DiPRO1 distinctly reprograms muscle and mesenchymal cancer cells.
DiPRO1
Mesenchymal Cancer
Methylation
Muscle
Retrotransposable Repeats
Journal
EMBO molecular medicine
ISSN: 1757-4684
Titre abrégé: EMBO Mol Med
Pays: Germany
ID NLM: 101487380
Informations de publication
Date de publication:
15 Jul 2024
15 Jul 2024
Historique:
received:
10
01
2023
accepted:
18
06
2024
revised:
13
06
2024
medline:
16
7
2024
pubmed:
16
7
2024
entrez:
15
7
2024
Statut:
aheadofprint
Résumé
We have recently identified the uncharacterized ZNF555 protein as a component of a productive complex involved in the morbid function of the 4qA locus in facioscapulohumeral dystrophy. Subsequently named DiPRO1 (Death, Differentiation, and PROliferation related PROtein 1), our study provides substantial evidence of its role in the differentiation and proliferation of human myoblasts. DiPRO1 operates through the regulatory binding regions of SIX1, a master regulator of myogenesis. Its relevance extends to mesenchymal tumors, such as rhabdomyosarcoma (RMS) and Ewing sarcoma, where DiPRO1 acts as a repressor via the epigenetic regulators TIF1B and UHRF1, maintaining methylation of cis-regulatory elements and gene promoters. Loss of DiPRO1 mimics the host defense response to virus, awakening retrotransposable repeats and the ZNF/KZFP gene family. This enables the eradication of cancer cells, reprogramming the cellular decision balance towards inflammation and/or apoptosis by controlling TNF-α via NF-kappaB signaling. Finally, our results highlight the vulnerability of mesenchymal cancer tumors to si/shDiPRO1-based nanomedicines, positioning DiPRO1 as a potential therapeutic target.
Identifiants
pubmed: 39009887
doi: 10.1038/s44321-024-00097-z
pii: 10.1038/s44321-024-00097-z
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Société Française de lutte contre les Cancers et les leucémies de l'Enfant et de l'Adolescent (SFCE)
ID : W381005059
Organisme : Institut National de la Santé et de la Recherche Médicale (Inserm)
ID : ENV201416
Organisme : Institut Gustave-Roussy (Gustave Roussy)
ID : X75390
Informations de copyright
© 2024. The Author(s).
Références
Abboud A, Masrouha K, Saliba M, Haidar R, Saab R, Khoury N, Tawil A, Saghieh S (2021) Extraskeletal Ewing sarcoma: diagnosis, management and prognosis. Oncol Lett 21(5):354
pubmed: 33747211
pmcid: 7967932
doi: 10.3892/ol.2021.12615
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Eberhard C et al (2016) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 44(W1):W3–W10
pubmed: 27137889
pmcid: 4987906
doi: 10.1093/nar/gkw343
Alhosin M, Sharif T, Mousli M, Etienne-Selloum N, Fuhrmann G, Schini-Kerth VB, Bronner C (2011) Down-regulation of UHRF1, associated with re-expression of tumor suppressor genes, is a common feature of natural compounds exhibiting anti-cancer properties. J Exp Clin Cancer Res 30:41
pubmed: 21496237
pmcid: 3096999
doi: 10.1186/1756-9966-30-41
Aygun O, Svejstrup J, Liu Y (2008) A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin. Proc Natl Acad Sci USA 105(25):8580–8584
pubmed: 18562274
pmcid: 2430918
doi: 10.1073/pnas.0804424105
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37(Web Server issue):W202–208
pubmed: 19458158
pmcid: 2703892
doi: 10.1093/nar/gkp335
Bardou P, Mariette J, Escudie F, Djemiel C, Klopp C (2014) jvenn: an interactive Venn diagram viewer. BMC Bioinforma 15:293
doi: 10.1186/1471-2105-15-293
Barrientos T, Frank D, Kuwahara K, Bezprozvannaya S, Pipes GC, Bassel-Duby R, Richardson JA, Katus HA, Olson EN, Frey N (2007) Two novel members of the ABLIM protein family, ABLIM-2 and -3, associate with STARS and directly bind F-actin. J Biol Chem 282(11):8393–8403
pubmed: 17194709
doi: 10.1074/jbc.M607549200
Barruet E, Garcia SM, Striedinger K, Wu J, Lee S, Byrnes L, Wong A, Xuefeng S, Tamaki S, Brack AS et al (2020) Functionally heterogeneous human satellite cells identified by single cell RNA sequencing. Elife 9:e51576
pubmed: 32234209
pmcid: 7164960
doi: 10.7554/eLife.51576
Barruet E, Striedinger K, Marangoni P, Pomerantz JH (2023) Loss of transcriptional heterogeneity in aged human muscle stem cells. PLoS ONE 18(5):e0285018
pubmed: 37192223
pmcid: 10187936
doi: 10.1371/journal.pone.0285018
Barton KM, Levine EM (2008) Expression patterns and cell cycle profiles of PCNA, MCM6, cyclin D1, cyclin A2, cyclin B1, and phosphorylated histone H3 in the developing mouse retina. Dev Dyn 237(3):672–682
pubmed: 18265020
doi: 10.1002/dvdy.21449
Benedict CA (2003) Viruses and the TNF-related cytokines, an evolving battle. Cytokine Growth Factor Rev 14(3-4):349–357
pubmed: 12787571
doi: 10.1016/S1359-6101(03)00030-3
Berlanga P, Pierron G, Lacroix L, Chicard M, Adam de Beaumais T, Marchais A, Harttrampf AC, Iddir Y, Larive A, Soriano Fernandez A et al (2022) The European MAPPYACTS Trial: precision medicine program in pediatric and adolescent patients with recurrent malignancies. Cancer Discov 12(5):1266–1281
pubmed: 35292802
pmcid: 9394403
doi: 10.1158/2159-8290.CD-21-1136
Bernasconi M, Remppis A, Fredericks WJ, Rauscher 3rd FJ, Schafer BW (1996) Induction of apoptosis in rhabdomyosarcoma cells through down-regulation of PAX proteins. Proc Natl Acad Sci USA 93(23):13164–13169
pubmed: 8917562
pmcid: 24064
doi: 10.1073/pnas.93.23.13164
Bertozzi TM, Elmer JL, Macfarlan TS, Ferguson-Smith AC (2020) KRAB zinc finger protein diversification drives mammalian interindividual methylation variability. Proc Natl Acad Sci USA 117(49):31290–31300
pubmed: 33239447
pmcid: 7733849
doi: 10.1073/pnas.2017053117
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, Galon J (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25(8):1091–1093
pubmed: 19237447
pmcid: 2666812
doi: 10.1093/bioinformatics/btp101
Blais A, Tsikitis M, Acosta-Alvear D, Sharan R, Kluger Y, Dynlacht BD (2005) An initial blueprint for myogenic differentiation. Genes Dev 19(5):553–569
pubmed: 15706034
pmcid: 551576
doi: 10.1101/gad.1281105
Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317(5845):1760–1764
pubmed: 17673620
doi: 10.1126/science.1147939
Brown G, Vicente-Duenas C, Sanchez-Garcia I (2020) Editorial: epigenetic reprogramming and cancer development. Front Cell Dev Biol 8:12
