                         SEQUENCE LISTING

<110>  Memorial Sloan-Kettering Cancer Center
 
<120>  Companion Diagnostic For CDK4 Inhibitors

<130>  072734.0158

<150>  US 61/812412
<151>  2013-04-16

<150>  US 61/893755
<151>  2013-10-21

<160>  10    

<170>  PatentIn version 3.5

<210>  1
<211>  497
<212>  PRT
<213>  Homo sapiens

<400>  1

Met Val Arg Ser Arg Gln Met Cys Asn Thr Asn Met Ser Val Pro Thr 
1               5                   10                  15      


Asp Gly Ala Val Thr Thr Ser Gln Ile Pro Ala Ser Glu Gln Glu Thr 
            20                  25                  30          


Leu Val Arg Pro Lys Pro Leu Leu Leu Lys Leu Leu Lys Ser Val Gly 
        35                  40                  45              


Ala Gln Lys Asp Thr Tyr Thr Met Lys Glu Val Leu Phe Tyr Leu Gly 
    50                  55                  60                  


Gln Tyr Ile Met Thr Lys Arg Leu Tyr Asp Glu Lys Gln Gln His Ile 
65                  70                  75                  80  


Val Tyr Cys Ser Asn Asp Leu Leu Gly Asp Leu Phe Gly Val Pro Ser 
                85                  90                  95      


Phe Ser Val Lys Glu His Arg Lys Ile Tyr Thr Met Ile Tyr Arg Asn 
            100                 105                 110         


Leu Val Val Val Asn Gln Gln Glu Ser Ser Asp Ser Gly Thr Ser Val 
        115                 120                 125             


Ser Glu Asn Arg Cys His Leu Glu Gly Gly Ser Asp Gln Lys Asp Leu 
    130                 135                 140                 


Val Gln Glu Leu Gln Glu Glu Lys Pro Ser Ser Ser His Leu Val Ser 
145                 150                 155                 160 


Arg Pro Ser Thr Ser Ser Arg Arg Arg Ala Ile Ser Glu Thr Glu Glu 
                165                 170                 175     


Asn Ser Asp Glu Leu Ser Gly Glu Arg Gln Arg Lys Arg His Lys Ser 
            180                 185                 190         


Asp Ser Ile Ser Leu Ser Phe Asp Glu Ser Leu Ala Leu Cys Val Ile 
        195                 200                 205             


Arg Glu Ile Cys Cys Glu Arg Ser Ser Ser Ser Glu Ser Thr Gly Thr 
    210                 215                 220                 


Pro Ser Asn Pro Asp Leu Asp Ala Gly Val Ser Glu His Ser Gly Asp 
225                 230                 235                 240 


Trp Leu Asp Gln Asp Ser Val Ser Asp Gln Phe Ser Val Glu Phe Glu 
                245                 250                 255     


Val Glu Ser Leu Asp Ser Glu Asp Tyr Ser Leu Ser Glu Glu Gly Gln 
            260                 265                 270         


Glu Leu Ser Asp Glu Asp Asp Glu Val Tyr Gln Val Thr Val Tyr Gln 
        275                 280                 285             


Ala Gly Glu Ser Asp Thr Asp Ser Phe Glu Glu Asp Pro Glu Ile Ser 
    290                 295                 300                 


Leu Ala Asp Tyr Trp Lys Cys Thr Ser Cys Asn Glu Met Asn Pro Pro 
305                 310                 315                 320 


Leu Pro Ser His Cys Asn Arg Cys Trp Ala Leu Arg Glu Asn Trp Leu 
                325                 330                 335     


Pro Glu Asp Lys Gly Lys Asp Lys Gly Glu Ile Ser Glu Lys Ala Lys 
            340                 345                 350         


Leu Glu Asn Ser Thr Gln Ala Glu Glu Gly Phe Asp Val Pro Asp Cys 
        355                 360                 365             


Lys Lys Thr Ile Val Asn Asp Ser Arg Glu Ser Cys Val Glu Glu Asn 
    370                 375                 380                 


Asp Asp Lys Ile Thr Gln Ala Ser Gln Ser Gln Glu Ser Glu Asp Tyr 
385                 390                 395                 400 


Ser Gln Pro Ser Thr Ser Ser Ser Ile Ile Tyr Ser Ser Gln Glu Asp 
                405                 410                 415     


Val Lys Glu Phe Glu Arg Glu Glu Thr Gln Asp Lys Glu Glu Ser Val 
            420                 425                 430         


Glu Ser Ser Leu Pro Leu Asn Ala Ile Glu Pro Cys Val Ile Cys Gln 
        435                 440                 445             


Gly Arg Pro Lys Asn Gly Cys Ile Val His Gly Lys Thr Gly His Leu 
    450                 455                 460                 


Met Ala Cys Phe Thr Cys Ala Lys Lys Leu Lys Lys Arg Asn Lys Pro 
465                 470                 475                 480 


