Array-based comparative genomic hybridization analysis reveals chromosomal copy number aberrations associated with clinical outcome in canine diffuse large B-cell lymphoma

Abstract

Canine Diffuse Large B-cell Lymphoma (cDLBCL) is an aggressive cancer with variable clinical response. Despite recent attempts by gene expression profiling to identify the dog as a potential animal model for human DLBCL, this tumor remains biologically heterogeneous with no prognostic biomarkers to predict prognosis. The aim of this work was to identify copy number aberrations (CNAs) by high-resolution array comparative genomic hybridization (aCGH) in 12 dogs with newly diagnosed DLBCL. In a subset of these dogs, the genetic profiles at the end of therapy and at relapse were also assessed. In primary DLBCLs, 90 different genomic imbalances were counted, consisting of 46 gains and 44 losses. Two gains in chr13 were significantly correlated with clinical stage. In addition, specific regions of gains and losses were significantly associated to duration of remission. In primary DLBCLs, individual variability was found, however 14 recurrent CNAs (>30%) were identified. Losses involving IGK, IGL and IGH were always found, and gains along the length of chr13 and chr31 were often observed (>41%). In these segments, MYC, LDHB, HSF1, KIT and PDGFRα are annotated. At the end of therapy, dogs in remission showed four new CNAs, whereas three new CNAs were observed in dogs at relapse compared with the previous profiles. One ex novo CNA, involving TCR, was present in dogs in remission after therapy, possibly induced by the autologous vaccine. Overall, aCGH identified small CNAs associated with outcome, which, along with future expression studies, may reveal target genes relevant to cDLBCL.

Figure 1. Genomic aberrations in cDLBCL.

Frequency plot of CNAs in 12 pre-treatment DLBCLs. Copy number gains/amplifications and losses are indicated as red and blue, respectively. The thresholds of log2 ratio values for single-copy number gains and losses were >0.25 and <−0.25, respectively; the thresholds for high-level gain or amplification were defined as a log 2 ratio >1 and 1.5 respectively.

Figure 2. Example of a single genomic aberration (CFA 26q22) at different time points in dog 2.

The log2 ratio value is plotted on the y-axis; the x-axis represents the genomic position of probes on the array. The genomic profiles indicate a focal loss in chr26, involving IGL, in pre-treatment DLBCL (upper plot) and during relapse (lower plot); the loss was not detected in clinical remission at the end of therapy (middle of plot).