pubmed: 32047749
pmcid: 6997552
doi: 10.3389/fcell.2020.00012
Brugmann SA, Pandur PD, Kenyon KL, Pignoni F, Moody SA (2004) Six1 promotes a placodal fate within the lateral neurogenic ectoderm by functioning as both a transcriptional activator and repressor. Development 131(23):5871–5881
pubmed: 15525662
doi: 10.1242/dev.01516
Carr CM, Munson M (2007) Tag team action at the synapse. EMBO Rep. 8(9):834–838
pubmed: 17767192
pmcid: 1973957
doi: 10.1038/sj.embor.7401051
Cassandri M, Smirnov A, Novelli F, Pitolli C, Agostini M, Malewicz M, Melino G, Raschella G (2017) Zinc-finger proteins in health and disease. Cell Death Discov 3:17071
pubmed: 29152378
pmcid: 5683310
doi: 10.1038/cddiscovery.2017.71
Chen B, Dias P, Jenkins 3rd JJ, Savell VH, Parham DM (1998) Methylation alterations of the MyoD1 upstream region are predictive of subclassification of human rhabdomyosarcomas. Am J Pathol 152(4):1071–1079
pubmed: 9546368
pmcid: 1858244
Cheneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B (2018) JASPAR 2020 ( https://jaspar2020.genereg.net/matrix/MA1118.1/ ) [DATASET]
Cheneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B (2018) ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Res 46(D1):D267–D275
pubmed: 29126285
doi: 10.1093/nar/gkx1092
Cheng CT, Kuo CY, Ann DK (2014) KAPtain in charge of multiple missions: Emerging roles of KAP1. World J Biol Chem 5(3):308–320
pubmed: 25225599
pmcid: 4160525
doi: 10.4331/wjbc.v5.i3.308
Chinnadurai G, Vijayalingam S, Rashmi R (2008) BIK, the founding member of the BH3-only family proteins: mechanisms of cell death and role in cancer and pathogenic processes. Oncogene 27(Suppl 1):S20–29
pubmed: 19641504
pmcid: 2928562
doi: 10.1038/onc.2009.40
Consortium, E. P. (2012). ENCODE project ( https://www.encodeproject.org/experiments/ENCSR211GNP/ ). [DATASET]
Consortium, E. P. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74
doi: 10.1038/nature11247
Cunha PM, Sandmann T, Gustafson EH, Ciglar L, Eichenlaub MP, Furlong EE (2010) Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity. PLoS Genet 6(7):e1001014
pubmed: 20617173
pmcid: 2895655
doi: 10.1371/journal.pgen.1001014
Danielli SG, Porpiglia E, De Micheli AJ, Navarro N, Zellinger MJ, Bechtold I, Kisele S, Volken L, Marques JG, Kasper S, et al (2023) Gene expression omnibus GSE218974 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218974 ). [DATASET]
Danielli SG, Porpiglia E, De Micheli AJ, Navarro N, Zellinger MJ, Bechtold I, Kisele S, Volken L, Marques JG, Kasper S et al (2023) Single-cell profiling of alveolar rhabdomyosarcoma reveals RAS pathway inhibitors as cell-fate hijackers with therapeutic relevance. Sci Adv 9(6):eade9238
pubmed: 36753540
pmcid: 9908029
doi: 10.1126/sciadv.ade9238
Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Jain K, Baymuradov UK, Narayanan AK et al (2018) The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res 46(D1):D794–D801
pubmed: 29126249
doi: 10.1093/nar/gkx1081
De Franco S, Vandenameele J, Brans A, Verlaine O, Bendak K, Damblon C, Matagne A, Segal DJ, Galleni M, Mackay JP et al (2019) Exploring the suitability of RanBP2-type zinc fingers for RNA-binding protein design. Sci Rep. 9(1):2484
pubmed: 30792407
pmcid: 6384913
doi: 10.1038/s41598-019-38655-y
De Preter K, Barriot R, Speleman F, Vandesompele J, Moreau Y (2008) Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions. Nucleic Acids Res 36(7):e43
pubmed: 18346969
pmcid: 2367735
doi: 10.1093/nar/gkn114
Demidenko E (2010) Three endpoints of in vivo tumour radiobiology and their statistical estimation. Int J Radiat Biol 86(2):164–173
pubmed: 20148701
pmcid: 2900851
doi: 10.3109/09553000903419304
Deng K, Wu M (2023) Leucine-rich repeats containing 4 protein (LRRC4) in memory, psychoneurosis, and glioblastoma. Chin Med J 136(1):4–12
pubmed: 36780420
pmcid: 10106153
doi: 10.1097/CM9.0000000000002441
DepMap portal of Broad Institute ( https://depmap.org/portal/ ) [DATASET]
Din FU, Aman W, Ullah I, Qureshi OS, Mustapha O, Shafique S, Zeb A (2017) Effective use of nanocarriers as drug delivery systems for the treatment of selected tumors. Int J Nanomed 12:7291–7309
doi: 10.2147/IJN.S146315
Dong J, Wang X, Cao C, Wen Y, Sakashita A, Chen S, Zhang J, Zhang Y, Zhou L, Luo M et al (2019) UHRF1 suppresses retrotransposons and cooperates with PRMT5 and PIWI proteins in male germ cells. Nat Commun 10(1):4705
pubmed: 31624244
pmcid: 6797737
doi: 10.1038/s41467-019-12455-4
Duteil D, Chambon C, Ali F, Malivindi R, Zoll J, Kato S, Geny B, Chambon P, Metzger D (2010) The transcriptional coregulators TIF2 and SRC-1 regulate energy homeostasis by modulating mitochondrial respiration in skeletal muscles. Cell Metab 12(5):496–508
pubmed: 21035760
pmcid: 3032428
doi: 10.1016/j.cmet.2010.09.016
Eisenstein M (2016) A simpler twist of fate. Nature 534(7607):421–423
pubmed: 27306187
doi: 10.1038/534421a
Enot DP, Vacchelli E, Jacquelot N, Zitvogel L, Kroemer G (2018) TumGrowth: an open-access web tool for the statistical analysis of tumor growth curves. Oncoimmunology 7(9):e1462431
pubmed: 30228932
pmcid: 6140814
doi: 10.1080/2162402X.2018.1462431
Ernst J, Kellis M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28(8):817–825
pubmed: 20657582
pmcid: 2919626
doi: 10.1038/nbt.1662
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al (2011) UCSC from ENCODE/Broad Institute ( https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone ) [DATASET]
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345):43–49
pubmed: 21441907
pmcid: 3088773
doi: 10.1038/nature09906
Esposito S, D’Abrosca G, Antolak A, Pedone PV, Isernia C, Malgieri G (2022) Host and viral zinc-finger proteins in COVID-19. Int J Mol Sci 23(7):3711
pubmed: 35409070
pmcid: 8998646
doi: 10.3390/ijms23073711
Faravelli I, Bucchia M, Rinchetti P, Nizzardo M, Simone C, Frattini E, Corti S (2014) Motor neuron derivation from human embryonic and induced pluripotent stem cells: experimental approaches and clinical perspectives. Stem Cell Res Ther 5(4):87
pubmed: 25157556
pmcid: 4100331
doi: 10.1186/scrt476
Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC (2015) Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol 26(1):64–70
