WO 2006/062811
`
`PCT/US2005/043578
`
`-48-
`
`hSepharase, Homo sapiens
`like 1 (S. cerevisiae) (ESPL1), mRNA
`extra spindle poles
`
`(GenBank accession number: NM_012291);
`protein (CaM kinase) kinase
`
`
`CamKIId, Homo sapiens
`calcium/calmodulin-dependent
`variant 3, mRNA (GenBank accession number:
`II delta (CAMK2D), transcript
`NM_001221);
`CDK6, Homo sapiens cyclin-dependent kinase
`accession number: NM_001259);
`and
`GRB2, Homo sapiens
`growth
`
`factor receptor-bound protein 2
`variant 1, mRNA
`(GenBank accession number: NM_002086).
`
`(GRB2),
`
`transcript
`
`6
`
`
`
`(CDK6), mRNA (GenBank
`
`(p21,
`
`accession
`
`16. A kit for predicting or monitoring cancer patient's a
`
`taxoid
`response to molecule of the
`
`
`family according to the method of Claim 8 wherein the kit
`comprises detectable-labeled
`antibodies, detectable-labeled antibody
`
`fragments or detectable-labeled oligonucleotides
`
`comprising nucleic acids capable of hybridizing under stringent conditions
`to said one or
`more genetic markers selected from the group consisting of:
`inhibitor Cipl)
`1A
`
`P21(Wafl), Homo sapiens
`cyclin-dependent
`kinase
`(CDKN1A), transcript
`variant 1, mRNA (GenBank
`accession number: NM_000389);
`Pim-1, Homo sapiens pim-1 oncogene (PIM1), mRNA (GenBank accession
`number:
`NM_002648);
`protein 1, interferon-inducible, 67kDa
`
`binding
`guanylate
`GBP-1, Homo sapiens
`(GBP1), mRNA (GenBank accession number: NM_002053);
`RXRA, Homo sapiens
`retinoid X receptor, alpha
`(RXRA), mRNA (GenBank
`accession number: NM_002957);
`
`
`accession number: NM_032905);
`Heel, Homo sapiens kinetochore associated 2 (KNTC2), mRNA
`number: NM_006101);
`Rafl, Human mRNA for raf oncogene (GenBank accession number: X03484);
`Aurora A, Homo sapiens aurora-related kinase 1 (ARK1) mRNA, complete cds
`(GenBank accession number: AF008551);
`TACC3, Homo sapiens transforming, acidic coiled-coil containing protein 3
`mRNA (GenBank accession number: NM_006342);
`
`SPF45, Homo sapiens RNA binding motif protein 17 (RBM17), mRNA
`
`(GenBank
`
`(GenBank
`
`(TACC3),
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01129
`
`MYLAN - EXHIBIT 1004 (Part 7 of 13)
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-49-
`
`B,
`(RELB),
`
`nuclear
`mRNA
`
`oncogene homolog
`RelB, Homo sapiens v-rel reticuloendotheliosis viral
`factor of kappa
`light
`
`polypeptide gene enhancer in B-cells 3
`(avian)
`
`(GenBank accession number: NM 006509);
`(PRKCD), transcript variant 1, mRNA
`PRKCD, Homo sapiens
`
`protein kinase C, delta
`(GenBank accession number: NM_006254);
`BRAF35, Homo sapiens
`high-mobility
`group
`accession number: NM_006339);
`HSPA1L, Homo sapiens
`heat
`shock 70kDa protein 1A (HSPA1 A), mRNA (GenBank
`
`accession number: NM_005345);
`kinase 11 (Peutz-Jeghers syndrome)
`
`STK11, Homo sapiens
`serine/threonine
`mRNA (GenBank accession
`number: NM_000455);
`and
`MKK3, Homo sapiens MAP
`kinase
`kinase
`3
`(MKK3)
`accession number: L36719).
`
`20B
`
`(HMG20B),
`
`mRNA
`
`(STK11),
`
`
`
`mRNA, (GenBank
`
`complete
`
`response to molecule of the taxoid
`
`the
`kit
`comprises
`the
`
`means
`
`17. A kit for predicting or monitoring a cancer patient's
`family according to
`
`the method of Claim 1 wherein
`
`a) obtaining total RNA from a bodily sample;
`cDNA; and
`
`b) reverse transcribing
`
`the total RNA to obtain
`reaction using a set of primers
`c) subjecting the cDNA to a polymerase chain
`wherein one or both primers are detectably-labeled
`and
`
`both primers are derived from
`a nucleotide sequence of one or more genetic markers selected from the group
`consisting of:
`to protein kinase (BUBR1) mRNA, complete cds
`BubRl, Homo sapiens similar
`(GenBank accession
`number: AF046079);
`
`Mad2, Homo sapiens mRNA for MAD2 protein
`AJ000186);
`Mpsl, Homo sapiens TTK protein kinase
`NM_003318);
`GEFT for Racl/CDC42, Homo sapiens RAC/CDC42
`factor (GEFT),
`
`exchange
`transcript variant 2, mRNA (GenBank accession
`number: NM_133483);
`Bubl, Homo sapiens BUB1
`budding uninhibited
`by
`benzimidazoles
`(BUB1), mRNA
`(GenBank
`
`accession number: NM_004336);
`
`
`
`(GenBank accession number:
`
`(TTK), mRNA (GenBank accession number:
`
`1
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01130
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-50-
`
`spindle poles like 1 (S. cerevisiae) (ESPL1), mRNA
`
`extra
`hSepharase, Homo sapiens
`(GenBank accession number: NM_012291);
`protein
`CamKIId, Homo sapiens
`calcium/calmodulin-dependent
`II delta (CAMK2D),
`
`transcript variant 3, mRNA (GenBank accession
`NM_p01221);
`CDK6, Homo sapiens cyclin-dependent kinase 6 (CDK6), mRNA (GenBank
`accession number: NM_001259); and
`GRB2, Homo sapiens growth
`(GRB2), transcript
`receptor-bound protein 2
`
`factor
`variant 1, mRNA (GenBank accession number: NM_002086).
