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Lubbers JM, Ważyńska MA, van Rooij N, Kol A, Workel HH, Plat A, Paijens ST, Vlaming MR, Spierings DCJ, Elsinga PH, Bremer E, Nijman HW, de Bruyn M. Expression of CD39 Identifies Activated Intratumoral CD8+ T Cells in Mismatch Repair Deficient Endometrial Cancer. Cancers (Basel) 2022; 14:cancers14081924. [PMID: 35454831 PMCID: PMC9028869 DOI: 10.3390/cancers14081924] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Identification of human cancer-reactive CD8+ T cells is crucial for the stratification of patients for immunotherapy and determination of immune-therapeutic effects. Here, we report on the CD103− CD39+ subset of CD8+ T cells in tumors and reveal this subset to be activated and likely tumor-reactive. Our data further suggest that TGF-β signaling in the tumor micro-environment causes the differentiation of these recently activated CD103− CD39+ CD8+ T cells towards a CD39+ CD103+ tissue-resident memory-like phenotype. Abstract Identification of human cancer-reactive CD8+ T cells is crucial for the stratification of patients for immunotherapy and determination of immune-therapeutic effects. To date, these T cells have been identified mainly based on cell surface expression of programmed cell death protein 1 (PD-1) or co-expression of CD103 and CD39. A small subset of CD103− CD39+ CD8+ T cells is also present in tumors, but little is known about these T cells. Here, we report that CD103− CD39+ CD8+ T cells from mismatch repair-deficient endometrial tumors are activated and characterized predominantly by expression of TNFRSF9. In vitro, transforming growth factor-beta (TGF-β) drives the disappearance of this subset, likely through the conversion of CD103− CD39+ cells to a CD103+ phenotype. On the transcriptomic level, T cell activation and induction of CD39 was associated with a number of tissue residence and TGF-β responsive transcription factors. Altogether, our data suggest CD39+ CD103− CD8+ tumor-infiltrating T cells are recently activated and likely rapidly differentiate towards tissue residence upon exposure to TGF-β in the tumor micro-environment, explaining their relative paucity in human tumors.
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Affiliation(s)
- Joyce M. Lubbers
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Marta A. Ważyńska
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Nienke van Rooij
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Arjan Kol
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Hagma H. Workel
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Annechien Plat
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Sterre T. Paijens
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Martijn R. Vlaming
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (M.R.V.); (E.B.)
| | - Diana C. J. Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Philip H. Elsinga
- Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Edwin Bremer
- Department of Hematology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (M.R.V.); (E.B.)
| | - Hans W. Nijman
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
| | - Marco de Bruyn
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (J.M.L.); (M.A.W.); (N.v.R.); (A.K.); (H.H.W.); (A.P.); (S.T.P.); (H.W.N.)
- Correspondence:
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2
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van den Berg JH, Heemskerk B, van Rooij N, Gomez-Eerland R, Michels S, van Zon M, de Boer R, Bakker NAM, Jorritsma-Smit A, van Buuren MM, Kvistborg P, Spits H, Schotte R, Mallo H, Karger M, van der Hage JA, Wouters MWJM, Pronk LM, Geukes Foppen MH, Blank CU, Beijnen JH, Nuijen B, Schumacher TN, Haanen JBAG. Tumor infiltrating lymphocytes (TIL) therapy in metastatic melanoma: boosting of neoantigen-specific T cell reactivity and long-term follow-up. J Immunother Cancer 2021; 8:jitc-2020-000848. [PMID: 32753545 PMCID: PMC7406109 DOI: 10.1136/jitc-2020-000848] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Treatment of metastatic melanoma with autologous tumor infiltrating lymphocytes (TILs) is currently applied in several centers. Robust and remarkably consistent overall response rates, of around 50% of treated patients, have been observed across hospitals, including a substantial fraction of durable, complete responses. PURPOSE Execute a phase I/II feasibility study with TIL therapy in metastatic melanoma at the Netherlands Cancer Institute, with the goal to assess feasibility and potential value of a randomized phase III trial. EXPERIMENTAL Ten patients were treated with TIL therapy. Infusion products and peripheral blood samples were phenotypically characterized and neoantigen reactivity was assessed. Here, we present long-term clinical outcome and translational data on neoantigen reactivity of the T cell products. RESULTS Five out of 10 patients, who were all anti-PD-1 naïve at time of treatment, showed an objective clinical response, including two patients with a complete response that are both ongoing for more than 7 years. Immune monitoring demonstrated that neoantigen-specific T cells were detectable in TIL infusion products from three out of three patients analyzed. For six out of the nine neoantigen-specific T cell responses detected in these TIL products, T cell response magnitude increased significantly in the peripheral blood compartment after therapy, and neoantigen-specific T cells were detectable for up to 3 years after TIL infusion. CONCLUSION The clinical results from this study confirm the robustness of TIL therapy in metastatic melanoma and the potential role of neoantigen-specific T cell reactivity. In addition, the data from this study supported the rationale to initiate an ongoing multicenter phase III TIL trial.
