Journal: Cell Communication and Signaling : CCS

Article Title: THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

doi: 10.1186/s12964-022-00928-x

Figure Lengend Snippet: High CDK7 protein expression is associated with a poor prognosis of GIST. A Based on data from the GSE136755 dataset, the mRNA levels of CDK4, CDK7 and CDK9 were relatively higher than those of other CDKs for CDK1-10. The mRNA level was calculated via GEO2R. B CDK7 expression was significantly elevated in high-risk GISTs based on the data from GSE136755. C Representative scanned images of GIST samples with low or high CDK7 protein expression, as determined by IHC. D Kaplan–Meier survival curves with a risk table showing that high CDK7 protein expression was significantly positively related to poor recurrence-free survival in GIST patients ( P = 0.044)

Article Snippet: IHC staining was performed with anti-CDK7 antibody (#2916, CST).

Techniques: Expressing

Journal: Cell Communication and Signaling : CCS

Article Title: THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

doi: 10.1186/s12964-022-00928-x

Figure Lengend Snippet: Knockdown of CDK7 decreases cell viability and proliferation and induces cell cycle arrest. A Immunoblotting analysis of CDK7 expression after targeting siRNA-mediated CDK7 knockdown in GIST-T1 and GIST-882 cells. A nontargeting siRNA and two independent siRNAs (siRNA1 and siRNA2) are represented by siNC, siCDK7-1, and siCDK7-2. B CCK-8 cell viability assay after CDK7 knockdown in GIST-T1 and GIST-882 cells. C Colony formation assays of GIST-T1 and GIST-882 cells after CDK7 knockdown. D Flow cytometry analysis was used to detect and analyse the cell cycle distribution after CDK7 knockdown. E Immunoblotting analysis of cyclin-D1, CDK4 and γH2AX expression after CDK7 knockdown

Article Snippet: IHC staining was performed with anti-CDK7 antibody (#2916, CST).

Techniques: Knockdown, Western Blot, Expressing, CCK-8 Assay, Viability Assay, Flow Cytometry

Journal: Cell Communication and Signaling : CCS

Article Title: THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

doi: 10.1186/s12964-022-00928-x

Figure Lengend Snippet: CDK7 inhibition leads to the suppression of RNA transcription in GIST cells. A Heatmap showing the change in global active transcripts in GIST-T1 cells following treatment with 50 nmol THZ1 and DMSO for 6 h. B Heatmap showing the transcriptional changes in cell cycle-related genes from the gene set (GOBP_CELL_CYCLE.v7.5.1) in GIST-T1 cells after THZ1 treatment. C The enriched GO functional terms of the transcripts that were reduced over twofold in GIST-T1 cells following treatment with 50 nmol/L THZ1 for 6 h. D Immunoblot analyses of RNAPII, RNAPII CTD phosphorylation (S2, S5, and S7), and CDK7 in GIST-T1 and GIST-882 cells treated either with THZ1 or DMSO at the indicated concentrations for 24 h

Article Snippet: IHC staining was performed with anti-CDK7 antibody (#2916, CST).

Techniques: Inhibition, Functional Assay, Western Blot, Phospho-proteomics

Journal: Cell Communication and Signaling : CCS

Article Title: THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

doi: 10.1186/s12964-022-00928-x

Figure Lengend Snippet: CDK7 inhibition leads to the suppression of c-KIT transcriptional activity and protein expression in GIST cells. A, B qRT–PCR and immunoblotting analysis of c-KIT expression after siRNA-mediated CDK7 knockdown in GIST-T1 and GIST-882 cells. C , D qRT–PCR and immunofluorescence assays showed that c-KIT expression changed after THZ1 treatment in GIST-T1 and GIST-882 cells. E Immunoblotting analysis showed that the expression of c-KIT and downstream ERK and AKT signalling pathway components was inhibited following THZ1 treatment at the indicated concentration in GIST-T1 and GIST-882 cells for 24 h. F Immunoblotting analysis indicated that combination treatment with imatinib and THZ1 enhanced c-KIT expression inhibition in GIST-T1 and GIST-882 cells for 24 h

Article Snippet: IHC staining was performed with anti-CDK7 antibody (#2916, CST).

