Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures
Background:T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and...
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creator | li, zhilang Ma, Lisha Gao, Zhaoya Wang, Xiya Che, Xuan Zhang, Pengchong Li, Yixian Bai, Yun Deng, Hongkui |
description | Background:T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and many tumor neoantigens are derive from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently need.Methods:In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulating of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot (ELISPOT) assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxic of TCRs were confirmed by transferring to primary peripheral blood T cells.Results: The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumors, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner.Conclusions: The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes (TILs) of patients with colorectal cancer (CRC), and tumor-specific TCRs can potentially be used for personalized TCR-Ts therapy. |
doi_str_mv | 10.6084/m9.figshare.25422793 |
format | Dataset |
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Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and many tumor neoantigens are derive from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently need.Methods:In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulating of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot (ELISPOT) assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxic of TCRs were confirmed by transferring to primary peripheral blood T cells.Results: The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumors, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner.Conclusions: The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes (TILs) of patients with colorectal cancer (CRC), and tumor-specific TCRs can potentially be used for personalized TCR-Ts therapy.</description><identifier>DOI: 10.6084/m9.figshare.25422793</identifier><language>eng</language><publisher>figshare</publisher><subject>Cellular interactions (incl. adhesion, matrix, cell wall)</subject><creationdate>2024</creationdate><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>780,1894</link.rule.ids><linktorsrc>$$Uhttps://commons.datacite.org/doi.org/10.6084/m9.figshare.25422793$$EView_record_in_DataCite.org$$FView_record_in_$$GDataCite.org$$Hfree_for_read</linktorsrc></links><search><creatorcontrib>li, zhilang</creatorcontrib><creatorcontrib>Ma, Lisha</creatorcontrib><creatorcontrib>Gao, Zhaoya</creatorcontrib><creatorcontrib>Wang, Xiya</creatorcontrib><creatorcontrib>Che, Xuan</creatorcontrib><creatorcontrib>Zhang, Pengchong</creatorcontrib><creatorcontrib>Li, Yixian</creatorcontrib><creatorcontrib>Bai, Yun</creatorcontrib><creatorcontrib>Deng, Hongkui</creatorcontrib><title>Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures</title><description>Background:T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and many tumor neoantigens are derive from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently need.Methods:In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulating of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot (ELISPOT) assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxic of TCRs were confirmed by transferring to primary peripheral blood T cells.Results: The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumors, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner.Conclusions: The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes (TILs) of patients with colorectal cancer (CRC), and tumor-specific TCRs can potentially be used for personalized TCR-Ts therapy.</description><subject>Cellular interactions (incl. adhesion, matrix, cell wall)</subject><fulltext>true</fulltext><rsrctype>dataset</rsrctype><creationdate>2024</creationdate><recordtype>dataset</recordtype><sourceid>PQ8</sourceid><recordid>eNqdj01qwzAQhbXpIqS9QRZzAbuO4_x4HVqaffZCyCNnQNKYkRzwAXrvxji5QFfDG74H71Nqs63KQ3VqPkNbOurTzQiW9b6p62O7W6nfS4cxkyNrMnEEEzu4G0_dEtlBHgNLkQa0MwVXsOg9CFocMksCJxwWCCg68lke1diDn8JwYztlTDCm-bNALL2JTB1YLuzo8yiY3tWbMz7hx_OuVfP9dT3_FI8ZxlJGPQgFI5PeVnq20aHVLxv9stn9s_YHnpZiBA</recordid><startdate>20240316</startdate><enddate>20240316</enddate><creator>li, zhilang</creator><creator>Ma, Lisha</creator><creator>Gao, Zhaoya</creator><creator>Wang, Xiya</creator><creator>Che, Xuan</creator><creator>Zhang, Pengchong</creator><creator>Li, Yixian</creator><creator>Bai, Yun</creator><creator>Deng, Hongkui</creator><general>figshare</general><scope>DYCCY</scope><scope>PQ8</scope></search><sort><creationdate>20240316</creationdate><title>Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures</title><author>li, zhilang ; Ma, Lisha ; Gao, Zhaoya ; Wang, Xiya ; Che, Xuan ; Zhang, Pengchong ; Li, Yixian ; Bai, Yun ; Deng, Hongkui</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-datacite_primary_10_6084_m9_figshare_254227933</frbrgroupid><rsrctype>datasets</rsrctype><prefilter>datasets</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Cellular interactions (incl. adhesion, matrix, cell wall)</topic><toplevel>online_resources</toplevel><creatorcontrib>li, zhilang</creatorcontrib><creatorcontrib>Ma, Lisha</creatorcontrib><creatorcontrib>Gao, Zhaoya</creatorcontrib><creatorcontrib>Wang, Xiya</creatorcontrib><creatorcontrib>Che, Xuan</creatorcontrib><creatorcontrib>Zhang, Pengchong</creatorcontrib><creatorcontrib>Li, Yixian</creatorcontrib><creatorcontrib>Bai, Yun</creatorcontrib><creatorcontrib>Deng, Hongkui</creatorcontrib><collection>DataCite (Open Access)</collection><collection>DataCite</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>li, zhilang</au><au>Ma, Lisha</au><au>Gao, Zhaoya</au><au>Wang, Xiya</au><au>Che, Xuan</au><au>Zhang, Pengchong</au><au>Li, Yixian</au><au>Bai, Yun</au><au>Deng, Hongkui</au><format>book</format><genre>unknown</genre><ristype>DATA</ristype><title>Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures</title><date>2024-03-16</date><risdate>2024</risdate><abstract>Background:T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current prediction algorithms for tumor neoantigens are not reliable and many tumor neoantigens are derive from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently need.Methods:In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulating of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot (ELISPOT) assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxic of TCRs were confirmed by transferring to primary peripheral blood T cells.Results: The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumors, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner.Conclusions: The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes (TILs) of patients with colorectal cancer (CRC), and tumor-specific TCRs can potentially be used for personalized TCR-Ts therapy.</abstract><pub>figshare</pub><doi>10.6084/m9.figshare.25422793</doi><oa>free_for_read</oa></addata></record> |
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subjects | Cellular interactions (incl. adhesion, matrix, cell wall) |
title | Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures |
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