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Affiliation(s)
| | - Bianca Heemskerk
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nienke van Rooij
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Raquel Gomez-Eerland
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Samira Michels
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Maaike van Zon
- BioTherapeutics Unit, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Renate de Boer
- BioTherapeutics Unit, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Noor A M Bakker
- BioTherapeutics Unit, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annelies Jorritsma-Smit
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marit M van Buuren
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hergen Spits
- AIMM Therapeutics, Amsterdam, The Netherlands.,Experimental Immunology, Amsterdam University Medical Centres, Amsterdam, Noord-Holland, The Netherlands
| | | | - Henk Mallo
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Matthias Karger
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joris A van der Hage
- Department of Surgery, Leiden Universitair Medisch Centrum, Leiden, Zuid-Holland, The Netherlands
| | - Michel W J M Wouters
- Surgical Oncology, Antoni van Leeuwenhoek Nederlands Kanker Instituut, Amsterdam, The Netherlands.,Dutch Institute for Clinical Auditing, Leiden, The Netherlands
| | - Loes M Pronk
- Department of Biometrics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marnix H Geukes Foppen
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christian U Blank
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, Noord-Holland, The Netherlands
| | - Jos H Beijnen
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht University Department of Pharmaceutical Sciences, Utrecht, Utrecht, The Netherlands
| | - Bastiaan Nuijen
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - John B A G Haanen
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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Kvistborg P, Shu CJ, Heemskerk B, Fankhauser M, Thrue CA, Toebes M, van Rooij N, Linnemann C, van Buuren MM, Urbanus JHM, Beltman JB, Thor Straten P, Li YF, Robbins PF, Besser MJ, Schachter J, Kenter GG, Dudley ME, Rosenberg SA, Haanen JBAG, Hadrup SR, Schumacher TNM. TIL therapy broadens the tumor-reactive CD8(+) T cell compartment in melanoma patients. Oncoimmunology 2021; 1:409-418. [PMID: 22754759 PMCID: PMC3382882 DOI: 10.4161/onci.18851] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
There is strong evidence that both adoptive T cell transfer and T cell checkpoint blockade can lead to regression of human melanoma. However, little data are available on the effect of these cancer therapies on the tumor-reactive T cell compartment. To address this issue we have profiled therapy-induced T cell reactivity against a panel of 145 melanoma-associated CD8(+) T cell epitopes. Using this approach, we demonstrate that individual tumor-infiltrating lymphocyte cell products from melanoma patients contain unique patterns of reactivity against shared melanoma-associated antigens, and that the combined magnitude of these responses is surprisingly low. Importantly, TIL therapy increases the breadth of the tumor-reactive T cell compartment in vivo, and T cell reactivity observed post-therapy can almost in full be explained by the reactivity observed within the matched cell product. These results establish the value of high-throughput monitoring for the analysis of immuno-active therapeutics and suggest that the clinical efficacy of TIL therapy can be enhanced by the preparation of more defined tumor-reactive T cell products.
