CITMIC: Comprehensive Estimation of Cell Infiltration in Tumor Microenvironment based on Individualized Intercellular
Xilong Zhao1, Jiashuo Wu1, Jiyin Lai1
1College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|November 5, 2024
Summary
This study introduces CITMIC, a novel method to analyze tumor microenvironment (TME) cell infiltration and crosstalk using gene expression data. CITMIC offers superior prognostic and treatment response predictions, especially for high-stage cancers.
Area of Science:
- Oncology
- Computational Biology
- Bioinformatics
Background:
- Tumor microenvironment (TME) cells critically influence tumor progression and treatment outcomes.
- Existing cell infiltration analysis methods are limited, failing to capture intercellular crosstalk.
- Comprehensive TME characterization is vital for advancing cancer biology and therapeutic strategies.
Purpose of the Study:
- To develop a novel computational approach for detailed TME cell infiltration and crosstalk analysis.
- To assess the efficacy of this new method in predicting cancer prognosis and treatment response.
- To provide a more holistic understanding of TME cellular dynamics.
Main Methods:
- Developed CITMIC, a method inferring TME cell infiltration by simultaneously measuring 86 cell types.
- Constructed individualized cell-cell crosstalk networks based on functional cell similarities.
- Utilized gene transcription data exclusively for analysis.
Main Results:
- CITMIC demonstrated superior estimation of relative cell infiltration levels compared to current methods.
- TME cell-based features derived from melanoma data effectively predicted prognosis and treatment response.
- The method showed significant prognostic performance in high-stage melanoma and adenocarcinomas.
Conclusions:
- CITMIC provides a comprehensive TME cell composition analysis by integrating cell-cell crosstalk.
- This approach enhances the discovery of predictive biomarkers for cancer.
- CITMIC offers a valuable tool for developing novel therapeutic strategies in oncology.
