cdk7 primary antibody  (Cell Signaling Technology Inc)

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: Proteins were transferred to PVDF membranes, blocked with 5% BSA, and immunoblotted with a CDK7 primary antibody (Cell Signaling Technology, 2090S) followed by a secondary HRP-conjugated antibody.

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: Proteins were transferred to PVDF membranes, blocked with 5% BSA, and immunoblotted with a CDK7 primary antibody (Cell Signaling Technology, 2090S) followed by a secondary HRP-conjugated antibody.

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: Proteins were transferred to PVDF membranes, blocked with 5% BSA, and immunoblotted with a CDK7 primary antibody (Cell Signaling Technology, 2090S) followed by a secondary HRP-conjugated antibody.

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: Proteins were transferred to PVDF membranes, blocked with 5% BSA, and immunoblotted with a CDK7 primary antibody (Cell Signaling Technology, 2090S) followed by a secondary HRP-conjugated antibody.

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: Proteins were transferred to PVDF membranes, blocked with 5% BSA, and immunoblotted with a CDK7 primary antibody (Cell Signaling Technology, 2090S) followed by a secondary HRP-conjugated antibody.

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: Proteins were transferred to PVDF membranes, blocked with 5% BSA, and immunoblotted with a CDK7 primary antibody (Cell Signaling Technology, 2090S) followed by a secondary HRP-conjugated antibody.

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: Proteins were transferred to PVDF membranes, blocked with 5% BSA, and immunoblotted with a CDK7 primary antibody (Cell Signaling Technology, 2090S) followed by a secondary HRP-conjugated antibody.

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

Journal: The Journal of investigative dermatology

Article Title: Cyclin-Dependent Kinase 7 Promotes Th17/Th1 Cell Differentiation in Psoriasis by Modulating Glycolytic Metabolism.

doi: 10.1016/j.jid.2021.04.018

Figure Lengend Snippet: Figure 1. CDK7 expression is upregulated in psoriatic CD4D T cells from peripheral blood and lesions. (a) Heat map showing gene expression profiles of differentially expressed proteins in circulating CD4þ T cells from Pso (Psoriasis) compared with age- and sex-matched HC (Healthy) (n ¼ 3 for each group). Colors represent high (red) and low (green) intensity. (b) Representative flow cytometry data showing CDK7 protein expression in circulating CD4þ T cells from Pso and HC. The MFI for CDK7 protein expression was analyzed by flow cytometry (n ¼ 21 for each group, mean SD, two-tailed Student’s t-test, ****P < 0.0001). (c) Correlation of CDK7 protein levels in circulating CD4þ T cells with PASI in Pso (n ¼ 21). The adjusted R2 and P-values are plotted in each graph. P-values were calculated by linear regression. (d) Representative images of immunofluorescence were analyzed for the expression of CD4 (green) and CDK7 (red) in healthy skin and psoriatic lesions. Arrowheads indicate double-positive CD4/CDK7 cells. Nuclei were counterstained with DAPI (blue). Bar ¼ 50 mm (n ¼ 3 for each group). HC, healthy control; MFI, mean fluorescence intensity; HC, healthy control; Pso, patients with psoriasis.

Article Snippet: Cells were stained with PECY7 rat anti-human CD4 antibody (BioLegend, San Diego, CA) for 30 minutes at 4 C, fixed and permeabilized with FOXP3 staining buffer kit (eBioscience, San Diego, CA), and incubated with mouse anti-CDK7 primary antibody (Santa Cruz Biotechnology) for 50 minutes at 4 C. The cells were then washed and stained with secondary FITC anti-mouse IgG antibody (BioLegend) for 30 minutes at 4 C. Gating was performed on single, live, CD4þ T cells.

Techniques: Expressing, Gene Expression, Cytometry, Two Tailed Test, Control

Journal: The Journal of investigative dermatology

Article Title: Cyclin-Dependent Kinase 7 Promotes Th17/Th1 Cell Differentiation in Psoriasis by Modulating Glycolytic Metabolism.

doi: 10.1016/j.jid.2021.04.018

Figure Lengend Snippet: Figure 2. Cdk7 knockdown of CD4D T cells ameliorates psoriasiform symptoms and reduces Th17/Th1 cell differentiation in the IMQ-induced psoriasis-like mouse model. (a) Schematic diagram of mouse experimental protocol. (b) H&E staining of the lesions. Bar ¼ 200 mm. (c) Mean thickness of the epidermis. (d) Representative images of immunofluorescence of IFN-g (green) or IL-17A (green) in the lesions. Bar ¼ 200 mm. (e) qRT-PCR for mRNA expression of Il17a and (f) Ifng in lesional skin. Data are mean SEM. *P < 0.05; ****P < 0.0001. P-values were calculated by one-way ANOVA with Tukey’s post hoc test. n ¼ 5 mice per group. IMQ, imiquimod; NC, normal control; shCDK7, CDK7 short hairpin RNA.

