Multi-omic analyses in immune cell development with lessons learned from T cell development

Abstract

Traditionally, flow cytometry has been the preferred method to characterize immune cells at the single-cell level. Flow cytometry is used in immunology mostly to measure the expression of identifying markers on the cell surface, but—with good antibodies—can also be used to assess the expression of intracellular proteins. The advent of single-cell RNA-sequencing has paved the road to study immune development at an unprecedented resolution. Single-cell RNA-sequencing studies have not only allowed us to efficiently chart the make-up of heterogeneous tissues, including their most rare cell populations, it also increasingly contributes to our understanding how different omics modalities interplay at a single cell resolution. Particularly for investigating the immune system, this means that these single-cell techniques can be integrated to combine and correlate RNA and protein data at the single-cell level. While RNA data usually reveals a large heterogeneity of a given population identified solely by a combination of surface protein markers, the integration of different omics modalities at a single cell resolution is expected to greatly contribute to our understanding of the immune system.

The recombinase activating genes: architects of immune diversity during lymphocyte development

“…While this kind of RAG1 gene therapy showed good efficacy in the mouse models, the occurrence of leukaemia due to insertional mutagenesis, forced the field to move to SIN LV vectors ( 164 , 194 ). For some types of SCID, these vectors became quickly available, however for RAG1-SCID this proved to be a formidable challenge due to the high expression of RAG1 in very strictly defined lymphoid progenitor populations ( 195 , 196 ). We first reported successful LV preclinical work with the spleen focus-forming virus (SFFV) promotor, which was later replaced by the more clinically acceptable myeloproliferative sarcoma virus enhancer, negative control region deleted, dl587rev primer-binding site substituted (MND) promotor, which has been used before in clinical trials for gene therapy ( 109 , 112 , 197 ).…”