Summary
Our aim was to utilise a 241-gene RNA hybridisation capture sequencing (CaptureSeq)
gene panel to identify unexpected fusions in undifferentiated, unclassified or partly
classified sarcomas of young individuals (<40 years). The purpose was to determine
the utility and yield of a large, targeted fusion panel as a tool for classifying
tumours that do not fit typical diagnostic entities at the time of the original diagnosis.
RNA hybridisation capture sequencing was performed on 21 archival resection specimens.
Successful sequencing was obtained in 12 of 21 samples (57%), two of which (16.6%)
harboured translocations. A novel NEAT1::GLI1 fusion, not previously reported in the literature, presented in a young patient with
a tumour in the retroperitoneum, which displayed low grade epithelioid cells. The
second case, a localised lung metastasis in a young male, demonstrated a EWSR1::NFATC2 translocation. No targeted fusions were identified in the remaining 83.4% (n=10) of cases. Forty-three per cent of the samples failed sequencing as a result of
RNA degradation.
RNA-based sequencing is an important tool, which helps to redefine the classification
of unclassified or partly classified sarcomas of young adults by identifying pathogenic
gene fusions in up to 16.6% of the cases. Unfortunately, 43% of the samples underwent
significant RNA degradation, falling below the sequencing threshold. As CaptureSeq
is not yet available in routine pathology practice, increasing awareness of the yield,
failure rate and possible aetiological factors for RNA degradation is fundamental
to maximise laboratory procedures to improve RNA integrity, allowing the potential
identification of significant gene alterations in solid tumours.
Key words
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to PathologyAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- WHO Classification of Tumours Editorial Board. World Health Organ Classification Tumours. Soft Tissue and Bone Tumours. IARC Press, Lyon2020
- The impact of translocations and gene fusions on cancer causation.Nat Rev Cancer. 2007; 7: 233-245
- Most gene fusions in cancer are stochastic events.Genes Chromosomes Cancer. 2019; 58: 607-611
- The role of next-generation sequencing in sarcomas: evolution from light microscope to molecular microscope.Curr Oncol Rep. 2017; 19: 78
- Is there value in molecular profiling of soft-tissue sarcoma?.Curr Treat Options Oncol. 2018; 19: 78
- Molecular analysis of gene fusions in bone and soft tissue tumors by anchored multiplex PCR-based targeted next-generation sequencing.J Mol Diagn. 2018; 20: 653-663
- Targeted RNA sequencing: a routine ancillary technique in the diagnosis of bone and soft tissue neoplasms.Genes Chromosomes Cancer. 2019; 58: 75-87
- Clinical value of NGS genomic studies for clinical management of pediatric and young adult bone sarcomas.Cancers (Basel). 2021; 13: 5436
- The 2020 WHO Classification: what's new in soft tissue tumor pathology?.Am J Surg Pathol. 2021; 45 (e1–e23)
- 'I can't keep up!': an update on advances in soft tissue pathology occurring after the publication of the 2020 World Health Organization classification of soft tissue and bone tumours.Histopathology. 2022; 80: 54-75
- Diagnosis of fusion genes using targeted RNA sequencing.Nat Commun. 2019; 10: 1388
- Molecular profiling of soft tissue sarcomas using next-generation sequencing: a pilot study toward precision therapeutics.Hum Pathol. 2014; 45: 1563-1571
- Targetable alterations in adult patients with soft-tissue sarcomas: insights for personalized therapy.JAMA Oncol. 2018; 4: 1398-1404
