CDK

Patient tumor cell sensitivity to combinatorial treatment with histone deacetylase (HDAC)/cyclin-dependent kinase (CDK) inhibitors in 3-D culture. The effect of each drug or drug combination was assessed by fluorescent dye to identify live (green) and dead cells (red). Cells from breast reduction patients were used as non-cancer control in the assay.

Inhibition of CDK5 by roscovitine resulted in defective neuronal migration, which was rescued by expression of GFP-Ndel1 (S251E). a, Granular neurons were treated with roscovitine. Western blotting was performed 24 h after start of culture. Aurora-A and NDEL1 displayed similar expression levels with untreated neurons, whereas the levels of phosphorylated Aurora-A and NDEL1 proteins were decreased after treatment with roscovitine. Relative intensities of the bands of Western blotting are shown at the bottom.

(C) In vivo treatment of Tg:Pomc-Pttg;Pomc-eGFP embryos with small-molecule CDK inhibitors (50 μM) or 0.2% DMSO as control from 18 to 40 hpf. One hundred to one hundred fifty embryos were treated with each compound. Representative images of live embryos are shown with gross morphology (Right) and pituitary Pomc-GFP-positive cells at higher magnification (Left) at 40 hpf. Embryos exposed to flavopiridol developed early developmental defect before pituitary POMC cell ontogeny occurs. (D) Relative expression of pituitary Pomc-eGFP fluorescence analyzed using Volocity 5.2 software (Improvision; mean ±SE of relative expression, n = 7). (E) R-roscovitine specifically suppresses expansion of pituitary POMC cells overexpressing zPttg from 18 to 48 hpf. Double transgenic Tg:Pomc-Pttg;Prl-RFP embryos were generated by breeding Tg:Pomc-Pttg fish with a previously generated PRL-RFP transgenic line, in which RFP was targeted to pituitary lactotrophs by a zebrafish Prolactin promoter (34). Representative fluorescent microscopy of pituitary POMC-eGFP (a and b) and PRL-RFP (c and d) expression in live Tg:Pomc-Pttg; Pomc-eGFP and Tg:Pomc-Pttg;Prl-RFP embryos treated with 0.2% DMSO (a and c) or 50 μM R-roscovitine (b and d). (F) Relative expression of pituitary POMC-eGFP or PRL-RFP fluorescence were analyzed (mean ±SE of relative expression; n = 10). Results represent one of three similar experiments;*P < 0.02 and **P < 0.000005. (Scale bar, 50 μm.)

Comparative efficacy of anticancer therapies (Flavopiridol, vincristine, daunorubicin, et al.) in NMC vs non-NMC cell lines. Mean IC50 (± s.e.m.) of the indicated agents in three NMC (PER-403, PER-624, and PER-704) and two non-NMC cell lines (PER-535 and SAOS2), ***P<0.001, unpaired t-test, corrected for multiple testing.

Hela cell was trypsinized and plated at 30% confluence in DMEM. 16 hours later, MK-8776 (SCH900776) was added at final concentrations of 0, 5, 10 and 25uM. Another 24 hours later, cells were harvested in RIPA with protease and phosphatase inhibitor cocktail. Total protein concentration was measured by BCA method. Lysates equivalent to 20ug total protein were subject to Western Blot, using total- CHK1, pS345-CHK1 and beta-actin (internal control) antibodies.

VEGF and P450 enzyme production in response to FAK or Src inhibitors. MCF10A cells were cultured in LD collagen gels ?vehicle control (V), 10 uM PF-562271 FAK ATP inhibitor (PF) or Src inhibitor PP2 for 24 h. Cells were also lysed and examined for CYP1A1 or CYP4B1 by immunoblot (B and C) and densitometry (D and E). VEGF data are displayed as the mean normalized to the vehicle control, N = 6, 盨EM, *p < 0.003 vs control (A). P450 data are displayed as the mean relative to GAPDH and normalized to the control. N > 4, ±SEM, *p < 0.05 vs respective control (D and E).

Dose-response inhibition of purified human recombinant cyclin-dependent kinase CDK7/cyclin H by inhibitor BS-181 (left panel). Immunoblotting of RNA polymerase II and its phosphorylated form (at Ser5), physiological substrate of CDK7, in MCF-7 cells treated with different doses of inhibitor BS-181 for 24 h (right panel).

B cells were pre-treated with the indicated concentrations of A-674563 for 1h prior to R848 treatment (500 ng/ml).  Thymidine incorporation was analyzed 24h later.

