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

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 investigat...

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Autores principales: Vos, Melissa, Boers, Ruben, Vriends, Anne L. M., Boers, Joachim, van Kuijk, Patricia F., van Houdt, Winan J., van Leenders, Geert J. L. H., Wagrodzki, Michal, van IJcken, Wilfred F. J., Gribnau, Joost, Grünhagen, Dirk J., Verhoef, Cornelis, Sleijfer, Stefan, Wiemer, Erik A. C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977735/
https://www.ncbi.nlm.nih.gov/pubmed/31971976
http://dx.doi.org/10.1371/journal.pone.0228014
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author Vos, Melissa
Boers, Ruben
Vriends, Anne L. M.
Boers, Joachim
van Kuijk, Patricia F.
van Houdt, Winan J.
van Leenders, Geert J. L. H.
Wagrodzki, Michal
van IJcken, Wilfred F. J.
Gribnau, Joost
Grünhagen, Dirk J.
Verhoef, Cornelis
Sleijfer, Stefan
Wiemer, Erik A. C.
author_facet Vos, Melissa
Boers, Ruben
Vriends, Anne L. M.
Boers, Joachim
van Kuijk, Patricia F.
van Houdt, Winan J.
van Leenders, Geert J. L. H.
Wagrodzki, Michal
van IJcken, Wilfred F. J.
Gribnau, Joost
Grünhagen, Dirk J.
Verhoef, Cornelis
Sleijfer, Stefan
Wiemer, Erik A. C.
author_sort Vos, Melissa
collection PubMed
description 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.
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spelling pubmed-69777352020-02-07 MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma Vos, Melissa Boers, Ruben Vriends, Anne L. M. Boers, Joachim van Kuijk, Patricia F. van Houdt, Winan J. van Leenders, Geert J. L. H. Wagrodzki, Michal van IJcken, Wilfred F. J. Gribnau, Joost Grünhagen, Dirk J. Verhoef, Cornelis Sleijfer, Stefan Wiemer, Erik A. C. PLoS One Research Article 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. Public Library of Science 2020-01-23 /pmc/articles/PMC6977735/ /pubmed/31971976 http://dx.doi.org/10.1371/journal.pone.0228014 Text en © 2020 Vos et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Vos, Melissa
Boers, Ruben
Vriends, Anne L. M.
Boers, Joachim
van Kuijk, Patricia F.
van Houdt, Winan J.
van Leenders, Geert J. L. H.
Wagrodzki, Michal
van IJcken, Wilfred F. J.
Gribnau, Joost
Grünhagen, Dirk J.
Verhoef, Cornelis
Sleijfer, Stefan
Wiemer, Erik A. C.
MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma
title MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma
title_full MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma
title_fullStr MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma
title_full_unstemmed MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma
title_short MicroRNA expression and DNA methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma
title_sort microrna expression and dna methylation profiles do not distinguish between primary and recurrent well-differentiated liposarcoma
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977735/
https://www.ncbi.nlm.nih.gov/pubmed/31971976
http://dx.doi.org/10.1371/journal.pone.0228014
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