Genome biology· 2016
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
- 4,044citations
- 2016year
Short summary
The MCP-counter method robustly quantifies eight immune and two stromal cell populations in tissues using transcriptomic data, validated by in vitro and ex vivo experiments.
AI-generated from the title and abstract; the full text is not read.
Key points
- MCP-counter quantifies absolute abundance of 8 immune and 2 stromal cell populations from transcriptomic data.
- Method validated using in vitro mRNA mixtures and ex vivo immunohistochemical data.
- MCP-counter overcomes limitations of previous computational approaches.
- Application to human tumors and healthy tissues reveals immune infiltration patterns.
- Microenvironment-based patient stratification associated with survival in lung, colorectal, and breast cancers.
AI-generated from the title and abstract; the full text is not read.
Abstract
We introduce the Microenvironment Cell Populations-counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data. We present in vitro mRNA mixture and ex vivo immunohistochemical data that quantitatively support the validity of our method's estimates. Additionally, we demonstrate that MCP-counter overcomes several limitations or weaknesses of previously proposed computational approaches. MCP-counter is applied to draw a global picture of immune infiltrates across human healthy tissues and non-hematopoietic human tumors and recapitulates microenvironment-based patient stratifications associated with overall survival in lung adenocarcinoma and colorectal and breast cancer.
The authors' abstract, as published at the source. Genome biology, 2016 · DOI ↗
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Field: Oncology
OncologyMedicine