دورية أكاديمية
أعرض في EDS

Systems Biology Analysis for Ewing Sarcoma.

التفاصيل البيبلوغرافية
العنوان: Systems Biology Analysis for Ewing Sarcoma.
المؤلفون: Petrizzelli M; Institut Curie, PSL Research University, Paris, France.; INSERM U900, Paris, France.; CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, Paris, France., Merlevede J; Institut Curie, PSL Research University, Paris, France.; INSERM U900, Paris, France.; CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, Paris, France., Zinovyev A; Institut Curie, PSL Research University, Paris, France. Andrei.Zinovyev@curie.fr.; INSERM U900, Paris, France. Andrei.Zinovyev@curie.fr.; CBIO-Centre for Computational Biology, Mines ParisTech, PSL Research University, Paris, France. Andrei.Zinovyev@curie.fr.
المصدر: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2226, pp. 303-333.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: Totowa, NJ : Humana Press
Original Publication: Clifton, N.J. : Humana Press,
مواضيع طبية MeSH: Systems Biology*/methods, Bone Neoplasms/*etiology , Bone Neoplasms/*metabolism , Sarcoma, Ewing/*etiology , Sarcoma, Ewing/*metabolism, Bone Neoplasms/pathology ; Databases, Genetic ; Genomics/methods ; Humans ; Metabolomics/methods ; Models, Theoretical ; Proteomics/methods ; Sarcoma, Ewing/pathology ; Web Browser
مستخلص: Ewing sarcoma (EwS) is a highly aggressive pediatric bone cancer that is defined by a somatic fusion between the EWSR1 gene and an ETS family member, most frequently the FLI1 gene, leading to expression of a chimeric transcription factor EWSR1-FLI1. Otherwise, EwS is one of the most genetically stable cancers. The situation when the major cancer driver is well known looks like a unique opportunity for applying the systems biology approach in order to understand the EwS mechanisms as well as to uncover some general mechanistic principles of carcinogenesis. A number of studies have been performed revealing the direct and indirect effects of EWSR1-FLI1 on multiple aspects of cellular life. Nevertheless, the emerging picture of the oncogene action appears to be highly complex and systemic, with multiple reciprocal influences between the immediate consequences of the driver mutation and intracellular and intercellular molecular mechanisms, including regulation of transcription, epigenome, and tumoral microenvironment. In this chapter, we present an overview of existing molecular profiling resources available for EwS tumors and cell lines and provide an online comprehensive catalogue of publicly available omics and other datasets. We further highlight the systems biology studies of EwS, involving mathematical modeling of networks and integration of molecular data. We conclude that despite the seeming simplicity, a lot has yet to be understood on the systems-wide mechanisms connecting the driver mutation and the major cellular phenotypes of this pediatric cancer. Overall, this chapter can serve as a guide for a systems biology researcher to start working on EwS.
References: Grunewald TGP, Cidre-Aranaz F, Surdez D, Tomazou EM, de Alava E, Kovar H, Sorensen PH, Delattre O, Dirksen U (2018) Ewing sarcoma. Nat Rev Dis Primers 4(1):5. (PMID: 2997705910.1038/s41572-018-0003-x29977059)
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortes ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, SA MC, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, CWM R, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499(7457):214–218. (PMID: 237705672377056710.1038/nature12213)
Boulay G, Sandoval GJ, Riggi N, Iyer S, Buisson R, Naigles B, Awad ME, Rengarajan S, Volorio A, McBride MJ, Broye LC, Zou L, Stamenkovic I, Kadoch C, Rivera MN (2017) Cancer-specific retargeting of BAF complexes by a prion-like domain. Cell 171(1):163–178.e19. (PMID: 28844694679182310.1016/j.cell.2017.07.036)
Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437(7062):1173–1178. (PMID: 1618951410.1038/nature0420916189514)
Romeo S, Dei Tos AP (2010) Soft tissue tumors associated with EWSR1 translocation. Virchows Arch 456(2):219–234. (PMID: 1993678210.1007/s00428-009-0854-3)
