Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches

Abstract

Osteosarcoma is a rare disease in children but is one of the most common cancers in adult large breed dogs. The mutational landscape of both the primary and pulmonary metastatic tumor in two dogs with appendicular osteosarcoma (OSA) was comprehensively evaluated using an automated whole genome sequencing, exome and RNA-seq pipeline that was adapted for this study for use in dogs. Chromosomal lesions were the most common type of mutation. The mutational landscape varied substantially between dogs but the lesions within the same patient were similar. Copy number neutral loss of heterozygosity in mutant TP53 was the most significant driver mutation and involved a large region in the middle of chromosome 5. Canine and human OSA is characterized by loss of cell cycle checkpoint integrity and DNA damage response pathways. Mutational profiling of individual patients with canine OSA would be recommended prior to targeted therapy, given the heterogeneity seen in our study and previous studies.

The genomic landscape of canine osteosarcoma cell lines reveals conserved structural complexity and pathway alterations

“…The highest contributions were made by signatures SBS1, SBS40, and SBS5 ( Fig 2B , S4 Fig ). Signatures SBS1, SBS5, SBS8, SBS17a, SBS17b, SBS30, and SBS40 have previously been reported in human OS samples [ 50 ], while signatures SBS1, SBS8, SBS9, and SBS17b have been reported in canine OS [ 16 – 19 ].…”

“…We identified five published WES or WGS datasets of canine OS tissue (Sakthikumar, et al [16], Gardner, et al [18], Das, et al [17], Chu, et al [19]) or cell lines (Das, et al [1]). Variant…”

“…We compared our simple somatic mutation calls to those previously reported in WES/ WGS canine OS tissue samples (S6 Table) [16][17][18][19]. Of the 3836 genes with SNVs/INDELs reported in at least one OS tumor in these studies, 272 (7%) were also mutated in at least one cell line.…”

“…A limited number of OS lines have been evaluated using RNA-seq and WES, demonstrating conserved transcriptional signatures and point mutations in TP53 with sequenced tumors [1,[15][16][17]. We and others have recently characterized canine primary OS using WGS, WES and RNA-sequencing, demonstrating significant structural complexity, including aberrations in SETD2, DMD, DLG2 and MYC, among others [16][17][18][19]. Several of these were not noted in the prior interrogation of canine OS cell lines, largely due to the fact that a defining feature of canine OS is the presence of large structural changes that are more difficult to detect via WES [18][19][20].…”

“…We and others have recently characterized canine primary OS using WGS, WES and RNA-sequencing, demonstrating significant structural complexity, including aberrations in SETD2, DMD, DLG2 and MYC, among others [16][17][18][19]. Several of these were not noted in the prior interrogation of canine OS cell lines, largely due to the fact that a defining feature of canine OS is the presence of large structural changes that are more difficult to detect via WES [18][19][20]. Therefore, we performed WGS in eight canine OS cell lines to characterize the tumor genome landscape and assess the similarities and differences between these cell lines and naturally occurring canine primary OS tumors.…”