Mission Bio De-risks CRISPR-Engineered T Cells Through Single-Cell Analysis of Genomic Edits and Gene Expression

First demonstration pairing single-cell targeted DNA and RNA readouts in multiplexed CRISPR cell therapy characterization.

SOUTH SAN FRANCISCO, Calif.--(BUSINESS WIRE)--Mission Bio, the single-cell multi-omics leader, today released data showing that its Targeted Single-Cell DNA+RNA Assay simultaneously resolves CRISPR edit co-occurrence, allelic zygosity, and downstream gene expression changes in individual cells of multiplex-engineered T cell populations, a capability legacy analytical methods cannot provide. The findings will be presented at the American Society of Gene & Cell Therapy (ASGCT) Annual Meeting in Boston.

As multiplexed CRISPR editing strategies grow more complex, the limitations of legacy bulk assays have become a critical bottleneck. Averaged signals across millions of cells mask clonal heterogeneity, stochastic editing variability, and rare off-target events with significant safety implications. The FDA and EMA are now focused on defining Critical Quality Attributes (CQAs) at a resolution that legacy assays cannot achieve.

Mission Bio scientists applied the Tapestri Platform's Targeted Single-Cell DNA+RNA Assay to characterize three engineered Jurkat T cell lines: a PDCD1 knockout, a TRAC knockout, and a double PDCD1/TRAC knockout carrying a defined off-target edit. The cells were spiked into healthy donor peripheral blood mononuclear cells to model a realistic cell therapy product background. Targeted DNA panels interrogated on-target gene editing efficiency and validated off-target loci while RNA panels quantified expression of PDCD1, TRAC, immune lineage markers, and downstream pathway genes within the same workflow.

The assay deconvoluted clonal heterogeneity across all sample types. In the double-knockout model, the platform quantified on-target edit co-occurrence per cell and segregated cells carrying the off-target edit from the intended population. Integrating genotyping with targeted transcriptomics revealed a dose-dependent relationship between editing zygosity and pathway gene expression: bi-allelic knockouts produced markedly greater downstream changes than mono-allelic events. Differential expression analysis further distinguished intended therapeutic signaling from aberrant patterns associated with off-target edits, delivering the orthogonal safety evidence regulators increasingly require.

"The Tapestri Platform was built on the foundational principle that genotype and phenotype must be resolved in the same cell simultaneously, because averages lie, and in cell therapy, the outlier cell is often the most consequential one," said Adam Sciambi, PhD, Co-Founder and Chief Technology Officer, Mission Bio. "This data demonstrates precisely what that platform was designed to deliver: single-cell co-occurrence resolution that links editing zygosity directly to downstream gene expression, providing the kind of orthogonal safety evidence that legacy bulk methods are fundamentally unable to generate."

The data will be presented under the title "Single-cell multiomic evaluation of allelic zygosity, edit co-occurrence, and gene expression for analytical characterization of CRISPR edited multiplex-engineered cell therapies" (Poster #1246) on May 12, 2026, from 5:00-6:30 PM ET at the ASGCT Annual Meeting, Boston. Visit booth #956 to learn more about single-cell multi-omics for CRISPR gene editing and cell & gene therapy development.

About Mission Bio

Mission Bio is the single-cell multi-omics leader. The company’s Tapestri Platform is unique in its capabilities, offering an unparalleled level of granularity and precision that is critical for complex research areas such as cancer studies, pharmaceutical development, and advanced cell and gene therapies. Unlike traditional standard of care methods, Tapestri provides a level of precision that opens the door for more tailored and effective treatment strategies. Researchers globally depend on Tapestri to identify rare cell populations, understand mechanisms of therapeutic resistance and response, and establish key quality metrics for next-generation medical treatments. With the Tapestri Platform, Mission Bio continues to set the standard in the field, contributing significantly to the progress of personalized medicine and targeted therapies. To learn more about Mission Bio and the Tapestri Platform, please visit missionbio.com.