Angiosarcoma is an aggressive malignancy that arises spontaneously or secondarily to ionizing radiation or chronic lymphoedema1. Previous work has identified aberrant angiogenesis, including occasional somatic mutations in angiogenesis signaling genes, as a key driver of angiosarcoma1. Here we employed whole-genome, whole-exome and targeted sequencing to study the somatic changes underpinning primary and secondary angiosarcoma. We identified recurrent mutations in two genes, PTPRB and PLCG1, which are intimately linked to angiogenesis. The endothelial phosphatase PTPRB, a negative regulator of vascular growth factor tyrosine kinases, harbored predominantly truncating mutations in 10 of 39 tumors (26%). PLCG1, a signal transducer of tyrosine kinases, encoded a recurrent, likely activating p.Arg707Gln missense variant in 3 of 34 cases (9%). Overall, 15 of 39 tumors (38%) harbored at least one driver mutation in angiogenesis signaling genes. Our findings inform and reinforce current therapeutic efforts to target angiogenesis signaling in angiosarcoma.
At a glance
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- Supplementary Figure 1: Genome-wide structural rearrangements. (54 KB)
CIRCOS plots representing rearrangement in the three genomes studied at the whole-genome level. Colors represent rearrangement class: orange, inversion type (tail to tail); blue, inversion type (head to head); green, deletion type; black, tandem duplication type; purple, interchromosomal.
- Supplementary Figure 2: Mutation frequency in tumor suppressor genes. (142 KB)
Publicly available catalogs of somatic mutations in cancers (n = 4,073) were analyzed for the frequency of 2 mutations (point mutations or LOH) in established tumor suppressor genes. For every gene, we selected all those samples in which the gene had a truncating mutation (nonsense, essential splice site or out-of-frame indel) and quantified the frequency of a second mutation, truncating, LOH, missense or in-frame indel, in the gene. Error bars represent the 95% confidence intervals of the total fraction of two-hit samples (using a Chi-square approximation, as implemented in the function prop.test in R (version 3.0.1).
- Supplementary Figure 3: Assessment of PTPRB silencing. (97 KB)
(A) PTPRB levels after silencing demonstrating ~80% reduction in PTPRP transcript levels. (B) Following PTPRB silencing, VE-cadherin expression is greatly reduced. (C) PTPRB silencing increases the phosphorylation levels of VEGFR2.
- Supplementary Figure 4: Activation of PLCγ enzymes by loss of autoinhibition. (137 KB)
(A) Diagram showing the domains in PLCγ. The regulatory region (comprising the spPH, nSH2, cSH2 and SH3 domains; amino acids 465–952 in PLCγ1) is inserted in a loop that connects two halves (X and Y boxes) of the catalytic domain (purple). The cSH2 domain (red), involved in autoinhibition, is in direct contact with the catalytic domain. Disruption of the cSH2 domain by deletion or point mutation can cause constitutive PLCγ activation. The R707Q alteration in the cSH2 domain is indicated in blue. Residue numbering is per human PLCγ1. (B) Structure of the PLCγ1 cSH2 domain (PDB 4EY0). The interface involved in autoinhibition and residue R707 are shown. (C) Possible impact of R707Q alterations on the PLCγ1 cSH2 domain. R707 is involved in interactions with several residues (left, doted lines) that are likely to be important for domain stability and conformational changes. These interactions are disrupted when R707 is replaced by glutamine (right).
- Supplementary Text and Figures (3,690 KB)
Supplementary Figures 1–4 and Supplementary Table 6
- Supplementary Table 1 (74 KB)
Clinical features of cases included in this study with likely driver mutations.
- Supplementary Table 2 (90 KB)
Coding mutations in 11 angiosarcomas subjected to whole-genome or whole-exome sequencing.
- Supplementary Table 3 (1,164 KB)
Substitutions and indels identified in three angiosarcoma genomes.
- Supplementary Table 4 (107 KB)
Rearrangements identified in three angiosarcoma genomes.
- Supplementary Table 5 (17 KB)
Amplification and homozygous deletions identified in three angiosarcoma genomes.
- Supplementary Table 7 (71 KB)
Cancer genes screened by targeted sequencing.