Calculation of immune cell proportion from batch tumor gene expression profile based on support vector regression.
Journal:
Journal of bioinformatics and computational biology
Published Date:
Aug 21, 2020
Abstract
In addition to tumor cells, a large number of immune cells are found in the tumor microenvironment (TME) of cancer patients. Tumor-infiltrating immune cells play an important role in tumor progression and patient outcome. We improved the relative proportion estimation algorithm of immune cells based on RNA-seq gene expression profiling and solved the multiple linear regression model by support vector regression ([Formula: see text]-SVR). These steps resulted in increased robustness of the algorithm and more accurate calculation of the relative proportion of different immune cells in cancer tissues. This method was applied to the analysis of infiltrating immune cells based on 41 pairs of colorectal cancer tissues and normal solid tissues. Specifically, we compared the relative fractions of six types of immune cells in colorectal cancer tissues to those found in normal solid tissue samples. We found that tumor tissues contained a higher proportion of CD8 T cells and neutrophils, while B cells and monocytes were relatively low. Our pipeline for calculating immune cell proportion using gene expression profile data can be freely accessed from GitHub at https://github.com/gutmicrobes/EICS.git.