Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach

Qi Wei,Amita Kashyap,Christiane V Löhr,Maureen K Larson,Stephen A Ramsey,Bernard Séguin,Charles Keller,Christopher Shiprack,Donasian Ochola,Noah E Berlow

doi:10.1186/s12885-019-5501-z

Abstract

BackgroundFeline injection-site sarcoma (FISS), an aggressive iatrogenic subcutaneous malignancy, is challenging to manage clinically and little is known about the molecular basis of its pathogenesis. Tumor transcriptome profiling has proved valuable for gaining insights into the molecular basis of cancers and for identifying new therapeutic targets. Here, we report the first study of the FISS transcriptome and the first cross-species comparison of the FISS transcriptome with those of anatomically similar soft-tissue sarcomas in dogs and humans.MethodsUsing high-throughput short-read paired-end sequencing, we comparatively profiled FISS tumors vs. normal tissue samples as well as cultured FISS-derived cell lines vs. skin-derived fibroblasts. We analyzed the mRNA-seq data to compare cancer/normal gene expression level, identify biological processes and molecular pathways that are associated with the pathogenesis of FISS, and identify multimegabase genomic regions of potential somatic copy number alteration (SCNA) in FISS. We additionally conducted cross-species analyses to compare the transcriptome of FISS to those of soft-tissue sarcomas in dogs and humans, at the level of cancer/normal gene expression ratios.ResultsWe found: (1) substantial differential expression biases in feline orthologs of human oncogenes and tumor suppressor genes suggesting conserved functions in FISS; (2) a genomic region with recurrent SCNA in human sarcomas that is syntenic to a feline genomic region of probable SCNA in FISS; and (3) significant overlap of the pattern of transcriptional alterations in FISS with the patterns of transcriptional alterations in soft-tissue sarcomas in humans and in dogs. We demonstrated that a protein, BarH-like homeobox 1 (BARX1), has increased expression in FISS cells at the protein level. We identified 11 drugs and four target proteins as potential new therapies for FISS, and validated that one of them (GSK-1059615) inhibits growth of FISS-derived cells in vitro.Conclusions(1) Window-based analysis of mRNA-seq data can uncover SCNAs. (2) The transcriptome of FISS-derived cells is highly consistent with that of FISS tumors. (3) FISS is highly similar to soft-tissue sarcomas in dogs and humans, at the level of gene expression. This work underscores the potential utility of comparative oncology in improving understanding and treatment of FISS.

Highlights

Feline injection-site sarcoma (FISS), an aggressive iatrogenic subcutaneous malignancy, is challenging to manage clinically and little is known about the molecular basis of its pathogenesis
Differential expression in feline injection site-sarcoma (FISS) vs. normal tissue In order to study transcriptome differences between FISS and normal tissue, we first compared the transcriptomes of FISS tumor tissue, normal skin, and normal skeletal muscle
In order to identify molecular functions and biological processes that are associated with the sets of genes that were up- and down-regulated in FISS vs. skin, we ranked genes

Summary

Introduction

Feline injection-site sarcoma (FISS), an aggressive iatrogenic subcutaneous malignancy, is challenging to manage clinically and little is known about the molecular basis of its pathogenesis. Feline injection-site sarcoma (FISS) is an aggressive subcutaneous soft-tissue cancer that occurs in approximately 1 in 10,000 domestic cats, frequently at vaccination sites [1]. The etiology of FISS appears to involve non-resolving local inflammation leading to neoplastic transformation of fibroblasts or myofibroblasts and the development of a tumor mass [2] The triggers of this inflammation probably include vaccine adjuvants and mechanical insult to the subcutis (with latency estimates ranging from months to years [3]), predisposing genetic factors for FISS have been noted [2, 4, 5]. Despite the promise of such systems-biology approaches, the tumor transcriptome of FISS has been neither systematically studied nor compared to the transcriptomes of soft tissue sarcomas in other species such as domestic dogs or humans

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