Li Y, Luo H, Liu T, Zacksenhaus E, Ben-David Y (2015) The ets transcription factor Fli-1 in development, cancer and disease. Oncogene 34(16):2022–2031. (PMID: 2490916110.1038/onc.2014.162)
Gangwal K, Sankar S, Hollenhorst PC, Kinsey M, Haroldsen SC, Shah AA, Boucher KM, Watkins WS, Jorde LB, Graves BJ, Lessnick SL (2008) Microsatellites as EWS/FLI response elements in Ewing’s sarcoma. Proc Natl Acad Sci U S A 105(29):10149–10154. (PMID: 18626011248130610.1073/pnas.0801073105)
Guillon N, Tirode F, Boeva V, Zynovyev A, Barillot E, Delattre O (2009) The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. PLoS One 4(3):e4932. (PMID: 19305498265472410.1371/journal.pone.0004932)
Tirode F, Laud-Duval K, Prieur A, Delorme B, Charbord P, Delattre O (2007) Mesenchymal stem cell features of Ewing tumors. Cancer Cell 11(5):421–429. (PMID: 1748213210.1016/j.ccr.2007.02.027)
Stoll G, Surdez D, Tirode F, Laud K, Barillot E, Zinovyev A, Delattre O (2013) Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis. Nucleic Acids Res 41(19):8853–8871. (PMID: 23935076379944210.1093/nar/gkt678)
Kovar H, Amatruda J, Brunet E, Burdach S, Cidre-Aranaz F, de Alava E, Dirksen U, van der Ent W, Grohar P, Grunewald TGP, Helman L, Houghton P, Iljin K, Korsching E, Ladanyi M, Lawlor E, Lessnick S, Ludwig J, Meltzer P, Metzler M, Mora J, Moriggl R, Nakamura T, Papamarkou T, Radic Sarikas B, Redini F, Richter GHS, Rossig C, Schadler K, Schafer BW, Scotlandi K, Sheffield NC, Shelat A, Snaar-Jagalska E, Sorensen P, Stegmaier K, Stewart E, Sweet-Cordero A, Szuhai K, Tirado OM, Tirode F, Toretsky J, Tsafou K, Uren A, Zinovyev A, Delattre O (2016) The second European interdisciplinary Ewing sarcoma research summit−A joint effort to deconstructing the multiple layers of a complex disease. Oncotarget 7(8):8613–8624. (PMID: 26802024489099110.18632/oncotarget.6937)
Maguire LH, Thomas AR, Goldstein AM (2015) Tumors of the neural crest: common themes in development and cancer. Dev Dyn 244(3):311–322. (PMID: 2538266910.1002/dvdy.2422625382669)
Sand LGL, Szuhai K, Hogendoorn PCW (2015) Sequencing overview of Ewing sarcoma: A journey across genomic, Epigenomic and transcriptomic landscapes. Int J Mol Sci 16(7):16176–16215. (PMID: 26193259451994510.3390/ijms160716176)
Amiel A, Ohali A, Fejgin M, Sardos-Albertini F, Bouaron N, Cohen I, Yaniv I, Zaizov R, Avigad S (2003) Molecular cytogenetic parameters in Ewing sarcoma. Cancer Genet Cytogenet 140(2):107–112. (PMID: 1264564710.1016/S0165-4608(02)00659-312645647)
Armengol G, Tarkkanen M, Virolainen M, Forus A, Valle J, Bohling T, Asko-Seljavaara S, Blomqvist C, Elomaa I, Karaharju E et al (1997) Recurrent gains of 1q, 8 and 12 in the Ewing family of tumours by comparative genomic hybridization. Br J Cancer 75(10):1403–1409. (PMID: 9166930222349310.1038/bjc.1997.242)
Brisset S, Schleiermacher G, Peter M, Mairal A, Oberlin O, Delattre O, Aurias A (2001) Cgh analysis of secondary genetic changes in Ewing tumors: correlation with metastatic disease in a series of 43 cases. Cancer Genet Cytogenet 130(1):57–61. (PMID: 1167277510.1016/S0165-4608(01)00454-X11672775)
Ozaki T, Paulussen M, Poremba C, Brinkschmidt C, Rerin J, Ahrens S, Homann C, Hillmann A, Wai D, Schaefer KL et al (2001) Genetic imbalances revealed by comparative genomic hybridization in Ewing tumors. Genes Chromosom Cancer 32(2):164–171. (PMID: 1155028410.1002/gcc.117811550284)
Tarkkanen M, Kiuru-Kuhlefelt S, Blomqvist C, Armengol G, Bohling T, Ekfors T, Virolainen M, Lindholm P, Monge O, Picci P et al (1999) Clinical correlations of genetic changes by compara-tive genomic hybridization in Ewing sarcoma and related tumors. Cancer Genet Cytogenet 114(1):35–41. (PMID: 1052653310.1016/S0165-4608(99)00031-X10526533)
Ferreira B, Alonso J, Carrillo J, Acquadro F, Largo C, Suela J, Teixeira M, Cerveira N, Molares A, Gomez-Lopez G et al (2008) Array cgh and gene-expression profiling reveals distinct genomic in-stability patterns associated with dna repair and cell-cycle checkpoint pathways in Ewing’s sarcoma. Oncogene 27(14):2084–2090. (PMID: 1795212410.1038/sj.onc.121084517952124)
