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Updated: Jun 10, 2025
Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies
Published on: September 15, 2023
Immunotherapy and pan-apoptotic characterization of the tumor microenvironment in gastric cancer (STAD): a
Sheng Zhang1, Jianhong Wang2, Huan Zhang2
1Department of Radiology, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, 637000, China.
Background:
The aim of this study was to elucidate the critical role of autophagy-related gene aggregation in gastric cancer tumor microenvironment cells and to investigate their major roles in cellular functions. In particular, the expression of these genes in tumor-associated fibroblast subtypes was scrutinized in an attempt to explain their cell-subpopulation-specific roles in cell-cell communication and regulation of cellular functions.
Methods:
In this study, single-cell RNA sequencing data were first analyzed in multiple steps, including data preprocessing, cell clustering, and cell classification. Cell subpopulations and gene expression patterns were identified and analyzed using unsupervised non-negative matrix factorization (NMF) techniques. The dynamic expression of autophagy-related gene aggregates in various cell types was deciphered by pseudotime trajectory analysis (PTA). Intercellular communication analysis was performed using the CellChat R software package, revealing the intricate communication patterns and exchange of key signaling molecules between cell subpopulations, and SCENIC analysis was used to identify gene regulatory networks and reveal the mechanisms behind cellular heterogeneity.
Result:
Cell subpopulations associated with pan-apoptosis were identified by NMF decomposition and SCENIC analysis. Cell-cell communication analysis revealed intricate communication patterns and exchange of key signaling molecules between cell subpopulations. Dynamic expression of autophagy-related genes aggregated in the pseudotemporal trajectory of STAD was observed by PTA. In the fibroblast subtype, different ligand-receptor interactions and their key roles in immunomodulation were observed.
Conclusion:
By deeply analyzing and comparing gene expression patterns within cellular subpopulations and intercellular communication, this study provides new insights into the role of pan-apoptosis-related genes in regulating immune responses and cellular functions in gastric cancer. These findings pave the way for further exploration of the role of these genes in tumorigenesis and immune regulation, as well as laying the foundation for potential therapeutic strategies.
Insights
This study reveals how autophagy-related gene aggregation in gastric cancer influences the tumor microenvironment, particularly in fibroblasts, impacting cellular functions and immune responses. Findings offer insights for potential therapeutic strategies.
Area of Science:
- Oncology
- Cell Biology
- Immunology
Background:
- Investigates autophagy-related gene aggregation within the gastric cancer tumor microenvironment.
- Focuses on tumor-associated fibroblast subtypes and their roles in cellular communication and function.
Purpose of the Study:
- Elucidate the critical role of autophagy-related gene aggregation in gastric cancer.
- Investigate the functions of these genes in cellular processes.
- Scrutinize gene expression in tumor-associated fibroblast subtypes for cell-specific roles.
Main Methods:
- Single-cell RNA sequencing analysis including preprocessing, clustering, and classification.
- Unsupervised non-negative matrix factorization (NMF) for cell subpopulation and gene expression identification.
- Pseudotime trajectory analysis (PTA) for dynamic gene expression, CellChat for intercellular communication, and SCENIC for gene regulatory networks.
Main Results:
- Identified cell subpopulations linked to pan-apoptosis using NMF and SCENIC analysis.
- Revealed intricate cell-cell communication patterns and key signaling molecule exchange.
- Observed dynamic autophagy-related gene expression in STAD pseudotemporal trajectory and immunomodulatory roles in fibroblast subtypes.
Conclusions:
- Provides novel insights into pan-apoptosis-related genes regulating immune responses and cellular functions in gastric cancer.
- Highlights the role of these genes in tumorigenesis and immune regulation.
- Lays the groundwork for potential therapeutic strategies targeting gastric cancer.
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