Application of Base Editing Screening Technology in Tumor Immunotherapy T Cell Research

Immune cell therapies, such as T cell transfer therapy and CAR T cell therapy, have become important clinical cancer treatment tools in certain disease fields. However, most cancer patients fail to benefit from cell therapies, possibly due to inherent changes in cancer cells (e.g., B2M loss, antigen loss, or CD58 loss or downregulation) or regulation of cellular products in an immunosuppressive tumor microenvironment. This study generates thousands of variants at known or potentially clinically relevant gene loci through base editing screening technology, exploring the impact of these variants on T cell biomarkers and proposing the possibility of leveraging these variants to improve existing and future cellular cancer immunotherapies.

Research Background

This study was conducted by Zachary H. Walsh, Parin Shah, Neeharika Kothapalli, Shivem B. Shah, and others from various research institutions, showcasing profound research backgrounds and professional capabilities. This research was published in “Nature Biotechnology,” with DOI 10.1038/s41587-024-02235-x, achieving large-scale parallel base editing screening in human T cells and uncovering multiple variants that may affect anti-tumor immune markers.

Research Process

The study initially modified clinically relevant single nucleotide variants (SNVs) to achieve gene editing. Subsequently, researchers designed a library (ClinVar library) containing 8142 types of ABE sgRNAs to generate variants of 102 genes associated with major T cell functions.

By adopting multiple screening procedures, researchers identified variants impacting T cell functional markers, including activation, short-term and long-term proliferation, and cytokine production.

The study generalized known clinical gene mutations and discovered novel gain-of-function (GOF) and loss-of-function (LOF) mutations, especially in key genes like PIK3CD and PIK3R1. Additionally, the study identified a range of other critical T cell-specific genes, such as LCK, SOS1, AKT1, and RHOA.

Research Findings

Through this screening technique, researchers not only identified GOF and LOF variants affecting T cell proliferation and function but also revealed that T cells harboring these variants exhibited enhanced signaling, cytokine production, and tumor cell lysis when co-cultured with tumor cell models. Experimental results demonstrated that the screened GOF variants could enhance nutrient-specific signaling, cytokine production, and leukemia cell-killing capability, showcasing enhanced antigen-specific activity in scenarios with known resistance to cell therapy, such as CD58 loss.

Research Conclusion and Significance

The study demonstrates that precise base editing screening technology is an effective tool for identifying and characterizing mutations that may improve existing and future cellular cancer immunotherapies. Optimized T cells, equipped with significantly beneficial variants, show enhanced activation signaling, cytokine production, and cytotoxic activity against specific melanoma and leukemia models. Meanwhile, the intrinsic properties of T cells determine their anti-tumor capability and clinical success rate, with the screened variants promising improvements in future cell therapies.

The methods and findings of this study not only potentially advance individualized cancer treatment development but also provide new tools for in-depth understanding and identification of SNVs associated with clinical immune syndromes. This method may be applicable for reclassifying previously described VUS, offering support for faster clinical diagnosis and decision-making.