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Manfredi F, Stasi L, Buonanno S, Marzuttini F, Noviello M, Mastaglio S, Abbati D, Potenza A, Balestrieri C, Cianciotti BC, Tassi E, Feola S, Toffalori C, Punta M, Magnani Z, Camisa B, Tiziano E, Lupo-Stanghellini MT, Branca RM, Lehtiö J, Sikanen TM, Haapala MJ, Cerullo V, Casucci M, Vago L, Ciceri F, Bonini C, Ruggiero E. Harnessing T cell exhaustion and trogocytosis to isolate patient-derived tumor-specific TCR. Sci Adv 2023; 9:eadg8014. [PMID: 38039364 PMCID: PMC10691777 DOI: 10.1126/sciadv.adg8014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/02/2023] [Indexed: 12/03/2023]
Abstract
To study and then harness the tumor-specific T cell dynamics after allogeneic hematopoietic stem cell transplant, we typed the frequency, phenotype, and function of lymphocytes directed against tumor-associated antigens (TAAs) in 39 consecutive transplanted patients, for 1 year after transplant. We showed that TAA-specific T cells circulated in 90% of patients but display a limited effector function associated to an exhaustion phenotype, particularly in the subgroup of patients deemed to relapse, where exhausted stem cell memory T cells accumulated. Accordingly, cancer-specific cytolytic functions were relevant only when the TAA-specific T cell receptors (TCRs) were transferred into healthy, genome-edited T cells. We then exploited trogocytosis and ligandome-on-chip technology to unveil the specificities of tumor-specific TCRs retrieved from the exhausted T cell pool. Overall, we showed that harnessing circulating TAA-specific and exhausted T cells allow to isolate TCRs against TAAs and previously not described acute myeloid leukemia antigens, potentially relevant for T cell-based cancer immunotherapy.
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Affiliation(s)
- Francesco Manfredi
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Lorena Stasi
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Silvia Buonanno
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Francesca Marzuttini
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Maddalena Noviello
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Sara Mastaglio
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
| | - Danilo Abbati
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Alessia Potenza
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Chiara Balestrieri
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milan 20132, Italy
| | - Beatrice Claudia Cianciotti
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Elena Tassi
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Sara Feola
- University of Helsinki, ImmunoVirotherapy Lab, Yliopistonkatu 4, 00100 Helsinki, Finland
| | - Cristina Toffalori
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Unit of Immunogenetics, Leukemia Genomics and Immunobiology, via Olgettina 60, Milan 20132, Italy
| | - Marco Punta
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Unit of Immunogenetics, Leukemia Genomics and Immunobiology, via Olgettina 60, Milan 20132, Italy
| | - Zulma Magnani
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Barbara Camisa
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Elena Tiziano
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
| | - Maria Teresa Lupo-Stanghellini
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
| | - Rui Mamede Branca
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, 171 65 Solna, Sweden
| | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, 171 65 Solna, Sweden
| | - Tiina M. Sikanen
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Chemistry and Technology, Helsinki University,, Viikinkaari 5E, 00014 Helsinki, Finland
| | - Markus J. Haapala
- Drug Research Program, Faculty of Pharmacy, Division of Pharmaceutical Chemistry and Technology, Helsinki University,, Viikinkaari 5E, 00014 Helsinki, Finland
| | - Vincenzo Cerullo
- University of Helsinki, ImmunoVirotherapy Lab, Yliopistonkatu 4, 00100 Helsinki, Finland
| | - Monica Casucci
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Innovative Immunotherapies Unit, via Olgettina 60, Milan 20132, Italy
| | - Luca Vago
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Unit of Immunogenetics, Leukemia Genomics and Immunobiology, via Olgettina 60, Milan 20132, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Fabio Ciceri
- IRCCS San Raffaele Scientific Institute, Hematology and Hematopoietic Stem Cell Transplantation Unit, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Innovative Immunotherapies Unit, via Olgettina 60, Milan 20132, Italy
| | - Chiara Bonini
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation and Infectious Disease, Innovative Immunotherapies Unit, via Olgettina 60, Milan 20132, Italy
| | - Eliana Ruggiero
- IRCCS San Raffaele Scientific Institute, Division of Immunology, Transplantation, and Infectious Diseases, Experimental Hematology Unit, via Olgettina 60, Milan 20132, Italy