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Affiliation(s)
- Pia Kvistborg
- The Netherlands Cancer Institute; Department of Immunology; Amsterdam, The Netherlands
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Lubbers JM, Koopman B, de Klerk‐Sluis JM, van Rooij N, Plat A, Pijper H, Koopman T, van Hemel BM, Hollema H, Wisman B, Nijman HW, de Bruyn M. Association of homozygous variants of STING1 with outcome in human cervical cancer. Cancer Sci 2021; 112:61-71. [PMID: 33040406 PMCID: PMC7780010 DOI: 10.1111/cas.14680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 01/04/2023] Open
Abstract
DNA-sensing receptor Cyclic GMP-AMP Synthase (cGAS) and its downstream signaling effector STimulator of INterferon Genes (STING) have gained significant interest in the field of tumor immunology, as a dysfunctional cGAS-STING pathway is associated with poor prognosis and worse response to immunotherapy. However, studies so far have not taken into account the polymorphic nature of the STING-encoding STING1 gene. We hypothesized that the presence of allelic variance in STING1 would cause variation between individuals as to their susceptibility to cancer development, cancer progression, and potential response to (immuno)therapy. To start to address this, we defined the genetic landscapes of STING1 in cervical scrapings and investigated their corresponding clinical characteristics across a unique cohort of cervical cancer patients and compared them with independent control cohorts. Although we did not observe an enrichment of particular STING1 allelic variants in cervical cancer patients, we did find that the occurrence of homozygous variants HAQ/HAQ and R232H/R232H of STING1 were associated with both younger age of diagnosis and higher recurrence rate. These findings were accompanied by worse survival, despite comparable mRNA and protein levels of STING and numbers of infiltrated CD8+ T cells. Our findings suggest that patients with HAQ/HAQ and R232H/R232H genotypes may have a dysfunctional cGAS-STING pathway that fails to promote efficient anticancer immunity. Interestingly, the occurrence of these genotypes coincided with homozygous presence of the V48V variant, which was found to be individually associated with worse outcome. Therefore, we propose V48V to be further evaluated as a novel prognostic marker for cervical cancer.
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Affiliation(s)
- Joyce M. Lubbers
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Bart Koopman
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Jessica M. de Klerk‐Sluis
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Nienke van Rooij
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Annechien Plat
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Harry Pijper
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Timco Koopman
- Department of PathologyPathologie FrieslandLeeuwardenThe Netherlands
| | - Bettien M. van Hemel
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Harry Hollema
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Bea Wisman
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Hans W. Nijman
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Marco de Bruyn
- Department of Obstetrics and GynecologyUniversity of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
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5
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Workel HH, van Rooij N, Plat A, Spierings DC, Fehrmann RSN, Nijman HW, de Bruyn M. Transcriptional Activity and Stability of CD39+CD103+CD8+ T Cells in Human High-Grade Endometrial Cancer. Int J Mol Sci 2020; 21:E3770. [PMID: 32471032 PMCID: PMC7312498 DOI: 10.3390/ijms21113770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Tumor-infiltrating CD8+ T cells (TIL) are of the utmost importance in anti-tumor immunity. CD103 defines tumor-resident memory T cells (TRM cells) associated with improved survival and response to immune checkpoint blockade (ICB) across human tumors. Co-expression of CD39 and CD103 marks tumor-specific TRM with enhanced cytolytic potential, suggesting that CD39+CD103+ TRM could be a suitable biomarker for immunotherapy. However, little is known about the transcriptional activity of TRM cells in situ. We analyzed CD39+CD103+ TRM cells sorted from human high-grade endometrial cancers (n = 3) using mRNA sequencing. Cells remained untreated or were incubated with PMA/ionomycin (activation), actinomycin D (a platinum-like chemotherapeutic that inhibits transcription), or a combination of the two. Resting CD39+CD103+ TRM cells were transcriptionally active and expressed a characteristic TRM signature. Activated CD39+CD103+ TRM cells differentially expressed PLEK, TWNK, and FOS, and cytokine genes IFNG, TNF, IL2, CSF2 (GM-CSF), and IL21. Findings were confirmed using qPCR and cytokine production was validated by flow cytometry of cytotoxic TIL. We studied transcript stability and found that PMA-responsive genes and mitochondrial genes were particularly stable. In conclusion, CD39+CD103+ TRM cells are transcriptionally active TRM cells with a polyfunctional, reactivation-responsive repertoire. Secondly, we hypothesize that differential regulation of transcript stability potentiates rapid responses upon TRM reactivation in tumors.
