Journal: eLife

Article Title: Distinct and diverse chromatin proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions

doi: 10.7554/eLife.73524

Figure Lengend Snippet:

Article Snippet: Antibody , Anti-RNF20 (rabbit polyclonal) , Cell Signaling Technology , Cat# 9425S;RRID: AB_2797700 , WB (1:1000).

Techniques: Software

Journal: eLife

Article Title: Distinct and diverse chromatin proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions

doi: 10.7554/eLife.73524

Figure Lengend Snippet:

Article Snippet: Antibody , Anti-RNF20 (rabbit polyclonal) , Cell Signaling Technology , Cat# 9425S;RRID: AB_2797700 , WB (1:1000).

Techniques: Software

Journal: Cancer Cell

Article Title: Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

doi: 10.1016/j.ccell.2020.03.001

Figure Lengend Snippet: In Vivo Screen Identifies CHD1 as Top Candidate Responsible for Resistance to Antiandrogen (A) Graphical representation of analyzed results of the library screen, using RIGER-E method. –Log10 of p value is presented and the area of p < 0.0001 is highlighted. The top eight candidate genes are presented as large red dots with gene symbol. Negative control gene TBC1D4 is presented as a large green dot. (B) Graphical representation of the percentage of tumors which have shRNAs targeting a specific gene and are enriched in resistant tumors. (C) Graphical representation of the number of genes which have multiple independent shRNAs enriched in resistant tumors. (D) Bee swarm plot of the normalized shRNA read counts of a representative pool in the plasmid, pregraft, and resistant tumors, median is presented as a red line (medians below 1 are not presented on log2 scale). shCHD1s are presented as large red dots. See also .

Article Snippet: Antibodies used for western blot are (also listed in ): (1) CHD1 (D8C2) Rabbit mAb, Cell Signaling, Cat #4351 (2) AR Antibody (N-20), Santa Cruz, sc-816 (3) KLK3 (D6B1) XP® Rabbit mAb, Cell Signaling, Cat # 5365 (4) PMEPA1 Antibody (P-15), Santa Cruz, Cat # sc-85829 (5) STEAP Antibody (B-4), Santa Cruz, Cat # sc-271872 (6) β-Actin (13E5) Rabbit mAb, Cell Signaling, Cat # 4970 (7) Glucocorticoid Receptor (D6H2L) XP® Rabbit mAb, Cell Signaling, Cat #12041 (8) SGK1 (D27C11) Rabbit mAb, Cell Signaling, Cat #12103 (9) c-Myc (D84C12) Rabbit mAb, Cell Signaling, Cat #5605

Techniques: In Vivo, Negative Control, shRNA, Plasmid Preparation

Journal: Cancer Cell

Article Title: Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

doi: 10.1016/j.ccell.2020.03.001

Figure Lengend Snippet: CHD1 Loss Confers Significant Resistance to Antiandrogen In Vitro and In Vivo (A) Western blot of CHD1 in LNCaP/AR cells transduced with annotated guide RNAs. (B) Relative cell number of LNCaP/AR cells transduced with annotated guide RNAs, normalized to sgNT + Veh group. Cells were treated with 10 μM enzalutamide (Enz) or DMSO (Veh) for 7 days and cell numbers were counted. p values were calculated using multiple t tests, three biological replicates in each group. (C) Histograms of representative fluorescence-activated cell sorting-based competition assay showing the distribution of shNT LNCaP/AR cells (GFP-negative) compared with cells transduced with cis -linked shCHD1-GFP or shNT-GFP shRNAs (GFP positive). The distribution on day 0 is shown in red and day 7 is shown in blue. (D) Relative cell number fold change compared with shNT group, based on the results of (C). Enz denotes enzalutamide of 10 μM and Veh denotes DMSO. p values were calculated using two-way ANOVA, three biological replicates in each group. (E) Tumor growth curve of xenografted LNCaP/AR cells transduced with annotated guide RNAs. Enz denotes enzalutamide treatment at 10 mg/kg from day 1 of grafting. Veh denotes 0.5% CMC + 0.1% Tween 80. p values were calculated using two-way ANOVA. For all panels, mean ± SEM is presented. ∗∗∗∗ p < 0.0001, ∗∗∗ p < 0.001, ∗∗ p < 0.01, ∗ p < 0.05. See also and .

