SIO: A Spatioimageomics Pipeline to Identify Prognostic Biomarkers Associated with the Ovarian Tumor Microenvironment
Abstract
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patient Samples
2.2. Preparation and Staining
2.3. Imaging Mass Cytometry
2.4. Microdissection and Microarray Analysis of Tissue Samples
2.5. Data Preprocessing and Cell Segmentation
2.6. Analysis Workflow
2.7. Clustering Analysis
2.8. Cell Density and Nearest-Neighbor Interactions in Tumor-Enriched Regions
2.9. Survival Prediction
2.10. Correlation of Cell Density with Gene Expression
2.11. Kaplan-Meier Analysis
2.12. Data and Code Availability
3. Results
3.1. Image Analysis Pipeline
3.2. Cell Segmentation and Annotation by Deep Learning-Based IMC Data Analysis
3.3. Spatially Resolved Cell Density and Nearest-Neighbor Cell-Cell Interactions Analyses of the Ovarian Tumor Microenvironment
3.4. Feature Selection for Overall Survival Prediction by Logistic Regression
3.5. Correlations between Cell Subtype Density and Transcriptomic Profiles from Microdissected Fibroblastic Stromal and Epithelial Compartments of HGSC
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Zhu, Y.; Ferri-Borgogno, S.; Sheng, J.; Yeung, T.-L.; Burks, J.K.; Cappello, P.; Jazaeri, A.A.; Kim, J.-H.; Han, G.H.; Birrer, M.J.; et al. SIO: A Spatioimageomics Pipeline to Identify Prognostic Biomarkers Associated with the Ovarian Tumor Microenvironment. Cancers 2021, 13, 1777. https://doi.org/10.3390/cancers13081777
Zhu Y, Ferri-Borgogno S, Sheng J, Yeung T-L, Burks JK, Cappello P, Jazaeri AA, Kim J-H, Han GH, Birrer MJ, et al. SIO: A Spatioimageomics Pipeline to Identify Prognostic Biomarkers Associated with the Ovarian Tumor Microenvironment. Cancers. 2021; 13(8):1777. https://doi.org/10.3390/cancers13081777
Chicago/Turabian StyleZhu, Ying, Sammy Ferri-Borgogno, Jianting Sheng, Tsz-Lun Yeung, Jared K. Burks, Paola Cappello, Amir A. Jazaeri, Jae-Hoon Kim, Gwan Hee Han, Michael J. Birrer, and et al. 2021. "SIO: A Spatioimageomics Pipeline to Identify Prognostic Biomarkers Associated with the Ovarian Tumor Microenvironment" Cancers 13, no. 8: 1777. https://doi.org/10.3390/cancers13081777
APA StyleZhu, Y., Ferri-Borgogno, S., Sheng, J., Yeung, T.-L., Burks, J. K., Cappello, P., Jazaeri, A. A., Kim, J.-H., Han, G. H., Birrer, M. J., Mok, S. C., & Wong, S. T. C. (2021). SIO: A Spatioimageomics Pipeline to Identify Prognostic Biomarkers Associated with the Ovarian Tumor Microenvironment. Cancers, 13(8), 1777. https://doi.org/10.3390/cancers13081777