HT29 cells were treated with DMSO control, 1 uM selumetinib (Sel), 5 uM PD0332991 (991), 0.3 uM LY2835219 (219) or serum-free (SF) medium for 48 h. Whole cell extracts were prepared, fractionated by SDS/PAGE and analysed by Western blotting with the indicated antibodies.

Viability at 250 nM and CI vs. Fa for U2932 following 24 hours exposure to ABT-199, additional drugs with activity against CDK9, or the combinations. Mean of quadruplicates ± SEM.

Analysis of apoptosis in leukemia cells induced by LEE011. Annexin V staining of cells following 48-h treatment with LEE011 at 2 or 5 µM compared with DMSO controls. Following 5-µM LEE011 treatment, the K562 apoptotic cell percentage was 5.9 ± 0.75 vs. 1.2 ± 0.66% for the DMSO group, P = 0.001; in MV4-11 cells, the apoptotic cell percentage was 24.2 ± 3.06 vs. 0.53 ± 0.40% for the DMSO group, P = 0.005; in U937 cells, the apoptotic cell percentage was 9.9 ± 2.81 vs. 0.57 ± 0.42% for the DMSO group, P = 0.027; in HL-60 cells, the apoptotic cell percentage was 28.23 ± 6.01 vs. 0.9 ± 0.8% for the DMSO group, P = 0.015; in THP-1 cells, the apoptotic cell percentage was 1.76 ± 0.4 vs. 1.56 ± 0.45% for the DMSO group, P = 0.59; in CCRF cells, the apoptotic cell percentage was 13.77 ± 3.16 vs. 1.2 ± 0.36% for the DMSO group, P = 0.019; in NB4 cells, the apoptotic cell percentage was 12.1 ± 1.35 vs. 0.86 ± 0.25% for the DMSO group, P = 0.004; and in SHI-1 cells the apoptotic cell percentage was 12.6 ± 2.81 vs. 1.87 ± 0.75% for the DMSO group, P = 0.017. These analyses were repeated three times. *P < 0.05; **P < 0.01

VEGF and P450 enzyme production in response to FAK or Src inhibitors. MCF10A cells were cultured in LD collagen gels ?vehicle control (V), 10 uM PF-562271 FAK ATP inhibitor (PF) or Src inhibitor PP2 for 24 h. Cells were also lysed and examined for CYP1A1 or CYP4B1 by immunoblot (B and C) and densitometry (D and E). VEGF data are displayed as the mean normalized to the vehicle control, N = 6, 盨EM, *p < 0.003 vs control (A). P450 data are displayed as the mean relative to GAPDH and normalized to the control. N > 4, ±SEM, *p < 0.05 vs respective control (D and E).

Predicted anticancer drugs inhibit the growth of neuroendocrine tumor cells. Multi-tyrosine kinase inhibitors sorafenib, sunitinib, regorafenib and cabozantinib effectively inhibit GOT1 cell growth with IC50 values in the micromolar range. Inhibitors of AKT (MK-2206), HDAC (vorinostat), HSP90 (alvespimycin) and CDK4/9 (P276-00) also inhibited GOT1 cell growth at micromolar concentrations, whereas inhibition of PARP1 (veliparib) had no effect. GOT1 cells were treated with anticancer drugs at various concentrations for 4 days. Cell viability was estimated using AlamarBlue®. Data points are the mean values of three individual experiments carried out in triplicate (n=9). Fitting of curves was done in GraphPad Prism software v6.04 using log (inhibitor) vs response nonlinear fit with variable slope. IC50 was interpolated at Y=50 and bars denote ±s.d.

Inhibition of CDK9 leads to a decrease in RNApol II activity and repetitive element expression. HEK293T cells were treated with DMSO control and the indicated amounts of LDC000067, a CDK9 inhibitor, for a total of 3 h. (A) Immunoblots showing the levels of phosphorylated RNApol II largest subunit (pRPB1), total RPB1 and GAPDH, in response to different doses of CDK9 inhibitor. (B) Quantification of immunoblots from 2 independent experiments in which each condition was performed in duplicates, and in which pRPB1 and total RPB1 protein levels were normalized to GAPDH or as pRPB1/Total RPB1 ratio. (C, D) qRT-PCR analyses show a significant response to CDK9 inhibition of repetitive elements belonging to the LTR (C) and SINE (D) classes. Statistical analyses were performed to compare all groups using a One-way ANOVA followed by Bonforreoni’s multiple comparison test, *P < 0.05, **P < 0.01, #P < 0.0001.

