Bioinformatics Screen Reveals Gli-Mediated Hedgehog Signaling as an Associated Pathway to Poor Immune Infiltration of Dedifferentiated Liposarcoma
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Hedgehog Signaling Is Enriched in Dedifferentiated Adipose Progenitors and DDLPS Tumors
2.2. Chromosome 12q13-12q15 Amplification Increases Gli1 Expression, but Not Gli2
2.3. Gli2 Expression and Downstream Hedgehog Signaling Are Elevated in DDLPS Tumors
2.4. Gli2-Focused Co-Expression Analysis Reveals an Inverse Relationship between Gli2 and Immune Cell Population Markers While Establishing a Positive Correlation to Fibroblasts and ECM Gene Markers
3. Discussion
4. Limitations
5. Methods
5.1. Software, Databases, and Computational Tools
5.2. Dataset Accession and Descriptions
5.3. Genomics Profiling
5.4. Transcriptional Profiling, Differentially Expressed Genes, and Co-Expression Analysis
5.5. Microarrays, Tissue RNA Sequencing, and Single-Cell RNA Sequencing
5.6. Gene Set Enrichment Analysis (GSEA) and Gene Ontology
5.7. Statistical Analyses
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Software/Database | Description | Location |
---|---|---|
Gene Expression Omnibus (GEO) |
| https://www.ncbi.nlm.nih.gov/geo/ (Accessed on 12 August 2022) |
GEO2R |
| https://www.ncbi.nlm.nih.gov/geo/geo2r/ (Accessed on 12 August 2022) |
ShinyGO (0.77) |
| http://bioinformatics.sdstate.edu/go/ (Accessed on 9 December 2022). |
CBioPortal |
| https://www.cbioportal.org/ (Accessed on 10 June 2021) |
GSEA |
| http://www.gsea-sigdb.org/gsea/index.jsp (Accessed on 17 April 2022) |
GraphPad Prism (9.5.0) |
| |
Biorender |
| https://www.biorender.com/ (Accessed on 19 February 2023) |
Human Protein Atlas |
| https://www.proteinatlas.org/ENSG00000074047-GLI2/single+cell+type (Accessed on 13 June 2022) |
Dataset | PMID/URL | Accession Location | Description |
---|---|---|---|
GSE30929 | 21335544 | Gene Expression Omnibus (GEO) GSE30929 | Expression analysis by UG133A array WDLPS (n = 52) DDLPS (n = 40) |
GSE20697 | 20887899 | Gene Expression Omnibus (GEO) GSE20697 | Whole-transcript expression data by UG133A array Time course of adipose stem cell differentiation |
MSK-IMPACT | 35705560 | CBioPortal Sarcoma_MSKCC_2022 | Genomics profiling by sequencing DDLPS (n = 167) |
TCGA-SARC | 29100075 | CBioPortal sarc_tcga_pan_can_atlas_2018 | Genomics and transcriptome profiling by sequencing DDLPS (n = 59) |
GSE21124 | 20601955 | CBioPortal, Sarc_mskcc (2010) Gene Expression Omnibus (GEO) GSE21122/GSE21123 | Expression and genomics analysis by UG133A array DDLPS (n = 50) Matched Normal (n = 50) Normal Fat (n = 9) |
Human Protein Atlas | 25613900 28495876 | https://www.proteinatlas.org/ENSG00000074047-GLI2 (Accessed on 13 June 2022) | Bulk RNA sequencing and single-cell sequencing of subcutaneous adipose tissue |
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Beadle, E.P.; Bennett, N.E.; Rhoades, J.A. Bioinformatics Screen Reveals Gli-Mediated Hedgehog Signaling as an Associated Pathway to Poor Immune Infiltration of Dedifferentiated Liposarcoma. Cancers 2023, 15, 3360. https://doi.org/10.3390/cancers15133360
Beadle EP, Bennett NE, Rhoades JA. Bioinformatics Screen Reveals Gli-Mediated Hedgehog Signaling as an Associated Pathway to Poor Immune Infiltration of Dedifferentiated Liposarcoma. Cancers. 2023; 15(13):3360. https://doi.org/10.3390/cancers15133360
Chicago/Turabian StyleBeadle, Erik P., Natalie E. Bennett, and Julie A. Rhoades. 2023. "Bioinformatics Screen Reveals Gli-Mediated Hedgehog Signaling as an Associated Pathway to Poor Immune Infiltration of Dedifferentiated Liposarcoma" Cancers 15, no. 13: 3360. https://doi.org/10.3390/cancers15133360