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Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]

ABSTRACT: We attempted to determine histological localization of chemoresistant cancer subpopulation by performing spatial transcriptomics.

ORGANISM(S): Homo sapiens

PROVIDER: GSE224335 | GEO | 2024/03/30

REPOSITORIES: GEO

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Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]

Project description:Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]

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Gene expression profile at single cell level of ovarian clear cell carcinoma (OCCC) [snRNA-seq OCCC]

Project description:The diversity of chemoresistant OCCC is unknown. We performed single nucleus RNA sequencing (snRNA-seq) to analyze the diversity of OCCC.

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Project description:We present a protocol to localize T cell receptor clones using the Visium spatial transcriptomics platform. This approach permits simultaneous localization of both gene expression and T cell clonotypes in situ within tissue sections. T cell receptor sequences identified by this protocol are readily recapitulated by single-cell sequencing. This technique enables detailed studies of the spatial organization of the human T cell repertoire, such as the localization of infiltrating T cell clones within the tumor microenvironment. For complete details on the use and execution of this protocol, please refer to Sudmeier et al. (2022).

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Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma - Spatial Transcriptomics - 10X Visium

Project description:Our understanding of how human skin cells differ according to anatomical site and tumour formation is limited. To address this we have created a multi-scale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single cell RNA sequencing, spatial global transcriptional profiling and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retained signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling. We propose that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.

2023-12-22 | E-MTAB-13085 | biostudies-arrayexpress

Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma - Spatial Transcriptomics - 10X Visium

Project description:Our understanding of how human skin cells differ according to body site and tumour formation is limited. To address this we have created a multi-scale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single cell RNA sequencing, spatial global transcriptional profiling and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retain signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling during cancer neovascularization. Our findings suggest that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.

2023-12-22 | E-MTAB-13084 | biostudies-arrayexpress

Resibufogenin inhibits ovarian clear cell carcinoma (OCCC) growth <i>in vivo</i>, and migration of OCCC cells <i>in vitro</i>, by down-regulating the PI3K/AKT and actin cytoskeleton signaling pathways.

Project description:Patients diagnosed with ovarian clear cell carcinoma (OCCC), a rare histologic subtype of ovarian cancer, often experience poor prognosis owing to the chemoresistance of their disease. Thus, there is an urgent need to identify new therapeutic options for these patients. A drug screen of 172 traditional Chinese herbs identified resibufogenin as a compound that inhibited the growth of cultured OCCC cells. Resibufogenin, a bioactive compound originally isolated from toad venom, is used in traditional Chinese medicine to treat several malignancies. The current study examined the impact of resibufogenin treatment on proliferation, migration, and invasion of ES-2 and TOV-21G OCCC cells in vitro. Flow cytometric analyses were employed to determine if resibufogenin affects apoptosis in OCCC cells. Additionally, the ability of resibufogenin to inhibit tumor growth in vivo was evaluated in murine xenograft models. RNA sequencing, quantitative polymerase chain reactions (qPCR), immunohistochemical assays, and western blotting were used to identify and verify cellular pathways potentially targeted by resibufogenin. Resibufogenin inhibited proliferation, migration, and invasion of OCCC cells, and induced apoptosis in them. Resibufogenin also suppressed the growth of xenograft tumors, which consequently showed lower Ki-67 and higher terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) expression. We observed down-regulation of (a) PI3K and AKT in the PI3K/AKT signaling pathway, and (b) MDM2 and myosin in the actin cytoskeleton pathway upon resibufogenin treatment. Thus, resibufogenin inhibits growth and migration of OCCC cells in vitro and suppresses OCCC growth in vivo through the PI3K/AKT and actin cytoskeleton signaling pathways.

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Spatial transcriptomics Visium data for human IPF and control lungs

Project description: Not available

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Spatial Visium FFPE Samples

Project description:Human Formalin fixed paraffin embedded Samples collected from Donated kidney samples, processed for cortex specific sections

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