Mouse Assay:Article Title: T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
Article Snippet: .. STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d RESOURCE AVAILABILITY B Lead contact B Materials availability B Data and code availability d EXPERIMENTAL MODEL AND STUDY PARTICIPANT DE- TAILS B Cell-lines B Mice B Human samples d METHOD DETAILS B T cell culture and stimulation B In vitro T cell killing assay B CyTOF phenotyping B Mouse tumor model B CODEX multiplexed imaging B RNA-seq B Spatial transcriptomics d QUANTIFICATION AND STATISTICAL ANALYSIS B CODEX multiplexed imaging data analysis B RNA-seq data analysis SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. celrep.2023.113494. .. This work was supported by the USNational Institutes of Health (P01HL108797, U01AI101984, 5U54CA209971, 5U01AI140498, U54HG010426, U19AI100627, R01HL120724, R01HL128173, 5P01AI131374, UH3DK114937, U19AI135976, U2CCA233238, U2CCA233195); the US Food and Drug Administration (HHSF223201610018C, DSTL/AGR/00980/01); Cancer Research UK (C27165/ A29073); the Bill and Melinda Gates Foundation (OPP1113682); the Cancer Research Institute; the Parker Institute for Cancer Immunotherapy (PICI0025); Hope Realized Medical Foundation (209477); the Kenneth Rainin Foundation (2020-1463); the Silicon Valley Community Foundation (2017-175329 and 2017-177799-5022); the Beckman Center for Molecular and Genetic Medicine; (D) Donut charts representing overall major cell-type compartments from CODEX multiplexed imaging (inside donut), and coarse grain cell-type percentages (outside donut, with legend) for all four groups shown. (E) Human cellular neighborhood (hCN) map from one of the patient’s tumor samples that was imaged by CODEX multiplexed imaging taken post-checkpoint inhibitor (CPI) therapy (black scale bar, 1 mm). (F) Magnified portion of the human cellular neighborhood (hCN) map indicating a location where the Immune Infiltrate hCN (sky blue) is adjacent to the Productive T cell & Tumor hCN (blue). (G) The same area magnified but showing a seven-color overlay (out of 58 total markers) highlighting immune cell infiltration (scale bar, 100 mm) next to areas where (H) CD8+ T cells are engaging with tumor cells with an inflamed phenotype (orange scale bar, 100 mm). (I and J) Significant two-combination neighborhoodmotifs enriched or depleted that are found associated with the Productive T cell & Tumor hCN compared with null distribution of permuted samples for (I) tumors from responders and (J) post therapy.
Cell Culture:Article Title: T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
Article Snippet: .. STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d RESOURCE AVAILABILITY B Lead contact B Materials availability B Data and code availability d EXPERIMENTAL MODEL AND STUDY PARTICIPANT DE- TAILS B Cell-lines B Mice B Human samples d METHOD DETAILS B T cell culture and stimulation B In vitro T cell killing assay B CyTOF phenotyping B Mouse tumor model B CODEX multiplexed imaging B RNA-seq B Spatial transcriptomics d QUANTIFICATION AND STATISTICAL ANALYSIS B CODEX multiplexed imaging data analysis B RNA-seq data analysis SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. celrep.2023.113494. .. This work was supported by the USNational Institutes of Health (P01HL108797, U01AI101984, 5U54CA209971, 5U01AI140498, U54HG010426, U19AI100627, R01HL120724, R01HL128173, 5P01AI131374, UH3DK114937, U19AI135976, U2CCA233238, U2CCA233195); the US Food and Drug Administration (HHSF223201610018C, DSTL/AGR/00980/01); Cancer Research UK (C27165/ A29073); the Bill and Melinda Gates Foundation (OPP1113682); the Cancer Research Institute; the Parker Institute for Cancer Immunotherapy (PICI0025); Hope Realized Medical Foundation (209477); the Kenneth Rainin Foundation (2020-1463); the Silicon Valley Community Foundation (2017-175329 and 2017-177799-5022); the Beckman Center for Molecular and Genetic Medicine; (D) Donut charts representing overall major cell-type compartments from CODEX multiplexed imaging (inside donut), and coarse grain cell-type percentages (outside donut, with legend) for all four groups shown. (E) Human cellular neighborhood (hCN) map from one of the patient’s tumor samples that was imaged by CODEX multiplexed imaging taken post-checkpoint inhibitor (CPI) therapy (black scale bar, 1 mm). (F) Magnified portion of the human cellular neighborhood (hCN) map indicating a location where the Immune Infiltrate hCN (sky blue) is adjacent to the Productive T cell & Tumor hCN (blue). (G) The same area magnified but showing a seven-color overlay (out of 58 total markers) highlighting immune cell infiltration (scale bar, 100 mm) next to areas where (H) CD8+ T cells are engaging with tumor cells with an inflamed phenotype (orange scale bar, 100 mm). (I and J) Significant two-combination neighborhoodmotifs enriched or depleted that are found associated with the Productive T cell & Tumor hCN compared with null distribution of permuted samples for (I) tumors from responders and (J) post therapy.