Savola S, Klami A, Tripathi A, Niini T, Serra M, Picci P, Kaski S, Zambelli D, Scotlandi K, Knuutila S (2009) Combined use of expression and cgh arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors. BMC Cancer 9(1):17. (PMID: 19144156263334510.1186/1471-2407-9-17)
Mackintosh C, Ordóñez JL, García-Domínguez DJ, Sevillano V, Llombart-Bosch A, Szuhai K, Scotlandi K, Alberghini M, Sciot R, Sinnaeve F, Hogendoorn PCW, Picci P, Knuutila S, Dirksen U, Debiec-Rychter M, Schaefer KL, de Alava E (2012) 1q gain and CDT2 overexpression underlie an aggressive and highly proliferative form of Ewing sarcoma. Oncogene 31(10):1287–1298. (PMID: 2182231010.1038/onc.2011.31721822310)
Postel-Vinay S, Veron AS, Tirode F, Pierron G, Reynaud S, Kovar H, Oberlin O, Lapouble E, Ballet S, Lucchesi C, Kontny U, Gonzalez-Neira A, Picci P, Alonso J, Patino-Garcia A, de Paillerets BB, Laud K, Dina C, Froguel P, Clavel-Chapelon F, Doz F, Michon J, Chanock SJ, Thomas G, Cox DG, Delattre O (2012) Common variants near TARDBP and EGR2 are associated with susceptibility to Ewing sarcoma. Nat Genet 44(3):323–327. (PMID: 2232751410.1038/ng.108522327514)
Machiela MJ, Grunewald TGP, Surdez D, Reynaud S, Mirabeau O, Karlins E, Rubio RA, Zaidi S, Grossetete-Lalami S, Ballet S, Lapouble E, Laurence V, Michon J, Pierron G, Kovar H, Gaspar N, Kontny U, Gonzalez-Neira A, Picci P, Alonso J, Patino-Garcia A, Corradini N, Berard PM, Freedman ND, Rothman N, Dagnall CL, Burdett L, Jones K, Manning M, Wyatt K, Zhou W, Yeager M, Cox DG, Hoover RN, Khan J, Armstrong GT, Leisenring WM, Bhatia S, Robison LL, Kulozik AE, Kriebel J, Meitinger T, Metzler M, Hartmann W, Strauch K, Kirchner T, Dirksen U, Morton LM, Mirabello L, Tucker MA, Tirode F, Chanock SJ, Delattre O (2018) Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility. Nat Commun 9(1):3184. (PMID: 30093639608537810.1038/s41467-018-05537-2)
Grunewald TGP, Bernard V, Gilardi-Hebenstreit P, Raynal V, Surdez D, Aynaud MM, Mirabeau O, Cidre-Aranaz F, Tirode F, Zaidi S, Perot G, Jonker AH, Lucchesi C, Le Deley MC, Oberlin O, Marec-Berard P, Veron AS, Reynaud S, Lapouble E, Boeva V, Rio Frio T, Alonso J, Bhatia S, Pierron G, Cancel-Tassin G, Cussenot O, Cox DG, Morton LM, Machiela MJ, Chanock SJ, Charnay P, Delattre O (2015) Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite. Nat Genet 47(9):1073–1078. (PMID: 26214589459107310.1038/ng.3363)
Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Holting TLB, Grossetete S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Perez L, Westermann F, Hartmann W, Dirksen U, Gymrek M, Anderson ND, Shlien A, Rotblat B, Kirchner T, Delattre O, TGP G (2019) Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes. Nat Commun 10(1):1–10. (PMID: 10.1038/s41467-019-12071-2)
Tirode F, Surdez D, Ma X, Parker M, Le Deley MC, Bahrami A, Zhang Z, Lapouble E, Reynaud S, Rusch M et al (2014) Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of stag2 and tp53 mutations. Cancer Discov 4(11):1342–1353. (PMID: 25223734426496910.1158/2159-8290.CD-14-0622)
Brohl AS, Solomon DA, Chang W, Wang J, Song Y, Sindiri S, Patidar R, Hurd L, Chen L, Shern JF et al (2014) The genomic landscape of the Ewing sarcoma family of tumors reveals recurrent stag2 mutation. PLoS Genet 10(7):e1004475. (PMID: 25010205409178210.1371/journal.pgen.1004475)
Crompton BD, Stewart C, Taylor-Weiner A, Alexe G, Kurek KC, Calicchio ML, Kiezun A, Carter SL, Shukla SA, Mehta SS et al (2014) The genomic landscape of pediatric Ewing sarcoma. Cancer Discov 4(11):1326–1341. (PMID: 2518694910.1158/2159-8290.CD-13-103725186949)
Aynaud MM, Mirabeau O, Gruel N, Grossetete S, Boeva V, Durand S, Surdez D, Saulnier O, Za di S, Gribkova S, Fouche A, Kairov U, Raynal V, Tirode F, Grunewald TG, Bohec M, Baulande S, Janoueix-Lerosey I, Vert JP, Barillot E, Delattre O, Zinovyev A (2020) Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single-cell resolution. Cell Rep 30(6):1767–1779.e6. (PMID: 3204900910.1016/j.celrep.2020.01.04932049009)
