Predictive value of micro-RNA expression profiling in pediatric desmoid fibromatosis

References

• Kasper B, Baumgarten C, Garcia J, et al. An update on the management of sporadic desmoid-type fibromatosis: a European consensus initiative between sarcoma PAtients EuroNet (SPAEN) and European organization for research and treatment of cancer (EORTC)/soft tissue and bone sarcoma group (STBSG). Ann Oncol. 2017;28(10):2399–2408. doi: 10.1093/annonc/mdx323.
   PubMed Web of Science ®Google Scholar
• Hawkins MM, Lancashire ER, Winter DL, et al. The british childhood cancer survivor study: objectives, methods, population structure, response rates and initial descriptive information. Pediatr Blood Cancer. 2008;50(5):1018–1025. doi: 10.1002/pbc.21335.
   PubMed Web of Science ®Google Scholar
• Martínez Trufero J, Pajares Bernad I, Torres Ramón I, et al. Desmoid-Type fibromatosis: who, when, and how to treat. Curr Treat Options Oncol. 2017;18(5):29. doi: 10.1007/s11864-017-0474-0.
   PubMed Web of Science ®Google Scholar
• Al-Jazrawe M, Au M, Alman B. Optimal therapy for desmoid tumors: current options and challenges for the future. Expert Rev Anticancer Ther. 2015;15(12):1443–1458. doi: 10.1586/14737140.2015.1096203.
   PubMed Web of Science ®Google Scholar
• Ganeshan D, Amini B, Nikolaidis P, et al. Current update on desmoid fibromatosis. J Comput Assist Tomogr. 2019;43(1):29–38. doi: 10.1097/RCT.0000000000000790.
   PubMed Web of Science ®Google Scholar
• Skubitz KM. Biology and treatment of aggressive fibromatosis or desmoid tumor. Mayo Clin Proc. 2017;92(6):947–964. doi: 10.1016/j.mayocp.2017.02.012.
   PubMed Web of Science ®Google Scholar
• Penel N, Le Cesne A, Bonvalot S, et al. Surgical versus non-surgical approach in primary desmoid-type fibromatosis patients: a nationwide prospective cohort from the french sarcoma group. Eur J Cancer. 2017;83:125–131. doi: 10.1016/j.ejca.2017.06.017.
   PubMed Web of Science ®Google Scholar
• Kasper B, Gruenwald V, Reichardt P, et al. Correlation of CTNNB1 mutation status with progression arrest rate in RECIST progressive Desmoid-Type fibromatosis treated with imatinib: translational research results from a phase 2 study of the german interdisciplinary sarcoma group (GISG-01). Ann Surg Oncol. 2016;23(6):1924–1927. doi: 10.1245/s10434-016-5132-4.
   PubMed Web of Science ®Google Scholar
• Nishida Y, Kawai A, Toguchida J, et al. Clinical features and treatment outcome of desmoid-type fibromatosis: based on a bone and soft tissue tumor registry in Japan. Int J Clin Oncol. 2019;24(11):1498–1505. doi: 10.1007/s10147-019-01512-z.
   PubMed Web of Science ®Google Scholar
• Von Mehren M, Randall L, Benjamin R, et al. Soft tissue sarcoma, version 2.2014: featured updates to the NCCN guidelines. J Natl Compr Canc Netw. 2014;12(4):473–483. doi: 10.6004/jnccn.2014.0053.
   PubMed Web of Science ®Google Scholar
• Kunder R, Jalali R, Sridhar E, et al. Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalinfixed paraffin embedded medulloblastomas. Neuro Oncol. 2013;15(12):1644–1651. doi: 10.1093/neuonc/not123.
   PubMed Web of Science ®Google Scholar
• Gulino R, Forte S, Parenti R, et al. MicroRNA and pediatric tumors: future perspectives. Acta Histochem. 2015;117(4-5):339–354. doi: 10.1016/j.acthis.2015.02.007.
