Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Obtainment
2.2. Pre-Processing of Microarray Data
2.3. Pre-Processing of RNA-Seq Data
2.4. Deconvolution of Cell Types with Cibersortx and Three Atlases
2.5. Accuracy and Robustness of Cell Fraction Estimation
2.6. Survival analysis, Statistics, and Data Visualisation
3. Results
3.1. Cibersortx Estimation of Cell Fraction
3.2. Difference of Cell Fraction between Tumour and Non-Tumour Liver Tissue
3.2.1. Hepatocytes and Cholangiocytes
3.2.2. Fibrogenesis
3.2.3. Vasculature
3.2.4. Immune Cells
3.2.5. Bi-Potent Stem Cells and Proliferative Cells
3.2.6. Other Cell Types
3.3. Cell Fraction of HCC TME Correlates with Clinical Outcome
3.4. Cell Abundance Estimation by Support Vector Regression
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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Zhang, S.; Bacon, W.; Peppelenbosch, M.P.; van Kemenade, F.; Stubbs, A.P. Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas. Cancers 2023, 15, 153. https://doi.org/10.3390/cancers15010153
Zhang S, Bacon W, Peppelenbosch MP, van Kemenade F, Stubbs AP. Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas. Cancers. 2023; 15(1):153. https://doi.org/10.3390/cancers15010153
Chicago/Turabian StyleZhang, Shaoshi, Wendi Bacon, Maikel P. Peppelenbosch, Folkert van Kemenade, and Andrew Peter Stubbs. 2023. "Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas" Cancers 15, no. 1: 153. https://doi.org/10.3390/cancers15010153
APA StyleZhang, S., Bacon, W., Peppelenbosch, M. P., van Kemenade, F., & Stubbs, A. P. (2023). Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas. Cancers, 15(1), 153. https://doi.org/10.3390/cancers15010153