Miller HE, Gorthi A, Bassani N, Lawrence LA, Iskra BS, Bishop AJR (2020) Reconstruction of Ewing sarcoma developmental context from mass-scale transcriptomics reveals characteristics of EWSR1-FLI1 permissibility. Cancers 12(4):948. (PMID: 722617510.3390/cancers120409487226175)
Savola S, Klami A, Myllykangas S, Manara C, Scotlandi K, Picci P, Knuutila S, Vakkila J (2011) High expression of complement component 5 (C5) at tumor site associates with superior survival in Ewing’s sarcoma family of tumour patients. ISRN Oncol 2011:1–10. (PMID: 10.5402/2011/168712)
Volchenboum SL, Andrade J, Huang L, Barkauskas DA, Krailo M, Womer RB, Ranft A, Potratz J, Dirksen U, Triche TJ, Lawlor ER (2015) Gene expression profiling of Ewing sarcoma tumors reveals the prognostic importance of tumor-stromal interactions: A report from the children’s oncology group. J Pathol Clin Res 1(2):83–94. (PMID: 26052443445739610.1002/cjp2.9)
Schaefer KL, Eisenacher M, Braun Y, Brachwitz K, Wai DH, Dirksen U, Lanvers-Kaminsky C, Juergens H, Herrero D, Stegmaier S, Koscielniak E, Eggert A, Nathrath M, Gosheger G, Schneider DT, Bury C, Diallo-Danebrock R, Ottaviano L, Gabbert HE, Poremba C (2008) Microarray analysis of Ewing’s sarcoma family of tumours reveals characteristic gene expression signatures associated with metastasis and resistance to chemotherapy. Eur J Cancer 44(5):699–709. (PMID: 1829484010.1016/j.ejca.2008.01.020)
Scotlandi K, Remondini D, Castellani G, Manara MC, Nardi F, Cantiani L, Francesconi M, Mercuri M, Caccuri AM, Serra M, Knuutila S, Picci P (2009) Overcoming resistance to conventional drugs in Ewing sarcoma and identification of molecular predictors of outcome. J Clin Oncol 27(13):2209–2216. (PMID: 1930750210.1200/JCO.2008.19.2542)
Svoboda LK, Harris A, Bailey NJ, Schwentner R, Tomazou E, von Levetzow C, Magnuson B, Ljung-man M, Kovar H, Lawlor ER (2014) Overexpression of HOX genes is prevalent in Ewing sarcoma and is associated with altered epigenetic regulation of developmental transcription programs. Epigenetics 9(12):1613–1625. (PMID: 2562584610.4161/15592294.2014.988048)
Ban J, Jug G, Mestdagh P, Schwentner R, Kauer M, Aryee DN, Schaefer KL, Nakatani F, Scotlandi K, Reiter M et al (2011) Hsa-mir-145 is the top ews-fli1-repressed microrna involved in a positive feedback loop in Ewing’s sarcoma. Oncogene 30(18):2173–2180. (PMID: 21217773495956710.1038/onc.2010.581)
De Vito C, Riggi N, Suva ML, Janiszewska M, Horlbeck J, Baumer K, Provero P, Stamenkovic I (2011) Let-7a is a direct ews-fli-1 target implicated in Ewing’s sarcoma development. PLoS One 6(8):e23592. (PMID: 21853155315450710.1371/journal.pone.0023592)
McKinsey E, Parrish J, Irwin A, Niemeyer B, Kern H, Birks D, Jedlicka P (2011) A novel onco-genic mechanism in Ewing sarcoma involving igf pathway targeting by ews/ i1-regulated micrornas. Oncogene 30(49):4910–4920. (PMID: 21643012469686210.1038/onc.2011.197)
Kawano M, Tanaka K, Itonaga I, Iwasaki T, Tsumura H (2015) C-myc represses tumor-suppressive micrornas, let-7a, mir-16 and mir-29b, and induces cyclin d2-mediated cell proliferation in Ewing’s sarcoma cell line. PLoS One 10(9):e0138560. (PMID: 26393798457888510.1371/journal.pone.0138560)
Kawano M, Tanaka K, Itonaga I, Iwasaki T, Tsumura H (2016) Microrna-301a promotes cell proliferation via pten targeting in Ewing’s sarcoma cells. Int J Oncol 48(4):1531–1540. (PMID: 2684673710.3892/ijo.2016.337926846737)
Kawano M, Tanaka K, Itonaga I, Iwasaki T, Tsumura H (2017) Microrna-20b promotes cell proliferation via targeting of tgf- receptor ii and upregulates myc expression in Ewing’s sarcoma cells. Int J Oncol 51(6):1842–1850. (PMID: 2903948010.3892/ijo.2017.415529039480)
Kawano M, Tanaka K, Itonaga I, Iwasaki T, Tsumura H (2018) Microrna-181c prevents apoptosis by targeting of fas receptor in Ewing’s sarcoma cells. Cancer Cell Int 18(1):37. (PMID: 29563856584843110.1186/s12935-018-0536-9)
