Journal: iScience

Article Title: Systematic fine-mapping and functional studies of prostate cancer risk variants

doi: 10.1016/j.isci.2023.106497

Figure Lengend Snippet: Key resources table

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-H3K27ac Abcam Cat# ab4729 RRID: AB_2118291 Chemicals, peptides, and recombinant proteins Biotin-dATP Thermo Fisher Cat# 19524016 Critical commercial assays TRIzol reagent Thermo Fisher Cat# 15596018 Streptavidin C-1 beads Life Technologies Cat# 65002 Dynabeads Protein G Invitrogen Cat#10004D Dual-Luciferase Reporter Assay System kit Promega Cat# E1910 PrimeScript RT reagent with a gDNA eraser Kit Takara Cat# RR047B Deposited data Prostate Cancer GWAS summary statistics GRASP https://grasp.nhlbi.nih.gov/Covid19GWASResults.aspx Epigenomic profiles CistromeDB http://cistrome.org/db/#/ 22Rv1 HiC This paper GSE197820 H3K27ac ChIP-seq This paper GSE197820 4C-seq This paper GSE197820 RNA-seq This paper GSE197820 PolII ChIA-PET (Ramanand et al., 2020) 36 GSE121020 Experimental models: Cell lines 22Rv1 ATCC Cat# CRL-2505 LNCaP ATCC Cat# CRL-1740 C4-2B ATCC Cat# CRL-3315 Oligonucleotides Primers are listed in Table S6 This paper N/A Recombinant DNA Plasmid: pGL3 Promoter vector Promega Cat# E1761 Plasmid: pGL3 basic vector Promega Cat# E1751 Plasmid: pRL-TK Renilla luciferase vector Promega Cat# E2241 Plasmid: pSpcas9n(sgRNAs) addgene Cat# 62987 Plasmid: pLVX-puro This paper N/A Software and algorithms GraphPad Prism9 GraphPad software https://www.graphpad.com ImageJ NIH https://imagej.nih.gov/ij Python (v3.7) The Python Language https://www.python.org GCTA (v1.94.0) (Yang et al., 2012) 53 https://yanglab.westlake.edu.cn/software/gcta/ FINEMAP (v1.4.1) (Benner et al., 2016) 54 http://www.christianbenner.com HiC-Pro (v3.0.0) (Servant et al., 2015) 55 https://github.com/nservant/HiC-Pro HiCRep (v0.2.6) (Yang et al., 2017) 56 https://github.com/dejunlin/hicrep FitHiC (v1.1.3) (Ay et al., 2014) 57 https://github.com/ay-lab/fithic FAN-C (Kruse et al., 2020) 58 https://github.com/vaquerizaslab/fanc VEP (release 96) (McLaren et al., 2016) 37 https://www.ensembl.org/info/docs/tools/vep/script/index.html BWA (v0.7.17) (Li and Durbin, 2009) 59 https://github.com/lh3/bwa Htseq (v0.11.3) (Anders et al., 2015) 60 https://github.com/simon-anders/htseq DEseq2 (v1.38.3) (Love et al., 2014) 61 https://bioconductor.org/packages/release/bioc/html/DESeq2.html DAVID (Huang da et al., 2009) 62 http://david.abcc.ncifcrf.gov/ Open in a separate window Key resources table .

Techniques: Recombinant, Reporter Assay, Plasmid Preparation, Luciferase, Software

Journal: Theranostics

Article Title: Bruceantin targets HSP90 to overcome resistance to hormone therapy in castration-resistant prostate cancer

doi: 10.7150/thno.51478

Figure Lengend Snippet: BCT downregulates AR-FL/AR-V7 levels through the ubiquitin-proteasome pathway. (A, B) Prostate cancer cells were treated with indicated concentrations (A) and time points (B) of BCT, and cell lysates were analyzed by immunoblot with indicated antibodies. (C) Immunoblot analyses of AR-FL, AR-V7, and HSPs in 22RV1 xenograft tumors treated p.o. with vehicle or BCT. (D, E) LNCaP, C4-2B (D), and 22RV1 (E) cells were treated with cycloheximide (CHX) and BCT as indicated for indicated time periods, and immunoblots were performed with indicated antibodies. (F) 22RV1 cells were treated with 10 nM BCT and 10 μM MG132 as indicated for indicated time periods, and immunoblots were performed with indicated antibodies. (G, H) 22RV1 cell lysates treated with BCT and MG132 as indicated for 4 h were immunoprecipitated with anti-AR (G) or anti-AR-V7 (H) antibody and immunoblotted with indicated antibodies.

