Novel Single-Cell RNA Technology Simplifies Measurement of Anti-BCMA CAR-Ts in Patient Samples

Introduction: There is a critical clinical need for a technology capable of characterizing cell therapies at time points post infusion. Targeted single cell RNA sequencing (scRNAseq) of anti-BCMA CAR-T cells was performed using a novel encapsulation and barcoding approach from Sampling Human Inc. This proof-of-concept study establishes the performance capability of BCMA antigen functionalized bioparticles for universal anti-BCMA CAR-T detection and mRNA capture directly from complex samples. The platform employs a highly streamlined and instrument free workflow, enabling routine testing of patient samples and providing high-resolution activity data of therapeutic cells in vivo.

Methods: The platform's performance was assessed using a dilution series of PBMCs from a patient receiving anti-BCMA CAR T-cell therapy and a healthy donor. Each sample, consisting of approximately 10,000 cells, was analyzed through an integrated one-step workflow using anti-BCMA CAR encapsulation reagent. Samples were processed directly into barcoded libraries, foregoing separate enrichment or isolation steps, and were sequenced using a standard NGS pipeline. The results were compared to those obtained from a benchmark workflow that employs FACS isolation, followed by analysis with 10X Genomics 3' kits.

Results: The results from the novel approach show strong alignment with existing single cell technologies that employ cell sorting in series with scRNAseq, based on median genes detected (2120 genes per cell) and transcript counts (2589 UMIs per cell). Notably, the platform consistently exhibited a significantly higher mean cell recovery rate (exceeding 70%) and lower false positive rate (<1% CAR-negative cells), permitting analysis on smaller sample sizes. Moreover, the approach demonstrated a decreased percentage of mitochondrial (MT) transcripts, indicating less cellular stress, and lower variability between samples compared to FACS-based methods.

Conclusion: This novel encapsulation and barcoding method from Sampling Human Inc consolidates scRNAseq of anti-BCMA CAR-T cells into a one-step protocol that greatly reduces the time and cost of analysis. The platform significantly increases access to translational scRNAseq data by eliminating isolation and sorting steps to simplify sample preparation at scale. Continued refinement of this platform promises to significantly improve the precision of CAR T-cell typing, with substantial promise for future applications such as precision re-dosing and advanced CAR T-cell engineering.