Tanaka K, Kawano M, Itonaga I, Iwasaki T, Miyazaki M, Ikeda S, Tsumura H (2016) Tumor suppressive microrna-138 inhibits metastatic potential via the targeting of focal adhesion kinase in Ewing’s sarcoma cells. Int J Oncol 48(3):1135–1144. (PMID: 2678292210.3892/ijo.2016.331726782922)
Parafioriti A, Bason C, Armiraglio E, Calciano L, Daolio PA, Berardocco M, Di Bernardo A, Colosimo A, Luksch R, Berardi AC (2016) Ewing’s sarcoma: an analysis of mirna expression profiles and target genes in paraffin-embedded primary tumor tissue. Int J Mol Sci 17(5):656. (PMID: 488148210.3390/ijms17050656)
Liu Y, Chen G, Liu H, Li Z, Yang Q, Gu X, Du Z, Zhang G, Wang J (2019) Integrated bioinformatics analysis of mirna expression in Ewing sarcoma and potential regulatory effects of mir-21 via targeting alcam/cd166. Artif Cells Nanomed Biotechnol 47(1):2114–2122. (PMID: 3114032810.1080/21691401.2019.162076031140328)
Nakatani F, Ferracin M, Manara MC, Ventura S, Del Monaco V, Ferrari S, Alberghini M, Grilli A, Knuutila S, Schaefer KL et al (2012) Mir-34a predicts survival of Ewing’s sarcoma patients and directly influences cell chemo-sensitivity and malignancy. J Pathol 226(5):796–805. (PMID: 2196005910.1002/path.300721960059)
Karnuth B, Dedy N, Spieker T, Lawlor ER, Gattenlohner S, Ranft A, Dirksen U, Jurgens H, Brauninger A (2014) Differentially expressed mirnas in Ewing sarcoma compared to mesenchymal stem cells: low mir-31 expression with effects on proliferation and invasion. PLoS One 9(3):e93067. (PMID: 24667836396552310.1371/journal.pone.0093067)
Teicher BA, Polley E, Kunkel M, Evans D, Silvers T, Delosh R, Laudeman J, Ogle C, Reinhart R, Selby M et al (2015) Sarcoma cell line screen of oncology drugs and investigational agents identifies patterns associated with gene and microrna expression. Mol Cancer Ther 14(11):2452–2462. (PMID: 26351324463647610.1158/1535-7163.MCT-15-0074)
De Feo A, Sciandra M, Ferracin M, Felicetti F, Astol A, Pignochino Y, Picci P, Care A, Scotlandi K (2019) Exosomes from cd99-deprived Ewing sarcoma cells reverse tumor malignancy by inhibiting cell migration and promoting neural differentiation. Cell Death Dis 10(7):1–15.
Rocchi A, Manara MC, Sciandra M, Zambelli D, Nardi F, Nicoletti G, Garofalo C, Meschini S, Astol A, Colombo MP et al (2010) Cd99 inhibits neural differentiation of human Ewing sarcoma cells and thereby contributes to oncogenesis. J Clin Invest 120(3):668–680. (PMID: 20197622282794310.1172/JCI36667)
Howarth MM, Simpson D, Ngok SP, Nieves B, Chen R, Siprashvili Z, Vaka D, Breese MR, Crompton BD, Alexe G et al (2014) Long noncoding rna ewsat1-mediated gene repression facilitates Ewing sarcoma oncogenesis. J Clin Invest 124(12):5275–5290. (PMID: 10.1172/JCI72124)
Patel N, Black J, Chen X, Marcondes AM, Grady WM, Lawlor ER, Borinstein SC (2012) DNA methylation and gene expression profiling of Ewing sarcoma primary tumors reveal genes that are potential targets of epigenetic inactivation. DOI https://doi.org/10.1155/2012/498472 , https://www.hindawi.com/journals/sarcoma/2012/498472/ , iSSN: 1357-714X library catalog: www.hindawi.com Pages: e498472 Publisher: Hindawi volume: 2012.
Park HR, Jung WW, Kim HS, Park YK (2014) Microarray-based DNA methylation study of Ewing’s sarcoma of the bone. Oncol Lett 8(4):1613–1617. (PMID: 25202378415618410.3892/ol.2014.2322)
Huertas-Mart Nez J, Court F, Rello-Varona S, Herrero-Mart ND, Almacellas-Rabaiget O, Sainz-Jaspeado M, Garcia-Monclus S, Lagares-Tena L, Buj R, Hontecillas-Prieto L, Sastre A, Azorin D, Sanjuan X, Lopez-Alemany R, Moran S, Roma J, Gallego S, Mora J et al (2017) DNA methylation profiling identifies PTRF/Cavin-1 as a novel tumor suppressor in Ewing sarcoma when co-expressed with caveolin-1. Cancer Lett 386:196–207. (PMID: 10.1016/j.canlet.2016.11.020)
Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schonegger A, Schuster M, Hadler J, Surdez D, Guillemot D, Lapouble E, Freneaux P, Champigneulle J, Bouvier R, Walder D, Ambros IM, Hutter C, Sorz E, Amaral AT, de Alava E, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, de Pinieux G, Terrier P, Laurence V, Michon J, Ladenstein R, Holter W, Windhager R, Dirksen U, Ambros PF, Delattre O, Kovar H, Bock C, Tomazou EM (2017) DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma. Nat Med 23(3):386–395. (PMID: 28134926595128310.1038/nm.4273)
