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CAFrgDB: a database for cancer-associated fibroblasts related genes and their functions in cancer
Qiang Yuan1, Yi Chu1, Xiaoyu Li1
1Department of Pathophysiology, State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
Abstract:
As one of the most essential components of the tumor microenvironment (TME), cancer-associated fibroblasts (CAFs) interact extensively with cancer cells and other stromal cells to remodel TME and participate in the pathogenesis of cancer, which earmarked themselves as new promising targets for cancer therapy. Numerous studies have highlighted the heterogeneity and versatility of CAFs in most cancer types. Thus, the identification and appropriate use of CAF-related genes (CAFGenes) in the context of specific cancer types will provide critical insights into disease mechanisms and CAF-related therapeutic targets. In this study, we collected and curated 5421 CAFGenes identified from small- or large-scale experiments, encompassing 4982 responsors that directly or indirectly participate in cancer malignant behaviors managed by CAFs, 1069 secretions that are secreted by CAFs and 281 regulators that contribute in modulating CAFs in human and mouse, which covered 24 cancer types. For these human CAFGenes, we performed gene expression and prognostic marker-based analyses across 24 cancer types using TCGA data. Furthermore, we provided annotations for CAF-associated proteins by integrating the knowledge of protein-protein interaction(s), drug-target relations and basic annotations, from 9 public databases. CAFrgDB (CAF related Gene DataBase) is free for academic research at http://caf.zbiolab.cn and we anticipate CAFrgDB can be a useful resource for further study of CAFs.
Insights
Cancer-associated fibroblasts (CAFs) are key in cancer. This study curated 5421 CAF-related genes (CAFGenes) across 24 cancer types, creating a database (CAFrgDB) for therapeutic target discovery.
Area of Science:
- Oncology
- Cancer Biology
- Bioinformatics
Background:
- Cancer-associated fibroblasts (CAFs) are crucial components of the tumor microenvironment (TME), influencing cancer progression and serving as therapeutic targets.
- CAFs exhibit significant heterogeneity and versatility across various cancer types, necessitating specific gene identification for targeted therapies.
Purpose of the Study:
- To curate and analyze cancer-associated fibroblast-related genes (CAFGenes) across 24 cancer types.
- To develop a comprehensive database (CAFrgDB) for CAF-related genes and proteins to aid in understanding cancer mechanisms and identifying therapeutic targets.
Main Methods:
- Collected and curated 5421 CAFGenes from experimental data, categorizing them into responders, secretions, and regulators.
- Performed gene expression and prognostic marker analyses on human CAFGenes using The Cancer Genome Atlas (TCGA) data.
- Integrated protein-protein interactions, drug-target relations, and annotations from 9 public databases for CAF-associated proteins.
Main Results:
- Identified 5421 CAFGenes, including 4982 responders, 1069 secretions, and 281 regulators, spanning 24 cancer types.
- Conducted gene expression and prognostic analyses, revealing CAFGene roles in cancer.
- Developed CAFrgDB (http://caf.zbiolab.cn), a publicly accessible resource integrating diverse CAF-related data.
Conclusions:
- CAFrgDB provides a valuable resource for exploring CAF heterogeneity and identifying novel therapeutic targets in cancer.
- The curated CAFGenes and integrated annotations facilitate deeper investigation into CAF functions and their impact on cancer pathogenesis.
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