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