Article Snippet: Cells were stained with PECY7 rat anti-human CD4 antibody (BioLegend, San Diego, CA) for 30 minutes at 4 C, fixed and permeabilized with FOXP3 staining buffer kit (eBioscience, San Diego, CA), and incubated with mouse anti-CDK7 primary antibody (Santa Cruz Biotechnology) for 50 minutes at 4 C. The cells were then washed and stained with secondary FITC anti-mouse IgG antibody (BioLegend) for 30 minutes at 4 C. Gating was performed on single, live, CD4þ T cells.

Techniques: Knockdown, Cell Differentiation, Staining, Quantitative RT-PCR, Expressing, Control, shRNA

Journal: The Journal of investigative dermatology

Article Title: Cyclin-Dependent Kinase 7 Promotes Th17/Th1 Cell Differentiation in Psoriasis by Modulating Glycolytic Metabolism.

doi: 10.1016/j.jid.2021.04.018

Figure Lengend Snippet: Figure 3. Inhibiting CDK7 suppresses CD4D T-cell activation and constrains Th17 and Th1 cell polarization in vitro. (a) Relative mRNA expression of CDK7 gene was measured by qRT-PCR in resting human CD4þ T cells and activated CD4þ T cells from healthy controls stimulated by CD3 and CD28 antibodies for 24 hours (n ¼ 3 for each group). (b) CDK7 gene expression was quantified by qRT-PCR in Th17 and Th1 subsets induced by IL-1b and IL- 23 or IL-12 acquired by in vitro differentiation for 5 days (n ¼ 3 for each group). (c) The percentage of CD69þ cells in the CD4þ T-cell population was evaluated by flow cytometry in human naive CD4þ T cells stimulated with different concentrations of THZ1 (0 nM, 2.5 nM, 5 nM, 10 nM) in the presence of CD3/CD28 antibodies for 24 hours (n ¼ 5 for each group). (d) mRNA expression of IL17A and IFNG (n ¼ 4 for each group). (e) The frequency of IL-17Aþ ROR-gtþ Th17 cells and (f) IFN-gþ T-betþ Th1 cells evaluated by flow cytometry (n ¼ 5 for each group). (g) Correlation of the percentage of ROR-gtþ cells and (h) T-betþ cells in the CD4þ T-cell population with CDK7 MFI (n ¼ 13 for each group). Data are mean SEM. *P < 0.05; **P < 0.01; ***P < 0.001. P-values were calculated by one-way ANOVA with Tukey’s post hoc test (a, b, c, d, e, f) or linear regression (g, h). MFI, mean fluorescence intensity; ns, not significant; Th, T helper type.

Article Snippet: Cells were stained with PECY7 rat anti-human CD4 antibody (BioLegend, San Diego, CA) for 30 minutes at 4 C, fixed and permeabilized with FOXP3 staining buffer kit (eBioscience, San Diego, CA), and incubated with mouse anti-CDK7 primary antibody (Santa Cruz Biotechnology) for 50 minutes at 4 C. The cells were then washed and stained with secondary FITC anti-mouse IgG antibody (BioLegend) for 30 minutes at 4 C. Gating was performed on single, live, CD4þ T cells.

Techniques: Activation Assay, In Vitro, Expressing, Quantitative RT-PCR, Gene Expression, Cytometry

Journal: The Journal of investigative dermatology

Article Title: Cyclin-Dependent Kinase 7 Promotes Th17/Th1 Cell Differentiation in Psoriasis by Modulating Glycolytic Metabolism.

doi: 10.1016/j.jid.2021.04.018

Figure Lengend Snippet: Figure 6. IL-23einduced CDK7 activates the Akt/mTOR/HIF1-a signaling pathway to promote glycolytic metabolism in psoriatic CD4D T cells. (a) Human CD4þ T cells were activated for 2 days in the presence of PBS (normal control) or IL-23 (50 nM)/IL-12 (2.5 ng/ml)/IL-1b (50 nM), respectively, and analyzed for CDK7 expression by flow cytometry. Quantification of MFI of CDK7 is shown (n ¼ 4 for each group). (b) Correlation of CDK7 protein levels in circulating CD4þ

Article Snippet: Cells were stained with PECY7 rat anti-human CD4 antibody (BioLegend, San Diego, CA) for 30 minutes at 4 C, fixed and permeabilized with FOXP3 staining buffer kit (eBioscience, San Diego, CA), and incubated with mouse anti-CDK7 primary antibody (Santa Cruz Biotechnology) for 50 minutes at 4 C. The cells were then washed and stained with secondary FITC anti-mouse IgG antibody (BioLegend) for 30 minutes at 4 C. Gating was performed on single, live, CD4þ T cells.

Techniques: Control, Expressing, Cytometry