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Affiliation(s)
- Hagma H. Workel
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Nienke van Rooij
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Annechien Plat
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Rudolf S. N. Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Hans W. Nijman
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
| | - Marco de Bruyn
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (H.H.W.); (N.v.R.); (A.P.); (H.W.N.)
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6
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Kvistborg P, Buuren MMV, Philips D, Rooij NV, Velds A, Behjati S, Braber MVD, Toebes M, Fanchi L, Slagter M, Svane MS, Hwu P, Berg JVD, Stratton M, Blank C, Haanen JB, Kesmir C, Schumacher TN. Abstract B022: Properties of T-cell-recognized neoantigens. Cancer Immunol Res 2019. [DOI: 10.1158/2326-6074.cricimteatiaacr18-b022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Over the past years we have learned that the T-cell-based immune system frequently responds to the neoantigens that arise as a consequence of the accumulated DNA damage causing the malignant transformation. Furthermore, recognition of neoantigens appears an important driver of the clinical activity of both T-cell checkpoint blockade and adoptive T-cell therapy as cancer immunotherapies. From the efforts dissecting the neoantigen-specific T-cell response it has become clear that only a very minor fraction of the accumulated mutations is recognized by the immune system, and the challenge to unravel the neoantigen-specific T-cell response lies in identifying which neoantigens are more likely to be true T-cell epitopes. We have analyzed neoantigen-specific T-cell reactivity in 12 melanoma patients using an in silico epitope prediction pipeline based on RNA expression, predicted HLA binding affinity, proteasomal processing and self-similarity to predict potential neoepitopes. We screened for T-cell recognition of 7000 epitopes from these 12 patients (average ~550 epitopes per patient, range: 96-1902) using our pMHC multimer combinatorial encoding technology and found 19 epitopes to be recognized by T-cells (hits) and 6981 to be “non-hits.” Based on these data we have examined the properties of T-cell recognized neoantigens. An intriguing observation is an enrichment within T-cell recognized epitopes of epitopes with the mutation positioned within the last 4 amino acids (C-terminal end of the peptide) compared to the screened set of epitopes. Fifteen out of 19 hits (approximately 80%) harbored a mutation within the last 4 amino acids of the peptide, whereas within the full set of screen epitopes it is 43%. While it is currently unclear what the reason is for this, this could reflect a biologic importance in T-cell recognition of the C-terminal part of the epitope. Furthermore, RNA expression and predicted binding affinity to HLA are important informative parameters for selecting T-cell recognized epitopes. A striking observation is that predicted binding affinity not only correlates with likelihood of observing a T-cell response but also the magnitude of this T-cell response, suggesting a hierarchy within neoantigens, and that not all neoantigens are of equal immunologic quality. In summary, our findings indicate that T-cell recognized neoantigens may differ from the neoantigen pool not recognized. In particular regarding position of the mutation with the epitope, RNA abundance and predicted HLA binding affinity. Importantly, our data reveal a hierarchy within neoantigens comparable to immunodominance known from viral infections. This hierarchy appears to depend mostly on binding affinity. These observations are likely to be highly relevant when selecting neoantigens for therapeutic manipulation such as vaccines.
Citation Format: Pia Kvistborg, Marit M. van Buuren, Daisy Philips, Nienke van Rooij, Arno Velds, Sam Behjati, Marlous van den Braber, Mireille Toebes, Lorenzo Fanchi, Maarten Slagter, Marie Stentoft Svane, Patrick Hwu, Joost van den Berg, Michael Stratton, Christian Blank, John B.A.G. Haanen, Can Kesmir, Ton N.M. Schumacher. Properties of T-cell-recognized neoantigens [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B022.