Article Snippet: Antibodies used for western blot are (also listed in ): (1) CHD1 (D8C2) Rabbit mAb, Cell Signaling, Cat #4351 (2) AR Antibody (N-20), Santa Cruz, sc-816 (3) KLK3 (D6B1) XP® Rabbit mAb, Cell Signaling, Cat # 5365 (4) PMEPA1 Antibody (P-15), Santa Cruz, Cat # sc-85829 (5) STEAP Antibody (B-4), Santa Cruz, Cat # sc-271872 (6) β-Actin (13E5) Rabbit mAb, Cell Signaling, Cat # 4970 (7) Glucocorticoid Receptor (D6H2L) XP® Rabbit mAb, Cell Signaling, Cat #12041 (8) SGK1 (D27C11) Rabbit mAb, Cell Signaling, Cat #12103 (9) c-Myc (D84C12) Rabbit mAb, Cell Signaling, Cat #5605

Techniques: In Vitro, In Vivo, Western Blot, Transduction, Fluorescence, FACS, Competitive Binding Assay

Journal: Cancer Cell

Article Title: Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

doi: 10.1016/j.ccell.2020.03.001

Figure Lengend Snippet: CHD1 mRNA Level Is Correlated with Clinical Outcome of Antiandrogen Treatment (A) Pearson correlation analysis of CHD1 mRNA and time of treatment on abiraterone (Abi)/enzalutamide (Enz)/apalutamide (Apa) of a 52 mCRPC patient cohort. (B) CHD1 expression distribution in all patients of the cohort in (A). (C) Probability of treatment duration of the top quartile compared with bottom quartile of all patients treated with abiraterone (Abi)/enzalutamide (Enz)/apalutamide (Apa); p value was calculated using Mantel-Cox test. (D) Cox hazard ratio analysis of the top and bottom quartile of all patients, p value was calculated using log rank test. (E) Probability of treatment duration of the above median compared with below median of patients who received enzalutamide (Enz)/apalutamide (Apa), p value was calculated using Mantel-Cox test. (F) Probability of treatment duration of the above median compared with below median of patients who received abiraterone (Abi), p value was calculated using Mantel-Cox test. (G) Pearson correlation analysis of CHD1 mRNA and time of treatment on patients who received enzalutamide (Enz)/apalutamide (Apa), n = 21 (2 patients received both apalutamide and abiraterone). (H) Pearson correlation analysis of CHD1 mRNA and time of treatment on patients who received abiraterone (Abi), n = 33.

Article Snippet: Antibodies used for western blot are (also listed in ): (1) CHD1 (D8C2) Rabbit mAb, Cell Signaling, Cat #4351 (2) AR Antibody (N-20), Santa Cruz, sc-816 (3) KLK3 (D6B1) XP® Rabbit mAb, Cell Signaling, Cat # 5365 (4) PMEPA1 Antibody (P-15), Santa Cruz, Cat # sc-85829 (5) STEAP Antibody (B-4), Santa Cruz, Cat # sc-271872 (6) β-Actin (13E5) Rabbit mAb, Cell Signaling, Cat # 4970 (7) Glucocorticoid Receptor (D6H2L) XP® Rabbit mAb, Cell Signaling, Cat #12041 (8) SGK1 (D27C11) Rabbit mAb, Cell Signaling, Cat #12103 (9) c-Myc (D84C12) Rabbit mAb, Cell Signaling, Cat #5605

Techniques: Expressing

Journal: Cancer Cell

Article Title: Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

doi: 10.1016/j.ccell.2020.03.001

Figure Lengend Snippet: CHD1 Loss Enhanced Prostate Cancer Cell Heterogeneity and Lineage Plasticity (A) Heatmap represents the expression fold changes (qPCR) of the top four resistance driver genes and CHD1 in different xenografts derived cell lines, three technical replicates for each line. (B) Heatmap represents the expression fold changes of the top four resistant driver genes (qPCR) in shCHD1 cell line treated with 10 μM enzalutamide (Enz) in charcoal-stripped serum medium, three biological replicates for each line. (C) Unsupervised clustering of 212 patients based on the gene expression level ( Z score) of CHD1 and the 4 TFs. (D) Relative gene expression level (qPCR) of lineage-specific markers and EMT genes in selective shCHD1-XE and sgCHD1-XE cell lines, three technical replicates for each line. See also Figure S7 .

