title: ETV transcriptional upregulation is more reliable than RNA sequencing algorithms and FISH in diagnosing round cell sarcomas with CIC gene rearrangements.
abstract: CIC rearrangements have been reported in two-thirds of EWSR1-negative small blue round cell tumors (SBRCTs). However, a number of SBRCTs remain unclassified despite exhaustive analysis. Fourteen SBRCTs lacking driver genetic events by RNA sequencing (RNAseq) analysis were collected. Unsupervised hierarchical clustering was performed using samples from our RNAseq database, including 13 SBRCTs with non-CIC genetic abnormalities and 2 CIC-rearranged angiosarcomas among others. Remarkably, all 14 study cases showed high mRNA levels of ETV1/4/5, and by unsupervised clustering most grouped into a distinct cluster, separate from other tumors. Based on these results indicating a close relationship with CIC-rearranged tumors, we manually inspected CIC reads in RNAseq data. FISH for CIC and DUX4 abnormalities and immunohistochemical stains for ETV4 were also performed. In the control group, only 2 CIC-rearranged angiosarcomas had high ETV1/4/5 expression. Upon manual inspection of CIC traces, 7 of 14 cases showed CIC-DUX4 fusion reads, 2 cases had DUX4-CIC reads, while the remaining 5 were negative. FISH showed CIC break-apart in 7 cases, including 5 cases lacking CIC-DUX4 or DUX4-CIC fusion reads on RNAseq manual inspection. However, no CIC abnormalities were detected by FISH in 6 cases with CIC-DUX4 or DUX4-CIC reads. ETV4 immunoreactivity was positive in 7 of 11 cases. Our results highlight the underperformance of FISH and RNAseq methods in diagnosing SBRCTs with CIC gene abnormalities. The downstream ETV1/4/5 transcriptional up-regulation appears highly sensitive and specific and can be used as a reliable molecular signature and diagnostic method for CIC fusion positive SBRCTs.
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.|Department of Pathology, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan.
authors.forename: Yu-Chien
authors.initials: YC
authors.lastname: Kao
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Yun-Shao
authors.initials: YS
authors.lastname: Sung
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Chun-Liang
authors.initials: CL
authors.lastname: Chen
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Pathology, Mount Sinai Hospital, Toronto, Canada.
authors.forename: Brendan C
authors.initials: BC
authors.lastname: Dickson
authors.affiliation: Department of Pathology, Mount Sinai Hospital, Toronto, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Swanson
authors.affiliation: Department of Musculoskeletal Pathology, The Royal Orthopaedic Hospital NHS Foundation Trust, Birmingham, United Kingdom.
authors.forename: Sumathi
authors.initials: S
authors.lastname: Vaiyapuri
authors.affiliation: Department of Human Molecular Genetics, School of Clinical and Experimental Medicine, The Medical School University of Birmingham Edgbaston, Birmingham, United Kingdom.
authors.forename: Farida
authors.initials: F
authors.lastname: Latif
authors.affiliation: Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham, Birmingham, United Kingdom.
authors.forename: Abdullah
authors.initials: A
authors.lastname: Alholle
authors.affiliation: Department of Anatomical Pathology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.
authors.forename: Shih-Chiang
authors.initials: SC
authors.lastname: Huang
authors.affiliation: Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Jason L
authors.initials: JL
authors.lastname: Hornick
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
authors.forename: Cristina R
authors.identifier: 0000-0002-9717-8205
authors.initials: CR
authors.lastname: Antonescu
mesh_terms: D000293:Adolescent; D000328:Adult; D000465:Algorithms; D002648:Child; D004268:DNA-Binding Proteins / Q000235:genetics*; D005260:Female; D015321:Gene Rearrangement; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D008875:Middle Aged; D012097:Repressor Proteins / Q000235:genetics*; D012512:Sarcoma, Ewing / Q000175:diagnosis* / Q000235:genetics; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic; D015854:Up-Regulation; D055815:Young Adult
chemical_list: C498610:CIC protein, human; D004268:DNA-Binding Proteins; C095239:ETV1 protein, human; D012097:Repressor Proteins; D014157:Transcription Factors