`
`kinase
`number:
`
`(CaM
`
`response to molecule
`
`the kit comprises the means of:
`
`of
`
`the
`
`18. A kit for predicting or monitoring a cancer patient's
`family according
`to
`
`the method of Claim 8 wherein
`a) obtaining total RNA
`
`from bodily sample; a
`
`b) reverse transcribing the total RNA to obtain cDNA; and
`
`c) subjecting the cDNA to a polymerase chain reaction using a set of primers
`
`wherein one or both primers are detectably-labeled
`and both
`
`primers are derived from
`
`a nucleotide sequence of one or more genetic markers selected from the group
`consisting of:
`cyclin-dependent kinase inhibitor 1A (p215 Cipl)
`
`sapiens
`P21(Wafl), Homo
`(CDKN1 A), transcript variant 1, mRNA (GenBank accession number: NM_000389);
`
`Pim-1, Homo sapiens pim-1 oncogene (PIM1), mRNA (GenBank
`accession
`number:
`NM_002648);
`GBP-1, Homo sapiens
`protein 1, interferon-inducible, 67kDa
`
`guanylate binding
`(GBP1), mRNA
`(GenBank
`
`accession number: NM_002053);
`RXRA, Homo sapiens
`retinoid X receptor, alpha (RXRA), mRNA
`accession number: NM_002957);
`binding motif protein 17 (RBM17), mRNA
`
`SPF45, Homo sapiens RNA
`accession number: NM_032905);
`Heel, Homo sapiens kinetochore associated 2
`number: NM_006101);
`Rafl, Human mRNA for raf oncogene (GenBank accession number: X03484);
`
`
`Aurora A, Homo sapiens aurora-related kinase 1 (ARK1) mRNA, complete
`(GenBank accession number: AF008551);
`
`(GenBank
`
`(GenBank
`
`(KNTC2), mRNA
`
`
`
`(GenBank accession
`
`cds
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01131
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-51-
`
`
`
`containing (TACC3),
`
`
`homolog nuclear
`B,
`3
`(avian)
`
`protein
`
`(RELB),
`
`
`
`20B mRNA (GenBank (HMG20B),
`
`coiled-coil
`acidic
`transforming,
`TACC3, Homo sapiens
`mRNA (GenBank accession number:
`NM_006342);
`
`RelB, Homo sapiens v-rel reticuloendotheliosis viral oncogene
`factor of kappa
`light polypeptide gene enhancer
`in B-cells
`(GenBank accession number: NM_006509);
`
`PRKCD, Homo sapiens protein kinase C, delta (PRKCD), transcript variant 1, mRNA
`(GenBank accession number: NM_006254);
`BRAF35, Homo sapiens high-mobility
`group
`accession number: NM_006339);
`HSPA1L, Homo sapiens
`heat shock
`accession number: NM_005345);
`kinase (Peutz-Jeghers syndrome) 11
`
`STK11, Homo sapiens
`serine/threonine
`
`NM 000455); and
`mRNA (GenBank accession number:
`
`MKK3, Homo sapiens MAP kinase kinase 3 (MKK3) mRNA,
`accession number: L36719).
`
`
`
`
`
`70kDa protein 1A (HSPA1 A), mRNA (GenBank
`
`
`
`(STK11),
`
`
`
`complete cds (GenBank
`
`19. The detectable
`label
`detectable
`one any of claims 15 — 18, wherein the
`
`
`
`of
`label
`
`from the group consisting of an enzyme, a radioactive isotope, or a chemical which
`fluoresces, a
`
`chemiluminescent molecule, radiopaque substances, liposomes, and haptenic
`molecules.
`
`is
`
`selected
`
`20. A method for predicting or monitoring a cancer patient's response to a molecule of the
`taxoid family, comprising the steps of:
`of said area patient;
`
`
`cancerous
`a) obtaining a test sample from a
`b) measuring the
`
`level of one or more genetic markers selected from the group
`consisting of:
`BubRl, Homo sapiens similar to protein kinase (BUBR1) mRNA, complete cds
`(GenBank accession number: AF046079);
`Mad25 Homo sapiens mRNA for MAD2 protein (GenBank
`AJ000186);
`Mpsl, Homo sapiens TTK protein kinase (TTK), mRNA
`number: NM_003318);
`
`(GenBank
`
`accession
`
`
`
`accession number:
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01132
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-52-
`
`6
`
`
`
`mRNA (CDK6), (GenBank
`
`
`
`protein
`
`2
`
`
`
`selected the
`
`from
`
`(GAPD),
`
`
`
`cds (GenBank
`
`(GEFT),
`factor
`sapiens RAC/CDC42 exchange
`
`GEFT for Racl/CDC42, Homo
`number:
`NM_133483);
`transcript variant 2, mRNA
`(GenBank
`accession
`by
`benzimidazoles 1 homolog
`
`Bubl, Homo sapiens BUB1
`budding
`uninhibited
`(yeast) (BUB1), mRNA
`
`(GenBank accession number: NM_004336);
`hSepharase, Homo sapiens
`
`extra spindle poles like 1 (S. cerevisiae) (ESPL1),
`mRNA (GenBank accession number: NM_012291);
`protein kinase (CaM
`
`CamKIId, Homo sapiens
`calcium/calmodulin-dependent
`kinase) II delta (CAMK2D), transcript variant 3, mRNA (GenBank accession
`number: NM_001221);
`CDK6, Homo sapiens cyclin-dependent kinase
`accession number: NM_001259);
`and
`receptor-bound
`GRB2, Homo sapiens growth
`factor
`variant 1, mRNA (GenBank
`
`accession number: NM_002086)
`c) measuring
`the level of one or more reference genetic markers
`group consisting of:
`GAPDH, Homo sapiens glyceraldehyde-3-phosphate dehydrogenase
`mRNA (GenBank accession
`number: NM_002046); and
`RPS9, Homo sapiens cDNA clone IMAGE:6647283, partial
`accession number: BC071941);
`d) comparing
`the measured
`
`levels of said one or more genetic markers and said
`more reference genetic markers in
`the test sample;
`
`wherein a decrease in the level of said one or more genetic markers as compared to the
`
`
`level of said one or more reference markers indicates an genetic increased resistance
`
`a molecule of the taxoid family.
