Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer

Abstract

We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole-genome and transcriptome sequence was obtained from nine anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 yr before death. Transcriptome analysis revealed increased expression of androgen receptor (AR)-regulated genes in liver metastases that harbored an AR p.L702H mutation, suggesting a dominant effect by the mutation despite being present in only one of an estimated 16 copies per cell. The metastases harbored several alterations to the PI3K/AKT pathway, including a clonal truncal mutation in PIK3CG and present in all metastatic sites studied. The list of truncal genomic alterations shared by all metastases included homozygous deletion of TP53, hemizygous deletion of RB1 and CHD1, and amplification of FGFR1. If the patient were treated today, given this knowledge, the use of second-generation androgen-directed therapies, cessation of glucocorticoid administration, and therapeutic inhibition of the PI3K/AKT pathway or FGFR1 receptor could provide personalized benefit. Three previously unreported truncal clonal missense mutations (ABCC4 p.R891L, ALDH9A1 p.W89R, and ASNA1 p.P75R) were expressed at the RNA level and assessed as druggable. The truncal status of mutations may be critical for effective actionability and merit further study. Our findings suggest that a large set of deeply analyzed cases could serve as a powerful guide to more effective prostate cancer basic science and personalized cancer medicine clinical trials.

Keywords: malignant genitourinary tract tumor; neoplasm of the genitourinary tract.

Figure 1.

Case A21 clinical timeline and pathology-genomic relationships. (A) Clinical events and serum PSA plotted with time in years on x-axis. (B) Three regions of radical prostatectomy tissue were microdissected (normal stroma, a mixed Gleason 3 + Gleason 5 cancer region, and a region of extraprostatic extension containing Gleason grade 5 cancer) and compared by targeted sequencing to whole-genome sequence data from nine metastatic sites. Mutation patterns show that the two primary cancer sites and nine metastatic sites are part of a clonal cancer lineage, as reflected by accretion of mutations in SPOP, ASNA1, and PIK3CG and others. The mixed Gleason 3 and Gleason 5 primary cancer region contains the earliest common ancestor identified, and cancer cells in the region of extraprostatic extension are more closely related to cells in all metastatic sites studied. All metastatic sites contain a PIK3CG p. R472 missense mutation that was not identified in the primary cancer. The pattern of spread of the metastatic tumor implied from the genomic data is shown. Numbers of unique high-confidence somatic mutations identified in metastases are listed in gray and horizontal lines are proportional in length to mutation number, with 1264 mutations shared by all metastases, an additional 557 somatic mutations unique to A, 178 mutations shared by all other metastases, and so forth. G, Gleason grade; EPE, extraprostatic extension; LN, lymph node.

Figure 2.

Evolution of androgen receptor (AR) region X Chromosome alterations by whole-genome and transcriptome sequencing in case A21. (A) AR regional structural instability signature in earlier metastases (right rib, left iliac crest, left clavicle LN, and left adrenal) in the clonal evolution map shown in Figure 1B contain four distinct patterns, the latter of which (left adrenal) is shared by all subsequent sites on the map, suggesting independent evolutionary selection of distinct AR structural response to androgen deprivation therapy (ADT) in at least these four studied independent sites. Whether these assorted AR-mutated subclones existed in small numbers before selection cannot be determined from the current study. (B) All four liver metastases and the left adrenal metastasis contained an AR p.L702H mutation in one copy of AR. The mutation is also present in the RNA-seq data from the same samples. The L702H mutant modifies the AR ligand binding domain and is known to alter ligand specificity, rendering the protein responsive to glucocorticoids administered during A21's treatment shown in Figure 1A (Zhao et al. 2000; Carreira et al. 2014). (C) Liver metastases containing the AR p.L702H mutation exhibited significantly increased expression of androgen-regulated genes KLK3, ACPP, FKBP5, SLC45A3, and PCA3 as compared with three metastatic sites where the AR p.L702H was not detected (*P < 0.05, **P < 0.01 and ***P < 0.001; see Methods).