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Affiliation(s)
- Pia Kvistborg
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Marit M. van Buuren
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Daisy Philips
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Nienke van Rooij
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Arno Velds
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Sam Behjati
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Marlous van den Braber
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Mireille Toebes
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Lorenzo Fanchi
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Maarten Slagter
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Marie Stentoft Svane
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Patrick Hwu
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Joost van den Berg
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Michael Stratton
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Christian Blank
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - John B.A.G. Haanen
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Can Kesmir
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
| | - Ton N.M. Schumacher
- The Netherlands Cancer Institute, Amsterdam, The Netherlands; Neon Therapeutics, Boston, MA; UMCG, Groningen, The Netherlands; Wellcome Sander Institute, Cambridgeshire, United Kingdom; Center for Cancer Immune Therapy/Herlev University Hospital, Herlev, Denmark; MD Anderson Cancer Center, Houston, TX; Utrecht University, Utrecht, The Netherlands
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7
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Dijkstra KK, Cattaneo CM, Weeber F, Chalabi M, van de Haar J, Fanchi LF, Slagter M, van der Velden DL, Kaing S, Kelderman S, van Rooij N, van Leerdam ME, Depla A, Smit EF, Hartemink KJ, de Groot R, Wolkers MC, Sachs N, Snaebjornsson P, Monkhorst K, Haanen J, Clevers H, Schumacher TN, Voest EE. Generation of Tumor-Reactive T Cells by Co-culture of Peripheral Blood Lymphocytes and Tumor Organoids. Cell 2018; 174:1586-1598.e12. [PMID: 30100188 DOI: 10.1016/j.cell.2018.07.009] [Citation(s) in RCA: 565] [Impact Index Per Article: 94.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 05/24/2018] [Accepted: 07/05/2018] [Indexed: 02/07/2023]
Abstract
Cancer immunotherapies have shown substantial clinical activity for a subset of patients with epithelial cancers. Still, technological platforms to study cancer T-cell interactions for individual patients and understand determinants of responsiveness are presently lacking. Here, we establish and validate a platform to induce and analyze tumor-specific T cell responses to epithelial cancers in a personalized manner. We demonstrate that co-cultures of autologous tumor organoids and peripheral blood lymphocytes can be used to enrich tumor-reactive T cells from peripheral blood of patients with mismatch repair-deficient colorectal cancer and non-small-cell lung cancer. Furthermore, we demonstrate that these T cells can be used to assess the efficiency of killing of matched tumor organoids. This platform provides an unbiased strategy for the isolation of tumor-reactive T cells and provides a means by which to assess the sensitivity of tumor cells to T cell-mediated attack at the level of the individual patient.
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Affiliation(s)
- Krijn K Dijkstra
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Chiara M Cattaneo
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Fleur Weeber
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Myriam Chalabi
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands; Department of Gastroenterologic Oncology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Joris van de Haar
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Lorenzo F Fanchi
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Maarten Slagter
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Daphne L van der Velden
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Sovann Kaing
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Sander Kelderman
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Nienke van Rooij
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Monique E van Leerdam
- Department of Gastroenterologic Oncology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Annekatrien Depla
- Department of Gastroenterology and Hepatology, EC Slotervaart Hospital, 1066 CX Amsterdam, the Netherlands
| | - Egbert F Smit
- Department of Thoracic Oncology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Koen J Hartemink
- Department of Surgery, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Rosa de Groot
- Department of Hematopoeisis, Sanquin Research, 1066 CX Amsterdam, the Netherlands
| | - Monika C Wolkers
- Department of Hematopoeisis, Sanquin Research, 1066 CX Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Norman Sachs
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Petur Snaebjornsson
- Department of Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - John Haanen
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands
| | - Emile E Voest
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands.