   PubMed Web of Science ®Google Scholar
• Sbaraglia M, Bellan E, Dei Tos AP. The 2020 WHO classification of soft tissue tumours: news and perspectives. Pathologica. 2021;113(2):70–84. doi: 10.32074/1591-951X-213.
   PubMed Web of Science ®Google Scholar
• Skapek SX, Ferguson WS, Granowetter L, et al. Vinblastine and methotrexate for desmoid fibromatosis in children: results of a pediatric oncology group phase II trial. J Clin Oncol. 2007;25(5):501–506. doi: 10.1200/JCO.2006.08.2966.
   PubMed Web of Science ®Google Scholar
• Stephen BD, Byrd D. AJCC. 7th ed. Cancer Staging Manual. New York: Springer; 2015.
   Google Scholar
• Andrews S. FastQC: a quality control tool for high throughput sequence data. 2019. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
   Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10. doi: 10.14806/ej.17.1.200.
   Google Scholar
• Ewels P, Magnusson M, Lundin S, et al. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048. doi: 10.1093/bioinformatics/btw354.
   PubMed Web of Science ®Google Scholar
• Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25.
   PubMed Web of Science ®Google Scholar
• Liao Y, Smyth GK, Shi W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–930. doi: 10.1093/bioinformatics/btt656.
   PubMed Web of Science ®Google Scholar
• Kozomara A, Birgaoanu M, Griffiths-Jones S. MiRBase: from microRNA sequences to function. Nucleic Acids Res. 2019;47(D1):D155–D162. doi: 10.1093/nar/gky1141.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi: 10.1186/s13059-014-0550-8.
   PubMed Web of Science ®Google Scholar
• Piper M, Kirchner R. Package ‘DEGreport‘. 2023.
   Google Scholar
• Create T, Data E. Using V, Description G. Package ‘ggplot2.’ 2023.
   Google Scholar
• Chang L, Zhou G, Soufan O, et al. miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology. Nucleic Acids Res. 2020;48(W1):W244–W251. doi: 10.1093/nar/gkaa467.
   PubMed Web of Science ®Google Scholar
• Dufresne A, Paturel M, Alberti L, et al. Prediction of desmoid tumor progression using miRNA expression profiling. Cancer Sci. 2015;106(5):650–655. doi: 10.1111/cas.12640.
   PubMed Web of Science ®Google Scholar
• Doudney CO, Rinaldi CN. Modification of UV-induced mutation frequency and cell survival of Escherichia coli B/r WP2 trp E65 by treatment before irradiation. J Bacteriol. 1984;160(1):233–238. doi: 10.1128/jb.160.1.233-238.1984.
   PubMed Web of Science ®Google Scholar
• Andy Bunn MK. A language and environment for statistical computing. R Foundation for Statistical Computing; 2017. http://www.gnu.org/copyleft/gpl.html.%0Ahttp://www.r-project.org/%0Ahttp://www.r-project.org.
   Google Scholar
• Salas S, Dufresne A, Bui B, et al. Prognostic factors influencing progression-free survival determined from a series of sporadic desmoid tumors: a wait-and-see policy according to tumor presentation. J Clin Oncol. 2011;29(26):3553–3558. doi: 10.1200/JCO.2010.33.5489.
   PubMed Web of Science ®Google Scholar
• Ruspi L, Cananzi FCM, Sicoli F, et al. Event-free survival in Desmoid-Type fibromatosis (DTF): a pre-post comparison of upfront surgery versus wait-and-see approach. Eur J Surg Oncol. 2021;47(5):1196–1200. doi: 10.1016/j.ejso.2020.08.009.
   PubMed Web of Science ®Google Scholar
• Salas S, Brulard C, Terrier P, et al. Gene expression profiling of desmoid tumors by cDNA microarrays and correlation with progression-free survival. Clin Cancer Res. 2015;21(18):4194–4200. doi: 10.1158/1078-0432.CCR-14-2910.
