Abstract
Adoptive cell transfer (ACT) with neoantigen-reactive T lymphocytes can mediate cancer regression. Here we isolated unique, personalized, neoantigen-reactive T cell receptors (TCRs) from tumor-infiltrating lymphocytes of patients with metastatic gastrointestinal cancers and incorporated the TCR α and β chains into gamma retroviral vectors. We transduced autologous peripheral blood lymphocytes and adoptively transferred these cells into patients after lymphodepleting chemotherapy. In a phase 2 single-arm study, we treated seven patients with metastatic, mismatch repair-proficient colorectal cancers who had progressive disease following multiple previous therapies. The primary end point of the study was the objective response rate as measured using RECIST 1.1, and the secondary end points were safety and tolerability. There was no prespecified interim analysis defined in this study. Three patients had objective clinical responses by RECIST criteria including regressions of metastases to the liver, lungs and lymph nodes lasting 4 to 7 months. All patients received T cell populations containing ≥50% TCR-transduced cells, and all T cell populations were polyfunctional in that they secreted IFNγ, GM-CSF, IL-2 and granzyme B specifically in response to mutant peptides compared with wild-type counterparts. TCR-transduced cells were detected in the peripheral blood of five patients, including the three responders, at levels ≥10% of CD3+ cells 1 month post-ACT. In one patient who responded to therapy, ~20% of CD3+ peripheral blood lymphocytes expressed transduced TCRs more than 2 years after treatment. This study provides early results suggesting that ACT with T cells genetically modified to express personalized neoantigen-reactive TCRs can be tolerated and can mediate tumor regression in patients with metastatic colorectal cancers. ClinicalTrials.gov registration: NCT03412877.
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Data availability
Next-generation sequencing data for all samples in this study have been deposited in raw fastq format to dbGaP under the study accession phs001003.
Code availability
All code used in this study is available from the corresponding author upon request for academic use. Upon request, the corresponding author will respond within 2 weeks and provide the requested code.
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Acknowledgements
We acknowledge the following people for significant contributions: for WES and RNA-seq analyses, S. Chatmon and T. Benzine; for peptide synthesis, S. Kivitz and M. Florentin; for TCR sequencing, B. Paria and V. Hill; for retroviral vector production, S. Feldman, A. Cuenca, A. Mason, N. Gill, Q. Richburg and T. Novsak; for T cell product production, R. Somerville, Z. Franco, L. Parker, A. Nahvi, M. Langhan, T. Shelton, H. Xu, N. Torres, F. Cobarde and X. Zhao; for quality control, R. Hurst, E. Pool, J. Lowe, A. Nguyen, C. Toy, A. Afzal and P. Chapman; for regulatory affairs, M. Toomey and J. Pappas; for patient care, R. Sherry, L. McIntyre, S. Seitter, A. Choi, A. Gustafson, A. El-Saadi, A. Dinerman, M. Dawson and K. Borkowski. The authors received no specific funding for this work.
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M.P., S.L.G., F.J.L., P.F.R. and S.A.R. conceived of and designed the study. M.P., S.L.G., F.J.L., R.K.B., H.H., P.F.R., T.D.P., J.J.G., S.S., S.K., N.Z., N.L., S.P.K. and S.A.R. developed the methodology. M.P., S.L.G., F.J.L., R.K.B., H.H., P.F.R., T.D.P., J.J.G., S.S., L.N., S.R., A.B., R.S., N.L., S.P.K., A.C., S.N., S.L., N.P. and S.A.R. acquired the data (acquired and managed patients, provided facilities and so on). M.P., S.L.G., F.J.L., P.F.R., T.D.P., J.J.G., S.S., J.C.Y. and S.A.R. analyzed and interpreted the data (for example, statistical analysis, biostatistics, computational analysis). M.P., S.L.G., F.J.L., R.K.B., H.H., P.F.R., J.J.G., S.S. and S.A.R. wrote, reviewed and revised the paper. S.L.G., A.C., S.N., S.L., N.P., M.L.M.K., N.D.K., J.C.Y. and S.A.R. were responsible for the clinical care of patients.
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Nature Medicine thanks George Coukos and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Ulrike Harjes, in collaboration with the Nature Medicine team.
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Extended data
Extended Data Fig. 1 Manufacture of clinical grade retroviral products.
Schematic diagram of our GLP process to generate retroviral products to transduce PBL for patient treatment using transiently transfected 293GP cells.
Extended Data Fig. 2 FACS strategy for evaluating persistence of TCR transduced cells in PBL.
Examples of FACs gating strategies to define persistence of GCLM and ALDH2 TCR transduced T cells in post-treatment PBL from patient 4378. Cryopreserved samples from the indicated days pre- and post-ACT were thawed and rested overnight without IL-2 prior to FACS. Cells were stained with antibodies against human CD3, murine TCRβ chain which stained all transduced cells, and human Vβ2 which stained the ALDH2 TCR. Analyses shown were performed on lymphocyte-size gated, live (PI negative), CD3+ T cells. The human Vβ2+ TCRβ- cells represent the endogenous Vβ2 repertoire in the patient’s PBL.
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Supplementary Results, Figs. 1–23 and Tables 1–8.
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Parkhurst, M., Goff, S.L., Lowery, F.J. et al. Adoptive transfer of personalized neoantigen-reactive TCR-transduced T cells in metastatic colorectal cancer: phase 2 trial interim results. Nat Med 30, 2586–2595 (2024). https://doi.org/10.1038/s41591-024-03109-0
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DOI: https://doi.org/10.1038/s41591-024-03109-0