Patient tumor cell sensitivity to combinatorial treatment with histone deacetylase (HDAC)/cyclin-dependent kinase (CDK) inhibitors in 3-D culture. The effect of each drug or drug combination was assessed by fluorescent dye to identify live (green) and dead cells (red). Cells from breast reduction patients were used as non-cancer control in the assay.

Inhibition of CDK5 by roscovitine resulted in defective neuronal migration, which was rescued by expression of GFP-Ndel1 (S251E). a, Granular neurons were treated with roscovitine. Western blotting was performed 24 h after start of culture. Aurora-A and NDEL1 displayed similar expression levels with untreated neurons, whereas the levels of phosphorylated Aurora-A and NDEL1 proteins were decreased after treatment with roscovitine. Relative intensities of the bands of Western blotting are shown at the bottom.

(C) In vivo treatment of Tg:Pomc-Pttg;Pomc-eGFP embryos with small-molecule CDK inhibitors (50 μM) or 0.2% DMSO as control from 18 to 40 hpf. One hundred to one hundred fifty embryos were treated with each compound. Representative images of live embryos are shown with gross morphology (Right) and pituitary Pomc-GFP-positive cells at higher magnification (Left) at 40 hpf. Embryos exposed to flavopiridol developed early developmental defect before pituitary POMC cell ontogeny occurs. (D) Relative expression of pituitary Pomc-eGFP fluorescence analyzed using Volocity 5.2 software (Improvision; mean ±SE of relative expression, n = 7). (E) R-roscovitine specifically suppresses expansion of pituitary POMC cells overexpressing zPttg from 18 to 48 hpf. Double transgenic Tg:Pomc-Pttg;Prl-RFP embryos were generated by breeding Tg:Pomc-Pttg fish with a previously generated PRL-RFP transgenic line, in which RFP was targeted to pituitary lactotrophs by a zebrafish Prolactin promoter (34). Representative fluorescent microscopy of pituitary POMC-eGFP (a and b) and PRL-RFP (c and d) expression in live Tg:Pomc-Pttg; Pomc-eGFP and Tg:Pomc-Pttg;Prl-RFP embryos treated with 0.2% DMSO (a and c) or 50 μM R-roscovitine (b and d). (F) Relative expression of pituitary POMC-eGFP or PRL-RFP fluorescence were analyzed (mean ±SE of relative expression; n = 10). Results represent one of three similar experiments;*P < 0.02 and **P < 0.000005. (Scale bar, 50 μm.)

Comparative efficacy of anticancer therapies (Flavopiridol, vincristine, daunorubicin, et al.) in NMC vs non-NMC cell lines. Mean IC50 (± s.e.m.) of the indicated agents in three NMC (PER-403, PER-624, and PER-704) and two non-NMC cell lines (PER-535 and SAOS2), ***P<0.001, unpaired t-test, corrected for multiple testing.

Hela cell was trypsinized and plated at 30% confluence in DMEM. 16 hours later, MK-8776 (SCH900776) was added at final concentrations of 0, 5, 10 and 25uM. Another 24 hours later, cells were harvested in RIPA with protease and phosphatase inhibitor cocktail. Total protein concentration was measured by BCA method. Lysates equivalent to 20ug total protein were subject to Western Blot, using total- CHK1, pS345-CHK1 and beta-actin (internal control) antibodies.

VEGF and P450 enzyme production in response to FAK or Src inhibitors. MCF10A cells were cultured in LD collagen gels ?vehicle control (V), 10 uM PF-562271 FAK ATP inhibitor (PF) or Src inhibitor PP2 for 24 h. Cells were also lysed and examined for CYP1A1 or CYP4B1 by immunoblot (B and C) and densitometry (D and E). VEGF data are displayed as the mean normalized to the vehicle control, N = 6, 盨EM, *p < 0.003 vs control (A). P450 data are displayed as the mean relative to GAPDH and normalized to the control. N > 4, ±SEM, *p < 0.05 vs respective control (D and E).

Dose-response inhibition of purified human recombinant cyclin-dependent kinase CDK7/cyclin H by inhibitor BS-181 (left panel). Immunoblotting of RNA polymerase II and its phosphorylated form (at Ser5), physiological substrate of CDK7, in MCF-7 cells treated with different doses of inhibitor BS-181 for 24 h (right panel).

B cells were pre-treated with the indicated concentrations of A-674563 for 1h prior to R848 treatment (500 ng/ml).  Thymidine incorporation was analyzed 24h later.

