                               SEQUENCE LISTING

<110> DANA-FARBER CANCER INSTITUTE, INC.
 
<120> METHODS OF TREATING CANCERS

<130> 00530-0339WO1

<140> PCT/US2018/055855
<141> 2018-10-15

<150> 62/719,276
<151> 2018-08-17

<150> 62/580,058
<151> 2017-11-01

<160> 17    

<170> PatentIn version 3.5

<210> 1
<211> 21
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide

<400> 1
tcggcaatac ttgctatctt a                                                 21


<210> 2
<211> 19
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide

<400> 2
ccatacaaac attggtaaa                                                    19


<210> 3
<211> 25
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide

<400> 3
caccggtcat acctagtgaa agtaa                                             25


<210> 4
<211> 20
<212> DNA
<213> Homo sapiens

<400> 4
gatccactca cagtttccat                                                   20


<210> 5
<211> 20
<212> DNA
<213> Homo sapiens

<400> 5
tcttgtgctg acttaccaga                                                   20


<210> 6
<211> 39
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide

<400> 6
ccagtgaatt gttgctcggt acctgctaac ggtaatcgg                              39


<210> 7
<211> 39
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide

<400> 7
ccgattaccg ttagcaggta ccgagcaaca attcactgg                              39


<210> 8
<211> 39
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide

<400> 8
cagctatggg acattcgata ccgagcaaca attcactgg                              39


<210> 9
<211> 770
<212> PRT
<213> Unknown

<220>
<223> Description of Unknown: 
      USP1 sequence

<400> 9
Met Pro Gly Val Ile Pro Ser Glu Ser Asn Gly Leu Ser Arg Gly Ser 
1               5                   10                  15      


Pro Ser Lys Lys Asn Arg Leu Ser Leu Lys Phe Phe Gln Lys Lys Glu 
            20                  25                  30          


Thr Lys Arg Ala Leu Asp Phe Thr Asp Ser Gln Glu Asn Glu Glu Lys 
        35                  40                  45              


Ala Ser Glu Tyr Arg Ala Ser Glu Ile Asp Gln Val Val Pro Ala Ala 
    50                  55                  60                  


Gln Ser Ser Pro Ile Asn Cys Glu Lys Arg Glu Asn Leu Leu Pro Phe 
65                  70                  75                  80  


Val Gly Leu Asn Asn Leu Gly Asn Thr Cys Tyr Leu Asn Ser Ile Leu 
                85                  90                  95      


Gln Val Leu Tyr Phe Cys Pro Gly Phe Lys Ser Gly Val Lys His Leu 
            100                 105                 110         


Phe Asn Ile Ile Ser Arg Lys Lys Glu Ala Leu Lys Asp Glu Ala Asn 
        115                 120                 125             


Gln Lys Asp Lys Gly Asn Cys Lys Glu Asp Ser Leu Ala Ser Tyr Glu 
    130                 135                 140                 


Leu Ile Cys Ser Leu Gln Ser Leu Ile Ile Ser Val Glu Gln Leu Gln 
145                 150                 155                 160 


Ala Ser Phe Leu Leu Asn Pro Glu Lys Tyr Thr Asp Glu Leu Ala Thr 
                165                 170                 175     


Gln Pro Arg Arg Leu Leu Asn Thr Leu Arg Glu Leu Asn Pro Met Tyr 
            180                 185                 190         


Glu Gly Tyr Leu Gln His Asp Ala Gln Glu Val Leu Gln Cys Ile Leu 
        195                 200                 205             


Gly Asn Ile Gln Glu Thr Cys Gln Leu Leu Lys Lys Glu Glu Val Lys 
    210                 215                 220                 


Asn Val Ala Glu Leu Pro Thr Lys Val Glu Glu Ile Pro His Pro Lys 
225                 230                 235                 240 


Glu Glu Met Asn Gly Ile Asn Ser Ile Glu Met Asp Ser Met Arg His 
                245                 250                 255     


Ser Glu Asp Phe Lys Glu Lys Leu Pro Lys Gly Asn Gly Lys Arg Lys 
            260                 265                 270         


Ser Asp Thr Glu Phe Gly Asn Met Lys Lys Lys Val Lys Leu Ser Lys 
        275                 280                 285             


Glu His Gln Ser Leu Glu Glu Asn Gln Arg Gln Thr Arg Ser Lys Arg 
    290                 295                 300                 


