Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA

Abstract

Cancers acquire resistance to systemic treatment as a result of clonal evolution and selection. Repeat biopsies to study genomic evolution as a result of therapy are difficult, invasive and may be confounded by intra-tumour heterogeneity. Recent studies have shown that genomic alterations in solid cancers can be characterized by massively parallel sequencing of circulating cell-free tumour DNA released from cancer cells into plasma, representing a non-invasive liquid biopsy. Here we report sequencing of cancer exomes in serial plasma samples to track genomic evolution of metastatic cancers in response to therapy. Six patients with advanced breast, ovarian and lung cancers were followed over 1-2 years. For each case, exome sequencing was performed on 2-5 plasma samples (19 in total) spanning multiple courses of treatment, at selected time points when the allele fraction of tumour mutations in plasma was high, allowing improved sensitivity. For two cases, synchronous biopsies were also analysed, confirming genome-wide representation of the tumour genome in plasma. Quantification of allele fractions in plasma identified increased representation of mutant alleles in association with emergence of therapy resistance. These included an activating mutation in PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) following treatment with paclitaxel; a truncating mutation in RB1 (retinoblastoma 1) following treatment with cisplatin; a truncating mutation in MED1 (mediator complex subunit 1) following treatment with tamoxifen and trastuzumab, and following subsequent treatment with lapatinib, a splicing mutation in GAS6 (growth arrest-specific 6) in the same patient; and a resistance-conferring mutation in EGFR (epidermal growth factor receptor; T790M) following treatment with gefitinib. These results establish proof of principle that exome-wide analysis of circulating tumour DNA could complement current invasive biopsy approaches to identify mutations associated with acquired drug resistance in advanced cancers. Serial analysis of cancer genomes in plasma constitutes a new paradigm for the study of clonal evolution in human cancers.

Cancer biomarkers: Written in blood

“…Last year, the researchers described how they had sequenced the complete exomes -the 1% of the genome that encodes protein -in blood samples from six people being treated for advanced breast, lung or ovarian cancers. In five cases, the unguided search revealed routes to resistance, such as mutations that prevent drugs from binding to their target proteins 12 .…”

Androgen receptor signaling pathways as a target for breast cancer treatment

“…The multiple inhibition of AR and other signaling pathways (including PI3K/MEK/WNT/MYC/ cell-cycle regulators) could also be useful in this subtype (Proverbs-Singh et al 2015) (Table 1). (Crowley et al 2013, Murtaza et al 2013. In prostate cancer, AR overexpression and point mutations in the AR LBD detected in cell-free DNA have been demonstrated as drivers of resistance to AR-directed therapies and prognostic factors.…”

Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma

“…A possible resolution to this problem is analysis of circulating tumor DNA (ctDNA) released by cancer cells into the plasma ( 20 ). Serial analysis of ctDNA can be used to track genomic evolution of metastatic cancers in response to therapy to complement invasive biopsy approaches and identify mutations associated with acquired drug resistance in advanced cancers ( 21 ), but it is unclear how this technology can be used in the routine setting of a hospital. Patientderived xenografts (PDX) also have the potential to assist personalized medicine decisions ( 22 ), but their development requires access to tumor tissue that is often inaccessible or…”