pubmed: 25319062
doi: 10.1093/annonc/mdu479
Ferreboeuf M, Mariot V, Bessieres B, Vasiljevic A, Attie-Bitach T, Collardeau S, Morere J, Roche S, Magdinier F, Robin-Ducellier J et al (2014) DUX4 and DUX4 downstream target genes are expressed in fetal FSHD muscles. Hum Mol Genet 23(1):171–181
pubmed: 23966205
doi: 10.1093/hmg/ddt409
Frese S, Ruebner M, Suhr F, Konou TM, Tappe KA, Toigo M, Jung HH, Henke C, Steigleder R, Strissel PL et al (2015) Long-term endurance exercise in humans stimulates cell fusion of myoblasts along with fusogenic endogenous retroviral genes in vivo. PLoS ONE 10(7):e0132099
pubmed: 26154387
pmcid: 4495930
doi: 10.1371/journal.pone.0132099
Garcia-Dominguez DJ, Hontecillas-Prieto L, Rodriguez-Nunez P, Pascual-Pasto G, Vila-Ubach M, Garcia-Mejias R, Robles MJ, Tirado OM, Mora J, Carcaboso AM et al (2018) The combination of epigenetic drugs SAHA and HCI-2509 synergistically inhibits EWS-FLI1 and tumor growth in Ewing sarcoma. Oncotarget 9(59):31397–31410
pubmed: 30140378
pmcid: 6101143
doi: 10.18632/oncotarget.25829
Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196(2):261–282
pubmed: 3656447
doi: 10.1016/0022-2836(87)90689-9
Garrick D, Fiering S, Martin DI, Whitelaw E (1998) Repeat-induced gene silencing in mammals. Nat Genet 18(1):56–59
pubmed: 9425901
doi: 10.1038/ng0198-56
Gastaldi T, Bonvini P, Sartori F, Marrone A, Iolascon A, Rosolen A (2006) Plakoglobin is differentially expressed in alveolar and embryonal rhabdomyosarcoma and is regulated by DNA methylation and histone acetylation. Carcinogenesis 27(9):1758–1767
pubmed: 16537559
doi: 10.1093/carcin/bgl008
Gatenby RA, Cunningham JJ, Brown JS (2014) Evolutionary triage governs fitness in driver and passenger mutations and suggests targeting never mutations. Nat Commun 5:5499
pubmed: 25407411
doi: 10.1038/ncomms6499
Gatto G, Morales D, Kania A, Klein R (2014) EphA4 receptor shedding regulates spinal motor axon guidance. Curr Biol 24(20):2355–2365
pubmed: 25264256
doi: 10.1016/j.cub.2014.08.028
Goldstein M, Meller I, Orr-Urtreger A (2007) FGFR1 over-expression in primary rhabdomyosarcoma tumors is associated with hypomethylation of a 5’ CpG island and abnormal expression of the AKT1, NOG, and BMP4 genes. Genes Chromosomes Cancer 46(11):1028–1038
pubmed: 17696196
doi: 10.1002/gcc.20489
Gonzalez-Cao M, Iduma P, Karachaliou N, Santarpia M, Blanco J, Rosell R (2016) Human endogenous retroviruses and cancer. Cancer Biol Med 13(4):483–488
pubmed: 28154780
pmcid: 5250606
doi: 10.20892/j.issn.2095-3941.2016.0080
Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27(7):1017–1018
pubmed: 21330290
pmcid: 3065696
doi: 10.1093/bioinformatics/btr064
Grifone R, Demignon J, Houbron C, Souil E, Niro C, Seller MJ, Hamard G, Maire P (2005) Six1 and Six4 homeoproteins are required for Pax3 and Mrf expression during myogenesis in the mouse embryo. Development 132(9):2235–2249
pubmed: 15788460
doi: 10.1242/dev.01773
Grifone R, Laclef C, Spitz F, Lopez S, Demignon J, Guidotti JE, Kawakami K, Xu PX, Kelly R, Petrof BJ et al (2004) Six1 and Eya1 expression can reprogram adult muscle from the slow-twitch phenotype into the fast-twitch phenotype. Mol Cell Biol 24(14):6253–6267
pubmed: 15226428
pmcid: 434262
doi: 10.1128/MCB.24.14.6253-6267.2004
Grobner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S et al (2018) The landscape of genomic alterations across childhood cancers. Nature 555(7696):321–327
pubmed: 29489754
doi: 10.1038/nature25480
Groner AC, Meylan S, Ciuffi A, Zangger N, Ambrosini G, Denervaud N, Bucher P, Trono D (2010) KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet 6(3):e1000869
pubmed: 20221260
pmcid: 2832679
doi: 10.1371/journal.pgen.1000869
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS (2007) Quantifying similarity between motifs. Genome Biol 8(2):R24
pubmed: 17324271
pmcid: 1852410
doi: 10.1186/gb-2007-8-2-r24
Gurria JP, Dasgupta R (2018) Rhabdomyosarcoma and extraosseous Ewing sarcoma. Child 5(12):165
doi: 10.3390/children5120165
Hajikhezri Z, Darweesh M, Akusjarvi G, Punga T (2020) Role of CCCH-type zinc finger proteins in human adenovirus infections. Viruses 12(11):1322
pubmed: 33217981
pmcid: 7698620
doi: 10.3390/v12111322
Hall TM (2005) Multiple modes of RNA recognition by zinc finger proteins. Curr Opin Struct Biol 15(3):367–373
pubmed: 15963892
doi: 10.1016/j.sbi.2005.04.004
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38(4):576–589
pubmed: 20513432
pmcid: 2898526
doi: 10.1016/j.molcel.2010.05.004
Helleboid PY, Heusel M, Duc J, Piot C, Thorball CW, Coluccio A, Pontis J, Imbeault M, Turelli P, Aebersold R, et al (2019a). Gene expression omnibus GSE78099 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78099 ). [DATASET]
Helleboid PY, Heusel M, Duc J, Piot C, Thorball CW, Coluccio A, Pontis J, Imbeault M, Turelli P, Aebersold R et al (2019b) The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. EMBO J 38(18):e101220
pubmed: 31403225
pmcid: 6745500
doi: 10.15252/embj.2018101220
Hewitt M, Weiner SL, Simone JV (2003) Childhood cancer survivorship: improving care and quality of life. National Academies Press, Washington (DC)
Hidaka K, Yamamoto I, Arai Y, Mukai T (1993) The MEF-3 motif is required for MEF-2-mediated skeletal muscle-specific induction of the rat aldolase A gene. Mol Cell Biol 13(10):6469–6478
pubmed: 8413246
pmcid: 364706
Hinson AR, Jones R, Crose LE, Belyea BC, Barr FG, Linardic CM (2013) Human rhabdomyosarcoma cell lines for rhabdomyosarcoma research: utility and pitfalls. Front Oncol 3:183
pubmed: 23882450
pmcid: 3713458
doi: 10.3389/fonc.2013.00183
Hirata T, Amano T, Nakatake Y, Amano M, Piao Y, Hoang HG, Ko MS (2012) Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells. Sci Rep. 2:208
pubmed: 22355722
pmcid: 3250575
doi: 10.1038/srep00208
Holliday R (1979) A new theory of carcinogenesis. Br J Cancer 40(4):513–522
pubmed: 497103
pmcid: 2010067
doi: 10.1038/bjc.1979.216
Hsu JY, Danis EP, Nance S, O’Brien JH, Gustafson AL, Wessells VM, Goodspeed AE, Talbot JC, Amacher SL, Jedlicka P et al (2022) Gene expression omnibus GSE173155 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE173155 ). [DATASET]
Hsu JY, Danis EP, Nance S, O’Brien JH, Gustafson AL, Wessells VM, Goodspeed AE, Talbot JC, Amacher SL, Jedlicka P et al (2022) SIX1 reprograms myogenic transcription factors to maintain the rhabdomyosarcoma undifferentiated state. Cell Rep. 38(5):110323
pubmed: 35108532
pmcid: 8917510
doi: 10.1016/j.celrep.2022.110323
Hua L, Fan L, Aichun W, Yongjin Z, Qingqing C, Xiaojian W (2014) Inhibition of Six1 promotes apoptosis, suppresses proliferation, and migration of osteosarcoma cells. Tumour Biol 35(3):1925–1931
pubmed: 24114014
doi: 10.1007/s13277-013-1258-1
Huang W, Loganantharaj R, Schroeder B, Fargo D, Li L (2013) PAVIS: a tool for peak annotation and visualization. Bioinformatics 29(23):3097–3099
pubmed: 24008416
pmcid: 3834791
doi: 10.1093/bioinformatics/btt520
Hu-Lieskovan S, Zhang J, Wu L, Shimada H, Schofield DE, Triche TJ (2005) EWS-FLI1 fusion protein up-regulates critical genes in neural crest development and is responsible for the observed phenotype of Ewing’s family of tumors. Cancer Res 65(11):4633–4644
pubmed: 15930281
doi: 10.1158/0008-5472.CAN-04-2857
Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L (2006) A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res 16(5):669–677
pubmed: 16606702
pmcid: 1457042
doi: 10.1101/gr.4842106
Imbeault M, Helleboid PY, Trono D (2017) KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks. Nature 543(7646):550–554
pubmed: 28273063
doi: 10.1038/nature21683
Ito J, Kimura I, Soper A, Coudray A, Koyanagi Y, Nakaoka H, Inoue I, Turelli P, Trono D, Sato K (2020) Endogenous retroviruses drive KRAB zinc-finger protein family expression for tumor suppression. Sci Adv 6(43):eabc3020
pubmed: 33087347
pmcid: 7577720
doi: 10.1126/sciadv.abc3020
Iyengar S, Farnham PJ (2011) KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem 286(30):26267–26276
pubmed: 21652716
pmcid: 3143589
doi: 10.1074/jbc.R111.252569
Janky R, Verfaillie A, Imrichova H, Van de Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Naval Sanchez M, Potier D et al (2014) iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PLoS Comput Biol 10(7):e1003731
pubmed: 25058159
pmcid: 4109854
doi: 10.1371/journal.pcbi.1003731
Jansz N, Faulkner GJ (2021) Endogenous retroviruses in the origins and treatment of cancer. Genome Biol 22(1):147
pubmed: 33971937
pmcid: 8108463
doi: 10.1186/s13059-021-02357-4
Jen J, Wang YC (2016) Zinc finger proteins in cancer progression. J Biomed Sci 23(1):53
pubmed: 27411336
pmcid: 4944467
doi: 10.1186/s12929-016-0269-9
Jurikova M, Danihel L, Polak S, Varga I (2016) Ki67, PCNA, and MCM proteins: markers of proliferation in the diagnosis of breast cancer. Acta Histochem 118(5):544–552
pubmed: 27246286
doi: 10.1016/j.acthis.2016.05.002
Kash JC, Tumpey TM, Proll SC, Carter V, Perwitasari O, Thomas MJ, Basler CF, Palese P, Taubenberger JK, Garcia-Sastre A et al (2006) Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus. Nature 443(7111):578–581
pubmed: 17006449
pmcid: 2615558
doi: 10.1038/nature05181
Katagiri T, Yamaguchi A, Komaki M, Abe E, Takahashi N, Ikeda T, Rosen V, Wozney JM, Fujisawa-Sehara A, Suda T (1994) Bone morphogenetic protein-2 converts the differentiation pathway of C2C12 myoblasts into the osteoblast lineage. J Cell Biol 127(6 Pt 1):1755–1766
pubmed: 7798324
doi: 10.1083/jcb.127.6.1755
Kedinger V, Meulle A, Zounib O, Bonnet ME, Gossart JB, Benoit E, Messmer M, Shankaranarayanan P, Behr JP, Erbacher P et al (2013) Sticky siRNAs targeting survivin and cyclin B1 exert an antitumoral effect on melanoma subcutaneous xenografts and lung metastases. BMC Cancer 13:338
pubmed: 23835136
pmcid: 3711931
doi: 10.1186/1471-2407-13-338
Keeney S, Kleckner N (1996) Communication between homologous chromosomes: genetic alterations at a nuclease-hypersensitive site can alter mitotic chromatin structure at that site both in cis and in trans. Genes Cells 1(5):475–489
pubmed: 9078379
doi: 10.1046/j.1365-2443.1996.d01-257.x
Kim E, Rich J, Karoutas A, Tarlykov P, Cochet E, Malysheva D, Mamchaoui K, Ogryzko V, Pirozhkova I (2015) ZNF555 protein binds to transcriptional activator site of 4qA allele and ANT1: potential implication in facioscapulohumeral dystrophy. Nucleic Acids Res 43(17):8227–8242
pubmed: 26184877
pmcid: 4787827
doi: 10.1093/nar/gkv721
Kim KY, Tanaka Y, Su J, Cakir B, Xiang Y, Patterson B, Ding J, Jung YW, Kim JH, Hysolli E et al (2018) Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. Nat Commun 9(1):2583
pubmed: 29968706
pmcid: 6030064
doi: 10.1038/s41467-018-04818-0
Klochkov D, Rincon-Arano H, Ioudinkova ES, Valadez-Graham V, Gavrilov A, Recillas-Targa F, Razin SV (2006) A CTCF-dependent silencer located in the differentially methylated area may regulate expression of a housekeeping gene overlapping a tissue-specific gene domain. Mol Cell Biol 26(5):1589–1597
pubmed: 16478981
pmcid: 1430243
doi: 10.1128/MCB.26.5.1589-1597.2006
Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F (2021). Gene transcription regulation database (GTRD) ( http://gtrd.biouml.org/ ). [DATASET]
Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F (2021) GTRD: an integrated view of transcription regulation. Nucleic Acids Res 49(D1):D104–D111
pubmed: 33231677
doi: 10.1093/nar/gkaa1057
Kong X, Chen J, Xie W, Brown SM, Cai Y, Wu K, Fan D, Nie Y, Yegnasubramanian S, Tiedemann RL et al (2019) Defining UHRF1 domains that support maintenance of human colon Cancer DNA methylation and oncogenic properties. Cancer Cell 35(4):633–648.e637
pubmed: 30956060
pmcid: 6521721
doi: 10.1016/j.ccell.2019.03.003
Korner A, Bernard A, Fitzgerald JC, Alarcon-Barrera JC, Kostidis S, Kaussen T, Giera M, Mirakaj V (2021) Sema7A is crucial for resolution of severe inflammation. Proc Natl Acad Sci USA 118(9):e2017527118
pubmed: 33637648
pmcid: 7936270
doi: 10.1073/pnas.2017527118
Kucukural A, Yukselen O, Ozata DM, Moore MJ, Garber M (2019) DEBrowser: interactive differential expression analysis and visualization tool for count data. BMC Genomics 20(1):6
pubmed: 30611200
pmcid: 6321710
doi: 10.1186/s12864-018-5362-x