Cys Pro Val Cys Arg Gln Pro Ile Gln Met Ile Val Leu Thr Tyr Phe 
                485                 490                 495     


Pro 
    


<210>  2
<211>  489
<212>  PRT
<213>  Mus musculus

<400>  2

Met Cys Asn Thr Asn Met Ser Val Ser Thr Glu Gly Ala Ala Ser Thr 
1               5                   10                  15      


Ser Gln Ile Pro Ala Ser Glu Gln Glu Thr Leu Val Arg Pro Lys Pro 
            20                  25                  30          


Leu Leu Leu Lys Leu Leu Lys Ser Val Gly Ala Gln Asn Asp Thr Tyr 
        35                  40                  45              


Thr Met Lys Glu Ile Ile Phe Tyr Ile Gly Gln Tyr Ile Met Thr Lys 
    50                  55                  60                  


Arg Leu Tyr Asp Glu Lys Gln Gln His Ile Val Tyr Cys Ser Asn Asp 
65                  70                  75                  80  


Leu Leu Gly Asp Val Phe Gly Val Pro Ser Phe Ser Val Lys Glu His 
                85                  90                  95      


Arg Lys Ile Tyr Ala Met Ile Tyr Arg Asn Leu Val Ala Val Ser Gln 
            100                 105                 110         


Gln Asp Ser Gly Thr Ser Leu Ser Glu Ser Arg Arg Gln Pro Glu Gly 
        115                 120                 125             


Gly Ser Asp Leu Lys Asp Pro Leu Gln Ala Pro Pro Glu Glu Lys Pro 
    130                 135                 140                 


Ser Ser Ser Asp Leu Ile Ser Arg Leu Ser Thr Ser Ser Arg Arg Arg 
145                 150                 155                 160 


Ser Ile Ser Glu Thr Glu Glu Asn Thr Asp Glu Leu Pro Gly Glu Arg 
                165                 170                 175     


His Arg Lys Arg Arg Arg Ser Leu Ser Phe Asp Pro Ser Leu Gly Leu 
            180                 185                 190         


Cys Glu Leu Arg Glu Met Cys Ser Gly Gly Ser Ser Ser Ser Ser Ser 
        195                 200                 205             


Ser Ser Ser Glu Ser Thr Glu Thr Pro Ser His Gln Asp Leu Asp Asp 
    210                 215                 220                 


Gly Val Ser Glu His Ser Gly Asp Cys Leu Asp Gln Asp Ser Val Ser 
225                 230                 235                 240 


Asp Gln Phe Ser Val Glu Phe Glu Val Glu Ser Leu Asp Ser Glu Asp 
                245                 250                 255     


Tyr Ser Leu Ser Asp Glu Gly His Glu Leu Ser Asp Glu Asp Asp Glu 
            260                 265                 270         


Val Tyr Arg Val Thr Val Tyr Gln Thr Gly Glu Ser Asp Thr Asp Ser 
        275                 280                 285             


Phe Glu Gly Asp Pro Glu Ile Ser Leu Ala Asp Tyr Trp Lys Cys Thr 
    290                 295                 300                 


Ser Cys Asn Glu Met Asn Pro Pro Leu Pro Ser His Cys Lys Arg Cys 
305                 310                 315                 320 


Trp Thr Leu Arg Glu Asn Trp Leu Pro Asp Asp Lys Gly Lys Asp Lys 
                325                 330                 335     


Val Glu Ile Ser Glu Lys Ala Lys Leu Glu Asn Ser Ala Gln Ala Glu 
            340                 345                 350         


Glu Gly Leu Asp Val Pro Asp Gly Lys Lys Leu Thr Glu Asn Asp Ala 
        355                 360                 365             


Lys Glu Pro Cys Ala Glu Glu Asp Ser Glu Glu Lys Ala Glu Gln Thr 
    370                 375                 380                 


Pro Leu Ser Gln Glu Ser Asp Asp Tyr Ser Gln Pro Ser Thr Ser Ser 
385                 390                 395                 400 


Ser Ile Val Tyr Ser Ser Gln Glu Ser Val Lys Glu Leu Lys Glu Glu 
                405                 410                 415     


Thr Gln Asp Lys Asp Glu Ser Val Glu Ser Ser Phe Ser Leu Asn Ala 
            420                 425                 430         


Ile Glu Pro Cys Val Ile Cys Gln Gly Arg Pro Lys Asn Gly Cys Ile 
        435                 440                 445             


Val His Gly Lys Thr Gly His Leu Met Ser Cys Phe Thr Cys Ala Lys 
    450                 455                 460                 


Lys Leu Lys Lys Arg Asn Lys Pro Cys Pro Val Cys Arg Gln Pro Ile 
465                 470                 475                 480 


Gln Met Ile Val Leu Thr Tyr Phe Asn 
                485                 


<210>  3
<211>  458
<212>  PRT
<213>  Rattus norvegicus

<400>  3

Met Cys Asn Thr Asn Met Ser Val Ser Thr Glu Gly Ala Ala Gly Thr 
1               5                   10                  15      