- Clinical effect of molecular methods in sarcoma diagnosis (GENSARC): a prospective, multicentre, observational study.Lancet Oncol. 2016; 17: 532-538
- Hedgehog/GLI signaling pathway: transduction, regulation, and implications for disease.Cancers (Basel). 2021; 13: 3410
- Long non-coding RNA NEAT1: a novel target for diagnosis and therapy in human tumors.Front Genet. 2018; 9: 471
- Involvement of the long noncoding RNA NEAT1 in carcinogenesis.Mol Oncol. 2019; 13: 46-60
- NEAT1 as a competing endogenous RNA in tumorigenesis of various cancers: role, mechanism and therapeutic potential.Int J Biol Sci. 2021; 17: 3428-3440
- A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains.BMC Genomics. 2007; 8: 39
- Gastroblastoma harbors a recurrent somatic MALAT1-GLI1 fusion gene.Mod Pathol. 2017; 30: 1443-1452
- Recurrent MALAT1-GLI1 oncogenic fusion and GLI1 up-regulation define a subset of plexiform fibromyxoma.J Pathol. 2016; 239: 335-343
- A distinct malignant epithelioid neoplasm with GLI1 gene rearrangements, frequent s100 protein expression, and metastatic potential: expanding the spectrum of pathologic entities with ACTB/MALAT1/PTCH1-GLI1 fusions.Am J Surg Pathol. 2018; 42: 553-560
- Activation of the GLI oncogene through fusion with the beta-actin gene (ACTB) in a group of distinctive pericytic neoplasms: pericytoma with t(7;12).Am J Pathol. 2004; 164: 1645-1653
- A case of pericytic neoplasm in the shoulder with a novel DERA-GLI1 gene fusion.Histopathology. 2021; 78: 466-469
- Head and neck mesenchymal neoplasms with GLI1 gene alterations: a pathologic entity with distinct histologic features and potential for distant metastasis.Am J Surg Pathol. 2020; 44: 729-737
- GLI1-amplifications expand the spectrum of soft tissue neoplasms defined by GLI1 gene fusions.Mod Pathol. 2019; 32: 1617-1626
- A malignant neoplasm from the jejunum with a MALAT1-GLI1 fusion and 26-year survival history.Int J Surg Pathol. 2020; 28: 553-562
- The NFATc2 gene is involved in a novel cloned translocation in a Ewing sarcoma variant that couples its function in immunology to oncology.Clin Cancer Res. 2009; 15: 2259-2268
- EWSR1-NFATC2 Translocation-associated sarcoma clinicopathologic findings in a rare aggressive primary bone or soft tissue tumor.Am J Surg Pathol. 2019; 43: 1112-1122
- NFATc2-rearranged sarcomas: clinicopathologic, molecular, and cytogenetic study of 7 cases with evidence of AGGRECAN as a novel diagnostic marker.Mod Pathol. 2020; 33: 1930-1944
- Multiscale-omic assessment of EWSR1-NFATc2 fusion positive sarcomas identifies the mTOR pathway as a potential therapeutic target.NPJ Precis Oncol. 2021; 5: 43
- Expanding the spectrum of EWSR1-NFATC2-rearranged benign tumors: a common genomic abnormality in vascular malformation/hemangioma and simple bone cyst.Am J Surg Pathol. 2021; 45: 1669-1681
- FUS-NFATC2 or EWSR1-NFATC2 fusions are present in a large proportion of simple bone cysts.Am J Surg Pathol. 2020; 44: 1623-1634
- Identification of EWSR1-NFATC2 fusion in simple bone cysts.Histopathology. 2021; 78: 849-856
- Next-generation sequencing for the management of sarcomas with no known driver mutations.Curr Opin Oncol. 2021; 33: 315-322
- A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen?.Arch Pathol Lab Med. 2014; 138: 1520-1530
- Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles.Sci Rep. 2019; 9: 6980
- Guideline: fixation of tissues.Aug 2020 (cited Jul 2022)
Article info
Publication history
Published online: March 09, 2023
Accepted:
November 22,
2022
Received in revised form:
October 14,
2022
Received:
August 3,
2022
Publication stage
In Press Corrected ProofIdentification
Copyright
© 2023 Royal College of Pathologists of Australasia. Published by Elsevier B.V. All rights reserved.