`
`one
`
`or
`
`to
`
`a
`
`1A
`
`
`
`response molecule of the to
`
`21. A method for predicting or monitoring a cancer patient's
`taxoid family, comprising the steps of:
`a) obtaining a
`
`test sample from a cancerous area of said patient;
`b) measuring the level of one or more genetic markers selected from the group
`consisting of:
`inhibitor (p21, Cipl)
`
`kinase
`cyclin-dependent
`P21(Wafl)5 Homo sapiens
`(CDKN1A), transcript variant 1, mRNA (GenBank
`accession number:
`NM 000389);
`
`
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01133
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-53-
`
`oncogene
`
`(PIM1),
`
`mRNA
`
`(GenBank
`
`Heel, Homo sapiens kinetochore associated 2 (KNTC2), mRNA nBank (Ge
`
`
`
`Pim-1, Homo sapiens pim-1
`number: NM_002648);
`GBP-1, Homo sapiens guanylate binding protein 1, interferon-inducible, 67kDa
`
`
`(GBP1), mRNA (GenBank
`accession
`number:
`NM_002053);
`RXRA, Homo sapiens retinoid X receptor, alpha
`
`(RXRA), mRNA (GenBank
`accession number: NM_002957);
`
`SPF45, Homo sapiens RNA binding motif protein 17 (RBM17), mRNA
`(GenBank accession number: NM_032905);
`
`accession number: NM_006101);
`number:
`accession
`Rafl, Human mRNA for raf oncogene (GenBank
`Aurora A, Homo sapiens
`aurora-related
`
`kinase 1 (ARK1) mRNA, complete
`(GenBank accession number: AF008551);
`
`TACC3, Homo sapiens transforming, acidic
`coiled-coil
`containing protein 3
`(TACC3), mRNA
`(GenBank accession number: NM 006342);
`B,
`RelB, Homo sapiens v-rel reticuloendotheliosis viral
`oncogene homolog
`nuclear factor of kappa
`light
`
`gene polypeptide enhancer in B-cells 3
`
`(avian)
`(RELB), mRNA (GenBank accession number: NM_006509);
`PRKCD, Homo sapiens
`
`protein kinase C, delta
`
`(PRKCD), transcript variant 1,
`mRNA (GenBank accession
`number: NM_006254);
`BRAF35, Homo sapiens
`high-mobility
`group
`20B
`(GenBank accession number: NM_006339);
`HSPA1L, Homo sapiens
`heat
`
`shock 70kDa protein 1A (HSPA1 A), mRNA
`(GenBank accession number: NM_005345);
`(Peutz-Jeghers syndrome)
`
`11
`STK11, Homo sapiens serine/threonine kinase
`(STK11), mRNA (GenBank
`
`accession number: NM_000455); and
`MKK3, Homo sapiens MAP
`
`kinase kinase 3 (MKK3) mRNA, complete cds
`(GenBank accession number: L36719);
`
`c) measuring the level of one or more reference genetic markers
`group consisting of:
`glyceraldehyde-3-phosphate
`GAPDH, Homo sapiens
`mRNA (GenBank accession
`
`number: NM_002046); and
`
`X03484);
`cds
`
`(HMG20B),
`
`mRNA
`
`selected
`
`
`
`from the
`
`dehydrogenase
`
`(GAPD),
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01134
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-54-
`
`clone IMAGE:6647283, partial cds (GenBank
`
`
`cDNA
`RPS9, Homo sapiens
`accession number: BC071941);
`
`
`
`d) comparing the measured
`levels
`
`said of or more genetic markers and said one one or
`more reference genetic markers in
`the test sample;
`.
`compared the
`to
`wherein a decrease in
`the
`
`level of said one or more genetic markers as
`
`level of said one or more reference genetic markers indicates an
`increased
`susceptibility
`to a molecule of the taxoid family.
`
`5
`
`22. The method of Claim 20 of 21 wherein
`of family is selected from the taxoid
`
`
`said molecule
`
`the group consisting of paclitaxel, docetaxel XRP9881 and XRP6258.
`
`
`
`10
`
`23. The method of Claim 20 or 21 wherein said level of
`
`measured by mRNA, DNA or protein.
`
`one
`
`or
`
`
`
`more markers is
`
`genetic
`
`24. The method of Claim 23 wherein
`from the group consisting of
`in situ
`reaction, nucleic acid hybridization,
`spectrometry.
`
`said measured by using a mRNA is technique selected
`
`
`
`
`hybridization,
`
`reverse-transcriptase polymerase chain
`
`electrophoresis. Northern blotting and mass
`
`said wherein DNA is measured by using a technique selected
`
`
`25. The method of Claim 23
`from the group consisting of quantitative polymerase chain
`reaction, genomic DNA-chips,
`in situ hybridization, electrophoresis,
`Southern blotting
`and
`mass
`spectrometry.