In Vitro:Article Title: T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
Article Snippet: .. STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d RESOURCE AVAILABILITY B Lead contact B Materials availability B Data and code availability d EXPERIMENTAL MODEL AND STUDY PARTICIPANT DE- TAILS B Cell-lines B Mice B Human samples d METHOD DETAILS B T cell culture and stimulation B In vitro T cell killing assay B CyTOF phenotyping B Mouse tumor model B CODEX multiplexed imaging B RNA-seq B Spatial transcriptomics d QUANTIFICATION AND STATISTICAL ANALYSIS B CODEX multiplexed imaging data analysis B RNA-seq data analysis SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. celrep.2023.113494. .. This work was supported by the USNational Institutes of Health (P01HL108797, U01AI101984, 5U54CA209971, 5U01AI140498, U54HG010426, U19AI100627, R01HL120724, R01HL128173, 5P01AI131374, UH3DK114937, U19AI135976, U2CCA233238, U2CCA233195); the US Food and Drug Administration (HHSF223201610018C, DSTL/AGR/00980/01); Cancer Research UK (C27165/ A29073); the Bill and Melinda Gates Foundation (OPP1113682); the Cancer Research Institute; the Parker Institute for Cancer Immunotherapy (PICI0025); Hope Realized Medical Foundation (209477); the Kenneth Rainin Foundation (2020-1463); the Silicon Valley Community Foundation (2017-175329 and 2017-177799-5022); the Beckman Center for Molecular and Genetic Medicine; (D) Donut charts representing overall major cell-type compartments from CODEX multiplexed imaging (inside donut), and coarse grain cell-type percentages (outside donut, with legend) for all four groups shown. (E) Human cellular neighborhood (hCN) map from one of the patient’s tumor samples that was imaged by CODEX multiplexed imaging taken post-checkpoint inhibitor (CPI) therapy (black scale bar, 1 mm). (F) Magnified portion of the human cellular neighborhood (hCN) map indicating a location where the Immune Infiltrate hCN (sky blue) is adjacent to the Productive T cell & Tumor hCN (blue). (G) The same area magnified but showing a seven-color overlay (out of 58 total markers) highlighting immune cell infiltration (scale bar, 100 mm) next to areas where (H) CD8+ T cells are engaging with tumor cells with an inflamed phenotype (orange scale bar, 100 mm). (I and J) Significant two-combination neighborhoodmotifs enriched or depleted that are found associated with the Productive T cell & Tumor hCN compared with null distribution of permuted samples for (I) tumors from responders and (J) post therapy.
Imaging:Article Title: T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
Article Snippet: .. STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d RESOURCE AVAILABILITY B Lead contact B Materials availability B Data and code availability d EXPERIMENTAL MODEL AND STUDY PARTICIPANT DE- TAILS B Cell-lines B Mice B Human samples d METHOD DETAILS B T cell culture and stimulation B In vitro T cell killing assay B CyTOF phenotyping B Mouse tumor model B CODEX multiplexed imaging B RNA-seq B Spatial transcriptomics d QUANTIFICATION AND STATISTICAL ANALYSIS B CODEX multiplexed imaging data analysis B RNA-seq data analysis SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. celrep.2023.113494. .. This work was supported by the USNational Institutes of Health (P01HL108797, U01AI101984, 5U54CA209971, 5U01AI140498, U54HG010426, U19AI100627, R01HL120724, R01HL128173, 5P01AI131374, UH3DK114937, U19AI135976, U2CCA233238, U2CCA233195); the US Food and Drug Administration (HHSF223201610018C, DSTL/AGR/00980/01); Cancer Research UK (C27165/ A29073); the Bill and Melinda Gates Foundation (OPP1113682); the Cancer Research Institute; the Parker Institute for Cancer Immunotherapy (PICI0025); Hope Realized Medical Foundation (209477); the Kenneth Rainin Foundation (2020-1463); the Silicon Valley Community Foundation (2017-175329 and 2017-177799-5022); the Beckman Center for Molecular and Genetic Medicine; (D) Donut charts representing overall major cell-type compartments from CODEX multiplexed imaging (inside donut), and coarse grain cell-type percentages (outside donut, with legend) for all four groups shown. (E) Human cellular neighborhood (hCN) map from one of the patient’s tumor samples that was imaged by CODEX multiplexed imaging taken post-checkpoint inhibitor (CPI) therapy (black scale bar, 1 mm). (F) Magnified portion of the human cellular neighborhood (hCN) map indicating a location where the Immune Infiltrate hCN (sky blue) is adjacent to the Productive T cell & Tumor hCN (blue). (G) The same area magnified but showing a seven-color overlay (out of 58 total markers) highlighting immune cell infiltration (scale bar, 100 mm) next to areas where (H) CD8+ T cells are engaging with tumor cells with an inflamed phenotype (orange scale bar, 100 mm). (I and J) Significant two-combination neighborhoodmotifs enriched or depleted that are found associated with the Productive T cell & Tumor hCN compared with null distribution of permuted samples for (I) tumors from responders and (J) post therapy.
