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Xenium Spatial Transcriptomics with human breast cell typing panel in human treatment naïve primary PDAC

ABSTRACT: Xenium Spatial Transcriptomics with human breast cell typing panel in human treatment naïve primary PDAC

PROVIDER: PRJNA1179871 | ENA |

REPOSITORIES: ENA

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Xenium Spatial Transcriptomics with human breast cell typing panel in human treatment naïve primary PDAC

Project description:In this study we provide evidence that cancer associated fibroblasts in mouse and human PDAC models are proficient in the synthesis of monounsaturated fatty acids and may feed these MUFAs to cancer cells, enabling their evasion of SFA-associated lipotoxicity in the tumor microenvironment. The desaturation of SFAs to MUFAs by SCD is an oxygen-dependent process and cancer cells experience hypoxia in the PDAC TME. Therefore, we hypothesized that CAFs would be spatially positioned more near to blood vessels and have greater access to molecular oxygen with which to perform SFA desaturation. We therefore profiled the spatial distribution of cells in 8 treatment-naive human PDAC cases to determine whether CAFs indeed have greater access to vasculature than cancer cells.

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Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [Xenium PDAC]

Project description:To explore the CAF niches in pancreatic ductal adenocarcinoma (PDAC), we performed Xenium assays in 3 treatment-naïve and 3 chemoradiotherapy-treated human PDAC samples. We found that after the chemoradiotherapy treatment, tissues became more desmoplastic with a larger CAF proportion. And interestingly, we found there was a reduction of cancer cell 1 in the chemoradiotherapy group while the ratio of cancer cell 2 remained similar, suggesting cancer cell 2 was the chemoradiotherapy-resistant cancer cell population. Through differential gene analysis, we found cancer 2 was marked by a high level of SPP1 expression.

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Spatial transcriptomic analysis of human dorsoal root ganglia neurons [Xenium]

Project description:Xenium platform was used for the spatial transcriptomic analysis of human DRG neurons, 100 marker genes were selected as the customized probe panel and hybridized to fresh frozen hDRG sections. Manual segmentation of each neuron soma was performed, based on expressions of pan-neuronal marker gene PGP9.5, satellite glia cell marker FAB7B, and the corresponding H.E. staining. In total, 1340 neurons were identified (excluding 75 region-of-interest with poor or unclear neuronal soma morphology in H & E staining) and clustered into 16 groups. The 16 clusters were assigned as different cell types based on marker genes expression.

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Project description:Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [Xenium PDAC]

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Xenium Spatial Transcriptomics of Head and Neck Single Cell Carcinoma

Project description:Recent work has shown that the spatial organization of immune responses is a critical determinant of anti-tumor immunity. Here, we profiled ten head and neck squamous cell carcinoma (HNSCC) patient tumors and one ameloblastoma tumor using Xenium V1 spatial transcriptomics. The 10X genomics human multi-tissue and cancer gene expression panel targeting 377 genes was used in combination with 100 custom Xenium probes targeting patient-specific CDR3 regions of T cell receptors (TCRs) in T cells, additoinal T cell specific genes, HPV oncoprotein genes, and tumor genes of interest. This enabled the detection of 477 transcripts within each tumor sample at a single-cell resolution. For seven of the ten HNSCC samples, different tissue sections run on different days were analyzed as technical replicates. Together, these findings introduce a scalable platform for spatial clonal T cell analysis and provide new insight into the spatial relationship of cells within the HNSCC tumor microenvironment.

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Class I Typing

Project description:Class I Typing