration” is meant a change (increase or decrease) in the expression levels or activity of a gene or polypeptide as detected by standard art known methods such as those described herein. As used herein, an alteration includes a 10% change in expression levels, preferably a 25% change, more preferably a 40% change, and most preferably a 50% or greater change in expression levels.
By “analog” is meant a molecule that is not identical, but has analogous functional or structural features. For example, a polypeptide analog retains the biological activity of a corresponding naturally-occurring polypeptide, while having certain biochemical modifications that enhance the analog's function relative to a naturally occurring polypeptide. Such biochemical modifications could increase the analog's protease resistance, membrane permeability, or half-life, without altering, for example, ligand binding. An analog may include an unnatural amino acid.
The term “cancer” refers to a malignant tumor of potentially unlimited growth that expands locally by invasion and systemically by metastasis.
The term “carcinoma” is art recognized and refers to malignancies of epithelial or endocrine tissues including respiratory system carcinomas, gastrointestinal system carcinomas, genitourinary system carcinomas, testicular carcinomas, breast carcinomas, prostatic carcinomas, endocrine system carcinomas, and melanomas. Exemplary carcinomas include those forming from tissue of the cervix, lung, prostate, breast, head and neck, colon, pancreas and ovary. The term also includes carcinosarcomas, e.g., which include malignant tumors composed of carcinomatous and sarcomatous tissues. An “adenocarcinoma” refers to a carcinoma derived from glandular tissue or in which the tumor cells form recognizable glandular structures.
In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
“Detect” refers to identifying the presence, absence or amount of the analyte to be detected.
By “detectable label” is meant a composition that when linked to a molecule of interest renders the latter detectable, via spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include radioactive isotopes, magnetic beads, metallic beads, colloidal particles, fluorescent dyes, electron-dense reagents, enzymes (for example, as commonly used in an ELISA), biotin, digoxigenin, or haptens.
By “disease” is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. Examples of diseases include cancer, in particular, any cancer that is amenable to treatment with ionizing radiation. Specific, non-limiting, examples of disease include prostate cancer, colon cancer, breast cancer, pancreatic cancer, and lung cancer.
By “effective amount” is meant the amount required to ameliorate the symptoms of a disease relative to an untreated patient. The effective amount of active compound(s) used to practice the present invention for therapeutic treatment of a disease varies depending upon the manner of administration, the age, body weight, and general health of the subject. Therapeutic treatment can be achieved upon single or multiple dose administration to a subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an “effective” amount.
The invention provides a number of targets that are useful for the development of highly specific drugs to treat or a disorder characterized by the methods delineated herein. In addition, the methods of the invention provide a facile means to identify therapies that are safe for use in subjects. In addition, the methods of the invention provide a route for analyzing virtually any number of compounds for effects on a disease described herein with high-volume throughput, high sensitivity, and low complexity.
By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides or amino acids.
“Hybridization” means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases. For example, adenine and thymine are complementary nucleobases that pair through the formation of hydrogen bonds.
By “inhibitory nucleic acid” is meant a double-stranded RNA, siRNA, shRNA, or antisense RNA, or a portion thereof, or a mimetic thereof, that when administered to a mammalian cell results in a decrease (e.g., by 10%, 25%, 50%, 75%, or even 90-100%) in the expression of a target gene. Typically, a nucleic acid inhibitor comprises at least a portion of a target nucleic acid molecule, or an ortholog thereof, or comprises at least a portion of the complementary strand of a target nucleic acid molecule. For example, an inhibitory nucleic acid molecule comprises at least a portion of any or all of the nucleic acids delineated herein.
By “isolated polynucleotide” is meant a nucleic acid (e.g., a DNA) that is free of the genes which, in the naturally-occurring genome of the organism from which the nucleic acid molecule of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA that is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule (for example, a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. In addition, the term includes an RNA molecule that is transcribed from a DNA molecule, as well as a recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequence.
By an “isolated polypeptide” is meant a polypeptide of the invention that has been separated from components that naturally accompany it. Typically, the polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, a polypeptide of the invention. An isolated polypeptide of the invention may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.
The term “neoplastic” refers to those cells having the capacity for autonomous growth, e.g., an abnormal state or condition characterized by rapidly proliferating cell growth. A neoplastic disease state may be categorized as pathologic, e.g., characterizing or constituting a disease state, or may be categorized as non-pathologic, e.g., a deviation from normal but not associated with a disease state. The term is meant to include all types of cancerous growths or oncogenic processes, metastatic tissues or malignantly transformed cells, tissues, or organs, irrespective of histopathologic type or stage of invasiveness. “Pathologic hyperproliferative” cells occur in disease states characterized by malignant tumor growth. Examples of non-pathologic hyperproliferative cells include proliferation of cells associated with wound repair.
The language “inhibiting the growth” of the neoplasm includes the slowing, interrupting, arresting or stopping its growth and metastases and does not necessarily indicate a total elimination of the neoplastic growth.
The common medical meaning of the term “neoplasia” refers to “new cell growth” that results as a loss of responsiveness to normal growth controls, e.g. to neoplastic cell growth. A “hyperplasia” refers to cells undergoing an abnormally high rate of growth. However, as used herein, the term neoplasia generally refers to cells experiencing abnormal cell growth rates. Neoplasias include “tumors,” which may be either benign, premalignant or malignant.
As used herein, “obtaining” as in “obtaining an agent” includes synthesizing, purchasing, or otherwise acquiring the agent.
“Primer set” means a set of oligonucleotides that may be used, for example, for PCR. A primer set would consist of at least 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 30, 40, 50, 60, 80, 100, 200, 250, 300, 400, 500, 600, or more primers.
By “reduces” is meant a negative alteration of at least 10%, 25%, 50%, 75%, or 100%.
By “reference” is meant a standard or control.
A “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset of or the entirety of a specified sequence; for example, a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence. For polypeptides, the length of the reference polypeptide sequence can be at least about 16 amino acids, at least about 20 amino acids, at least about 25 amino acids, or about 35 amino acids, about 50 amino acids, or about 100 amino acids. For nucleic acids, the length of the reference nucleic acid sequence can be at least about 50 nucleotides, at least about 60 nucleotides, at least about 75 nucleotides, or about 100 nucleotides or about 300 nucleotides or any integer thereabout or therebetween.
By “siRNA” is meant a double stranded RNA. Optimally, an siRNA is 18, 19, 20, 21, 22, 23 or 24 nucleotides in length and has a 2 base overhang at its 3′ end. These dsRNAs can be introduced to an individual cell or to a whole animal; for example, they may be introduced systemically via the bloodstream. Such siRNAs are used to downregulate mRNA levels or promoter activity.
By “specifically binds” is meant a compound or antibody that recognizes and binds a polypeptide of the invention, but which does not substantially recognize and bind other molecules in a sample, for example, a biological sample, which naturally includes a polypeptide of the invention.
Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. Nucleic acid molecules useful in the methods of the invention include any nucleic acid molecule that encodes a polypeptide of the invention or a fragment thereof. Such nucleic acid molecules need not be 100% identical with an endogenous nucleic acid sequence, but will typically exhibit substantial identity. Polynucleotides having “substantial identity” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. By “hybridize” is meant a pair to form a double-stranded molecule between complementary polynucleotide sequences (e.g., a gene described herein), or portions thereof, under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A. R. (1987) Methods Enzymol. 152:507).
For example, stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate, preferably less than about 500 mM NaCl and 50 mM trisodium citrate, and more preferably less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide. Stringent temperature conditions can include temperatures of at least about 30° C., of at least about 37° C., or at least about 42° C. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed. In embodiments, hybridization will occur at 30° C. in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In other embodiments, hybridization will occur at 37° C. in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 μg/ml denatured salmon sperm DNA (ssDNA). In embodiments, hybridization will occur at 42° C. in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200 μg/ml ssDNA. Useful variations on these conditions will be readily apparent to those skilled in the art.
For most applications, washing steps that follow hybridization will also vary in stringency. Wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature. For example, stringent salt concentration for the wash steps can be less than about 30 mM NaCl and 3 mM trisodium citrate, or less than about 15 mM NaCl and 1.5 mM trisodium citrate. Stringent temperature conditions for the wash steps can include a temperature of at least about 25° C., of at least about 42° C., or of at least about 68° C. In embodiments, wash steps will occur at 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In other embodiments, wash steps will occur at 42° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In related embodiments, wash steps will occur at 68° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additional variations on these conditions will be readily apparent to those skilled in the art. Hybridization techniques are well known to those skilled in the art and are described, for example, in Benton and Davis (Science 196:180, 1977); Grunstein and Hogness (Proc. Natl. Acad. Sci., USA 72:3961, 1975); Ausubel et al. (Current Protocols in Molecular Biology, Wiley Interscience, New York, 2001); Berger and Kimmel (Guide to Molecular Cloning Techniques, 1987, Academic Press, New York); and Sambrook et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York).
By “substantially identical” is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein). Such a sequence can be at least 60%, 80% or 85%, 90%, 95% or even 99% identical at the amino acid level or nucleic acid to the sequence used for comparison.
Sequence identity is typically measured using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and/or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e−3 and e−100 indicating a closely related sequence.
By “subject” is meant a mammal, including, but not limited to, a human or non-human mammal, such as a bovine, equine, canine, ovine, or feline.
Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive. Unless specifically stated or obvious from context, as used herein, the terms “a”, “an”, and “the” are understood to be singular or plural.
Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.
The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a plot showing the results of a screen for radiosensitization target genes and their cognate siRNAs. An siRNA library screen for candidate radiosensitization targets was carried out in DU145 cells. Cells were transfected with library siRNAs or controls. Transfected cells were untreated or irradiated (6 Gy) 72 hours later. Radiosensitization was calculated as percent increased cell death associated with a gene-specific siRNA after radiation therapy compared with irradiated cells transfected with a control siRNA. Each diamond represents an siRNA (triplicate, average) organized alphabetically. Mean library radiosensitization and SD are shown by solid and dashed lines, respectively.
FIGS. 2A-2F are graphs showing the confirmation of siRNA mediated radiosensitization using clonogenic survival assays. Radiosensitization was confirmed by clonogenic survival assays (n=3). DU145 cells were reverse transfected with 5 nM control siRNA or (FIG. 2A) DNAPK, (FIG. 2B) MAD2L2, (FIG. 2C) BRCA2, (FIG. 2D) NBN, (FIG. 2E) RAD23B, or (FIG. 2F) RAD54L siRNA 72 hours prior to irradiation. DMF0.1 values are shown for each. Open diamonds, control siRNA; closed squares, candidate siRNA. SF, surviving fraction.
FIGS. 3A-3F are graphs showing the siRNA-mediated knock-down of radiosensitization target genes. DU145 cells were transfected with Candidate siRNAs (5 nM), 48 hours later the mRNA level of target genes were evaluated by qRTPCR. Data are normalized to GAPDH mRNA. (FIG. 3A) DNA-PK, (FIG. 3B) MAD2L2, (FIG. 3C) BRCA2, (FIG. 3D) NBN, (FIG. 3E) Rad23B, and (FIG. 3F) RAD54L. Columns represent mean±S.E.M, n=3.
FIG. 4 is a graph showing the results of siRNA-mediated radiation sensitization of a panel of radiosensitization target genes. LNCaP cells were seeded in 6-well plates at 2×105 cells per well. After 24 hours, cells were either transfected with 100 nM of DNA-PK, BRCA2, NBN, MAD2L2, RAD23B, RAD54L siRNAs or control siRNAs separately using HiPerfectTransfection Reagent. 48 hours later, cells were seeded in 96 well plate at 2000 cells per well. 24 hours later, cells were then irradiated with Gy IR using a Gammacell 40 (Nordion, Ottawa, ONT, Canada) 137Cs radiator at approximately 0.6 Gy/min. Cell viability was assessed after 12 days by MTS. means±S.E.M, n=3.
FIGS. 5A -5F demonstrate the ability of aptamer-shRNA chimeras to mediate target gene knock-down in PSMA expressing cells. FIGS. 5A and 5B include structures of illustrative examples of aptamer-shRNA chimeras, including the secondary structure of (FIG. 5A) A10-3-DNAPK (SEQ ID NO: 44) and (FIG. 5B) Neg-DNAPK (SEQ ID NO: 47). Aptamer and shRNA portions are shown by brackets. FIGS. 5C-5C are graphs showing the results of aptamer-shRNA chimera-mediated RNAi in the absence of transfection reagents. (FIG. 5C) LNCaP cells were treated with 0, 4, 40, or 400 nM A10-3-DNAPK for 48 hours, and DNAPK mRNA levels were quantified by qRT-PCR. LNCaP cells were treated with 400 nM of (FIG. 5D) A10-3-DNAPK, (FIG. 5E) A10-3-BRCA2, or (FIG. 5F) A10-3-ATM for 48 hours. Respective target gene mRNA levels were quantified by qRT-PCR. Appropriate siRNAs were transfected (100 nM) as positive controls. Expression was normalized to GAPDH. Mean±SEM (n=3). *P<0.05.
FIG. 6 is a graph showing that aptamer-shRNA chimeras do not illicit an interferon response. 2×105 LNCaP cells were either transfected with DNA-PK siRNA or incubated with 400 nM A10-3-Con, A10-3-DNA-PK or NegDNA-PK for 48 hours before interferon β secretion into the cell culture supernatant was analyzed. Cells were separately treated with 5 μg/ml Poly(I:C) (Invitrogen, Carlsbad, Calif.) as a positive control. Detection of interferon β was accomplished by using a commercially available sandwich interferon β ELISA kit (PBL) following manufacturer's recommendations. 25-2,000 pg/ml of interferon-beta standard was used as a positive control for assay integrity. means±S.E.M, n=3.
FIGS. 7A-7H show the PSMA selectivity of the aptamer-shRNA chimeras. FIGS. 7A and 7B include graphs depicting PSMA selectivity. (FIG. 7A) PC3-PIP or (FIG. 7B) PC3-Flu cells were treated with 400 nM aptamer-shRNA chimeras for 48 hours, and DNAPK expression was quantified by qRT-PCR. siRNA DNAPK (100 nM transfected) was included as a positive control. Expression is normalized to GAPDH. Mean±SEM (n=3). *P<0.05. FIG. 7C is a gel showing aptamer-shRNA chimera processing by Dicer in vitro. Cleavage products were analyzed by denaturing PAGE and ethidium bromide staining. Image was inverted for clarity. FIG. 7D includes a gel showing the results from a cell-based RNAi processing assay. LNCaP cells were treated with 400 nM aptamer-shRNA chimeras, and RNA was extracted 48 hours later for Northern blot assay. Probes are specific to corresponding antisense siRNAs. ds, double-stranded; ss, single-stranded. FIGS. 7E and 7F show the results from targeted in vivo knockdown. Subcutaneous LNCaP tumors were injected with aptamer-shRNA chimeras (200 pmol/injection) on days −3 and −2 and harvested on day 0, and DNAPK expression was determined. FIG. 7E is a graph showing qRT-PCR results. Mean±SEM. *P<0.05. FIG. 7F includes immunohistochemistry results. Original magnification, x400. FIGS. 7G and 7H include gels showing results from 5′-RACE PCR analysis to assess siRNA-mediated cleavage of DNAPK. LNCaP cells transfected with DNAPK siRNA or with A10-3-DNAPK chimeras produced a specific DNAPK cleavage product (FIG. 7G). In vivo treatment of LNCaP xenografts with A10-3-DNAPK chimera resulted in siRNA-mediated DNAPK cleavage (FIG. 7H).
FIGS. 8A and 8B include flow cytometry results showing the cell surface expression of PSMA. PSMA positive PC3-PIP cells and PSMA negative PC3-Flu cells were incubated with anti-PSMA (J591) antibody and stained with secondary antibody conjugated with Alexa488. PSMA expression was then determined by flow cytometry. 48.2% of PC3-PIP (FIG. 8A) cells expressed PSMA when compared to PC3-Flu (FIG. 8B) cells.
FIGS. 9A-9D are graphs showing aptamer-shRNA mediated radiosensitization in vitro and in vivo PCa models. FIG. 9A shows in vitro radiosensitization results. LNCaP cells treated with 400 nM A10-3-DNAPK or A10-3-Con or transfected with control siRNA were irradiated 48 hours later with 6 Gy IR, and cell viability was assessed 12 days later by MTS. Percent cell death is relative to nonirradiated cells. FIGS. 9B-9D show in vivo radiosensitization. Established tumors were treated with aptamer-shRNA chimeras (days −3 and −2) and either 6 Gy IR or no radiation (day 0). FIG. 9B shows results for the PC3 tumor model (n=3 per group). A10-3-DNAPK provided no significant therapeutic benefit to nonirradiated or irradiated PC3 tumors. Radiation similarly affected growth in all treatment groups. Mean±SEM. FIG. 9C shows results for the LNCaP tumor model (n≧6 per group). Radiation similarly affected growth in all treatment groups except irradiated A10-3-DNAPK. *P<0.05, *** P<0.001, A10-3-DNAPK IR vs. A 10-3-Con IR and A10-3-DNAPK IR vs. Neg-DNAPK IR; 2-way ANOVA. Mean±SEM. FIG. 9D shows the extension of tumor quadrupling for LNCaP tumor model. Events (animals whose tumor volume was not yet 4-fold the size at injection) were plotted by Kaplan-Meier curve. P<0.01, A10-3-Con IR vs. A10-3-Con and Neg-DNAPK IR vs. Neg-DNAPK; P<0.0001, A10-3-DNAPK IR vs. A10-3-Con IR and A10-3-DNAPK IR vs. Neg-DNAPK IR; log-rank (Mantel-Cox) test.
FIGS. 10A-10G are graphs showing aptamer-shRNA chimera mediated radiosensitization in individual LNCaP tumors in vivo. Established LNCaP tumors were intratumorally injected with 200 pmol aptamer-shRNAs on days −3 and day −2. On day 0, animals were divided into groups that received either 6 Gy radiation (+R) or no radiation (−R). Tumors were measured every other day until reaching four times the volume at time of radiation. FIG. 10A: PBS(−R) (n=6); FIG. 10B: A10-3-Con (−R) (n=6); FIG. 10C: A10-3-DNA-PK(−R) (n=6); FIG. 10D: NegDNA-PK(−R) (n=6); FIG. 10E: A10-3-Con(+R) (n=6); FIG. 10F: Neg-DNA-PK(+R) (n=6); FIG. 10G: A10-3-DNAPK(+R) (n=8).
FIG. 11 shows the result of ex vivo treatment of human prostate tissue with aptamer-shRNA chimeras. Sections of normal human prostate tissue were obtained from fresh radical prostatectomy specimens and maintained ex vivo. These were treated with 200 nM aptamer-shRNA chimeras, and DNAPK levels were detected by immunohistochemistry 48 hours after treatment. Quantitative image analysis determined a 25% reduction in DNAPK Staining for A10-3-DNAPK-treated samples. Original magnification, ×400.
FIGS. 12A-12C illustrate an the design of an aptamer-siRNA chimera. FIG. 12A is a table showing the sequences of the three oligonculeotides (SEQ ID NOS 63-65, respectively, in order of appearance) that comprise the aptamer-siRNA chimera. FIG. 12B shows the structure of the aptamer-siRNA chimera. To generate the aptamer-siRNA molecule the aptamer olignucleotide, sense strand-siRNA olignucleotide, and the antisense strand-siRNA are mixed and annealed. FIG. 12C is a graph showing the ability of the aptamer-siRNA chimera to knock-down expression of the target gene DNAPK.
FIG. 13 shows the structure of the A10-3 aptamer.



