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US 2015/0030615 A1Published application
Biomarkers for cancer stem cells and related methods of use
AssigneeVerastem, Inc.
InventorsAlan G. Derr, David T. Weaver, Irina Shapiro, Daniel W. Paterson, Jonathan A. Pachter
Life of this patent
Estimating the term…
Abstract
Novel methods of classifying subjects as candidates for treatment with a cancer associated mesenchymal cell, tumor initiating cancer cell, or cancer stem cell inhibitor treatment and subsequent administration of the cancer associated mesenchymal cell, tumor initiating cancer cell, or cancer stem cell inhibitor are disclosed within.
Claims34
A method of evaluating or treating a subject, comprising:
- a) optionally, acquiring a subject sample;
- b) acquiring a value or values that is a function of the level of gene expression for (each of) a plurality of genes selected from a first and/or second and/or third and/or fourth and or/fifth and/or sixth set of genes, wherein
- (i) said first set of genes comprises or consists of:
- S100A4, SDC2, CYP1B1, FERMT2, CYBRD1, SNAI2, CD44, BIN1, PMP22, CTGF, IGFBP3, ANXA6, MAP1B, TAGLN, ENPP2, FBLN5, PCOLCE, FN1, VIM, PPAP2B, SEM5A, VCAN, NID2, NID1, HAS2, PRRX1, TNFAIP6, CLDN4, FADS2, DDIT4, GNG11, PER1, ISCU, KPNA3, SLC44A1, FKBP5, NR2F1, MLPH, DOCK10, RGS4, IGFBP4;
- and
- (ii) said second set of genes comprises or consists of:
- S100A4, SDC2, CYP1B1, FERMT2, CYBRD1, SNAI2, CD44, BIN1, ENPP2, FBLN5, PCOLCE, FN1, VIM, PPAP2B, SEM5A, VCAN, CLDN4, FADS2, DDIT4, GNG11, PER1, ISCU, KPNA3, SLC44A1, FKBP5, IGFBP4;
- and
- (iii) said third set of genes comprises or consists of:
- SDC2, CYBRD1, SNAI2, PMP22, CTGF, IGFBP3, ANXA6, MAP1B, TAGLN, PPAP2B, HAS2, NRF2, MLPH, DOCK10, RGS4;
- and
- (iv) said fourth set of genes comprises or consists of:
- FERMT2, BIN1, PMP22, CHN1, CTGF, IGFBP3, NID2, CLDN4, CYBRD1, PRR16, ANXA6, PCOLCE, PPAP2B, HAS2, CDH11, MLPH, DOCK10, RGS4, PVRL3, NID2, SLC44A1, FKBP5;
- and
- (v) said fifth set of genes comprises or consists of:
- FERMT2, BIN1, PMP22, CHN1, CTGF, IGFBP3, NID2, CLDN4;
- and
- (vi) said sixth set of genes comprises or consists of:
- HAS2, BIN1, PCOLCE, FERMT2, CTGF, IGFBP3, NID2, SLC44A1, FKBP5, and MLPH;
- and
- (c) responsive to said value or values:
- (i) classifying said subject;
- or
- (ii) administering treatment comprising an agent that inhibits or kills cancer associated mesenchymal cells, tumor initiating cancer cells, or cancer stem cells, to said subject;
- provided that, if (c)(ii) is not performed the acquisition in (a) or (b) comprises directly acquiring;
- thereby evaluating or treating said subject.