RNA Sequencing:Article Title: T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
Article Snippet: .. STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d RESOURCE AVAILABILITY B Lead contact B Materials availability B Data and code availability d EXPERIMENTAL MODEL AND STUDY PARTICIPANT DE- TAILS B Cell-lines B Mice B Human samples d METHOD DETAILS B T cell culture and stimulation B In vitro T cell killing assay B CyTOF phenotyping B Mouse tumor model B CODEX multiplexed imaging B RNA-seq B Spatial transcriptomics d QUANTIFICATION AND STATISTICAL ANALYSIS B CODEX multiplexed imaging data analysis B RNA-seq data analysis SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. celrep.2023.113494. .. This work was supported by the USNational Institutes of Health (P01HL108797, U01AI101984, 5U54CA209971, 5U01AI140498, U54HG010426, U19AI100627, R01HL120724, R01HL128173, 5P01AI131374, UH3DK114937, U19AI135976, U2CCA233238, U2CCA233195); the US Food and Drug Administration (HHSF223201610018C, DSTL/AGR/00980/01); Cancer Research UK (C27165/ A29073); the Bill and Melinda Gates Foundation (OPP1113682); the Cancer Research Institute; the Parker Institute for Cancer Immunotherapy (PICI0025); Hope Realized Medical Foundation (209477); the Kenneth Rainin Foundation (2020-1463); the Silicon Valley Community Foundation (2017-175329 and 2017-177799-5022); the Beckman Center for Molecular and Genetic Medicine; (D) Donut charts representing overall major cell-type compartments from CODEX multiplexed imaging (inside donut), and coarse grain cell-type percentages (outside donut, with legend) for all four groups shown. (E) Human cellular neighborhood (hCN) map from one of the patient’s tumor samples that was imaged by CODEX multiplexed imaging taken post-checkpoint inhibitor (CPI) therapy (black scale bar, 1 mm). (F) Magnified portion of the human cellular neighborhood (hCN) map indicating a location where the Immune Infiltrate hCN (sky blue) is adjacent to the Productive T cell & Tumor hCN (blue). (G) The same area magnified but showing a seven-color overlay (out of 58 total markers) highlighting immune cell infiltration (scale bar, 100 mm) next to areas where (H) CD8+ T cells are engaging with tumor cells with an inflamed phenotype (orange scale bar, 100 mm). (I and J) Significant two-combination neighborhoodmotifs enriched or depleted that are found associated with the Productive T cell & Tumor hCN compared with null distribution of permuted samples for (I) tumors from responders and (J) post therapy.
Spatial Transcriptomics:Article Title: T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
Article Snippet: .. STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: d KEY RESOURCES TABLE d RESOURCE AVAILABILITY B Lead contact B Materials availability B Data and code availability d EXPERIMENTAL MODEL AND STUDY PARTICIPANT DE- TAILS B Cell-lines B Mice B Human samples d METHOD DETAILS B T cell culture and stimulation B In vitro T cell killing assay B CyTOF phenotyping B Mouse tumor model B CODEX multiplexed imaging B RNA-seq B Spatial transcriptomics d QUANTIFICATION AND STATISTICAL ANALYSIS B CODEX multiplexed imaging data analysis B RNA-seq data analysis SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j. celrep.2023.113494. .. This work was supported by the USNational Institutes of Health (P01HL108797, U01AI101984, 5U54CA209971, 5U01AI140498, U54HG010426, U19AI100627, R01HL120724, R01HL128173, 5P01AI131374, UH3DK114937, U19AI135976, U2CCA233238, U2CCA233195); the US Food and Drug Administration (HHSF223201610018C, DSTL/AGR/00980/01); Cancer Research UK (C27165/ A29073); the Bill and Melinda Gates Foundation (OPP1113682); the Cancer Research Institute; the Parker Institute for Cancer Immunotherapy (PICI0025); Hope Realized Medical Foundation (209477); the Kenneth Rainin Foundation (2020-1463); the Silicon Valley Community Foundation (2017-175329 and 2017-177799-5022); the Beckman Center for Molecular and Genetic Medicine; (D) Donut charts representing overall major cell-type compartments from CODEX multiplexed imaging (inside donut), and coarse grain cell-type percentages (outside donut, with legend) for all four groups shown. (E) Human cellular neighborhood (hCN) map from one of the patient’s tumor samples that was imaged by CODEX multiplexed imaging taken post-checkpoint inhibitor (CPI) therapy (black scale bar, 1 mm). (F) Magnified portion of the human cellular neighborhood (hCN) map indicating a location where the Immune Infiltrate hCN (sky blue) is adjacent to the Productive T cell & Tumor hCN (blue). (G) The same area magnified but showing a seven-color overlay (out of 58 total markers) highlighting immune cell infiltration (scale bar, 100 mm) next to areas where (H) CD8+ T cells are engaging with tumor cells with an inflamed phenotype (orange scale bar, 100 mm). (I and J) Significant two-combination neighborhoodmotifs enriched or depleted that are found associated with the Productive T cell & Tumor hCN compared with null distribution of permuted samples for (I) tumors from responders and (J) post therapy.
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