DETAILED DESCRIPTION OF THE INVENTION
The invention features compositions comprising aptamer-inhibitory nucleic acid (e.g., shRNA) chimeras and methods of using the composition to sensitize a cancer cell to radiation.
The invention is based, at least in part, on the discovery that an aptamer that binds to prostate-specific membrane antigen (PSMA) is able to target an attached shRNA to prostate cancer cells and silence the gene that the shRNA targets. In addition, the invention is further based, at least in part, on the discovery of a set of genes, the inhibition of which results in the cancer cell becoming sensitized to ionizing radiation treatment. As described in more detail below, the discovery of these compositions and target genes demonstrates that the therapeutic index for local treatment of prostate cancer (PCa) can be improved by selectively sensitizing PCa cells to IR. The therapeutic strategy to deliver dose-escalated radiation therapy to the prostate, historically considered as more than approximately 70 Gy, has been constrained by the limited tolerance of the urinary tract and rectum (Leibel S A, Hanks G E, Kramer S. Patterns of care outcome studies: results of the national practice in adenocarcinoma of the prostate. Int J Radiat Oncol Biol Phys. 1984; 10(3):401-409; Smit W G, Helle P A, van Putten W L, Wijnmaalen A J, Seldenrath J J, van der Werf-Messing B H. Late radiation damage in prostate cancer patients treated by high dose external radiotherapy in relation to rectal dose. Int J Radiat Oncol Biol Phys. 1990; 18(1):23-29). Thus, the invention provides the benefits of dose-escalated radiation without the associated risks to normal tissue, the concomitant expensive high-tech infrastructure, and/or the added use of androgen suppression. Accordingly, the invention will have a significant impact on PCa morbidity and mortality.
The present invention provides methods of treating a disease or disorder or symptoms thereof which comprise administering a therapeutically effective amount of a pharmaceutical composition comprising an aptamer-inhibitory nucleic acid (e.g., shRNA) chimera to a subject (e.g., a mammal such as a human). Thus, one embodiment is a method of treating a subject suffering from cancer or symptom thereof. The method includes the step of administering to the mammal a therapeutic amount of an aptamer-inhibitory nucleic acid (e.g., shRNA) chimera followed by treating the mammal with ionizing radiation to treat the cancer or symptom thereof, under conditions such that the disease or disorder is treated. In certain embodiments the mammal is suffering from prostate cancer.
The methods herein include administering to the subject (including a subject identified as in need of such treatment) an effective amount of an aptamer-inhibitory nucleic acid (e.g., shRNA) chimera wherein the aptamer binds to a cell surface molecule on the cancer cell and the shRNA inhibits the expression of a target gene wherein the knock-down of the target gene product results in the cancer cell becoming radiosensitized. Following treatment with an aptamer-inhibitory nucleic acid (e.g., shRNA) chimera the cancer is further treated with ionizing radiation. Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g. opinion) or objective (e.g. measurable by a test or diagnostic method).
As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
As used herein, the terms “prevent,” “preventing,” “prevention,” “prophylactic treatment” and the like refer to reducing the probability of developing a disorder or condition in a subject, who does not have, but is at risk of or susceptible to developing a disorder or condition.
The therapeutic methods of the invention in general comprise administration of therapeutically effective amount of the compounds herein, such as a compound of the formulae herein to a subject (e.g., animal, human) in need thereof, including a mammal, particularly a human. Such treatment will be suitably administered to subjects, particularly humans, suffering from, having, susceptible to, or at risk for a disease, disorder, or symptom thereof. Determination of those subjects “at risk” can be made by any objective or subjective determination by a diagnostic test or opinion of a subject or health care provider (e.g., genetic test, enzyme or protein marker, Marker (as defined herein), family history, and the like).
In one embodiment, the invention provides a method of monitoring treatment progress. The method includes the step of determining a level of diagnostic marker (Marker) (e.g., any target delineated herein modulated by a compound herein, a protein or indicator thereof, etc.) or diagnostic measurement (e.g., screen, assay) in a subject suffering from or susceptible to a disorder or symptoms thereof, in which the subject has been administered a therapeutic amount of a compound herein sufficient to treat the disease or symptoms thereof. The level of Marker determined in the method can be compared to known levels of Marker in either healthy normal controls or in other afflicted patients to establish the subject's disease status. In preferred embodiments, a second level of Marker in the subject is determined at a time point later than the determination of the first level, and the two levels are compared to monitor the course of disease or the efficacy of the therapy. In certain preferred embodiments, a pre-treatment level of Marker in the subject is determined prior to beginning treatment according to this invention; this pre-treatment level of Marker can then be compared to the level of Marker in the subject after the treatment commences, to determine the efficacy of the treatment.
Localized Cancer Cells
As used herein, “localized cancer cell” and “localized neoplastic cell” are used interchangeably and refer to a cancer/neoplastic cell present at the site of a tumor/cancer.
The aptamer-inhibitory nucleic acid chimeras are suitable for use to target any localized cancer cell. Cancers can affect a variety of cell types, tissues, or organs, including but not limited to bladder, bone, brain, breast, cartilage, glia, esophagus, fallopian tube, gallbladder, heart, intestines, kidney, liver, lung, lymph node, nervous tissue, ovaries, pancreas, prostate, skeletal muscle, skin, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea, urogenital tract, ureter, urethra, uterus, and vagina, or a tissue or cell type thereof. Examples of such include, but are not limited to, melanoma, renal cancer, prostate cancer, breast cancer, colon cancer and lung cancer, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular malignant melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, testicular cancer, uterine cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina, carcinoma of the vulva, Hodgkin's Disease, non-Hodgkin's lymphoma, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, sarcoma of soft tissue, cancer of the urethra, cancer of the penis, chronic or acute leukemias including acute myeloid leukemia, chronic myeloid leukemia, acute lymphoblastic leukemia, chronic lymphocytic leukemia, solid tumours of childhood, lymphocytic lymphoma, cancer of the bladder, cancer of the kidney or ureter, carcinoma of the renal pelvis, neoplasm of the central nervous system (CNS), primary CNS lymphoma, tumour angiogenesis, spinal axis tumour, brain stein glioma, pituitary adenoma, Kaposi's sarcoma, epidermoid cancer, squamous cell cancer, T-cell lymphoma, environmentally induced cancers including those induced by asbestos, and combinations of said cancers.
In embodiments, the localized cancer cell is a prostate cancer cell.
An estimated 1 in 6 men will be diagnosed with prostate cancer (PCa). Although the majority of these men can be successfully treated with surgery or radiation therapy, approximately 20%-40% will biochemically recur within 10 years of treatment (Ward J F, Moul J W. Rising prostate-specific antigen after primary prostate cancer therapy. Nat Clin Pract Urol. 2005; 2(4):174-182). This risk of recurrence is elevated to approximately 50% for men with locally advanced disease, a condition that is primarily managed by radiation therapy (Bolla M, et al. Long-term results with immediate androgen suppression and external irradiation in patients with locally advanced prostate cancer (an EORTC study): a phase III randomised trial. Lancet. 2002; 360(9327):103-106; Walz J, et al. A nomogram predicting 10-year life expectancy in candidates for radical prostatectomy or radiotherapy for prostate cancer. J Clin Oncol. 2007; 25(24):3576-3581). Thus, new technologies that improve the therapeutic index of radiation therapy for local disease will significantly affect the morbidity and mortality of PCa.
Ionizing radiation (IR) causes multiple types of cellular injury, of which DNA double-strand breaks (DSBs) are considered the most cytotoxic (Smith G C, Jackson S P. The DNA-dependent protein kinase. Genes Dev. 1999; 13(8):916-934). Naturally occurring mutations in genes that sense or repair DNA damage are associated with increased sensitivity to IR (Helleday T, Lo J, van Gent D C, Engelward B P. DNA double-strand break repair: from mechanistic understanding to cancer treatment. DNA Repair (Amst). 2007; 6(7):923-935; Pollard J M, Gatti R A. Clinical radiation sensitivity with DNA repair disorders: an overview. Int J Radiat Oncol Biol Phys. 2009; 74(5):1323-1331). Chemical or siRNA inhibition of DNA repair proteins, such as ataxia telangiectasia mutated (ATM) or NBS1, also results in cellular hypersensitivity to IR (Chalmers A J, Bentzen S M, Buffa F M, A general framework for quantifying the effects of DNA repair inhibitors on radiation sensitivity as a function of dose. Theor Biol Med. Model. 2007; 4:25; Collis S J, Swartz M J, Nelson W G, DeWeese T L. Enhanced radiation and chemotherapy-mediated cell killing of human cancer cells by small inhibitory RNA silencing of DNA repair factors. Cancer Res. 2003; 63(7):1550-1554; Ohnishi K, Scuric Z, Schiestl R H, Okamoto N, Takahashi A, Ohnishi T. siRNA targeting NBS1 or XIAP increases radiation sensitivity of human cancer cells independent of TP53 status. Radiat Res. 2006; 166(3):454-462). Although these approaches have potential, they lack a means to selectively target cancer cells or specific tissues. Prostate-targeted radiosensitization approaches will both increase the therapeutic effect of IR and reduce radiation-associated damage to other pelvic tissues. RNAi is a promising new therapeutic approach. The challenge for translating RNAi therapy is delivery, particularly for specific cell types.
A prostate-specific membrane antigen-targeted (PSMA-targeted) RNA aptamers was previously developed (Lupold S E, Hicke B J, Lin Y, Coffey D S. Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res. 2002; 62(14):4029-4033), which are capable of targeting drugs, nanoparticles, and toxins to PSMA-expressing PCa cells and tumors (Cheng J, et al. Formulation of functionalized PLGA-PEG nanoparticles for in vivo targeted drug delivery. Biomaterials. 2007; 28(5):869-876; Chu T C, et al. Aptamer:toxin conjugates that specifically target prostate tumor cells. Cancer Res. 2006; 66(12):5989-5992; Chu T C, et al. Labeling tumor cells with fluorescent nanocrystal-aptamer bioconjugates. Biosens Bioelectron. 2006; 21(10):1859-1866; Farokhzad O C, et al. Targeted nanoparticle aptamer bioconjugates for cancer chemotherapy in vivo. Proc Natl Acad Sci USA. 2006; 103(16):6315-6320; Farokhzad O C, Jon S, Khademhosseini A, Tran T N, Lavan D A, Langer R. Nanoparticle-aptamer bioconjugates: a new approach for targeting prostate cancer cells. Cancer Res. 2004; 64(21):7668-7672). When conjugated to siRNAs and shRNAs, these PSMA aptamers are also capable of delivering cell-selective gene knockdown (Chu T C, Twu K Y, Ellington A D, Levy M. Aptamer mediated siRNA delivery. Nucleic Acids Res. 2006; 34(10):e73; Dassie J P, et al. Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat. Biotechnol. 2009; 27(9):839-849; McNamara J O 2nd, et al. Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat Biotechnol. 2006; 24(8):1005-1015; Pastor F, Kolonias D, Giangrande P H, Gilboa E. Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay. Nature. 2010; 465(7295):227-230; Wullner U, Neef I, Eller A, Kleines M, Tur M K, Barth S. Cell-specific induction of apoptosis by rationally designed bivalent aptamer-siRNA transcripts silencing eukaryotic elongation factor 2. Curr Cancer Drug Targets. 2008; 8(7):554-565). Because PSMA is highly expressed in PCa, targeted aptamer-inhibitory nucleic acid (e.g., shRNA) chimeras could be used to inhibit DNA repair pathways in prostatic cells for enhanced radiation therapy of locally advanced PCa.
Dose-escalated radiation therapy for localized prostate cancer (PCa) has a clear therapeutic benefit; however, escalated doses may also increase injury to noncancerous tissues. Radiosensitizing agents can improve ionizing radiation (IR) potency, but without targeted delivery, these agents will also sensitize surrounding normal tissues. The prostate-targeted RNAi agents of the invention selectively sensitized prostate-specific membrane antigen-positive (PSMA-positive) cells to IR. siRNA library screens identified DNA-activated protein kinase, catalytic polypeptide (DNAPK) as a preferred radiosensitization target. As described herein, DNAPK shRNAs, delivered by PSMA-targeting RNA aptamers, selectively reduced DNAPK in PCa cells, xenografts, and human prostate tissues. Aptamer-targeted DNAPK shRNAs, combined with IR, dramatically and specifically enhanced PSMA-positive tumor response to IR.
Cancer cells on which the claimed chimeric aptamer-inhibitory nucleic acid (e.g., shRNA) molecules exert a therapeutic effect are not particularly limited. The results described herein demonstrate that the chimeric aptamers are effective in treating any localized cancer cells (e.g., prostate cancer cells). Therefore, in aspects of the invention, the chimeric aptamers are used in combination with radiotherapy, and in embodiments, use of the chimeric aptamers enhances the efficacy of the radiotherapy. It is readily within the skill of the ordinary artisan to choose the appropriate aptamer and shRNA for use with a particular type of cancer cell.
Use of the chimeric aptamers reduces the dosage of radiotherapy, and can suppress the side effects that accompany radiotherapy.
Aptamers
The aptamers of the invention may be prepared by any known method, including synthetic, recombinant, and purification methods, and may be used alone or in combination with other aptamers specific for the same target. Illustrative methods of preparing aptamers are disclosed in U.S. Pat. Nos. 5,582,981 and 5,840,867, both of which are incorporated by reference in their entirety. Further, as described more fully herein, the term “aptamer” specifically includes “secondary aptamers” containing a consensus sequence derived from comparing two or more known aptamers to a given target.
As used herein, the term “binding” refers to an interaction or complexation between a target and an oligonucleotide or aptamer, resulting in a sufficiently stable complex so as to permit separation of oligonucleotide:target complexes from uncomplexed oligonucleotides under given binding complexation or reaction conditions. Binding is mediated through hydrogen bonding or other molecular forces. As used herein, the term “binding” specifically excludes the normal “Watson-Crick”-type binding interactions (i.e., adenine-thymine and guanine-cytosine base-pairing) traditionally associated with the DNA double helix.
In general, a minimum of approximately 3 nucleotides, at least 5 nucleotides, and the like, are necessary to effect specific binding. The only apparent limitations on the binding specificity of the target/oligonucleotide complexes of the invention concern sufficient sequence to be distinctive in the binding oligonucleotide and sufficient binding capacity of the target substance to obtain the necessary interaction. Oligonucleotides of sequences shorter than 10 can be used when the appropriate interaction can be obtained in the context of the environment in which the target is placed. Although the oligonucleotides generally described herein are single-stranded or double-stranded, it is contemplated that aptamers may sometimes assume triple-stranded or quadruple-stranded structures.
As further explained below, the specifically binding oligonucleotides need to contain the sequence-conferring specificity, but may be extended with flanking regions and otherwise derivatized.
The aptamers found to bind to the targets may be isolated, sequenced, and then resynthesized as conventional DNA or RNA moieties, or may be “modified” oligomers which are those conventionally recognized in the art. As the resulting aptamers of the invention include intermediates in their synthesis, any of the hydroxyl groups ordinarily present may be replaced by phosphonate groups, phosphate groups, protected by a standard protecting group, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid supports. The 5′ terminal OH is conventionally free but may be phosphorylated; OH substituents at the 3′ terminus may also be phosphorylated. The hydroxyls may also be derivatized to standard protecting groups. One or more phosphodiester linkages may be replaced by alternative linking groups. These alternative linking groups include, but are not limited to embodiments wherein P(O)O is replaced by P(O)S, P(O)NR2, P(O)R, P(O)OR′, CO, or CNR2, wherein R is H or alkyl (1-20C) and R′ is alkyl (1-20C); in addition, this group may be attached to adjacent nucleotide through O or S, Not all linkages in an oligomer need to be identical.
“Analogous” forms of purines and pyrimidines are those generally known in the art, many of which are used as chemotherapeutic agents. An exemplary but not exhaustive list includes 2′-fluoro-modified pyrimidine, aziridinylcytosine, 4-acetylcytosine, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethylaminomethyluracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5-methoxyuracil, 2-methylthio-N-6-isopentenyladenine, uracil-5-oxyacetic acid methylester, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid, and 2,6-diaminopurine.
Aptamer oligonucleotides may contain analogous forms of ribose or deoxyribose that are generally known in the art. An exemplary, but not exhaustive list includes locked-nucleic acids (LNA), 2′ substituted sugars such as 2′-O-methyl-, 2′-fluoro- or 2′-azido-ribose, carbocyclic sugar analogs, α-anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, sedoheptuloses, acyclic analogs and abasic nucleoside analogs such as methyl riboside.
In most instances, the conventional sugars and bases will be used in applying the method of the invention; substitution of analogous forms of sugars, purines and pyrimidines may be advantageous in designing the final product.
Aptamers containing the specific binding sequences discerned through the method of the invention can also be derivatized in various ways. For example, if the aptamer is to be used for separation of the target substance, conventionally the oligonucleotide will be derivatized to a solid support to permit chromatographic separation. If the oligonucleotide is to be used to label cellular components or otherwise for attaching a detectable moiety to target, the oligonucleotide will be derivatized to include a radionuclide, a fluorescent molecule, a chromophore or the like. If the oligonucleotide is to be used in specific binding assays, coupling to solid support or detectable label is also desirable. If it is to be used therapeutically, the oligonucleotide may be derivatized to include ligands which permit easier transit of cellular barriers, toxic moieties which aid in the therapeutic effect, or enzymatic activities which perform desired functions at the targeted site. The aptamer may also be included in a suitable expression system to provide for in situ generation of the desired sequence.
The oligonucleotides used as starting materials in the process of the invention to determine specific binding sequences may be single-stranded or double-stranded DNA or RNA. In embodiments of this invention, the sequences are single-stranded RNA.
In aspects of the invention, the aptamer specifically targets antigens specific to cancer cells, which are also known as cancer antigens or tumor antigens. Such antigens are well known in the art, and it is within the skill of the ordinary artisan to select the appropriate cancer antigen for use with a specific cancer. For example, as described in detail herein, the aptamer in an aptamer-inhibitory nucleic acid chimera can be specific to PSMA. Other illustrative non-limiting examples of aptamer targeted cancer cell antigens includes Muc1, HER2, TGFbeta-receptor, Guanylyl cyclase C (GC-C), and PSCA.
Inhibitory Nucleic Acids
Inhibitory nucleic acid molecules are those oligonucleotides that inhibit the expression or activity of a target gene in a cancer cell, wherein such inhibition results in the cancer cell becoming radiosensitized. Such oligonucleotides include single and double stranded nucleic acid molecules (e.g., DNA, RNA, and analogs thereof) that bind a nucleic acid molecule that encodes a target radiosensitivity protein (e.g., antisense molecules, siRNA, shRNA) as well as nucleic acid molecules that bind directly to a radiosensitivity protein and thereby modulate its biological activity.
shRNA
Small hairpin RNAs consist of a stem-loop structure with optional 3′ UU-overhangs. A “stem-loop structure” refers to a nucleic acid having a secondary structure that includes a region of nucleotides which are known or predicted to form a double strand or duplex (stem portion) that is linked on one side by a region of predominantly single-stranded nucleotides (loop portion). The term “hairpin” is also used herein to refer to stem-loop structures. Such structures are well known in the art and the term is used consistently with its known meaning in the art. As is known in the art, the secondary structure does not require exact base-pairing. Thus, the stem can include one or more base mismatches or bulges. Alternatively, the base-pairing can be exact, i.e. not include any mismatches. The multiple stem-loop structures can be linked to one another through a linker, such as, for example, a nucleic acid linker, a miRNA flanking sequence, other molecule, or some combination thereof.
While there may be variation, stems can range from 21 to 31 bp (e.g., 25 to 29 bp), and the loops can range from 4 to 30 bp (desirably 4 to 23 bp). For expression of shRNAs within cells, any method well known in the art for introducing a nucleic acid construct into cells can be employed. A non-limiting example includes use of plasmid vectors containing either the polymerase III H1-RNA or U6 promoter, a cloning site for the stem-looped RNA insert, and a 4-5-thymidine transcription termination signal can be employed. The Polymerase III promoters generally have well-defined initiation and stop sites and their transcripts lack poly(A) tails. The termination signal for these promoters is defined by the polythymidine tract, and the transcript is typically cleaved after the second uridine. Cleavage at this position generates a 3′ UU overhang in the expressed shRNA, which is similar to the 3′ overhangs of synthetic siRNAs. Furthermore, as described herein, shRNAs may be covalently linked to aptamers to generate the aptamer-shRNA chimeras of the invention.
