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Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas

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Abstract

Injection-site-associated sarcomas (ISAS), commonly arising at the site of routine vaccine administration, afflict as many as 22,000 domestic cats annually in the USA. These tumors are typically more aggressive and prone to recurrence than spontaneous sarcomas (non-ISAS), generally receiving a poorer long-term prognosis and warranting a more aggressive therapeutic approach. Although certain clinical and histological factors are highly suggestive of ISAS, timely diagnosis and optimal clinical management may be hindered by the absence of definitive markers that can distinguish between tumors with underlying injection-related etiology and their spontaneous counterpart. Specific nonrandom chromosome copy number aberrations (CNAs) have been associated with the clinical behavior of a vast spectrum of human tumors, providing an extensive resource of potential diagnostic and prognostic biomarkers. Although similar principles are now being applied with great success in other species, their relevance to feline molecular oncology has not yet been investigated in any detail. We report the construction of a genomic microarray platform for detection of recurrent CNAs in feline tumors through cytogenetic assignment of 210 large-insert DNA clones selected at intervals of ∼15 Mb from the feline genome sequence assembly. Microarray-based profiling of 19 ISAS and 27 non-ISAS cases identified an extensive range of genomic imbalances that were highly recurrent throughout the combined panel of 46 sarcomas. Deletions of two specific regions were significantly associated with the non-ISAS phenotype. Further characterization of these regions may ultimately permit molecular distinction between ISAS and non-ISAS, as a tool for predicting tumor behavior and prognosis, as well as refining means for therapeutic intervention.

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Abbreviations

BAC:

Bacterial artificial chromosome

BLAST:

Basic Local Alignment Search Tool

BLAT:

BLAST-like alignment tool

CNA:

Copy number aberration

DSH/DMH/DLH:

Domestic short/medium/long hair

FBS:

Fetal bovine serum

FCA:

Felis catus

FeLV:

Feline leukemia virus

FFPE:

Formalin-fixed paraffin-embedded

FISH:

Fluorescence in situ hybridization

H&E:

Hematoxylin and eosin

ISAS:

Injection-site-associated sarcoma

Mb:

Megabase

NCBI:

National Center for Biotechnology Information

RPCI:

Roswell Park Cancer Institute

UCSC:

University of California Santa Cruz

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Acknowledgements

We thank Katie Saylor and Emily Smith for technical assistance and Dr. Steven Suter for his clinical advice and expertise. We are grateful to Drs. Steve O’Brien, Sagarika Kanjilal, Naoya Yuhki, and Vivek Kapur for assistance with retrieval of feline DNA sequences, and we gratefully acknowledge Dr. Peter de Jong for provision of feline BAC clones. We thank Sandra Horton and the NCSU Histology Service for their invaluable assistance with retrieving clinical samples and data and thank the owners and veterinarians who contributed feline clinical samples. This study was supported by funding from the Morris Animal Foundation (D06FE-308 awarded to RT) and was sponsored by the Blue Buffalo Foundation for Cancer Research and Carolyn S. Norgren. KLT is a European Science Foundation EURYI award recipient.

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Authors and Affiliations

  1. Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC, 27606, USA

    Rachael Thomas & Matthew Breen

  2. Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, 27606, USA

    Rachael Thomas & Matthew Breen

  3. VDx Veterinary Diagnostics, 2019 Anderson Road, Suite C, Davis, CA, 95616, USA

    Victor E. Valli

  4. Microarray Facility, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

    Peter Ellis & Cordelia F. Langford

  5. Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, Grafton, MA, 01536, USA

    Jerold Bell

  6. Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, MA, 02141, USA

    Elinor K. Karlsson & Kerstin Lindblad-Toh

  7. FAS Center for Systems Biology, Harvard University, Cambridge, MA, 02138, USA

    Elinor K. Karlsson

  8. Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA

    John Cullen

  9. Department of Medical Biochemistry and Microbiology, Uppsala University, 751 24, Uppsala, Sweden

    Kerstin Lindblad-Toh

  10. Cancer Genetics Program, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA

    Matthew Breen

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  1. Rachael Thomas
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Correspondence to Rachael Thomas.

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Responsible Editor: Dean A. Jackson

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S1

Signalment and aCGH data for all sarcoma cases analyzed (n = 46). The breed, age, and gender of each case are shown at the top of the chart, along with the anatomical location of the tumor. ISAS cases are listed to the left, and non-ISAS cases to the right. The first two columns indicate the chromosome and megabase location of arrayed BAC clones, which are listed in genomic order. Colored cells indicate the copy number status at each locus in each tumor case, based on the tumor DNA/reference DNA fluorescence intensity (red cells indicates genomic loss, test/reference ≤ 0.85:1; green cells indicates genomic gain, test/reference ≥ 1.15:1; yellow cells indicates genomic balance). M male, F female, DSH domestic short hair, DMH domestic medium hair, DLH domestic long hair (PDF 180 kb)

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Thomas, R., Valli, V.E., Ellis, P. et al. Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas. Chromosome Res 17, 987–1000 (2009). https://doi.org/10.1007/s10577-009-9096-0

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  • DOI: https://doi.org/10.1007/s10577-009-9096-0

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