Article Snippet: Antibodies used for western blot are (also listed in ): (1) CHD1 (D8C2) Rabbit mAb, Cell Signaling, Cat #4351 (2) AR Antibody (N-20), Santa Cruz, sc-816 (3) KLK3 (D6B1) XP® Rabbit mAb, Cell Signaling, Cat # 5365 (4) PMEPA1 Antibody (P-15), Santa Cruz, Cat # sc-85829 (5) STEAP Antibody (B-4), Santa Cruz, Cat # sc-271872 (6) β-Actin (13E5) Rabbit mAb, Cell Signaling, Cat # 4970 (7) Glucocorticoid Receptor (D6H2L) XP® Rabbit mAb, Cell Signaling, Cat #12041 (8) SGK1 (D27C11) Rabbit mAb, Cell Signaling, Cat #12103 (9) c-Myc (D84C12) Rabbit mAb, Cell Signaling, Cat #5605

Techniques: Expressing, Derivative Assay

Journal: Cancer Cell

Article Title: Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

doi: 10.1016/j.ccell.2020.03.001

Figure Lengend Snippet: GR Inhibition Has Significant Antitumor Effect on Antiandrogen-Resistant Tumors with CHD1 Loss (A) Relative gene expression of NR3C1 and GR target genes in tumors collected from LNCaP/AR xenografts, all normalized and compared with shNT + Veh group. Mean ± SEM is presented. p values were calculated using two-way ANOVA, and numbers of biological replicates are presented. (B) Western blot showing AR, GR, and their downstream target genes in xenografted LNCaP/AR tumors. For (A) and (B), Enz denotes enzalutamide at 10 mg/kg from day 1 of grafting. Veh denotes 0.5% CMC + 0.1% Tween 80. (C) Histograms of representative FACS-based competition assay showing the distribution of shCHD1-XE-1 cells (RFP-negative) versus shCHD1-XE-1 cells transduced with shGR (RFP-positive). The distributions on different days are presented in different colors. (D) Relative cell number of shCHD1-XE-1 cells transduced with annotated inducible shRNAs, normalized to shCHD1-XE-1 + Veh. Cells were treated with 250 ng/mL doxycycline for 48 h, and then 7 days of 10 μM enzalutamide (Enz) or DMSO (Veh) before cell numbers were counted. Mean ± SEM is presented, and p values were calculated by two-way ANOVA, with three biological replicates in each group. (E) Model depicting the chromatin dysregulation (plasticity) and antiandrogen resistance in mCRPC due to CHD1 loss. For all panels, ∗∗∗∗ p < 0.0001, ∗∗∗ p < 0.001, ∗∗ p < 0.01, ∗ p < 0.05. See also Figure S8 .

Article Snippet: Antibodies used for western blot are (also listed in ): (1) CHD1 (D8C2) Rabbit mAb, Cell Signaling, Cat #4351 (2) AR Antibody (N-20), Santa Cruz, sc-816 (3) KLK3 (D6B1) XP® Rabbit mAb, Cell Signaling, Cat # 5365 (4) PMEPA1 Antibody (P-15), Santa Cruz, Cat # sc-85829 (5) STEAP Antibody (B-4), Santa Cruz, Cat # sc-271872 (6) β-Actin (13E5) Rabbit mAb, Cell Signaling, Cat # 4970 (7) Glucocorticoid Receptor (D6H2L) XP® Rabbit mAb, Cell Signaling, Cat #12041 (8) SGK1 (D27C11) Rabbit mAb, Cell Signaling, Cat #12103 (9) c-Myc (D84C12) Rabbit mAb, Cell Signaling, Cat #5605

Techniques: Inhibition, Expressing, Western Blot, Competitive Binding Assay, Transduction

Journal: Cancer Cell

Article Title: Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation

doi: 10.1016/j.ccell.2020.03.001

Figure Lengend Snippet:

