Characterization Of Tumor-Specific T-Cells With Checkpoint Modifications For Adoptive Transfer Using RNA-Seq–Based Gene Expression

By James Goward, Nathalie Labarriere, Tiffany Beauvais, Kathleen Ducoin, Nantes University, and Samuel Rulli, Katja Heitz, Christin Meerschiff, Ioanna Andreou, Yasmin Fries, Gabriele Christoffel, QIAGEN

Reliable transcriptomic analysis is essential for understanding how engineered T-cells respond to checkpoint modification and immune stimulation. A scalable RNA-seq workflow was used to characterize melanoma-derived T-cells with CRISPR-mediated deletion of PD-1, TIGIT, or both targets. Across 192 samples, automated RNA purification using QIAsprint Connect, followed by QIAseq FastSelect library preparation, delivered strong technical performance, including approximately 90% total mapping, highly efficient rRNA depletion, and highly reproducible expression profiles across plates and experimental conditions.

Gene-expression results showed that stimulation, rather than checkpoint status, shaped the global transcriptional landscape. Checkpoint deletion instead produced more limited, pathway-specific effects, suggesting focused regulation rather than widespread cellular reprogramming.

Examine the methods, quality metrics, and biological findings supporting sensitive analysis of engineered T-cell populations.