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8
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Strønen E, Toebes M, Kelderman S, van Buuren MM, Yang W, van Rooij N, Donia M, Böschen ML, Lund-Johansen F, Olweus J, Schumacher TN. Targeting of cancer neoantigens with donor-derived T cell receptor repertoires. Science 2016; 352:1337-41. [PMID: 27198675 DOI: 10.1126/science.aaf2288] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 05/04/2016] [Indexed: 12/14/2022]
Abstract
Accumulating evidence suggests that clinically efficacious cancer immunotherapies are driven by T cell reactivity against DNA mutation-derived neoantigens. However, among the large number of predicted neoantigens, only a minority is recognized by autologous patient T cells, and strategies to broaden neoantigen-specific T cell responses are therefore attractive. We found that naïve T cell repertoires of healthy blood donors provide a source of neoantigen-specific T cells, responding to 11 of 57 predicted human leukocyte antigen (HLA)-A*02:01-binding epitopes from three patients. Many of the T cell reactivities involved epitopes that in vivo were neglected by patient autologous tumor-infiltrating lymphocytes. Finally, T cells redirected with T cell receptors identified from donor-derived T cells efficiently recognized patient-derived melanoma cells harboring the relevant mutations, providing a rationale for the use of such "outsourced" immune responses in cancer immunotherapy.
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Affiliation(s)
- Erlend Strønen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway. K. G. Jebsen Centers for Cancer Immunotherapy and for Inflammation Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Mireille Toebes
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sander Kelderman
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marit M van Buuren
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Weiwen Yang
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway. K. G. Jebsen Centers for Cancer Immunotherapy and for Inflammation Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Nienke van Rooij
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marco Donia
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Maxi-Lu Böschen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway. K. G. Jebsen Centers for Cancer Immunotherapy and for Inflammation Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Fridtjof Lund-Johansen
- K. G. Jebsen Centers for Cancer Immunotherapy and for Inflammation Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. Department of Immunology and Transfusion Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Johanna Olweus
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway. K. G. Jebsen Centers for Cancer Immunotherapy and for Inflammation Research, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Ton N Schumacher
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.
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9
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Kelderman S, Heemskerk B, Fanchi L, Philips D, Toebes M, Kvistborg P, van Buuren MM, van Rooij N, Michels S, Germeroth L, Haanen JBAG, Schumacher NM. Antigen-specific TIL therapy for melanoma: A flexible platform for personalized cancer immunotherapy. Eur J Immunol 2016; 46:1351-60. [DOI: 10.1002/eji.201545849] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 02/01/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Sander Kelderman
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Bianca Heemskerk
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Lorenzo Fanchi
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Daisy Philips
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Mireille Toebes
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Pia Kvistborg
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Marit M. van Buuren
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Nienke van Rooij
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - Samira Michels
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | | | - John B. A. G. Haanen
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
| | - N. M. Schumacher
- Division of Immunology; The Netherlands Cancer Institute; Amsterdam The Netherlands
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10
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Beltman JB, Urbanus J, Velds A, van Rooij N, Rohr JC, Naik SH, Schumacher TN. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. BMC Bioinformatics 2016; 17:151. [PMID: 27038897 PMCID: PMC4818877 DOI: 10.1186/s12859-016-0999-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Results Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences. Conclusions Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0999-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joost B Beltman
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC, Leiden, The Netherlands.
| | - Jos Urbanus
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Nienke van Rooij
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jan C Rohr
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Shalin H Naik
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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11
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Gomez-Eerland R, Nuijen B, Heemskerk B, van Rooij N, van den Berg JH, Beijnen JH, Uckert W, Kvistborg P, Schumacher TN, Haanen JBAG, Jorritsma A. Manufacture of gene-modified human T-cells with a memory stem/central memory phenotype. Hum Gene Ther Methods 2014; 25:277-87. [PMID: 25143008 DOI: 10.1089/hgtb.2014.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Advances in genetic engineering have made it possible to generate human T-cell products that carry desired functionalities, such as the ability to recognize cancer cells. The currently used strategies for the generation of gene-modified T-cell products lead to highly differentiated cells within the infusion product, and on the basis of data obtained in preclinical models, this is likely to impact the efficacy of these products. We set out to develop a good manufacturing practice (GMP) protocol that yields T-cell receptor (TCR) gene-modified T-cells with more favorable properties for clinical application. Here, we show the robust clinical-scale production of human peripheral blood T-cells with an early memory phenotype that express a MART-1-specific TCR. By combining selection and stimulation using anti-CD3/CD28 beads for retroviral transduction, followed by expansion in the presence of IL-7 and IL-15, production of a well-defined clinical-scale TCR gene-modified T-cell product could be achieved. A major fraction of the T-cells generated in this fashion were shown to coexpress CD62L and CD45RA, and express CD27 and CD28, indicating a central memory or memory stemlike phenotype. Furthermore, these cells produced IFNγ, TNFα, and IL-2 and displayed cytolytic activity against target cells expressing the relevant antigen. The T-cell products manufactured by this robust and validated GMP production process are now undergoing testing in a phase I/IIa clinical trial in HLA-A*02:01 MART-1-positive advanced stage melanoma patients. To our knowledge, this is the first clinical trial protocol in which the combination of IL-7 and IL-15 has been applied for the generation of gene-modified T-cell products.
