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Biernacki MA, Lok J, Black RG, Foster KA, Cummings C, Woodward KB, Monahan T, Oehler VG, Stirewalt DL, Wu D, Rongvaux A, Deeg HJ, Bleakley M. Discovery of U2AF1 neoantigens in myeloid neoplasms. J Immunother Cancer 2023; 11:e007490. [PMID: 38164756 PMCID: PMC10729103 DOI: 10.1136/jitc-2023-007490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) arise from somatic mutations acquired in hematopoietic stem and progenitor cells, causing cytopenias and predisposing to transformation into secondary acute myeloid leukemia (sAML). Recurrent mutations in spliceosome genes, including U2AF1, are attractive therapeutic targets as they are prevalent in MDS and sAML, arise early in neoplastic cells, and are generally absent from normal cells, including normal hematopoietic cells. MDS and sAML are susceptible to T cell-mediated killing, and thus engineered T-cell immunotherapies hold promise for their treatment. We hypothesized that targeting spliceosome mutation-derived neoantigens with transgenic T-cell receptor (TCR) T cells would selectively eradicate malignant cells in MDS and sAML. METHODS We identified candidate neoantigen epitopes from recurrent protein-coding mutations in the spliceosome genes SRSF2 and U2AF1 using a multistep in silico process. Candidate epitopes predicted to bind human leukocyte antigen (HLA) class I, be processed and presented from the parent protein, and not to be subject to tolerance then underwent in vitro immunogenicity screening. CD8+ T cells recognizing immunogenic neoantigen epitopes were evaluated in in vitro assays to assess functional avidity, confirm the predicted HLA restriction, the potential for recognition of similar peptides, and the ability to kill neoplastic cells in an antigen-specific manner. Neoantigen-specific TCR were sequenced, cloned into lentiviral vectors, and transduced into third-party T cells after knock-out of endogenous TCR, then tested in vitro for specificity and ability to kill neoplastic myeloid cells presenting the neoantigen. The efficacy of neoantigen-specific T cells was evaluated in vivo in a murine cell line-derived xenograft model. RESULTS We identified two neoantigens created from a recurrent mutation in U2AF1, isolated CD8+ T cells specific for the neoantigens, and demonstrated that transferring their TCR to third-party CD8+ T cells is feasible and confers specificity for the U2AF1 neoantigens. Finally, we showed that these neoantigen-specific TCR-T cells do not recognize normal hematopoietic cells but efficiently kill malignant myeloid cells bearing the specific U2AF1 mutation, including primary cells, in vitro and in vivo. CONCLUSIONS These data serve as proof-of-concept for developing precision medicine approaches that use neoantigen-directed T-cell receptor-transduced T cells to treat MDS and sAML.
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MESH Headings
- Humans
- Mice
- Animals
- CD8-Positive T-Lymphocytes
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Antigens, Neoplasm
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Myelodysplastic Syndromes/genetics
- Myelodysplastic Syndromes/therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/metabolism
- Epitopes/metabolism
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Affiliation(s)
- Melinda Ann Biernacki
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica Lok
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Ralph Graeme Black
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kimberly A Foster
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Carrie Cummings
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kyle B Woodward
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Tim Monahan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Vivian G Oehler
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Derek L Stirewalt
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Anthony Rongvaux
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Hans Joachim Deeg
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Marie Bleakley
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
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Kim JY, Cha H, Kim K, Sung C, An J, Bang H, Kim H, Yang JO, Chang S, Shin I, Noh SJ, Shin I, Cho DY, Lee SH, Choi JK. MHC II immunogenicity shapes the neoepitope landscape in human tumors. Nat Genet 2023; 55:221-231. [PMID: 36624345 DOI: 10.1038/s41588-022-01273-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/30/2022] [Indexed: 01/11/2023]
Abstract
Despite advances in predicting physical peptide-major histocompatibility complex I (pMHC I) binding, it remains challenging to identify functionally immunogenic neoepitopes, especially for MHC II. By using the results of >36,000 immunogenicity assay, we developed a method to identify pMHC whose structural alignment facilitates T cell reaction. Our method predicted neoepitopes for MHC II and MHC I that were responsive to checkpoint blockade when applied to >1,200 samples of various tumor types. To investigate selection by spontaneous immunity at the single epitope level, we analyzed the frequency spectrum of >25 million mutations in >9,000 treatment-naive tumors with >100 immune phenotypes. MHC II immunogenicity specifically lowered variant frequencies in tumors under high immune pressure, particularly with high TCR clonality and MHC II expression. A similar trend was shown for MHC I neoepitopes, but only in particular tissue types. In summary, we report immune selection imposed by MHC II-restricted natural or therapeutic T cell reactivity.
