Tracking the clonal origin of lethal prostate cancer

Abstract

Recent controversies surrounding prostate cancer overtreatment emphasize the critical need to delineate the molecular features associated with progression to lethal metastatic disease. Here, we have used whole-genome sequencing and molecular pathological analyses to characterize the lethal cell clone in a patient who died of prostate cancer. We tracked the evolution of the lethal cell clone from the primary cancer to metastases through samples collected during disease progression and at the time of death. Surprisingly, these analyses revealed that the lethal clone arose from a small, relatively low-grade cancer focus in the primary tumor, and not from the bulk, higher-grade primary cancer or from a lymph node metastasis resected at prostatectomy. Despite being limited to one case, these findings highlight the potential importance of developing and implementing molecular prognostic and predictive markers, such as alterations of tumor suppressor proteins PTEN or p53, to augment current pathological evaluation and delineate clonal heterogeneity. Furthermore, this case illustrates the potential need in precision medicine to longitudinally sample metastatic lesions to capture the evolving constellation of alterations during progression. Similar comprehensive studies of additional prostate cancer cases are warranted to understand the extent to which these issues may challenge prostate cancer clinical management.

Figure 1. Common genomic consensus alterations found in 3 distant metastases (M5, M38, and M40) by whole-genome sequencing are plotted.

Genes with nonsynonymous single nucleotide variants (SNVs) and indels in coding sequences are indicated in the outermost circle. Copy number alterations are color-coded and shown in the adjacent circle. Regions of high copy number gain (>4; dark red), and significant copy number loss (<0.5; blue) are indicated. LOH of individual regions (orange) is indicated in the middle circle. Arcs in the interior connect regions of structural rearrangements (blue, intrachromosomal; orange, interchromosomal), and associated genes are shown in the inner circle.

Figure 2. Consensus genomic alterations and their phenotypic consequences in the autopsy metastases.

(A) Anatomic distribution of study samples. Asterisks denote the 3 anatomically distinct autopsy metastases on which whole-genome sequencing was performed. (B–E) Molecular phenotypes of genomic alterations evaluated by immunohistochemistry (IHC) and telomere-specific FISH in representative metastasis M63. (B) AR amplification was associated with strong immunoreactivity for AR. (C) Mutations in TP53 (R248Q) resulted in nuclear accumulation of p53. (D) A frameshift deletion in the coding sequence of PTEN resulted in loss of PTEN immunostaining in neoplastic cells. Original magnification, ×20. (E) The genomic inversion within the ATRX gene was associated with strong nuclear accumulation of telomeric sequence, consistent with ALT. Arrows indicate neoplastic cells. Scale bar: 10 μm.

Figure 3. Molecular and pathological findings in the primary tumor and their clonal relationship to the distant metastases.

(A) PTEN staining in a cross-section of the primary prostatectomy specimen (LA, left anterior; RA, right anterior; LP, left posterior; RP, right posterior). Individual tumor areas that were further analyzed are indicated; green dotted outline denotes areas containing tumor glands. P1 was the only lesion in the primary tumor devoid of PTEN staining in neoplastic cells. The adjacent P2 stained positive for PTEN, and in this regard was representative of the bulk tumor outside P1. Arrows indicate tumor cells. Note that the surrounding normal stroma showed strong immunoreactivity for PTEN. Original magnification, ×2 (top); ×40 (bottom). Scale bar: 10 mm. (B) Summary of the analyzed consensus genomic alterations in the primary tumor and metastases. The presence and absence of the consensus mutations are denoted by blue and gray, respectively. (C) Proposed model of disease progression in this index case, based on sequencing and molecular pathological analyses. Phylogenetic relationships of distant metastases were calculated based on structural rearrangements.