Techniques: Inhibition, Activity Assay, Expressing, Quantitative RT-PCR, Western Blot, Knockdown, Immunofluorescence, Concentration Assay

Journal: Cell Communication and Signaling : CCS

Article Title: THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

doi: 10.1186/s12964-022-00928-x

Figure Lengend Snippet: CDK7 inhibits c-KIT expression through OSR1 in GIST. A Volcano plot of RNA-seq data displaying the distribution of differential gene expression between THZ1 treatment and DMSO treatment. The upregulated and downregulated genes are highlighted in red and blue, respectively. The results illustrated that OSR1 was the top downregulated gene with the lowest P value. B , C qRT–PCR and immunoblotting analyses showed that OSR1 expression was inhibited by CDK7 knockdown or THZ1 treatment in a dose-dependent manner. OSR1 expression was inhibited by CDK7 knockdown in GIST-T1 and GIST-882 cells. D Gene expression profile in the Oncomine database. The results showed that OSR1 was significantly upregulated in GIST compared with normal gastric tissue. E Gene expression profile in the MediSapiens IST Online transcriptome database. The results showed that OSR1 was uniquely overexpressed in GIST and prostate cancer compared with other cancer types. F Immunoblot analyses of OSR1 expression in clinical sample tissues of GIST, gastrointestinal leiomyoma and schwannoma. The expression of OSR1 was significantly higher in GIST than in leiomyoma and schwannoma. G Data from the MediSapiens database showed that c-KIT and OSR1 expression levels were positively correlated (n = 77, r = 0.407, P < 0.001). H , I qRT–PCR and immunoblotting analyses showed that OSR1 knockdown significantly inhibited c-KIT mRNA and protein expression in GIST-T1 and GIST-882 cells. J Immunoblot analyses showed that OSR1 overexpression promoted c-KIT expression in GIST-T1 and GIST-882 cells. K The inhibitory effect of c-KIT expression was reversed when CDK7 siRNA and OSR1 plasmid were cotransfected into GIST-T1 and GIST-882 cells

Article Snippet: IHC staining was performed with anti-CDK7 antibody (#2916, CST).

Techniques: Expressing, RNA Sequencing, Gene Expression, Quantitative RT-PCR, Western Blot, Knockdown, Over Expression, Plasmid Preparation

Journal: Cell Communication and Signaling : CCS

Article Title: THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours

doi: 10.1186/s12964-022-00928-x

Figure Lengend Snippet: Relationship between CDK7 expression and clinicopathological characteristics of GIST patients

Article Snippet: IHC staining was performed with anti-CDK7 antibody (#2916, CST).

Techniques: Expressing, Modification

Journal: Journal of Biological Chemistry

Article Title: c-Myc Mediates Activation of the cad Promoter via a Post-RNA Polymerase II Recruitment Mechanism

doi: 10.1074/jbc.m109014200

Figure Lengend Snippet: FIG. 6. The c-Myc transactivation domain interacts with P- TEFb. GST fusions of the c-Myc and USF transactivation domains were immobilized on a glutathione column and HeLa nuclear extract was poured over the column. After washing the column, proteins were eluted and analyzed by Western blot using antibodies for cdk7, cyclin H, cdk8, cyclin C, cdk9, and cyclin T1.

Article Snippet: Eluates were analyzed by Western blot analysis with anti-cdk7 sc-529 (Santa Cruz), anti-cyclin H sc-855 (Santa Cruz), anti-cdk8 sc-1521 (Santa Cruz), anti-cyclin C sc-1061 (Santa Cruz), anti-cdk9 sc-7331 (Santa Cruz), and anti-cyclin T1 sc-8128 (Santa Cruz) antibodies.

