What has single-cell RNA sequencing revealed about microglial neuroimmunology?

The use of single-cell RNA sequencing (scRNA-seq) in microglial research is increasing rapidly. The basic workflow of this approach consists of isolating single cells, followed by sequencing. scRNA-seq is capable of examining microglial heterogeneity on a cellular level. However, the results gained from applying this technique suffer from discrepancies due to differences between applied methods characteristics such as the number of cells sequenced and the depth of sequencing. This review aims to shed more light on the recent developments that happened in this field and how they are related to the methods used. To do that, we track the progress and limitations of various scRNA-seq methods currently available. The review then summarizes the current knowledge gained using scRNA-seq in the field of microglia, including novel subpopulations associated with function and development under homeostasis as well during several pathological conditions such as Alzheimer, lipopolysaccharide response, and HIV in relation to the methods employed. Our review points out that despite major developments found using this technique, current scRNA-seq methods suffer from high cost, low yields, and nonstandardization of generated data. Additional development of scRNA-seq methods will raise our awareness of microglia's heterogeneity and plasticity under healthy and pathological conditions.