Bilke S, Schwentner R, Yang F, Kauer M, Jug G, Walker RL, Davis S, Zhu YJ, Pineda M, Meltzer PS, Kovar H (2013) Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer. Genome Res 23(11):1797–1809. (PMID: 23940108381488010.1101/gr.151340.112)
Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suva ML, Rossetti NE, Boonseng WE, Oksuz O, Cook EB, Formey A, Patel A, Gymrek M, Thapar V, Deshpande V, Ting DT, Hornicek FJ, Nielsen GP, Stamenkovic I, Aryee MJ, Bernstein BE, Rivera MN (2014) EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell 26(5):668–681. (PMID: 25453903449234310.1016/j.ccell.2014.10.004)
Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schonegger A, Datlinger P, Kubicek S, Bock C, Kovar H (2015) Epigenome mapping reveals distinct modes of gene regulation and widespread enhancer reprogramming by the oncogenic fusion protein EWS-FLI1. Cell Rep 10(7):1082–1095. (PMID: 25704812454231610.1016/j.celrep.2015.01.042)
Elzi DJ, Song M, Hakala K, Weintraub ST, Shiio Y (2014) Proteomic analysis of the EWS-FLI-1 interactome reveals the role of the lysosome in EWS-FLI-1 turnover. J Proteome Res 13(8):3783–3791. (PMID: 24999758412394410.1021/pr500387m)
Hawkins AG, Basrur V, da Veiga LF, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER (2018) The Ewing sarcoma secretome and its response to activation of wnt/beta-catenin signaling. Mol Cell Proteomics 17(5):901–912. (PMID: 29386236593041210.1074/mcp.RA118.000596)
Madoz-Gurpide J, Herrero-Martin D, Gomez-Lopez G, Hontecillas-Prieto L, Biscuola M, Chamizo C, Garcia-Dominguez D, Marcilla D, Amaral AT, Ordonez JL, Ed A (2016) Proteomic profiling of Ewing sarcoma reveals a role for TRAF6 in proliferation and ribonucleoproteins/RNA processing. J Proteomics Bioinform 9(6):1–10.
Franzetti GA, Laud-Duval K, van der Ent W, Brisac A, Irondelle M, Aubert S, Dirksen U, Bouvier C, de Pinieux G, Snaar-Jagalska E, Chavrier P, Delattre O (2017) Cell-to-cell heterogeneity of EWSR1-FLI1 activity determines proliferation/migration choices in Ewing sarcoma cells. Oncogene 36(25):3505–3514. (PMID: 28135250554126710.1038/onc.2016.498)
Kikuta K, Tochigi N, Shimoda T, Yabe H, Morioka H, Toyama Y, Hosono A, Beppu Y, Kawai A, Hirohashi S, Kondo T (2009) Nucleophosmin as a candidate prognostic biomarker of Ewing’s sarcoma revealed by proteomics. Clin Cancer Res 15(8):2885–2894. (PMID: 1935176910.1158/1078-0432.CCR-08-191319351769)
Lamhamedi-Cherradi SE, Menegaz BA, Ramamoorthy V, Vishwamitra D, Wang Y, Maywald RL, Buford AS, Fokt I, Skora S, Wang J, Naing A, Lazar AJ, Rohren EM, Daw NC, Subbiah V, Benjamin RS, Ratan R, Priebe W, Mikos AG, Amin HM, Ludwig JA (2016) IGF-1R and mTOR blockade: novel resistance mechanisms and synergistic drug combinations for Ewing sarcoma. J Natl Cancer Inst 108(12):djw182. (PMID: 27576731524189410.1093/jnci/djw182)
Puerto-Camacho P, Amaral AT, Lamhamedi-Cherradi SE, Menegaz BA, Castillo-Ecija H, Ordóñez JL, Domínguez S, Jordan-Perez C, Diaz-Martin J, Romero-Pérez L, Lopez-Alvarez M, Civantos-Jubera G, Robles-Frías MJ, Biscuola M, Ferrer C, Mora J, Cuglievan B, Schadler K, Seifert O, Kontermann R, Pfizenmaier K, Simón L, Fabre M, Carcaboso AM, Ludwig JA, Ed Á (2019) Preclinical efficacy of endoglin-targeting antibody–drug conjugates for the treatment of Ewing sarcoma. Clin Cancer Res 25(7):2228–2240. (PMID: 3042044710.1158/1078-0432.CCR-18-093630420447)
Town J, Pais H, Harrison S, Stead LF, Bataille C, Bunjobpol W, Zhang J, Rabbitts TH (2016) Exploring the surfaceome of Ewing sarcoma identifies a new and unique therapeutic target. Proc Natl Acad Sci 113(13):3603–3608. (PMID: 2697995310.1073/pnas.152125111326979953)
Jonker A (2014) Synthetic Lethality and Metabolism in Ewing Sarcoma: Knowledge Through Silence. PhD thesis, Paris 11. http://www.theses.fr/2014PA11T039.