`
`15
`
`20
`
`26. The method of Claim 23 wherein
`said is measured by using a technique selected protein
`
`
`from the group consisting of immunoassay, Western blots, ELIS A, and mass spectrometry.
`
`25
`
`taxoid
`to a molecule of the
`27. A kit for predicting or monitoring a cancer patient's response
`family according
`
`
`to the method of Claim 20 wherein the kit comprises detectable-labeled
`antibodies, detectable-labeled
`antibody
`fragments
`or
`
`detectable-labeled oligonucleotides
`
`comprising nucleic acids capable of hybridizing under stringent conditions
`to said one or
`more genetic markers and said one or more reference
`
`markers genetic selected from the
`
`group consisting of:
`
`30
`
`01135
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-55-
`
`(BUBR1) mRNA, complete
`
`cds
`
`(GenBank
`
`accession
`
`number:
`
`BubRl, Homo sapiens similar
`to protein kinase
`(GenBank accession number: AF046079);
`Mad2, Homo sapiens mRNA
`for MAD2 protein
`AJ000186);
`Mpsl, Homo sapiens TTK protein kinase (TTK), mRNA (GenBank accession number:
`NM_003318);
`GEFT for Racl/CDC42, Homo sapiens RAC/CDC42
`
`exchange factor (GEFT),
`transcript variant 2, mRNA
`(GenBank
`
`
`number: accession NM_133483);
`Bubl, Homo sapiens BUB1 budding uninhibited
`by
`
`benzimidazoles 1 homolog (yeast)
`(BUB1), mRNA (GenBank
`accession number:
`NM_004336);
`hSepharase, Homo sapiens
`
`extra spindle poles
`
`like 1 (S. cerevisiae) (ESPL1), mRNA
`(GenBank accession number: NM_012291);
`protein (CaM kinase) kinase
`
`
`CamKIId, Homo sapiens
`calcium/calmodulin-dependent
`II delta (CAMK2D),
`transcript variant 3, mRNA (GenBank accession number:
`NM_001221);
`
`accession number: NM_001259);
`
`GRB2, Homo sapiens growth factor receptor-bound protein 2 (GRB2), transcript
`variant 1, mRNA (GenBank
`
`accession number: NM_002086);
`GAPDH, Homo sapiens
`glyceraldehyde-3-phosphate
`dehydrogenase
`(GenBank accession number: NM_002046);
`and
`RPS9, Homo sapiens cDNA clone IMAGE:6647283, partial cds (GenBank accession
`number: BC071941).
`
`CDK6, Homo sapiens cyclin-dependent kinase 6 (CDK6), mRNA (GenBank
`
`(GAPD),
`
`the taxoid
`response to a molecule of
`
`28. A kit for predicting or monitoring a cancer patient's
`family according
`
`to the method of Claim 21 wherein the kit comprises detectable-labeled
`antibodies, detectable-labeled
`antibody
`
`fragments detectable-labeled oligonucleotides or
`
`comprising nucleic acids capable of hybridizing under
`stringent
`
`conditions to said one or
`
`more genetic markers and said one or more genetic markers
`selected
`from the
`group
`consisting of:
`(p21,
`1A
`inhibitor
`kinase
`cyclin-dependent
`P21(Wafl), Homo sapiens
`(CDKN1A), transcript variant mRNA (GenBank accession number: NM_000389); 1,
`
`
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01136
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-56-
`
`oncogene
`
`
`
`(PIM1), mRNA (GenBank accession
`
`number:
`
`1,
`
`
`
`interferon-inducible, 67kDa
`
`(RXRA), mRNA (GenBank
`
`associated
`
`
`
`
`
`(KNTC2), 2 mRNA (GenBank accession
`
`
`
`group (HMG20B), mRNA 20B
`
`
`
`(GenBank
`
`(GenBank
`
`(STK11),
`
`
`
`cds (GenBank
`
`(GAPD), mRNA
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`Pim-1, Homo sapiens pim-1
`NM 002648);
`protein
`GBP-1, Homo sapiens guanylate binding
`
`number: NM_002053);
`accession
`(GBP1), mRNA (GenBank
`RXRA, Homo sapiens
`
`retinoid X receptor, alpha
`
`accession number: NM_002957);
`SPF45, Homo sapiens RNA
`
`binding motif protein 17 (RBM17), mRNA (GenBank
`accession number: NM_032905);
`Heel, Homo sapiens kinetochore
`number: NM_006101);
`Rafl, Human mRNA for raf oncogene (GenBank
`X03484);
`number:
`accession
`
`Aurora A, Homo sapiens
`aurora-related
`kinase
`
`1 mRNA, complete cds (ARK1)
`(GenBank accession number: AF008551);
`TACC3, Homo sapiens
`
`transforming, acidic coiled-coil containing protein 3 (TACC3),
`mRNA (GenBank accession
`number: NM_006342);
`oncogene B, nuclear
`homolog
`
`viral
`RelB, Homo sapiens v-rel
`reticuloendotheliosis
`factor of kappa
`
`in light polypeptide gene enhancer B-cells 3 (avian) (RELB), mRNA
`
`(GenBank accession number: NM_006509);
`PRKCD, Homo sapiens protein kinase C, delta (PRKCD), transcript variant 1, mRNA
`(GenBank accession number: NM_006254);
`BRAF35, Homo sapiens
`high-mobility
`accession number: NM_006339);
`HSPA1L, Homo sapiens heat shock 70kDa protein 1A (HSPA1A), mRNA
`accession number: NM_005345);
`kinase 11 (Peutz-Jeghers syndrome)
`
`STK11, Homo sapiens
`serine/threonine
`mRNA (GenBank accession number: NM_000455);
`and
`MKK3, Homo sapiens MAP kinase kinase 3 (MKK3) mRNA, complete
`accession number: L36719);
`GAPDH, Homo sapiens glyceraldehyde-3-phosphate dehydrogenase
`(GenBank accession number: NM_002046); and
`RPS9, Homo sapiens cDNA
`clone IMAGE:6647283:,
`number: BC071941).