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Potenza A, Balestrieri C, Spiga M, Albarello L, Pedica F, Manfredi F, Cianciotti BC, De Lalla C, Botrugno OA, Faccani C, Stasi L, Tassi E, Bonfiglio S, Scotti GM, Redegalli M, Biancolini D, Camisa B, Tiziano E, Sirini C, Casucci M, Iozzi C, Abbati D, Simeoni F, Lazarevic D, Elmore U, Fiorentini G, Di Lullo G, Casorati G, Doglioni C, Tonon G, Dellabona P, Rosati R, Aldrighetti L, Ruggiero E, Bonini C. Revealing and harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells. Gut 2023; 72:1887-1903. [PMID: 37399271 DOI: 10.1136/gutjnl-2022-328042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/02/2023] [Indexed: 07/05/2023]
Abstract
OBJECTIVE Colorectal tumours are often densely infiltrated by immune cells that have a role in surveillance and modulation of tumour progression but are burdened by immunosuppressive signals, which might vary from primary to metastatic stages. Here, we deployed a multidimensional approach to unravel the T-cell functional landscape in primary colorectal cancers (CRC) and liver metastases, and genome editing tools to develop CRC-specific engineered T cells. DESIGN We paired high-dimensional flow cytometry, RNA sequencing and immunohistochemistry to describe the functional phenotype of T cells from healthy and neoplastic tissue of patients with primary and metastatic CRC and we applied lentiviral vectors (LV) and CRISPR/Cas9 genome editing technologies to develop CRC-specific cellular products. RESULTS We found that T cells are mainly localised at the front edge and that tumor-infiltrating T cells co-express multiple inhibitory receptors, which largely differ from primary to metastatic sites. Our data highlighted CD39 as the major driver of exhaustion in both primary and metastatic colorectal tumours. We thus simultaneously redirected T-cell specificity employing a novel T-cell receptor targeting HER-2 and disrupted the endogenous TCR genes (TCR editing (TCRED)) and the CD39 encoding gene (ENTPD1), thus generating TCREDENTPD1KOHER-2-redirected lymphocytes. We showed that the absence of CD39 confers to HER-2-specific T cells a functional advantage in eliminating HER-2+ patient-derived organoids in vitro and in vivo. CONCLUSION HER-2-specific CD39 disrupted engineered T cells are promising advanced medicinal products for primary and metastatic CRC.
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Affiliation(s)
- Alessia Potenza
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Balestrieri
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martina Spiga
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Albarello
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Pedica
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Manfredi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Claudia De Lalla
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Cristina Faccani
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lorena Stasi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elena Tassi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Bonfiglio
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Maria Scotti
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Miriam Redegalli
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Donatella Biancolini
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Camisa
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elena Tiziano
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Sirini
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monica Casucci
- Innovative Immunotherapies Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Iozzi
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Danilo Abbati
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Simeoni
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dejan Lazarevic
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ugo Elmore
- Gastrointestinal Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Guido Fiorentini
- Gastrointestinal Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Di Lullo
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Casorati
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Doglioni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Functional Genomics of Cancer Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Paolo Dellabona
- Experimental Immunology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Riccardo Rosati
- Vita-Salute San Raffaele University, Milan, Italy
- Gastrointestinal Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luca Aldrighetti
- Vita-Salute San Raffaele University, Milan, Italy
- Hepatobiliary Surgery Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eliana Ruggiero
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Bonini
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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3
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Potenza A, Balestrieri C, Albarello L, Pedica F, Spiga M, Manfredi F, Cianciotti BC, De Lalla C, Stasi L, Tassi E, Bonfiglio S, Scotti GM, Redegalli M, Biancolini D, Abbati D, Simeoni F, Lazarevic D, Elmore U, Fiorentini G, Lullo GD, Casorati G, Doglioni C, Tonon G, Dellabona P, Rosati R, Aldrighetti L, Ruggiero E, Bonini C. Abstract 902: Harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-902] [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: 04/07/2023]
