Electronic Sorting of Immune Cell Subpopulations Based on Highly Plastic Genes

Abstract

Immune cells are highly heterogeneous and plastic with regard to gene expression and cell phenotype. In this study, we categorized genes into those with low and high gene plasticity, and those categories revealed different functions and applications. We proposed that highly plastic genes could be suited for the labeling of immune cell subpopulations; thus, novel immune cell subpopulations could be identified by gene plasticity analysis. For this purpose, we systematically analyzed highly plastic genes in human and mouse immune cells. In total, 1,379 human and 883 mouse genes were identified as being extremely plastic. We also expanded our previous immunoinformatic method, electronic sorting, which surveys big data to perform virtual analysis. This approach used correlation analysis and took dosage changes into account, which allowed us to identify the differentially expressed genes. A test with human CD4+ T cells supported the method’s feasibility, effectiveness, and predictability. For example, with the use of human nonregulatory T cells, we found that FOXP3hiCD4+ T cells were highly expressive of certain known molecules, such as CD25 and CTLA4, and that this process of investigation did not require isolating or inducing these immune cells in vitro. Therefore, the sorting process helped us to discover the potential signature genes or marker molecules and to conduct functional evaluations for immune cell subpopulations. Finally, in human CD4+ T cells, 747 potential immune cell subpopulations and their candidate signature genes were identified, which provides a useful resource for big data–driven knowledge discoveries.

Virtual Sorting Has a Distinctive Advantage in Identification of Anticorrelated Genes and Further Negative Regulators of Immune Cell Subpopulations

“…We have established an ImmuCo database for gene coexpression analysis for immune cells based on the Pearson correlation, and negative correlation can also be illustrated between queried gene pairs (10). However, Pearson-based negative correlation is not suitable for negative biomarker identification because genes with higher negative correlation strength tend to coexist (11). Therefore, novel methods of negative correlation (anticorrelation or inverse correlation) are urgently needed.…”

“…In the current study, we continued to use our previously established method, virtual sorting (in silico sorting, or expanded electronic sorting) (11), for highly plastic genes. Highly plastic genes indicate a large variation in gene expression and can be used as biomarkers to label immune cell subpopulations (11). During virtual sorting, we mainly considered dosage change, which was measured by the d value of the average rank score (ARS) (11).…”

“…Highly plastic genes indicate a large variation in gene expression and can be used as biomarkers to label immune cell subpopulations (11). During virtual sorting, we mainly considered dosage change, which was measured by the d value of the average rank score (ARS) (11). We first tested the relationships between the Pearson coefficient, mutual repulsion rate [or absent-present and present-absent (APA) rate] (11), and d value in healthy human CD4 + T cells and B cells, and found that virtual sorting had a distinctive advantage in identification of anticorrelated gene sets.…”

“…All data (generated by Affymetrix human U133 plus 2.0 arrays) were from the Gene Expression Omnibus (GEO) database and downloaded according to the method previously described (10,12). Healthy human CD4 + T cells (470 GEO samples, or 470 arrays and measurements) were taken directly from our recent study (11). We updated the datasets of B cells and CD8 + T cells in the ImmuSort database (12), and finally obtained 400 and 166 GEO samples for healthy human B cells and CD8 + T cells.…”

Cysteine and glycine-rich protein 2 (CSRP2) transcript levels correlate with leukemia relapse and leukemia-free survival in adults with B-cell acute lymphoblastic leukemia and normal cytogenetics

“…CSRP2 was moderately expressed in normal human B-cells (ARS = 43.16). In our previous study we reported moderately expressed genes had more plastic or variable expression in diverse experimental conditions [31]. The gene plastic (GPL) score of CSRP2 was 19 in normal B-cells (400 GSMs) making it suitable for virtual sorting, an immune informatics method to evaluate immune cell subpopulations and their functions based on highly plastic genes.…”