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Melanoma Til Study RNAseq

ABSTRACT: In this study, mutations present in a series of human melanomas (stage IV disease) will be determined, using autologous blood cells to obtain a reference genome. From each of the samples that are analyzed, tumour-infiltrating T lymphocytes have also been isolated. This offers a unique opportunity to determine which (fraction of) mutations in human cancer leads to epitopes that are recognized by T cells. The resulting information is likely to be of value to understand how T cell activating drugs exert their action.

PROVIDER: EGAS00001000251 | EGA |

REPOSITORIES: EGA

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RNA-seq of human melanoma samples

Project description:In this study, mutations present in a series of human melanomas (stage IV disease) will be determined, using autologous blood cells to obtain a reference genome. From each of the samples that are analyzed, tumour-infiltrating T lymphocytes have also been isolated. This offers a unique opportunity to determine which (fraction of) mutations in human cancer leads to epitopes that are recognized by T cells. The resulting information is likely to be of value to understand how T cell activating drugs exert their action.

2013-01-22 | E-ERAD-61 | biostudies-arrayexpress

Melanoma TIL Study Exomes

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Project description:Multi-modal single cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states, but does not allow for simultaneous integration of critical post-translational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq); a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes and the transcriptome at the single cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.

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Single-cell RNA-seq reveals intratumoral heterogeneity in primary uveal melanomas and discloses new targetable vulnerability

Project description:Lack of specific markers for invasive uveal melanoma cells prevents early diagnosis of metastasis, while no systemic treatment options are available for patients with disseminated uveal melanomas. Intra-tumor heterogeneity has been recognized in numerous cancers as the main cause of metastasis development and therapy resistance. However, in uveal melanomas the specific subpopulations and their biological function which influence tumor behavior remained unknown. Here, using scRNA-seq analysis of six different primary uveal melanomas, we uncovered previously unrecognized intratumor heterogeneity. We localized diverse tumor-associated populations and transcriptional states in primary uveal melanomas. We also unraveled a gene regulatory network underlying a poor prognosis melanoma state. Heterogeneity was demonstrated in uveal melanoma tissue using the RNAscope assay. Thus, single-cell analysis offers an unprecedented view of intratumor heterogeneity in primary uveal melanoma, identified bona fide biomarkers for metastatic cells in the primary tumor, and unravel targetable modules driving metastase formation and growth, with critical implications for prognosis and therapeutic opportunity.

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Project description:Antigen-antibody interactions play a key role in the immune response post vaccination and the mechanism of action of antibody-based biopharmaceuticals. 4CMenB is a multicomponent vaccine against Neisseria meningitidis serogroup B in which factor H binding protein (fHbp) is one of the key antigens. In this study, we use hydrogen/deuterium exchange mass spectrometry (HDX-MS) to identify epitopes in fHbp recognized by polyclonal antibodies (pAb) from two human donors (HDs) vaccinated with 4CMenB. Our HDX-MS data reveal several epitopes recognized by the complex mixture of human pAb. Furthermore, we show that the pAb from the two HDs recognize the same epitope regions. Epitope mapping of total pAb and purified fHbp-specific pAb from the same HD reveals that the two antibody samples recognize the same main epitopes, showing that HDX-MS based epitope mapping can, in this case at least, be performed directly using total IgG pAb samples that have not undergone Ab-selective purification. Two monoclonal antibodies (mAb) were previously produced from B-cell repertoire sequences from one of the HDs and used for epitope mapping of fHbp with HDX-MS. The epitopes identified for the pAb from the same HD in this study, overlap with the epitopes recognized by the two individual mAbs. Overall, HDX-MS epitope mapping appears highly suitable for simultaneous identification of epitopes recognized by pAb from human donors and to thus both guide vaccine development and study basic human immunity to pathogens, including viruses.

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Epitope Mapping of Human Polyclonal Antibodies to the fHbp Antigen of a Neisseria Meningitidis Vaccine by Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) - part 2

2024-05-22 | PXD047712 | Pride

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Project description:Tumor-targeted T-cell therapies of various types have been booming, but T-cell therapy is limited by its inability to penetrate the collagen barrier surrounding tumors. The destruction of tumor collagen is significant because collagen both suppresses T cells and contributes to the formation of the extracellular matrix. Our previously reported cell surface vimentin (CSV)–targeted and membrane-anchored IL12-armed (attIL12) T cells can reduce collagen production by killing cancer-associated fibroblasts, but fail to reduce collagen expression by tumor cells, resulting in resistance to attIL12-T cell treatment. In this study, we discovered that CCKAR directly boosts collagen production by tumor cells in vitro and in vivo. attIL12-modified tumor-infiltrating lymphocytes (TILs) disabled collagen production by CCKAR-high autologous tumor cells in vitro and sarcoma patient-derived xenografts (PDXs) in vivo. This disruption of collagen production by tumor cells by attIL12-TILs overcomes resistance to attIL12-T cell treatment and required a simultaneous interaction between the CSV on autologous tumor cells, which is targeted by attIL12, and HLA-TCR on attIL12-TILs; when either interaction was abrogated, collagen production and CCKAR expression were not shut down. Mechanistically, the interaction between attIL12-TILs and autologous tumor cells induced IFNγ production synergistically, which in combination with CCKAR downregulation reduced collagen expression through suppression of both TGFβ-stimulated SMAD activation and CCKAR-AKT signaling. Diminishing collagen expression from tumor cells significantly increased T-cell infiltration and improved tumor growth inhibition in PDX sarcomas. Thus, this attIL12-TIL therapy holds great clinical potential for boosting T-cell infiltration in high-grade, collagen-rich tumors.

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