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Affiliation(s)
- Raquel Gomez-Eerland
- 1 Division of Immunology, The Netherlands Cancer Institute , 1066 CX Amsterdam, The Netherlands
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12
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Kelderman S, Heemskerk B, Toebes M, van Buuren M, van Rooij N, Bies L, Fanchi L, Germeroth L, Kvistborg P, Schumacher T. Antigen-specific TIL therapy for melanoma: a flexible platform for personalized cancer immunotherapy. J Immunother Cancer 2013. [PMCID: PMC3990297 DOI: 10.1186/2051-1426-1-s1-p19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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van Rooij N, van Buuren MM, Philips D, Velds A, Toebes M, Heemskerk B, van Dijk LJA, Behjati S, Hilkmann H, El Atmioui D, Nieuwland M, Stratton MR, Kerkhoven RM, Kesmir C, Haanen JB, Kvistborg P, Schumacher TN. Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma. J Clin Oncol 2013; 31:e439-42. [PMID: 24043743 DOI: 10.1200/jco.2012.47.7521] [Citation(s) in RCA: 660] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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14
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Naik S, Perie L, Zwart E, Gerlach C, van Rooij N, de Boer R, Schumacher T. Diverse and heritable lineage imprinting of early hematopoietic progenitors. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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van Rooij N, Haanen JBAG, van Buren M, Philips D, Toebes M, Heemskerk B, van Dijk L, Behjati S, Stratton MR, Kerkhoven RM, Kesmir C, Kvistborg P, Schumacher T. Use of tumor exome analysis to reveal neo-antigen-specific T-cell reactivity in ipilimumab-responsive melanoma. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.9085] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9085 Background: Evidence for T cell mediated regression of human cancer in particular melanoma following immunotherapy is strong. Anti-CTLA4 treatment has been approved for treatment of metastatic melanoma and blockade of PD-1 has shown encouraging results. However, it is unknown which T cell reactivities are involved in cancer regression. Reactivity against non-mutated tumor self-antigens has been analyzed in patients treated with Ipilimumab or with autologous TILs, but the size of these responses are modest. Therefore, T cell recognition of patient-specific mutant epitopes may be a potentially important component. Animal model data recently suggested that analysis of T cell reactivity against patient-specific neo-antigens may be feasible through exploitation of cancer genome data. However, human data have thus far been lacking. Methods: To address this we have used MHC class I peptide exchange technology allowing production of very large collections of pMHC complexes, together with a pMHC "combinatorial coding" strategy for parallel detection of dozens of different T cell populations within a single sample. Results: From a melanoma patient responding to ipilimumab treatment, we identified tumor specific mutations via exome sequencing of tumor material. The exome contained 1,075 non-synonymous mutations. Possible MHC epitopes covering these mutations were predicted based on; 1) predicted to bind the patient’s MHC; 2) predicted to be cleaved by the proteasome; 3) genes of which the mutated peptides arose had evidence of RNA expression. The analysis yielded 1,952 epitopes restricted to the HLA-A and HLA-B. To screen for T cell reactivity against these epitopes we used the pMHC combinatorial coding approach. We found T cell reactivity against 2 neo-antigens, including a dominant T cell response against a mutant epitope of the ATR gene product. Analysis of PBMC samples collected before and during Ipilimumab therapy showed that this particular response increased strongly after treatment from 0.06% to 0.28% of CD8 T cells after being stable in magnitude for 10 months. Conclusions: These data provide the first demonstration of cancer exome-guided analysis to dissect the effects of melanoma immunotherapy.