Lys Ala Thr Ser Asp Thr Leu Glu Ser Pro Pro Lys Ile Ile Pro Lys 
305                 310                 315                 320 


Tyr Ile Ser Glu Asn Glu Ser Pro Arg Pro Ser Gln Lys Lys Ser Arg 
                325                 330                 335     


Val Lys Ile Asn Trp Leu Lys Ser Ala Thr Lys Gln Pro Ser Ile Leu 
            340                 345                 350         


Ser Lys Phe Cys Ser Leu Gly Lys Ile Thr Thr Asn Gln Gly Val Lys 
        355                 360                 365             


Gly Gln Ser Lys Glu Asn Glu Cys Asp Pro Glu Glu Asp Leu Gly Lys 
    370                 375                 380                 


Cys Glu Ser Asp Asn Thr Thr Asn Gly Cys Gly Leu Glu Ser Pro Gly 
385                 390                 395                 400 


Asn Thr Val Thr Pro Val Asn Val Asn Glu Val Lys Pro Ile Asn Lys 
                405                 410                 415     


Gly Glu Glu Gln Ile Gly Phe Glu Leu Val Glu Lys Leu Phe Gln Gly 
            420                 425                 430         


Gln Leu Val Leu Arg Thr Arg Cys Leu Glu Cys Glu Ser Leu Thr Glu 
        435                 440                 445             


Arg Arg Glu Asp Phe Gln Asp Ile Ser Val Pro Val Gln Glu Asp Glu 
    450                 455                 460                 


Leu Ser Lys Val Glu Glu Ser Ser Glu Ile Ser Pro Glu Pro Lys Thr 
465                 470                 475                 480 


Glu Met Lys Thr Leu Arg Trp Ala Ile Ser Gln Phe Ala Ser Val Glu 
                485                 490                 495     


Arg Ile Val Gly Glu Asp Lys Tyr Phe Cys Glu Asn Cys His His Tyr 
            500                 505                 510         


Thr Glu Ala Glu Arg Ser Leu Leu Phe Asp Lys Met Pro Glu Val Ile 
        515                 520                 525             


Thr Ile His Leu Lys Cys Phe Ala Ala Ser Gly Leu Glu Phe Asp Cys 
    530                 535                 540                 


Tyr Gly Gly Gly Leu Ser Lys Ile Asn Thr Pro Leu Leu Thr Pro Leu 
545                 550                 555                 560 


Lys Leu Ser Leu Glu Glu Trp Ser Thr Lys Pro Thr Asn Asp Ser Tyr 
                565                 570                 575     


Gly Leu Phe Ala Val Val Met His Ser Gly Ile Thr Ile Ser Ser Gly 
            580                 585                 590         


His Tyr Thr Ala Ser Val Lys Val Thr Asp Leu Asn Ser Leu Glu Leu 
        595                 600                 605             


Asp Lys Gly Asn Phe Val Val Asp Gln Met Cys Glu Ile Gly Lys Pro 
    610                 615                 620                 


Glu Pro Leu Asn Glu Glu Glu Ala Arg Gly Val Val Glu Asn Tyr Asn 
625                 630                 635                 640 


Asp Glu Glu Val Ser Ile Arg Val Gly Gly Asn Thr Gln Pro Ser Lys 
                645                 650                 655     


Val Leu Asn Lys Lys Asn Val Glu Ala Ile Gly Leu Leu Gly Gly Gln 
            660                 665                 670         


Lys Ser Lys Ala Asp Tyr Glu Leu Tyr Asn Lys Ala Ser Asn Pro Asp 
        675                 680                 685             


Lys Val Ala Ser Thr Ala Phe Ala Glu Asn Arg Asn Ser Glu Thr Ser 
    690                 695                 700                 


Asp Thr Thr Gly Thr His Glu Ser Asp Arg Asn Lys Glu Ser Ser Asp 
705                 710                 715                 720 


Gln Thr Gly Ile Asn Ile Ser Gly Phe Glu Asn Lys Ile Ser Tyr Val 
                725                 730                 735     


Val Gln Ser Leu Lys Glu Tyr Glu Gly Lys Trp Leu Leu Phe Asp Asp 
            740                 745                 750         


Ser Glu Val Lys Val Thr Glu Glu Lys Asp Phe Leu Asn Ser Leu Ser 
        755                 760                 765             


