Genomic and transcriptomic characterisation of undifferentiated pleomorphic sarcoma of bone
Authors
Ali, Naser M.Niada, Stefania
Brini, Anna T.
Morris, Mark R.
Kurusamy, Sathishkumar
Alholle, Abdullah
Huen, David
Antonescu, Cristina R.
Tirode, Franck
Sumathi, Vaiyapuri
Latif, Farida
Issue Date
2018-12-27
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Undifferentiated pleomorphic sarcoma of bone (UPSb), is a rare primary bone sarcoma that lacks a specific line of differentiation. There is very little information about the genetic alterations leading to tumourigenesis or malignant transformation. Distinguishing between UPSb and other malignant bone sarcomas, including dedifferentiated chondrosarcoma and osteosarcoma, can be challenging due to overlapping features. To explore the genomic and transcriptomic landscape of UPSb tumours, whole-exome sequencing (WES) and RNA Sequencing (RNA-Seq) were performed on UPSb tumours. All tumours lacked hotspot mutations in IDH1/2 132 or 172 codons, thereby excluding the diagnosis of dedifferentiated chondrosarcoma. Recurrent somatic mutations in TP53 were identified in 4/14 samples (29%). Moreover, recurrent mutations in histone chromatin remodelling genes, including H3F3A, ATRX and DOT1L, were identified in 5/14 samples (36%), highlighting the potential role of deregulated chromatin remodelling pathways in UPSb tumourigenesis. The majority of recurrent mutations in chromatin remodelling genes identified here are reported in COSMIC, including the H3F3A G35 and K36 hotspot residues. Copy number alteration analysis identified gains and losses in genes that have been previously altered in UPSb or UPS of soft tissue. Eight somatic gene fusions were identified by RNA-Seq, two of which, CLTC-VMP1 and FARP1-STK24, were reported previously in multiple cancers. Five gene fusions were genomically characterised. Hierarchical clustering analysis, using RNA-Seq data, distinctly clustered UPSb tumours from osteosarcoma and other sarcomas, thus molecularly distinguishing UPSb from other sarcomas. RNA-Seq expression profiling analysis and quantitative RT-PCR showed an elevated expression in FGF23 which can be a potential molecular biomarker in UPSb. To our knowledge, this study represents the first comprehensive WES and RNA-Seq analysis of UPSb tumours revealing novel protein-coding recurrent gene mutations, gene fusions and identifying a potential UPSb molecular biomarker, thereby broadening the understanding of the pathogenic mechanisms and highlighting the possibility of developing novel targeted therapeutics.Citation
Ali, N.M. et al (2018) Genomic and transcriptomic characterisation of undifferentiated pleomorphic sarcoma of bone, Journal of Pathology, 247 (2), pp. 166-176. DOI: 10.1002/path.5176Publisher
WileyJournal
Journal of PathologyAdditional Links
https://onlinelibrary.wiley.com/doi/abs/10.1002/path.5176Type
Journal articleLanguage
enDescription
This is an accepted manuscript of an article published by Wiely in The Journal of Pathology on 27/12/2018, available online: https://doi.org/10.1002/path.5176 The accepted version of the publication may differ from the final published version.ISSN
0022-3417ae974a485f413a2113503eed53cd6c53
10.1002/path.5176
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