`
`
`
`
`
`cds partial (GenBank accession
`
`01137
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-57-
`
`response to a molecule of the taxoid
`
`
`29. A kit for predicting or monitoring a cancer patient's
`
`
`family according to the method of Claim 20 wherein the kit comprises
`
`the means of:
`a) obtaining total RNA
`
`from a bodily sample;
`b) reverse transcribing
`
`the total RNA to obtain cDNA; and
`reaction using a set of primers wherein
`
`c) subjecting the cDNA to a polymerase chain
`
`one or both primers are detectable-labeled and both
`
`are primers derived from a
`
`nucleotide sequence of
`one or more
`genetic
`
`selected markers the group consisting
`
`of:
`BubRl, Homo sapiens similar to protein kinase
`(GenBank accession number: AF046079);
`Mad2, Homo sapiens mRNA for MAD2
`AJ000186);
`
`Mpsl, Homo sapiens TTK protein kinase (TTK), mRNA (GenBank
`number: NM 003318);
`GEFT for Racl/CDC42, Homo sapiens RAC/CDC42 exchange factor (GEFT),
`
`transcript variant 2, mRNA (GenBank
`accession
`number:
`Bubl, Homo sapiens BUB1 budding uninhibited
`by benzimidazoles
`(yeast) (BUB1), mRNA
`
`(GenBank accession number: NM_004336);
`hSepharase, Homo
`sapiens extra
`spindle poles like 1 (S. cerevisiae) (ESPL1), mRNA
`
`(GenBank accession
`number: NM_012291);
`kinase
`protein
`CamKIId, Homo sapiens
`calcium/calmodulin-dependent
`kinase) II delta
`
`(CAMK2D), anscript variant 3, mRNA (GenBank accession tr
`
`number: NM_001221);
`
`accession number: NM_001259);
`and
`GRB2, Homo sapiens
`
`growth factor receptor-bound protein 2
`variant 1, mRNA (GenBank accession
`number: NM_002086);
`
`GAPDH, Homo sapiens glyceraldehyde-3-phosphate dehydrogenase (GAPD),
`mRNA (GenBank accession number: NM_002046); and
`RPS9, Homo sapiens
`
`cDNA clone IMAGE:6647283, partial
`accession number: BC071941).
`
`CDK6, Homo sapiens cyclin-dependent kinase 6 (CDK6), mRNA (GenBank
`
`(GRB2),
`
`transcript
`
`
`
`cds (GenBank
`
`from
`
`(BUBR1) mRNA,
`
`complete
`
`cds
`
`protein
`
`(GenBank
`
`accession
`
`accession
`
`NM_133483);
`1
`homolog
`
`(CaM
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01138
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-58-
`
`(PIM1), mRNA
`
`(GenBank
`
`accession
`
`number:
`
`(GenBank
`
`SPF45, Homo sapiens RNA binding motif protein 17 (RBM17), mRNA (GenBank
`
`(KNTC2), mRNA
`
`(GenBank
`
`30. A kit for predicting or monitoring a
`cancer patient's response to a molecule of the taxoid
`
`family according
`to
`the method of
`
`
`
`
`claim the kit comprises 19 wherein the means of:
`
`a) obtaining total RNA from a bodily sample;
`cDNA; and
`
`b) reverse transcribing the total RNA
`to obtain
`of set primers wherein
`
`
`c) subjecting the cDNA to a polymerase chain reaction using a
`
`one or both primers
`
`
`are detectable-labeled and both primers derived from a are
`nucleotide sequence of one or more genetic markers selected from
`the group consisting
`of:
`kinase inhibitor 1A (p21, Cipl)
`
`sapiens cyclin-dependent
`P21(Wafl), Homo
`(CDKN1 A), transcript variant
`1, mRNA (GenBank accession
`number:
`NM_000389);
`Pim-1, Homo sapiens pim-1 oncogene
`NM 002648);
`GBP-1, Homo sapiens guanylate binding protein 1,
`interferon-inducible, 67kDa
`(GBP1), mRNA
`(GenBank accession
`
`number: NM_002053);
`
`RXRA, Homo sapiens retinoid X receptor, alpha (RXRA), mRNA
`accession number: NM_002957);
`
`accession number: NM_032905);
`Heel, Homo sapiens kinetochore associated 2
`accession number: NM_006101);
`number: X03484);
`
`Rafl, Human mRNA for raf oncogene (GenBank accession
`Aurora A, Homo
`
`sapiens aurora-related kinase 1 (ARK1) mRNA, complete cds
`(GenBank accession number: AF008551);
`TACC3, Homo sapiens
`
`transforming, acidic coiled-coil containing
`(TACC3), mRNA
`(GenBank
`
`accession number: NM_006342);
`homolog
`RelB, Homo sapiens v-rel reticuloendotheliosis
`viral oncogene
`factor of kappa
`light polypeptide gene enhancer
`
`in B-cells 3 (avian) (RELB),
`mRNA (GenBank accession number: NM_006509);
`PRKCD, Homo sapiens protein kinase C, delta (PRKCD), transcript variant 1,
`mRNA (GenBank accession number: NM_006254);
`BRAF35, Homo sapiens high-mobility
`
`group (HMG20B), mRNA (GenBank 20B
`accession number: NM_006339);
`
`protein 3
`
`B,
`
`nuclear
`
`
`
`5
`
`10
`
`15
`
`20
`
`25
`
`30
`
`01139
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`-59-
`
`HSPA1L, Homo sapiens heat
`shock 70kDa protein 1A (HSPA1 A), mRNA
`
`NM_005345);
`(GenBank accession number:
`
`STK11, Homo sapiens serine/threonine
`
`kinase (Peutz-Jeghers syndrome) 11
`(STK11), mRNA (GenBank
`
`accession number: NM_000455);
`and
`MKK3, Homo sapiens MAP kinase kinase 3 (MICK3) mRNA,
`complete
`(GenBank accession number:
`L36719);
`GAPDH, Homo sapiens glyceraldehyde-3-phosphate
`mRNA (GenBank accession
`number: NM_002046); and
`RPS9, Homo sapiens cDNA clone IMAGE:6647283,
`
`partial cds (GenBank
`accession number: BC071941).