   PubMed Web of Science ®Google Scholar
• Rotelli MT, Refolo MG, Lippolis C, et al. The role of miRNA-133b and its target gene SIRT1 in FAP-derived desmoid tumor. Oncotarget. 2020;11(26):2484–2492. doi: 10.18632/oncotarget.27622.
   PubMedGoogle Scholar
• Tornin J, Martinez-Cruzado L, Santos L, et al. Inhibition of SP1 by the mithramycin analog EC-8042 efficiently targets tumor initiating cells in sarcoma. Oncotarget. 2016;7(21):30935–30950. doi: 10.18632/oncotarget.8817.
   PubMedGoogle Scholar
• Schmit K, Michiels C. TMEM proteins in cancer: a review. Front Pharmacol. 2018;9:1345. doi: 10.3389/fphar.2018.01345.
   PubMed Web of Science ®Google Scholar
• Wang Y, Gu W, Wen W, et al. SERPINH1 is a potential prognostic biomarker and correlated with immune infiltration: a Pan-Cancer analysis. Front Genet. 2021;12:756094. doi: 10.3389/fgene.2021.756094.
   PubMed Web of Science ®Google Scholar
• Gungormez C, Gumushan Aktas H, Dilsiz N, et al. Novel miRNAs as potential biomarkers in stage II Colon cancer: microarray analysis. Mol Biol Rep. 2019;46(4):4175–4183. doi: 10.1007/s11033-019-04868-7.
   PubMed Web of Science ®Google Scholar
• Crimi S, Falzone L, Gattuso G, et al. Droplet digital pcr analysis of liquid biopsy samples unveils the diagnostic role of hsa-mir-133a-3p and hsa-mir-375-3p in oral cancer. Biology (Basel). 2020;9(11):1–14. doi: 10.3390/biology9110379.
   Google Scholar
• Je EM, An CH, Yoo NJ, et al. Mutational analysis of PIK3CA, JAK2, BRAF, FOXL2, IDH1, AKT1 and EZH2 oncogenes in sarcomas. APMIS. 2012;120(8):635–639. doi: 10.1111/j.1600-0463.2012.02878.x.
   PubMed Web of Science ®Google Scholar
• Zhai Y, Jiang S, Li B, et al. Potential mechanisms of yanghe decoction in the treatment of soft tissue sarcoma and arteriosclerosis obliterans based on network pharmacology. Chinese Med Nat Prod. 2022;02(02):e77–e88. doi: 10.1055/s-0042-1755401.
   Google Scholar
• Gong H, Jiang A, Jiang R, et al. PTBP1 as a promising predictor of poor prognosis by regulating cell proliferation, immunosuppression, and drug sensitivity in SARC. Oxid Med Cell Longev. 2022;2022:5687238. doi: 10.1155/2022/5687238.
   PubMed Web of Science ®Google Scholar
• Wu N, Ren D, Li S, et al. RCC2 over-expression in tumor cells alters apoptosis and drug sensitivity by regulating Rac1 activation. BMC Cancer. 2018;18(1):67. doi: 10.1186/s12885-017-3908-y.
   PubMedGoogle Scholar
• Claesson-Welsh L, Welsh M. VEGFA and tumour angiogenesis. J Intern Med. 2013;273(2):114–127. doi: 10.1111/joim.12019.
   PubMed Web of Science ®Google Scholar
• Zhang H, Zhang Z, Gao L, et al. miR-1-3p suppresses proliferation of hepatocellular carcinoma through targeting SOX9. Onco Targets Ther. 2019;12:2149–2157. doi: 10.2147/OTT.S197326.
   PubMed Web of Science ®Google Scholar
• Riquelme I, Tapia O, Leal P, et al. miR-101-2, miR-125b-2 and miR-451a act as potential tumor suppressors in gastric cancer through regulation of the PI3K/AKT/mTOR pathway. Cell Oncol (Dordr). 2016;39(1):23–33. doi: 10.1007/s13402-015-0247-3.
   PubMed Web of Science ®Google Scholar