Kurmasheva RT, Peterson CA, Parham DM, Chen B, McDonald RE, Cooney CA (2005) Upstream CpG island methylation of the PAX3 gene in human rhabdomyosarcomas. Pediatr Blood Cancer 44(4):328–337
pubmed: 15602708
doi: 10.1002/pbc.20285
Laclef C, Hamard G, Demignon J, Souil E, Houbron C, Maire P (2003) Altered myogenesis in Six1-deficient mice. Development 130(10):2239–2252
pubmed: 12668636
doi: 10.1242/dev.00440
Lazzerini Denchi E, Helin K (2005) E2F1 is crucial for E2F-dependent apoptosis. EMBO Rep. 6(7):661–668
pubmed: 15976820
pmcid: 1369111
doi: 10.1038/sj.embor.7400452
Leo E, Deveraux QL, Buchholtz C, Welsh K, Matsuzawa S, Stennicke HR, Salvesen GS, Reed JC (2001) TRAF1 is a substrate of caspases activated during tumor necrosis factor receptor-alpha-induced apoptosis. J Biol Chem 276(11):8087–8093
pubmed: 11098060
doi: 10.1074/jbc.M009450200
Lerdrup M, Johansen JV, Agrawal-Singh S, Hansen K (2016) An interactive environment for agile analysis and visualization of ChIP-sequencing data. Nat Struct Mol Biol 23(4):349–357
pubmed: 26926434
doi: 10.1038/nsmb.3180
Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P (2015). Molecular signatures database (MSigDB) hallmark gene set collection ( https://www.gsea-msigdb.org/gsea/msigdb/ ). [DATASET]
Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P (2015) The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst 1(6):417–425
pubmed: 26771021
pmcid: 4707969
doi: 10.1016/j.cels.2015.12.004
Lim K-H, Park SG (2016) Transcriptional regulation of KRAB-ZFPs in cancer. Mol Cell Toxicol 11(4):389–394
doi: 10.1007/s13273-015-0040-4
Liu A, Cerniglia GJ, Bernhard EJ, Prendergast GC (2001) RhoB is required to mediate apoptosis in neoplastically transformed cells after DNA damage. Proc Natl Acad Sci USA 98(11):6192–6197
pmcid: 33444
doi: 10.1073/pnas.111137198
Liu W, Yu Z, Tang H, Wang X, Zhang B, Zhao J, Liu X, Zhang J, Wei M (2020) Silencing KIF18B enhances radiosensitivity: identification of a promising therapeutic target in sarcoma. EBioMedicine 61:103056
pubmed: 33038765
pmcid: 7648128
doi: 10.1016/j.ebiom.2020.103056
Liu X, Gao Q, Li P, Zhao Q, Zhang J, Li J, Koseki H, Wong J (2013) UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9. Nat Commun 4:1563
pubmed: 23463006
doi: 10.1038/ncomms2562
Liu X, Zhou Y, Qin C, Zhu X (2022) TNFRSF9 suppressed the progression of breast cancer via the p38MAPK/PAX6 signaling pathway. J Oncol 2022:8549781
pubmed: 35799609
pmcid: 9256432
Liu Y, Chu A, Chakroun I, Islam U, Blais A (2010) Cooperation between myogenic regulatory factors and SIX family transcription factors is important for myoblast differentiation. Nucleic Acids Res 38(20):6857–6871
pubmed: 20601407
pmcid: 2978361
doi: 10.1093/nar/gkq585
Liu Y, Xu C, Asiamah CA, Ye R, Pan Y, Lu LL, Zhao Z, Jiang P, Su Y (2021) Decorin regulates myostatin and enhances proliferation and differentiation of embryonic myoblasts in Leizhou black duck. Gene 804:145884
pubmed: 34364913
doi: 10.1016/j.gene.2021.145884
Liu Y, Zhang B, Kuang H, Korakavi G, Lu LY, Yu X (2016) Zinc finger protein 618 regulates the function of UHRF2 (ubiquitin-like with PHD and ring finger domains 2) as a specific 5-hydroxymethylcytosine reader. J Biol Chem 291(26):13679–13688
pubmed: 27129234
pmcid: 4919451
doi: 10.1074/jbc.M116.717314
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) Method. Methods 25(4):402–408
pubmed: 11846609
doi: 10.1006/meth.2001.1262
Louis DN, Perry A, Reifenberger G, von Deimling A, Figarella-Branger D, Cavenee WK, Ohgaki H, Wiestler OD, Kleihues P, Ellison DW (2016) The 2016 World Health Organization classification of tumors of the central nervous system: a summary. Acta Neuropathol 131(6):803–820
pubmed: 27157931
doi: 10.1007/s00401-016-1545-1
Mackeh R, Marr AK, Fadda A, Kino T (2018) C2H2-type zinc finger proteins: evolutionarily old and new partners of the nuclear hormone receptors. Nucl Recept Signal 15:1550762918801071
pubmed: 30718982
pmcid: 6348741
doi: 10.1177/1550762918801071
Maiorano D, Lutzmann M, Mechali M (2006) MCM proteins and DNA replication. Curr Opin Cell Biol 18(2):130–136
pubmed: 16495042
doi: 10.1016/j.ceb.2006.02.006
Maire P, Dos Santos M, Madani R, Sakakibara I, Viaut C, Wurmser M (2020) Myogenesis control by SIX transcriptional complexes. Semin Cell Dev Biol 104:51–64
pubmed: 32247726
doi: 10.1016/j.semcdb.2020.03.003
Mamchaoui K, Trollet C, Bigot A, Negroni E, Chaouch S, Wolff A, Kandalla PK, Marie S, Di Santo J, St Guily JL et al (2011) Immortalized pathological human myoblasts: towards a universal tool for the study of neuromuscular disorders. Skelet Muscle 1:34
pubmed: 22040608
pmcid: 3235972
doi: 10.1186/2044-5040-1-34
Marshall AD, Grosveld GC (2012) Alveolar rhabdomyosarcoma - the molecular drivers of PAX3/7-FOXO1-induced tumorigenesis. Skelet Muscle 2(1):25
pubmed: 23206814
pmcid: 3564712
doi: 10.1186/2044-5040-2-25
Marthiens V, Gavard J, Lambert M, Mege RM (2002) Cadherin-based cell adhesion in neuromuscular development. Biol Cell 94(6):315–326
pubmed: 12500939
doi: 10.1016/S0248-4900(02)00005-9
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28(5):495–501
pubmed: 20436461
pmcid: 4840234
doi: 10.1038/nbt.1630
Megiorni F (2020) Epigenetics in rhabdomyosarcoma: cues to new biomarkers and targeted therapies. EBioMedicine 52:102673
pubmed: 32058940
pmcid: 7026726
doi: 10.1016/j.ebiom.2020.102673
Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY et al (2013) The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods 10(8):730–736
pubmed: 23921808
pmcid: 3773500
doi: 10.1038/nmeth.2557
Min WP, Wei XF (2021) Silencing SIX1 inhibits epithelial mesenchymal transition through regulating TGF-beta/Smad2/3 signaling pathway in papillary thyroid carcinoma. Auris Nasus Larynx 48(3):487–495
pubmed: 33077306
doi: 10.1016/j.anl.2020.10.002
Moio P, Kulyyassov A, Vertut D, Camoin L, Ramankulov E, Lipinski M, Ogryzko V (2011) Exploring the use of dimethylsulfate for in vivo proteome footprinting. Proteomics 11(2):249–260
pubmed: 21204252
doi: 10.1002/pmic.200900832
Nakamura K, Baba Y, Kosumi K, Harada K, Shigaki H, Miyake K, Kiyozumi Y, Ohuchi M, Kurashige J, Ishimoto T et al (2016) UHRF1 regulates global DNA hypomethylation and is associated with poor prognosis in esophageal squamous cell carcinoma. Oncotarget 7(36):57821–57831
