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

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 approximately 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.

Cat Mammary Tumors: Genetic Models for the Human Counterpart

“…Moreover, some of these chromosomes are syntenic to human chromosome regions already reported as being associated with human breast cancer (e.g., [ 25 , 26 , 27 , 28 , 29 ]). In most of these HBC chromosomes, the observed genomic imbalances were determined via comparative genomic hybridization (CGH), a technology now being applied also in the analysis of cat tumors, but for now only reported in feline sarcomas [ 30 ].…”

Cell Lines Derived From Feline Fibrosarcoma Display Unstable Chromosomal Aneuploidy and Additionally Centrosome Number Aberrations

“…38 Kalat et al 28 found, in addition to structural chromosomal aberrations, a chromosomal hyperdiploidy with 40 to 46 chromosomes per cell in feline fibrosarcoma cell lines. An extensive range of genomic imbalances was also shown by Thomas et al, 50 who used a genomic microarray to investigate nonrandom chromosome copy number aberrations in 46 feline sarcomas. A further study of Santos et al analyzed the cat satellite DNA family and telomere sequences by in situ hybridization.…”

Cytogenomics of Feline Cancers: Advances and Opportunities

“…Remarkably, combined CGH and FISH analyses showed that a subset of genomic regions exhibited in excess of 30 copies within individual tumor cells, which were distributed across as many as ten different chromosome structures. Also of note, ISS cases showed non-random reorganization of FCA E1 in conjunction with copy number amplification of a discrete region on FCA E1p12 [ 35 ], consistent with the location of a nucleolar organizing region (NOR) [ 36 ]. Elevated argyrophilic nucleolar organizing region (AgNOR) scores, as defined by silver staining analysis, are common indicators of increased cellular proliferation, and have been associated with decreased overall survival for canine soft tissue sarcomas [ 37 ].…”

“…Towards this goal, a microarray platform was developed to permit CGH-based identification of recurrent genomic DNA copy number aberrations (CNAs) in feline tumors [ 35 ]. This “aneuploidy array” comprised 210 large-insert clones representing loci anchored at ~15 Mb intervals throughout the initial 2x-coverage cat genome sequence assembly.…”

“…Statistical comparison of genomic profiles across the cohort identified two subchromosomal regions that showed significant differences in DNA copy number status in ISS versus non-ISS cases. While providing support for molecular discrimination, the limited resolution capabilities of the aneuploidy array confounded the ability to refine the boundaries of these regions and in turn to assess their gene content [ 35 ].…”