Article Snippet: All cell lines used, except C4-2B-MDVR (an ENZ-resistant C4-2B cell line), were purchased from American Type Culture Collection (ATCC) or Korean Cell Line Bank (KCLB).

Techniques: Western Blot, Immunoprecipitation

Journal: Cell Cycle

Article Title: Discovery of thalicthuberine as a novel antimitotic agent from nature that disrupts microtubule dynamics and induces apoptosis in prostate cancer cells

doi: 10.1080/15384101.2017.1356512

Figure Lengend Snippet: Measurement of cytotoxic activity of TH against a panel of human malignant and non-malignant cell lines of the prostate and cervix.

Article Snippet: LNCaP (lymph node metastasis), C4–2B (LNCaP-derivative) and PC-3 (metastatic prostate cancer) cells were obtained from the American Type Culture Collection (ATCC).

Techniques: Activity Assay

Journal: PLoS ONE

Article Title: IGF-IR Promotes Prostate Cancer Growth by Stabilizing α 5 β 1 Integrin Protein Levels

doi: 10.1371/journal.pone.0076513

Figure Lengend Snippet: (A) LNCaP and C4-2B cells were transfected with either control siRNA or IGF-IR siRNA and 24 h later, cells were trypsinized and counted. Cells were replated in triplicates at 3×10 5 cells per well in 6-well plates with 2% CSS-containing medium in the presence of 1 nM R1881, harvested and counted at day 1, 2 and 3 after re-plating. Each experimental assay was carried out in triplicates and error bars represent standard deviation from three independent values ( * P<0.01), relative to respective control siRNA treatments. A parallel set of LNCaP and C4-2B cell lysates was analyzed for efficiency of IGF-IR and β 1 integrin subunit downregulation by immunoblotting (lower panels). (B) Representative images of relative C4-2B cell densities on day 2 and day 3 are shown.

Article Snippet: LNCaP and C4-2B cells were purchased from ATCC.

Techniques: Transfection, Standard Deviation, Western Blot

Journal: PLoS ONE

Article Title: Inhibition of β2-Microglobulin/Hemochromatosis Enhances Radiation Sensitivity by Induction of Iron Overload in Prostate Cancer Cells

doi: 10.1371/journal.pone.0068366

Figure Lengend Snippet: A. Iron staining in control and anti-β2-M Ab (5 µg/ml) treated cells using iron staining kit in ARCaP M prostate cancer cell lines. B. Mitochondrial superoxide levels in response to anti-β2-M Ab treatment in a time and dose dependent manner in i. ARCaP M , ii. ARCaP E prostate cancer cell lines (***p<0.001, Student’s t test) and iii. p69 immortalized prostate epithelial cells using MitoSOX dye. C. Mitochondrial superoxide in ARCaP M , KD HFE1 and KD HFE3 using MitoSOX dye (*p<0.05, Student’s t test). D. Expression of stress response proteins and DNA repair enzymes in C4-2B Neo control and β2-M knockdown cell lines. i. β2-M protein expression, ii. HSP27 and HSP70 protein expression and iii. NUDT1 and MPG protein expression. NUDT1 and MPG protein expression in response to anti- β2-M Ab treatment in LNCaP and C4-2 prostate cancer cells.

Article Snippet: ARCaP M , ARCaP E , C4-2, and C4-2B prostate cancer cells were derived in our laboratory as described previously, and p69 (non-tumorigenic cells), LNCaP, PC-3, DU145, TRAMP C1 and TRAMP C2 prostate cancer cells were purchased from ATCC.

Techniques: Staining, Expressing

Journal: PLoS ONE

Article Title: Inhibition of β2-Microglobulin/Hemochromatosis Enhances Radiation Sensitivity by Induction of Iron Overload in Prostate Cancer Cells

doi: 10.1371/journal.pone.0068366

Figure Lengend Snippet: A. Cell viability of C4-2B Neo control cells and KD β2-M cells in response to: taxotere (0.3 µM), cisplatin (10 µM) and PS341 (1 µM). (***p<0.001, Student’s t test) B. Cell viability of DU154 prostate cancer cells in response to combination of anti-β2-M Ab (0.5 µg/ml) and cisplatin (100 µM)/doxorubicin (100 µM). (***p<0.001, Student’s t test). C. Cell viability of PC-3 prostate cancer cells in response to combination of anti-β2-M Ab (1 µg/ml) and cisplatin (100 µM). (***p<0.001, Student’s t test).

Article Snippet: ARCaP M , ARCaP E , C4-2, and C4-2B prostate cancer cells were derived in our laboratory as described previously, and p69 (non-tumorigenic cells), LNCaP, PC-3, DU145, TRAMP C1 and TRAMP C2 prostate cancer cells were purchased from ATCC.

Techniques: