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Innovative breakthroughs facilitated by single-cell multi-omics: manipulating natural killer cell functionality
Zhijie Zhao1,2, Yantao Ding3,4, Lisa Jia Tran5
1Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Background:
Melanoma is typically regarded as the most dangerous form of skin cancer. Although surgical removal of in situ lesions can be used to effectively treat metastatic disease, this condition is still difficult to cure. Melanoma cells are removed in great part due to the action of natural killer (NK) and T cells on the immune system. Still, not much is known about how the activity of NK cell-related pathways changes in melanoma tissue. Thus, we performed a single-cell multi-omics analysis on human melanoma cells in this study to explore the modulation of NK cell activity.
Materials And Methods:
Cells in which mitochondrial genes comprised > 20% of the total number of expressed genes were removed. Gene ontology (GO), gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), and AUCcell analysis of differentially expressed genes (DEGs) in melanoma subtypes were performed. The CellChat package was used to predict cell-cell contact between NK cell and melanoma cell subtypes. Monocle program analyzed the pseudotime trajectories of melanoma cells. In addition, CytoTRACE was used to determine the recommended time order of melanoma cells. InferCNV was utilized to calculate the CNV level of melanoma cell subtypes. Python package pySCENIC was used to assess the enrichment of transcription factors and the activity of regulons in melanoma cell subtypes. Furthermore, the cell function experiment was used to confirm the function of TBX21 in both A375 and WM-115 melanoma cell lines.
Results:
Following batch effect correction, 26,161 cells were separated into 28 clusters and designated as melanoma cells, neural cells, fibroblasts, endothelial cells, NK cells, CD4+ T cells, CD8+ T cells, B cells, plasma cells, monocytes and macrophages, and dendritic cells. A total of 10137 melanoma cells were further grouped into seven subtypes, i.e., C0 Melanoma BIRC7, C1 Melanoma CDH19, C2 Melanoma EDNRB, C3 Melanoma BIRC5, C4 Melanoma CORO1A, C5 Melanoma MAGEA4, and C6 Melanoma GJB2. The results of AUCell, GSEA, and GSVA suggested that C4 Melanoma CORO1A may be more sensitive to NK and T cells through positive regulation of NK and T cell-mediated immunity, while other subtypes of melanoma may be more resistant to NK cells. This suggests that the intratumor heterogeneity (ITH) of melanoma-induced activity and the difference in NK cell-mediated cytotoxicity may have caused NK cell defects. Transcription factor enrichment analysis indicated that TBX21 was the most important TF in C4 Melanoma CORO1A and was also associated with M1 modules. In vitro experiments further showed that TBX21 knockdown dramatically decreases melanoma cells' proliferation, invasion, and migration.
Conclusion:
The differences in NK and T cell-mediated immunity and cytotoxicity between C4 Melanoma CORO1A and other melanoma cell subtypes may offer a new perspective on the ITH of melanoma-induced metastatic activity. In addition, the protective factors of skin melanoma, STAT1, IRF1, and FLI1, may modulate melanoma cell responses to NK or T cells.
Insights
This study reveals that the C4 Melanoma CORO1A subtype is more sensitive to natural killer (NK) and T cell immunity, unlike other melanoma subtypes. This finding offers insights into melanoma's heterogeneity and potential therapeutic strategies targeting immune responses.
Area of Science:
- Immunology
- Oncology
- Genomics
Background:
- Melanoma is a dangerous skin cancer, often difficult to cure despite surgical options.
- Natural killer (NK) and T cells are crucial for eliminating melanoma cells.
- Understanding NK cell activity modulation in melanoma tissue is limited.
Purpose of the Study:
- To explore the modulation of NK cell activity in human melanoma using single-cell multi-omics analysis.
- To investigate how different melanoma subtypes interact with NK and T cells.
- To identify key factors influencing immune response within the tumor microenvironment.
Main Methods:
- Single-cell multi-omics analysis of human melanoma cells.
- Gene ontology, GSEA, GSVA, and AUCell analyses for differentially expressed genes.
- CellChat for cell-cell contact prediction, Monocle and CytoTRACE for cell trajectory and ordering.
- pySCENIC for transcription factor enrichment and regulon activity.
- In vitro experiments to confirm TBX21 function.
Main Results:
- Identified 28 cell clusters, including seven melanoma subtypes.
- C4 Melanoma CORO1A showed higher sensitivity to NK and T cells, suggesting differential immune response.
- TBX21 identified as a key transcription factor in C4 Melanoma CORO1A, crucial for melanoma cell proliferation and invasion.
- Intratumor heterogeneity (ITH) contributes to NK cell defects and varying cytotoxicity.
Conclusions:
- Differential NK and T cell immunity among melanoma subtypes provides insight into ITH.
- TBX21 plays a significant role in melanoma progression and immune evasion.
- STAT1, IRF1, and FLI1 may influence melanoma cell responses to immune cells.
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