`
`
`
`dehydrogenase (GAPD),
`
`cds
`
`31. The detectable
`label of any one of claims 24 — 27, wherein the detectable label comprises
`
`
`an enzyme, a radioactive isotope, or a
`
`chemical fluoresces, a chemiluminescent which
`
`molecule, radiopaque substances,
`
`liposomes, and haptenic molecules.
`
`5
`
`10
`
`15
`
`20
`
`01140
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 1 of 16
`
`3
`
`2 r>—
`
`RBI
`
`BabRI
`
`\ v q
`
`-v. -a—.
`I
`
`Mpsl
`
`v R
`
`<3
`to
`0
`Q 3
`O
`
`MR=103
`
`1
`
`1
`
`MR-3.01
`
`1
`
`Mad2
`
`2 -
`
`i
`\
`\
`\
`
`k
`
`MR-S.C0
`
`1
`
`0
`
`1
`10
`100
`Bomtm&t
`
`MR~2.92 1
`1
`(nM)
`
`1
`10
`
`100
`
`Figure 1
`
`01141
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 2 of
`
`16
`
`[=
`
`10
`D-
`
`0.1 =
`
`-MR=4.21
`
`o
`io 0
`M-
`Q 10 i
`O
`
`0.1 =
`
`BubR1
`
`N-
`
`\
`
`U n. Ck m N
`
`•a
`
`MPS-1
`
`i
`
`o»
`
`0
`
`-MR=1.73
`
`1
`I
`10
`1
`Docetaxel (nM)
`
`100
`
`Figure 2
`
`01142
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 3 of 16
`
`Quantitate Knockdown
`
`Vector BubR1
`Control shRNA
`
`Vector Mps1
`Control shRNA
`
`Figure 3
`
`O)
`.5
`.5 <0
`S
`<D oc
`so
`OS
`
`120
`1 0 0 - i w ®
`80 -
`60 -
`40 -
`2 0 -
`0
`
`01143
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 4 of 16
`
`- Docetaxel
`72 hours
`16 hours
`
`+ Docetaxel
`72 hours
`16 hours
`
`Control mM
`siRNA y®|
`
`Mad2 ||
`siRNA 1
`p.
`
`tdafr
`i"1 r
`%• *
`
`te
`
`—'-A .^'T'V
`
`t
`
`^
`
`j^Sil PilfcN
`
`^la^-
`
`BubR1
`siRNA
`
`f A
`
`ISiJ
`
`^ '
`
`•
`
`*
`
`• '"4
`
`1
`
`tktaf
`
`m
`
`l#¥|
`•y
`'-'U
`
`"f'v
`
`il
`
`Mpsi •pB|
`siRNA ^3c.
`
`pplf
`J t l
`
`m
`
`&m:Sik
`Figure 4
`
`IBS
`
`^^*5
`
`1^3
`
`01144
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 5 of 16
`
`80
`
`SO
`OS
`
`><
`60 -
`0)
`T3
`C 40 -
`.o
`p 20 -
`
`o
`
`• Control
`O Mpsl
`A Mad2
`• BubR1
`
`20
`
`60
`40
`Time (hours)
`
`80
`
`Figure 5
`
`01145
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 6 of 16
`
`Quantitate Knockdown
`
`X
`
`140 o c: 1 2 0 -
`[5 1 0 0 -
`"i5 80 -
`S 6 0 -
`oc
`CD 4 0 -
`2 0 -
`SO oS
`0
`
`Control Mpsi
`siRNA siRNA
`
`Control BubR1
`siRNA siRNA
`
`Control Mad2
`siRNA siRNA
`
`Figure 6
`
`01146
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 7 of 16
`
`Mpsl
`2
`
`4
`
`i
`
`' * - * •
`
`1
`
`BubR1
`
`Mad2
`2
`
`.li ,
`
`i
`
`8
`
`<U
`ra
`o
`O
`O
`+ Q
`
`JL
`it
`
`1 0 102 103 104
`
`Control
`2
`
`i
`
`W SW
`C
`Si
`o
`O
`0)
`o
`i
`uL
`0 10 102 103 104 0
`
`4
`i .
`
`i
`
`i
`
`Ji
`
`8
`4
`2 J 116
`i
`i
`10 102 103 104 0
`10 102 103 104 0
`DNA content
`
`816
`4
`2
`
`;32
`
`Figure 7
`
`01147
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 8 of 16
`
`stable knockdown cell
`BubR1
`
`5nM
`line +
`Vector control
`
`i
`
`Docetaxel
`
`* * «
`
`,<#'
`
`*
`**» .
