Abstract
BackgroundBevacizumab, a monoclonal antibody against soluble VEGFA, is an approved and commonly administered anti-angiogenic drug in patients with metastasized colorectal cancer (mCRC). The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months, and acquired resistance mechanisms are largely unknown. Here, we employed whole-genome sequencing of plasma DNA to evaluate the tumor genome of patients undergoing treatment with bevacizumab to determine novel aberrations associated with resistance.MethodsUsing longitudinal plasma analyses, we studied the evolution of tumor genomes in a mCRC cohort (n = 150) and conducted analyses of CRC cases from The Cancer Genome Atlas (TCGA) database (n = 619) to identify associations between genomic aberrations and clinical features. We employed whole-genome sequencing to identify the most frequently occurring focal somatic copy number alterations (SCNAs). Using the TCGA data as a comparative and supporting dataset, we defined the minimally amplified overlapping region and studied the mechanistic consequences of copy number gain of the involved genes in this segment. In addition, we established an in vitro cell model and conducted downstream gene expression and cell viability assays to confirm our findings from the patient dataset.ResultsWe observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of CRC cases from the TCGA database suggested that this amplicon is associated with more advanced stages. We confirmed that this 13q12.2 amplicon frequently emerges later during the clinical course of disease. After defining the minimally amplified region, we observed that the amplification and expression of one gene, POLR1D, impacted cell proliferation and resulted in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab treatment. In fact, in several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with therapy resistance.ConclusionsNon-invasive analyses of cell-free DNA from patients undergoing treatment with bevacizumab enabled the tracking of evolving tumor genomes and helped identify a recurrent focal SCNA of clinical relevance. Here, we describe a novel resistance mechanism against a widely applied treatment in patients with mCRC which will impact the clinical management of patients.
Highlights
Bevacizumab, a monoclonal antibody against soluble vascular endothelial growth factor A (VEGFA), is an approved and commonly administered anti-angiogenic drug in patients with metastasized colorectal cancer
The focal amplification 12p12.1 harboring the KRAS oncogene was present in 6.7% of our patients, compared to only 1.6% of patient of the The Cancer Genome Atlas (TCGA) cohort (p = 0.002; chi-square test; Fig. 1a, Additional file 2: Figure S1A, Additional file 4), which may reflect a higher number of patients who received anti-epidermal growth factor receptor (EGFR) therapy in our cohort [28, 36]
Given the specificity of bevacizumab to the VEGFA ligand [54] and as recent publications showed that bevacizumab treatment induces autocrine VEGF signaling [55, 70], we investigated the occurrence of POLR1D amplifications in patients receiving bevacizumab to provide in vivo data
Summary
Bevacizumab, a monoclonal antibody against soluble VEGFA, is an approved and commonly administered anti-angiogenic drug in patients with metastasized colorectal cancer (mCRC). The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months, and acquired resistance mechanisms are largely unknown. Surgical removal of early-stage or metastatic lesions represents a potential curative approach [5], therapeutic options for metastatic CRC (mCRC) are commonly limited to palliative approaches that improve quality of life and survival for a median time of about 2 to 3 years. The identification of molecular targets and pathways involved in the initiation and progression of CRC have helped to better characterize the disease and further tailor patient treatment more precisely to minimize primary resistance, or to avoid it altogether [6]. Advances in genome sequencing technology have enabled high-resolution detection of potential molecular targets, such as somatic copy number alterations (SCNAs) or mutations, the significance of many such aberrations remains elusive in terms of guiding therapy decision-making
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