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Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones

ABSTRACT: Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones

PROVIDER: PRJNA1078932 | ENA |

REPOSITORIES: ENA

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Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones.

Project description:High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised by the presence of subclones with distinct genotypes. Intratumoural heterogeneity is linked to recurrence, chemotherapy resistance, and poor prognosis. Here, we use spatial transcriptomics to identify HGSOC subclones and study their association with infiltrating cell populations. Visium spatial transcriptomics reveals multiple tumour subclones with different copy number alterations present within individual tumour sections. These subclones differentially express various ligands and receptors and are predicted to differentially associate with different stromal and immune cell populations. In one sample, CosMx single molecule imaging reveals subclones differentially associating with immune cell populations, fibroblasts, and endothelial cells. Cell-to-cell communication analysis identifies subclone-specific signalling to stromal and immune cells and multiple subclone-specific autocrine loops. Our study highlights the high degree of subclonal heterogeneity in HGSOC and suggests that subclone-specific ligand and receptor expression patterns likely modulate how HGSOC cells interact with their local microenvironment.

| S-EPMC10991508 | biostudies-literature

Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments

Project description:Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments

| PRJNA873051 | ENA

Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity

Project description:Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity

| PRJNA740308 | ENA

Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Liver)

Project description:Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Liver)

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Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Skin)

Project description:Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Skin)

| PRJNA740314 | ENA

Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Salivary Gland)

Project description:Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Salivary Gland)

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human HG-3 B-lymphome cell line subclones

Project description:Genetic heterogeneity though common in tumors has been rarely documented in cell lines. To examine how often B-lymphoma cell lines are comprised of subclones, we performed immunoglobulin (Ig) heavy chain hypermutation analysis. Revealing that subclones are not rare in B-cell lymphoma cell lines, 6/49 Ig hypermutated cell lines (12%) consisted of subclones with individual Ig mutations. Subclones were also identified in 2/284 leukemia/lymphoma cell lines exhibiting bimodal CD marker expression. We successfully isolated 10 subclones from four cell lines HG3, SU-DHL-5, TMD-8, U-2932). Whole exome sequencing was performed to molecularly characterize these subclones. We in detail describe the clonal structure of cell line HG3, derived from chronic lymphocytic leukemia. HG3 consists of three lineages each bearing clone-specific aberrations, gene expression and DNA methylation patterns. While donor patient leukemic cells were CD5+ , two of three HG3 subclones had independently lost this marker. CD5 on HG3 cells was regulated by epigenetic/transcriptional mechanisms rather than by alternative splicing as reported hitherto. In conclusion, we show that the presence of subclones in cell lines carrying individual mutations and characterized by sets of differentially expressed genes is not uncommon. We show also that these subclones can be useful isogenic models for regulatory and functional studies.

2016-09-30 | E-MTAB-4955 | biostudies-arrayexpress

Expression data from the subclones of Lewis Lung Carcinoma (LLC) cells

Project description:Medium conditioned by LLC cells stimulates thermogenic gene expression when added onto primary adipocytes. We generated single cell colonies from parental LLC cells. Media conditioned by the subclones stimulated thermogenic gene expression in primary adipocytes at varying degrees. Subclones 2, 3, 6 and 28 produce significantly larger amount of thermogenic activity than the subclones 18, 19, 23 and 24. We compared gene expression profiles of these subclones to identify secreted factors enriched in the more thermogenic clones.

2014-07-13 | GSE57797 | GEO

Expression data from U87MG subclones

Project description:U87MG is a glioblastoma cell line that shows substantial heterogeneity despite long-term passaging. We used microarrays to identify variations in gene expression that are associated with phenotypic differences among subclones derived from U87MG.

2015-02-12 | GSE54967 | GEO

Expression data from the subclones of Lewis Lung Carcinoma (LLC) cells

2014-07-13 | E-GEOD-57797 | biostudies-arrayexpress