CRISPR/methotrexate-integrated strategy for TCR-T cell engineering with reduced chromosome 14 loss

Adoptive T cell therapy, particularly T cell receptor-engineered T (TCR-T) cell therapy, holds promise for cancer treatment in solid tumors and hematological malignancies. Conventional lentiviral TCR-T cell therapies face insertional mutagenesis risks, while CRISPR-mediated T cell receptor α constant (TRAC) locus targeting suffers from suboptimal knockin efficiency and chromosome 14 loss. To address these challenges, we introduced a non-viral strategy combining CRISPR-Cas9 electroporation with methotrexate (MTX) metabolic selection. Primary human T cells were engineered to integrate a CMV-pp65-specific TCR and an MTX-resistant dihydrofolate reductase (DHFR)-FS cassette into the TRAC locus via homology-directed repair (HDR). Systematic optimization of electroporation timing, buffer systems, and HDR enhancers achieved initial TCR integration efficiency of ∼20%. Subsequent 6-day MTX treatment enriched engineered cells to ∼70% purity while selectively depleting unedited and chromosomally aberrant clones. Fluorescence <i>in situ</i> hybridization revealed that MTX enrichment reduced CRISPR-associated chromosome 14 loss comparable to unedited T cells. Functionally, TRAC-TCR-T cells exhibited enhanced interferon (IFN)-γ/tumor necrosis factor alpha (TNF-α) secretion and reduced exhaustion markers versus lentiviral counterparts, while maintaining equivalent tumor clearance efficacy <i>in vitro</i> and in xenograft models. In conclusion, this integrated platform mitigates viral vector risks, alleviates concerns of CRISPR-associated genomic instability, and provides a good manufacturing practice (GMP)-compatible approach that may facilitate the development of safer adoptive TCR-T immunotherapies.