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Integrated Genomic and Transcriptomic Analysis Revealed Mutation Patterns of De-differentiated Liposarcoma and Leiomyosarcoma
Yuhong Zhou
Zhongshan Hospital Fudan University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6333-8226
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This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Cancer.
Background Treating patients with advanced sarcomas is challenging due to great histologic diversity among its subtypes. Leiomyosarcoma (LMS) and de-differentiated liposarcoma (DDLPS) are two common and aggressive subtypes of soft tissue sarcoma (STS). They differ significantly in histology and clinical behaviors. However, the molecular driving force behind the difference is unclear.
Methods We collected 20 LMS and 12 DDLPS samples and performed whole exome sequencing (WES) to obtain their somatic mutation profiles. We also performed RNA-Seq to analyze the transcriptomes of 8 each of the LMS and DDLPS samples and obtained information about differential gene expression, pathway enrichment, immune cell infiltration in tumor microenvironment, and chromosomal rearrangement including gene fusions. Selected gene fusion events from the RNA-seq prediction were checked by RT-PCR in tandem with Sanger sequencing.
Results We detected loss of function mutation and deletion of tumor suppressors mostly in LMS, and oncogene amplification mostly in DDLPS. A focal amplification affecting chromosome 12q13–15 region which encodes MDM2, CDK4 and HMGA2 is notable in DDLPS. Mutations in TP53, ATRX, PTEN, and RB1 are identified in LMS but not DDLPS, while mutation of HERC2 is only identified in DDLPS but not LMS. RNA-seq revealed overexpression of MDM2, CDK4 and HMGA2 in DDLPS and down-regulation of TP53 and RB1 in LMS. It also detected more fusion events in DDLPS than LMS (4.5 vs. 1, p=0.0195), and the ones involving chromosome 12 in DDLPS stand out. RT-PCR and Sanger sequencing verified the majority of the fusion events in DDLPS but only one event in LMS selected to be tested. The tumor microenvironmental signatures are highly correlated with histologic types. DDLPS has more endothelial cells and fibroblasts content than LMS.
Conclusions Our analysis revealed different recurrent genetic variations in LMS and DDLPS including simultaneous upregulation of gene expression and gene copy number amplification of MDM2 and CDK4. Up-regulation of tumor related genes is favored in DDLPS, while loss of suppressor function is favored in LMS. DDLPS harbors more frequent fusion events which can generate neoepitopes and potentially targeted by personalized immune treatment.
Keywords
Soft tissue sarcoma, gene fusion, tumor microenvironment, immune infiltration
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This is a list of supplementary files associated with this preprint. Click to download.
- SupplementaryTableS1genefusion.xlsx
Supplementary Table S1: list of gene fusion events and their sequences, and the oligos used and products detected by RT-PCR.
- SupplementaryTableS2SNV.xlsx
Supplementary Table S2: SNV list
- SupplementaryTableS3LMSampgenes.xlsx
Supplementary Table S3: LMS_amplified_gene list in 0.95 confidence level
- SupplementaryTableS4LMSdelgenes.xlsx
Supplementary Table S4: LMS_deleted_gene list in 0.95 confidence level
- SupplementaryTableS5DDLPSampgenes.xlsx
Supplementary Table S5: DDLPS_ amplified_gene list in 0.95 confidence level
- SupplementaryTableS6RNAexpression.xlsx
Supplementary Table S6: RNA expression from RNA-seq analysis
- SupplementaryTableS7RNApathways.xlsx
Supplementary Table S7: Pathways enriched from RNA-seq analysis
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CURRENT STATUS: Published
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Editorial decision: Minor revision
On 17 Sep, 2020
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Received 02 Sep, 2020
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Received 25 Aug, 2020
Reviewer #2 agreed
On 14 Aug, 2020
Reviewers invited
Invitations sent on 12 Aug, 2020
Reviewer #1 agreed
On 12 Aug, 2020
Editor assigned
On 03 Aug, 2020
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On 19 Jul, 2020
No comments provided
Editorial decision: Major revision
On 21 May, 2020
Review #3 received
Received 20 May, 2020
Review #1 received
Received 14 May, 2020
Review #2 received
Received 13 May, 2020
Reviewer #3 agreed
On 28 Apr, 2020
Reviewer #1 agreed
On 21 Apr, 2020
Reviewer #2 agreed
On 21 Apr, 2020
Editor assigned
On 10 Apr, 2020
Reviewers invited
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This preprint is under consideration at BMC Cancer. A preprint is 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.
