PMID- 36232302
OWN - NLM
STAT- MEDLINE
DCOM- 20221017
LR  - 20221019
IS  - 1422-0067 (Electronic)
IS  - 1422-0067 (Linking)
VI  - 23
IP  - 19
DP  - 2022 Sep 20
TI  - mRNA Capture Sequencing and RT-qPCR for the Detection of Pathognomonic, Novel, 
      and Secondary Fusion Transcripts in FFPE Tissue: A Sarcoma Showcase.
LID - 10.3390/ijms231911007 [doi]
LID - 11007
AB  - We assess the performance of mRNA capture sequencing to identify fusion 
      transcripts in FFPE tissue of different sarcoma types, followed by RT-qPCR 
      confirmation. To validate our workflow, six positive control tumors with a 
      specific chromosomal rearrangement were analyzed using the TruSight RNA 
      Pan-Cancer Panel. Fusion transcript calling by FusionCatcher confirmed these 
      aberrations and enabled the identification of both fusion gene partners and 
      breakpoints. Next, whole-transcriptome TruSeq RNA Exome sequencing was applied to 
      17 fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated 
      round cell sarcoma (URCS) tumors, for whom fluorescence in situ hybridization 
      (FISH) did not identify the classical pathognomonic rearrangements. For six 
      patients, a pathognomonic fusion transcript was readily detected, i.e., 
      PAX3-FOXO1 in two ARMS patients, and EWSR1-FLI1, EWSR1-ERG, or EWSR1-NFATC2 in 
      four URCS patients. For the 11 remaining patients, 11 newly identified fusion 
      transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, 
      WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2, and BRD4-LEUTX fusion transcripts in 
      ARMS patients. Additionally, recurrently detected secondary fusion transcripts in 
      patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed 
      (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53, and UBE2F-ALS2). In conclusion, this 
      study shows that mRNA capture sequencing enhances the detection rate of 
      pathognomonic fusions and enables the identification of novel and secondary 
      fusion transcripts in sarcomas.
FAU - Decock, Anneleen
AU  - Decock A
AUID- ORCID: 0000-0002-1091-0927
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
FAU - Creytens, David
AU  - Creytens D
AUID- ORCID: 0000-0002-6064-1673
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
AD  - Department of Pathology, Ghent University Hospital, 9000 Ghent, Belgium.
AD  - Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium.
FAU - Lefever, Steve
AU  - Lefever S
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
FAU - Van der Meulen, Joni
AU  - Van der Meulen J
AUID- ORCID: 0000-0002-1916-2769
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
AD  - Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, 
      9000 Ghent, Belgium.
FAU - Anckaert, Jasper
AU  - Anckaert J
AUID- ORCID: 0000-0001-8144-4639
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
FAU - De Ganck, Ariane
AU  - De Ganck A
AUID- ORCID: 0000-0002-6120-1987
AD  - Biogazelle, 9052 Zwijnaarde, Belgium.
FAU - Deleu, Jill
AU  - Deleu J
AUID- ORCID: 0000-0003-0921-6003
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
FAU - De Wilde, Bram
AU  - De Wilde B
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
AD  - Department of Internal Medicine and Pediatrics, Ghent University Hospital, 9000 
      Ghent, Belgium.
FAU - Fierro, Carolina
AU  - Fierro C
AD  - Biogazelle, 9052 Zwijnaarde, Belgium.
FAU - Kuersten, Scott
AU  - Kuersten S
AD  - Illumina, San Diego, CA 92122, USA.
FAU - Luypaert, Manuel
AU  - Luypaert M
AUID- ORCID: 0000-0003-3966-849X
AD  - Biogazelle, 9052 Zwijnaarde, Belgium.
FAU - Rottiers, Isabelle
AU  - Rottiers I
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
AD  - Department of Pathology, Ghent University Hospital, 9000 Ghent, Belgium.
FAU - Schroth, Gary P
AU  - Schroth GP
AD  - Illumina, San Diego, CA 92122, USA.
