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PLoS One. 2020 Jan 23;15(1):e0228014. doi: 10.1371/journal.pone.0228014. eCollection 2020.

MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma.

Author information

1
Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
2
Department of Surgical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
3
Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands.
4
Department of Surgical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
5
Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands.
6
Department of Pathology, Maria Skłodowska-Curie Institute-Oncology Center, Warsaw, Poland.
7
Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands.

Abstract

Approximately one-third of the patients with well-differentiated liposarcoma (WDLPS) will develop a local recurrence. Not much is known about the molecular relationship between the primary tumor and the recurrent tumor, which is important to reveal potential drivers of recurrence. Here we investigated the biology of recurrent WDLPS by comparing paired primary and recurrent WDLPS using microRNA profiling and genome-wide DNA methylation analyses. In total, 27 paired primary and recurrent WDLPS formalin-fixed and paraffin-embedded tumor samples were collected. MicroRNA expression profiles were determined using TaqMan® Low Density Array (TLDA) cards. Genome-wide DNA methylation and differentially methylated regions (DMRs) were assessed by methylated DNA sequencing (MeD-seq). A supervised cluster analysis based on differentially expressed microRNAs between paired primary and recurrent WDLPS did not reveal a clear cluster pattern separating the primary from the recurrent tumors. The clustering was also not based on tumor localization, time to recurrence, age or status of the resection margins. Changes in DNA methylation between primary and recurrent tumors were extremely variable, and no consistent DNA methylation changes were found. As a result, a supervised clustering analysis based on DMRs between primary and recurrent tumors did not show a distinct cluster pattern based on any of the features. Subgroup analysis for tumors localized in the extremity or the retroperitoneum also did not yield a clear distinction between primary and recurrent WDLPS samples. In conclusion, microRNA expression profiles and DNA methylation profiles do not distinguish between primary and recurrent WDLPS and no putative common drivers could be identified.

Conflict of interest statement

Ruben Boers, Joachim Boers, Wilfred F.J. van IJcken and Joost Gribnau declare a conflict of interest as shareholders of Methylomics B.V. This does not alter our adherence to PLOS ONE policies on sharing data and materials. The other authors declare no conflicts of interest.

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