Dynamic single-cell measurements of gene expression in primary lymphocytes: challenges, tools and prospects

Lymphocyte populations show a high level of phenotypic variability and are highly heterogeneous in their gene expression patterns. Studying this cell-to-cell variability, the processes which generate it and its implications for lymphocyte function can be advanced by live cell imaging combined with measurements of gene expression at the single-cell level. However, until recently such studies were limited due to the high motility of primary lymphocytes following their activation, their clustering that precludes single-cell analysis and the prolonged duration of relevant processes such as cell differentiation. In this review, we describe recent methodological advances, which enable single-cell studies of primary lymphocytes, and present some applications of these new techniques. We focus our discussion on microwell arrays. These arrays are typically comprised of thousands of small microwells in which primary lymphocytes can be trapped and imaged over long periods of time. This allows for quantitative evaluation of various cellular processes including cell proliferation, cell death, cytokine secretion and measurements of gene expression at the single-cell level. These advances pave the way for future studies of population variability, dynamic cell responses, stochasticity in gene expression and intercellular interactions between functional lymphocytes in controlled microenvironments.