Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis.
Chromosomal translocation that results in fusion of the genes encoding RNA-binding protein EWS and transcription factor FLI1 (EWS-FLI1) is pathognomonic for Ewing sarcoma. EWS-FLI1 alters gene expression through mechanisms that are not completely understood. We performed RNA sequencing (RNAseq) analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify gene targets of this oncoprotein. We determined that long noncoding RNA-277 (Ewing sarcoma-associated transcript 1 [EWSAT1]) is upregulated by EWS-FLI1 in pMPCs. Inhibition of EWSAT1 expression diminished the ability of Ewing sarcoma cell lines to proliferate and form colonies in soft agar, whereas EWSAT1 inhibition had no effect on other cell types tested. Expression of EWS-FLI1 and EWSAT1 repressed gene expression, and a substantial fraction of targets that were repressed by EWS-FLI1 were also repressed by EWSAT1. Analysis of RNAseq data from primary human Ewing sarcoma further supported a role for EWSAT1 in mediating gene repression. We identified heterogeneous nuclear ribonucleoprotein (HNRNPK) as an RNA-binding protein that interacts with EWSAT1 and found a marked overlap in HNRNPK-repressed genes and those repressed by EWS-FLI1 and EWSAT1, suggesting that HNRNPK participates in EWSAT1-mediated gene repression. Together, our data reveal that EWSAT1 is a downstream target of EWS-FLI1 that facilitates the development of Ewing sarcoma via the repression of target genes.
Michelle
M
Marques Howarth
David
D
Simpson
Siu P
SP
Ngok
Bethsaida
B
Nieves
Ron
R
Chen
Zurab
Z
Siprashvili
Dedeepya
D
Vaka
Marcus R
MR
Breese
Brian D
BD
Crompton
Gabriela
G
Alexe
Doug S
DS
Hawkins
Damon
D
Jacobson
Alayne L
AL
Brunner
Robert
R
West
Jaume
J
Mora
Kimberly
K
Stegmaier
Paul
P
Khavari
E Alejandro
EA
Sweet-Cordero
D045744:Cell Line, Tumor; D002471:Cell Transformation, Neoplastic / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D015536:Down-Regulation / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D034641:Heterogeneous-Nuclear Ribonucleoprotein K; D006801:Humans; D015514:Oncogene Proteins, Fusion / Q000096:biosynthesis / Q000235:genetics; D051789:Proto-Oncogene Protein c-fli-1 / Q000096:biosynthesis / Q000235:genetics; D062085:RNA, Long Noncoding / Q000096:biosynthesis* / Q000235:genetics; D012334:RNA, Neoplasm / Q000096:biosynthesis* / Q000235:genetics; D034802:RNA-Binding Protein EWS / Q000096:biosynthesis / Q000235:genetics; D012261:Ribonucleoproteins / Q000235:genetics / Q000378:metabolism*; D012512:Sarcoma, Ewing / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D017423:Sequence Analysis, RNA; D015854:Up-Regulation / Q000235:genetics
C106031:EWS-FLI fusion protein; D034641:Heterogeneous-Nuclear Ribonucleoprotein K; D015514:Oncogene Proteins, Fusion; D051789:Proto-Oncogene Protein c-fli-1; D062085:RNA, Long Noncoding; D012334:RNA, Neoplasm; D034802:RNA-Binding Protein EWS; D012261:Ribonucleoproteins; C072074:HNRNPK protein, human