Mapping variant effects on anti-tumor hallmarks of primary human T cells with base-editing screens

Area of Science:

• Immunology
• Genetics
• Biotechnology

Background:

• Single-nucleotide variants (SNVs) in T cell genes can cause disease.
• These SNVs hold potential for enhancing cancer immunotherapies.

Purpose of the Study:

• To identify novel gain-of-function (GOF) and loss-of-function (LOF) mutations in T cell genes.
• To evaluate the therapeutic potential of these mutations in cellular cancer immunotherapies.

Main Methods:

• Massively parallel base-editing screens were employed to generate thousands of gene variants.
• Engineered T cells, including chimeric antigen receptor (CAR) T cells, were used to test variant function.
• Specific gene loci with clinical relevance were targeted for mutation generation.

Main Results:

• A wide range of GOF and LOF mutations were discovered in genes such as PIK3CD, PIK3R1, LCK, SOS1, AKT1, and RHOA.
• Engineered T cells with PIK3CD and PIK3R1 GOF mutations showed enhanced signaling, cytokine production, and cancer cell lysis.
• PIK3CD GOF mutations improved CD19 CAR T cell efficacy against leukemia models.

Conclusions:

• Novel GOF mutations in T cell genes can significantly enhance cellular immunotherapy efficacy.
• Base editing screens are effective for discovering clinically relevant gene variants.
• Targeted genetic engineering of T cells with specific GOF mutations represents a promising strategy for improved cancer treatment.