shRNA also includes micro-RNA embedded shRNAs (miRNA-based shRNAs), wherein the guide strand and the passenger strand of the miRNA duplex are incorporated into an existing (or natural) miRNA or into a modified or synthetic (designed) miRNA. In some instances the precursor miRNA molecule can include more than one stem-loop structure. MicroRNAs are endogenously encoded RNA molecules that are about 22-nucleotides long and generally expressed in a highly tissue- or developmental-stage-specific fashion and that post-transcriptionally regulate target genes. More than 200 distinct miRNAs have been identified in plants and animals. These small regulatory RNAs are believed to serve important biological functions by two prevailing modes of action: (1) by repressing the translation of target mRNAs, and (2) through RNA interference (RNAi), that is, cleavage and degradation of mRNAs. In the latter case, miRNAs function analogously to small interfering RNAs (siRNAs). Thus, one of ordinary skill in the art can readily design and express artificial miRNAs based on the features of existing miRNA genes.
siRNA
Short twenty-one to twenty-five nucleotide double-stranded RNAs are effective at down-regulating gene expression (Zamore et al., Cell 101: 25-33; Elbashir et al., Nature 411: 494-498, 2001, each of which is hereby incorporated by reference). The therapeutic effectiveness of an siRNA in vivo is well known in the art (see McCaffrey et al, (Nature 418: 38-39.2002), which is hereby incorporated by reference). Given the sequence of a target gene, siRNAs may be designed to inactivate that gene. Such siRNAs, for example, could be administered directly to an affected tissue, or administered systemically. The nucleic acid sequence of a gene can be used to design small interfering RNAs (siRNAs) for that gene. The 21 to 25 nucleotide siRNAs may be used, for example, when screening for additional target genes the inhibition of which would radiosensitize a cancer cell. Further, as described herein, siRNA may be coupled with an aptamer to deliver the siRNA to a cancer cell.
Ribozymes
Catalytic RNA molecules or ribozymes that target an antisense target sequence of the present invention can be used to inhibit expression of a target gene nucleic acid molecule in vivo, wherein inhibition of the target gene sensitizes the cancer cell to radiation. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs. The design and use of target RNA-specific ribozymes is described in Haseloff et al., Nature 334:585-591. 1988, and U.S. Patent Application Publication No. 2003/0003469 A1, each of which is incorporated by reference.
Accordingly, the invention also features a catalytic RNA molecule that includes, in the binding arm, an antisense RNA having between eight and nineteen consecutive nucleobases. In embodiments of this invention, the catalytic nucleic acid molecule is formed in a hammerhead or hairpin motif. Examples of such hammerhead motifs are well known in the art (see Rossi et al., Aids Research and Human Retroviruses, 8:183, 1992, which is hereby incorporate by reference). Example of hairpin motifs are also well known in the art (see Hampel et al., “RNA Catalyst for Cleaving Specific RNA Sequences,” filed Sep. 20, 1989, which is a continuation-in-part of U.S. Ser. No. 07/247,100 filed Sep. 20, 1988, Hampel and Tritz, Biochemistry, 28:4929, 1989, and Hampel et al., Nucleic Acids Research, 18: 299, 1990, each of which is hereby incorporated by reference). These specific motifs are not limiting in the invention and those skilled in the art will recognize that all that is important in an enzymatic nucleic acid molecule of this invention is that it has a specific substrate binding site which is complementary to one or more of the target gene RNA regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart an RNA cleaving activity to the molecule. Further, catalytic RNAs of the invention may be covalently linked to an aptamer wherein the aptamer delivers the catalytic RNA to a cancer cell and the catalytic RNA inhibits the production of a target protein and thereby radiosensitizes the cancer cell.
The inhibitory nucleic acid molecules of the present invention may be employed as double-stranded RNAs for RNA interference (RNAi)-mediated knock-down of the expression of a target radiosensitivity protein. In one embodiment, DNAPK expression is reduced in a prostate cancer cell. RNAi is a method for decreasing the cellular expression of specific proteins of interest (reviewed in Tuschl, Chembiochem 2:239-245, 2001; Sharp, Genes & Devel, 15:485-490, 2000; Hutvagner and Zamore, Curr. Opin. Genet. Devel. 12:225-232, 2002; and Hannon, Nature 418:244-251, 2002).
In one embodiment of the invention, a double-stranded RNA (dsRNA) molecule is made that includes between eight and nineteen consecutive nucleobases of a nucleobase oligomer of the invention. The dsRNA can be two distinct strands of RNA that have duplexed, or a single RNA strand that has self-duplexed (small hairpin (sh)RNA). Typically, dsRNAs are about 21 or 22 base pairs, but may be shorter or longer (up to about 29 nucleobases) if desired. dsRNA can be made using standard techniques (e.g., chemical synthesis or in vitro transcription). Kits are available, for example, from Ambion (Austin, Tex.) and Epicentre (Madison, Wis.). Methods for expressing dsRNA in mammalian cells are described in Brummelkamp et al. Science 296:550-553, 2002; Paddison et al. Genes & Devel. 16:948-958, 2002. Paul et al. Nature Biotechnol. 20:505-508, 2002; Sui et al. Proc. Natl. Acad. Sci. USA 99:5515-5520, 2002; Yu et al. Proc. Natl. Acad. Sci. USA 99:6047-6052, 2002; Miyagishi et al. Nature Biotechnol. 20:497-500, 2002; and Lee et al. Nature Biotechnol. 20:500-505 2002, each of which is hereby incorporated by reference.
In aspects of the invention, shRNA are coupled with an aptamer to deliver the shRNA to a cancer cell.
Pharmaceutical Compositions
For therapeutic uses, the compositions or agents identified using the methods disclosed herein may be administered systemically, for example, formulated in a pharmaceutically-acceptable carrier. Preferable routes of administration include, for example, subcutaneous, intravenous, interperitoneally, intramuscular, or intradermal injections that provide continuous, sustained levels of the drug in the patient. Treatment of human patients or other animals will be carried out using a therapeutically effective amount of a radiosensitizing aptamer-inhibitory nucleic acid (e.g., shRNA) chimeric therapeutic in a physiologically-acceptable carrier. Suitable carriers and their formulation are described, for example, in Remington's Pharmaceutical Sciences by E. W. Martin. The amount of the therapeutic aptamer-inhibitory nucleic acid (e.g., shRNA) chimera to be administered varies depending upon the manner of administration, the age and body weight of the patient, and the clinical symptoms of the cancer. Generally, amounts will be in the range of those used for other agents used in the treatment of cancer, although in certain instances lower amounts will be needed because of the increased specificity of the compound. A compound is administered at a dosage that radiosenitizes a cancer cell as determined by a diagnostic method known to one skilled in the art, or using any assay that measures sensitivity to ionizing radiation (e.g., induction of apoptosis).
Formulation of Pharmaceutical Compositions
The administration of an agent of the invention or analog thereof for the treatment of cancer may be by any suitable means that results in a concentration of the therapeutic that, combined with ionizing radiation, is effective in ameliorating, reducing, or stabilizing cancer or a symptom thereof. In one embodiment, administration of the agent and ionizing radiation results in an increase in apoptosis of the cancer cells. In another embodiment, the agent and ionizing radiation results in an increase in the average survival time or quality of life of the subject.
Methods of administering such agents are known in the art. The invention provides for the therapeutic administration of an agent by any means known in the art. The compound may be contained in any appropriate amount in any suitable carrier substance, and is generally present in an amount of 1-95% by weight of the total weight of the composition. The composition may be provided in a dosage form that is suitable for parenteral (e.g., subcutaneously, intravenously, intramuscularly, or intraperitoneally) administration route. In embodiments, the therapeutic composition is administered directly to the cancer mass. In related embodiments, the therapeutic composition is administered directly to the prostate of a subject. The pharmaceutical compositions may be formulated according to conventional pharmaceutical practice (see, e.g., Remington: The Science and Practice of Pharmacy (20th ed.), ed. A. R, Gennaro, Lippincott Williams & Wilkins, 2000 and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York). Suitable formulations include forms for oral administration, depot formulations, formulations for delivery by a patch, semisolid dosage forms to be topically or transdermally delivered.
Pharmaceutical compositions according to the invention may be formulated to release the active compound substantially immediately upon administration or at any predetermined time or time period after administration. The latter types of compositions are generally known as controlled release formulations, which include (i) formulations that create a substantially constant concentration of the drug within the body over an extended period of time; (ii) formulations that after a predetermined lag time create a substantially constant concentration of the drug within the body over an extended period of time; (iii) formulations that sustain action during a predetermined time period by maintaining a relatively, constant, effective level in the body with concomitant minimization of undesirable side effects associated with fluctuations in the plasma level of the active substance (sawtooth kinetic pattern); (iv) formulations that localize action by, e.g., spatial placement of a controlled release composition adjacent to or in the central nervous system or cerebrospinal fluid; (v) formulations that allow for convenient dosing, such that doses are administered, for example, once every one or two weeks; and (vi) formulations that target cancer by using carriers or chemical derivatives to deliver the therapeutic agent to a particular cell type (e.g., prostate cancer cell). For some applications, controlled release formulations obviate the need for frequent dosing during the day to sustain the plasma level at a therapeutic level.
Any of a number of strategies can be pursued in order to obtain controlled release in which the rate of release outweighs the rate of metabolism of the compound in question. In one example, controlled release is obtained by appropriate selection of various formulation parameters and ingredients, including, e.g., various types of controlled release compositions and coatings. Thus, the therapeutic is formulated with appropriate excipients into a pharmaceutical composition that, upon administration, releases the therapeutic in a controlled manner. Examples include single or multiple unit tablet or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, molecular complexes, nanoparticles, patches, and liposomes.
Parenteral Compositions
The pharmaceutical composition may be administered parenterally by injection, infusion or implantation (subcutaneous, intravenous, intramuscular, intraperitoneal, or the like) in dosage forms, formulations, or via suitable delivery devices or implants containing conventional, non-toxic pharmaceutically acceptable carriers and adjuvants. The formulation and preparation of such compositions are well known to those skilled in the art of pharmaceutical formulation. Formulations can be found in Remington: The Science and Practice of Pharmacy, supra. Compositions for parenteral use may be provided in unit dosage forms (e.g., in single-dose ampoules), or in vials containing several doses and in which a suitable preservative may be added (see below). The composition may be in the form of a solution, a suspension, an emulsion, an infusion device, or a delivery device for implantation, or it may be presented as a dry powder to be reconstituted with water or another suitable vehicle before use. Apart from the active therapeutic (s), the composition may include suitable parenterally acceptable carriers and/or excipients. The active therapeutic (s) may be incorporated into microspheres, microcapsules, nanoparticles, liposomes, or the like for controlled release. Furthermore, the composition may include suspending, solubilizing, stabilizing, pH-adjusting agents, tonicity adjusting agents, and/or dispersing, agents.
As indicated above, the pharmaceutical compositions according to the invention may be in the form suitable for sterile injection. To prepare such a composition, the suitable active therapeutic(s) are dissolved or suspended in a parenterally acceptable liquid vehicle.
Dosage
Human dosage amounts can initially be determined by extrapolating from the amount of compound used in mice, as a skilled artisan recognizes it is routine in the art to modify the dosage for humans compared to animal models. In certain embodiments it is envisioned that the dosage may vary from between about 1 mg compound/Kg body weight to about 5000 mg compound/Kg body weight; or from about 5 mg/Kg body weight to about 4000 mg/Kg body weight or from about 10 mg/Kg body weight to about 3000 mg/Kg body weight; or from about 50 mg/Kg body weight to about 2000 mg/Kg body weight; or from about 100 mg/Kg body weight to about 1000 mg/Kg body weight; or from about 150 mg/Kg body weight to about 500 mg/Kg body weight. In other embodiments this dose may be about 1, 5, 10, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1600, 1700, 1800, 1900, 2000, 2500, 3000, 3500, 4000, 4500, 5000 mg/Kg body weight. In other embodiments, it is envisaged that higher does may be used, such doses may be in the range of about 5 mg compound/Kg body to about 20 mg compound/Kg body. In other embodiments the doses may be about 8, 10, 12, 14, 16 or 18 mg/Kg body weight. Of course, this dosage amount may be adjusted upward or downward, as is routinely done in such treatment protocols, depending on the results of the initial clinical trials and the needs of a particular patient.
Therapeutic Methods
The present invention provides methods of treating cancer by increasing the cancer's sensitivity to ionizing radiation, and exposing the cancer to ionizing radiation when the cancer is in the sensitive state. The methods comprise administering a therapeutically effective amount of a pharmaceutical composition comprising an aptamer-inhibitory nucleic acid (e.g., shRNA) chimera. Not wishing to be bound by any theory, it is believed that the aptamer portion delivers the aptamer-inhibitory nucleic acid (e.g., shRNA) chimera to a cancer cell; the shRNA portion enters the cell, is processed to an siRNA that knocks-down the levels of a target protein; and knock-down of the target protein results in the sentization of the cancer cell to ionizing radiation. Once the cancer cell has been sensitized to ionizing radiation the cancer is exposed to therapeutic amounts of ionizing radiation.
The methods herein include administering to the subject (including a subject identified as in need of such treatment) an effective amount of a compound described herein, or a composition described herein to produce such effect. Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g., opinion) or objective (e.g., measurable by a test or diagnostic method).
The therapeutic methods of the invention, which include prophylactic treatment, in general comprise administration of a therapeutically effective amount of the agent herein to a subject (e.g., animal, human) in need thereof, including a mammal, e.g., a human.
Combination Therapies
The present invention also provides combination therapies. The chimeric aptamers of the present invention are suitable for use in combination with other chemotherapeutics, including, but not limited to, an alkylation agent, nitrosourea agent, antimetabolite, anticancer antibiotics, vegetable-origin alkaloid, topoisomerase inhibitor, hormone drug, hormone antagonist, aromatase inhibitor, P-glycoprotein inhibitor, platinum complex derivative, other immunotherapeutic drugs and other anticancer drugs well known in the art. Further, the chimeric aptamers can be used with a cancer treatment adjunct, such as a leucopenia (neutrophenia) treatment drug, thrombocytopenia treatment drug, antiemetic and cancer pain intervention drug, or combinations thereof.
In aspects, the chimeric aptamers can be used with other immunomodulators. Immunomodulators are well known in the art. Examples of the immunomodulator include, but are not limited to, various cytokines that stimulate immune responses such as GM-CSF, M-CSF, G-CSF, interferon-α, β, or γ, IL-1, IL-2, IL-3 and IL-12.
In other aspects, the chimeric aptamers can be used with targeted radiation-therapeutics such as radio-labeled antibodies (e.g., I131, Bi213, or Y90) or radioactive substances that are taken up by bone (e.g., MDP). In addition, the chimeric aptamers can be used in combination with radiation mimetic drugs such as bleomycin or neocarzinostatin.
Kits
The invention provides kits for the treatment or amelioration of cancer or its symptoms. In one embodiment, the kit includes a therapeutic or prophylactic composition containing an effective amount of an agent of the invention (e.g., aptamer-inhibitory nucleic acid chimera) in unit dosage form. In embodiments, the kit comprises a container which contains a therapeutic or prophylactic compound; such containers can be sterile, and such containers can be in the form of boxes, ampoules, bottles, vials, tubes, bags, pouches, blister-packs, and the like. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments.
If desired, an agent of the invention is provided together with instructions for administering it to a subject having cancer. The instructions will generally include information about the use of the composition for the treatment of cancer. In other embodiments, the instructions include at least one of the following: description of the compound; dosage schedule and administration for treatment of cancer or symptoms thereof; precautions; warnings; indications; counter-indications; overdosage information; adverse reactions; animal pharmacology; clinical studies; and/or references. The instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.
Neovascularization
Angiogenesis is the growth of new blood vessels from pre-existing vessels. Angiogenesis plays a critical role in tumor formation and is essential for growth of tumors beyond 1 mm in diameter. Tumor-associated neovascular endothelial cells express antigens that can serve as targets for the claimed aptamer-inhibitory nucleic acid chimeras. For example, tumor-associate neovascular endothelia cells express prostate-specific membrane antigen (PSMA). (Chang et al., Five different anti-prostate-specific membrane antigen (PSMA) antibodies cofirm PSMA expression in tumor-associated neovasculature, Cancer Res., vol. 59, pages 3192-3198). In one aspect of the invention, methods are provided for targeting neoplasia associated neovascularization by contacting neovascular endothelia cells with aptamer-inhibitory nucleic acid chimeras and exposing neovascular endothelia cells to ionizing radiation.
The practice of the present invention employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are well within the purview of the skilled artisan. Such techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook, 1989); “Oligonucleotide Synthesis” (Gait, 1984); “Animal Cell Culture” (Freshney, 1987); “Methods in Enzymology” “Handbook of Experimental Immunology” (Weir, 1996); “Gene Transfer Vectors for Mammalian Cells” (Miller and Calos, 1987); “Current Protocols in Molecular Biology” (Ausubel, 1987); “PCR: The Polymerase Chain Reaction”, (Mullis, 1994); “Current Protocols in Immunology” (Coligan, 1991). These techniques are applicable to the production of the polynucleotides and polypeptides of the invention, and, as such, may be considered in making and practicing the invention. Particularly useful techniques for particular embodiments will be discussed in the sections that follow.
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the agents and therapeutic methods of the invention, and are not intended to limit the scope of what the inventors regard as their invention.
EXAMPLES
It should be appreciated that the invention should not be construed to be limited to the examples that are now described; rather, the invention should be construed to include any and all applications provided herein and all equivalent variations within the skill of the ordinary artisan.
Example 1
Identification of siRNAs that Radiosensitize a Cell
To explore the combination of IR with siRNA, a custom siRNA library was screened against 249 mRNAs, primarily encoding critical DNA repair proteins. The goal was to identify radiosensitizing target genes and corresponding siRNAs. Radiosensitization was calculated as percent increased cell death associated with a gene-specific siRNA after radiation therapy (6 Gy) compared with irradiated cells transfected with a control siRNA. Candidate targets were defined as those for which 2 separate siRNAs, targeting the same gene, enhanced radiation-induced cell death above the SD of the library mean (FIG. 1 and Table 1). In total, 10 candidate genes were identified as PCa radiosensitization targets, 6 of which were separately confirmed by clonogenic survival assays (FIG. 2). Effective target gene knockdown at the time of irradiation was confirmed by quantitative RT-PCR (qRT-PCR; FIG. 3). The dose-modifying factor (DMF0.1) was calculated for each target as the ratio of IR dose required for 90% cell kill by control siRNA versus gene-specific siRNA, and 3 target genes—specifically, the catalytic subunit of DNA-activated protein kinase, catalytic polypeptide (DNAPK); mitotic spindle assembly checkpoint protein MAD2B (MAD2L2); and breast cancer type 2 susceptibility protein (BRCA2)-achieved DMF0.1 of 1.6 by siRNA inhibition. The remaining 3 target genes achieved DMF0.1 of 1.3 in clonogenic survival assays. All 6 candidate genes were verified as radiosensitizing targets in a second cell line, the PSMA-positive cell and tumor model LNCaP (FIG. 4). Interestingly, the siRNA screen primarily identified genes involved in DSB repair, except RAD23B, a gene involved in excision repair (Mu D, Hsu D S, Sancar A. Reaction mechanism of human DNA repair excision nuclease. J Biol. Chem. 1996; 271(14):8285-8294).