Abstract
Abstract
Colorectal cancer (CRC) is the 2nd cause of cancer-related death. Standard therapies often fail, with more than 50% of patients experiencing relapse, eventually with metastatic disease. Colorectal tumors are densely infiltrated by immune cells that have a role in surveillance and modulation of tumor progression. However, exhaustion mechanisms acting within the tumor microenvironment impede their functional capacity against tumor cells. We paired high-dimensional flow cytometry, RNA sequencing, immunohistochemistry and immunofluorescence to describe the T cell functional landscape in tumor and peritumoral tissues from primary colorectal cancers and liver metastases. Analysis of the healthy, peritumoral and neoplastic tissues of treatment-naïve primary CRCs and of the peritumoral and tumoral tissues of CRC patients undergoing surgery for liver metastasis, revealed extensive transcriptional and spatial remodeling across tumors, being metabolic pathways among the major drivers of this variance. Regarding the immune infiltrate, we found that T cells are mainly localized at the front edge and that tumor-infiltrating T cells co-express multiple inhibitory receptors. Unsupervised analysis of flow cytometry data performed by an advanced pipeline of data handling by dimensionality reduction and clustering algorithms allowed the definition of a peculiar inhibitory receptors signature in TILs enriched both in primary CRCs and liver metastases. Among the highly co-expressed inhibitory receptors, CD39 was found to represent the major driver of exhaustion in both primary and metastatic colorectal tumors. CD39 is a diphosphohydrolase converting ATP into AMP that is emerging as exhaustion marker for tumor-specific T cells, thus highlighting its relevance as molecular target for T cells engineering. We leveraged on these findings to generate a novel cellular product for the adoptive cell therapy of CRC. By CRISPR/Cas9 genome editing tools, we simultaneously redirected T cell specificity by disrupting the alpha and beta genes of the endogenous T cell receptor with 90% efficiency for both genes, and disrupted CD39 with 100% efficiency, generating triple-knockout engineered lymphocytes. By lentiviral transduction, we redirected the specificity of our engineered T cell product employing a novel T-cell receptor targeting the HER-2 antigen. Triple-edited, HER2-redirected T cells were challenged in vitro against HER2+ patient-derived organoids from liver metastases (mPDOs). Measurement of Cas3/7 displayed a functional advantage for CD39-disrupted, HER2-redirected T cells in recognizing and killing mPDOs. We then evaluated the efficacy of our T cell product in two different in vivo models: subcutaneous injection of mPDOs, and intra-hepatic injection of mPDOs. In both models, CD39-disrupted, HER2-redirected T cells displayed a superior capacity of controlling tumor outgrowth long term.
Citation Format: Alessia Potenza, Chiara Balestrieri, Luca Albarello, Federica Pedica, Martina Spiga, Francesco Manfredi, Beatrice C. Cianciotti, Claudia De Lalla, Lorena Stasi, Elena Tassi, Silvia Bonfiglio, Giulia M. Scotti, Miriam Redegalli, Donatella Biancolini, Danilo Abbati, Fabio Simeoni, Dejan Lazarevic, Ugo Elmore, Guido Fiorentini, Giulia Di Lullo, Giulia Casorati, Claudio Doglioni, Giovanni Tonon, Paolo Dellabona, Riccardo Rosati, Luca Aldrighetti, Eliana Ruggiero, Chiara Bonini. Harnessing CD39 for the treatment of colorectal cancer and liver metastases by engineered T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 902.
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Affiliation(s)
| | | | | | | | - Martina Spiga
- 1IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | | | - Lorena Stasi
- 1IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elena Tassi
- 1IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | | | | | - Danilo Abbati
- 1IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Simeoni
- 1IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Ugo Elmore
- 1IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | | | | | | | | | | | | | | | - Chiara Bonini
- 1IRCCS San Raffaele Scientific Institute, Milan, Italy
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4
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Potenza A, Balestrieri C, Albarello L, Pedica F, Stasi L, Manfredi F, Spiga M, Tassi E, Cianciotti BC, Abbati D, Elmore U, Biondi A, Aldrighetti L, De Lalla C, Lullo GD, Dellabona P, Ruggiero E, Rosati R, Bonini C. Abstract 567: CRISPR/Cas9-mediated CD39 disruption can be combined with TCR editing in T cells to improve the adoptive T cell therapy of colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-567] [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
