Clonal diversity revealed by morphoproteomic and copy number profiles of single prostate cancer cells at diagnosis

Abstract

Tumor heterogeneity is prevalent in both treatment-naïve and end-stage metastatic castrationresistant prostate cancer (PCa), and may contribute to the broad range of clinical presentation, treatment response, and disease progression. To characterize molecular heterogeneity associated with de novo metastatic PCa, multiplatform single cell profiling was performed using high definition single cell analysis (HD-SCA). HD-SCA enabled morphoproteomic and morphogenomic profiling of single cells from touch preparations of tissue cores (prostate and bone marrow biopsies) as well as liquid samples (peripheral blood and bone marrow aspirate). Morphology, nuclear features, copy number alterations, and protein expression were analyzed. Tumor cells isolated from prostate tissue touch preparation (PTTP) and bone marrow touch preparation (BMTP) as well as metastatic tumor cells (MTCs) isolated from bone marrow aspirate were characterized by morphology and cytokeratin expression. Although peripheral blood was examined, circulating tumor cells were not definitively observed. Targeted proteomics of PTTP, BMTP, and MTCs revealed cell lineage and luminal prostate epithelial differentiation associated with PCa, including co-expression of EpCAM, PSA, and PSMA. Androgen receptor expression was highest in MTCs. Hallmark PCa copy number alterations, including PTEN and ETV6 deletions and NCOA2 amplification, were observed in cells within the primary tumor and bone

SMURF-seq: efficient copy number profiling on long-read sequencers

“…However, many diagnostic amplifications and deletions of important genes (including loss of TP53 or amplification of ERBB2 [26]) are in the megabase size range. For instance, the focal amplification of androgen receptor (AR) [21, 27] and MYCN [28] as well as loss of PTEN [29] and RB1 [28] can be detected with CNV profiling using 5000 bins.…”

“…CNV profiles were generated using the procedure described in [19, 20] with the modification employed in [27, 29]. Briefly, the human reference genome (hg19) was split into 5000 (20,000 or 50,000) bins containing an equal number of uniquely mappable locations, and the bin counts were determined using uniquely mapped fragments.…”

“…Circular binary segmentation (CBS) [30], implemented in DNAcopy [31] package, then identifies breakpoints in the normalized bin counts. Following [27, 29], after CBS, spurious segmentation calls were removed. The influence of the GC content correction can be seen in Additional file 1: Figure S14.…”

Liquid Biopsy in Colorectal Carcinoma: Clinical Applications and Challenges

“…Genomic information from CTCs may be used to better understand cancer cell biology, provide confidence around diagnostic [ 61 ] or treatment decisions [ 62 ], and to track treatment response [ 63 ]. Genomic information also allows for the assessment of clonality and the characterization of different cell populations [ 64 , 65 ]. CTCs can be detected in the peripheral blood as single cells or as cell clusters [ 66 ].…”

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“…Venous peripheral blood was collected in Cellfree DNA Blood Collection Tubes ® (Streck, La Vista, NE, USA) prior to surgery (before anesthesia) and postsurgery. Five touch prep slides were collected from each piece of resected tumor tissue immediately after resection, by gently touching the tissue against standard microscope glass slides [30]. At the time of data analysis, pre-surgery liquid biopsies and a minimum of 1 hepatic touch prep had been collected from 43 patients ( Table 1).…”