TABLE 1







0 Gy Avg
0 Gy St dev
6 Gy Avg
6 Gy St dev
Relative Sensitization





















control siRNA
1
0.124472004
1
0.094211712
0.00%


ACLY
1.860022981
0.121168192
1.495426898
0.442145785
19.60%


ACLY
1.336293046
0.125416099
1.016535256
0.152135228
23.93%


AHCY
1.647376301
0.074640222
2.111917098
0.261125426
28.20%


AHCY
2.065322609
0.029588199
2.424329804
0.104705175
17.38%


AKT1
1.026513645
0.043308969
1.297762747
0.15662083
26.42%


AKT1
1.165931683
0.039687706
1.559469303
0.020034444
−33.75%


AKT2
1.062967649
0.05816065
1.359677419
0.119615338
27.91%


AKT2
1.220621724
0.177839016
1.418938606
0.023089508
16.25%


ALKBH2
0.992821292
0.041468292
1.044196918
0.198307671
5.17%


ALKBH2
1.134315823
0.090214712
1.2873918
0.182010182
13.50%


ALKBH3
1.840593335
0.072838311
1.821536382
0.208577626
1.04%


ALKBH3
0.654305512
0.097023714
0.509484118
0.060718889
22.13%


APEX1
0.758026278
0.040990649
0.815590223
0.027601053
7.59%


APEX1
0.826198015
0.027713131
0.846079577
0.040360728
2.41%


APEX1
1.019446955
0.078334922
1.447086368
0.062142199
−41.95%


APEX2
0.99622068
0.166587825
0.913306046
0.090975723
8.32%


APEX2
1.077546042
0.066916344
1.029546624
0.234397258
4.45%


AR
1.057364902
0.108014404
1.334313215
0.051292945
26.19%


AR
0.826369058
0.078424208
0.969927159
0.058317607
17.37%


ARMET
0.464436401
0.041606696
0.499541479
0.035553201
7.56%


ARMET
1.083684937
0.078618231
1.215325773
0.059524345
12.15%


ATM
1.811971169
0.297400989
1.717774273
0.609641954
5.20%


ATM
1.879487447
0.047891941
1.301148907
0.172167965
30.77%


ATR
0.827678681
0.021027422
0.839313521
0.253657593
1.41%


ATR
1.139033091
0.041048611
1.133949574
0.102873886
0.45%


BIRC2
1.041596304
0.044036623
1.047771889
0.067265294
0.59%


BIRC2
0.689337914
0.103040786
0.686322809
0.037473851
0.44%


BIRC4
1.093635358
0.028595307
1.275185987
0.125032344
16.60%


BIRC4
1.212271201
0.150139005
1.339478988
0.04263207
10.49%


BIRC5
0.965236126
0.037132307
1.044786146
0.021190889
8.24%


BIRC5
1.152700945
0.045995234
1.30989525
0.031959076
13.64%


BLM
0.838862632
0.026110645
0.843013703
0.118823653
0.49%


BLM
0.731519295
0.04504036
0.857191253
0.005359138
17.18%


BRCA1
0.933036602
0.04001633
1.032488101
0.024911891
10.66%


BRCA1
0.891096529
0.036928642
0.850381964
0.030689307
4.57%


BRCA2
1.963229917
0.170562503
1.35791845
0.222474753
30.83%


BRCA2
1.704899196
0.066633739
1.498715927
0.254634012
12.09%


C18orf37
1.001514005
0.113452665
1.140479212
0.19351858
13.88%


C18orf37
0.819561715
0.067014617
0.959145082
0.072471853
17.03%


CANX
1.552491382
0.344356396
1.886911467
0.886718735
21.54%


CANX
1.215057203
0.01066571
1.524633072
0.071152097
25.48%


CARM1
0.526865164
0.051063897
0.72835447
0.41977691
−38.24%


CARM1
1.064868324
0.032061914
1.198975598
0.049979816
12.59%


CBX3
1.207602411
0.028772199
1.164993539
0.165527336
3.53%


CBX3
0.950717211
0.035486509
1.000646911
0.120997246
5.25%


CCNH
1.123477774
0.141124798
1.094947326
0.152009453
2.54%


CCNH
1.098082345
0.0691399
1.069784607
0.112084229
2.58%


CCT4
0.405966926
0.021478927
0.527947393
0.083764296
−30.05%


CCT4
0.294367014
0.011728925
0.43405131
0.051809487
−47.45%


CCT5
1.010978024
0.037455863
1.12570176
0.0223163
11.35%


CCT5
0.381291368
0.065450694
0.434632848
0.06932378
13.99%


CDC2
1.306876615
0.110871263
1.173740185
0.011830356
10.19%


CDC2
0.578121415
0.052542672
0.685739452
0.015592135
18.62%


CDK7
1.484940283
0.19507667
1.660103627
0.105763156
11.80%


CDK7
0.623245935
0.11527591
0.65857175
0.076873494
5.67%


CDKN1A
1.100953046
0.028537044
1.264711005
0.090780349
14.87%


CDKN1A
1.128535104
0.014977281
1.305665447
0.092554062
15.70%


CDKN2A
0.877570938
0.145223487
1.143704475
0.042522887
−30.33%


CDKN2A
0.778022772
0.104083061
0.88371488
0.097923994
13.58%


CDKN2B
1.116985966
0.033413553
1.305789853
0.035445274
16.90%


CDKN2B
1.097556241
0.077339843
1.221293324
0.03406237
11.27%


CDKN2C
1.088782779
0.082766972
1.427483765
0.158641889
−31.11%


CDKN2C
1.194103146
0.075179945
1.537956259
0.098110371
28.80%


CDKN2D
0.572041383
0.033747449
0.705033465
0.0791769
23.25%


CDKN2D
1.117529455
0.106303492
1.512876017
0.154025732
−35.38%


CDKN3
1.163690536
0.043745101
1.085933481
0.142287485
6.68%


CDKN3
0.719730449
0.037050282
0.728734707
0.213212127
1.25%


CETN2
0.623747687
0.06176773
0.616511679
0.052325066
1.16%


CETN2
0.930421083
0.084747927
1.028270407
0.02810361
10.52%


CHEK1
0.991817264
0.142118845
1.447037621
0.830679326
−45.90%


CHEK1
1.002715972
0.03867027
0.836629872
0.029912339
16.56%


CHEK2
1.28579161
0.105754821
1.399794586
0.037026965
8.87%


CHEK2
0.720797198
0.041990255
0.814099632
0.047447296
12.94%


CKS2
1.811205126
0.194266251
1.917503942
0.247453229
5.87%


CKS2
1.46840071
0.068376853
1.039062852
0.16501012
29.24%


CLU
1.138744929
0.079983171
1.345226543
0.0921184
18.13%


CLU
1.067741998
0.151957353
1.400636959
0.095978125
−31.18%


COL1A2
0.359429204
0.053593975
0.458834443
0.011955923
27.66%


COL1A2
1.266232009
0.094068616
1.210780903
0.181226478
4.38%


COPB2
0.239756844
0.037202802
0.299693574
0.054748087
25.00%


COPB2
1.149373113
0.048861171
1.251403521
0.034123819
8.88%


CRIP2
0.652390404
0.139328733
0.577607569
0.146551051
11.46%


CRIP2
1.095512621
0.068560075
1.149935575
0.109379194
4.97%


DCLRE1A
1.591281033
0.111652076
1.091732372
0.418836143
31.39%


DCLRE1A
1.052335445
0.05026272
1.12643005
0.040626099
7.04%


DCLRE1B
0.833270011
0.105735905
0.906439419
0.111711577
8.78%


DCLRE1B
0.685756564
0.043878988
0.654767496
0.136268103
4.52%


DCLRE1C
0.993012287
0.055026948
1.133835933
0.175782264
14.18%


DCLRE1C
1.005726043
0.097130704
1.145355925
0.128195999
13.88%


DDB1
0.770155555
0.039104923
0.851262767
0.012161393
10.53%


DDB1
0.856499544
0.079866395
0.988878107
0.085105856
15.46%


DDB2
1.157631626
0.048063944
1.282426357
0.041339678
10.78%


DDB2
1.0688876
0.068378244
1.271354761
0.058499126
18.94%


DMC1
1.033828469
0.072739098
1.060052321
0.022626912
2.54%


DMC1
1.033586095
0.055406574
1.105989614
0.035412173
7.01%


DNMT1
1.735506111
0.026980137
1.486776301
0.172839324
14.33%


DNMT1
1.533166197
0.172790108
1.286821356
0.450139636
16.07%


DNMT3A
0.745025161
0.032365367
0.74117926
0.015546111
0.52%


DNMT3A
0.821945885
0.076881199
0.901400816
0.046183218
9.67%


DNMT3A
1.094108079
0.145429841
1.472372529
0.0492144
−34.57%


DNMT3B
1.043382053
0.091970002
1.356821179
0.129786815
−30.04%


DNMT3B
0.959238339
0.035026724
1.163096216
0.206177031
21.25%


DOT1L
0.583786444
0.025379453
0.780671239
0.192908096
−33.73%


DOT1L
1.264805019
0.061232483
1.299605738
0.091357589
2.75%


DUT
1.10487393
0.037379504
1.497847777
0.123138745
−35.57%


DUT
0.792367864
0.048672338
0.918140877
0.177527823
15.87%


DVL3
0.405515512
0.033604624
0.807163776
0.447926414
−99.05%


DVL3
0.980367716
0.064516677
1.146382414
0.082073988
16.93%


E2F5
1.061978463
0.080035003
1.159404162
0.06011161
9.17%


E2F5
1.156427726
0.059250675
1.443308203
0.064070848
24.81%


EHMT1
0.892199404
0.038581048
0.918137288
0.168632819
2.91%


EHMT1
0.76504688
0.036265048
0.84316615
0.105879905
10.21%


EIF4A3
0.195084885
0.023282535
0.219374175
0.014285702
12.45%


EIF4A3
0.267511379
0.011053333
0.420766657
0.064542057
−57.29%


ERCC1
0.392806156
0.075434221
0.429691372
0.074023734
9.39%


ERCC1
1.744733452
0.185704447
1.267447623
0.342173015
27.36%


ERCC2
0.786482816
0.218273403
0.800450552
0.333277067
1.78%


ERCC2
0.961999238
0.043331064
1.025028308
0.065354518
6.55%


ERCC3
0.53626519
0.16759708
0.39288128
0.079007759
26.74%


ERCC3
0.856012603
0.069645025
0.913240405
0.059447555
6.69%


ERCC4
1.017000796
0.063861889
1.283862403
0.134446188
26.24%


ERCC4
1.060316471
0.060040828
1.061301784
0.090313161
0.09%


ERCC5
0.998164548
0.031775952
1.090282365
0.039962071
9.23%


ERCC5
0.987503633
0.008047825
0.978894592
0.077568635
0.87%


ERCC6
0.920310931
0.046930892
0.990726641
0.012528521
7.65%


ERCC6
0.923288667
0.029801806
0.946897817
0.056996782
2.56%


ERCC8
0.863625935
0.009022114
0.915053272
0.10272711
5.95%


ERCC8
0.96050001
0.06268134
1.215247195
0.160933046
26.52%


EXO1
0.785190963
0.010413493
0.86552501
0.096729266
10.23%


EXO1
0.835987091
0.037022998
0.908938462
0.109179185
8.73%


EZH2
1.357805388
0.025484382
1.674783819
0.106377867
23.34%


EZH2
1.125274171
0.044033774
1.231793188
0.064529549
9.47%


FANCA
0.921970535
0.091443109
1.06678112
0.124781298
15.71%


FANCA
0.877016246
0.152461723
0.922047225
0.075566524
5.13%


FANCC
0.867300301
0.013956345
0.945706923
0.102383262
9.04%


FANCC
1.012032132
0.056223141
1.073991644
0.032935617
6.12%


FANCD2
0.867092552
0.148666839
0.977216821
0.05624289
12.70%


FANCD2
1.034065102
0.064945126
1.093802095
0.063329712
5.78%


FANCE
0.990079983
0.022110333
1.122779275
0.057955865
13.40%


FANCE
1.078944635
0.05420914
1.17105931
0.106630156
8.54%


FANCF
0.876489393
0.045808435
1.004861358
0.043934195
14.65%


FANCF
0.888939874
0.054700626
0.958432847
0.037646362
7.82%


FANCG
1.039463649
0.05237549
0.751350098
0.040050399
27.72%


FANCG
1.138147374
0.09357871
1.254812312
0.084518567
10.25%


FAP
0.783324921
0.092675649
0.8783136
0.034157238
12.13%


FAP
0.934107282
0.066698723
1.015109169
0.053117056
8.67%


FEN1
1.956370347
0.101173521
1.916197342
0.327589619
2.05%


FEN1
0.9836917
0.039574795
0.856409355
0.080129664
12.94%


FLJ35220
0.909145138
0.090843227
1.037163135
0.021970932
14.08%


FLJ35220
0.892304869
0.044923291
0.961159951
0.038823588
7.72%


G3BP1
1.152515685
0.131429656
1.113507604
0.060789059
3.38%


G3BP1
1.137040226
0.01768681
1.253652718
0.04649044
10.26%


GTF2H1
1.028694835
0.006924532
1.075376322
0.043473843
4.54%


GTF2H1
1.201796039
0.104581252
1.431037339
0.059869531
19.07%


GTF2H2
1.024306638
0.079546063
1.116590528
0.076126393
9.01%


GTF2H2
0.900765209
0.072862706
0.978856741
0.035748865
8.67%


GTF2H3
1.264952639
0.094175773
1.507106649
0.019866063
19.14%


GTF2H3
1.121294132
0.027453019
1.338203625
0.196008137
19.34%


GTF2H4
0.827905295
0.15953647
1.114360042
0.056431067
−34.60%


GTF2H4
0.958792698
0.03563308
1.38280437
0.024077758
−44.22%


H2AFX
0.909705991
0.791921993
1.579365868
0.180969505
−73.61%


H2AFX
1.433854103
0.068855513
1.807606931
0.036722217
26.07%


H2AFZ
1.43657509
0.113374705
1.54629421
0.409551322
7.64%


H2AFZ
1.892370904
0.085788012
1.956431629
0.470600702
3.39%


HDAC1
1.076726189
0.035884843
1.162361046
0.080159851
7.95%


HDAC1
1.378250707
0.121219923
1.776364179
0.029219212
28.89%


HDAC10
1.167302251
0.093962651
1.316469536
0.186286463
12.78%


HDAC10
1.265100258
0.040689297
1.405360633
0.063882576
11.09%


HDAC11
0.526505315
0.021192524
0.631193628
0.041775621
19.88%


HDAC11
1.048976836
0.056671452
1.080258483
0.137293172
2.98%


HDAC2
0.993750769
0.030449241
1.12066395
0.245415742
12.77%


HDAC2
1.390134088
0.062017949
1.54527383
0.113485364
11.16%


HDAC4
0.953083342
0.083100984
1.03145133
0.039446365
8.22%


HDAC4
0.918648939
0.080711928
0.964058412
0.062250727
4.94%


HDAC6
1.118438681
0.042367796
1.235008611
0.07702996
10.42%


HDAC6
1.164950309
0.070419053
1.199467669
0.164185371
2.96%


HLTF
1.368384795
0.083804062
1.726567936
0.0217327
26.18%


HLTF
0.986074548
0.070984414
1.009376139
0.074536946
2.36%


HNRNPA2B1
0.922302866
0.166113356
1.051784117
0.346638883
14.04%


HNRNPA2B1
1.235354902
0.105006002
1.528973263
0.123246142
23.77%


HSP90B1
1.770152164
0.100831368
1.929218292
0.6011219
8.99%


HSP90B1
0.687175737
0.133561854
0.609191259
0.048822099
11.35%


HSPD1
0.906482962
0.08775712
1.101746016
0.10132525
21.54%


HSPD1
1.05752245
0.040245058
1.131597257
0.144315988
7.00%


HSPE1
0.793203106
0.193945844
0.848884884
0.070819712
7.02%


HSPE1
0.651833281
0.040807423
0.75791845
0.098718014
16.27%


HUS1
2.100630245
0.106357851
2.471908087
0.44322413
17.67%


HUS1
0.966569717
0.050318208
1.073796416
0.053323535
11.09%


IARS
1.631393851
0.211565456
1.701419239
0.097191131
4.29%


IARS
1.405236951
0.173116431
1.407794548
0.334264592
0.18%


IFNGR2
0.535583595
0.452033381
0.707441455
0.54022995
−32.09%


IFNGR2
1.027375072
0.135597374
1.136661522
0.008499378
10.64%


IGF1R
0.939071022
0.080118676
1.292851633
0.2689938
−37.67%


IGF1R
1.283545876
0.239291152
1.374337538
0.055778733
7.07%


ILF2
0.763082645
0.053578429
0.826544991
0.029521512
8.32%


ILF2
1.015317243
0.022874379
0.949965331
0.056634536
6.44%


ITGB3
0.864865389
0.015373447
1.119827822
0.159795099
−29.48%


ITGB3
0.709136435
0.167351123
0.687492225
0.169761376
3.05%


KDELR2
1.089923814
0.011828729
1.174998322
0.157686543
7.81%


KDELR2
1.15283249
0.023051809
1.13945738
0.094693411
1.16%


KIAA0101
1.125698118
0.039174475
1.104860352
