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


Autoři: Melissa Vos aff001;  Ruben Boers aff003;  Anne L. M. Vriends aff001;  Joachim Boers aff003;  Patricia F. van Kuijk aff001;  Winan J. van Houdt aff004;  Geert J. L. H. van Leenders aff005;  Michal Wagrodzki aff006;  Wilfred F. J. van IJcken aff007;  Joost Gribnau aff003;  Dirk J. Grünhagen aff002;  Cornelis Verhoef aff002;  Stefan Sleijfer aff001;  Erik A. C. Wiemer aff001
Působiště autorů: Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands aff001;  Department of Surgical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands aff002;  Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, the Netherlands aff003;  Department of Surgical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands aff004;  Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands aff005;  Department of Pathology, Maria Skłodowska-Curie Institute-Oncology Center, Warsaw, Poland aff006;  Center for Biomics, Erasmus University Medical Center, Rotterdam, the Netherlands aff007
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0228014

Souhrn

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.

Klíčová slova:

DNA methylation – Gene pool – Hierarchical clustering – Methylation – MicroRNAs – Surgical resection – Tumor resection – Liposarcoma


Zdroje

1. Fletcher CDM, Bridge JA, Hogendoorn PCW, Mertens F, World Health Organization, International Agency for Research on Cancer. WHO classification of tumours of soft tissue and bone. Lyon: IARC Press; 2013.

2. The Netherlands Comprehensive Cancer Registry. Bijlage D Deelrapportage voor wekedelensarcomen. The Netherlands Comprehensive Cancer Organisation (IKNL), 2014.

3. Hayes J, Peruzzi PP, Lawler S. MicroRNAs in cancer: biomarkers, functions and therapy. Trends in Molecular Medicine. 2014;20(8):460–9. doi: 10.1016/j.molmed.2014.06.005 25027972

4. Di Leva G, Garofalo M, Croce CM. MicroRNAs in cancer. Annu Rev Pathol. 2014;9:287–314. doi: 10.1146/annurev-pathol-012513-104715 24079833.

5. Lujambio A, Lowe SW. The microcosmos of cancer. Nature. 2012;482(7385):347–55. doi: 10.1038/nature10888 22337054.

6. Gits CM, van Kuijk PF, Jonkers MB, Boersma AW, Smid M, van Ijcken WF, et al. MicroRNA expression profiles distinguish liposarcoma subtypes and implicate miR-145 and miR-451 as tumor suppressors. Int J Cancer. 2014;135(2):348–61. doi: 10.1002/ijc.28694 24375455.

7. Sun R, Shen JK, Choy E, Yu Z, Hornicek FJ, Duan Z. The emerging roles and therapeutic potential of microRNAs (miRs) in liposarcoma. Discov Med. 2015;20(111):311–24. 26645903.

8. Ugras S, Brill E, Jacobsen A, Hafner M, Socci ND, Decarolis PL, et al. Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Res. 2011;71(17):5659–69. Epub 2011/06/23. doi: 0008-5472.CAN-11-0890 [pii] doi: 10.1158/0008-5472.CAN-11-0890 21693658; PubMed Central PMCID: PMC3165140.

9. Vincenzi B, Iuliani M, Zoccoli A, Pantano F, Fioramonti M, De Lisi D, et al. Deregulation of dicer and mir-155 expression in liposarcoma. Oncotarget. 2015;6(12):10586–91. doi: 10.18632/oncotarget.3201 25888631.

10. Kapodistrias N, Mavridis K, Batistatou A, Gogou P, Karavasilis V, Sainis I, et al. Assessing the clinical value of microRNAs in formalin-fixed paraffin-embedded liposarcoma tissues: Overexpressed miR-155 is an indicator of poor prognosis. Oncotarget. 2016. doi: 10.18632/oncotarget.14320 28036291.

11. Lee DH, Amanat S, Goff C, Weiss LM, Said JW, Doan NB, et al. Overexpression of miR-26a-2 in human liposarcoma is correlated with poor patient survival. Oncogenesis. 2013;2:e47. doi: 10.1038/oncsis.2013.10 23689287.

12. Renner M, Czwan E, Hartmann W, Penzel R, Brors B, Eils R, et al. MicroRNA profiling of primary high-grade soft tissue sarcomas. Genes Chromosomes Cancer. 2012;51(11):982–96. doi: 10.1002/gcc.21980 22811003.

13. Subramanian S, Lui WO, Lee CH, Espinosa I, Nielsen TO, Heinrich MC, et al. MicroRNA expression signature of human sarcomas. Oncogene. 2008;27(14):2015–26. Epub 2007/10/09. doi: 1210836 [pii] doi: 10.1038/sj.onc.1210836 17922033.

14. Zhang P, Bill K, Liu J, Young E, Peng T, Bolshakov S, et al. MiR-155 is a liposarcoma oncogene that targets casein kinase-1alpha and enhances beta-catenin signaling. Cancer Res. 2012;72(7):1751–62. doi: 10.1158/0008-5472.CAN-11-3027 22350414.

15. Nezu Y, Hagiwara K, Yamamoto Y, Fujiwara T, Matsuo K, Yoshida A, et al. miR-135b, a key regulator of malignancy, is linked to poor prognosis in human myxoid liposarcoma. Oncogene. 2016;35(48):6177–88. doi: 10.1038/onc.2016.157 27157622.

16. Schubeler D. Function and information content of DNA methylation. Nature. 2015;517(7534):321–6. doi: 10.1038/nature14192 25592537.

17. Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol. 2010;28(10):1057–68. doi: 10.1038/nbt.1685 20944598.

