CytoF data analysis with Bioconductor packages

Mass cytometry or Cytometry by Time Of Flight (CyTOF) is used to study cell population variation between different experimental conditions. This technology measures the expression of more than 50 proteins at single cell resolution by using heavy metal isotope labelled antibodies. Although the technology is well established, the CyTOF data analysis field is still expanding. Bioconductor provides a panel of methods and tools designed to analyze this high-throughput data. Using a selection of Bioconductor packages, we have studied the impact of the dengue virus (DENV) on Natural Killers (NK) cells during pediatric and adult infections. The FlowCore package allows importing the data in R. The SingleCellExperiment package provides a core data structure and framework for downstream analysis. Integrated into the CATALYST package, the combination of the flowSOM and ConsensusClusterPlus algorithms allow clustering the cells for cell phenotyping. Using this workflow, we identified different subsets within the NK cells population. With the help of the diffcyt package, we performed differential abundance tests between healthy and DENV positive patients within the pediatric and adult populations. We found that pediatric DENV infection leads to changes in the total NK cell frequency within two NK cells subsets. Next, we used a custom-made package CytoGLMM to identify different proteins within adult and pediatric samples that are predictive of the DENV infection. The results of these analysis suggest that the disease severity in pediatric may be partially explained by a diminution in the NK cell activation.