Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comprehensive analysis of metastatic gastric cancer tumor cells using Single-cell RNA-seq

ABSTRACT: Gastric cancer (GC) is a leading cause of cancer-induced mortality with poor prognosis with metastasis. However, the mechanism of gastric carcinoma lymph node metastasis remains unknown due to traditional bulk-leveled approaches mask roles of subpopulations. To answer questions from the gastric carcinoma intratumoral perspective in the metastasis, we performed single-cell level analysis on three gastric cancer patients with primary cancer and paired metastatic lymph node cancer tissues using scRNA-seq. Results showed distinct carcinoma profiles from each patient, and diverse microenvironmental subsets were shared by a different patient. Clustering data showed significant intratumoral heterogeneity. Results also revealed a subgroup of cells bridging the metastatic group and primary group, implying the transition state of cancer during the metastatic process. In the present study we obtained a more comprehensive picture over gastric cancer lymph node metastasis, and we discovered some GC lymph node metastasis marker genes (ERBB2, CLDN11 and CDK12), as well as potential gastric cancer evolutionary driving genes (FOS and JUN), which provide a basis for the treatment of heterogeneity.

ORGANISM(S): Homo sapiens

PROVIDER: GSE158631 | GEO | 2020/12/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features in Breast Cancer

Project description:Ductal carcinoma in situ (DCIS) is a nonobligate precursor of invasive breast cancer. Its biological features, particularly its intratumoral heterogeneity, remain obscure. Moreover, mechanism of lymph node metastasis is unclear. To address this deficiency, we performed single-cell transcriptome profiling of DCIS, invasive ductal carcinoma (IDC) and lymph node metastasis. Single-cell transcriptome analysis revealed that breast cancer exhibits intratumoral heterogeneity at the transcriptional level, defining specific functions, and that DCIS has similar heterogeneity to IDC.

2022-08-02 | GSE195861 | GEO

SAGE Hiroshima gastric cancer tissue

Project description:Human primary gastric cancer tissue SAGE libraries. Profile of the genes expressed in well and poorly differentiated gastric cancer, early and advanced gastric cancer, scirrhous type gastric cancer, and　lymph node metastasis determined through SAGE. Keywords = gastric cancer, histology, early gastric cancer, advanced gastric cancer, lymph node metastasis, scirrhous type gastric cancer Keywords: other

2003-07-21 | GSE545 | GEO

Differential expression of miRNA in tissue microarray

Project description:The expression of miRNA in cancer tissues of gastric cancer patients with different lymph node stages was compared. N0 indicated no lymph node metastasis, and N3 indicated 7 or more lymph node metastasis

2021-07-05 | GSE173215 | GEO

HOXA11 promotes lymphatic metastasis of gastric cancer via transcriptional activation of TGFβ1

Project description:Most gastric cancer (GC) patients with early stage often have no lymph node (LN) metastases, while LN metastases appear in the advanced stage. However, there are some patients who present with early stage LN metastases and no LN metastases in the advanced stage. To explore the deeper molecular mechanisms involved, we collected clinical samples from early and advanced stage GC with and without LN metastases, as well as metastatic lymph nodes. Herein, we identified a keytarget, HOXA11, that was upregulated in GC tissues and closely associated with lymphatic metastases. HOXA11 transcriptionally regulates TGFβ1 expression and activates the TGFβ1/Smad2 pathway, which in turn promotes the development of EMT. In addition, enhanced Smad2 expression promotes the secretion of VEGF-C, which in turn induces lymphangiogenesis. These findings provide a plausible mechanism forHOXA11-modulated tumor in lymphatic metastasis and suggest thatHOXA11 may represent a potential therapeutic target for clinical intervention in LN-metastatic gastric cancer.

2023-11-08 | GSE246963 | GEO

Gene expression profiles in lymph nodes with metastasis of oral squamous cell carcinoma (OSCC)

Project description:Background: Cervical lymph node metastasis is a potent prognostic factor in oral squamous cell carcinoma (OSCC). However, lymph nodes resected by sentinel node biopsy or neck dissection are usually diagnosed by examining only one or two sections of the maximal cut surface. Accurate diagnosis of the metastasis in lymph nodes is important but depends on a heavy workload of the pathologist. In this study, we have attempted to identify novel molecular markers to find the harboring cancer cells in the lymph node and establish rapid detection method. Methods: We determined the gene expression profiles of 7 metastatic lymph nodes from patients with OSCC and 1 normal lymph node and 5 salivary glands from non-cancerous patients by microarray analysis. We found the overexpression genes in all metastatic lymph nodes. Subsequently, we examined the expression of these genes in newly 23 metastatic lymph nodes and 9 normal lymph nodes by real-time quantitative RT-PCR (qRT-PCR) assay. Moreover, the rapid detection of lymph node metastasis by these genes was examined using the reverse transcription loop-mediated isothermal amplification (RT-LAMP) method. Result: Among the 4 genes identified by microarray analysis, annexin A8 (ANXA8) and desmoglein 3 (DSG3) were detected in all metastatic lymph nodes at a much higher level but not in normal lymph nodes at all by qRT-PCR. Furthermore, RT-LAMP method targeting ANXA8 rapidly detected almost lymph nodes with metastasis. Conclusions: ANXA8 could be a useful marker for detecting lymph node metastasis in OSCC. Using AB1700 system, we determined the gene expression profiles of lymph nodes with metastasis of OSCC. Normal lymph node and salivary gland tissues were used as control samples.

