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.
This is a preview of subscription content, log in via an institution to check access.
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.
References
Parkhurst, M. R. et al. Unique neoantigens arise from somatic mutations in patients with gastrointestinal cancers. Cancer Discov. 9, 1022–1035 (2019).
Prickett, T. D. et al. Durable complete response from metastatic melanoma after transfer of autologous T cells recognizing 10 mutated tumor antigens. Cancer Immunol. Res. 4, 669–678 (2016).
Stevanovic, S. et al. Landscape of immunogenic tumor antigens in successful immunotherapy of virally induced epithelial cancer. Science 356, 200–205 (2017).
Tran, E. et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science 344, 641–645 (2014).
Zacharakis, N. et al. Breast cancers are immunogenic: immunologic analyses and a phase II pilot clinical trial using mutation-reactive autologous lymphocytes. J. Clin. Oncol. 40, 1741–1754 (2022).
Crompton, J. G., Sukumar, M. & Restifo, N. P. Uncoupling T-cell expansion from effector differentiation in cell-based immunotherapy. Immunol. Rev. 257, 264–276 (2014).
Krishna, S. et al. Stem-like CD8 T cells mediate response of adoptive cell immunotherapy against human cancer. Science 370, 1328–1334 (2020).
Sade-Feldman, M. et al. Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell 175, 998–1013.e20 (2018).
Morgan, R. A. et al. Cancer regression in patients after transfer of genetically engineered lymphocytes. Science 314, 126–129 (2006).
Robbins, P. F. et al. A pilot trial using lymphocytes genetically engineered with an NY-ESO-1-reactive T-cell receptor: long-term follow-up and correlates with response. Clin. Cancer Res. 21, 1019–1027 (2015).
Robbins, P. F. et al. Tumor regression in patients with metastatic synovial cell sarcoma and melanoma using genetically engineered lymphocytes reactive with NY-ESO-1. J. Clin. Oncol. 29, 917–924 (2011).
Parkhurst, M. R. et al. T cells targeting carcinoembryonic antigen can mediate regression of metastatic colorectal cancer but induce severe transient colitis. Mol. Ther. 19, 620–626 (2011).
Linette, G. P. et al. Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T cells in myeloma and melanoma. Blood 122, 863–871 (2013).
Morgan, R. A. et al. Cancer regression and neurological toxicity following anti-MAGE-A3 TCR gene therapy. J. Immunother. 36, 133–151 (2013).
Dudley, M. E., Wunderlich, J. R., Shelton, T. E., Even, J. & Rosenberg, S. A. Generation of tumor-infiltrating lymphocyte cultures for use in adoptive transfer therapy for melanoma patients. J. Immunother. 26, 332–342 (2003).
Cohen, C. J., Zhao, Y., Zheng, Z., Rosenberg, S. A. & Morgan, R. A. Enhanced antitumor activity of murine–human hybrid T-cell receptor (TCR) in human lymphocytes is associated with improved pairing and TCR/CD3 stability. Cancer Res. 66, 8878–8886 (2006).
Chatani, P. D. et al. Cell surface marker-based capture of neoantigen-reactive CD8+ T-cell receptors from metastatic tumor digests. J. Immunother. Cancer 11, e006264 (2023).
Rosenberg, S. A. et al. Durable complete responses in heavily pretreated patients with metastatic melanoma using T-cell transfer immunotherapy. Clin. Cancer Res. 17, 4550–4557 (2011).
Wang, Q. J. et al. Identification of T-cell receptors targeting KRAS-mutated human tumors. Cancer Immunol. Res. 4, 204–214 (2016).
Foy, S. P. et al. Non-viral precision T cell receptor replacement for personalized cell therapy. Nature 615, 687–696 (2023).
Hanada, K. I. et al. A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers. Cancer Cell 40, 479–493 e476 (2022).
Yossef, R. et al. Phenotypic signatures of circulating neoantigen-reactive CD8+ T cells in patients with metastatic cancers. Cancer Cell 41, 2154–2165.e5 (2023).
Cohen, C. J. et al. Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes. J. Clin. Invest. 125, 3981–3991 (2015).
Cafri, G. et al. Memory T cells targeting oncogenic mutations detected in peripheral blood of epithelial cancer patients. Nat. Commun. 10, 449 (2019).
Kim, S. P. et al. Adoptive cellular therapy with autologous tumor-infiltrating lymphocytes and T-cell receptor-engineered T cells targeting common p53 neoantigens in human solid tumors. Cancer Immunol. Res. 10, 932–946 (2022).
Abate-Daga, D. et al. Expression profiling of TCR-engineered T cells demonstrates overexpression of multiple inhibitory receptors in persisting lymphocytes. Blood 122, 1399–1410 (2013).
Pasetto, A. et al. Tumor- and neoantigen-reactive T-cell receptors can be identified based on their frequency in fresh tumor. Cancer Immunol. Res. 4, 734–743 (2016).
Favero, F. et al. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann. Oncol. 26, 64–70 (2015).
McGranahan, N. et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 351, 1463–1469 (2016).
Roth, A. et al. PyClone: statistical inference of clonal population structure in cancer. Nat. Methods 11, 396–398 (2014).
Dilthey, A. T. et al. HLA*LA–HLA ty** from linearly projected graph alignments. Bioinformatics 35, 4394–4396 (2019).
Bai, Y., Wang, D. & Fury, W. PHLAT: inference of high-resolution HLA types from RNA and whole exome sequencing. Methods Mol. Biol. 1802, 193–201 (2018).
McGranahan, N. et al. Allele-specific HLA loss and immune escape in lung cancer evolution. Cell 171, 1259–1271.e11 (2017).
Rosenberg, S. A. et al. Immunologic and therapeutic evaluation of a synthetic peptide vaccine for the treatment of patients with metastatic melanoma. Nat. Med. 4, 321–327 (1998).
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.
Author information
Authors and Affiliations
Contributions
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.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
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.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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.
Supplementary information
Supplementary Information
Supplementary Results, Figs. 1–23 and Tables 1–8.
Rights and permissions
About this article
Cite this article
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 (2024). https://doi.org/10.1038/s41591-024-03109-0
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41591-024-03109-0
- Springer Nature America, Inc.