`_
`+ , - r " *
`
`/
`
`£
`»'.:*& m
`4 A
`
`* ?
`
`•
`
`•
`
`«
`
`i
`g
`?
` *
`
`
`* . i " » * ' ' f , - ' j * •
`
`
`
`
`
`
`
`*
`
`t*
`
`A ..
`
`& "
`
`••
`
`^
`
`^
`
`"C
`*>» «
`
`" i - 5 '
`
`* * ^ •<*
`
`^ •
`•*. V* <•:
`
`*
`
`"
`
`J"
`
`&
`
`X L .
`
`*3k-^
`
`Figure 8
`
`01148
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`10 E
`
`IVIR=0.25
`
`o
`io 0
`Q
`3
`O
`
`Sheet 9 of 16
`
`siRNA
`p21
`
`t
`
`-•a.
`
`CL
`
`Pim-1
`
`NPO
`•o-..
`
`MR=0.3
`6
`
`Aurora A
`
`r>ACC3
`
`.
`
`\
`\
`\
`
`a B \
`
`\ s m \
`
`\
`\
`
`IR=0.73
`
`0
`
`1
`
`IR=0.29
`
`100
`10
`1
`Docetaxel (nM)
`
`I
`10
`
`100
`
`Figure 9
`
`01149
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 10 of
`
`16
`
`Q
`O
`
`3
`
`0
`
`Aurora A
`
`\
`\
`\
`i
`
`%
`
`IR=0J8
`
`1
`1
`10
`1
`Docetaxel (nM)
`
`100
`
`Figure 10
`
`01150
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 11 of 16
`
`120
`S5 100 -
`•S
`•S 80 -
`<o
`S
`60 -
`0) oc
`^ 20 -
`0
`
`Quantitate Knockdown
`
`i
`
`1
`
`Vector
`Control
`
`Aurora A
`shRNA
`
`Figure 11
`
`01151
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 12 of 16
`
`TACC3
`
`-—Q~"
`
`4 —
`
`•
`•
`•
`•
`
`i
`
`i
`
`Pim~1
`
`& - •
`
`•
`•
`•
`/
`•
`/
`•
`
`— — s
`
`I
`I
`1
`60
`40
`20
`Time (Hours)
`
`80
`
`Figure 12
`
`O 1
`><
`0
`to
`CD
`O
`o
`*
`
`4 —
`3
`
`—
`
`1
`0
`
`01152
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 13 of 16
`
`Quantitate Knockdown
`0> 120
`•5 ioo|- ii
`I
`•5 80- Ii
`<o
`g 60 - HI
`0 40 - III
`o:
`2 0 -
`0 Control TACC3
`Control Pim-1
`siRNA
`
`NO
`OS
`
`Figure 13
`
`01153
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 14 of 16
`
`0 nM
`
`5 nM
`
`•
`40 nM
`
`j-iii-i
`
`1135.5
`
`855
`
`wM
`
`800
`
`111 Null
`600 -
`Pim-1
`BubR1
`400 -
`
`"5 c
`<i>
`H-J c
`a) 200 —
`o c:
`0
`CD
`O
`(0 800
`Q>
`o 600 -
`^3
`u. 400 -
`c
`03
`0) 200
`0
`CO
`® 1400
`a
`to
`CQ
`O 600 -
`CD
`^ 400 -
`o
`
`sy
`
`200 -
`
`0
`
`72
`48
`24
`Time (hours)
`
`Figure 14
`
`01154
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 15 of 16
`
`CJ) c:
`to
`c:
`=3
`
`•HM
`-iC
`
`Q.
`
`2.5
`
`2.0 -
`
`1.5 -
`
`1 . 0 -
`
`0.5 "
`
`0
`
`;
`
`0
`
`I Null
`Pim-1
`BubR1
`
`• ;:l
`
`40
`
`5
`Taxotere (nM)
`
`Figure 15
`
`01155
`
`

`
`WO 2006/062811
`
`PCT/US2005/043578
`
`Sheet 16 of 16
`
`Ab O
`i
`
`MM 4P
`
`SiRNA
`
`1
`
`Ab
`-BubR1
`
`~cc^u b u I i n
`
`Figure 16
`
`•**
`
`i
`
`a-Tubulm-?
`
`i «
`
`•
`
`01156
`
`

`
`
`APPLICATION
`(12) INTERNATIONAL
`PUBLISHED THE PATENT COOPERATION UNDER
`Property
`Organization
`(19) World Intellectual
`International Bureau
`
`
`
`TREATY
`
`(PCT)
`
`Date
`(43) International Publication
`14 October 2010
`(14.10.2010)
`
`m
`
`PCT
`
`(10) International Publication
`Number
`WO 2010/117668 A1
`
`(51) International Patent Classification:
`A61K9/00
`(2006.01)
`(21) International Application
`
`Number:
`PCT/US2010/028770
`
`(22) International Filing Date:
`26 March 2010
`
`(25) Filing Language:
`(26) Publication Language:
`(30) Priority Data:
`US
`(30.03.2009)
`30 March 2009
`61/164,734
`US
`(30.03.2009)
`30 March 2009
`61/164,722
`us
`61/164,720
`(30.03.2009)
`30 March 2009
`us
`61/164,725
`(30.03.2009)
`30 March 2009
`us
`61/164,728
`(30.03.2009)
`30 March 2009
`us
`61/164,731
`(30.03.2009)
`30 March 2009
`61/262,993
`US
`(20.11.2009)
`20 November 2009
`61/262,994
`US
`(20.11.2009)
`20 November 2009
`(71) Applicant
`(for all designated States except US):
`CERULEAN PHARMA INC. [US/US]; 840 Memorial
`Drive, 5th Floor, Cambridge,
`MA
`02139
`(72) Inventors; and
`__ (75) Inventors/Applicants (for US only): ELIASOF, Scott
`[US/US]; 35 Brandon St., Lexington, MA 02420 (US).
