Serial biopsy of pancreatic ductal adenocarcinoma (PDAC), to chart tumour evolution presents a significant challenge. We examined the utility of circulating free DNA (cfDNA) as a minimally invasive ...approach across a cohort of 55 treatment-naïve patients with PDAC; 31 with metastatic and 24 with locally advanced disease. Somatic mutations in cfDNA were detected using next generation sequencing in 15/24 (62.5%) and 27/31 (87%) of patients with locally advanced and metastatic disease, respectively. Copy number changes were detected in cfDNA of 10 patients of whom 7 exhibited gain of chromosome 12p harbouring KRAS as well as a canonical KRAS codon 12 mutation. In multivariable Cox Regression analysis, we show for the first time that patients with KRAS copy number gain and KRAS mutation have significantly worse outcomes, suggesting that this may be linked to PDAC progression. The simple cfDNA assay we describe will enable determination of the presence of KRAS copy number gain and KRAS mutations in larger studies and clinical trials.
Next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) supports blood-based genomic profiling but is not yet routinely implemented in the setting of a phase I trials clinic. TARGET is a ...molecular profiling program with the primary aim to match patients with a broad range of advanced cancers to early phase clinical trials on the basis of analysis of both somatic mutations and copy number alterations (CNA) across a 641 cancer-associated-gene panel in a single ctDNA assay. For the first 100 TARGET patients, ctDNA data showed good concordance with matched tumor and results were turned round within a clinically acceptable timeframe for Molecular Tumor Board (MTB) review. When a 2.5% variant allele frequency (VAF) threshold was applied, actionable mutations were identified in 41 of 100 patients, and 11 of these patients received a matched therapy. These data support the application of ctDNA in this early phase trial setting where broad genomic profiling of contemporaneous tumor material enhances patient stratification to novel therapies and provides a practical template for bringing routinely applied blood-based analyses to the clinic.
SCLC accounts for approximately 250,000 deaths worldwide each year. Acquisition of adequate tumor biopsy samples is challenging, and liquid biopsies present an alternative option for patient ...stratification and response monitoring.
We applied whole genome next-generation sequencing to circulating free DNA (cfDNA) from 39 patients with limited-stage (LS) SCLC and 30 patients with extensive-stage SCLC to establish genome-wide copy number aberrations and also performed targeted mutation analysis of 110 SCLC associated genes. Quantitative metrics were calculated for copy number aberrations, including percent genome amplified (PGA the percentage of genomic regions amplified), Z-score (a measure of standard deviation), and Moran’s I (a measure of spatial autocorrelation). In addition CellSearch, an epitope-dependent enrichment platform, was used to enumerate circulating tumor cells (CTCs) from a parallel blood sample.
Genome-wide and targeted cfDNA sequencing data identified tumor-related changes in 94% of patients with LS SCLC and 100% of patients with extensive-stage SCLC. Parallel analysis of CTCs based on at least 1 CTC/7.5 mL of blood increased tumor detection frequencies to 95% for LS SCLC. Both CTC counts and cfDNA readouts correlated with disease stage and overall survival.
We demonstrate that a simple cfDNA genome-wide copy number approach provides an effective means of monitoring patients through treatment and show that targeted cfDNA sequencing identifies potential therapeutic targets in more than 50% of patients. We are now incorporating this approach into additional studies and trials of targeted therapies.
A single maintenance course of a PARP inhibitor (PARPi) improves progression-free survival (PFS) in germline BRCA1/2-mutant high-grade serous ovarian cancer (gBRCAm-HGSOC). The feasibility of a ...second maintenance course of PARPi was unknown.
Phase II trial with two entry points (EP1, EP2). Patients were recruited prior to rechallenge platinum. Patients with relapsed, gBRCAm-HGSOC were enrolled at EP1 if they were PARPi-naïve. Patients enrolled at EP2 had received their first course of olaparib prior to trial entry. EP1 patients were retreated with olaparib after RECIST complete/partial response (CR/PR) to platinum. EP2 patients were retreated with olaparib ± cediranib after RECIST CR/PR/stable disease to platinum and according to the platinum-free interval. Co-primary outcomes were the proportion of patients who received a second course of olaparib and the proportion who received olaparib retreatment for ≥6 months. Functional homologous recombination deficiency (HRD), somatic copy-number alteration (SCNA), and BRCAm reversions were investigated in tumor and liquid biopsies.
