Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE260801 | GEO | 2024/10/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2

Project description:While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. We profiled inducible genetic CRC mouse models that recapitulate key features of human CRC, assigned cell types and epithelial expression programs to spatial tissue locations in tumors, and computationally used them to identify the regional features spanning different cells in the same spatial niche. We find that tumors were organized in cellular neighborhoods, each with a distinct composition of cell subtypes, expression programs, and local cellular interactions. Comparing to scRNA-seq and Slide-seq data from human CRC, we find that both cell composition and layout features were conserved between the species, with mouse neighborhoods correlating with malignancy and clinical outcome in human patient tumors, highlighting the relevance of our findings to human disease. Our work offers a comprehensive framework that is applicable across various tissues, tumors, and disease conditions, with tools for the extrapolation of findings from experimental mouse models to human diseases.

2024-10-18 | GSE260798 | GEO

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - Slide-Seq

2024-10-18 | GSE260797 | GEO

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2 with cell multiplexing

2024-10-18 | GSE260799 | GEO

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v3 with cell multiplexing

2024-10-18 | GSE260800 | GEO

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics

Project description:Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics

| PRJNA1083516 | ENA

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2

Project description:Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2

| PRJNA1083530 | ENA

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - Slide-Seq

Project description:Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - Slide-Seq

| PRJNA1083531 | ENA

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2 with cell multiplexing

Project description:Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v2 with cell multiplexing

| PRJNA1083529 | ENA

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v3 with cell multiplexing

Project description:Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics - scRNAseq v3 with cell multiplexing

| PRJNA1083528 | ENA

Spatially resolved transcriptomics revealed local invasion-related genes in colorectal cancer.

Project description:ObjectiveLocal invasion is the first step of metastasis, the main cause of colorectal cancer (CRC)-related death. Recent studies have revealed extensive intertumoral and intratumoral heterogeneity. Here, we focused on revealing local invasion-related genes in CRC.MethodsWe used spatial transcriptomic techniques to study the process of local invasion in four CRC tissues. First, we compared the pre-cancerous, cancer center, and invasive margin in one section (S115) and used pseudo-time analysis to reveal the differentiation trajectories from cancer center to invasive margin. Next, we performed immunohistochemical staining for RPL5, STC1, AKR1B1, CD47, and HLA-A on CRC samples. Moreover, we knocked down AKR1B1 in CRC cell lines and performed CCK-8, wound healing, and transwell assays to assess cell proliferation, migration, and invasion.ResultsWe demonstrated that 13 genes were overexpressed in invasive clusters, among which the expression of CSTB and TM4SF1 was correlated with poor PFS in CRC patients. The ribosome pathway was increased, while the antigen processing and presentation pathway was decreased along CRC progression. RPL5 was upregulated, while HLA-A was downregulated along cancer invasion in CRC samples. Pseudo-time analysis revealed that STC1, AKR1B1, SIRPA, C4orf3, EDNRA, CES1, PRRX1, EMP1, PPIB, PLTP, SULF2, and EGFL6 were unpregulated along the trajectories. Immunohistochemic3al staining showed the expression of STC1, AKR1B1, and CD47 was increased along cancer invasion in CRC samples. Knockdown of AKR1B1 inhibited CRC cells' proliferation, migration, and invasion.ConclusionsWe revealed the spatial heterogeneity within CRC tissues and uncovered some novel genes that were associated with CRC invasion.

| S-EPMC9928961 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data