論文 - 詳細
| RRC ID | 51935 |
|---|---|
| 著者 | Komura D, Isagawa T, Kishi K, Suzuki R, Sato R, Tanaka M, Katoh H, Yamamoto S, Tatsuno K, Fukayama M, Aburatani H, Ishikawa S. |
| タイトル | CASTIN: a system for comprehensive analysis of cancer-stromal interactome. |
| ジャーナル | BMC Genomics |
| Abstract |
BACKGROUND:Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer therapy. However, identifying relevant and druggable cancer-stromal interactions is challenging due to the lack of quantitative methods to analyze whole cancer-stromal interactome. RESULTS:We present CASTIN (CAncer-STromal INteractome analysis), a novel framework for the evaluation of cancer-stromal interactome from RNA-Seq data using cancer xenograft models. For each ligand-receptor interaction which is derived from curated protein-protein interaction database, CASTIN summarizes gene expression profiles of cancer and stroma into three evaluation indices. These indices provide quantitative evaluation and comprehensive visualization of interactome, and thus enable to identify critical cancer-microenvironment interactions, which would be potential drug targets. We applied CASTIN to the dataset of pancreas ductal adenocarcinoma, and successfully characterized the individual cancer in terms of cancer-stromal relationships, and identified both well-known and less-characterized druggable interactions. CONCLUSIONS:CASTIN provides comprehensive view of cancer-stromal interactome and is useful to identify critical interactions which may serve as potential drug targets in cancer-microenvironment. CASTIN is available at: http://github.com/tmd-gpat/CASTIN . |
| 巻・号 | 17(1) |
| ページ | 899 |
| 公開日 | 2016-11-9 |
| DOI | 10.1186/s12864-016-3207-z |
| PII | 10.1186/s12864-016-3207-z |
| PMID | 27829362 |
| PMC | PMC5103609 |
| MeSH | Animals Cell Communication* / genetics Cell Line, Tumor Computational Biology Disease Models, Animal Female Gene Expression Profiling / methods Heterografts Humans Mice Neoplasms / etiology* Neoplasms / metabolism* Neoplasms / pathology Protein Interaction Mapping / methods Stromal Cells / metabolism* Stromal Cells / pathology Transcriptome Tumor Microenvironment* / genetics Workflow |
| IF | 3.594 |
| 引用数 | 7 |
| リソース情報 | |
| ヒト・動物細胞 | KLM-1(RCB2138) PK-8(RCB2700) PK-45P(RCB2141) PK-45H(RCB1973) PANC-1(RCB2095) |