pubmed: 27507047
pmcid: 5295392
doi: 10.18632/oncotarget.11067
Nakatani Y, Ogryzko V (2003) Immunoaffinity purification of mammalian protein complexes. Methods Enzymol 370:430–444
pubmed: 14712665
doi: 10.1016/S0076-6879(03)70037-8
Niemeyer BA, Mery L, Zawar C, Suckow A, Monje F, Pardo LA, Stuhmer W, Flockerzi V, Hoth M (2001) Ion channels in health and disease. 83rd Boehringer Ingelheim Fonds International Titisee Conference. EMBO Rep. 2(7):568–573
pubmed: 11463739
pmcid: 1083959
doi: 10.1093/embo-reports/kve145
Niinuma T, Kitajima H, Kai M, Yamamoto E, Yorozu A, Ishiguro K, Sasaki H, Sudo G, Toyota M, Hatahira T et al (2019) UHRF1 depletion and HDAC inhibition reactivate epigenetically silenced genes in colorectal cancer cells. Clin Epigenetics 11(1):70
pubmed: 31064417
pmcid: 6505222
doi: 10.1186/s13148-019-0668-3
Ohshima K, Hatakeyama K, Nagashima T, Watanabe Y, Kanto K, Doi Y, Ide T, Shimoda Y, Tanabe T, Ohnami S et al (2017) Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. Sci Rep. 7(1):641
pubmed: 28377632
pmcid: 5428069
doi: 10.1038/s41598-017-00219-3
Oluwole SO, Yao Y, Conradi S, Kristensson K, Karlsson H (2007) Elevated levels of transcripts encoding a human retroviral envelope protein (syncytin) in muscles from patients with motor neuron disease. Amyotroph Lateral Scler 8(2):67–72
pubmed: 17453631
doi: 10.1080/17482960600864207
Ostrovidov S, Hosseini V, Ahadian S, Fujie T, Parthiban SP, Ramalingam M, Bae H, Kaji H, Khademhosseini A (2014) Skeletal muscle tissue engineering: methods to form skeletal myotubes and their applications. Tissue Eng Part B Rev 20(5):403–436
pubmed: 24320971
pmcid: 4193686
doi: 10.1089/ten.teb.2013.0534
Oyler-Yaniv J, Oyler-Yaniv A, Maltz E, Wollman R (2021) TNF controls a speed-accuracy tradeoff in the cell death decision to restrict viral spread. Nat Commun 12(1):2992
pubmed: 34016976
pmcid: 8137918
doi: 10.1038/s41467-021-23195-9
Pankow S, Bamberger C, Calzolari D, Bamberger A, Yates 3rd JR (2016) Deep interactome profiling of membrane proteins by co-interacting protein identification technology. Nat Protoc 11(12):2515–2528
pubmed: 27854364
pmcid: 5444904
doi: 10.1038/nprot.2016.140
Parmacek MS, Ip HS, Jung F, Shen T, Martin JF, Vora AJ, Olson EN, Leiden JM (1994) A novel myogenic regulatory circuit controls slow/cardiac troponin C gene transcription in skeletal muscle. Mol Cell Biol 14(3):1870–1885
pubmed: 8114720
pmcid: 358545
Patel AG, Chen X, Huang X, Clay MR, Komorova N, Krasin MJ, Pappo A, Tillman H, Orr BA, McEvoy J et al (2022) The myogenesis program drives clonal selection and drug resistance in rhabdomyosarcoma. Dev Cell 57(10):1226–1240.e1228
pubmed: 35483358
pmcid: 9133224
doi: 10.1016/j.devcel.2022.04.003
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14(4):417–419
pubmed: 28263959
pmcid: 5600148
doi: 10.1038/nmeth.4197
Portney BA, Arad M, Gupta A, Brown RA, Khatri R, Lin PN, Hebert AM, Angster KH, Silipino LE, Meltzer WA et al (2020) ZSCAN4 facilitates chromatin remodeling and promotes the cancer stem cell phenotype. Oncogene 39(26):4970–4982
pubmed: 32507861
pmcid: 7314663
doi: 10.1038/s41388-020-1333-1
Pritt ML, Hall DG, Recknor J, Credille KM, Brown DD, Yumibe NP, Schultze AE, Watson DE (2008) Fabp3 as a biomarker of skeletal muscle toxicity in the rat: comparison with conventional biomarkers. Toxicol Sci 103(2):382–396
pubmed: 18308699
doi: 10.1093/toxsci/kfn042
Qian Y, Pei D, Cheng T, Wu C, Pu X, Chen X, Liu Y, Shen H, Zhang W, Shu Y (2015) CD137 ligand-mediated reverse signaling inhibits proliferation and induces apoptosis in non-small cell lung cancer. Med Oncol 32(3):44
pubmed: 25631633
doi: 10.1007/s12032-015-0499-9
Quenneville S, Turelli P, Bojkowska K, Raclot C, Offner S, Kapopoulou A, Trono D (2012) The KRAB-ZFP/KAP1 system contributes to the early embryonic establishment of site-specific DNA methylation patterns maintained during development. Cell Rep. 2(4):766–773
pubmed: 23041315
pmcid: 3677399
doi: 10.1016/j.celrep.2012.08.043
Randolph K, Hyder U, D’Orso I (2022) KAP1/TRIM28: transcriptional activator and/or repressor of viral and cellular programs? Front Cell Infect Microbiol 12:834636
pubmed: 35281453
pmcid: 8904932
doi: 10.3389/fcimb.2022.834636
Reichenberger KJ, Coletta RD, Schulte AP, Varella-Garcia M, Ford HL (2005) Gene amplification is a mechanism of Six1 overexpression in breast cancer. Cancer Res 65(7):2668–2675
pubmed: 15805264
doi: 10.1158/0008-5472.CAN-04-4286
Repo H, Loyttyniemi E, Kurki S, Kallio L, Kuopio T, Talvinen K, Kronqvist P (2020) A prognostic model based on cell-cycle control predicts outcome of breast cancer patients. BMC Cancer 20(1):558
pubmed: 32546141
pmcid: 7296704
doi: 10.1186/s12885-020-07045-3
Rich J, Ogryzko VV, Pirozhkova IV (2014) Satellite DNA and related diseases. Biopolym Cell 30(4):249–259
doi: 10.7124/bc.00089E
Roberti A, Valdes AF, Torrecillas R, Fraga MF, Fernandez AF (2019) Epigenetics in cancer therapy and nanomedicine. Clin Epigenetics 11(1):81
pubmed: 31097014
pmcid: 6524244
doi: 10.1186/s13148-019-0675-4
Rowe HM, Friedli M, Offner S, Verp S, Mesnard D, Marquis J, Aktas T, Trono D (2013) De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET. Development 140(3):519–529
pubmed: 23293284
doi: 10.1242/dev.087585
Sakai H, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada SI, Ohkawa Y, Kikugawa T et al (2022) Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience 25(3):103928
pubmed: 35243267
pmcid: 8886052
doi: 10.1016/j.isci.2022.103928
Salminen M, Spitz F, Fiszman MY, Demignon J, Kahn A, Daegelen D, Maire P (1995) Myotube-specific activity of the human aldolase A M-promoter requires an overlapping binding site for NF1 and MEF2 factors in addition to a binding site (M1) for unknown proteins. J Mol Biol 253(1):17–31
pubmed: 7473711
doi: 10.1006/jmbi.1995.0532
Samuels-Lev Y, O’Connor DJ, Bergamaschi D, Trigiante G, Hsieh JK, Zhong S, Campargue I, Naumovski L, Crook T, Lu X (2001) ASPP proteins specifically stimulate the apoptotic function of p53. Mol Cell 8(4):781–794
pubmed: 11684014
doi: 10.1016/S1097-2765(01)00367-7
