Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma

Abstract

Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24 and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near two-fold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22% versus 40%). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly-distinct subtypes of canine hemangiosarcoma.

Comparative oncology: what dogs and other species can teach us about humans with cancer

“…Despite the presence of multiple passenger alterations, potential recurrent driver alternations were seen in CDKN2A, VEGFA and SKI. Interestingly, VEGFA gains were observed at nearly half the rate in golden retrievers compared with the other breeds (22 versus 40%) [96]. These data support an alternative origin of tumorigenesis among breeds and multiple haemangiosarcoma molecular subtypes owing to alternative activating pathways as demonstrated in the gene expression studies.…”

“…The authors investigated haemangiosarcoma cell lines and discovered expression of multiple and distinct markers for early endothelial, haematopoietic and myeloid cells along with several phagocytic and adipogenic functional experiments [95], further supporting the multipotent potential and origin of this blood vessel sarcoma. Genome-wide DNA copy number profiling of canine haemangiosarcoma has also been performed using high-resolution oaCGH [96]. In this study, primary intra-abdominal haemangiosarcomas (N ¼ 75; golden retriever (n ¼ 40), Australian shepherd (n ¼ 10), German shepherd (n ¼ 10), flat-coated retriever (n ¼ 9) and BMD (n ¼ 6)) were assessed and the data revealed a relatively low rate of CNAs with small amplitudes.…”

Genome-wide assessment of recurrent genomic imbalances in canine leukemia identifies evolutionarily conserved regions for subtype differentiation

“…Identification of CNAs using oligonucleotide array comparative genomic hybridization Oligonucleotide array comparative genomic hybridization (oaCGH) was performed using a 180,000 feature CGH microarray (Agilent Technologies, Santa Clara, CA) as previously described (Thomas et al , 2014Shapiro et al 2015). The array contains repeatmasked 60mer oligonucleotides spaced approximately every 13 kb across the dog genome (CanFam version 2.0, Lindblad-Toh et al 2005).…”

“…Fluorescence in situ hybridization (FISH) of canine leukemia cases was performed as previously described (Breen et al 2004;Thomas et al 2014) to verify copy number data obtained by oaCGH. FISH analysis was performed using panels of cytogenetically validated clones (Thomas et al 2008) from the CHORI-82 dog bacterial artificial chromosome (BAC) library (www.…”

“…To compliment traditional small animal models, we propose that the domestic dog offers a suitable large animal model for evaluating spontaneously occurring leukemias, exhibiting similar morphology and clinical characteristics to human leukemias. Evaluation of recurrent genetic changes using cross-species comparison between dogs and humans has identified orthologous regions of importance in brain tumors (Thomas et al 2009), colorectal cancer (Tang et al 2010), non-Hodgkin lymphoma , osteosarcoma (Angstadt et al 2012), hemangiosarcoma (Thomas et al 2014), melanoma (Poorman et al 2015), and urothelial carcinoma (Shapiro et al 2015). Each of these studies has led to the identification of genomic regions harboring candidate genes associated with pathogenesis and therapeutic potential.…”