Expansion and Precise CRISPR-Cas9 Gene Repair of Autologous T-Memory Stem Cells from Patients with T-Cell Immunodeficiencies

Xun Li; Van Trung Chu; Christine Kocks; Klaus Rajewsky

doi:10.21769/BioProtoc.5085

Expansion and Precise CRISPR-Cas9 Gene Repair of Autologous T-Memory Stem Cells from Patients with T-Cell Immunodeficiencies

Bio Protoc. 2024 Oct 20;14(20):e5085. doi: 10.21769/BioProtoc.5085.

Authors

Xun Li¹, Van Trung Chu^{1

2}, Christine Kocks^{1

2}, Klaus Rajewsky¹

Affiliations

¹ Immune Regulation and Cancer, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
² Genome Engineering and Disease Models, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.

Abstract

The adoptive transfer of autologous, long-lived, gene-repaired T cells is a promising way to treat inherited T-cell immunodeficiencies. However, adoptive T-cell therapies require a large number of T cells to be manipulated and infused back into the patient. This poses a challenge in primary immunodeficiencies that manifest early in childhood and where only small volumes of blood samples may be available. Our protocol describes the ex vivo expansion of potentially long-lived human T memory stem cells (T_SCM), starting from a limited number of peripheral blood mononuclear cells (PBMCs). Using the perforin gene as an example, we provide detailed instructions for precise gene repair of human T cells and the expansion of T_SCM. The efficiency of precise gene repair can be increased by suppressing unintended non-homologous end-joining (NHEJ) events. Our protocol yields edited T-cell populations that are ready for phenotyping, genome-wide off-target analysis, and functional characterization. Key features • Expansion and enrichment of T_SCM from PBMCs using IL-7 and IL-15. • Phenotyping of T_SCM. • Design of "off-the-shelf" gene-repair strategies based on knock-in of a single exon or complete cDNA and design of effective guide RNAs and DNA donor templates. • High-efficiency gene targeting using CRISPR-Cas9, recombinant adeno-associated virus serotype 6 (rAAV6), and a selective small molecule inhibitor of DNA-dependent protein kinase (DNA-PK).

Keywords: Adeno-associated virus 6 (AAV6); CRISPR-Cas9 systems; Gene editing efficiency; Gene therapy; Genome editing; Humans; Immunodeficiencies; Memory T cells; Perforin; Ribonucleoproteins.