Comprehensive mutational profiling identifies new driver events in cutaneous leiomyosarcoma

Abstract

Background: Cutaneous leiomyosarcoma (cLMS) is a rare soft-tissue neoplasm, showing smooth muscle differentiation, that arises from the mesenchymal cells of the dermis. To date, genetic investigation of these tumours has involved studies with small sample sizes and limited analyses that identified recurrent somatic mutations in RB1 and TP53, copy number gain of MYOCD and IGF1R, and copy number loss of PTEN.

Objectives: To better understand the molecular pathogenesis of cLMS, we comprehensively explored the mutational landscape of these rare tumours to identify candidate driver events.

Methods: In this retrospective, multi-institutional study, we performed whole-exome sequencing and RNA sequencing in 38 cases of cLMS.

Results: TP53 and RB1 were identified as significantly mutated and thus represent validated driver genes of cLMS. COSMIC mutational signatures SBS7a/b and DBS1 were recurrent; thus, ultraviolet light exposure may be an aetiological factor driving cLMS. Analysis of significantly recurrent somatic copy number alterations, which represent candidate driver events, found focal (< 10 Mb) deletions encompassing TP53 and KDM6B, and amplifications encompassing ZMYM2, MYOCD, MAP2K4 and NCOR1. A larger (24 Mb) recurrent deletion encompassing CYLD was also identified as significant. Significantly recurrent broad copy number alterations, involving at least half of a chromosome arm, included deletions of 6p/q, 10p/q, 11q, 12q, 13q and 16p/q, and amplification of 15q. Notably PTEN is located on 10q, RB1 on 13q and IGFR1 on 15q. Fusion gene analysis identified recurrent CRTC1/CRTC3::MAML2 fusions, as well as many novel fusions in individual samples.

Conclusions: Our analysis of the largest number of cases of cLMS to date highlights the importance of large cohort sizes and exploration beyond small targeted gene panels when performing molecular analyses, as it allowed a comprehensive exploration of the mutational landscape of these tumours and identification of novel candidate driver events. It also uniquely afforded the opportunity to compare the molecular phenotype of cLMS with LMS of other tissue types, such as uterine and soft-tissue LMS. Given that molecular profiling has resulted in the development of novel targeted treatment approaches for uterine and soft-tissue LMS, our study now allows the same opportunities to become available for patients with cLMS.

Figure 1

Overall somatic mutational landscape of cutaneous leiomyosarcoma. Tumour mutational burden (TMB) is shown as mutations per megabase. Ultraviolet (UV) signature indicates samples with the COSMIC signature SBS7. Significantly recurrent broad deletions or amplifications include the short (p) or long (q) arm of the chromosomes listed. The significantly recurrent focal copy number alterations shown include amplifications/deletions < 10 Mb in size. Specifically, the focal deletion is a 242-kb region overlapping 17p13.1 and the focal amplifications are a 0.9-Mb region within 13q12.11 and a 4.1-Mb region overlapping 17p12. Loss of heterozygosity (LOH) status is shown for TP53 and RB1 and includes copy number loss (LOH), copy neutral LOH (cn-LOH) and copy gain LOH. Both focal and broad copy number losses encompassing either TP53 or RB1 were used to determine LOH status. The oncoplot panel shows OncoKB^TM cancer genes for which a mutation was present in at least three samples. TP53 and RB1 are significantly mutated genes. For tumour site, the locations are either the extremities (arms, hands, legs and feet) or trunk (shoulders, torso and buttocks/genital areas).

Figure 2

CRTC1::MAML2 and CRTC3::MAML2 fusion genes in cutaneous leiomyosarcoma. Schematic of the CRTC1::MAML2 and CRTC3::MAML2 fusions found in two representative cutaneous leiomyosarcoma samples. The vertical red bars on the chromosome images denote the location of the gene within the chromosome. The grey blocks on the gene images represent the exons that are present in the gene fusion that is formed, with the red arc representing the joining of the two genes. The breakpoints for these interchromosomal fusions were different between the individual tumours; however, the resulting transcript involved exons 1–3 of CRTC1 or 1–2 of CRTC3 being spliced to exons 2–5 of MAML2. Chr., chromosome.