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Novel CAF-identifiers via transcriptomic and protein level analysis in HNSC patients
Nehanjali Dwivedi1,2, Nidhi Shukla1, K M Prathima3
1Molecular Immunology, Mazumdar Shaw Medical Foundation, Narayana Health City, Bommasandra, Bangalore, Karnataka, 560099, India.
Scientific Reports
|August 25, 2023
Summary
New markers like TIMP-1 and COL1A2 can help identify cancer-associated fibroblasts (CAFs) in head and neck tumors. This research aids in distinguishing CAFs from other cells for better cancer understanding.
Area of Science:
- Oncology
- Cancer Biology
- Bioinformatics
Background:
- Cancer-associated fibroblasts (CAFs) are key players in tumor progression and drug resistance.
- Traditional CAF markers show significant variability across CAF subpopulations and cancer types.
- Accurate identification of CAFs is crucial for understanding the tumor microenvironment.
Purpose of the Study:
- To identify novel, reliable CAF markers using an unbiased, data-driven approach.
- To distinguish CAF populations from tumor epithelial cells and normal fibroblasts in head and neck squamous cell carcinoma (HNSC).
- To validate potential CAF markers through experimental methods.
Main Methods:
- Differential gene expression analysis of public and in-house RNA sequencing (RNAseq) data, including single-cell sequencing.
- Bioinformatic analysis to identify potential CAF markers (TIMP-1, SPARC, COL1A2, COL3A1, COL1A1).
- Experimental validation using quantitative polymerase chain reaction (qPCR), immunofluorescence, and immunohistochemistry (IHC).
Main Results:
- TIMP-1, SPARC, COL1A2, COL3A1, and COL1A1 were identified as potential CAF markers.
- Experimental validation confirmed higher expression of TIMP-1 and COL1A2 in novel CAF cells.
- Immunohistochemistry indicated COL1A2 as a promising marker for differential staining between tumor epithelia and stroma.
Conclusions:
- The study identified and validated novel CAF markers, including TIMP-1 and COL1A2, for HNSC.
- A data science-driven approach using omics data is effective for identifying CAF markers.
- These findings can be applied to identify CAF markers in other cancer types.