Techniques: Western Blot

Journal: bioRxiv

Article Title: Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

doi: 10.1101/2025.11.23.690049

Figure Lengend Snippet: ( A ) Chemical structure of Q901. ( B ) Assessment of the covalent binding site was conducted via mass spectrometry analysis of the recombinant CDK7-cyclin H-MAT1 (CAK) trimetric complex. The recombinant CAK complex was incubated with Q901 or DMSO for 1 h, digested for 18 h, and analyzed by mass spectrometry. ( C ) KinMap image illustrating the kinase inhibition profile of Q901 against a panel of 410 kinases (397 protein kinase assays and 13 lipid kinase assays). The inhibition profile was determined by measuring the residual activity at 1 μM for 1 h using the PanQinase® Activity Assay. ATP concentration was set at the apparent ATP-Km value for each kinase. A red dot indicates 99% inhibition of CDK7 by Q901 at this concentration. ( D ) Efficacy and selectivity of Q901 against other CDKs at ATP concentrations corresponding to the apparent ATP-Km value for each kinase. Residual activity (%) was measured after a 1 h incubation with Q901 at the indicated concentrations. ( E ) CDK7 target occupancy assay using Bio-QS, a biotinylated analog of Q901. Cell lysates were prepared from A2780 cells treated with Q901 or DMSO for 4 h at the indicated concentrations and subjected to immunoprecipitation (IP) using Bio-QS and streptavidin agarose beads (SA). IP samples and whole-cell lysates were immunoblotted with an anti-CDK7 antibody. ( F ) Washout-based target occupancy assay to measure the duration of CDK7 inhibition. A2780 cells treated with 6 nM Q901 for 4 h were washed with fresh medium and incubated for the indicated times. Cells were lysed, treated with Bio-QS, and immunoprecipitated with streptavidin agarose beads (SA). The percentage of free CDK7 was calculated by normalizing CDK7 levels in IP samples from Q901 treatment to those in IP samples from the DMSO-treated group (n = 3; two-way ANOVA with Tukey’s multiple comparisons test, data represent mean ± SD).

Article Snippet: The following antibodies were used for ChIP-seq: pan pol II (Cell Signaling Technology, 2629 RRID: AB_2167468), Ser5P (Abcam, Cambridge, UK, ab5408, RRID:AB_304868), Ser2P (Abcam, ab5095, RRID:AB_304749), CDK7 (Bethyl, Montgomery, TX, USA, A300-405A, RRID: AB_2275973), MYC (Cell Signaling Technology, 13987, RRID: AB_2631168), E2F1 (Cell Signaling Technology, 3742, RRID: AB_2096936), and TOP1 (Abcam, ab109374, RRID: AB_10861978).

Techniques: Binding Assay, Mass Spectrometry, Recombinant, Incubation, Inhibition, Activity Assay, Concentration Assay, Immunoprecipitation

Journal: bioRxiv

Article Title: Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

doi: 10.1101/2025.11.23.690049

Figure Lengend Snippet: A ) 1 H NMR spectrum of Q901 was acquired using variable temperature (VT) NMR in DMSO-d□. ( B ) Targeted proteomics analysis to determine the Q901 binding sites on CDK7. The recombinant CAK trimeric complex was incubated with Q901 or DMSO, followed by protease digestion and peptide mapping via LC-MS/MS. Chromatograms show peptide fragments generated by ArgC (Clostripain) digestion (right) and ArgC/Trypsin digestion (left). The expanded boxes highlight the peak of C312 containing peptides, which are reduced following Q901 treatment, indicating covalent modification at this site. ( C ) Representative Western blot images from the pulse-chase assay described in . A2780 cells were treated with 6 nM Q901 for 4 h and then divided into two groups. One group (- wash out) remained in the Q901-containing medium for continuous incubation, while the other group (+ wash out) underwent a drug washout, where the medium was completely removed and replaced with fresh drug-free medium before further incubation for the indicated times. Bio-QS-labeled CDK7 was immunoprecipitated using streptavidin agarose beads (SA), and the levels of free CDK7 were analyzed by immunoblotting. These images in this figure were quantified in .

