Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2

Abstract

Osteosarcoma (OS) is a rare, metastatic, human adolescent cancer that also occurs in pet dogs. To define the genomic underpinnings of canine OS, we performed multi-platform analysis of OS tumors from 59 dogs, including whole genome sequencing (n = 24) and whole exome sequencing (WES; n = 13) of primary tumors and matched normal tissue, WES (n = 10) of matched primary/metastatic/normal samples and RNA sequencing (n = 54) of primary tumors. We found that canine OS recapitulates features of human OS including low point mutation burden (median 1.98 per Mb) with a trend towards higher burden in metastases, high structural complexity, frequent TP53 (71%), PI3K pathway (37%), and MAPK pathway mutations (17%), and low expression of immune-associated genes. We also identified novel features of canine OS including putatively inactivating somatic SETD2 (42%) and DMD (50%) aberrations. These findings set the stage for understanding OS development in dogs and humans, and establish genomic contexts for future comparative analyses.

Keywords: Bone cancer; Cancer genomics; Dog; Sarcoma.

Fig. 1

Analysis Pipeline for WGS, WES and RNA-seq. Flow-chart demonstrates sequential use of tools in evaluation of DNA and RNA samples

Fig. 2

Recurrently mutated genes in canine osteosarcoma. a Single nucleotide variants were reported in samples subjected to both WGS and WES. Copy number variants (Log2FC < −0.9 and >0.4) and structural variants were reported in WGS samples. All mutations were clustered based on mutational burden in genes associated with chromatin/histones, TP53 and DMD. b, c Circos plots on DogID #14 and #18. Blue triangles = SNVs; red dots = amplifications; green dots = deletions; dark red arrows = intra-chromosomal translocations; dark blue arrows = inter-chromosomal translocations. WGS whole genome sequencing, WES whole exome sequencing, SNV single nucleotide variant

Fig. 3

Somatic CNVs, SNVs, and SVs. Frequency of somatic coding and non-coding CNVs, SNVs and SVs across both WGS and WES samples. a WGS and WES somatic coding and non-coding SNVs. b WGS somatic coding SVs. Whiskers represent the 5-95th percentile. c WGS copy number changes. Whiskers represent the 5-95th percentile. d Rainfall plots illustrating the density and distribution of somatic mutations in two WGS samples. Base-pair distance between events represented on the y-axis

Fig. 4

SETD2 mutation burden in primary canine OS. a Lollipop plot demonstrating location of SETD2 single nucleotide variants in canine OS. b Recurrent Copy Number Variations and Structural variants mutations found in five tumors defined by the region surrounding SETD2. c All somatic and germline SNV and SV calls affecting SETD2

Fig. 5

DMD mutation burden in primary canine OS. a Lollipop plot demonstrating location of DMD single nucleotide variants in canine OS. b Recurrent Copy Number Variations and Structural variants found in eleven tumors defined by the region surrounding DMD