Tanner JM, Bensard C, Wei P, Krah NM, Schell JC, Gardiner J, Schiman J, Lessnick SL, Rutter J (2017) EWS/FLI is a master regulator of metabolic reprogramming in Ewing sarcoma. Mol Cancer Res 15(11):1517–1530. (PMID: 28720588566817110.1158/1541-7786.MCR-17-0182)
Dasgupta A, Trucco M, Rainusso N, Bernardi RJ, Shuck R, Kurenbekova L, Loeb DM, Yustein JT (2017) Metabolic modulation of Ewing sarcoma cells inhibits tumor growth and stem cell properties. Oncotarget 8(44):77292–77308. (PMID: 29100387565278010.18632/oncotarget.20467)
Sen N, Cross AM, Lorenzi PL, Khan J, Gryder BE, Kim S, Caplen NJ (2018) EWS-FLI1 reprograms the metabolism of Ewing sarcoma cells via positive regulation of glutamine import and serine-glycine biosynthesis. Mol Carcinog 57(10):1342–1357. (PMID: 29873416617524510.1002/mc.22849)
Issaq SH, Mendoza A, Fox SD, Helman LJ (2019) Glutamine synthetase is necessary for sarcoma adaptation to glutamine deprivation and tumor growth. Oncogenesis 8(3):1–12. (PMID: 10.1038/s41389-019-0129-z)
Barretina J, Caponigro G, Stransky N, Venkatesan K, AA M, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jane-Valbuena J, FA M, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, LA G (2012) The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483(7391):603–607. (PMID: 22460905332002710.1038/nature11003)
Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O’Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH (2012) Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483(7391):570–575. (PMID: 22460902334923310.1038/nature11005)
Brenner JC, Feng FY, Han S, Patel S, Goyal SV, Bou-Maroun LM, Liu M, Lonigro R, Prensner JR, Tomlins SA, Chinnaiyan AM (2012) PARP-1 inhibition as a targeted strategy to treat Ewing’s sarcoma. Cancer Res 72(7):1608–1613. (PMID: 22287547331978610.1158/0008-5472.CAN-11-3648)
He T, Surdez D, Rantala JK, Haapa-Paananen S, Ban J, Kauer M, Tomazou E, Fey V, Alonso J, Kovar H, Delattre O, Iljin K (2017) High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability. Gene 596:137–146. (PMID: 2776038110.1016/j.gene.2016.10.021)
Shukla N, Somwar R, Smith RS, Ambati S, Munoz S, Merchant M, D’Arcy P, Wang X, Kobos R, Antczak C, Bhinder B, Shum D, Radu C, Yang G, Taylor BS, Ng CK, Weigelt B, Khodos I, De Stanchina E, Reis-Filho JS, Ouerfelli O, Linder S, Djaballah H, Ladanyi M (2016) Proteasome ad-diction defined in Ewing sarcoma is effectively targeted by a novel class of 19S proteasome inhibitors. Cancer Res 76(15):4525–4534. (PMID: 27256563548400210.1158/0008-5472.CAN-16-1040)
Tsafou K, Katschnig AM, Radic-Sarikas B, Mutz CN, Iljin K, Schwentner R, Kauer MO, Muhlbacher K, Aryee DN, Westergaard D, Haapa-Paananen S, Fey V, Superti-Furga G, Toretsky J, Brunak S, Kovar H (2018) Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers. Oncotarget 9(57):31018–31031. (PMID: 30123424608955210.18632/oncotarget.25760)
Branka RS, Kalliopi PT, Kristina BE, Theodore P, Huber KV, Cornelia M, Jerey AT, Keiryn LB, Jesper VO, Sren B, Heinrich K, Giulio SF (2017) Combinatorial drug screening identifies Ewing sarcoma-specific sensitivities. Mol Cancer Ther 16(1):88–101.
Stolte B, Iniguez AB, Dharia NV, Robichaud AL, Conway AS, Morgan AM, Alexe G, Schauer NJ, Liu X, Bird GH, Tsherniak A, Vazquez F, Buhrlage SJ, Walensky LD, Stegmaier K (2018) Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in TP53 wild-type Ewing sarcoma. J Exp Med 215(8):2137–2155. (PMID: 30045945608091510.1084/jem.20171066)
Pessetto ZY, Chen B, Alturkmani H, Hyter S, Flynn CA, Baltezor M, Ma Y, Rosenthal HG, Neville KA, Weir SJ, Butte AJ, Godwin AK (2017) In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma. Oncotarget 8(3):4079–4095. (PMID: 2786342210.18632/oncotarget.1338527863422)
Pauwels E, Surdez D, Stoll G, Lescure A, Del Nery E, Delattre O, Stoven V (2012) A probabilistic model for cell population phenotyping using HCS data. PLoS One 7(8):1–12. (PMID: 10.1371/journal.pone.0042715)
Chakraborty S, Hosen MI, Ahmed M, Shekhar HU (2018) Onco-multi-OMICS approach: A new frontier in cancer research. Biomed Res Int 2018:9836256. (PMID: 30402498619216610.1155/2018/9836256)