18. De Carvalho DD, Sharma S, You JS, Su SF, Taberlay PC, Kelly TK, et al. DNA methylation screening identifies driver epigenetic events of cancer cell survival. Cancer Cell. 2012;21(5):655–67. doi: 10.1016/j.ccr.2012.03.045 22624715.

19. Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer. 2003;3(4):253–66. doi: 10.1038/nrc1045 12671664.

20. Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet. 2012;13(10):679–92. doi: 10.1038/nrg3270 22945394.

21. Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, et al. DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia. Cancer cell. 2010;17(1):13–27. doi: 10.1016/j.ccr.2009.11.020 PubMed PMID: PMC3008568. 20060365

22. Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010;17(5):510–22. doi: 10.1016/j.ccr.2010.03.017 20399149.

23. Brock MV, Hooker CM, Ota-Machida E, Han Y, Guo M, Ames S, et al. DNA methylation markers and early recurrence in stage I lung cancer. N Engl J Med. 2008;358(11):1118–28. doi: 10.1056/NEJMoa0706550 18337602.

24. Boers R, Boers J, de Hoon B, Kockx C, Ozgur Z, Molijn A, et al. Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI. Genome Res. 2018;28(1):88–99. Epub 2017/12/10. doi: gr.222885.117 [pii] doi: 10.1101/gr.222885.117 29222086; PubMed Central PMCID: PMC5749185.

25. Cancer Genome Atlas Research Network. Electronic address edsc, Cancer Genome Atlas Research N. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell. 2017;171(4):950–65 e28. Epub 2017/11/04. doi: S0092-8674(17)31203-5 [pii] doi: 10.1016/j.cell.2017.10.014 29100075; PubMed Central PMCID: PMC5693358.

26. Davidovic R, Sopta J, Mandusic V, Krajnovic M, Stanojevic M, Tulic G, et al. p14(ARF) methylation is a common event in the pathogenesis and progression of myxoid and pleomorphic liposarcoma. Med Oncol. 2013;30(3):682. doi: 10.1007/s12032-013-0682-9 23918242.

27. Taylor BS, DeCarolis PL, Angeles CV, Brenet F, Schultz N, Antonescu CR, et al. Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discov. 2011;1(7):587–97. doi: 10.1158/2159-8290.CD-11-0181 22328974.

28. Mazzu YZ, Hu Y, Soni RK, Mojica KM, Qin LX, Agius P, et al. miR-193b-Regulated Signaling Networks Serve as Tumor Suppressors in Liposarcoma and Promote Adipogenesis in Adipose-Derived Stem Cells. Cancer Res. 2017;77(21):5728–40. doi: 10.1158/0008-5472.CAN-16-2253 28882999.

29. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8(1):118–27. Epub 2006/04/25. doi: kxj037 [pii] doi: 10.1093/biostatistics/kxj037 16632515.

30. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, et al. MicroRNA expression in zebrafish embryonic development. Science. 2005;309(5732):310–1. doi: 10.1126/science.1114519 15919954.

31. Zhou J, Sears RL, Xing X, Zhang B, Li D, Rockweiler NB, et al. Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. BMC genomics. 2017;18(1):724–. doi: 10.1186/s12864-017-4115-6 28899353.

32. Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome research. 2013;23(9):1522–40. doi: 10.1101/gr.156539.113 23804400.

33. Su M, Qin B, Liu F, Chen Y, Zhang R. miR-885-5p upregulation promotes colorectal cancer cell proliferation and migration by targeting suppressor of cytokine signaling. Oncol Lett. 2018;16(1):65–72. doi: 10.3892/ol.2018.8645 29928388.

34. Lam CS, Ng L, Chow AK, Wan TM, Yau S, Cheng NS, et al. Identification of microRNA 885-5p as a novel regulator of tumor metastasis by targeting CPEB2 in colorectal cancer. Oncotarget. 2017;8(16):26858–70. doi: 10.18632/oncotarget.15844 28460469.

35. Liu Y, Bao Z, Tian W, Huang G. miR-885-5p suppresses osteosarcoma proliferation, migration and invasion through regulation of β-catenin. Oncology letters. 2019;17(2):1996–2004. Epub 2018/11/28. doi: 10.3892/ol.2018.9768 30675266.

36. Garsed DW, Marshall OJ, Corbin VD, Hsu A, Di Stefano L, Schroder J, et al. The architecture and evolution of cancer neochromosomes. Cancer Cell. 2014;26(5):653–67. Epub 2014/12/18. doi: S1535-6108(14)00373-0 [pii] doi: 10.1016/j.ccell.2014.09.010 25517748.

37. Hoekstra HJ, Haas RLM, Verhoef C, Suurmeijer AJH, van Rijswijk CSP, Bongers BGH, et al. Adherence to Guidelines for Adult (Non-GIST) Soft Tissue Sarcoma in the Netherlands: A Plea for Dedicated Sarcoma Centers. Ann Surg Oncol. 2017;24(11):3279–88. Epub 2017/07/28. doi: 10.1245/s10434-017-6003-3 [pii]. 28748443; PubMed Central PMCID: PMC5596052.

38. Otsu H, Watanabe M, Inoue N, Masutani R, Iwatani Y. Intraindividual variation of microRNA expression levels in plasma and peripheral blood mononuclear cells and the associations of these levels with the pathogenesis of autoimmune thyroid diseases. Clin Chem Lab Med. 2017;55(5):626–35. doi: 10.1515/cclm-2016-0449 28195542.

39. Flanagan JM, Popendikyte V, Pozdniakovaite N, Sobolev M, Assadzadeh A, Schumacher A, et al. Intra- and interindividual epigenetic variation in human germ cells. American journal of human genetics. 2006;79(1):67–84. Epub 2006/05/25. doi: 10.1086/504729 16773567.


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2020 Číslo 1