Sannino G, Marchetto A, Kirchner T, Grunewald TGP (2017) Epithelial-to-mesenchymal and mesenchymal-to-epithelial transition in mesenchymal tumors: a paradox in sarcomas? Cancer Res 77(17):4556–4561
pubmed: 28811330
doi: 10.1158/0008-5472.CAN-17-0032
Santolini M, Sakakibara I, Gauthier M, Ribas-Aulinas F, Takahashi H, Sawasaki T, Mouly V, Concordet JP, Defossez PA, Hakim V et al (2016) MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis. Nucleic Acids Res 44(18):8621–8640
pubmed: 27302134
pmcid: 5062961
doi: 10.1093/nar/gkw512
Schrader C, Janssen D, Klapper W, Siebmann JU, Meusers P, Brittinger G, Kneba M, Tiemann M, Parwaresch R (2005) Minichromosome maintenance protein 6, a proliferation marker superior to Ki-67 and independent predictor of survival in patients with mantle cell lymphoma. Br J Cancer 93(8):939–945
pubmed: 16189522
pmcid: 2361659
doi: 10.1038/sj.bjc.6602795
Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher 3rd FJ (2002) SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev 16(8):919–932
pubmed: 11959841
pmcid: 152359
doi: 10.1101/gad.973302
Schulze A, Harris AL (2012) How cancer metabolism is tuned for proliferation and vulnerable to disruption. Nature 491(7424):364–373
pubmed: 23151579
doi: 10.1038/nature11706
Shang Z, Wu X, Zheng S, Wei Y, Hong Z, Ye D (2023) A systematic pan-cancer analysis identifies TRIM28 as an immunological and prognostic predictor and involved in immunotherapy resistance. J Cancer 14(15):2798–2810
pubmed: 37781084
pmcid: 10539564
doi: 10.7150/jca.86742
Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D, Fan X (2019) Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC Med Genet 20(1):175
pubmed: 31706287
pmcid: 6842483
doi: 10.1186/s12881-019-0909-5
Shi J, Wei L (2007) Rho kinase in the regulation of cell death and survival. Arch Immunol Ther Exp (Warsz) 55(2):61–75
pubmed: 17347801
doi: 10.1007/s00005-007-0009-7
Sidhu H, Capalash N (2017) UHRF1: The key regulator of epigenetics and molecular target for cancer therapeutics. Tumour Biol 39(2):1010428317692205
pubmed: 28218043
doi: 10.1177/1010428317692205
Singh K, Cassano M, Planet E, Sebastian S, Jang SM, Sohi G, Faralli H, Choi J, Youn HD, Dilworth FJ et al (2015) A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation. Genes Dev 29(5):513–525
pubmed: 25737281
pmcid: 4358404
doi: 10.1101/gad.254532.114
Smit AFA, Hubley R, Green P (1996–2010) UCSC: 2022-10-18 ( https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2241691764_NAblzqhTDxKwTWYEwHHlyISn3tgh&db=hg38&g=rmsk ) [DATASET]
Smit AFA, Hubley R, Green P (1996–2010). RepeatMasker Open-3.0. ( http://www.repeatmasker.org )
Sobocinska J, Molenda S, Machnik M, Oleksiewicz U (2021) KRAB-ZFP transcriptional regulators acting as oncogenes and tumor suppressors: an overview. Int J Mol Sci 22(4):2212
pubmed: 33672287
pmcid: 7926519
doi: 10.3390/ijms22042212
Spitz F, Demignon J, Porteu A, Kahn A, Concordet JP, Daegelen D, Maire P (1998) Expression of myogenin during embryogenesis is controlled by Six/sine oculis homeoproteins through a conserved MEF3 binding site. Proc Natl Acad Sci USA 95(24):14220–14225
pubmed: 9826681
pmcid: 24354
doi: 10.1073/pnas.95.24.14220
Spitz F, Salminen M, Demignon J, Kahn A, Daegelen D, Maire P (1997) A combination of MEF3 and NFI proteins activates transcription in a subset of fast-twitch muscles. Mol Cell Biol 17(2):656–666
pubmed: 9001219
pmcid: 231791
doi: 10.1128/MCB.17.2.656
Srinivasan R, Nady N, Arora N, Hsieh LJ, Swigut T, Narlikar GJ, Wossidlo M, Wysocka J (2020) Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage. Sci Adv 6(12):eaaz9115
pubmed: 32219172
pmcid: 7083622
doi: 10.1126/sciadv.aaz9115
Stirzaker C, Song JZ, Ng W, Du Q, Armstrong NJ, Locke WJ, Statham AL, French H, Pidsley R, Valdes-Mora F et al (2017) Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer. Oncogene 36(10):1328–1338
pubmed: 27593931
doi: 10.1038/onc.2016.297
Su Lim C, Sun Kim E, Yeon Kim J, Taek Hong S, Jai Chun H, Eun Kang D, Rae Cho B (2015) Measurement of the nucleus area and nucleus/cytoplasm and mitochondria/nucleus ratios in human colon tissues by dual-colour two-photon microscopy imaging. Sci Rep. 5:18521
pubmed: 26673743
pmcid: 4682082
doi: 10.1038/srep18521
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102(43):15545–15550
pubmed: 16199517
pmcid: 1239896
doi: 10.1073/pnas.0506580102
Sun X, Guo W, Shen JK, Mankin HJ, Hornicek FJ, Duan Z (2015) Rhabdomyosarcoma: advances in molecular and cellular biology. Sarcoma 2015:232010
pubmed: 26420980
pmcid: 4569767
doi: 10.1155/2015/232010
Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126(4):663–676
pubmed: 16904174
doi: 10.1016/j.cell.2006.07.024
Tamaru H, Selker EU (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414(6861):277–283
pubmed: 11713521
doi: 10.1038/35104508
Tang D, Kang R, Berghe TV, Vandenabeele P, Kroemer G (2019) The molecular machinery of regulated cell death. Cell Res 29(5):347–364
pubmed: 30948788
pmcid: 6796845
doi: 10.1038/s41422-019-0164-5
Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E et al (2019) COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acids Res 47(D1):D941–D947
pubmed: 30371878
doi: 10.1093/nar/gky1015
Tenente IM, Hayes MN, Ignatius MS, McCarthy K, Yohe M, Sindiri S, Gryder B, Oliveira ML, Ramakrishnan A, Tang Q et al (2017) Myogenic regulatory transcription factors regulate growth in rhabdomyosarcoma. Elife 6:e19214
pubmed: 28080960
pmcid: 5231408
doi: 10.7554/eLife.19214
Tremblay P, Dietrich S, Mericskay M, Schubert FR, Li Z, Paulin D (1998) A crucial role for Pax3 in the development of the hypaxial musculature and the long-range migration of muscle precursors. Dev Biol 203(1):49–61
pubmed: 9806772
doi: 10.1006/dbio.1998.9041
Tsukihara H, Nakagawa F, Sakamoto K, Ishida K, Tanaka N, Okabe H, Uchida J, Matsuo K, Takechi T (2015) Efficacy of combination chemotherapy using a novel oral chemotherapeutic agent, TAS-102, together with bevacizumab, cetuximab, or panitumumab on human colorectal cancer xenografts. Oncol Rep 33(5):2135–2142
pubmed: 25812794
pmcid: 4391594
Turelli P, Castro-Diaz N, Marzetta F, Kapopoulou A, Raclot C, Duc J, Tieng V, Quenneville S, Trono D (2014) Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements. Genome Res 24(8):1260–1270
