Germinal GLT8D1, GATAD2A and SLC25A39 mutations in a patient with a glomangiopericytal tumor and five different sarcomas over a 10-year period

Abstract

Soft tissue sarcoma represents about 1% of all adult cancers. Occurrence of multiple sarcomas in a same individual cannot be fortuitous. A 72-year-old patient had between 2007 and 2016 a glomangiopericytal tumor of the right forearm and a succession of sarcomas of the extremities: a leiomyosarcoma of the left buttock, a myxofibrosarcoma (MFS) of the right forearm, a MFS of the left scapula, a left latero-thoracic MFS and two undifferentiated sarcomas on the left forearm. Pathological examination of the six locations was not in favor of disease with local/distant recurrences but could not confirm different diseases. An extensive molecular analysis including DNA-array, RNA-sequencing and DNA-Sanger-sequencing, was thus performed to determine the link between them. The genomic profile of the glomangiopericytal tumor and the six sarcomas revealed that five sarcomas were different diseases and one was the local recurrence of the glomangiopericytal tumor. While the chromosomal alterations in the six tumors were different, a common somatic CDKN2A/CDKN2B deletion was identified. RNA-sequencing of five tumors identified mutations in GLT8D1, GATAD2A and SLC25A39 in all samples. The germline origin of these mutations was confirmed by Sanger-sequencing. Innovative molecular analysis methods have made possible a better understanding of the complex tumorigenesis of multiple sarcomas.

Figure 1

Location and histological subtypes of the seven soft tissue tumors. LMS leiomyosarcoma, MFS myxofibrosarcoma, UPS undifferentiated pleomorphic sarcoma.

Figure 2

Histological characteristics of the soft tissue tumors. (A) S2007A: glomangiopericytal tumor with uncertain potential: ovoid cells embedded in a myxoid background and concentrically arranged around rounded vascular structures. The tumor is classified according to the WHO classification as a tumor with uncertain potential because of its size. (B) S2007B: grade 3 LMS: proliferation consisting of long bundles composed of spindle cells with abundant eosinophilic cytoplasm. Black arrow: atypical mitosis. (C) S2008: Low grade MFS: slightly atypical fusiform cells embedded in myxoid background. Numerous thin-walled vessels. (D) S2012A: MFS: High Power magnification of atypical spindle cells. Black arrow: atypical mitosis. (E) S2012B: MFS: At low magnification power, juxtaposition of dense spindle cell area and paucicellular myxoid proliferation. (F) S2016A: grade 2 UPS: proliferation of spindle cells dissecting adipose tissue (at the bottom). (G) S2016B: grade 2 UPS: atypical spindle and pleomorphic cells on a myxoid background. Black arrow: atypical mitosis. LMS leiomyosarcoma, HE hematoxylin and eosin staining, MFS myxofibrosarcoma, UPS undifferentiated pleomorphic sarcoma. Scale bar: 100 µm.

Figure 3

Tumor genomic profiles. Copy number variations (CNVs) and allele frequency differences, plotted on the upper and lower lane of each panel respectively, demonstrate that all tumors present different genomic profiles except for S2007A and S2008 which have alterations in common. Deletion of CDKN2A and CDKN2B genes on the chromosome 9 is highlited. Ploidie of each tumor is indicated near each profile and the status of the CDKN2A/CDKN2B deletion in each tumor is defined. x axis: chromosome 1 to chromosome Y; y axis: weighted log2(ratio) (upper lane) and allele difference (lower lane).

Figure 4

Validated genomic mutations. Sequence chromatograms showing GLT8D1, GATAD2A and SLC25A39 mutations observed on genomic DNA in two healthy tissues (HT2012, HT2013) and two tumors (S2008, S2012A) (Sequence viewer: FinchTV, Geospiza). Frames indicate mutation sites (hg38, GLT8D1: chr3:g.52695006G > C, GATAD2A: chr19:g.19465410A > G, SLC25A39: chr17:g.44320429C > T). Allelic status is indicated for each case and number of copies of each gene, determined according to DNA-array data, in each tumor is also presented. MUT mutated allele, WT wild-type allele.