Learn more about In Review
Research article
Integrated Genomic and Transcriptomic Analysis Revealed Mutation Patterns of De-differentiated Liposarcoma and Leiomyosarcoma
Yuhong Zhou
Zhongshan Hospital Fudan University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6333-8226
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 28 Sep, 2020
No comments provided
Editorial decision: Minor revision
On 17 Sep, 2020
Review #1 received
Received 02 Sep, 2020
Review #2 received
Received 25 Aug, 2020
Reviewer #2 agreed
On 14 Aug, 2020
Reviewers invited
Invitations sent on 12 Aug, 2020
Reviewer #1 agreed
On 12 Aug, 2020
Editor assigned
On 03 Aug, 2020
Editor invited
On 02 Aug, 2020
Submission checks complete
On 19 Jul, 2020
No comments provided
Editorial decision: Major revision
On 21 May, 2020
Review #3 received
Received 20 May, 2020
Review #1 received
Received 14 May, 2020
Review #2 received
Received 13 May, 2020
Reviewer #3 agreed
On 28 Apr, 2020
Reviewer #1 agreed
On 21 Apr, 2020
Reviewer #2 agreed
On 21 Apr, 2020
Editor assigned
On 10 Apr, 2020
Reviewers invited
Invitations sent on 10 Apr, 2020
Submission checks complete
On 07 Apr, 2020
Editor invited
On 07 Apr, 2020
First submitted
On 02 Apr, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Cancer.
Background Treating patients with advanced sarcomas is challenging due to great histologic diversity among its subtypes. Leiomyosarcoma (LMS) and de-differentiated liposarcoma (DDLPS) are two common and aggressive subtypes of soft tissue sarcoma (STS). They differ significantly in histology and clinical behaviors. However, the molecular driving force behind the difference is unclear.
Methods We collected 20 LMS and 12 DDLPS samples and performed whole exome sequencing (WES) to obtain their somatic mutation profiles. We also performed RNA-Seq to analyze the transcriptomes of 8 each of the LMS and DDLPS samples and obtained information about differential gene expression, pathway enrichment, immune cell infiltration in tumor microenvironment, and chromosomal rearrangement including gene fusions. Selected gene fusion events from the RNA-seq prediction were checked by RT-PCR in tandem with Sanger sequencing.
Results We detected loss of function mutation and deletion of tumor suppressors mostly in LMS, and oncogene amplification mostly in DDLPS. A focal amplification affecting chromosome 12q13–15 region which encodes MDM2, CDK4 and HMGA2 is notable in DDLPS. Mutations in TP53, ATRX, PTEN, and RB1 are identified in LMS but not DDLPS, while mutation of HERC2 is only identified in DDLPS but not LMS. RNA-seq revealed overexpression of MDM2, CDK4 and HMGA2 in DDLPS and down-regulation of TP53 and RB1 in LMS. It also detected more fusion events in DDLPS than LMS (4.5 vs. 1, p=0.0195), and the ones involving chromosome 12 in DDLPS stand out. RT-PCR and Sanger sequencing verified the majority of the fusion events in DDLPS but only one event in LMS selected to be tested. The tumor microenvironmental signatures are highly correlated with histologic types. DDLPS has more endothelial cells and fibroblasts content than LMS.
Conclusions Our analysis revealed different recurrent genetic variations in LMS and DDLPS including simultaneous upregulation of gene expression and gene copy number amplification of MDM2 and CDK4. Up-regulation of tumor related genes is favored in DDLPS, while loss of suppressor function is favored in LMS. DDLPS harbors more frequent fusion events which can generate neoepitopes and potentially targeted by personalized immune treatment.
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