Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

Abstract

Background: There are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potential to cost-efficiently accelerate precision medicine trials to improve clinical efficacy and diminish costs and toxicity. However, comprehensive ctDNA profiling in metastatic prostate cancer to date has been limited. Methods:A combination of targeted-and low-pass whole genome sequencing was performed on plasma cell-free DNA and matched white blood cell germline DNA in 364 blood samples from 217 metastatic prostate cancer patients.Results: ctDNA was detected in 85.9% of baseline samples, correlated to line of therapy and was mirrored by circulating tumor cell enumeration of synchronous blood samples. Comprehensive profiling of the androgen receptor (AR) revealed a continuous increase in the fraction of patients with intra-AR structural variation, from 15.4% during first line mCRPC therapy to 45.2% in fourth line, indicating a continuous evolution of AR during the course of the disease. Patients displayed frequent alterations in DNA repair deficiency genes (18.0%).Additionally, the microsatellite instability phenotype was identified in 3.81% of eligible samples (≥0.1 ctDNA fraction). Sequencing of non-repetitive intronic-and exonic regions of PTEN, RB1and TP53 detected biallelic inactivation in 47.5%, 20.3% and 44.1% of samples with ≥0.2 ctDNA fraction, respectively. Only one patient carried a clonal high-impact variant without a detectable second hit. Intronic high-impact structural variation was twice as common as exonic mutations in PTEN and RB1. Finally, 14.6% of patients presented false positive variants due to clonal hematopoiesis, commonly ignored in commercially available assays.Conclusions: ctDNA profiles appear to mirror the genomic landscape of metastatic prostate cancer tissue and may cost-efficiently provide somatic information in clinical trials designed to identify predictive biomarkers. However, intronic sequencing of the interrogated tumor suppressors challenge the ubiquitous focus on coding regions and is vital, together with profiling of synchronous white blood cells, to minimize erroneous assignments which in turn may confound results and impede true associations in clinical trials.

Clinical Implications of Mismatch Repair Deficiency in Prostate Cancer

“…Among the 1033 patients who had adequate tumor quality for study, 3.1% had MSI-H/dMMR prostate cancers. As an aside, this estimate is remarkably similar to that of another recent study using circulating cell-free tumor DNA, which also estimated an MSI-high prevalence of 3.8% in men with mCRPC [59]. Seven of these 32 patients in the Abida study (21.9%) had a pathogenic germline mutation in a LS-associated gene, including five in MSH2, one in MSH6 and one in PMS2.…”

“…However, given the frequency of bone-only disease in prostate cancer, and poor yield from these metastatic sites, alternate methods of detection are needed. For this purpose, circulating tumor DNA (ctDNA) remains promising and may eliminate the need for tissue biopsy or archival tissue altogether [59].…”

Clinical and genomic insights into circulating tumor DNA-based alterations across the spectrum of metastatic hormone-sensitive and castrate-resistant prostate cancer

“…The emergence of somatic alterations in the mCRPC state in 2 independent cohorts (the biochemical progressive mCRPC group and the clinical mCRPC group), has not been consistently reported. Mayrhofer et al [38] recently conducted a small study in which plasma-based genomes of hormone-naive and castrate-resistant patients were compared using ctDNA genome profiling. The authors reported ctDNA and ctDNA-based somatic variations in 6 hormone- sensitive, 23 hormone-naive, and 188 castrate-resistant patients, which were used to evaluate variations in cfDNA/ctDNA and genomic alterations from the hormone-naive to the castrate-resistant state.…”

Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

“…Assessing the filtering of putative clonal hematopoiesis (CH) mutations. Several recent studies have suggested that CH mutations present a challenge for proper filtering in highly sensitive NGS-based liquid biopsy assays [27][28][29][30] . We observed that the use of patient-matched normal WBC DNA in MSK-ACCESS eliminated 7,760 (77%) of variant calls below 10% VAF (Fig.…”