0.167193939
1.85%


KIAA0101
0.991867078
0.125229112
0.975964768
0.098017306
1.60%


KPNA2
0.66307224
0.067796131
0.680810339
0.040902805
2.68%


KPNA2
0.856375901
0.019620509
0.900824906
0.031907025
5.19%


LDHA
1.235070859
0.159647246
0.916062176
0.090692611
25.83%


LDHA
1.583899161
0.114930832
1.439513404
0.210851066
9.12%


LIG1
1.316863401
0.218038446
1.658301419
0.344683257
25.93%


LIG1
1.817995056
0.116370189
2.256273936
0.168285885
24.11%


LIG3
0.515364744
0.014590155
0.797800086
0.066154726
−54.80%


LIG3
0.312289334
0.02141388
0.582248285
0.056561565
−86.45%


LIG4
1.188668258
0.218374363
1.233783683
0.058202656
3.80%


LIG4
1.134882276
0.031025365
1.376651489
0.108683022
21.30%


MAD2L2
1.131775126
0.100003295
0.969817447
0.080246876
14.31%


MAD2L2
0.584499938
0.097607811
0.488520028
0.078809175
16.42%


MAPK1
1.090312669
0.01643541
1.508818939
0.07590002
−38.38%


MAPK1
1.149358395
0.021244124
1.542611863
0.020252454
−34.22%


MBD1
1.032162891
0.033178014
1.324550272
0.193153997
28.33%


MBD1
0.825928298
0.009873938
1.0271205
0.178708358
24.36%


MBD2
0.884241604
0.132033611
1.060563894
0.149834619
19.94%


MBD2
1.020128496
0.065484971
1.340125899
0.125954093
−31.37%


MBD3
0.712131816
0.033331493
0.867946051
0.051206979
21.88%


MBD3
0.882666995
0.200837669
1.022959944
0.051471831
15.89%


MBD4
1.103881301
0.046525652
1.240466125
0.053908808
12.37%


MBD4
0.94057725
0.053769515
0.775530599
0.063311909
17.55%


MCL1
0.904772996
0.055246785
1.083750093
0.151223466
19.78%


MCL1
1.134726994
0.056068185
1.530243089
0.118152703
−34.86%


MCM3
1.123037853
0.164055084
1.152653828
0.271277652
2.64%


MCM3
0.900477914
0.074173861
0.750922633
0.220000661
16.61%


MECP2
1.028622167
0.156557379
0.739761207
0.07149122
28.08%


MECP2
1.138672484
0.098527939
1.118347585
0.264519109
1.78%


MGMT
0.832090224
0.061160229
0.659307969
0.151432941
20.76%


MGMT
0.937411095
0.031078032
0.971289192
0.030613894
3.61%


MLH1
1.341202688
0.12140842
1.141833746
0.296881041
14.86%


MLH1
1.042796302
0.064639691
1.075865839
0.134241881
3.17%


MLH3
1.026020567
0.076563554
1.017453438
0.105029182
0.83%


MLH3
0.926041342
0.041804849
0.87786498
0.024686386
5.20%


MLL
0.937778186
0.038073653
0.936090926
0.047482141
0.18%


MLL
0.984291592
0.013820563
1.0191236
0.021751586
3.54%


MMP9
1.013177628
0.139768588
1.053814668
0.194962418
4.01%


MMP9
1.036513428
0.079869992
1.105124248
0.144166699
6.62%


MMS19
1.009518287
0.0758167
1.110000224
0.155881203
9.95%


MMS19
0.997996299
0.039405677
1.075850738
0.061939209
7.80%


MNAT1
0.868856972
0.016039672
0.91034436
0.122152111
4.77%


MNAT1
0.955903272
0.03020709
1.031251588
0.022277812
7.88%


MPG
1.127739281
0.025061122
1.396432037
0.17750059
23.83%


MPG
1.004017935
0.024471619
1.260481202
0.195839574
25.54%


MRE11A
0.756796654
0.137423182
0.929066031
0.060433439
22.76%


MRE11A
1.056120064
0.060981219
1.422158169
0.127685446
−34.66%


MRPL3
1.511925903
0.203105158
1.303717053
0.065137095
13.77%


MRPL3
0.79346283
0.082893271
0.921088595
0.034167244
16.08%


MRPS12
0.794995335
0.031077941
0.863983604
0.097011025
8.68%


MRPS12
0.67566038
0.022143849
0.751410133
0.075278165
11.21%


MSH2
1.048071347
0.059056559
0.974792547
0.045328435
6.99%


MSH2
0.97716411
0.060961516
1.115703773
0.187484054
14.18%


MSH3
0.849364634
0.087060425
0.950763344
0.074436738
11.94%


MSH3
1.096343617
0.035353941
1.234489087
0.092999264
12.60%


MSH4
0.98332814
0.032249944
1.071687947
0.023182138
8.99%


MSH4
0.865517122
0.030142067
0.979364336
0.092463868
13.15%


MSH5
0.997166094
0.028414811
1.120972357
0.127389282
12.42%


MSH5
1.033211048
0.07621348
1.30280411
0.030119616
26.09%


MSH6
0.963906497
0.033863944
1.069180702
0.190779091
10.92%


MSH6
0.928860949
0.05137645
0.981435371
0.081732297
5.66%


MTHFD2
0.64122458
0.138498582
0.828580375
0.116876916
−29.22%


MTHFD2
0.848636791
0.15836051
0.851948637
0.059538097
0.39%


MUTYH
0.982433665
0.11341215
1.162797641
0.169143086
18.36%


MUTYH
0.648789767
0.081549299
0.768405862
0.110945125
18.44%


NBN
1.493506041
0.211299898
1.236494706
0.429566775
17.21%


NBN
0.865246004
0.405302674
0.523090786
0.046915698
39.54%


NCBP2
0.76796654
0.043102805
0.61892456
0.097193977
19.41%


NCBP2
1.132921835
0.072889009
1.321688935
0.00044993
16.66%


NEIL1
1.4067659
0.089279444
1.798562104
0.030132906
27.85%


NEIL1
1.366096691
0.146802815
1.891230163
0.109594132
−38.44%


NEIL2
0.92867283
0.054608129
1.044941627
0.013051774
12.52%


NEIL2
1.065787196
0.119529982
1.215825231
0.105074406
14.08%


NEIL3
1.114399408
0.095004343
1.172068264
0.170227137
5.17%


NEIL3
0.815445326
0.012160387
0.837034402
0.005685218
2.65%


NFKB1
0.89081698
0.093046762
1.038117987
0.172160929
16.54%


NFKB1
1.267047109
0.196696199
1.311910627
0.108812065
3.54%


NME1
1.294944028
0.02940933
1.556969155
0.029324398
20.23%


NME1
1.270070119
0.074679937
1.41467051
0.071370835
11.39%


NONO
1.21936697
0.183332247
1.063708042
0.193841121
12.77%


NONO
1.84397089
0.062994624
1.693174138
0.199637423
8.18%


NTHL1
1.001350369
0.131660656
1.147143805
0.028701554
14.56%


NTHL1
0.574183719
0.115223842
0.645347702
0.083707156
12.39%


NUDT1
0.733691246
0.02877895
0.802191846
0.043445081
9.34%


NUDT1
0.764389177
0.059789195
0.806341786
0.004894415
5.49%


NUP205
0.662804988
0.079274607
0.800806452
0.040496562
20.82%


NUP205
0.730562082
0.081662056
0.909885536
0.09129767
24.55%


OGG1
1.345697704
0.198202209
1.414246971
0.036288628
5.09%


OGG1
0.769677206
0.070479563
0.904829439
0.120057041
17.56%


OGT
0.80438673
0.049329366
0.922861934
0.006202001
14.73%


OGT
0.787301772
0.148415465
1.006394466
0.153674726
27.83%


PAFAH1B3
1.340924127
0.194142412
1.888533453
0.766722412
−40.84%


PAFAH1B3
1.699745813
0.053856671
1.745167831
0.189695117
2.67%


PAICS
0.763027884
0.056611495
0.800057591
0.007461821
4.85%


PAICS
0.979213509
0.037642874
1.002134255
0.028226997
2.34%


PARP1
1.494063164
0.097813841
1.335751295
0.318840968
10.60%


PARP1
1.343744559
0.052759186
1.841450777
0.909471525
−37.04%


PARP2
1.069814409
0.577670361
1.261365172
0.855459643
17.91%


PARP2
1.041099685
0.038000202
1.139920347
0.203874733
9.49%


PCNA
0.239193013
0.024341727
0.40204751
0.062477143
−68.08%


PCNA
0.285742404
0.044824887
0.364907398
0.101843788
27.71%


PIK3CB
1.113006852
0.11716295
1.551939489
0.212096704
−39.44%


PIK3CB
1.118131175
0.090924768
1.541290339
0.154474956
−37.85%


PLK1
0.202583655
0.019092656
0.228835323
0.036005583
12.96%


PLK1
0.258539643
0.034356536
0.296868664
0.058995452
14.83%


PMS1
0.846372688
0.08377974
1.010688212
0.030975732
19.41%


PMS1
0.920999098
0.045914146
1.013652455
0.055106511
10.06%


PMS2
0.846212077
0.085815047
1.029160757
0.194627073
21.62%


PMS2
1.02962014
0.026774353
1.363986962
0.148601365
−32.47%


PMS2L3
1.042924273
0.02122765
1.436602497
0.037274537
−37.75%


PMS2L3
0.730327128
0.046156347
0.849869927
0.113296622
16.37%


PNKP
0.757307392
0.027266692
0.840811694
0.040156354
11.03%


PNKP
0.900686765
0.020236289
1.062638684
0.031067462
17.98%


POLB
1.692921063
0.031845939
1.971705339
0.359410185
16.47%


POLB
0.718136491
0.102179626
0.606477685
0.091200501
15.55%


POLD1
1.171269172
0.091136261
1.289896889
0.133305242
10.13%


POLD1
0.65189128
0.083766021
0.635923235
0.019171176
2.45%


POLE
0.36006371
0.015961676
0.404298934
0.015887855
12.29%


POLE
0.470378449
0.078029927
0.493576979
0.046345196
4.93%


POLG
0.944969905
0.221379113
1.073833009
0.220369446
13.64%


POLG
0.779944631
0.066445735
0.809255213
0.060983479
3.76%


POLH
1.177088124
0.071660795
1.268782572
0.107372389
7.79%


POLH
0.909068661
0.063508841
0.921845622
0.03107983
1.41%


POLH
1.00422917
0.019700222
1.425858481
0.056130679
−41.99%


POLI
1.365580022
0.056515253
1.609846602
0.113150911
17.89%


POLI
1.350941075
0.067718606
1.484974986
0.095899691
9.92%


POLK
1.084093984
0.037743481
1.247390915
0.114134048
15.06%


POLK
1.392372986
0.057872984
1.782824769
0.097741764
28.04%


POLL
0.713837777
0.065188911
0.804749564
0.081876458
12.74%


POLL
0.685357684
0.034839121
0.795568881
0.008595048
16.08%


POLM
1.03348222
0.062915947
1.069833275
0.064646037
3.52%


POLM
1.072140854
0.030338963
1.096462458
0.039015514
2.27%


POLN
0.776518454
0.040834685
0.894710097
0.023406799
15.22%


POLN
0.831107848
0.033379191
0.814895743
0.051254906
1.95%


POLN
0.977173324
0.136833629
1.430306972
0.053064726
−46.37%


POLN
1.070522321
0.10944335
1.474115505
0.026108428
−37.70%


POLQ
1.817925415
0.038128927
1.969002027
0.204668642
8.31%


POLQ
1.079758319
0.030115834
1.120026551
0.068909376
3.73%


PPP2R5C
0.780877652
0.033221846
0.838660501
0.081104022
7.40%


PPP2R5C
0.743679163
0.014577188
0.781763979
0.053803136
5.12%


PRDX2
0.53556403
0.053850774
0.469370175
0.070958632
12.36%


PRDX2
1.306975028
0.070782665
1.613391644
0.183006563
23.44%


PRDX4
0.955348037
0.052991499
0.908832674
0.134937811
4.87%


PRDX4
0.681417345
0.049799999
0.858149366
0.395648804
25.94%


PRKDC
1.831923117
0.152474241
1.346834873
0.258136718
26.48%


PRKDC
1.154253282
0.586521468
0.782879027
0.072359299
32.17%


PRMT1
0.666284281
0.021117386
0.722716263
0.055869548
8.47%


PRMT1
0.391012405
0.05150105
0.486118875
0.027183459
24.32%


PSMA1
0.479104796
0.02879132
0.547809211
0.02634527
14.34%


PSMA1
0.349269202
0.002616508
0.423552537
0.016236708
21.27%


PSMC4
0.251666872
0.034694173
0.331279197
0.020436708
−31.63%


PSMC4
1.407651618
0.106571263
1.728920253
0.060840825
22.82%


PSME2
0.944288633
0.070159459
1.05595252
0.054089041
11.83%


PSME2
0.785637616
0.051126589
0.85705361
0.04163169
9.09%


PTMA
1.092683317
0.168241686
1.213737726
0.157280281
11.08%


PTMA
1.177508049
0.097012191
1.190297256
0.255281267
1.09%


RAD1
0.825203812
0.092998017
0.867506818
0.068775224
5.13%


RAD1
0.718548769
0.06679937
0.792198113
0.093348839
10.25%


RAD17
0.792180976
0.057811504
0.84131985
0.103258346
6.20%


RAD17
1.072846911
0.048075596
1.352243039
0.202140925
26.04%


RAD18
2.044047495
0.111956878
2.491777427
0.415969557
21.90%


RAD18
0.957394135
0.12954875
1.024520714
0.087694526
7.01%


RAD23A
0.723549761
0.083643221
0.651144065
0.138278479
10.01%


RAD23A
1.100861845
0.075767502
1.223847547
0.065045321
11.17%


RAD23B
1.588948083
0.088358794
1.44217166
0.314714968
9.24%


RAD23B
1.044117135
0.140404355
0.772065781
0.2128863
26.06%


RAD50
0.974337547
0.024550727
0.921468799
0.122931539
5.43%


RAD50
1.272432033
0.033422429
1.686015307
0.05132537
−32.50%


RAD51
0.511182187
0.131272877
0.559586522
0.035667246
9.47%


RAD51
0.925017955
0.147411912
0.798785798
0.137513654
13.65%


RAD51C
0.768457762
0.093630788
0.724393177
0.052532638
5.73%


RAD51C
0.717585157
0.073467415
0.673763911
0.026263698
6.11%


RAD51L1
0.817873018
0.094902225
1.194446518
0.211469443
−46.04%


RAD51L1
1.201168501
0.170081516
1.232813316
0.056555848
2.63%


RAD51L3
0.70513791
0.149672924
0.646015277
0.136603096
8.38%


RAD51L3
0.979560939
0.032141582
1.16006071
0.155376595
18.43%


RAD52
1.030707118
0.042929649
1.185290239
0.242449811
15.00%


RAD52
0.937906403
0.037925306
1.214674927
0.165845884
−29.51%


RAD54B
1.352737114
0.064491212
1.583341616
0.166379203
17.05%


RAD54B
1.113199656
0.057171838
1.272206209
0.152437673
14.28%


RAD54L
0.972644924
0.053778984
0.819365228
0.367401917
15.76%


RAD54L
0.776457272
0.164819999
0.686010468
0.009817277
11.65%


RAD9A
0.850043592
0.014605471
0.923031319
0.039630503
8.59%


RAD9A
0.660196699
0.019886843
0.618815319
0.033428832
6.27%


RBM4
0.994264213
0.084276284
1.069414096
0.065704696
7.56%


RBM4
1.012618731
0.035887922
1.050866406
0.061712412
3.78%


RECQL4
0.998043697
0.040026929
1.101089376
0.024145818
10.32%


RECQL4
0.945621689
0.029731666
0.995334036
0.029924898
5.26%


REV1
1.058741041
0.054179002
1.246378509
0.147637522
17.72%


REV1
0.973667809
0.0044165
0.918140643
0.023286175
5.70%


REV3L
0.875296349
0.039583261
0.964191947
0.026776987
10.16%


REV3L
0.848988207
0.044018351
0.812998628
0.026009492
4.24%


RFC4
0.751851396
0.069120099
1.080011927
0.161376804
−43.65%


RFC4
0.539180711
0.045344645
0.609647815
0.102207721
13.07%


RPA1
0.474494591
0.027492229
0.56901295
0.108270301
19.92%


RPA1
0.396088704
0.047348825
0.535485025
0.104865168
−35.19%


RPA2
0.542762303
0.016064604
0.619293655
0.099365573
14.10%


RPA2
0.969049084
0.064344594
0.940927012
0.462411173
2.90%


RPA3
0.781107083
0.063542864
0.791808527
0.050814142
1.37%


RPA3
0.817204301
0.045263551
0.819672409
0.029970272
0.30%


RPA4
1.090301582
0.080537699
1.252547733
0.031526223
14.88%


RPA4
1.060783906
0.089242319
1.165631955
0.063527532
9.88%


RPL13
0.982410581
0.015371703
1.045761587
0.03335435
6.45%


RPL13
1.134950313
