TimiGP: An R package to depict the tumor microenvironment from bulk transcriptomics
Chenyang Li1, Jianjun Zhang2, Chao Cheng3
1Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA.
STAR Protocols
|November 29, 2023
Summary
This study introduces a new R package for analyzing the tumor immune microenvironment (TIME) and its link to patient outcomes. It maps immune cell interactions and abundance using gene expression data for better cancer treatment strategies.
Area of Science:
- Oncology
- Immunology
- Bioinformatics
Background:
- The tumor microenvironment (TME) plays a critical role in cancer progression and treatment response.
- Understanding the diverse immune cell populations within the TME is essential for developing effective cancer therapies.
Purpose of the Study:
- To present a novel protocol for illustrating the tumor immune microenvironment (TIME) using gene pairs.
- To introduce an R package designed to infer cell-cell interactions and analyze immune cell abundance in relation to patient prognoses.
Main Methods:
- Utilizing bulk gene expression and survival data to correlate immune cell relative abundance with patient outcomes.
- Employing cell-type markers identified from single-cell RNA sequencing (scRNA-seq) data.
- Mapping the TIME across various cancer types using the developed R package.
Main Results:
- The protocol enables the deduction of cell-cell interactions within the TIME.
- It reveals associations between immune cell relative abundance and patient prognoses.
- The method is applicable across a wide range of cancer types.
Conclusions:
- The developed R package and protocol offer a valuable tool for dissecting the tumor immune microenvironment.
- This approach facilitates a deeper understanding of the clinical relevance of immune cells in cancer.
- It holds potential for improving prognostic predictions and guiding therapeutic strategies.