Article Snippet: Antibodies used for western blot are (also listed in ): (1) CHD1 (D8C2) Rabbit mAb, Cell Signaling, Cat #4351 (2) AR Antibody (N-20), Santa Cruz, sc-816 (3) KLK3 (D6B1) XP® Rabbit mAb, Cell Signaling, Cat # 5365 (4) PMEPA1 Antibody (P-15), Santa Cruz, Cat # sc-85829 (5) STEAP Antibody (B-4), Santa Cruz, Cat # sc-271872 (6) β-Actin (13E5) Rabbit mAb, Cell Signaling, Cat # 4970 (7) Glucocorticoid Receptor (D6H2L) XP® Rabbit mAb, Cell Signaling, Cat #12041 (8) SGK1 (D27C11) Rabbit mAb, Cell Signaling, Cat #12103 (9) c-Myc (D84C12) Rabbit mAb, Cell Signaling, Cat #5605

Techniques: Recombinant, SYBR Green Assay, Bicinchoninic Acid Protein Assay, Transfection, Purification, Cell Viability Assay, Software

Journal: Molecular cancer research : MCR

Article Title: Targeting USP22 Suppresses Tumorigenicity and Enhances Cisplatin Sensitivity Through ALDH1A3 Downregulation in Cancer-initiating Cells from Lung Adenocarcinoma

doi: 10.1158/1541-7786.MCR-18-0042

Figure Lengend Snippet: A. Images of tumorspheres from 3 lung adenocarcinoma tissues (Samples 1, 2, and 3). B. Western Blot analysis of CD133 (as a surface biomarker of CICs), CD44 (as another surface biomarker of CICs), USP22, RNF20, and H2Bub1, shows enriched USP22 protein in tumorspheres compared to original cancer tissues. C. Flow cytometry analysis of CD133 expression demonstrates a strong CD133 expression in about 30% of tumorsphere cells. D. Western Blot analysis demonstrates USP22 is markedly elevated, while H2Bub1 were significantly deceased in CD133+ cancer cells compared to CD133− cells sorted from tumorspheres. E. Flow cytometry analysis of CD44 expression demonstrates a strong CD44 expression in about 12% to 44% of tumorsphere cells. F. Western Blot analysis demonstrates USP22 and CD133 are markedly elevated, while H2Bub1 and RNF20 were markedly or moderately deceased in CD44+ cancer cells compared to CD44− cells sorted from tumorspheres. G. Mouse xenografts generated by both CD133− and CD133+ cancer cells isolated from tumorspheres, indicating CD133+ cells may represent CICs with stem cell characteristics in tumorspheres.

Article Snippet: Rabbit anti-RNF20 antibody (#9425) was purchased from Cell Signaling Technology (Beverly, CA, USA).

Techniques: Western Blot, Biomarker Assay, Flow Cytometry, Expressing, Generated, Isolation

Journal: Molecular cancer research : MCR

Article Title: Targeting USP22 Suppresses Tumorigenicity and Enhances Cisplatin Sensitivity Through ALDH1A3 Downregulation in Cancer-initiating Cells from Lung Adenocarcinoma

doi: 10.1158/1541-7786.MCR-18-0042

Figure Lengend Snippet: A. Morphology changes of tumorspheres in differentiating culture medium (left panel); Western Blot analysis of USP22, CD133, RNF20 and H2Bub1 in tumorspheres in differentiating conditions (right panel). B. Western Blot analysis of USP22, CD133 and H2Bub1 in GFP-CTRL and USP22-KD cells (left panel); Quantitative analysis of tumorsphere formation upon USP22 knockdown, GFP-CTRL for cells transfected with control shRNA, USP22-KD for specific shRNA targeting USP22 (**P < 0.01, compared with Control, middle panel) and Tumorspheres (right panel). C. In vivo tumorigenesis of GFP-CTRL and USP22-KD tumorsphere cells, demonstrating USP22 knockdown suppressed both tumorsphere formation and tumorigenesis of lung adenocarcinoma CICs.

Article Snippet: Rabbit anti-RNF20 antibody (#9425) was purchased from Cell Signaling Technology (Beverly, CA, USA).

Techniques: Western Blot, Transfection, shRNA, In Vivo