Colorectal cancer (CRC) is the 2nd cause of cancer-related death. Despite standard therapies, more than 50% of patients experience relapse, eventually with metastatic disease. The CRC microenvironment is densely infiltrated by T-cells, which presence correlates with improved overall survival, thus sustaining the rational for immunotherapy. Here, we paired high-dimensional flow cytometry, bulk RNA sequencing and immunohistochemistry to describe the phenotype and the exhaustion status of T-cells infiltrating primary and metastatic CRC. Analysis of the healthy, peritumoral and neoplastic tissues of treatment-naïve primary CRCs and of the peritumoral and tumoral tissues of CRC patients undergoing surgery for liver metastasis, revealed extensive transcriptional and spatial remodeling across tumors. Unsupervised analysis of flow cytometry data performed by an advanced pipeline of data handling by dimensionality reduction and clustering algorithms allowed the definition of a peculiar inhibitory receptors signature on TILs enriched both in primary CRCs and liver metastases. Of note, CD39 was upregulated in both the signatures retrieved from primary and metastatic CRC, thus suggesting its relevance as molecular target for T-cells engineering. By CRISPR/Cas9 we disrupted the CD39 gene in T cells with >80% efficiency. We combined CD39 knock-out with the genetic disruption of alpha and beta chains of the endogenous TCR, observing >90% efficiency for both genes, thus generating triple-knockout T-cells. By repetitively stimulating healthy donors’ peripheral blood mononuclear cells with autologous antigen-presenting cells loaded with a pool of peptides selected to be immunogenic and expressed by CRC, we obtained a library of anti-tumor TCRs to redirected the specificity of triple knock-out lymphocytes. Our preliminary experiments showed a functional advantage for TCR-redirected, CD39 disrupted T-cells in recognizing and killing CRC target cells.
Citation Format: Alessia Potenza, Chiara Balestrieri, Luca Albarello, Federica Pedica, Lorena Stasi, Francesco Manfredi, Martina Spiga, Elena Tassi, Beatrice Claudia Cianciotti, Danilo Abbati, Ugo Elmore, Andrea Biondi, Luca Aldrighetti, Claudia De Lalla, Giulia Di Lullo, Paolo Dellabona, Eliana Ruggiero, Riccardo Rosati, Chiara Bonini. CRISPR/Cas9-mediated CD39 disruption can be combined with TCR editing in T cells to improve the adoptive T cell therapy of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 567.
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Affiliation(s)
| | | | | | | | - Lorena Stasi
- 1San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Elena Tassi
- 1San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Ugo Elmore
- 1San Raffaele Scientific Institute, Milan, Italy
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5
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Ruggiero E, Carnevale E, Prodeus A, Magnani ZI, Camisa B, Merelli I, Politano C, Stasi L, Potenza A, Cianciotti BC, Manfredi F, Di Bono M, Vago L, Tassara M, Mastaglio S, Ponzoni M, Sanvito F, Liu D, Balwani I, Galli R, Genua M, Ostuni R, Doglio M, O'Connell D, Dutta I, Yazinski SA, McKee M, Arredouani MS, Schultes B, Ciceri F, Bonini C. CRISPR-based gene disruption and integration of high-avidity, WT1-specific T cell receptors improve antitumor T cell function. Sci Transl Med 2022; 14:eabg8027. [PMID: 35138911 DOI: 10.1126/scitranslmed.abg8027] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
T cell receptor (TCR)-based therapy has the potential to induce durable clinical responses in patients with cancer by targeting intracellular tumor antigens with high sensitivity and by promoting T cell survival. However, the need for TCRs specific for shared oncogenic antigens and the need for manufacturing protocols able to redirect T cell specificity while preserving T cell fitness remain limiting factors. By longitudinal monitoring of T cell functionality and dynamics in 15 healthy donors, we isolated 19 TCRs specific for Wilms' tumor antigen 1 (WT1), which is overexpressed by several tumor types. TCRs recognized several peptides restricted by common human leukocyte antigen (HLA) alleles and displayed a wide range of functional avidities. We selected five high-avidity HLA-A*02:01-restricted TCRs, three that were specific to the less explored immunodominant WT137-45 and two that were specific to the noncanonical WT1-78-64 epitopes, both naturally processed by primary acute myeloid leukemia (AML) blasts. With CRISPR-Cas9 genome editing tools, we combined TCR-targeted integration into the TCR α constant (TRAC) locus with TCR β constant (TRBC) knockout, thus avoiding TCRαβ mispairing and maximizing TCR expression and function. The engineered lymphocytes were enriched in memory stem T cells. A unique WT137-45-specific TCR showed antigen-specific responses and efficiently killed AML blasts, acute lymphoblastic leukemia blasts, and glioblastoma cells in vitro and in vivo in the absence of off-tumor toxicity. T cells engineered to express this receptor are being advanced into clinical development for AML immunotherapy and represent a candidate therapy for other WT1-expressing tumors.