Twenty-seven patients were treated (EP1 = 17, EP2 = 10), and 19 were evaluable. Twelve patients (63%) received a second course of olaparib and 4 received olaparib retreatment for ≥6 months. Common grade ≥2 adverse events during olaparib retreatment were anemia, nausea, and fatigue. No cases of MDS/AML occurred. Mean duration of olaparib treatment and retreatment differed (12.1 months vs. 4.4 months; P < 0.001). Functional HRD and SCNA did not predict PFS. A BRCA2 reversion mutation was detected in a post-olaparib liquid biopsy.
A second course of olaparib can be safely administered to women with gBRCAm-HGSOC but is only modestly efficacious. See related commentary by Gonzalez-Ochoa and Oza, p. 2563.
Abstract
Background: Prostate cancer (CaP) is the second-leading cause of male cancer-related mortality in Western societies. Localised prostate cancer (Loc-CaP) can be classified into low-, ...intermediate-, or high-risk groups. Active surveillance is recommended for low-risk patients, whereas radiotherapy or surgery is often indicated in intermediate- and high-risk patients, with possible intensification using hormone therapy treatment. Despite advances in radiation delivery and surgery, ~20% of patients will not be cured with local treatment and require androgen deprivation therapy (ADT). The majority will develop resistance to ADT resulting in castration resistant prostate cancer (CRPC) with poor prognosis and increased risk of metastatic disease (mCRPC). Biomarkers are being developed based on tumour biopsies which may help stratify patients and allow more effective treatment. However tumour biopsies are invasive, demanding for patients and surgeons as well as challenging for longitudinal sampling. Here we evaluate a range of blood biomarkers suitable for longitudinal sampling including circulating tumour cells (CTCs), circulating tumour DNA (ctDNA) and Tumour educated platelet mRNA (TEP-RNA).
Methods: A blood sampling, processing and banking pipeline has been established for CaP patients providing ctDNA, enriched and single CTCs as well as TEP-RNA. Following ctDNA isolation, next generation sequencing (NGS) libraries are prepared to generate copy number alteration (CNA) data and mutation profiles. CTCs are enriched using both the epitope independent Parsortix (P-CTC) (Chudziak J. et al, 2016) and the epitope dependent (EPCAM and KRT19) CellSearch (CS-CTC) platforms. Genomic analysis of CTCs is carried out by NGS of whole genome amplified (WGA) single and pooled CTCs. CTC and TEP-RNA mRNA profiles are established using both the Fluidigm RT qPCR (Fluidigm Biomark™ HD system) and RNA-Seq.
Results: Over 160 Loc-CaP and 100 mCRPC blood samples have been collected, processed and banked. In keeping with published data 53% of the 100 mCRPC patients have >5 CS-CTCs (a poor prognostic indicator) compared to 100% of Loc-CaP having <2 CTCs. Control cell “spike in” RNA data showed =>1000 fold enrichment of epithelial mRNAs post Parsortix CTC enrichment indicate an equivalent enrichment of the “spiked in” cells. Similar epithelial mRNA enrichment was seen in 3/5 mCRPC clinical samples tested. Tumour associated CNA changes were clearly detected in at least 15 of the 1st 22 mCRPC ctDNA samples. Sample processing and statistical analysis is ongoing to evaluate if these blood biomarkers, either alone or in combination, can be linked to clinical status or outcome.
Note: This abstract was not presented at the meeting.
Citation Format: Jenny Antonello, Jakub Chudziak, Alan Redfern, Victoria Foy, Shambhavi Srivastava, Adnan Syed, Deborah Burt, Mahmood Ayub, Bedirhan Kilerci, Marina Parry, Richard Marais, Esther Baena, Crispin Miller, Dominic Rothwell, Noel Clarke, Caroline Dive, Ged Brady. An evaluation of DNA and RNA based blood biomarkers in prostate cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5685. doi:10.1158/1538-7445.AM2017-5685
PDF
