Integrating Methylomic and Fragmentomic Profiling in Soft Tissue Sarcoma: Unravelling Novel Epigenetic Signatures

Background: DNA sequencing and copy number variation (CNV) analysis have become central to genomic research. Methylomic and fragmentomic profiles are inherently present in cell-free DNA (cfDNA) and circulating tumour DNA (ctDNA). We integrated these epigenetic profiles in plasma-derived DNA from patients with liposarcoma (LPS) and leiomyosarcoma (LMS).

Method: Plasma-derived ctDNA samples were sequenced using the PromethION platform (Oxford Nanopore Technologies). Reference-based alignment enabled the detection of epigenetic modification. Methylation deconvolution and fragmentation analysis were performed using two validated computational tools.

Results: 80 LPS and 24 LMS ctDNA were analysed. ONT data revealed a significantly reduced global methylation in LPS samples compared to LMS. Interestingly, locus gene methylation (RASSF1A) was generally higher in LMS compared to LPS. Cell type deconvolution revealed that granulocytes were the predominant cell origin in both LPS and LMS, with average cfDNA signals of 36.9% and 40.5%, respectively (p = 0.2795). The adipocyte and smooth muscle signals were 0.152% and 0.092% in LPS, in contrast to 0% and 0.05% in LMS, which reflects a low cell-type-specific tumour signal. A higher density of total whole genome DNA fragments was associated with a gained MDM2 copy number compared to a normal copy number in LPS.

Conclusions: Hypermethylation of locus RASSF1A is associated with LMS. Whole-genome hypomethylation is a feature of LPS. Methylation deconvolution may help detect the cell origin in cancer of unknown primary (CUP). Whole-genome fragment size density appears to be more abundant in samples with a gained copy number of the MDM2 gene in LPS.