Article Snippet: The following antibodies were used for ChIP-seq: pan pol II (Cell Signaling Technology, 2629 RRID: AB_2167468), Ser5P (Abcam, Cambridge, UK, ab5408, RRID:AB_304868), Ser2P (Abcam, ab5095, RRID:AB_304749), CDK7 (Bethyl, Montgomery, TX, USA, A300-405A, RRID: AB_2275973), MYC (Cell Signaling Technology, 13987, RRID: AB_2631168), E2F1 (Cell Signaling Technology, 3742, RRID: AB_2096936), and TOP1 (Abcam, ab109374, RRID: AB_10861978).

Techniques: Targeted Proteomics, Binding Assay, Recombinant, Incubation, Liquid Chromatography with Mass Spectroscopy, Generated, Modification, Western Blot, Pulse Chase, Labeling, Immunoprecipitation

Journal: bioRxiv

Article Title: Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

doi: 10.1101/2025.11.23.690049

Figure Lengend Snippet: ( A ) MCF-7 cells were treated with Q901 at the indicated concentrations for 72, 96, or 120 h. Cell viability was measured using the ATP Lite™ system. Inhibition (%) was plotted against the log-transformed Q901 concentration (µM) (n = 3 to 4). Data represent mean ± SD. ( B and C ) RNAPII ChIP-seq was performed following treatment with 100 nM Q901 for the indicated duration. (B) Volcano plot of pan RNAPII ChIP-seq signals after Q901 treatment (n = 2; blue dot indicates p-value ≤ 0.05 and log2FC ≤ -0.58; red dot indicates p-value ≤ 0.05 and log2FC ≥ 0.58). (C) Average ChIP-seq signal plots of various RNAPII forms for genes downregulated by Q901. ( D ) Average CDK7 ChIP-seq signal plots of downregulated and upregulated genes at the TSS. CDK7 ChIP-seq was performed with 100 nM Q901 for the indicated durations.

Article Snippet: The following antibodies were used for ChIP-seq: pan pol II (Cell Signaling Technology, 2629 RRID: AB_2167468), Ser5P (Abcam, Cambridge, UK, ab5408, RRID:AB_304868), Ser2P (Abcam, ab5095, RRID:AB_304749), CDK7 (Bethyl, Montgomery, TX, USA, A300-405A, RRID: AB_2275973), MYC (Cell Signaling Technology, 13987, RRID: AB_2631168), E2F1 (Cell Signaling Technology, 3742, RRID: AB_2096936), and TOP1 (Abcam, ab109374, RRID: AB_10861978).

Techniques: Inhibition, Transformation Assay, Concentration Assay, ChIP-sequencing

Journal: bioRxiv

Article Title: Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

doi: 10.1101/2025.11.23.690049

Figure Lengend Snippet: ( A ) The results of SE calling using the ROSE program with H3K27ac ChIP-seq (GSE62229). ( B ) Expression levels of enhancer target genes (pan RNAPII ChIP-seq; n = 2, Q901 1h treatment condition, data represent mean ± SEM). ( C ) Average fastGRO signals of four enhancer groups. ( D ) GO analysis results of target genes regulated by CDK7-bound SE and CDK7-bound TE. ( E ) Track images showing ChIP-seq signals for H3K27ac, CDK7, pan RNAPII, MYC, and E2F1, along with fastGRO, at a representative CDK7-bound SE region (highlighted in yellow) and it associated target genes.

Article Snippet: The following antibodies were used for ChIP-seq: pan pol II (Cell Signaling Technology, 2629 RRID: AB_2167468), Ser5P (Abcam, Cambridge, UK, ab5408, RRID:AB_304868), Ser2P (Abcam, ab5095, RRID:AB_304749), CDK7 (Bethyl, Montgomery, TX, USA, A300-405A, RRID: AB_2275973), MYC (Cell Signaling Technology, 13987, RRID: AB_2631168), E2F1 (Cell Signaling Technology, 3742, RRID: AB_2096936), and TOP1 (Abcam, ab109374, RRID: AB_10861978).

