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Primary research
Geng Chen
East China Normal University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-3452-9434
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This work is licensed under a CC BY 4.0 License. Read Full License
Background
Synovial sarcoma (SS) is a rare type of cancer but relatively common in soft tissue tumors. The transcriptome landscape of SS is crucial for understanding the SS biology; however, the transcriptomic profile of SS is still poorly understood.
Methods
Here we collected 10 paired SS and adjacent normal tissues, and then performed deeply total RNA sequencing to systematically dissect the transcriptomic changes of SS in terms of differential expression, alternative splicing, gene fusion, and circular RNAs.
Results
By comparing SS with adjacent normal tissues, we identified 2309 upregulated and downregulated genes in SS. Those upregulated genes could lead to the upregulation of cell cycle, ribosome, and DNA replication pathways, while the downregulated genes may result in the downregulation of a set of metabolic biological processes and signaling pathways. Moreover, 2511 genes (including 21 splicing factors) were differentially alternative spliced, indicating that the deregulation of alternative splicing could be one important factor contributes to the tumorigenesis. Additionally, we not only detected the common fusion events of SS18-SSX1/SSX2 in SS, but also uncovered 11 novel gene fusions. Interestingly, 49 circular RNAs (circRNAs) were differentially expressed and their parental genes could function in muscle contraction and muscle system processes. Interaction network reconstruction and exploration revealed that these differentially expressed circRNAs may function as the miRNA sponge to regulate the expression of an abundance of differentially expressed and alternatively spliced genes.
Conclusions
Collectively, our results provide novel insights into the transcriptome and underlying mechanism of SS, which could benefit the diagnosis and treatment of SS.
Keywords
synovial sarcoma, gene expression, alternative splicing, gene fusion, circular RNA
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Primary research
Geng Chen
East China Normal University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-3452-9434
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 18 Feb, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Cancer Biology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Synovial sarcoma (SS) is a rare type of cancer but relatively common in soft tissue tumors. The transcriptome landscape of SS is crucial for understanding the SS biology; however, the transcriptomic profile of SS is still poorly understood.
Methods
Here we collected 10 paired SS and adjacent normal tissues, and then performed deeply total RNA sequencing to systematically dissect the transcriptomic changes of SS in terms of differential expression, alternative splicing, gene fusion, and circular RNAs.
Results
By comparing SS with adjacent normal tissues, we identified 2309 upregulated and downregulated genes in SS. Those upregulated genes could lead to the upregulation of cell cycle, ribosome, and DNA replication pathways, while the downregulated genes may result in the downregulation of a set of metabolic biological processes and signaling pathways. Moreover, 2511 genes (including 21 splicing factors) were differentially alternative spliced, indicating that the deregulation of alternative splicing could be one important factor contributes to the tumorigenesis. Additionally, we not only detected the common fusion events of SS18-SSX1/SSX2 in SS, but also uncovered 11 novel gene fusions. Interestingly, 49 circular RNAs (circRNAs) were differentially expressed and their parental genes could function in muscle contraction and muscle system processes. Interaction network reconstruction and exploration revealed that these differentially expressed circRNAs may function as the miRNA sponge to regulate the expression of an abundance of differentially expressed and alternatively spliced genes.
Conclusions
Collectively, our results provide novel insights into the transcriptome and underlying mechanism of SS, which could benefit the diagnosis and treatment of SS.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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