title: Overexpression of HOX genes is prevalent in Ewing sarcoma and is associated with altered epigenetic regulation of developmental transcription programs.
abstract: The polycomb proteins BMI-1 and EZH2 are highly overexpressed by Ewing sarcoma (ES), a tumor of stem cell origin that is driven by EWS-ETS fusion oncogenes, most commonly EWS-FLI1. In the current study we analyzed expression of transcription programs that are controlled by polycomb proteins during embryonic development to determine if they are abnormal in ES. Our results show that polycomb target gene expression in ES deviates from normal tissues and stem cells and that, as expected, most targets are relatively repressed. However, we also discovered a paradoxical up regulation of numerous polycomb targets and these were highly enriched for homeobox (HOX) genes. Comparison of HOX profiles between malignant and non-malignant tissues revealed a distinctive HOX profile in ES, which was characterized by overexpression of posterior HOXD genes. In addition, ectopic expression of EWS-FLI1 during stem cell differentiation led to aberrant up regulation of posterior HOXD genes. Mechanistically, this up regulation was associated with altered epigenetic regulation. Specifically, ES and EWS-FLI1+ stem cells displayed a relative loss of polycomb-dependent H3K27me3 and gain of trithorax-dependent H3K4me3 at the promoters of posterior HOXD genes and also at the HOXD11.12 polycomb response element. In addition, a striking correlation was evident between HOXD13 and other genes whose regulation is coordinately regulated during embryonic development by distal enhancer elements. Together, these studies demonstrate that epigenetic regulation of polycomb target genes, in particular HOXD genes, is altered in ES and that these changes are mediated downstream of EWS-FLI1.
authors.affiliation: a Translational Oncology Program and the Departments of Pediatric and Communicable Diseases; University of Michigan ; Ann Arbor , MI USA.
authors.forename: Laurie K
authors.initials: LK
authors.lastname: Svoboda
authors.forename: Ashley
authors.initials: A
authors.lastname: Harris
authors.forename: Natashay J
authors.initials: NJ
authors.lastname: Bailey
authors.forename: Raphaela
authors.initials: R
authors.lastname: Schwentner
authors.forename: Eleni
authors.initials: E
authors.lastname: Tomazou
authors.forename: Cornelia
authors.initials: C
authors.lastname: von Levetzow
authors.forename: Brian
authors.initials: B
authors.lastname: Magnuson
authors.forename: Mats
authors.initials: M
authors.lastname: Ljungman
authors.forename: Heinrich
authors.initials: H
authors.lastname: Kovar
authors.forename: Elizabeth R
authors.initials: ER
authors.lastname: Lawlor
mesh_terms: D001859:Bone Neoplasms / Q000235:genetics*; D002454:Cell Differentiation; D045744:Cell Line, Tumor; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D005801:Genes, Homeobox; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D005810:Multigene Family; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D063146:Polycomb-Group Proteins / Q000235:genetics; D051789:Proto-Oncogene Protein c-fli-1 / Q000235:genetics; D034802:RNA-Binding Protein EWS / Q000235:genetics; D012512:Sarcoma, Ewing / Q000235:genetics*; D013234:Stem Cells / Q000166:cytology / Q000502:physiology; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: C106031:EWS-FLI fusion protein; C489493:HOXD11 protein, human; C513184:HOXD13 protein, human; D018398:Homeodomain Proteins; D015514:Oncogene Proteins, Fusion; D063146:Polycomb-Group Proteins; D051789:Proto-Oncogene Protein c-fli-1; D034802:RNA-Binding Protein EWS; D014157:Transcription Factors; C072064:HOXD10 protein, human
keywords: ARMS, alveolar rhabdomyosarcoma; BM-MSC, adult bone marrow-derived mesenchymal stem cells; ChIP, chromatin immunoprecipitation; ChIP-seq, chromatin immunoprecipitation/high throughput sequencing; ERMS, embryonal rhabdomyosarcoma; ES, Ewing sarcoma; Ewing sarcoma; GCR, global control region; HOX; HOX, homeobox; MSC, mesenchymal stem cells; NC-MSC, neural crest stem cell-derived mesenchymal stem cells; NCSC, neural crest stem cells; OS, osteosarcoma; PCA, principal components analysis; PRE, polycomb response element; RT-PCR, reverse transcriptase polymerase chain reaction; epigenetic; hESC, human embryonic stem cells; polycomb; qPCR, quantitative polymerase chain reaction