Ser Gln Ile Pro Ala Ser Glu Gln Glu Thr Leu Ile Ile Phe Tyr Ile 
            20                  25                  30          


Gly Gln Tyr Ile Met Thr Lys Arg Leu Tyr Asp Glu Lys Gln Gln His 
        35                  40                  45              


Ile Val Tyr Cys Ser Asn Asp Leu Leu Gly Asp Val Phe Gly Val Pro 
    50                  55                  60                  


Ser Phe Ser Val Lys Glu His Arg Lys Ile Tyr Ala Met Ile Tyr Arg 
65                  70                  75                  80  


Asn Leu Val Val Val Ser Gln Gln Asp Ser Gly Thr Ser Pro Ser Glu 
                85                  90                  95      


Ser Arg Cys Gln Pro Glu Gly Gly Ser Asp Leu Lys Asp Pro Val Gln 
            100                 105                 110         


Ala Ser Gln Glu Glu Lys Pro Ser Ser Ser Asp Val Val Ser Arg Pro 
        115                 120                 125             


Ser Thr Ser Ser Arg Arg Arg Ala Ile Ser Glu Thr Glu Glu Asn Thr 
    130                 135                 140                 


Asp Glu Leu Pro Gly Glu Arg Gln Arg Lys Arg His Arg Ala Leu Ser 
145                 150                 155                 160 


Phe Asp Glu Ser Leu Gly Leu Cys Val Leu Arg Glu Ile Cys Cys Glu 
                165                 170                 175     


Arg Ser Ser Ser Ser Glu Ala Thr Asp Thr Pro Ser His Gln Asp Leu 
            180                 185                 190         


Asp Asp Gly Val Ser Asp His Ser Ala Asp Cys Leu Asp Gln Asp Ser 
        195                 200                 205             


Val Ser Asp Gln Phe Ser Val Glu Phe Glu Val Glu Ser Leu Asp Ser 
    210                 215                 220                 


Glu Asp Tyr Ser Leu Ser Asp Glu Gly His Glu Leu Ser Asp Glu Asp 
225                 230                 235                 240 


Asp Glu Val Tyr Arg Val Thr Val Tyr Gln Ala Gly Glu Ser Asp Ala 
                245                 250                 255     


Asp Ser Phe Glu Gly Asp Pro Glu Ile Ser Leu Ala Asp Tyr Trp Lys 
            260                 265                 270         


Cys Thr Ser Cys Asn Glu Met Asn Pro Pro Leu Pro Ser His Cys Asn 
        275                 280                 285             


Arg Cys Trp Thr Leu Arg Glu Asn Trp Leu Pro Asp Asp Lys Gly Lys 
    290                 295                 300                 


Asp Lys Val Glu Ile Ser Glu Lys Ala Lys Leu Glu Ser Ser Asp Gln 
305                 310                 315                 320 


Ala Glu Glu Gly Leu Asp Val Pro Asp Gly Lys Lys Val Thr Glu Asp 
                325                 330                 335     


Asp Ala Lys Glu Ser Ser Ala Glu Asp Ser Glu Glu Lys Val Ala Gln 
            340                 345                 350         


Met Leu Leu Ser Gln Glu Ser Asp Asp Tyr Ser Gln Pro Ser Thr Ser 
        355                 360                 365             


Ser Ser Ile Val Tyr Ser Ser Gln Glu Ser Gly Lys Glu Leu Lys Glu 
    370                 375                 380                 


Asp Thr Gln Asp Lys Glu Glu Ser Met Glu Ser Ser Phe Ser Leu Asn 
385                 390                 395                 400 


Ala Ile Glu Pro Cys Val Ile Cys Gln Gly Arg Pro Lys Asn Gly Cys 
                405                 410                 415     


Ile Val His Gly Lys Thr Gly His Leu Met Ser Cys Phe Thr Cys Ala 
            420                 425                 430         


Lys Lys Leu Lys Lys Arg Asn Lys Pro Cys Pro Val Cys Arg Gln Pro 
        435                 440                 445             


Ile Gln Met Ile Val Leu Thr Tyr Phe Asn 
    450                 455             


<210>  4
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  CDK4 shRNA

<400>  4
gagattactt tgctgcctta a                                                 21


<210>  5
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  MDM2 shRNA (M376)

<400>  5
ttcactattc cactaccaaa g                                                 21


<210>  6
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  MDM2 shRNA (M380)

<400>  6
tactagaagt tgatggctga g                                                 21


<210>  7
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  HAUSP shRNA (4057)

<400>  7
ccagctaagt atcaaaggaa a                                                 21


<210>  8
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  HAUSP shRNA (845)

<400>  8
cgtggtgtca aggtgtacta a                                                 21


<210>  9
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  CDK6 shRNA

<400>  9
gacctggaaa ggtgcaaaga a                                                 21


<210>  10
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  MDM2 shRNA (mismatch)

<400>  10
actattctca accctcaact tcta                                              24