2015-12-21 | E-GEOD-70604 | biostudies-arrayexpress

Gene Expression Profiling of Fixed Tissues of Lymph Node Metastasis in Hepatocellular Carcinoma

Project description:RNA was extracted from formalin-fixed specimens of paired intratumoral and peritumoral tissues of patients with lymph node-positive (n=20) or negative (n=20) HCC. A cDNA-mediated annealing, selection, extension, and ligation assay was performed with an array of 502 known cancer-related genes to identify differentially expressed genes in 80 RNA samples. Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. DASL experiments were performed to identify genes that were differentially expressed between the lymph node metastasis (LNM) and non-lymph node metastasis (NLNM) groups of matched intratumoral and peritumoral tissues by using A cDNA-mediated annealing, selection, extension, and ligation assay.

2011-08-03 | E-GEOD-28248 | biostudies-arrayexpress

A reductionist approach using primary and metastatic cell-derived extracellular vesicles reveals hub proteins associated with oral cancer prognosis

Project description:Oral squamous cell carcinoma (OSCC) has high mortality rates that are largely associated with lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Extracellular vesicles (EVs) are membrane-bound particles that play a role in intercellular communication and impact cancer development and progression. Thus, profiling EVs would be of great significance to decipher the role of EV cargo in OSCC metastasis. For that purpose, we used a reductionist approach to map the proteomic, miRNA, metabolomic, and lipidomic profiles of extracellular vesicles (EVs) derived from human primary tumor (SCC-9) cells and matched lymph node metastases (LN1) cells. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites, and 64 lipids differentially abundant between LN1- and SCC-9-derived EVs. A multi-omics integration identified 11 ‘hub proteins’ significantly decreased at the metastatic site compared to primary tumor-derived EVs. We confirmed the validity of these findings with analysis of data from multiple public databases, and found that low abundance of seven hub proteins in metastatic EVs is correlated with reduced survival and tumor aggressiveness in cancer patients. In summary, this multi-omics approach identified proteins transported by EVs that are associated with metastasis, and which may potentially serve as prognostic markers in OSCC.

2021-04-26 | ST001755 | MetabolomicsWorkbench

In vitro and In vivo Evidence of Long Non-coding OR3A4 in Gastric Cancer Progression and Tumorigenicity

Project description:LncRNA and mRNA expression profiling for 7 human gastric cancr samples (3 tumor tissues and 3 tumor lymph node and 1 normal tissue) We have completed the metastasis-related Long Noncoding RNA expression profiling data microarray analysis of the 7 human gastric cancer related samples In the study presented here, a consecutively operated, well-defined cohort of three gastric cancer tissues and three metastatic lymph nodes tissues compared with the normal tissues and lymph nodes tissues, followed up more than five years, was used to acquire expression profiles of a total of 1942 lncRNA and 1976 mRNA, leading to the successful construction of supervised

2014-02-11 | E-GEOD-54835 | biostudies-arrayexpress

Gene expression profiles in lymph nodes with metastasis of oral squamous cell carcinoma (OSCC)

2015-12-21 | GSE70604 | GEO

Reductionist approach using primary and metastatic cell-derived extracellular vesicles prospect proteins associated with oral cancer prognosis

Project description:Oral squamous cell carcinoma (OSCC) shows high mortality rates that are largely associated with the presence of lymph node metastasis. However, the molecular mechanisms that drive OSCC metastasis are unknown. Here, we used a reductionist approach mapping the proteomic, miRNA, metabolomic and lipidomic profiles of extracellular vesicles (EVs) from human primary tumor (SCC-9 cells) and matched lymph node metastasis (LN1 cells) to explore the role of EV cargo in OSCC metastasis. Distinct omics profiles were associated with the metastatic phenotype, including 670 proteins, 217 miRNAs, 26 metabolites and 64 lipids differentially abundant between LN1 and SCC-9-derived EVs. A multi-omics integration indicated 11 ‘hub proteins’ significantly modulated in the metastatic site when compared to primary site-derived EVs, seven of them correlated with aggressiveness in cancer patients. The multi-omics approach allowed the prospection of proteins transported by EVs that potentially serves as prognostic markers in OSCC.

2021-07-19 | PXD019216 | Pride

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