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

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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 twofold 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.

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Abbreviations

ASD:

Australian Shepherd Dog

BAC:

bacterial artificial chromosome

BMD:

Bernese Mountain Dog

CFA:

Canis familiaris

CNA:

copy number aberration

CNV:

copy number variant

FCR:

Flat-Coated Retriever

FFPE:

formalin-fixed, paraffin-embedded

FISH:

fluorescence in situ hybridization

GR:

Golden Retriever

GSD:

German Shepherd Dog

H&E:

hematoxylin and eosin

oaCGH:

oligonucleotide array comparative genomic hybridization

SSC:

saline–sodium citrate

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Acknowledgments

This study was supported by grant D10CA-501 (MB, JFM, KLT) from the Golden Retriever Foundation and Morris Animal Foundation, and grant 1131 from the American Kennel Club Canine Health Foundation (JFM). We thank Sandra Horton and staff members of the North Carolina State University Histopathology laboratory for their expertise in the preparation and diagnostic evaluation of clinical specimens. Additional pathology support was provided by Drs Gerry O’Sullivan and Sandra Yi, and the Comparative Pathology Shared Resource Core of the Masonic Cancer Center, University of Minnesota, supported by grant P30CA077598 from the National Institutes of Health. We thank Mitzi Lewellyn for co-ordination of clinical specimen collection, Katie Kennedy for assistance with FISH analysis and Kate Kelley, Alex Hanes Sparrow, Milcah Scott, and Megan Duckett for technical assistance. Enrollment and diagnostic evaluation of cases recruited by North Carolina State University was supported by the Canine Cancer Genomics Fund. Cases recruited through University of Minnesota were supported in part by the Starlight Fund, The Land of PureGold Foundation, the WillPower Fund, and other philanthropic funding at the University of Minnesota Animal Cancer Care and Research Program. We gratefully acknowledge the many dog owners, breeders, and veterinarians who have supported this study through provision of clinical specimens and patient data.

Ethical standards

Experiments described in this manuscript comply with the current laws of the country in which they were performed (USA). All institutional and national guidelines for the care and use of laboratory animals were followed.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, 1060 William Moore Drive, Raleigh, NC, 27607, USA

    Rachael Thomas & Matthew Breen

  2. Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, USA

    Rachael Thomas, Luke Borst, Alison Motsinger-Reif & Matthew Breen

  3. Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA

    Luke Borst

  4. Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC, USA

    Daniel Rotroff & Alison Motsinger-Reif

  5. Broad Institute, Cambridge, MA, USA

    Kerstin Lindblad-Toh

  6. Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

    Kerstin Lindblad-Toh

  7. Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA

    Jaime F. Modiano

  8. Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA

    Jaime F. Modiano

  9. Cancer Genetics Program, University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA

    Matthew Breen

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  1. Rachael Thomas
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  2. Luke Borst
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  4. Alison Motsinger-Reif
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  6. Jaime F. Modiano
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  7. Matthew Breen
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Correspondence to Matthew Breen.

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Responsible Editor: Conly Rieder

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Supplementary figure 1

Comparison of oaCGH data obtained using DNA isolated from fresh and FFPE-derived tissue from the same tumor specimen. Examples are provided from two tumors for which the genomic profile shown in blue (1) was obtained using DNA isolated from fresh, unfixed tissue. The profile shown in red (2) was obtained using FFPE-derived tissue. These two profiles are then overlaid (3), showing that, although the data derived from FFPE tissue exhibit a higher level of background noise in oaCGH analysis, the regions of genomic balance identified are highly consistent with those derived from fresh, unfixed tissue from the same specimen (PPT 201 kb)

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Thomas, R., Borst, L., Rotroff, D. et al. Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma. Chromosome Res 22, 305–319 (2014). https://doi.org/10.1007/s10577-014-9406-z

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  • DOI: https://doi.org/10.1007/s10577-014-9406-z

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