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Affiliation(s)
- Jeong Yeon Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.,Penta Medix Co., Ltd., Seongnam-si, Republic of Korea
| | - Hongui Cha
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyeonghui Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Changhwan Sung
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.,Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Jinhyeon An
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Hyoeun Bang
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.,Penta Medix Co., Ltd., Seongnam-si, Republic of Korea
| | - Hyungjoo Kim
- Penta Medix Co., Ltd., Seongnam-si, Republic of Korea.,Department of Life Science, Hanyang University, Seoul, Republic of Korea
| | - Jin Ok Yang
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea.,Korea Bioinformation Center, KRIBB, Daejeon, Republic of Korea
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Incheol Shin
- Department of Life Science, Hanyang University, Seoul, Republic of Korea.,Natural Science Institute, Hanyang University, Seoul, Republic of Korea
| | - Seung-Jae Noh
- Penta Medix Co., Ltd., Seongnam-si, Republic of Korea
| | - Inkyung Shin
- Penta Medix Co., Ltd., Seongnam-si, Republic of Korea
| | - Dae-Yeon Cho
- Penta Medix Co., Ltd., Seongnam-si, Republic of Korea.
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea. .,Department of Health Sciences and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea. .,Penta Medix Co., Ltd., Seongnam-si, Republic of Korea.
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Ferrari V, Tarke A, Fields H, Tanaka TN, Searles S, Zanetti M. Tumor-specific T cell-mediated upregulation of PD-L1 in myelodysplastic syndrome cells does not affect T-cell killing. Front Oncol 2022; 12:915629. [PMID: 35992887 PMCID: PMC9389224 DOI: 10.3389/fonc.2022.915629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
The PD-1:PD-L1 axis is a binary interaction that delivers inhibitory signals to T cells, impeding both immune surveillance and response to immunotherapy. Here we analyzed a phenomenon whereby tumor-specific T cells induce PD-L1 upregulation in autologous MDS cells in short-term culture, through a mechanism that is cell-contact-independent and partially IFNγ-dependent. After investigating a panel of small-molecule inhibitors, we determined that PD-L1 upregulation was attributed to the PKR-like ER kinase (PERK) branch of the unfolded protein response. Interestingly, we found that the cytotoxic capacity of tumor-specific T cells was not impaired by the expression of PD-L1 on MDS target cells. These results highlight a little appreciated aspect of PD-1:PD-L1 regulation in hematologic cancers and indicate that this phenomenon, while likely to hinder autochthonous immune surveillance, may not be an obstacle to immunotherapies such as personalized adoptive T-cell therapy.
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Affiliation(s)
- Valentina Ferrari
- PersImmune, Inc., San Diego, CA, United States
- *Correspondence: Valentina Ferrari, ; Maurizio Zanetti,
| | | | | | - Tiffany N. Tanaka
- Moores Cancer Center, Department of Hematology and Oncology, University of California San Diego, La Jolla, CA, United States
| | - Stephen Searles
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Maurizio Zanetti
- The Laboratory of Immunology, Department of Medicine and Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
- *Correspondence: Valentina Ferrari, ; Maurizio Zanetti,
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Simoni Y, Chapuis N. Diagnosis of Myelodysplastic Syndromes: From Immunological Observations to Clinical Applications. Diagnostics (Basel) 2022; 12:diagnostics12071659. [PMID: 35885563 PMCID: PMC9324119 DOI: 10.3390/diagnostics12071659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Myelodysplastic syndromes (MDS) constitute a very heterogeneous group of diseases with a high prevalence in elderly patients and a propensity for progression to acute myeloid leukemia. The complexity of these hematopoietic malignancies is revealed by the multiple recurrent somatic mutations involved in MDS pathogenesis and the paradoxical common phenotype observed in these patients characterized by ineffective hematopoiesis and cytopenia. In the context of population aging, the incidence of MDS will strongly increase in the future. Thus, precise diagnosis and evaluation of the progression risk of these diseases are imperative to adapt the treatment. Dysregulations of both innate and adaptive immune systems are frequently detected in MDS patients, and their critical role in MDS pathogenesis is now commonly accepted. However, different immune dysregulations and/or dysfunctions can be dynamically observed during the course of the disease. Monitoring the immune system therefore represents a new attractive tool for a more precise characterization of MDS at diagnosis and for identifying patients who may benefit from immunotherapy. We review here the current knowledge of the critical role of immune dysfunctions in both MDS and MDS precursor conditions and discuss the opportunities offered by the detection of these dysregulations for patient stratification.