FAU - Steyaert, Sandra
AU  - Steyaert S
AD  - Biogazelle, 9052 Zwijnaarde, Belgium.
FAU - Vanderheyden, Katrien
AU  - Vanderheyden K
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
FAU - Vanden Eynde, Eveline
AU  - Vanden Eynde E
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
FAU - Verniers, Kimberly
AU  - Verniers K
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
FAU - Verreth, Joke
AU  - Verreth J
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
FAU - Van Dorpe, Jo
AU  - Van Dorpe J
AUID- ORCID: 0000-0001-8175-2930
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
AD  - Department of Pathology, Ghent University Hospital, 9000 Ghent, Belgium.
AD  - Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium.
FAU - Vandesompele, Jo
AU  - Vandesompele J
AUID- ORCID: 0000-0001-6274-0184
AD  - OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, 
      Ghent University, 9000 Ghent, Belgium.
AD  - Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
AD  - Biogazelle, 9052 Zwijnaarde, Belgium.
LA  - eng
PT  - Journal Article
DEP - 20220920
PL  - Switzerland
TA  - Int J Mol Sci
JT  - International journal of molecular sciences
JID - 101092791
RN  - 0 (AP1B1 protein, human)
RN  - 0 (Adaptor Protein Complex 1)
RN  - 0 (Adaptor Protein Complex beta Subunits)
RN  - 0 (BRD4 protein, human)
RN  - 0 (Cell Cycle Proteins)
RN  - 0 (Nuclear Proteins)
RN  - 0 (Oncogene Proteins, Fusion)
RN  - 0 (RNA, Messenger)
RN  - 0 (Transcription Factors)
RN  - 63231-63-0 (RNA)
RN  - 9BZQ3U62JX (Dithionitrobenzoic Acid)
SB  - IM
MH  - Adaptor Protein Complex 1/genetics
MH  - Adaptor Protein Complex beta Subunits
MH  - Cell Cycle Proteins/genetics
MH  - Dithionitrobenzoic Acid
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - Nuclear Proteins/genetics
MH  - Oncogene Proteins, Fusion/genetics
MH  - RNA
MH  - RNA, Messenger/genetics
MH  - Reverse Transcriptase Polymerase Chain Reaction
MH  - *Sarcoma/diagnosis/genetics/pathology
MH  - *Soft Tissue Neoplasms/pathology
MH  - Transcription Factors/genetics
PMC - PMC9569610
OTO - NOTNLM
OT  - RT-qPCR
OT  - alveolar rhabdomyosarcoma
OT  - formalin-fixed paraffin-embedded (FFPE) tissue
OT  - fusion gene
OT  - fusion transcript
OT  - mRNA capture sequencing
OT  - sarcoma
OT  - undifferentiated round cell sarcoma
COIS- C.F. is an employee, A.D.G., M.L. and S.S. are former employees, and J.V. (Jo 
      Vandesompele) is co-founder and CSO at Biogazelle, a CRO providing RNA sequencing 
      services. G.S. and S.K. are employees of Illumina, providing the TruSight RNA 
      Pan-Cancer Panel. The other authors declare no potential conflict of interest. 
      The sponsors had no role in the design, execution, interpretation, or writing of 
      the study.
EDAT- 2022/10/15 06:00
MHDA- 2022/10/18 06:00
PMCR- 2022/09/20
CRDT- 2022/10/14 02:06
PHST- 2022/08/09 00:00 [received]
PHST- 2022/09/12 00:00 [revised]
PHST- 2022/09/12 00:00 [accepted]
PHST- 2022/10/14 02:06 [entrez]
PHST- 2022/10/15 06:00 [pubmed]
PHST- 2022/10/18 06:00 [medline]
PHST- 2022/09/20 00:00 [pmc-release]
AID - ijms231911007 [pii]
AID - ijms-23-11007 [pii]
AID - 10.3390/ijms231911007 [doi]
PST - epublish
SO  - Int J Mol Sci. 2022 Sep 20;23(19):11007. doi: 10.3390/ijms231911007.