Dissecting T follicular helper cell development in vivo using CRISPR

T follicular helper (Tfh) cells are specialized CD4 helper T cells that signal B cells to produce high affinity antibodies and provide long-term humoral immunity. Identifying genes that govern Tfh differentiation and function could provide targets for improving vaccines and therapies for autoimmunity. However, Tfh differentiation is only partially understood, and not fully recapitulated in vitro. To discover novel Tfh-regulating genes, we developed a CRISPR-based functional genetic system to mutate genes in primary mouse T cells, and measured the effects on Tfh cells in vivo. Transgenic Cas9-expressing mouse CD4 T cells were transduced in vitro with an optimized retroviral vector encoding an sgRNA and GFP. With a guide targeting Tcf7 (encoding a Tfh-essential transcription factor Tcf1), >90% cells could be transduced; up to >80% of GFP+ cells were Tcf1neg by flow and mutational analyses. To evaluate the functional consequence of CRISPR editing, we adoptively transferred virus-specific CD4 T cells that were transduced with either a control or Tcf7 sgRNA construct into wild-type hosts. After viral challenge, control T cells differentiated into both Tfh and non-Tfh cells, while very few Tcf7-edited T cells became Tfh cells. Similarly, guides against the Tfh master transcription factor Bcl6 abrogated Tfh differentiation in vivo. Next, we constructed sgRNA libraries of up to 400 guides, targeting up to 80 genes, including ones implicated in primary immunodeficiencies and druggable targets. NGS analysis of T cells post-viral challenge revealed depletion of multiple guides targeting known Tfh-required genes in the Tfh vs non-Tfh populations, validating this approach. We are currently following up on potential hits from these screens.