Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells [CROPSeq_Data]

CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the chromosome, including in pre-clinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells, dramatically reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic. Overall design: Primary human T cells were transduced with a lentiviral vector (CROP-seq) containing a unique Cas9 guide RNA and co-expressing GFP at an MOI <0.3. After FACS to isolate GFP+ T cells, Cas9 protein was electroporated. Genome edited T cells were barcoded using MULTI-seq before pooling and performing 10x Genomics 3' scRNA-seq. Along with the MULTI-seq barcodes and gene expression data, the sequence of the guide RNA was also sequenced.