Techniques: ChIP-sequencing, Expressing

Journal: bioRxiv

Article Title: Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

doi: 10.1101/2025.11.23.690049

Figure Lengend Snippet: ( A ) Average ChIP-seq signal plots of CDK7 and pan RNAPII ChIP-seq across four enhancer groups. ( B ) Average ChIP-seq signal plots for CDK7 and pan RNAPII for protein-coding genes regulated by four enhancer groups. ( C ) Bar graph shows the proportion of downregulated genes in each enhancer groups (Pan RNAPII ChIP-seq; n = 2; p-value ≤ 0.05 and log2FC ≤ -0.58). ( D ) Scatter plot shows the expression levels and log2FC of target genes regulated by CDK7-bound SE and CDK7-bound TE (pan RNAPII ChIP-seq; n = 2; p-value ≤ 0.05).

Article Snippet: The following antibodies were used for ChIP-seq: pan pol II (Cell Signaling Technology, 2629 RRID: AB_2167468), Ser5P (Abcam, Cambridge, UK, ab5408, RRID:AB_304868), Ser2P (Abcam, ab5095, RRID:AB_304749), CDK7 (Bethyl, Montgomery, TX, USA, A300-405A, RRID: AB_2275973), MYC (Cell Signaling Technology, 13987, RRID: AB_2631168), E2F1 (Cell Signaling Technology, 3742, RRID: AB_2096936), and TOP1 (Abcam, ab109374, RRID: AB_10861978).

Techniques: ChIP-sequencing, Expressing

Journal: bioRxiv

Article Title: Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

doi: 10.1101/2025.11.23.690049

Figure Lengend Snippet: ( A and B ) Average ChIP-seq signal plots of CDK7 (A) and pan RNAPII (B) for gene sets related to DNA repair, MYC targets V1, and E2F targets. ( C ) Track image of SRSF6 gene, a representative gene from the DNA repair pathway. ( D ) Track image of RPLP0 gene, a representative gene from the MYC targets V1 pathway. ( E ) Track image of EZH2 gene, a representative gene from the E2F targets pathway. ( F ) Heatmap showing log2FC values of DNA damage/repair genes expression from pan RNAPII ChIP-seq and mRNA-seq data (right; n = 3, FDR ≤ 0.1).

Article Snippet: The following antibodies were used for ChIP-seq: pan pol II (Cell Signaling Technology, 2629 RRID: AB_2167468), Ser5P (Abcam, Cambridge, UK, ab5408, RRID:AB_304868), Ser2P (Abcam, ab5095, RRID:AB_304749), CDK7 (Bethyl, Montgomery, TX, USA, A300-405A, RRID: AB_2275973), MYC (Cell Signaling Technology, 13987, RRID: AB_2631168), E2F1 (Cell Signaling Technology, 3742, RRID: AB_2096936), and TOP1 (Abcam, ab109374, RRID: AB_10861978).

