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

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

PROVIDER: PRJNA1147623 | ENA |

REPOSITORIES: ENA

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

Project description:One of the most common origins of Peritoneal metastasis (PM) is colon cancer, which occurs in about 20% of colon cancer patients. Given the cancer cell heterogeneity in PM, we first tried to dissect the spatial distribution of CAF and the associated niches at a single cell resolution, we exploited the Xenium In Situ high-plex spatial imaging platform. We performed the Xenium assays with 8 human PM samples of colon origin including one PM-adjacent tissue. Among the 8 PM samples, 3 samples carried a distinct iCMS3 epithelial signature (PM1, PM2, PM3), 2 carried iCMS2 signature (PM6, PM7), while the other 2 samples had a mix of both iCMS2 and iCMS3 signatures (PM4, PM5). We found that the presence of iCMS3 cancer cells was associated with an increase infiltration of lymphocytes and the formation of tertiary lymphoid structures (TLS).

2025-09-15 | GSE274623 | GEO

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

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

| PRJNA1147630 | ENA

Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [scRNA-seq]

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

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Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [xenium]

Project description:Precision use of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as Juvenile Idiopathic Arthritis. Progress has been obstructed by a lack of understanding of the cellular basis of joint inflammation in children, given the difficulties in obtaining and studying synovial tissue itself. To this end, we combine single-cell RNA-sequencing, multiplexed immunofluorescence imaging and spatial transcriptomics to define the cellular and transcriptomic landscape of the synovium in children with Juvenile Idiopathic Arthritis. We identify spatial niches of resident and infiltrating cell populations that correlate with the degree of inflammation, and gene programs associated with arthritis severity. Combined with analyses of synovial fluid and peripheral blood from the same children, we distinguish differences in cellular composition, signalling pathways and transcriptional programs across anatomical compartments. Whilst we identify several pathogenic populations shared with adult-onset arthritis, our analyses highlight increased vascularity of the inflamed developing joint and TGFb-driven stromal subsets that upregulate expression of disease risk-associated genes. Overall, these findings illustrate the need for treatment algorithms informed by a tissue-based classification of arthritis. Slides were prepared, processed, imaged and underwent post-run staining according to Xenium (10X Genomics) protocols: “CG000580 Rev C”, “CG000582 Rev D”, “CG000584 Rev B” and “CG000613 Rev A”, according to manufacturer’s instructions. For gene detection, slides hybridized with probes from the predesigned Xenium Human Multi-Tissue and Cancer Gene Expression and hMulti_v1 design (chemistry v1: 10x Genomics), consisting of 377 genes was used.

2025-05-11 | GSE278969 | GEO

Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [xenium]

Project description:Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [xenium]

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Antigen Presenting Dendritic Cells

Project description:Assessing the gene expression repertoire of antigen presenting dendritic cells Keywords: other

2004-09-30 | GSE702 | GEO

Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches [scRNA-seq]

Project description:To understand the microenvironmental changes caused by Spp1 knockout, we digested the tumors from the control and knockout groups into single cell suspension and performed scRNA-seq. The scRNA-seq data suggested a significant increase of T cell infiltration into the stromal Spp1 knockout tumors.

2025-09-15 | GSE274609 | GEO

Antigen presenting cells of myeloid origin

Project description:Transcriptional profiles of four different myeloid antigen presenting cell (APC) subsets (BDCA-1+ circulating myeloid dendritic cells, CD14+ monocytes, and in vitro generated immature and mature monocyte-derived dendritic cells) were used for comprehensive transcriptome analysis. Based on the gene expression profiling data, a quantitative relationship between myeloid APC in functionally related gene spaces was established. Keywords = myeloid antigen presenting cells Keywords = dendritic cell subsets Keywords: repeat sample

2017-12-21 | GSE2215 | GEO

Identification of PM-localized proteins

Project description:In order to assess the quality of alleged PM identifications from Arabidopsis, PM-enriched fractions were compared to PM-depleted fractions using 18O isotopic labeling and mass spectrometry. The two samples submitted are biological replicates. Keywords: Protein Localization via MS

2005-06-21 | GSE2830 | GEO

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