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

// Darko Stefanovski 1 , George Tang 2 , Kolja Wawrowsky 3 , Raymond C. Boston 1 , Nils Lambrecht 4, 5 and Jian Tajbakhsh 2, 6 1 Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA 2 Translational Cytomics Group, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA 3 Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA 4 Pathology and Laboratory Medicine Service, Veterans Affairs Medical Center, Long Beach, CA, USA 5 Department of Pathology and Laboratory Medicine, University of California Irvine, Orange, CA, USA 6 Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA Correspondence to: Jian Tajbakhsh, email: tajbakhshj@cshs.org Keywords: prostate cancer, epigenetics, 3D high-content imaging, tissue diagnostics, cell heterogeneity Received: September 07, 2016     Accepted: June 02, 2017     Published: July 05, 2017 ABSTRACT Background: Prostate cancer (PCa) management can benefit from novel concepts/biomarkers for reducing the current 20-30% chance of false-negative diagnosis with standard histopathology of biopsied tissue. Method: We explored the potential of selected epigenetic markers in combination with validated histopathological markers, 3D high-content imaging, cell-by-cell analysis, and probabilistic classification in generating novel detailed maps of biomarker heterogeneity in patient tissues, and PCa diagnosis. We used consecutive biopsies/radical prostatectomies from five patients for building a database of ~140,000 analyzed cells across all tissue compartments and for model development; and from five patients and the two well-characterized HPrEpiC primary and LNCaP cancer cell types for model validation. Results: Principal component analysis presented highest covariability for the four biomarkers 4’,6-diamidino-2-phenylindole, 5-methylcytosine, 5-hydroxymethylcytosine, and alpha-methylacyl-CoA racemase in the epithelial tissue compartment. The panel also showed best performance in discriminating between normal and cancer-like cells in prostate tissues with a sensitivity and specificity of 85%, correctly classified 87% of HPrEpiC as healthy and 99% of LNCaP cells as cancer-like, identified a majority of aberrant cells within histopathologically benign tissues at baseline diagnosis of patients that were later diagnosed with adenocarcinoma. Using k-nearest neighbor classifier with cells from an initial patient biopsy, the biomarkers were able to predict cancer stage and grade of prostatic tissue that occurred at later prostatectomy with 79% accuracy. Conclusion: Our approach showed favorable diagnostic values to identify the portion and pathological category of aberrant cells in a small subset of sampled tissue cells, correlating with the degree of malignancy beyond baseline.