Pro Ser 
    770 


<210> 10
<211> 370
<212> PRT
<213> Unknown

<220>
<223> Description of Unknown: 
      USP12 sequence

<400> 10
Met Glu Ile Leu Met Thr Val Ser Lys Phe Ala Ser Ile Cys Thr Met 
1               5                   10                  15      


Gly Ala Asn Ala Ser Ala Leu Glu Lys Glu Ile Gly Pro Glu Gln Phe 
            20                  25                  30          


Pro Val Asn Glu His Tyr Phe Gly Leu Val Asn Phe Gly Asn Thr Cys 
        35                  40                  45              


Tyr Cys Asn Ser Val Leu Gln Ala Leu Tyr Phe Cys Arg Pro Phe Arg 
    50                  55                  60                  


Glu Lys Val Leu Ala Tyr Lys Ser Gln Pro Arg Lys Lys Glu Ser Leu 
65                  70                  75                  80  


Leu Thr Cys Leu Ala Asp Leu Phe His Ser Ile Ala Thr Gln Lys Lys 
                85                  90                  95      


Lys Val Gly Val Ile Pro Pro Lys Lys Phe Ile Thr Arg Leu Arg Lys 
            100                 105                 110         


Glu Asn Glu Leu Phe Asp Asn Tyr Met Gln Gln Asp Ala His Glu Phe 
        115                 120                 125             


Leu Asn Tyr Leu Leu Asn Thr Ile Ala Asp Ile Leu Gln Glu Glu Arg 
    130                 135                 140                 


Lys Gln Glu Lys Gln Asn Gly Arg Leu Pro Asn Gly Asn Ile Asp Asn 
145                 150                 155                 160 


Glu Asn Asn Asn Ser Thr Pro Asp Pro Thr Trp Val His Glu Ile Phe 
                165                 170                 175     


Gln Gly Thr Leu Thr Asn Glu Thr Arg Cys Leu Thr Cys Glu Thr Ile 
            180                 185                 190         


Ser Ser Lys Asp Glu Asp Phe Leu Asp Leu Ser Val Asp Val Glu Gln 
        195                 200                 205             


Asn Thr Ser Ile Thr His Cys Leu Arg Gly Phe Ser Asn Thr Glu Thr 
    210                 215                 220                 


Leu Cys Ser Glu Tyr Lys Tyr Tyr Cys Glu Glu Cys Arg Ser Lys Gln 
225                 230                 235                 240 


Glu Ala His Lys Arg Met Lys Val Lys Lys Leu Pro Met Ile Leu Ala 
                245                 250                 255     


Leu His Leu Lys Arg Phe Lys Tyr Met Asp Gln Leu His Arg Tyr Thr 
            260                 265                 270         


Lys Leu Ser Tyr Arg Val Val Phe Pro Leu Glu Leu Arg Leu Phe Asn 
        275                 280                 285             


Thr Ser Gly Asp Ala Thr Asn Pro Asp Arg Met Tyr Asp Leu Val Ala 
    290                 295                 300                 


Val Val Val His Cys Gly Ser Gly Pro Asn Arg Gly His Tyr Ile Ala 
305                 310                 315                 320 


Ile Val Lys Ser His Asp Phe Trp Leu Leu Phe Asp Asp Asp Ile Val 
                325                 330                 335     


Glu Lys Ile Asp Ala Gln Ala Ile Glu Glu Phe Tyr Gly Leu Thr Ser 
            340                 345                 350         


Asp Ile Ser Lys Asn Ser Glu Ser Gly Tyr Ile Leu Phe Tyr Gln Ser 
        355                 360                 365             


Arg Asp 
    370 


<210> 11
<211> 354
<212> PRT
<213> Unknown

<220>
<223> Description of Unknown: 
      USP46 sequence

<400> 11
Met Thr Val Arg Asn Ile Ala Ser Ile Cys Asn Met Gly Thr Asn Ala 
1               5                   10                  15      


Ser Ala Leu Glu Lys Asp Ile Gly Pro Glu Gln Phe Pro Ile Asn Glu 
            20                  25                  30          


His Tyr Phe Gly Leu Val Asn Ala Leu Tyr Phe Cys Arg Pro Phe Arg 
        35                  40                  45              


