US 12,072,336 B2
Methods for single-cell prostate tissue classification and prediction of cancer progression
Jian Tajbakhsh, Encino, CA (US); and Darko Stefanovski, West Chester, PA (US)
Assigned to Cedars-Sinai Medical Center, Los Angeles, CA (US); and Trustees of The University of Pennsylvania, Philadelphia, PA (US)
Appl. No. 16/342,297
Filed by CEDARS-SINAI MEDICAL CENTER, Los Angeles, CA (US); and TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, Philadelphia, PA (US)
PCT Filed Oct. 20, 2017, PCT No. PCT/US2017/057557
§ 371(c)(1), (2) Date Apr. 16, 2019,
PCT Pub. No. WO2018/075873, PCT Pub. Date Apr. 26, 2018.
Claims priority of provisional application 62/410,689, filed on Oct. 20, 2016.
Prior Publication US 2020/0057069 A1, Feb. 20, 2020
Int. Cl. G01N 33/574 (2006.01); C12Q 1/6804 (2018.01); G01N 1/30 (2006.01); G01N 21/64 (2006.01)
CPC G01N 33/57434 (2013.01) [C12Q 1/6804 (2013.01); G01N 1/30 (2013.01); G01N 21/6428 (2013.01); G01N 21/6447 (2013.01); G01N 21/6458 (2013.01); G01N 2001/302 (2013.01); G01N 2021/6439 (2013.01); G01N 2201/12 (2013.01)] 15 Claims
 
1. A method, comprising:
obtaining a prostate tissue sample from a prostate of a human subject;
quantifying four biomarkers in one or more prostate cells of the prostate tissue sample, wherein the four biomarkers are global DNA (gDNA), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and alpha-methylacyl-CoA racemase (AMACR);
determining if the one or more prostate cells are cancerous or non-cancerous, based on a quantity of the four biomarkers relative to cancerous and/or noncancerous cells, wherein a significantly higher quantity of gDNA and AMACR and a significantly lower quantity of 5mC and 5hmC, relative to non-cancerous cells, is indicative of presence of one or more cancerous prostate cells in the prostate tissue sample;
classifying the one or more cancerous prostate cells according to cancer grade (Gleason score) and cancer stage in the one or more cancerous prostate cells;
determining proportions of cancer grades (Gleason scores) and cancer stages in the prostate tissue sample based on a composition of the classified one or more cancerous prostate cells in the prostate tissue sample;
classifying the prostate tissue sample according to the proportions of cancer grades (Gleason scores) and cancer stages in the prostate tissue sample; and
predicting cancer progression in the prostate of the human subject based on the cancer grade (Gleason score) and the cancer stage in the one or more cancerous prostate cells.