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Affiliation(s)
- Yannick Simoni
- Institut Cochin, Université Paris Cité, CNRS UMR8104, INSERM U1016, 75014 Paris, France;
| | - Nicolas Chapuis
- Institut Cochin, Université Paris Cité, CNRS UMR8104, INSERM U1016, 75014 Paris, France;
- Assistance Publique-Hôpitaux de Paris, Centre-Université Paris Cité, Service d’Hématologie Biologique, Hôpital Cochin, 75014 Paris, France
- Correspondence:
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5
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Inflammation and myeloid malignancy: Quenching the flame. Blood 2022; 140:1067-1074. [PMID: 35468199 DOI: 10.1182/blood.2021015162] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/22/2022] [Indexed: 01/19/2023] Open
Abstract
Chronic inflammation with aging ("inflammaging") plays a prominent role in the pathogenesis of myeloid malignancies. Aberrant inflammatory activity impacts many different cells in the marrow, including normal blood and stromal marrow elements and leukemic cells, in unique and distinct ways. Inflammation can promote selective clonal expansion through differential immune-mediated suppression of normal hematopoietic cells and malignant clones. We review these complex roles, how they can be understood by separating cell-intrinsic from extrinsic effects, and how this informs future clinical trials.
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6
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Neoantigen reactive T cells correlate with the low mutational burden in hematological malignancies. Leukemia 2022; 36:2734-2738. [PMID: 36209321 PMCID: PMC9613475 DOI: 10.1038/s41375-022-01705-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
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Tanaka TN, Ferrari V, Tarke A, Fields H, Ferrari L, Ferrari F, McCarthy CL, Sanchez AP, Vitiello A, Lane TA, Bejar R. Adoptive transfer of neoantigen-specific T-cell therapy is feasible in older patients with higher-risk myelodysplastic syndrome. Cytotherapy 2020; 23:236-241. [PMID: 33279399 DOI: 10.1016/j.jcyt.2020.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/27/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) represent the most common type of acquired bone marrow failure in adults and is characterized by ineffective maturation of myeloid precursor cells and peripheral cytopenias associated with higher rates of infection, bleeding and transfusion dependence. In higher-risk patients with MDS who relapse or do not respond after standard hypomethylating agent (HMA) therapy, the 2-year survival rate is 15%. METHODS Here the authors report the feasibility and safety of a novel experimental T-cell therapy called personalized adoptive cell therapy, which selects, immunizes and expands T cells against MDS-specific mutations and is targeted to patient-specific tumor cell neoantigens. Somatic mutations serve as the pathogenic drivers of cancer, including MDS, as these transformative genetic mutations may generate novel immunogenic proteins (i.e., neopeptides and possible neoantigens) that may be targeted therapeutically. RESULTS The authors demonstrate that the adaptive immune system can be trained ex vivo to recognize neopeptides as neoantigens and that the infusion of culture-expanded, neoantigen-immunized autologous T cells has been feasible and safe in the three patients treated to date. DISCUSSION The authors report on early results from their first-in-human phase 1 clinical trial that aims to assess the safety and tolerability of this novel form of adoptive T-cell immunotherapy for HMA-refractory patients with higher-risk MDS.
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Affiliation(s)
- Tiffany N Tanaka
- University of California San Diego Moores Cancer Center, La Jolla, California, USA
| | | | | | | | | | - Franco Ferrari
- University of California San Diego Moores Cancer Center, La Jolla, California, USA
| | - Colin L McCarthy
- University of California San Diego Moores Cancer Center, La Jolla, California, USA
| | - Amber P Sanchez
- University of California San Diego Apheresis Program and Division of Nephrology, La Jolla, California, USA
| | | | | | - Rafael Bejar
- University of California San Diego Moores Cancer Center, La Jolla, California, USA.
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