Forget A, Martignetti L, Puget S, Calzone L, Brabetz S, Picard D, Montagud A, Liva S, Sta A, Dingli F, Arras G, Rivera J, Loew D, Besnard A, Lacombe J, Pages M, Varlet P, Dufour C, Yu H, Mercier AL, Indersie E, Chivet A, Leboucher S, Sieber L, Beccaria K, Gombert M, Meyer FD, Qin N, Bartl J, Chavez L, Okonechnikov K, Sharma T, Thatikonda V, Bourdeaut F, Pouponnot C, Ramaswamy V, Korshunov A, Borkhardt A, Reifenberger G, Poullet P, Taylor MD, Kool M, Pster SM, Kawauchi D, Barillot E, Remke M, Ayrault O (2018) Aberrant ERBB4-SRC signaling as a Hallmark of group 4 Medulloblastoma revealed by integrative Phosphoproteomic Profiling. Cancer Cell 34(3):379–395.e7. (PMID: 3020504310.1016/j.ccell.2018.08.00230205043)
Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A (2012) Antagonism pattern detection between MicroRNA and target expression in Ewing’s sarcoma. PLoS One 7(7):e41770. (PMID: 22848594340496610.1371/journal.pone.0041770)
von Levetzow C, Jiang X, Gwye Y, von Levetzow G, Hung L, Cooper A, Hsu JHR, Lawlor ER (2011) Modeling initiation of Ewing sarcoma in human neural crest cells. PLoS One 6(4):e19305. (PMID: 10.1371/journal.pone.0019305)
Hancock JD, Lessnick SL (2008) A transcriptional profiling meta-analysis reveals a core EWS-FLI gene expression signature. Cell Cycle 7(2):250–256. (PMID: 1825652910.4161/cc.7.2.522918256529)
Kauer M, Ban J, Koer R, Walker B, Davis S, Meltzer P, Kovar H (2009) A molecular function map of Ewing’s sarcoma. PLoS One 4(4):e5415. (PMID: 19404404267184710.1371/journal.pone.0005415)
Avila Cobos F, Vandesompele J, Mestdagh P, De Preter K (2018) Computational deconvolution of transcriptomics data from mixed cell populations. Bioinformatics 34(11):1969–1979. (PMID: 2935158610.1093/bioinformatics/bty01929351586)
Stahl D, Gentles AJ, Thiele R, Gutgemann I (2019) Prognostic profiling of the immune cell mi-croenvironment in Ewing’s sarcoma family of tumors. Onco Targets Ther 8(12):e1674113.
Lutsik P, Slawski M, Gasparoni G, Vedeneev N, Hein M, Walter J (2017) MeDeCom: discovery and quantification of latent components of heterogeneous methylomes. Genome Biol 18(1):55. (PMID: 28340624536615510.1186/s13059-017-1182-6)
Scherer M, Nebel A, Franke A, Walter J, Lengauer T, Bock C, Muller F, List M (2020) Quantitative comparison of within-sample heterogeneity scores for DNA methylation data. Nucleic Acids Res 48(8):e46. (PMID: 32103242719261210.1093/nar/gkaa120)
Selvanathan SP, Graham GT, Erkizan HV, Dirksen U, Natarajan TG, Dakic A, Yu S, Liu X, Paulsen MT, Ljungman ME, Wu CH, Lawlor ER, Uren A, Toretsky JA (2015) Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing. Proc Natl Acad Sci U S A 112(11):E1307–E1316. (PMID: 25737553437196910.1073/pnas.1500536112)
Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DPA, Barillot E, Zinovyev A (2015) NaviCell web service for network-based data visualization. Nucleic Acids Res 43(W1):W560–W565. (PMID: 25958393448928310.1093/nar/gkv450)
Stoll G, Caron B, Viara E, Dugourd A, Zinovyev A, Naldi A, Kroemer G, Barillot E, Calzone L (2017) MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinformatics 33(14):2226–2228. (PMID: 2888195910.1093/bioinformatics/btx12328881959)
Schwentner R, Papamarkou T, Kauer MO, Stathopoulos V, Yang F, Bilke S, Meltzer PS, Girolami M, Kovar H (2015) EWS-FLI1 employs an E2F switch to drive target gene expression. Nucleic Acids Res 43(5):2780–2789. (PMID: 25712098435772410.1093/nar/gkv123)
Sompairac N, Nazarov PV, Czerwinska U, Cantini L, Biton A, Molkenov A, Zhumadilov Z, Barillot E, Radvanyi F, Gorban A, Kairov U, Zinovyev A (2019) Independent component analysis for unraveling the complexity of cancer omics datasets. Int J Mol Sci 20(18):4414. (PMID: 677112110.3390/ijms20184414)
Khoogar R, Lawlor ER, Chen Y, Ignatius M, Kitagawa K, H-M Huang T, Houghton PJ (2019) Single-cell RNA profiling identifies diverse cellular responses to EWSR1-FLI1 Down-regulation in Ewing sarcoma. bioRxiv 750539.
فهرسة مساهمة: Keywords: Cancer systems biology; Data integration; EWSR1-FLI1; Ewing sarcoma; Mathematical modeling; Network; Omics data
تواريخ الأحداث: Date Created: 20201216 Date Completed: 20210401 Latest Revision: 20210401
رمز التحديث: 20240628
DOI: 10.1007/978-1-0716-1020-6_23
PMID: 33326111
قاعدة البيانات: MEDLINE
الوصف
تدمد:1940-6029
DOI:10.1007/978-1-0716-1020-6_23