0.01694113
1.14710476
0.133957623
1.07%


RPL27
0.317302885
0.021821095
0.424388826
0.050024839
−33.75%


RPL27
0.404767142
0.047657271
0.588718155
0.072362476
−45.45%


RPL35
0.260419931
0.010107865
0.425816625
0.17020649
−63.51%


RPL35
0.346634632
0.053329427
0.43852219
0.033930958
26.51%


RRM2B
1.835265852
0.088012263
2.067402568
0.263075495
12.65%


RRM2B
1.732616038
0.311187984
1.787474656
0.143368398
3.17%


SDHC
0.746738249
0.063002438
0.71617799
0.058123403
4.09%


SDHC
0.839902721
0.064063922
0.795450311
0.065602835
5.29%


SDHC
1.072763419
0.061501225
1.397684703
0.047562692
−30.29%


SETD7
1.268470907
0.138721625
1.657721234
0.068811337
−30.69%


SETD7
0.91142822
0.188260736
1.046449988
0.189063493
14.81%


SETD8
0.328771893
0.060194006
0.308267628
0.052808991
6.24%


SETD8
1.725512727
0.107258939
1.267312458
0.291727995
26.55%


SMARCA4
1.083999862
0.03674433
1.058021944
0.028473389
2.40%


SMARCA4
1.052491257
0.101614772
1.248526024
0.102740888
18.63%


SMUG1
0.469722694
0.070949326
0.543709877
0.025514302
15.75%


SMUG1
0.814282874
0.046241008
0.907566441
0.012424282
11.46%


SND1
1.120638285
0.08028654
1.164821401
0.01387382
3.94%


SND1
0.764382411
0.048384332
0.866380371
0.060316309
13.34%


SNRPE
0.250774748
0.04218319
0.254021176
0.034499364
1.29%


SNRPE
1.093036945
0.058778876
1.176291437
0.094178192
7.62%


SNRPF
0.360808144
0.044821314
0.393053766
0.030910898
8.94%


SNRPF
0.458969565
0.216341599
0.373257585
0.02361055
18.67%


SOX4
1.368212572
0.065414864
1.668455753
0.146408279
21.94%


SOX4
1.126756059
0.144170173
1.208726767
0.143286316
7.27%


SPO11
0.962674423
0.053744433
1.072683613
0.024790567
11.43%


SPO11
0.938592847
0.039822107
1.099918004
0.082286484
17.19%


SSBP1
1.114802047
0.190161168
1.027618833
0.079890785
7.82%


SSBP1
2.017305616
0.105782625
1.961883307
0.321744314
2.75%


SSR1
0.923155753
0.048337445
0.964801735
0.032101674
4.51%


SSR1
0.902292785
0.018146642
0.923065196
0.043842017
2.30%


SSR1
1.178185433
0.371732748
1.469901145
0.040405264
24.76%


SUV39H1
1.130696475
0.046219036
1.220559619
0.112912001
7.95%


SUV39H1
1.034445311
0.014717011
0.986652438
0.081736941
4.62%


SUV39H2
1.156991741
0.084704866
1.140530989
0.310941747
1.42%


SUV39H2
1.066428043
0.076814973
1.08658212
0.224213368
1.89%


TARS
1.092703313
0.135950105
1.185712049
0.181531826
8.51%


TARS
1.315167917
0.160206793
1.513997946
0.436690366
15.12%


TDG
1.043664473
0.059542555
0.94854697
0.131023792
9.11%


TDG
1.965110206
0.130389798
2.049921153
0.455489286
4.32%


TDP1
1.364669701
0.084413264
1.605672067
0.071219197
17.66%


TDP1
1.120892628
0.016110377
1.1483347
0.159712848
2.45%


TGIF1
1.080145189
0.098050022
1.461869573
0.227788929
−35.34%


TGIF1
0.948912052
0.041567691
1.074693339
0.210315008
13.26%


TMEM30A
0.9571411
0.045285335
1.170162012
0.181927153
22.26%


TMEM30A
1.328010825
0.160492727
1.59742239
0.102380157
20.29%


TOP2A
0.709872223
0.068846446
0.758393165
0.084125223
6.84%


TOP2A
0.690695675
0.081985123
0.734594824
0.030496926
6.36%


TP53BP1
1.65385285
0.098191519
1.349628295
0.498273727
18.39%


TP53BP1
1.145060761
0.03948085
1.156386574
0.164304495
0.99%


TPX2
0.345317843
0.044176878
0.49504574
0.10285601
−43.36%


TPX2
0.847127517
0.017319157
0.964526158
0.058915548
13.86%


TRAF4
0.75428712
0.120454756
0.769903588
0.070453027
2.07%


TRAF4
0.58248247
0.180237487
0.938872875
0.305702298
−61.18%


TRDMT1
1.013820144
0.055052864
1.27108059
0.056221051
25.38%


TRDMT1
1.003455036
0.064872547
1.369734518
0.192587955
36.50%


TREX1
0.803082358
0.163382387
0.895175537
0.096258278
11.47%


TREX1
1.003493857
0.032700862
1.246846309
0.153152632
24.25%


TREX2
1.114725058
0.078651636
0.794619488
0.317513264
28.72%


TREX2
0.604256366
0.064314841
0.970910778
0.077896404
−60.68%


TSTA3
0.904537183
0.129294758
0.790154108
0.331863616
12.65%


TSTA3
0.73016857
0.172535519
0.864076584
0.205934855
18.34%


TUBB
0.811779371
0.068025776
0.805962282
0.048349847
0.72%


TUBB
0.957394135
0.077029388
0.939713404
0.141855363
1.85%


UBE2A
0.791691522
0.033880413
0.786828599
0.056549419
0.61%


UBE2A
1.36456453
0.181344495
1.344878207
0.055772107
1.44%


UBE2A
1.020187963
0.067432635
1.40991155
0.07672793
−38.20%


UBE2B
1.077871265
0.026494129
1.126469095
0.066458707
4.51%


UBE2B
1.014317371
0.020335035
1.135801023
0.048036463
11.98%


UBE2N
0.923202105
0.100131378
1.107473351
0.028225986
19.96%


UBE2N
1.045687476
0.024308099
1.22086213
0.084046203
16.75%


UBE2S
1.144693955
0.040318695
1.221230625
0.187321024
6.69%


UBE2S
0.978823812
0.06026047
1.158156076
0.15539387
18.32%


UBE2V2
1.610606219
0.109388676
1.593872494
0.224505875
1.04%


UBE2V2
0.947681867
0.057566223
1.10214361
0.036703067
16.30%


UNG
0.726633042
0.040307347
0.806248551
0.061815077
10.96%


UNG
1.121411518
0.055191263
1.315767212
0.047598982
17.33%


WRN
1.088721752
0.182807012
0.989637306
0.345886214
9.10%


WRN
0.989820297
0.061506019
1.149818437
0.06864358
16.16%


XAB2
0.205523006
0.031549473
0.244671095
0.014958665
19.05%


XAB2
0.27561039
0.052777351
0.370596524
0.117461503
−34.46%


XPA
1.022956269
0.050251198
1.032232244
0.084341859
0.91%


XPA
1.006665282
0.022237175
1.125727227
0.043821683
11.83%


XPC
1.013901873
0.058506357
0.981179962
0.042709163
3.23%


XPC
1.019112912
0.036188718
1.140291281
0.01786393
11.89%


XRCC1
0.393049897
0.030277741
0.365307502
0.062157112
7.06%


XRCC1
0.996953014
0.123844963
0.975635469
0.003643983
2.14%


XRCC2
0.598558446
0.087284639
0.596891192
0.057007034
0.28%


XRCC2
1.121637062
0.026148695
1.111026512
0.093941714
0.95%


XRCC3
1.478139993
0.029208955
1.932478548
0.027419033
−30.74%


XRCC3
0.503628983
0.004624957
0.469668356
0.013361831
6.74%


XRCC4
1.015334149
0.01682787
1.197805479
0.181934329
17.97%


XRCC4
1.054678856
0.02970874
1.198054291
0.211292253
13.59%


XRCC5
1.064328421
0.080256697
0.931825807
0.618120205
12.45%


XRCC5
0.248575256
0.049170377
0.625690577
0.629193334
−151.71%


XRCC6
0.972196254
0.069516122
1.048572879
0.021400333
7.86%


XRCC6
0.8919705
0.151343437
0.818378822
0.105603542
8.25%


ZDHHC17
1.244753352
0.097540066
1.332637577
0.169147293
7.06%


ZDHHC17
1.258531185
0.057937462
1.293708379
0.021835192
2.80%









Example 2
Generation of Aptamer-shRNAs Chimeras that Selectively Target PSMA-expressing Cells
Candidate and previously identified radiosensitizing siRNAs (Collis S J, Swartz M J, Nelson W G, DeWeese T L. Enhanced radiation and chemotherapy-mediated cell killing of human cancer cells by small inhibitory RNA silencing of DNA repair factors. Cancer Res. 2003; 63(7):1550-1554) were linked to the PSMA-targeting A10-3 aptamer for selective cell delivery. Aptamer-shRNA chimeras were designed as a single intact nuclease-stabilized 2′ fluoro-modified pyrimidine transcript. The 3′-terminus of the A10-3 aptamer was conjugated to the passenger (sense) strand of the siRNA, followed by a 10-mer loop sequence and then by the guide or silencing (antisense) strand of the siRNA. The secondary structures of each aptamer-shRNA chimera were evaluated by mFold to predict proper folding of the aptamer portion (FIG. 5A). Control chimeras were generated with nonspecific shRNAs (referred to herein as A10-3-Con) or nontargeting aptamer portions (denoted by the prefix Neg− followed by the target gene; FIG. 5B). LNCaP cells were treated with aptamer-shRNA chimeras, in the absence of transfection reagents, and changes in target gene mRNA were evaluated by qRT-PCR relative to untreated cells. The efficiency of chimera A10-3-DNAPK was first evaluated at 4, 40, and 400 nM in LNCaP cells, and 400 nM was determined to be the most effective dose (FIG. 5C). Within 48 hours of treatment at 400 nM, aptamer targeted shRNA caused significant reductions in DNAPK, BRCA2, and ATM mRNA levels (FIGS. 5D-5F). A10-3-Con and aptamer control chimeras (Neg-DNAPK, Neg-BRCA2, and Neg-ATM) had no detectable effect on target mRNA levels. Transfected siRNA served as a positive control for knockdown of each gene. Because delivered shRNAs could potentially induce nonspecific inflammatory responses that cause cellular toxicity (Sledz C A, Holko M, de Veer M J, Silverman R H, Williams B R. Activation of the interferon system by short-interfering RNAs. Nat Cell Biol. 2003; 5(9):834-839), whether INF-β was induced in LNCaP cells transfected with DNAPK siRNAs or treated with aptamer-shRNA chimeras was evaluated by ELISA. The applied treatment conditions failed to cause any detectable increases in INF-β (FIG. 6).
To further confirm PSMA-selective targeting, a second and previously described isogenic cell model of PSMA-expressing PC3 cells (PC3-PIP) and PSMA-negative control cells (PC3-Flu) (Chang S S, Reuter V E, Heston W D, Bander N H, Grauer L S, Gaudin P B. Five different anti-prostate-specific membrane antigen (PSMA) antibodies confirm PSMA expression in tumor-associated neovasculature. Cancer Res. 1999; 59(13):3192-3198) was subjected to aptamer-shRNA chimera treatment. A10-3-DNAPK treatment selectively reduced DNAPK levels in PC3-PIP cells, but not in PC3-Flu cells (FIGS. 7A and 7B).
Example 3
Aptamer-shRNA Chimeras Enter Cells and are Processed by the RNAi Machinery
The processing of aptamer-shRNA chimeras by RNAi machinery was evaluated. Aptamer-shRNA himeras were incubated in the presence or absence of recombinant human Dicer for 1 hour at 37° C. shRNA cleavage products were obtained in samples treated with Dicer, whereas no cleavage products were detected in its absence (FIG. 7C). Aptamer-shRNA chimera processing was further interrogated in an intact cell model. LNCaP cells were treated with A10-3 aptamer-shRNA chimeras in the absence of transfection reagents and evaluated for the presence of the desired siRNA product by Northern blotting. A10-3-DNAPK and A10-3-Con were effectively internalized and processed to produce antisense siRNAs (FIG. 7D). Collectively, these results support that A10-3 aptamer-shRNA bound PSMA, were internalized into cells, and were processed by RNAi machinery, whereas Neg-DNAPK could not enter cells to be processed. In the absence of extensive cell washing, the unprocessed chimeras were detectable by Northern blot, and levels indicated that approximately half of the A10-3 aptamer-shRNA chimeras were internalized and processed to the mature siRNAs in the experimental time period. Processed siRNAs from aptamer-shRNA chimeras resulted in products that were slightly different compared with reference siRNA.
Example 4
Aptamer-shRNA Chimeras Target PSMA Expressing Cells In Vivo
Aptamer-targeted DNAPK RNAi was evaluated in vivo. LNCaP xenografts were established subcutaneously in nude male mice and treated with 200 pmol of targeted and control aptamer-shRNA chimeras by 2 consecutive intratumoral injections. qRT-PCR and immunohistochemistry demonstrated reduction of DNAPK mRNA and DNAPK protein after treatment with A10-3-DNAPK, but not controls (FIGS. 7E and 7F). Quantification of total DNAPK protein staining per nuclear area by FrIDA image analysis (Gurel B, et. al. Nuclear MYC protein overexpression is an early alteration in human prostate carcinogenesis. Mod Pathol. 2008; 21(9):1156-1167) indicated a 52% protein reduction in A10-3-DNAPK-treated tumors compared with A10-3-Con treatment. That aptamer-shRNA chimera-mediated DNAPK knockdown occurs through RNAi was confirmed by identifying DNAPK mRNA cleavage products with 5′-rapid amplification of cDNA ends (5′-RACE) in cell line and animal model treatments (FIGS. 7G and 7H).
Example 5
Aptamer-targeted Radiosensitization in Human PCa Cell and Tumor Models
The aptamer-shRNA chimera targeting the catalytic subunit of DNAPK was used in targeted radiosensitization studies in LNCaP cells. LNCaP, rather than PC3-PIP, was selected for these studies due to the cells' consistent and high-level PSMA expression (FIG. 8). Treatment of LNCaP cells with A10-3-DNAPK in the absence of transfection reagents significantly increased cell death after IR compared with controls (FIG. 9A).
