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Genomic profiling of canine mast cell tumors identifies DNA copy number aberrations associated with KIT mutations and high histological grade

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Abstract

Mast cell tumor (MCT) is the most common skin malignancy of domestic dogs and presents with a widely variable clinical behavior. Although activating KIT mutations are present in approximately 20% of canine MCTs, molecular etiology is largely unknown for the majority of this cancer. Characterization of genomic alterations in canine MCTs may identify genomic regions and/or genes responsible for their development and progression, facilitating the discovery of new therapeutic targets and improved clinical management of this heterogeneous cancer. We performed genome-wide DNA copy number analysis of 109 primary MCTs derived from three popular canine breeds (the Boxer, Labrador Retriever, and Pug) as well as nontarget breeds using oligonucleotide array comparative genomic hybridization (oaCGH). We demonstrated a stepwise accumulation of numerical DNA copy number aberrations (CNAs) as tumor grade increases. DNA sequencing analysis revealed that KIT mutations were found less frequently in the Pug tumors and were strongly associated with high histological grade. Tumors with KIT mutations showed genome-wide aberrant copy number profiles, with frequent CNAs involving genes in the p53 and RB pathways, whereas CNAs were very limited in tumors with wild-type KIT. We evaluated the presence of four CNAs to predict aggressive tumor phenotypes. This approach predicted aggressive tumors with a sensitivity of 78–94% and specificity of 88–93%, when using oaCGH and droplet digital PCR platforms. Further investigation of genome regions identified in this study may lead to the development of a molecular tool for classification and prognosis, as well as identification of therapeutic target molecules.

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Abbreviations

CFA:

Canis familiaris (also used as a prefix to chromosome numbers)

CI:

Confidence interval

CNA:

Copy number aberration

ddPCR:

Droplet digital PCR

FFPE:

Formalin fixed paraffin embedded

GISTIC:

Genomic Identification of Significant Targets in Cancer

ITD:

Internal tandem duplication

MCT:

Mast cell tumor

mut-KIT :

Mutant KIT

oaCGH:

Oligonucleotide array comparative genomic hybridization

OR:

Odds ratio

ROC:

Receiver operating characteristic

wt-KIT :

Wild-type KIT

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Acknowledgements

This study was funded in part by a grant from Antech Diagnostics (awarded to MB) and by the NCSU Cancer Genomics fund (MB). HM was supported in part by a Morris Animal Foundation Fellowship (awarded to HM, study ID: D14CA-401) and a Postdoctoral Fellowship for Research Abroad, provided by the Japan Society for the Promotion of Science (HM).

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Authors and Affiliations

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

    Hiroyuki Mochizuki, Rachael Thomas & Matthew Breen

  2. Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA

    Hiroyuki Mochizuki, Rachael Thomas & Matthew Breen

  3. Antech Diagnostics Inc., 1111 Marcus Ave. Suite M28, New Hyde Park, NY, USA

    Scott Moroff

  4. Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA

    Matthew Breen

  5. Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA

    Matthew Breen

Authors
  1. Hiroyuki Mochizuki
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  2. Rachael Thomas
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  3. Scott Moroff
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  4. Matthew Breen
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Correspondence to Matthew Breen.

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Responsible Editor: Conly Rieder

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Mochizuki, H., Thomas, R., Moroff, S. et al. Genomic profiling of canine mast cell tumors identifies DNA copy number aberrations associated with KIT mutations and high histological grade. Chromosome Res 25, 129–143 (2017). https://doi.org/10.1007/s10577-016-9543-7

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  • DOI: https://doi.org/10.1007/s10577-016-9543-7

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