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Non-Viral Engineering of Primary Human T Cells via Homology-Mediated End-Joining Targeted Integration of Large DNA Templates
Published on: May 9, 2025
Non-viral precision T cell receptor replacement for personalized cell therapy
Susan P Foy1, Kyle Jacoby2, Daniela A Bota3
1PACT Pharma, South San Francisco, CA, USA. sfoy@pactpharma.com.
Abstract:
T cell receptors (TCRs) enable T cells to specifically recognize mutations in cancer cells1-3. Here we developed a clinical-grade approach based on CRISPR-Cas9 non-viral precision genome-editing to simultaneously knockout the two endogenous TCR genes TRAC (which encodes TCRα) and TRBC (which encodes TCRβ). We also inserted into the TRAC locus two chains of a neoantigen-specific TCR (neoTCR) isolated from circulating T cells of patients. The neoTCRs were isolated using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with different refractory solid cancers received up to three distinct neoTCR transgenic cell products. Each product expressed a patient-specific neoTCR and was administered in a cell-dose-escalation, first-in-human phase I clinical trial ( NCT03970382 ). One patient had grade 1 cytokine release syndrome and one patient had grade 3 encephalitis. All participants had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease and the other eleven had disease progression as the best response on the therapy. neoTCR transgenic T cells were detected in tumour biopsy samples after infusion at frequencies higher than the native TCRs before infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs that recognize mutational neoantigens. Moreover, simultaneous knockout of the endogenous TCR and knock-in of neoTCRs using single-step, non-viral precision genome-editing are achieved. The manufacture of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene-edited neoTCR T cell products and the ability of the transgenic T cells to traffic to the tumours of patients are also demonstrated.
Insights
This study developed a clinical-grade CRISPR-Cas9 gene-editing method to engineer T-cells with neoantigen-specific T-cell receptors (neoTCRs) for cancer therapy. The approach successfully knocked out endogenous TCRs and inserted neoTCRs, demonstrating feasibility and T-cell trafficking to tumors.
Area of Science:
- Immunology
- Genetics
- Oncology
Background:
- T-cell receptors (TCRs) are crucial for T-cells to identify cancer-specific mutations.
- Current T-cell therapies often face challenges in specificity and efficacy against solid tumors.
Purpose of the Study:
- To develop and evaluate a clinical-grade, non-viral CRISPR-Cas9 genome-editing approach for engineering T-cells with neoantigen-specific TCRs (neoTCRs).
- To assess the safety, feasibility, and in vivo T-cell trafficking of neoTCR-engineered T-cell products in patients with refractory solid cancers.
Main Methods:
- Simultaneous knockout of endogenous TRAC and TRBC genes using CRISPR-Cas9 non-viral genome editing.
- Insertion of neoantigen-specific TCRs (neoTCRs) into the TRAC locus, with neoTCRs isolated using personalized neoantigen-HLA capture reagents.
- Phase I clinical trial administering up to three distinct neoTCR transgenic T-cell products in a dose-escalation manner to patients with refractory solid cancers.
Main Results:
- Successful simultaneous knockout of endogenous TCR genes and knock-in of neoTCRs using a single-step, non-viral precision genome-editing method.
- neoTCR transgenic T-cells were detected in tumor biopsies post-infusion at higher frequencies than endogenous TCRs pre-infusion, indicating successful tumor trafficking.
- Observed manageable side effects, including cytokine release syndrome and encephalitis in one patient each, alongside expected chemotherapy-related side effects.
Conclusions:
- Demonstrated the feasibility of isolating and cloning multiple TCRs targeting mutational neoantigens.
- Established the clinical-grade manufacture and safety of infusing multiple gene-edited neoTCR T-cell products.
- Confirmed the ability of engineered T-cells to traffic to tumor sites in patients, supporting the potential of this approach for cancer immunotherapy.
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