LNCaP tumors and PC3 tumors were then established subcutaneously in male nude mice and intratumorally injected twice with 200 pmol targeted or control aptamer-shRNA chimeras (days −3 and −2). Half of each cohort then received either no radiation treatment or a single radiation treatment (6 Gy) 2 days after aptamer-shRNA chimera injection (day 0). No differences in tumor volume were observed between nonirradiated cohorts (FIGS. 9B and 9C; see FIG. 10 for individual tumor curves), which suggests that chimera treatment alone had no detectable therapeutic effect in either tumor model. In both LNCaP and PC3 tumor models, irradiated tumors treated with control aptamer-shRNA chimeras resulted in a significant but temporary reduction in tumor volume compared with nonirradiated samples (FIG. 9D). Notably, the combination of A10-3-DNAPK and radiation resulted in a significant and extended tumor response in LNCaP tumors, but not PC3 tumors. This combination treatment dramatically extended the time to reach quadruple tumor volume, by approximately 10 weeks compared with 1 week in tumors treated with radiation and control aptamer-shRNA chimeras (FIG. 9D). Thus, in cell and tumor models, aptamer-targeted knockdown of DNAPK selectively enhanced radiosensitivity and increased therapeutic effect.
Example 6
Aptamer-shRNA Chimera-specific Knockdown of the Target Gene in Human Prostate Tissue
To determine whether aptamer-shRNA chimeras would be effective in human tissue, a unique human tissue model was used in which fresh sections of histologically normal human prostate were obtained from radical prostatectomy specimens and immediately maintained ex vivo (Kiviharju-af Hallstrom T M, et al. Human prostate epithelium lacks Weel A-mediated DNA damage-induced checkpoint enforcement. Proc Natl Acad Sci USA. 2007; 104(17):7211-7216). PSMA expression in these noncancerous tissue sections was confirmed by qRT-PCR prior to treatment. Tissue was then treated with A10-3-DNAPK and control aptamer-shRNA chimeras in the absence of transfection reagents. Quantitative image analysis found DNAPK immunostaining to be decreased by 25% in normal prostate epithelial cells 2 days after treatment with A10-3-DNAPK compared with those treated with control aptamer-shRNA chimeras (FIG. 11). Thus, aptamer-shRNA chimeras are effective in treating human prostate tissues. Further, knockdown in cancer specimens is expected to be much more substantial because PSMA expression is known to be elevated in primary prostate tumors compared to normal prostatic epithelium.
DNA repair pathways are an attractive therapeutic target for radiosensitization. Double stranded breaks (DSBs) are generally regarded as the most lethal of all DNA lesions; if unrepaired, they severely threaten not only the integrity of the genome, but also the survival of the organism (Hoeijmakers J H. Genome maintenance mechanisms for preventing cancer. Nature. 2001; 411(6835):366-374; van Gent D C, Hoeijmakers J H, Kanaar R. Chromosomal stability and the DNA double-stranded break connection. Nat Rev Genet. 2001; 2(3):196-206; Vilenchik M M, Knudson A G. Endogenous DNA double-strandbreaks: production, fidelity of repair, and induction of cancer. Proc Natl Acad Sci USA. 2003; 100(22):12871-12876). To combat the intricate nature of DSBs, complex repair pathways have evolved. Thus, multiple steps of DSB repair pathways, enzymes, and proteins are targets for RNAi induced radiosensitization therapy. Described herein is the first high-throughput screen of DNA repair pathways by RNAi in combination with radiation therapy. Of 249 mRNAs screened, 10 candidates were identified, 6 of which were identified by at least 2 siRNAs and confirmed in separate PCa cell line models. Given the ubiquity of the identified target genes, these target genes are suitable targets for radiosensitization in a variety of tissue and cancer types.
Since the discovery of RNAi, this pathway has been widely recognized as a new frontier for human therapeutics, and many human clinical trials using this technology are currently planned or in progress. As with other therapeutic approaches, there is a need for selective tissue targeting to minimize damage to normal tissues (Aagaard L, Rossi J J. RNAi therapeutics: principles, prospects and challenges. Adv Drug Deliv Rev. 2007; 59(2-3):75-86; Castanotto D, Rossi J J. The promises and pitfalls of RNA-interference-based therapeutics. Nature. 2009; 457(7228):426-433; Jinek M, Doudna J A. A three-dimensional view of the molecular machinery of RNA interference. Nature. 2009; 457(7228):405-412; Siomi H, Siomi M C. On the road to reading the RNA-interference code, Nature. 2009; 457(7228):396-404). PSMA-targeting aptamers were previously developed as a means to selectively deliver therapeutic and imaging agents to PCa cells (Lupold S E, Hicke B J, Lin Y, Coffey D S. Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res. 2002; 62(14):4029-4033). These aptamers have been used to target therapeutics, including siRNAs and shRNAs (Chu T C, Twu K Y, Ellington A D, Levy M. Aptamer mediated siRNA delivery. Nucleic Acids Res. 2006; 34(10):e73; Dassie J P, et al. Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat. Biotechnol. 2009; 27(9):839-849; McNamara J O 2nd, et al. Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat. Biotechnol. 2006; 24(8):1005-1015; Wullner U, Neef I, Eller A, Kleines M, Tur M K, Barth S. Cell-specific induction of apoptosis by rationally designed bivalent aptamer-siRNA transcripts silencing eukaryotic elongation factor 2. Curr Cancer Drug Targets. 2008; 8(7):554-565).
The present invention relates to aptamer-inhibitory nucleic acid chimeras suitable for use as selective radiosensitizing agents. Described in detail herein is the generation of 2′ fluoro-modified pyrimidine aptamer-shRNA chimera radiosensitizing agents. The conjugates retained PSMA targeting ability, and the inhibitory nucleic acid portion of the chimera was effectively processed by RNAi machinery to the predicted antisense siRNA. There was a slight difference in the siRNA product size compared with the reference siRNA, which may be caused by 2′-fluoro-modifications or by cleavage somewhere in the aptamer loop. Similar size differences have been seen in aptamer-siRNA chimera studies (Dassie J P, et al. Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat. Biotechnol. 2009; 27(9):839-849). The resulting siRNA product was then free to degrade the target transcript at the predicted site, as demonstrated by 5′-RACE. These results demonstrate that aptamer-inhibitory nucleic acid (e.g., shRNA) chimeras can be developed for virtually any target gene, including those that sensitize cancer cells to standard therapeutic approaches.
Advantages of aptamer-inhibitory nucleic acid (e.g., shRNA) chimeras include their simplicity, potential for chemical synthesis, safety, and low toxicity (Behlke M A. Chemical modification of siRNAs for in vivo use. Oligonucleotides. 2008; 18(4):305-319; Reynolds A, Leake D, Boese Q, Scaringe S, Marshall W S, Khvorova A. Rational siRNA design for RNA interference. Nat. Biotechnol. 2004; 22(3):326-330; Soundararajan S, Chen W, Spicer E K, CourtenayLuck N, Fernandes D J. The nueleolin targeting aptamer AS1411 destabilizes Bcl-2 messenger RNA in human breast cancer cells. Cancer Res. 2008; 68(7):2358-2365). The invention described herein demonstrates the utility of such agents in individuals being treated with radiation therapy for localized cancers. Although radiation therapy is highly successful, there are treatment-related risks that would be diminished with a radiation dose-reducing strategy predicated on the claimed aptamer-shRNA chimera method. Moreover, treatment efficacy of local tumors would be improved with radiosensitization while also minimizing side effects.
Also described herein, DNAPK knockdown improved therapeutic efficacy by almost 10-fold. Further, the current A10-3-DNAPK chimeras are suitable for targeting metastatic disease. In addition, inhibition of DNA repair pathways can also sensitize cells to chemotherapeutics, such as alkylating agents and topoisomerase inhibitors, therefore providing a mechanism for systemic chemosensitization (Collis S J, Swartz M J, Nelson W G, DeWeese T L. Enhanced radiation and chemotherapy-mediated cell killing of human cancer cells by small inhibitory RNA silencing of DNA repair factors. Cancer Res. 2003; 63(7):1550-1554).
In summary, the claimed aptamer-inhibitory nucleic acid (e.g., shRNA) chimeras retain cancer cell antigen (e.g., PSMA)-selective targeting, proper Dicer shRNA processing, and subsequent target gene knockdown in cancerous cells (e.g., PCa cells, tumor xenografts, and normal human prostatic tissue models). Targeted treatment markedly enhances the benefits of radiation therapy in both cellular and tumor models, demonstrating the utility of these chimeras to enhance radiation therapy for locally advanced cancers.
Example 7
Generation of Aptamer-siRNA Chimeras
An aptamer-inhibitory nucleic acid chimera was generated that comprises an aptamer that is bonded to an siRNA molecule by Watson-Crick binding. To generate aptamer-siRNA chimeras, three oligonucleotides were synthesized (FIG. 12A) where the first oligonucleotide corresponds to the aptamer, the second oligonucleotide corresponds to the sense strand of the siRNA molecule, and the third strand corresponds to the anti-sense strand of the siRNA. The anti-sense siRNA strand includes a two-nucleotide 3′-overhang. The three oligonucleotides were mixed in a 1:1:1 molar ratio, heated to 90° C. for 5 minutes followed by a 25° C. incubation for 30 minutes. Once formed the aptamer-siRNA chimeras were stored at −20° C. The structure of the annealed aptamer-siRNA is shown in FIG. 12B. LNCaP cells were treated with 400 nM aptamer-siRNA (A10-3-DNAPK) or A10-3 Con as a control. In addition, LNCaP cells were Hyperfect transfected with DNAPK siRNA as an additional control. The levels of DNAPK expression were measured by quantitative reverse transcription coupled to polymerase chain reaction (QT-PCR). As shown in FIG. 12C, the aptamer-siRNA chimera treatment resulted in a significant decrease in DNAPK expression.
The results described above were obtained using the following methods and materials.
Cell Culture.
PCa cell lines DU145 (ATCC no. HTB-81), LNCaP (ATCC no. CRL1740), PC3 (ATCC no. CRL-1435), PC3-PIP, and PC3-Flu (gift of W. Heston, Lerner Research Institute, Cleveland, Ohio, USA) were grown in RPMI 1640 supplemented with 10% FBS and maintained at 37° C. and 5% CO2.
DNA Repair siRNA Library Screen.
A custom siRNA library included 496 siRNAs targeting 249 genes and controls (Qiagen). 2×103 DU145 were Hiperfect reverse transfected (Qiagen) in triplicate in 96-well plates formatted with 5 nM siRNA. 72 hours later, cells were irradiated (6 Gy in a Gammacell 40 [Nordion] 137Cs radiator at approximately 0.6 Gy/min) and grown for 72 hours. Cell viability was quantified by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS; Promega). Irradiated and nonirradiated viability was normalized to the control siRNA for each siRNA, and radiosensitization was determined as the ratio of increased cell death relative to the control siRNA. Significance was assigned as P<0.05 by Student's t test. Candidate sensitizing siRNAs were confirmed by repeat assays and clonogenic survival assays.
Clonogenic Survival Assays.
Clonogenic survival assays were confirmed in a larger format, in which 1.7×105 DU145 cells were reverse transfected with 5 nM control and candidate siRNAs and grown for 72 hours, after which cell dilutions were plated into 100-mm culture dishes and irradiated immediately. Exposures were carried out as described above. The cells were grown for 14 days and stained with crystal violet; colonies with greater than 30 cells were scored, and survival fraction was calculated.
qRT-PCR.
mRNA (1 μg) from PCa cells treated with the various siRNAs or aptamer-shRNA chimeras was reverse transcribed using QuantiTect Reverse Transcription Kit (Qiagen). Sybrgreen-based real-time qRT-PCR was performed using SYBR GreenER qPCR SuperMix (Invitrogen) according to the manufacturer's instructions. All reactions were done in triplicate. Standard curves were generated by serial dilution of each sample, and the relative amount of target gene mRNA was normalized to GAPDH mRNA (see Table 2 for primers).







TABLE 2







(TABLE 2 discloses SEQ ID NOS 12-27, respectively, in


order of appearance)


 Primers for q-PCR









Name
Forward
Reverse





DNA-PK
AGAAGGCGGCTTACCTGAGT
GACATTTTTGTCAGCCAATCTTT


 


BRCA2
GCGCGGTTTTTGTCAGCTTA
TGGTCCTAAATCTGCTTTGTTGC


 


ATM
TGGATCCAGCTATTTGGTTTGA
CCAAGTATGTAACCAACAATAGAAGAAGTAG


 


MAD2L2
CGAGTTCCTGGAGGTGGCTGTGCATC
CTTGACGCAGTGCAGCGTGTCCTGGATA


 


RAD23B
ATGGTAGACAAAACTATAATCCAGCATC
GCCACATCTCCCAACCCA


 


NBN
ATGGAGGCCATATTTCCATGAC
CAAGCAGCCAGAACTTGGAAG


 


RAD54L
CGAAGCCGTAGCAGTGACAAAG
ATGGACATCGTGCCATCCAG


 


GAPDH
TCGCTCTCTGCTCCTCCTGTTC
CGCCCAATACGACCAAATCC









Aptamer-shRNA Chimeras.

Aptamer-shRNA chimeras were generated as follows. PSMA-targeting (A10-3) or nontargeting (Neg) template primers (Table 3) were fused to a corresponding shRNA by PCR with Pfu polymerase (NEB).