HT29 cells were treated with DMSO control, 1 uM selumetinib (Sel), 5 uM PD0332991 (991), 0.3 uM LY2835219 (219) or serum-free (SF) medium for 48 h. Whole cell extracts were prepared, fractionated by SDS/PAGE and analysed by Western blotting with the indicated antibodies.

Viability at 250 nM and CI vs. Fa for U2932 following 24 hours exposure to ABT-199, additional drugs with activity against CDK9, or the combinations. Mean of quadruplicates ± SEM.

Analysis of apoptosis in leukemia cells induced by LEE011. Annexin V staining of cells following 48-h treatment with LEE011 at 2 or 5 µM compared with DMSO controls. Following 5-µM LEE011 treatment, the K562 apoptotic cell percentage was 5.9 ± 0.75 vs. 1.2 ± 0.66% for the DMSO group, P = 0.001; in MV4-11 cells, the apoptotic cell percentage was 24.2 ± 3.06 vs. 0.53 ± 0.40% for the DMSO group, P = 0.005; in U937 cells, the apoptotic cell percentage was 9.9 ± 2.81 vs. 0.57 ± 0.42% for the DMSO group, P = 0.027; in HL-60 cells, the apoptotic cell percentage was 28.23 ± 6.01 vs. 0.9 ± 0.8% for the DMSO group, P = 0.015; in THP-1 cells, the apoptotic cell percentage was 1.76 ± 0.4 vs. 1.56 ± 0.45% for the DMSO group, P = 0.59; in CCRF cells, the apoptotic cell percentage was 13.77 ± 3.16 vs. 1.2 ± 0.36% for the DMSO group, P = 0.019; in NB4 cells, the apoptotic cell percentage was 12.1 ± 1.35 vs. 0.86 ± 0.25% for the DMSO group, P = 0.004; and in SHI-1 cells the apoptotic cell percentage was 12.6 ± 2.81 vs. 1.87 ± 0.75% for the DMSO group, P = 0.017. These analyses were repeated three times. *P < 0.05; **P < 0.01

VEGF and P450 enzyme production in response to FAK or Src inhibitors. MCF10A cells were cultured in LD collagen gels ?vehicle control (V), 10 uM PF-562271 FAK ATP inhibitor (PF) or Src inhibitor PP2 for 24 h. Cells were also lysed and examined for CYP1A1 or CYP4B1 by immunoblot (B and C) and densitometry (D and E). VEGF data are displayed as the mean normalized to the vehicle control, N = 6, 盨EM, *p < 0.003 vs control (A). P450 data are displayed as the mean relative to GAPDH and normalized to the control. N > 4, ±SEM, *p < 0.05 vs respective control (D and E).

Predicted anticancer drugs inhibit the growth of neuroendocrine tumor cells. Multi-tyrosine kinase inhibitors sorafenib, sunitinib, regorafenib and cabozantinib effectively inhibit GOT1 cell growth with IC50 values in the micromolar range. Inhibitors of AKT (MK-2206), HDAC (vorinostat), HSP90 (alvespimycin) and CDK4/9 (P276-00) also inhibited GOT1 cell growth at micromolar concentrations, whereas inhibition of PARP1 (veliparib) had no effect. GOT1 cells were treated with anticancer drugs at various concentrations for 4 days. Cell viability was estimated using AlamarBlue®. Data points are the mean values of three individual experiments carried out in triplicate (n=9). Fitting of curves was done in GraphPad Prism software v6.04 using log (inhibitor) vs response nonlinear fit with variable slope. IC50 was interpolated at Y=50 and bars denote ±s.d.

Inhibition of CDK9 leads to a decrease in RNApol II activity and repetitive element expression. HEK293T cells were treated with DMSO control and the indicated amounts of LDC000067, a CDK9 inhibitor, for a total of 3 h. (A) Immunoblots showing the levels of phosphorylated RNApol II largest subunit (pRPB1), total RPB1 and GAPDH, in response to different doses of CDK9 inhibitor. (B) Quantification of immunoblots from 2 independent experiments in which each condition was performed in duplicates, and in which pRPB1 and total RPB1 protein levels were normalized to GAPDH or as pRPB1/Total RPB1 ratio. (C, D) qRT-PCR analyses show a significant response to CDK9 inhibition of repetitive elements belonging to the LTR (C) and SINE (D) classes. Statistical analyses were performed to compare all groups using a One-way ANOVA followed by Bonforreoni’s multiple comparison test, *P < 0.05, **P < 0.01, #P < 0.0001.