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Affiliation(s)
- Nienke van Rooij
- The Netherlands Cancer Institute-Antoni Van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - John B. A. G. Haanen
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Marit van Buren
- The Netherlands Cancer Institute-Antoni Van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Daisy Philips
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mireille Toebes
- The Netherlands Cancer Institute-Antoni Van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Bianca Heemskerk
- The Netherlands Cancer Institute-Antoni Van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Laura van Dijk
- The Netherlands Cancer Institute-Antoni Van Leeuwenhoek Hospital, Amsterdam, Netherlands
| | - Sam Behjati
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Ron M Kerkhoven
- Netherlands Cancer Institute (NKI-AVL), Amsterdam, Netherlands
| | - Can Kesmir
- Utrecht University, Utrecht, Netherlands
| | - Pia Kvistborg
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ton Schumacher
- The Netherlands Cancer Institute-Antoni Van Leeuwenhoek Hospital, Amsterdam, Netherlands
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16
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Gerlach C, Rohr JC, Perié L, van Rooij N, van Heijst JWJ, Velds A, Urbanus J, Naik SH, Jacobs H, Beltman JB, de Boer RJ, Schumacher TNM. Heterogeneous differentiation patterns of individual CD8+ T cells. Science 2013; 340:635-9. [PMID: 23493421 DOI: 10.1126/science.1235487] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Upon infection, antigen-specific CD8(+) T lymphocyte responses display a highly reproducible pattern of expansion and contraction that is thought to reflect a uniform behavior of individual cells. We tracked the progeny of individual mouse CD8(+) T cells by in vivo lineage tracing and demonstrated that, even for T cells bearing identical T cell receptors, both clonal expansion and differentiation patterns are heterogeneous. As a consequence, individual naïve T lymphocytes contributed differentially to short- and long-term protection, as revealed by participation of their progeny during primary versus recall infections. The discordance in fate of individual naïve T cells argues against asymmetric division as a singular driver of CD8(+) T cell heterogeneity and demonstrates that reproducibility of CD8(+) T cell responses is achieved through population averaging.
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Affiliation(s)
- Carmen Gerlach
- Division of Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
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17
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Gerlach C, Rohr J, Perié L, van Heijst J, van Rooij N, Velds A, Urbanus J, Hauptmann M, Jacobs H, de Boer R, Schumacher T. The CD8+ T cell response to infection is dominated by the progeny of few naïve T cells (110.12). The Journal of Immunology 2012. [DOI: 10.4049/jimmunol.188.supp.110.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Following infection, antigen-specific CD8+ T cell numbers increase dramatically. Analysis of antigen-specific T cell responses at the bulk cell level has provided insight into the average number of cell divisions that T cells undergo upon activation. However, it is unclear whether all naïve T cells of a given affinity for antigen produce equal numbers of progeny, or whether the total effector T cell pool is predominantly created by the output of few. To quantify how many daughter cells individual naïve T cells produce, we have generated naïve OT-I T cells harboring unique genetic tags (barcodes) and have measured the number of progeny per labeled cell by second-generation sequencing of barcode sequences after infection. Our data reveal that upon infection, individual OT-I T cells that are recruited into the response produce highly variable numbers of daughter cells. These data indicate that the bulk of pathogen protection provided by an antigen-specific T cell response is due to the progeny of only a handful of cells.
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Affiliation(s)
- Carmen Gerlach
- 1Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jan Rohr
- 1Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Leila Perié
- 1Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
- 4Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | | | - Nienke van Rooij
- 1Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Arno Velds
- 2Deep sequencing Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jos Urbanus
- 1Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Michael Hauptmann
- 3Bioinformatics and Statistics group, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Heinz Jacobs
- 1Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rob de Boer
- 4Theoretical Biology, Utrecht University, Utrecht, Netherlands
| | - Ton Schumacher
- 1Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
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