Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: Imaging was performed to acquire four categories of tissue frames corresponding to a sampling spectrum of epithelial and stromal compartments: epithelia only (E), epithelia with minor bordering stroma (E+s), mixed epithelia and stroma at various ratios (ES), and stroma only (S).

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques: Imaging, Sampling

Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: Differential levels and cellular heterogeneity of Biomarkers I and II between biopsied benign and cancerous prostatic tissues (represented by AC with GS6), as visualized by confocal scanning microscopy (A). Each marker (false-colored) was recorded in a separate channel. For each tissue sample all channels —including the multi-color overlay image— are presented as maximum intensity projections. (B) Quantitative presentation of biomarker levels as bar plots indicate for Biomarkers I: significant increase in DNA content (DAPI) and AMACR levels and simultaneous loss of the two epigenetic DNA modifications 5mC and 5hmC in both basal and luminal epithelial cells in AC versus benign tissue; luminal cells seemingly exhibit a stronger loss of 5hmC compared to basal cells. Biomarkers II: concurrent loss of suppressive chromatin-state marker H3K27me3 and decrease of chromatin-associated SAFB levels, while H3K9me3 and nuclear AR levels are highly elevated in AC versus benign tissue. Scale bar is 10 μm.

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques: Microscopy, Marker, Biomarker Discovery

Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: The data was separated into subsets representing the first biopsy (blue), the second biopsy (red), and finally prostatectomy (green). Each dot represents one cell. The results show a high overlap when epithelial and stromal compartments are analyzed together (ES). The overlap is reduced in the case of only a minor involvement of stroma (E+s). The best segregation is seen when the epithelial compartment is analyzed by itself, indicating the highest change (variance) for the analyzed markers. The latter subdata is missing data from two biopsies, as most patients for which epithelial (E) compartments could be analyzed were initially diagnosed with lots of AC and thus only underwent one biopsy prior to prostatectomy.

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques:

Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: Performance of Logistic regression model with the development data set and Biomarkers I, utilizing epithelial cell only (A) and all subsets of all imaged cells (B). 5mC shows best performance as single marker in both cases, and is only exceeded by the combined marker panel.

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques: Marker

Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: Logistic regression model coefficients for epithelial cells only

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques:

Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: Predictions of the logistic model based on epithelial cells only

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques:

Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: Validation of KNN classification for predicting tissue pathological categories (including cancer stages) using epithelial cells only and Biomarkers I

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques: Biomarker Discovery

Journal: Oncotarget

Article Title: Prostate cancer diagnosis using epigenetic biomarkers, 3D high-content imaging and probabilistic cell-by-cell classifiers

doi: 10.18632/oncotarget.18985

Figure Lengend Snippet: Validation of KNN classification for predicting GS based on epithelial cells only with Biomarkers I

Article Snippet: Cultured cells included primary human prostate epithelial cells (HPrEpiC, ScienCell, Carlsbad, CA) as normal primary cells, and LNCaP (American Type Culture Collection, Manassas, VA), an androgen-sensitive prostate cancer cell line.

Techniques: Biomarker Discovery

Journal: Conditioning medicine

Article Title: Is there a central role for the cerebral endothelium and the vasculature in the brain response to conditioning stimuli?

doi:

Figure Lengend Snippet: Effects of hypoxia- or ischemia-related conditioning on BBB permeability and endothelial cell death after stroke in vivo or oxygen glucose deprivation in vitro.

Article Snippet: Rat , HpreC (single) , pMCAO , ↑[ 14 C]AIB permeability , ( Chi et al. , 2017 ).

Techniques: Permeability, In Vivo, In Vitro

Journal: Conditioning medicine

Article Title: Is there a central role for the cerebral endothelium and the vasculature in the brain response to conditioning stimuli?

doi:

Figure Lengend Snippet: Effects of hypoxia- or ischemia-related preconditioning on cerebral blood flow.

Article Snippet: Rat , HpreC (single) , pMCAO , ↑[ 14 C]AIB permeability , ( Chi et al. , 2017 ).

Techniques:

Journal: PLoS ONE

Article Title: Repression of Androgen Receptor Transcription through the E2F1/DNMT1 Axis

doi: 10.1371/journal.pone.0025187

Figure Lengend Snippet: (A) Primary cultures of human prostate epithelial cells (hPrEC) and (B) immortalized benign prostate epithelial cells (BPH-1) transduced with either control (shVector (shV) and shNon-targeting (NT)) or DNMT1 shRNA constructs. AR and DNMT1 protein expression relative to actin loading control were analyzed by Western blot. The exposures in (B) were taken from different sections of the same blot at the same intensity. AR transcription was analyzed using qRTPCR with readings done in triplicate (graphs A and B). Mean values are represented with standard error bars. (C) shRNA transduced BPH-1 cells (described in A and B) were transfected with the human AR promoter luciferase reporter (hAR-Luc) construct. The histograms represent the mean value of three independent experiments with the indicated standard deviation. were normalized to β-galactosidase (B-gal) expression from a co-transfected CMV promoter driven B-gal reporter construct. All western blots are representative of 3 separate experimental replicates.

Article Snippet: Human prostate epithelial cells (hPrEC) purchased from Lonza/Clonetics, Walkersville, MD were maintained in Prostate Epithelial Cell Growth Medium (Lonza/Clonetics).

Techniques: Transduction, Control, shRNA, Construct, Expressing, Western Blot, Transfection, Luciferase, Standard Deviation

Journal: PLoS ONE

Article Title: Repression of Androgen Receptor Transcription through the E2F1/DNMT1 Axis

doi: 10.1371/journal.pone.0025187

Figure Lengend Snippet: (A) Map of a region of the AR promoter depicting two types of E2F consensus sequences +80→+96 and +13,318→+13,334 (shown as solid ovals) and +999→+1,015 (shown as open ovals). Primer flanked regions are designated as sites A, B, and C. The 243 bp region (+22→+293) analyzed by bisulfite sequencing is indicated. (B) qPCR analysis of target (DNMT1) and non-specific (IgG) ChIPed DNA from BPH-1 cells using primers that flank sites A, B, and C. Primers flanking a region in the PS2 (targeted DNMT1) promoter and ABCB1 (non-targeted DNMT1) region were used as ChIP controls. Data is representative of the mean from 3 qPCR reactions and shown as a percent of input with the standard error indicated. (C) Bisulfite sequencing analysis of the 243 bp region in the AR minimal promoter in hPrEC compared to DU145 cells infected with both non-targeting (NT) (control) and DNMT1 shRNA constructs (4-1 and 4-2). Solid circles (methylated) and open circles (un-methylated) were used to represent the methylation status of cytosines within CpG dinucleotides. Each horizontal strand of circles depicts a separate DNA clone. Lysates were probed on a western blot for AR and actin. Cell lines were also treated with either 1 µM 5Aza (5A) or DMSO matched vehicle (V) and extracted cDNA was PCR amplified with both human AR and GAPDH. All data shown except for the 5Aza treatments are representative of 3 separate experimental replicates.

Article Snippet: Human prostate epithelial cells (hPrEC) purchased from Lonza/Clonetics, Walkersville, MD were maintained in Prostate Epithelial Cell Growth Medium (Lonza/Clonetics).

Techniques: Methylation Sequencing, Infection, Control, shRNA, Construct, Methylation, Western Blot, Amplification