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Affiliation(s)
- Eliana Ruggiero
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Erica Carnevale
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Zulma Irene Magnani
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Barbara Camisa
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy.,National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Claudia Politano
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Lorena Stasi
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Alessia Potenza
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy.,School of Medicine and Surgery, Milano-Bicocca University, 20126 Milan, Italy
| | - Beatrice Claudia Cianciotti
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Francesco Manfredi
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy.,Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Mattia Di Bono
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Luca Vago
- Immunogenetics, Leukemia Genomics and Immunobiology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy.,Hematology and Bone Marrow Transplantation Unit, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Michela Tassara
- Immunohematology and Transfusion Medicine Unit, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sara Mastaglio
- Hematology and Bone Marrow Transplantation Unit, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maurilio Ponzoni
- Vita-Salute San Raffaele University, 20132 Milan, Italy.,Pathology Unit, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Francesca Sanvito
- Pathology Unit, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Dai Liu
- Intellia Therapeutics, Cambridge, MA 02139, USA
| | | | - Rossella Galli
- Neural Stem Cell Biology Unit, Division of Neurosciences, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Marco Genua
- Genomics of the Innate Immune System Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Renato Ostuni
- Vita-Salute San Raffaele University, 20132 Milan, Italy.,Genomics of the Innate Immune System Unit, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Matteo Doglio
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Ivy Dutta
- Intellia Therapeutics, Cambridge, MA 02139, USA
| | | | - Mark McKee
- Intellia Therapeutics, Cambridge, MA 02139, USA
| | | | | | - Fabio Ciceri
- Vita-Salute San Raffaele University, 20132 Milan, Italy.,Hematology and Bone Marrow Transplantation Unit, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Chiara Bonini
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy.,Vita-Salute San Raffaele University, 20132 Milan, Italy
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6
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Manfredi F, Abbati D, Cianciotti BC, Stasi L, Potenza A, Ruggiero E, Magnani Z, Carnevale E, Doglio M, Noviello M, Tassi E, Balestrieri C, Buonanno S, Clemente F, De Lalla C, Protti MP, Mondino A, Casorati G, Dellabona P, Bonini C. Flow cytometry data mining by cytoChain identifies determinants of exhaustion and stemness in TCR-engineered T cells. Eur J Immunol 2021; 51:1992-2005. [PMID: 34081326 DOI: 10.1002/eji.202049103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/03/2020] [Revised: 04/09/2021] [Accepted: 05/31/2021] [Indexed: 12/17/2022]
Abstract
The phenotype of infused cells is a major determinant of Adoptive T-cell therapy (ACT) efficacy. Yet, the difficulty in deciphering multiparametric cytometry data limited the fine characterization of cellular products. To allow the analysis of dynamic and complex flow cytometry samples, we developed cytoChain, a novel dataset mining tool and a new analytical workflow. CytoChain was challenged to compare state-of-the-art and innovative culture conditions to generate stem-like memory cells (TSCM ) suitable for ACT. Noticeably, the combination of IL-7/15 and superoxides scavenging sustained the emergence of a previously unidentified nonexhausted Fit-TSCM signature, overlooked by manual gating and endowed with superior expansion potential. CytoChain proficiently traced back this population in independent datasets, and in T-cell receptor engineered lymphocytes. CytoChain flexibility and function were then further validated on a published dataset from circulating T cells in COVID-19 patients. Collectively, our results support the use of cytoChain to identify novel, functionally critical immunophenotypes for ACT and patients immunomonitoring.
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Affiliation(s)
- Francesco Manfredi
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
| | - Danilo Abbati
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | | | - Lorena Stasi
- Vita Salute San Raffaele University, Milan, Italy
| | - Alessia Potenza
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy.,School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Eliana Ruggiero
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Zulma Magnani
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Erica Carnevale
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Doglio
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
| | - Maddalena Noviello
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Elena Tassi
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Balestrieri
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Buonanno
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy
| | | | - Claudia De Lalla
- Experimental Immunology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Maria Pia Protti
- Tumor Immunology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Anna Mondino
- Lymphocyte Activation Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Casorati
- Experimental Immunology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Dellabona
- Experimental Immunology Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Bonini
- Experimental Hematology Unit, San Raffaele Scientific Institute, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
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