TABLE 3







(TABLE 3 discloses the “Forward” primers as SEQ ID NOS 28, 33, 37 and 40,


respectively, in order of appearance and the “Reverse” primers as SEQ ID NOS


29-32, 34-36, 38-39 and 41-42, respectively, in order of appearance)


Primers and templates for aptamer-shRNAs synthesis










Name
Forward
Reverse
Name










1st PCR primers










A10-3  
TAATACGACTCACTATAGGGAGGACG
AATTCTCCGAACGTGTCACGTCAAGCTTCATACGTGA
Con-S1RNA-


Temlate
ATGCGGATCA
CACGTTCGGAGAATTGCCGATGAGCATTGACAAG
loop primer


primer
GCCATGTTTACGTCACTCCTTGTCAA
TTCGGCTAACTCGCCAGTTTACAAGCTTCATTAAACT
DNA-PK-loop 



TCCTCATCGGC
GGCGAGTTAGCCGAAGCCGATGAGGATTGACAAG
primer




CAGGACACAATTACAACTAAACAAGCTTCATTTTAGT
BRCA2-loop 




TGTAATTGTGTCCTGGCCGATGAGGATTGACAAG
primer




AGGCTATTCAGTGTGCGAGACAAGCTTCATTCTCGC
ATM-loop 




ACACTGAATAGCCTTGCCGATGAGGATTGACAAG
primer


 


Neg  
TAATACGACTCACTATACAGGCATGC
TTCGGCTAACTCGCCAGTTTACAAGCTTCATTAAACT
Neg-DNA-PK-


Temlate
CTAGCTAAGCA
GGCGAGTTAGCCGAAGAACGGAAGCCAATATTCC
loop primer


primer
GCCCATGGCTTATGCGCGGAATATTG
CAGGACACAATTACAACTAAACAAGCTTCATTTTAGT
Neg-BRCA2-



GCTTCCGTTC
TGTAATTGTGTTCCTGGAACGGAAGCCAATATTCC
loop primer




AAGGCTATTCAGTGTGCGAGACAAGCTTCATTCTCG
Neg-ATM-




CACACTGAATAGCCTTGAACGGAAGCCAATATTCC
loop primer








2nd PCR primers











A10-3 5′-
TAATACGACTCACTATAGGGAGGAC
AATTCTCCGAACGTGTCACGTCAAGC
Con-loop 2nd 


primer
GATGCGG

primer




TTCGGCTAACTCGCCAGTTTACAAGC
DNA-PK-loop 





2nd primer


 


Neg 5′-
TAATACGACTCACTATACAGGCATG
CAGGACACAATTACAACTAAACAAGC
BRCA2-loop 


primer
CCTAGCT

2nd primer




AAGGCTATTCAGTGTGCGAGACAAGC
ATM-loop 





2nd primer









These first DNA templates were column purified (Qiagen) and separately used as templates for secondary PCR with A10-3 or Neg 5′-primer and the appropriate second primer for each gene by Taq polymerase (Qiagen). After column purification, products were TA cloned (Promega) and sequenced. PCR products from plasmid or the secondary PCR were used as templates for DuraScribe T7 transcription according to the manufacturer's instructions (Epicenter Biotechnologies). Aptamer-shRNA chimeras (Table 4) were purified by gel electrophoresis (Lupold S E, Hicke B J, Lin Y, Coffey D S.








TABLE 4







(TABLE 4 discloses SEQ ID NOS 43-49, respectively,


in order of appearance)


Aptamer-shRNA








Name






A10-3-Con
GGGAGGACGAUGCGGAUCAGCCAUGUUUACGUCACUCCUUGUCAAUCCUCAUCG



GCAAUUCUCCGAACGUGUCACGUAUGAAGCUUGACGUGACACGUUCGGAGAAUU


 


A10-3-DNA-PK
GGGAGGACGAUGCGGAUCAGCCAUGUUUACGUCACUCCUUGUCAAUCCUCAUCG



GCUUCGGCUAACUCGCCAGUUUAAUGAAGCUUGUAAACUGGCGAGUUAGCCGAA


 


A10-3-BRCA2
GGGAGGACGAUGCGGAUCAGCCAUGUUUACGUCACUCCUUGUCAAUCCUCAUCG



GCCAGGACACAAUUACAACUAAAAUGAAGCUUGUUUAGUUGUAAUUGUGUCCUG


 


A10-3-ATM
GGGAGGACGAUGCGGAUCAGCCAUGUUUACGUCACUCCUUGUCAAUCCUCAUCG



GCAAGGCUAUUCAGUGUGCGAGAAUGAAGCUUGUCUCGCACACUGAAUAGCCUU


 


Neg-DNA-PK
CAGGCAUGCCUAGCUAAGCAGCCCAUGGCUUAUGCGCGGAAUAUUGGCUUCCGU



UCUUCGGCUAACUCGCCAGUUUAAUGAAGCUUGUAAACUGGCGAGUUAGCCGAA


 


Neg-BRCA2
CAGGCAUGCCUAGCUAAGCAGCCCAUGGCUUAUGCGCGGAAUAUUGGCUUCCGU



UCCAGGACACAAUUACAACUAAAAUGAAGCUUGUUUAGUUGUAAUUGUGUCCUG


 


Neg-ATM
CAGGCAUGCCUAGCUAAGCAGCCCAUGGCUUAUGCGCGGAAUAUUGGCUUCCGU



UCAAGGCUAUUCAGUGUGCGAGAAUGAAGCUUGUCUCGCACACUGAAUAGCCUU









Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res. 2002; 62(14):4029-4033).

Aptamer-shRNA Chimera-Mediated Gene Silencing and Radiosensitization Assay.

2×105 cells (LNCaP, PC3-PIP, or PC3-Flu) were Hiperfect transfected with 100 nM siRNA (Table 5) in 6-well plates or treated with 4, 40, or 400 nM of aptamer-shRNA chimeras.







TABLE 5







(TABLE 5 discloses SEQ ID NOS 50-57,


respectively, in order of appearance)


siRNA









Name
sense
anti-sense





DNA-PK
UUCGGCUAACUCGCC
UAAACUGGCGAGUUA



AGUUUA
GCCGAA


 


BRCA2
CAGGACACAAUUACA
UUUAGUUGUAAUUGU



ACUAAA
GUCCUG


 


ATM
AAGGCUAUUCAGUGU
UCUCGCACACUGAAU



GCGAGA
AGCCUU


 


Con siRNA
AAUUCUCCGAACGUG
ACGUGACACGUUCGG



UCACGU
AGAAUU









After 48 hours, cells were either collected for qRT-PCR or seeded in 96-well plates at 2,000 cells/well. 24 hours later, cells were irradiated with 6 Gy using a Gammacell 40 (Nordion) 137Cs radiator at approximately 0.6 Gy/min. Cell viability was assessed after 12 days by MTS.

Dicer Processing Analysis

For in vitro Dicer assay, 1 μg of each aptamer-shRNA chimera was incubated with recombinant human Dicer following the manufacturer's recommendations (Recombinant Human Turbo Dicer Kit; GTS). For cellular Dicer assay, RNA from aptamer-shRNA chimera-treated LNCaP cells (as described above) were evaluated by Northern blot. Probes were as follows: DNAPK siRNA antisense, 5′-TTCGGCTAACTCGCCAGTTTA-3′ (SEQ ID NO: 58); control siRNA antisense, 5′-AATTCTCCGAACGTGTCACGT-3′ (SEQ ID NO: 59).
5′ RACE mRNA (5 μg) from LNCaP cells or LNCaP tumor treated with aptamer-shRNA chimeras was ligated to GeneRacer adaptor (Invitrogen). Ligated RNA was reverse transcribed using a gene-specific primer (GSP[DNAPK] reverse 1, 5′-GAGGGCTCCTTGACAAACACATCCAT-3′ (SEQ
ID NO: 60)). To detect cleavage products, PCR was performed using primers complementary to the RNA adaptor (GR 5′ primer, 5′-CTCTAGAGCGACTGGAGCACGAGGACACTA-3′ (SEQ ID NO: 61)) and gene-specific primer (GSP[DNAPK] reverse 2, 5′-GGAAGGCCCGGAGTGCGTGTACCAT-3′ (SEQ ID NO: 62)). Amplification products were resolved by agarose gel electrophoresis, visualized by ethidium bromide staining, and confirmed by sequencing.
Animal Model Studies.
Studies were performed according to the protocols approved by the Animal Care and Use Committee at Johns Hopkins University. 8-week-old athymic nude mice (nu/nu; Harlan Laboratories Inc.) were obtained from the Animal Center Isolation Facility at Johns Hopkins University and maintained in a sterile environment according to guidelines established by the Association for Assessment and Accreditation of Laboratory Animal Care. Mice were inoculated with 5×106 (50% Matrigel) PC3 cells or LNCaP cells subcutaneously, and tumors were grown to at least 0.8 cm in diameter. For aptamer-shRNA chimera knockdown, tumors were injected with 200 pmol chimeras on days −3 and −2. On day 0, the tumor was harvested and partitioned for RNA extraction or formalin fixation. For radiosensitization, LNCaP or PC3 tumors were randomized into no-radiation and radiation groups and treated with aptamer-shRNA chimeras as above. On day 0, radiation groups received 6 Gy local IR (5.8 Gy/min) to the tumor-bearing leg from a J.L. Shepherd Mark 137Cs irradiator with the remainder of the body shielded from the source. Tumors were measured every 2 days to calculate tumor volume: (w×l×h)×0.52. Tumor response was determined as reaching 4 times its volume at the start of radiation treatment.
Immunohistochemistry.
Paraffin-embedded sections (4 μm) were taken from xenograft tumors or human tissues. Slides were deparaffinized and rehydrated through a series of ethanol gradients, then treated with 0.1% Tween 20 detergent in deionized water and incubated in Target Retrieval solution (Dako) and in steam (Black and Decker Vegetable Steamer), then washed in PBS with Tween. After 3% hydrogen peroxide incubation, primary antibody anti-DNAPK (Ab-2, mouse mAb; Calbiochem) was added to each slide, A second antibody, Powervision (Poly-HRP anti-mouse IgG; Leica Biosystems) was applied to the specimens according to the manufacturer's standard protocol. The staining was developed with diaminobenzidine (DAB kit; Vector Laboratories) and counterstained with Mayer hematoxylin. Images were captured for presentation using a Nikon 50i microscopy with Nikon NIS-Elements software and an attached charge-coupled device digital camera. Brightfield setting was the same for all images. For quantification of DNAPK, whole DAB staining slides were scanned via ScanScope CS system (Aperio Technologies Inc.) at the Tissue Micro Array Core of Johns Hopkins University School of Medicine, and total DNAPK expression per cell nucleus was measured from 5-8 areas of tissue specimen for 500-1,000 cells using Framework for Image Dataset Analysis (FrIDA) software as previously described (Gurel B, et al. Nuclear MYC protein overexpression is an early alteration in human prostate carcinogenesis. Mod Pathol. 2008; 21(9):1156-1167).
Ex Vivo Human Prostate Tissue Model.
Fresh human prostate tissue samples were obtained from the Department of Pathology of Johns Hopkins University. This study was approved by the Institutional Review Board at Johns Hopkins Medical Institution (approval no. NA—00015481), and informed consent was obtained from patients participating in the study. Fresh tissue representing histologically normal areas was bored from radical prostatectomy specimens and sliced at 300 μm with a Krumdieck precision tissue slicer (Alabama Research and Development Corp.; Kiviharju-af Hallstrom T M, et al. Human prostate epithelium lacks Weel A-mediated DNA damage-induced checkpoint enforcement, Proc Natl Aced Sci USA. 2007; 104(17):7211-7216). The tissue slices were loaded onto titanium grids in 6-well plates containing culture medium with 200 nM aptamer-shRNA chimeras and rotated on an inclined plane in a humidified tissue culture incubator at 37° C. for 48 hours before being processed for immunohistochemical staining and quantification as above.
Statistics.
Statistical analysis data of tumor size was evaluated by 2-way ANOVA. A P value of 0.05 or less was considered significant. For the extension of tumor quadrupling experiments, events (animals whose tumor volume was not yet 4-fold the size at injection) were plotted on Kaplan-Meier curve and analyzed by log-rank (Mantel-Cox) test. Paired samples were evaluated by 2-tailed Student's t test.
Materials.
Unless otherwise noted, all DNA primers were purchased from Sigma-Aldrich, siRNAs were purchased from IDT and all cell culture products were purchased from Gibco BRL/LifeTechnologies.
Interferon Assay.
For evaluating the interferon β response, 2×105 LNCaP cells were either transfected with siRNA DNA-PK or incubated with 400 nM A10-3-Con, A10-3-DNA-PK or NegDNA-PK, Poly(I:C) (invivogen) as a positive control, for 48 hours before the secretion of interferon β into the cell culture supernatant was analyzed. Detection of interferon β was accomplished by using a commercially available sandwich interferon β ELISA kit (PBL) following the manufacturer's recommendations. The results obtained were compared to serial dilutions of an interferon β positive control provided with the kit.
RNA Secondary Structure.
M-fold was used to predict the structures of Aptamer-shRNAs. The most stable structures with the lowest energies for each RNA oligo were compared.
PSMA Cell-Surface Expression.
PSMA cell-surface expression was determined by flow cytometry using antibodies specific to human PSMA (J591 from Neil Bander, Weill Medical College of Cornell University). PC3—PIP or PC3-Flu cells were trypsinized and washed three times in PBS. 1×106 cells were resuspended in 100 μl cell sorting buffer (1×PBS, 0.5% bovine serum albumin (BSA), 2 mmol/L EDTA) with a 1:5000 dilution of Human PSMA antibody J591 and incubated at 4° C. for 20 min. Cells were then washed in 1 ml cold cell sorting buffer and incubated at 4° C. for 20 min with a 1:1,000 dilution of Alexa Fluor 488 F(ab′)2 fragment of antihuman IgG (A11013; Invitrogen) in cell sorting buffer. Cells were washed and incubated at 4° C. for 20 min with 4% PFA (1 ml). After fixation, cells were then resuspended in cell sorting buffer and analyzed by flow cytometry (Becton Dickson Calibur FACS Analytic cytometer).
Other Embodiments
From the foregoing description, it will be apparent that variations and modifications may be made to the invention described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.
The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
Incorporation by Reference
All patents, publications, and nucleotide accession numbers mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent, publication, and accession number record was specifically and individually indicated to be incorporated by reference.

## Claims

1. A method of inducing cell death or terminal differentiation in a neoplastic cell, the method comprising:
a) contacting the neoplastic cell with an effective amount of an aptamer-inhibitory nucleic acid chimera, wherein the aptamer-inhibitory nucleic acid chimera comprises a 2′fluoro-modified pyrimidine RNA aptamer-shRNA chimera, wherein the aptamer-shRNA chimera specifically binds prostate-specific membrane antigen (PSMA), and wherein the shRNA decreases the expression of DNA-activated protein kinase (DNAPK); and
b) exposing the neoplastic cell to ionizing radiation, thereby inducing cell death or terminal differentiation in the neoplastic cell.

2. A method of reducing the growth, proliferation or survival of a neoplastic cell, the method comprising:
a) contacting the neoplastic cell with an effective amount of an aptamer-inhibitory nucleic acid chimera, wherein the aptamer-inhibitory nucleic acid chimera comprises a 2′fluoro-modified pyrimidine RNA aptamer-shRNA chimera, wherein the aptamer-shRNA chimera specifically binds prostate-specific membrane antigen (PSMA), and wherein the shRNA decreases the expression of DNA-activated protein kinase (DNAPK); and
b) exposing the neoplastic cell to ionizing radiation, thereby reducing growth, proliferation or survival of the neoplastic cell.

3. A method of treating neoplasia in a subject comprising:
a) administering an aptamer-inhibitory nucleic acid chimera to the subject, wherein the aptamer-inhibitory nucleic acid chimera comprises a 2′fluoro-modified pyrimidine RNA aptamer-shRNA chimera, wherein the aptamer-shRNA chimera specifically binds prostate-specific membrane antigen (PSMA), and wherein the shRNA decreases the expression of DNA-activated protein kinase (DNAPK); and
b) exposing the neoplasia to ionizing radiation, thereby treating neoplasia in the subject.

4. A method of treating prostate cancer in a subject in need thereof comprising:
a) administering an aptamer-shRNA chimera to the subject, wherein the aptamer-shRNA chimera comprises a 2′fluoro-modified pyrimidine RNA aptamer-shRNA chimera, wherein the aptamer-shRNA chimera specifically binds prostate-specific membrane antigen (PSMA), and wherein the shRNA decreases the expression of DNA-activated protein kinase (DNAPK); and
b) exposing the subject to ionizing radiation, thereby treating prostate cancer in the subject.

5. The method of claim 4, wherein the aptamer-shRNA chimera comprises an A10-3 aptamer, wherein the A10-3 aptamer comprises SEQ ID NO: 11 or SEQ ID NO: 63.

6. The method of claim 4, wherein the aptamer-shRNA chimera comprises A10-3 aptamer-DNAPK shRNA, wherein said A10-3 aptamer-DNAPK shRNA comprises SEQ ID NO: 44.

7. The method of claim 4, wherein the DNAPK shRNA comprises SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 64, or SEQ ID NO: 65.

8. The method of claim 1, wherein the aptamer-shRNA chimera comprises an A10-3 aptamer, wherein the A10-3 aptamer comprises SEQ ID NO: 11 or SEQ ID NO: 63.

9. The method of claim 1, wherein the shRNA comprises SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 64, or SEQ ID NO: 65.

10. The method of claim 1, wherein the aptamer-shRNA chimera comprises A10-3 aptamer-DNAPK shRNA, wherein said A10-3 aptamer-DNAPK shRNA comprises SEQ ID NO: 44.