Glu Asn Val Leu Ala Tyr Lys Ala Gln Gln Lys Lys Lys Glu Asn Leu 
    50                  55                  60                  


Leu Thr Cys Leu Ala Asp Leu Phe His Ser Ile Ala Thr Gln Lys Lys 
65                  70                  75                  80  


Lys Val Gly Val Ile Pro Pro Lys Lys Phe Ile Ser Arg Leu Arg Lys 
                85                  90                  95      


Glu Asn Asp Leu Phe Asp Asn Tyr Met Gln Gln Asp Ala His Glu Phe 
            100                 105                 110         


Leu Asn Tyr Leu Leu Asn Thr Ile Ala Asp Ile Leu Gln Glu Glu Lys 
        115                 120                 125             


Lys Gln Glu Lys Gln Asn Gly Lys Leu Lys Asn Gly Asn Met Asn Glu 
    130                 135                 140                 


Pro Ala Glu Asn Asn Lys Pro Glu Leu Thr Trp Val His Glu Ile Phe 
145                 150                 155                 160 


Gln Gly Thr Leu Thr Asn Glu Thr Arg Cys Leu Asn Cys Glu Thr Val 
                165                 170                 175     


Ser Ser Lys Asp Glu Asp Phe Leu Asp Leu Ser Val Asp Val Glu Gln 
            180                 185                 190         


Asn Thr Ser Ile Thr His Cys Leu Arg Asp Phe Ser Asn Thr Glu Thr 
        195                 200                 205             


Leu Cys Ser Glu Gln Lys Tyr Tyr Cys Glu Thr Cys Cys Ser Lys Gln 
    210                 215                 220                 


Glu Ala Gln Lys Arg Met Arg Val Lys Lys Leu Pro Met Ile Leu Ala 
225                 230                 235                 240 


Leu His Leu Lys Arg Phe Lys Tyr Met Glu Gln Leu His Arg Tyr Thr 
                245                 250                 255     


Lys Leu Ser Tyr Arg Val Val Phe Pro Leu Glu Leu Arg Leu Phe Asn 
            260                 265                 270         


Thr Ser Ser Asp Ala Val Asn Leu Asp Arg Met Tyr Asp Leu Val Ala 
        275                 280                 285             


Val Val Val His Cys Gly Ser Gly Pro Asn Arg Gly His Tyr Ile Thr 
    290                 295                 300                 


Ile Val Lys Ser His Gly Phe Trp Leu Leu Phe Asp Asp Asp Ile Val 
305                 310                 315                 320 


Glu Lys Ile Asp Ala Gln Ala Ile Glu Glu Phe Tyr Gly Leu Thr Ser 
                325                 330                 335     


Asp Ile Ser Lys Asn Ser Glu Ser Gly Tyr Ile Leu Phe Tyr Gln Ser 
            340                 345                 350         


Arg Glu 
        


<210> 12
<211> 39
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide


<220>
<221> CDS
<222> (1)..(39)

<400> 12
atc tta gag tgt ccc atc tgt ctg gag ttg atc aag gaa                     39
Ile Leu Glu Cys Pro Ile Cys Leu Glu Leu Ile Lys Glu                       
1               5                   10                                    


<210> 13
<211> 38
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide


<220>
<221> CDS
<222> (1)..(27)

<400> 13
atc tta gag tgt ccc atc gtc tgg agt tgatcaagga a                        38
Ile Leu Glu Cys Pro Ile Val Trp Ser                                       
1               5                                                         


<210> 14
<211> 38
<212> DNA
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      oligonucleotide


<220>
<221> CDS
<222> (1)..(27)

<400> 14
atc tta gag tgt ccc atc ttc tgg agt tgatcaagga a                        38
Ile Leu Glu Cys Pro Ile Phe Trp Ser                                       
1               5                                                         


<210> 15
<211> 13
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      peptide

<400> 15
Ile Leu Glu Cys Pro Ile Cys Leu Glu Leu Ile Lys Glu 
1               5                   10              


<210> 16
<211> 9
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      peptide

<400> 16
Ile Leu Glu Cys Pro Ile Val Trp Ser 
1               5                   


<210> 17
<211> 9
<212> PRT
<213> Artificial Sequence

<220>
<223> Description of Artificial Sequence: Synthetic
      peptide

<400> 17
Ile Leu Glu Cys Pro Ile Phe Trp Ser 
1               5                   