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A method of assaying in a subject sample the level of gene expression product of a plurality of genes selected from a first and/or second and/or third and/or fourth and/or fifth and/or sixth set of genes, wherein:
- (i) said first set of genes comprises or consists of:
- S100A4, SDC2, CYP1B1, FERMT2, CYBRD1, SNAI2, CD44, BIN1, PMP22, CTGF, IGFBP3, ANXA6, MAP1B, TAGLN, ENPP2, FBLN5, PCOLCE, FN1, VIM, PPAP2B, SEM5A, VCAN, NID2, NID1, HAS2, PRRX1, TNFAIP6, CLDN4, FADS2, DDIT4, GNG11, PER1, ISCU, KPNA3, SLC44A1, FKBP5, NR2F1, MLPH, DOCK10, RGS4, IGFBP4;
- and
- (ii) said second set of genes comprises or consists of:
- S100A4, SDC2, CYP1B1, FERMT2, CYBRD1, SNAI2, CD44, BIN1, ENPP2, FBLN5, PCOLCE, FN1, VIM, PPAP2B, SEM5A, VCAN, CLDN4, FADS2, DDIT4, GNG11, PER1, ISCU, KPNA3, SLC44A1, FKBP5, IGFBP4;
- and
- (iii) said third set of genes comprises or consists of:
- SDC2, CYBRD1, SNAI2, PMP22, CTGF, IGFBP3, ANXA6, MAP1B, TAGLN, PPAP2B, HAS2, NRF2, MLPH, DOCK10, RGS4;
- and
- (iv) said fourth set of genes comprises or consists of:
- FERMT2, BIN1, PMP22, CHN1, CTGF, IGFBP3, NID2, CLDN4, CYBRD1, PRR16, ANXA6, PCOLCE, PPAP2B, HAS2, CDH11, MLPH, DOCK10, RGS4, PVRL3, NID2, SLC44A1, FKBP5;
- and
- (v) said fifth set of genes comprises or consists of:
- FERMT2, BIN1, PMP22, CHN1, CTGF, IGFBP3, NID2, CLDN4;
- and
- (vi) said sixth set of genes comprises or consists of:
- HAS2, BIN1, PCOLCE, FERMT2, CTGF, IGFBP3, NID2, SLC44A1, FKBP5, and MLPH;
- comprising a first agent capable of interacting with a gene expression product of a plurality of genes selected from a first and/or second and/or third and/or fourth and/or fifth and/or sixth set of genes;
- and wherein the method comprises assaying the level of gene expression product of the plurality of genes.
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A reaction mixture comprising:
- a plurality of detection reagents;
- and
- a plurality of target nucleic acid molecules derived from a subject, wherein each of the plurality of detection reagents comprises a plurality probes to measure the level of gene expression product of a plurality of genes selected from a first and/or second and/or third and/or fourth and/or fifth and/or sixth set of genes, wherein:
- (i) said first set of genes comprises or consists of:
- S100A4, SDC2, CYP1B1, FERMT2, CYBRD1, SNAI2, CD44, BIN1, PMP22, CTGF, IGFBP3, ANXA6, MAP1B, TAGLN, ENPP2, FBLN5, PCOLCE, FN1, VIM, PPAP2B, SEM5A, VCAN, NID2, NID1, HAS2, PRRX1, TNFAIP6, CLDN4, FADS2, DDIT4, GNG11, PER1, ISCU, KPNA3, SLC44A1, FKBP5, NR2F1, MLPH, DOCK10, RGS4, IGFBP4;
- and
- (ii) said second set of genes comprises or consists of:
- S100A4, SDC2, CYP1B1, FERMT2, CYBRD1, SNAI2, CD44, BIN1, ENPP2, FBLN5, PCOLCE, FN1, VIM, PPAP2B, SEM5A, VCAN, CLDN4, FADS2, DDIT4, GNG11, PER1, ISCU, KPNA3, SLC44A1, FKBP5, IGFBP4;
- and
- (iii) said third set of genes comprises or consists of:
- SDC2, CYBRD1, SNAI2, PMP22, CTGF, IGFBP3, ANXA6, MAP1B, TAGLN, PPAP2B, HAS2, NRF2, MLPH, DOCK10, RGS4;
- and
- (iv) said fourth set of genes comprises or consists of:
- FERMT2, BIN1, PMP22, CHN1, CTGF, IGFBP3, NID2, CLDN4, CYBRD1, PRR16, ANXA6, PCOLCE, PPAP2B, HAS2, CDH11, MLPH, DOCK10, RGS4, PVRL3, NID2, SLC44A1, FKBP5;
- and
- (v) said fifth set of genes comprises or consists of:
- FERMT2, BIN1, PMP22, CHN1, CTGF, IGFBP3, NID2, CLDN4;
- and
- (vi) said sixth set of genes comprises or consists of:
- HAS2, BIN1, PCOLCE, FERMT2, CTGF, IGFBP3, NID2, SLC44A1, FKBP5, and MLPH.
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Dependencies are inferred from the claim text.