Integrative Transcriptomic Meta-Analysis Reveals Risk Signatures and Immune Infiltration Patterns in High-Grade Serous Ovarian Cancer
Abstract
1. Introduction
2. Materials and Methods
2.1. Search Strategy and Information Sources
2.2. Meta-Analysis of Differentially Expressed Genes
2.3. Functional Enrichment Analysis
2.4. Protein-Protein Interaction (PPI)
2.5. Cox Regression Analysis of DEGs
2.6. Survival Analysis
2.7. Estimation of Immune and Stromal Infiltration
2.8. Analysis of Immunotherapy-Associated Gene Expression
2.9. Convergence Analysis
2.10. Single Cell Analysis
3. Results
3.1. Selection of Gene Expression Datasets
3.2. Functional Enrichment and Pathway Analysis of Differentially Expressed Genes
3.3. Protein-Protein Interaction Networks of Key Differentially Expressed Genes in HGSOC
3.4. Identification of Oncogenes and Tumor Suppressor Genes Among Differentially Expressed Genes in HGSOC
3.5. Survival Analysis of Key Upregulated Genes and Risk Stratification in Ovarian Cancer
3.6. Estimation of Immune Cell Infiltration Between High- and Low-Risk Ovarian Cancer Patients
Differential Expression of Immunotherapy-Associated Genes
3.7. Single-Cell Analysis Reveals Cellular Expression Patterns of Survival Associated Genes and Dysregulation of Extracellular Matrix Pathways in HGSOC
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
HGSOC | High Grade Serous Ovarian Cancer |
DEGs | Differentially Expressed Genes |
GEO | Gene Expression Omnibus |
NCBI | National Center of Biotechnology Information |
SRA | Sequence Read Archive |
RNA-seq | RNA Sequencing |
PCA | Principal Component Analysis |
UMAP | Uniform Manifold Approximation and Projection |
CNVs | Copy Number Variations |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
GSEA | Gene Set Enrichment Analysis |
MHC | Major histocompatibility Complex |
aDC | Activated Dendritic Cells |
DC | Dendritic Cells |
CLP | Common lymphoid progenitors |
ECM | Extracellular Matrix |
iDC | Immature Dendritic Cells |
MEP | Megakaryocyte-erythroid Progenitors |
NKT | Natural Killer T-Cells |
FDR | False Discovery Rate |
GO | Gene Ontology |
BP | Biological Process |
MF | Molecular Function |
CC | Cellular Component |
WebGestalt | WEB-based Gene SeT AnaLysis |
PPI | Protein Protein Interaction |
STRING | Search Tool for the Retrieval of Interacting Genes |
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Author/Year | NCBI GEO | Cases (n = 291) | Controls (n = 96) | Platform | PMID |
---|---|---|---|---|---|
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Yoshihara K, et al., 2009 | GSE12470 | 43 | 10 | Agilent-012097 Human 1A Microarray (V2) | 19486012 [31] |
Tung CS et al., 2009 | GSE14001 | 10 | 3 | Affymetrix Human Genome U133 Plus 2.0 | 19525924 [32] |
Bowen NJ et al., 2009 | GSE14407 | 12 | 12 | Affymetrix Human Genome U133 Plus 2.0 | 20040092 [33] |
Mok SC, et al., 2009 | GSE18520 | 53 | 10 | Affymetrix Human Genome U133 Plus 2.0 | 19962670 [34] |
Shahab S, et al., 2011 | GSE23391 | 3 | 5 | Affymetrix U133 Plus 2.0 3’ expression | 21811625 [35] |
Bonome T, et al., 2008 | GSE26712 | 107 | 10 | Affymetrix Human Genome U133A | 18593951 [36] |
King ER, et al., 2011 | GSE27651 | 22 | 6 | Affymetrix Human Genome U133 Plus 2.0 | 21451362 [37] |
Elgaaen BV, et al., 2012 | GSE36668 | 8 | 4 | Affymetrix Human Genome U133 Plus | 23029477 [38] |
Yeung TL, et al., 2013 | GSE40595 | 32 | 8 | Affymetrix human genome U133 Plus 2.0 | 23824740 [39] |
Wu R et al., 2007 | GSE6008 | 41 | 4 | Affymetrix HG_U133A array | 23824740 [40] |
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Morales-Suárez, P.D.; Zambrano-O, Y.T.; Mejía-Garcia, A.; Tsao, H.M.; Lopez-Kleine, L.; Bonilla, D.A.; Combita, A.L.; Parra-Medina, R.; Lopez-Correa, P.; Serrano-G, S.J.; et al. Integrative Transcriptomic Meta-Analysis Reveals Risk Signatures and Immune Infiltration Patterns in High-Grade Serous Ovarian Cancer. Immuno 2025, 5, 23. https://doi.org/10.3390/immuno5030023
Morales-Suárez PD, Zambrano-O YT, Mejía-Garcia A, Tsao HM, Lopez-Kleine L, Bonilla DA, Combita AL, Parra-Medina R, Lopez-Correa P, Serrano-G SJ, et al. Integrative Transcriptomic Meta-Analysis Reveals Risk Signatures and Immune Infiltration Patterns in High-Grade Serous Ovarian Cancer. Immuno. 2025; 5(3):23. https://doi.org/10.3390/immuno5030023
Chicago/Turabian StyleMorales-Suárez, Paula D., Yina T. Zambrano-O, Alejandro Mejía-Garcia, Hsuan Megan Tsao, Liliana Lopez-Kleine, Diego A. Bonilla, Alba L. Combita, Rafel Parra-Medina, Patricia Lopez-Correa, Silvia J. Serrano-G, and et al. 2025. "Integrative Transcriptomic Meta-Analysis Reveals Risk Signatures and Immune Infiltration Patterns in High-Grade Serous Ovarian Cancer" Immuno 5, no. 3: 23. https://doi.org/10.3390/immuno5030023
APA StyleMorales-Suárez, P. D., Zambrano-O, Y. T., Mejía-Garcia, A., Tsao, H. M., Lopez-Kleine, L., Bonilla, D. A., Combita, A. L., Parra-Medina, R., Lopez-Correa, P., Serrano-G, S. J., Rodriguez, J. L., & Orozco, C. A. (2025). Integrative Transcriptomic Meta-Analysis Reveals Risk Signatures and Immune Infiltration Patterns in High-Grade Serous Ovarian Cancer. Immuno, 5(3), 23. https://doi.org/10.3390/immuno5030023