Techniques: ChIP-sequencing, Expressing

Journal: bioRxiv

Article Title: Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

doi: 10.1101/2025.11.23.690049

Figure Lengend Snippet: ( A ) A model illustrating how Q901 enhances the activity of TOP1i and TOP1i-ADCs. (Left) Q901 promotes CDK7 accumulation at the TSS while reducing RNAPII binding. This also decreases MYC and E2F1 binding at the TSS, leading to downregulation of genes involved in the DNA damage response pathway. (Middle) The dual inhibition of CDK7 (by Q901) and TOP1 (by TOP1i) blocks the repair of TOP1i-induced DNA damage, ultimately leading to cell death. (Right) The combination of Q901 and a TOP1i-ADC shows potent enhanced anticancer activity, effectively inducing cancer cell death in vitro and significantly reducing tumor growth in vivo. ( B and C ) HCT116, HER2 ultra low/negative human colon cancer cell line, was treated with Q901, T-DXd (10 μg/ml), or their combination at the indicated concentrations for 72 h (B). Dose-response curves were plotted as a function of log-transformed concentration relative to IC□□ values. Cell viability was measured using the ATP Lite™ system (n = 2, data represent mean ± SD). (C) For in vivo efficacy study, HCT116 cells mixed with Matrigel (1:1) were subcutaneously implanted into BALB/c nude mice. When tumors reached an average size of 117 mm3, mice were randomized into groups (n = 8 per group) and treated with Q901 (10 mg/kg, intraperitoneally once daily), T-DXd alone (10 mg/kg, intravenous single injection on day 0) or the combination. ( D and F ) H292, TROP2 positive human lung cancer cell line, was treated with Q901 in combination with SG at the indicated concentrations for 72 h (D). Dose-response curves were generated using log-transformed concentrations normalized to IC□□ values. Cell viability was assessed using the ATP Lite™ system (n = 2, data represent mean ± SD). ( E and F ) For in vivo efficacy study, H292 cells were mixed with Matrigel (1:1) and implanted subcutaneously into BALB/c nude mice. When tumors reached an average size of 140 mm3, mice were randomized into groups (n = 8 per group) and treated with Q901 (10 or 3 mg/kg, intraperitoneally once daily), SG alone (3 or 10 mg/kg, intravenous single injection on day 1 and 8) or the combination of both. The graph shows the mean tumor volume ± SEM. Statistical significance was calculated using GraphPad Prism software (*: p < 0.01, ****: p < 0.0001 by two-way ANOVA followed by Tukey’s multiple comparison test).

Article Snippet: The following antibodies were used for ChIP-seq: pan pol II (Cell Signaling Technology, 2629 RRID: AB_2167468), Ser5P (Abcam, Cambridge, UK, ab5408, RRID:AB_304868), Ser2P (Abcam, ab5095, RRID:AB_304749), CDK7 (Bethyl, Montgomery, TX, USA, A300-405A, RRID: AB_2275973), MYC (Cell Signaling Technology, 13987, RRID: AB_2631168), E2F1 (Cell Signaling Technology, 3742, RRID: AB_2096936), and TOP1 (Abcam, ab109374, RRID: AB_10861978).

Techniques: Activity Assay, Binding Assay, Inhibition, In Vitro, In Vivo, Transformation Assay, Concentration Assay, Injection, Generated, Software, Comparison

Journal: Frontiers in Oncology

Article Title: PKM2 Interacts With the Cdk1-CyclinB Complex to Facilitate Cell Cycle Progression in Gliomas

doi: 10.3389/fonc.2022.844861

Figure Lengend Snippet: PKM2 physically interacts with the Cdk1-cyclin B complex. (A) Levels (top) and activity (bottom) of Cdk7 in control and PKM2 knock-down U87, T98G and LN319 cells 10 hrs following release from serum deprivation-induced arrest. (B) Levels of cyclin B1, PKM2, and Cdk1 in total cell lysates in control or PKM2 shRNA U87 cells measured at the times indicated following release from serum deprivation-induced arrest. (C) Levels of Cdk1, cyclin B, or PKM2 from Cdk1, cyclin B or PKM2 immunoprecipitates measured at the times indicated following release of control or PKM2 shRNA U87 cells from serum deprivation-induced arrest. Data in M lanes were derived from cells isolated by mitotic shake-off. I:B = Immuno Blot, IP = immunoprecipitate. Bottom panel: Densitometric analysis of Cdk1, cyclin B, or PKM2 levels in U87 cells from Cdk1, cyclin B or PKM2 immunoprecipitates. (D) Western blot analysis of cyclin B1 in control and PKM2 knock-down U87, T98G and LN319 cells. Densitometric analysis (bottom right panel) of western blot demonstrating levels of cyclin B1 in different experimental groups. *p<.05, n=3.

Article Snippet: For Cdk1-cyclin B activity analysis, cell lysates were diluted and pipetted into recombinant Cdc7 pre-coated wells (MBL International Corp), after which Mg2+ and ATP were added, and the amount of phosphorylated substrate was measured by binding to an anti-phospho-Cdk7 (T 376) antibody and a horseradish peroxidase-conjugated anti-mouse IgG.

Techniques: Activity Assay, Control, Knockdown, shRNA, Derivative Assay, Isolation, Western Blot