Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma

Abstract

Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, we present the largest sequencing study of osteosarcoma to date, comprising 112 childhood and adult tumours encompassing all major histological subtypes. A key finding of our study is the identification of mutations in insulin-like growth factor (IGF) signalling genes in 8/112 (7%) of cases. We validate this observation using fluorescence in situ hybridization (FISH) in an additional 87 osteosarcomas, with IGF1 receptor (IGF1R) amplification observed in 14% of tumours. These findings may inform patient selection in future trials of IGF1R inhibitors in osteosarcoma. Analysing patterns of mutation, we identify distinct rearrangement profiles including a process characterized by chromothripsis and amplification. This process operates recurrently at discrete genomic regions and generates driver mutations. It may represent an age-independent mutational mechanism that contributes to the development of osteosarcoma in children and adults alike.

Figure 1. The cancer gene landscape of osteosarcoma.

The driver mutations of 112 osteosarcomas are shown in a. For each mutated cancer gene the percentage of 112 tumours with at least one driver mutation is shown, subdivided by mutation type. Blue: point mutation (substitutions; indels). Green: structural variant (amplification; homozygous deletion; disruptive breakpoint). (b) Driver events that were found in IGF1R signalling genes operative at the level of IGF1R. Blue square: amplification. Red circle: truncating mutation. An example of an amplicon is shown in c, found in case PD7193a. The x axis shows genomic position in mega bases and the y axis shows absolute copy number. Each dot in the plot represents the copy number of a particular genomic position. Lines and arcs: breakpoint with rearrangements coded by colour. Brown: tandem duplication; blue: deletion; green and turquoise: inversion; grey with arrowheads: interchromosomal rearrangement. (d) The key components of IGF signalling. At the level of the cell membrane, IGF signalling is mediated by IGF1R. IGF2R is a nonsignalling receptor that acts as a negative regulator of IGF1R. A number of circulating binding proteins modulate the function of IGF1R signalling, including IGFBP5 that is thought to inhibit IGF1R. Note that both IGF1 and IGF2 have autocrine, paracrine as well as endocrine sources.

Figure 2. Patterns of rearrangement in osteosarcoma.

In a the rare case of a tumour is shown in which rearrangements are confined to a single chromosome as a consequence of chromothripsis. This causes multiple driver events in this tumour, that is, loss of heterozygosity (LOH) of TP53 and MAP2K4 and disruption of NF1 by insertion of breakpoints into the gene footprint. (b–d) Examples of chromothripsis-amplification. The x axis shows genomic position in mega bases and the y axis shows absolute copy number. Each dot in the plot represents the copy number of a particular genomic position. Lines and arcs: breakpoint with rearrangements coded by colour. Brown: tandem duplication; blue: deletion; green and turquoise: inversion; grey with arrowheads: interchromosomal rearrangement.

Figure 3. Aggregate copy number profiles.

Aggregate copy number profiles of chromosomes 12 (a), 5 (b) and 17 (c) in 112 osteosarcomas are shown in comparison with chromosome 12 of 643 cases of glioblastoma multiforme (d) and to chromosome 17 of 267 soft tissue sarcomas (e). Using copy number calls from this and other studies, aggregate copy number profiles for each chromosome and tumour type were generated. Blue shaded area highlights the first and third quartiles of copy numbers in each genomic position. Black represents the mean copy number in each genomic position. The x axis shows genomic position and the y axis shows copy number change (log2). Putative target genes are indicated with arrows.