`CRAWFORD, Thomas, C. [US/US]; 13 Clark Ln., Es­
`sex, CT 06426 (US). GANGEL, Geeti [IN/US]; 118
`Sherman St., Cambridge, MA 02140 (US). REITER,
`Lawrence, Alan [US/US]; 32 W. Mystic Ave., Mystic,
`
`CT 06355 (US). NG, Pei-Sze [SG/US]; 21 Wendell St.
`02138
`(US).
`#17, Cambridge, MA
`(74) Agent: LAWRENCE, Laurie, Butler; Lando & Anas-
`tasi, LLP, One Main Street, Eleventh Floor, Cambridge,
`(US).
`MA 02142
`
`(26.03.2010) (81) Designated States (unless otherwise indicated, for every
`kind of national protection available): AE, AG, AL, AM,
`English
`AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ,
`CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO,
`English
`DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT,
`HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP,
`KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD,
`ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI,
`NO, NZ, OM,
`PT,
`PE,
`PG,
`PH,
`PL,
`TN,
`ST, SV, SY, TH, TJ, TM,
`SE, SG, SK, SL,
`SM,
`ZM,
`TT, TZ, UA, UG, US, UZ, VC, VN,
`ZA,
`(84) Designated States (unless otherwise indicated, for every
`kind of regional protection available): ARIPO (BW, GH,
`GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG,
`ZM, ZW), Eurasian
`(AM,
`AZ,
`BY,
`TM), European
`(AT,
`BE,
`
`
`DE, BG, CH, CY, CZ, DK, EE,
`(US).
`ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV,
`MC, MK, MT, NL, NO, PL, PT, RO, SE, SI, SK, SM,
`TR), OAPI
`(BF, BJ,
`
`CF, CM, GA, GN, GQ, GW, CG, CI,
`
`
`ML, MR, NE,
`SN,
`TD,
`TG).
`Published:
`with international search
`
`TR,
`ZW.
`
`KG,
`
`
`
`report (Art. 21(3))
`
`<
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`00
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`o
`o
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`
`(54) Title: POLYMER-AGENT
`PARTICLES,
`CONJUGATES,
`(57) Abstract: Described herein
`
`and particles, which
`
`are polymer-agent conjugates
`are
`cancer.
`Also
`described
`herein
`treat a
`disorder),
`
`
`kits polymer-agent conjugates including
`(e.g., to
`gates and particles, methods
`of
`storing
`the
`
`
`
`the and
`
`AND
`COMPOSITIONS,
`in the treatment of
`can be used, for example,
`compositions
`mixtures,
`particles, methods of making the polymer- agent
`
`
`particles
`and
`
`conju­
`methods
`
`01157
`
`

`
`WO 2010/117668
`
`PCT/US2010/028770
`
`T2021-7000W O
`
`POLYMER-AGENT CONJUGATES.
`PARTICLES.
`RELATED METHODS OF
`USE
`
`COMPOSITIONS.
`
`RELATED APPLICATIONS
`claims priority
`to
`U.S.S.N.
`This application
`filed
`March
`2009;
`U.S.S.N. 61/164,722,
`2009; U.S.S.N.
`61/164,728,
`filed
`30,
`filed
`30, 2009; U.S.S.N.
`61/164,734,
`November 20, 2009;
`and
`U.S.S.N.
`disclosures of the prior applications
`are
`reference
`in)
`the
`disclosure
`of
`
`30,
`March
`
`30,
`March
`filed
`61/262,994,
`The
`part
`considered
`this
`application.
`
`61/164,720,
`U.S.S.N.
`2009;
`
`filed
`
`2009;
`November 20,
`(and
`
`of
`
`The delivery
`to provide optimal
`increase
`the
`efficacy
`
`INVENTION
`BACKGROUND OF
`is
`agent
`
`of
`a
`drug
`
`with release of the controlled active
`
`systems
`use
`and
`
`effectiveness. Controlled release
`
`polymer
`
`
`
`the and minimize drug problems
`with
`patient
`
`of
`
`desirable
`may
`compliance.
`
`INVENTION
`SUMMARY OF
`are
`polymer-agent
`conjugates
`Described herein
`can be
`and
`the
`
`treatment cancer, cardiovascular of
`
`diseases,
`used, for example,
`in
`inflammatory
`disorders (e.g.,
`an
`inflammatory
`disorder
`that
`includes
`caused by, e.g.,
`an
`infectious
`disease)
`
`or Also described autoimmune
`
`herein are mixtures,
`
`compositions dosage forms containing and
`
`the
`particles,
`of using
`the
`particles
`
`to (e.g., treat a disorder),
`kits
`
`
`including the polymer-agent
`and
`conjugates and
`particles,
`methods
`
`
`
`making of the polymer-agent conjugates
`particles, methods
`
`of storing the particles
`and
`
`methods analyzing
`the
`
`of particles.
`Accordingly,
`in
`one
`aspect,
`the
`
`invention a polymer-agent
`features conjugate
`
`comprising:
`a polymer; and
`an agent (e.g.,
`
`or
`
`
`
`diagnostic the polymer.
`
`agent)
`
`a
`
`therapeutic
`
`particles,
`
`methods
`
`attached
`
`1005052.1
`
`1
`
`01158
`
`

`
`WO 2010/117668
`
`PCT/US2010/028770
`
`T2021-7000W O
`
`biodegradable
`poly(lactic-co-gly