Comprehensive Analysis of Lung Adenocarcinoma and Brain Metastasis through Integrated Single-Cell Transcriptomics
Abstract
:1. Introduction
2. Results
2.1. Processing for Single-Cell RNA Sequencing Data
2.2. Principal Component Analysis and Batch Effect Correction
2.3. Primary Tumors and Brain Metastases Exhibit Different Immune and Stromal Infiltration Patterns
2.4. Complex Intercellular Communication Networks in Brain Metastasis
2.5. Immune Cells Reveal Potential Roles of the Human Leukocyte Antigen Complex (HLA) in Brain Metastasis Progression
2.6. Stage-Specific Subclustering Unveils Distinctive Profiles of Dendritic Cells in the Tumor Microenvironment
2.7. Comprehensive Subclustering of T and B Cells Reveals Stage-Specific Profiles
3. Discussion
4. Materials and Methods
4.1. Data Collection
4.2. Pre-Processing and Quality Control of scRNA-Seq Data
4.3. Dimensionality Reduction, Clustering, and Cell Type Annotations
4.4. scRNA-Seq Pathway Analysis
4.5. Differential Expression Analysis of Immune Cells and Enrichment Analysis
4.6. Cell Communication Analysis
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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Database | Access | Platform | Stage | No. of Samples | No. of Cells * | Ref |
---|---|---|---|---|---|---|
Brain metastasis | ||||||
GEO | GSE131907 | Illumina HiSeq 2500 | III/IV | 10 | 29,057 | [16] |
GEO | GSE202371 | Illumina NovaSeq 6000 | IV | 10 | 38,476 | [16] |
GEO | GSE143423 | HiSeq X Ten | IV | 3 | 12,196 | NA |
Primary tumor | ||||||
GEO | GSE131907 | Illumina HiSeq 2500 | I | 8 | 31,025 | [16] |
GEO | GSE131907 | Illumina HiSeq 2500 | II | 1 | 3840 | [16] |
GEO | GSE131907 | Illumina HiSeq 2500 | III | 2 | 10,282 | [16] |
GEO | GSE131907 | Illumina HiSeq 2500 | IV | 4 | 12,070 | [16] |
Stage I | Stage II | Stage III | Stage IV | |
---|---|---|---|---|
Immune cells | ||||
Macrophages | 3801 | 483 | 1411 | 526 |
NK cells | 3439 | 517 | 292 | 732 |
Neutrophils | 651 | 353 | 636 | |
Dendritic cells | 1161 | 232 | 295 | 457 |
B cells | 324 | 133 | 748 | 390 |
Mast cells | 1480 | 222 | 235 | |
T cells | 13,125 | 1373 | 4865 | 2696 |
Non-immune cells | ||||
Endothelial | 456 | 100 | 174 | 153 |
Fibroblasts | 418 | 228 | ||
Epithelial cells | 2670 | 220 | 467 | 4970 |
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Souza, V.G.P.; Telkar, N.; Lam, W.L.; Reis, P.P. Comprehensive Analysis of Lung Adenocarcinoma and Brain Metastasis through Integrated Single-Cell Transcriptomics. Int. J. Mol. Sci. 2024, 25, 3779. https://doi.org/10.3390/ijms25073779
Souza VGP, Telkar N, Lam WL, Reis PP. Comprehensive Analysis of Lung Adenocarcinoma and Brain Metastasis through Integrated Single-Cell Transcriptomics. International Journal of Molecular Sciences. 2024; 25(7):3779. https://doi.org/10.3390/ijms25073779
Chicago/Turabian StyleSouza, Vanessa G. P., Nikita Telkar, Wan L. Lam, and Patricia P. Reis. 2024. "Comprehensive Analysis of Lung Adenocarcinoma and Brain Metastasis through Integrated Single-Cell Transcriptomics" International Journal of Molecular Sciences 25, no. 7: 3779. https://doi.org/10.3390/ijms25073779