pubmed: 24879559
pmcid: 4120080
doi: 10.1101/gr.172833.114
Turelli P, Playfoot C, Grun D, Raclot C, Pontis J, Coudray A, Thorball C, Duc J, Pankevich EV, Deplancke B et al (2020) Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons. Sci Adv 6(35):eaba3200
pubmed: 32923624
pmcid: 7455193
doi: 10.1126/sciadv.aba3200
Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, Mann M, Cox J (2016) The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 13(9):731–740
pubmed: 27348712
doi: 10.1038/nmeth.3901
Verdikt R, Bendoumou M, Bouchat S, Nestola L, Pasternak AO, Darcis G, Avettand-Fenoel V, Vanhulle C, Ait-Ammar A, Santangelo M et al (2022) Novel role of UHRF1 in the epigenetic repression of the latent HIV-1. EBioMedicine 79:103985
pubmed: 35429693
pmcid: 9038550
doi: 10.1016/j.ebiom.2022.103985
Vinciguerra M, Fulco M, Ladurner A, Sartorelli V, Rosenthal N (2010) SirT1 in muscle physiology and disease: lessons from mouse models. Dis Model Mech 3(5-6):298–303
pubmed: 20354108
pmcid: 2860850
doi: 10.1242/dmm.004655
Vishnubalaji R, Elango R, Al-Toub M, Manikandan M, Al-Rikabi A, Harkness L, Ditzel N, Atteya M, Hamam R, Alfayez M et al (2019) Neoplastic transformation of human mesenchymal stromal cells mediated via LIN28B. Sci Rep 9(1):8101
pubmed: 31147574
pmcid: 6542832
doi: 10.1038/s41598-019-44536-1
Wakelam MJ (1985) The fusion of myoblasts. Biochem J 228(1):1–12
pubmed: 3890835
pmcid: 1144947
doi: 10.1042/bj2280001
Wang C, Ivanov A, Chen L, Fredericks WJ, Seto E, Rauscher 3rd FJ, Chen J (2005) MDM2 interaction with nuclear corepressor KAP1 contributes to p53 inactivation. EMBO J 24(18):3279–3290
pubmed: 16107876
pmcid: 1224681
doi: 10.1038/sj.emboj.7600791
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et al (2013). USCS from ENCODE 3 Nov 2018 ( https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=2241966598_fSlgbau4A0NavVvfQSrqfanUAuxx&g=encRegTfbsClustered&hgTracksConfigPage=configure ) [DATASET]
Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et al (2013) Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res 41(Database issue):D171–176
pubmed: 23203885
doi: 10.1093/nar/gks1221
Wang YN, Yang WC, Li PW, Wang HB, Zhang YY, Zan LS (2018) Myocyte enhancer factor 2 A promotes proliferation and its inhibition attenuates myogenic differentiation via myozenin 2 in bovine skeletal muscle myoblast. PLoS ONE 13(4):e0196255
pubmed: 29698438
pmcid: 5919640
doi: 10.1371/journal.pone.0196255
Wanigasekara Y, Airaksinen MS, Heuckeroth RO, Milbrandt J, Keast JR (2004) Neurturin signalling via GFRalpha2 is essential for innervation of glandular but not muscle targets of sacral parasympathetic ganglion neurons. Mol Cell Neurosci 25(2):288–300
pubmed: 15019945
doi: 10.1016/j.mcn.2003.10.019
Wei Y, Qin Q, Yan C, Hayes MN, Garcia SP, Xi H, Do D, Jin AH, Eng TC, McCarthy KM et al (2022) Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma. Nat Cancer 3(8):961–975
pubmed: 35982179
pmcid: 10430812
doi: 10.1038/s43018-022-00414-w
Wolf G, de Iaco A, Sun MA, Bruno M, Tinkham M, Hoang D, Mitra A, Ralls S, Trono D, Macfarlan TS (2020) KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage. Elife 9:e56337
pubmed: 32479262
pmcid: 7289599
doi: 10.7554/eLife.56337
Wu W, Huang R, Wu Q, Li P, Chen J, Li B, Liu H (2014) The role of Six1 in the genesis of muscle cell and skeletal muscle development. Int J Biol Sci 10(9):983–989
pubmed: 25210496
pmcid: 4159689
doi: 10.7150/ijbs.9442
Wu W, Ren Z, Li P, Yu D, Chen J, Huang R, Liu H (2015) Six1: a critical transcription factor in tumorigenesis. Int J Cancer 136(6):1245–1253
pubmed: 24488862
doi: 10.1002/ijc.28755
Wurmser M, Chaverot N, Madani R, Sakai H, Negroni E, Demignon J, Saint-Pierre B, Mouly V, Amthor H, Tapscott S et al (2020) SIX1 and SIX4 homeoproteins regulate PAX7+ progenitor cell properties during fetal epaxial myogenesis. Development 147(19):dev185975
pubmed: 32591430
doi: 10.1242/dev.185975
Xiao W, Mohseny AB, Hogendoorn PC, Cleton-Jansen AM (2013) Mesenchymal stem cell transformation and sarcoma genesis. Clin Sarcoma Res 3(1):10
pubmed: 23880362
pmcid: 3724575
doi: 10.1186/2045-3329-3-10
Yang Y, Tan S, Han Y, Huang L, Yang R, Hu Z, Tao Y, Oyang L, Lin J, Peng Q et al (2023) The role of tripartite motif-containing 28 in cancer progression and its therapeutic potentials. Front Oncol 13:1100134
pubmed: 36756159
pmcid: 9899900
doi: 10.3389/fonc.2023.1100134
Yoshida H, Miyachi M, Sakamoto K, Ouchi K, Yagyu S, Kikuchi K, Kuwahara Y, Tsuchiya K, Imamura T, Iehara T et al (2014) PAX3-NCOA2 fusion gene has a dual role in promoting the proliferation and inhibiting the myogenic differentiation of rhabdomyosarcoma cells. Oncogene 33(49):5601–5608
pubmed: 24213582
doi: 10.1038/onc.2013.491
Yu Y, Davicioni E, Triche TJ, Merlino G (2006) The homeoprotein six1 transcriptionally activates multiple protumorigenic genes but requires ezrin to promote metastasis. Cancer Res 66(4):1982–1989
pubmed: 16488997
doi: 10.1158/0008-5472.CAN-05-2360
Zapata JM, Perez-Chacon G, Carr-Baena P, Martinez-Forero I, Azpilikueta A, Otano I, Melero I (2018) CD137 (4-1BB) signalosome: complexity is a matter of TRAFs. Front Immunol 9:2618
pubmed: 30524423
pmcid: 6262405
doi: 10.3389/fimmu.2018.02618
Zhang K, Sha J, Harter ML (2010) Activation of Cdc6 by MyoD is associated with the expansion of quiescent myogenic satellite cells. J Cell Biol 188(1):39–48
pubmed: 20048262
pmcid: 2812847
doi: 10.1083/jcb.200904144
Zhou J, Wang M, Zhou Z, Wang W, Duan J, Wu G (2021) Expression and prognostic value of MCM family genes in osteosarcoma. Front Mol Biosci 8:668402
pubmed: 34239894
pmcid: 8257954
doi: 10.3389/fmolb.2021.668402
Zhou Y, Basu S, Laue E, Seshia AA (2016) Single cell studies of mouse embryonic stem cell (mESC) differentiation by electrical impedance measurements in a microfluidic device. Biosens Bioelectron 81:249–258
pubmed: 26963790
pmcid: 4833703
doi: 10.1016/j.bios.2016.02.069
Zhu Q, Pao GM, Huynh AM, Suh H, Tonnu N, Nederlof PM, Gage FH, Verma IM (2011) BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature 477(7363):179–184
pubmed: 21901007
pmcid: 3240576
doi: 10.1038/nature10371