Gene expression signatures of neoplasm responsiveness to therapy

1. A method of determining if a hematological neoplasm is sensitive to treatment with histone deacetylase inhibitor (HDACi) and mechanistic Target of Rapamycin (mTOR) inhibitor (mTORi) combination therapy and treating the neoplasm, comprising:

obtaining a blood sample from a subject with a hematological neoplasm;

detecting the level of expression of six or more genes in the blood sample, wherein the six or more genes are selected from the group consisting of ATPase family, AAA domain containing 2 (ATAD2); Bloom syndrome, RecQ helicase-like (BLM); chromosome 9 open reading frame 140 (C9orf140); cyclin B2 (CCNB2); cell division cycle 20 homolog ( S. cerevisiae ) (CDC20); cell division cycle 25 homolog A ( S. pombe ) (CDC25A); cell division cycle 6 homolog ( S. cerevisiae ) (CDC6); cell division cycle associated 3 (CDCA3); cell division cycle associated 5 (CDCA5); E2F transcription factor 2 (E2F2); Holliday junction recognition protein (HJURP); major histocompatibility complex, class II, DP beta 1 (HLA-DPB1); Hs.193784; Hs.202577; KIAA2013; kinesin family member 22 (KIF22); kinesin family member 2C (KIF2C); lactate dehydrogenase A (LDHA); minichromosome maintenance complex component 2 (MCM2); minichromosome maintenance complex component 4 (MCM4); minichromosome maintenance complex component 5 (MCM5); v-myb myeloblastosis viral oncogene homolog (avian)-like 2 (MYBL2); non-SMC condensin I complex, subunit H (NCAPH); NAD(P) dependent steroid dehydrogenase-like (NSDHL); polyhomeotic homolog 3 ( Drosophila ) (PHC3); PHD finger protein 19 (PHF19); RAD51 homolog (RecA homolog, E. coli ) ( S. cerevisiae ) (RAD51); ribonucleotide reductase M2 (RRM2); solute carrier family 19 (folate transporter), member 1 (SLC19A1); sperm associated antigen 5 (SPAG5); aurora kinase A (STK6); suppressor of variegation 3-9 homolog 1 ( Drosophila ) (SUV39H1); transforming, acidic coiled-coil containing protein 3 (TACC3); transmembrane protein 48 (TMEM48); thyroid hormone receptor interactor 13 (TRIP13); ubiquitin-conjugating enzyme E2C (UBE2C); and Zinc finger protein 107 (ZNF107);

wherein the six or more genes comprise at least CDC25A, E2F2, RRM2, RAD51, MCM4, BLM, CDC6, CDCA5, HJURP, MCM2, MCM5, MYBL2, PHF19, SLC19A1, UBE2C, Hs.193784, Hs.202577, and HLA-DPB1;

identifying the neoplasm as sensitive to treatment with HDACi and mTORi combination therapy if there is a difference in the level of expression of the six or more genes in the neoplasm sample as compared to a control; and

administering a therapeutically effective amount of a HDACi and mTORi combination therapy to the subject if the neoplasm is identified as sensitive to treatment with HDACi and mTORi combination therapy.

2. The method of claim 1 , wherein the six or more genes comprise each of ATAD2, BLM, C9orf140, CCNB2, CDC20, CDC25A, CDC6, CDCA3, CDCA5, E2F2, HJURP, HLA-DPB1, Hs.193784, Hs.202577, KIAA2013, KIF22, KIF2C, LDHA, MCM2, MCM4, MCM5, MYBL2, NCAPH, NSDHL, PHC3, PHF19, RAD51, RRM2, SLC19A1, SPAG5, STK6, SUV39H1, TACC3, TMEM48, TRIP13, UBE2C, and ZNF107.

3. The method of claim 2 , wherein identifying the neoplasm as sensitive to treatment with HDACi and mTORi combination therapy occurs prior to HDACi and mTORi combination therapy, and wherein the difference in the level of expression comprises:

(a) an increase in the level of expression of one or more of ATAD2, BLM, C9orf140, CCNB2, CDC20, CDC25A, CDC6, CDCA3, CDCA5, E2F2, HJURP, KIAA2013, KIF22, KIF2C, LDHA, MCM2, MCM4, MCM5, MYBL2, NCAPH, NSDHL, PHF19, RAD51, RRM2, SLC19A1, SPAG5, STK6, SUV39H1, TACC3, TMEM48, TRIP13, UBE2C, and ZNF107; and

(b) a decrease in the level of expression of one or more of Hs.193784, Hs.202577, HLA-DPB1, and PHC3.

4. The method of claim 3 , wherein the difference in the level of expression comprises:

(c) an increase in an aggregate gene expression value calculated from the level of expression of two or more of ATAD2, BLM, C9orf140, CCNB2, CDC20, CDC25A, CDC6, CDCA3, CDCA5, E2F2, HJURP, KIAA2013, KIF22, KIF2C, LDHA, MCM2, MCM4, MCM5, MYBL2, NCAPH, NSDHL, PHF19, RAD51, RRM2, SLC19A1, SPAG5, STK6, SUV39H1, TACC3, TMEM48, TRIP13, UBE2C, and ZNF107; and

(d) a decrease in an aggregate gene expression value calculated from the level of expression of two or more of Hs.193784, Hs.202577, HLA-DPB1, and PHC3.

5. The method of claim 1 , wherein detecting the level of expression of the six or more genes comprises microarray analysis.

6. The method of claim 1 , wherein the control comprises the level of expression of the six or more genes in a control sample.

7. The method of claim 1 , wherein identifying the neoplasm as sensitive to treatment with HDACi and mTORi combination therapy occurs prior to HDACi and mTORi combination therapy, and wherein the difference in the level of expression comprises:

(a) an increase in the level of expression of BLM, CDC25A, CDC6, CDCA5, E2F2, HJURP, MCM2, MCM4, MCM5, MYBL2, PHF19, RAD51, RRM2, SLC19A1, and UBE2C; and

(b) a decrease in the level of expression of Hs.193784, Hs.202577, and HLA-DPB1.

8. The method of claim 7 , wherein the difference in the level of expression comprises:

(c) an increase in an aggregate gene expression value calculated from the level of expression of BLM, CDC25A, CDC6, CDCA5, E2F2, HJURP, MCM2, MCM4, MCM5, MYBL2, PHF19, RAD51, RRM2, SLC19A1, and UBE2C; and

(d) a decrease in an aggregate gene expression value calculated from the level of expression of Hs.193784, Hs.202577, and HLA-DPB1.

9. The method of claim 1 , wherein the HDACi is MS-275 and the mTORi is Rapamycin.

10. The method of claim 1 , wherein detecting the level of expression of the six or more genes comprises:

contacting RNA or cDNA prepared from the blood sample with probes for each of the six or more genes, wherein the probes are spatially arranged in addressable locations on a substrate; and

performing an array analysis to detect the level of expression of the six or more genes.