Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenomic analysis reveals a unique DNA methylation program of metastasis-competent circulating tumor cells in colorectal cancer

ABSTRACT: Metastasis is the main cause of cancer-related deaths in patients with solid tumors, including colorectal cancer (CRC). Circulating tumor cells (CTCs) and epigenetic alterations are involved in the development of metastasis. It is important to characterize the DNA methylation pattern of metastasis-competent CTCs to better understand the metastatic process and obtain new clinical applications for cancer patients. Therefore, the aim of this study was to investigate the DNA methylation landscape of metastasis-competent CTCs in CRC. The DNA methylome of the human colorectal cancer-derived cell line CTC-MCC-41 was compared with primary (HT29, Caco2, HCT116, RKO) and metastatic (SW620 and COLO205) CRC cells using a genome-wide methylation analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE220096 | GEO | 2023/09/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Metabolomic analysis of colorectal cancer cells using mass spectrometry

Project description:Colorectal cancer (CRC) is one of the most prevalent tumors, with a high mortality rate. Nearly half of CRC patients develop metastasis, which accounts for as many as 90% of CRC-related deaths. In the metastasis process, cancer cells exhibit altered dependency on specific metabolic pathways and some of the metabolites discovered might be useful as potential diagnostic biomarkers. To identify metabolic pathway dependencies in CRC metastasis, mass spectrometry-based untargeted metabolomic analysis was performed in two pairs of CRC cell lines with different metastatic abilities. Each pair of cell lines was comprised of primary and metastatic colorectal cancer cell lines (SW480 vs. SW620; HT-29 vs. COLO 205). Relative levels of intracellular metabolites distinguished high-metastatic CRC cells from low-metastatic CRC cells.

2022-10-06 | ST002341 | MetabolomicsWorkbench

Single-cell metabolic fingerprints discover a cluster of circulating tumor cells with distinct metastatic potential

Project description:Circulating tumor cells (CTCs) are recognized as direct seeds of metastasis. However, CTC count may not be the 'best' indicator of metastatic risk because their heterogeneity is generally neglected. In this study, we develop a molecular typing system to predict colorectal cancer metastasis potential based on the metabolic fingerprints of single CTCs. After identification of the metabolites potentially related to metastasis using mass spectrometry-based untargeted metabolomics, setup of a home-built single-cell quantitative mass spectrometric platform for target metabolite analysis in individual CTCs and use of a machine learning method composed of non-negative matrix factorization and logistic regression, CTCs are divided into two subgroups, C1 and C2, based on a 4-metabolite fingerprint. Both in vitro and in vivo experiments demonstrate that CTC count in C2 subgroup is closely associated with metastasis incidence. This is an interesting report on the presence of a specific population of CTCs with distinct metastatic potential at the single-cell metabolite level.

2023-08-21 | MTBLS5028 | MetaboLights

Expression data from human Circulating Tumor Cells (CTC) and HT-29 cells

Project description:Unraveling the yet unknown molecular mechanisms regulating the biology of metastasis-competent Circulating Tumor Cells (CTCs) is important for better understanding metastatic growth and disease relapses in patients with colon cancer. We investigated and compared the transcriptome profiles of the CTC line and of a cell line derived from a primary colon cancer to get some insight into the specific molecular mechanism of metastasis-competent CTCs. We used microarrays to establish the molecular portrait of the metastasis-competent CTC and of HT-29 cells

2019-06-02 | GSE82198 | GEO

Human derived and patient derived xenografts epigenome analysis of primary and metastasis colorectal cancer

Project description:Genome wide DNA methylation profiling of primary (PR) and liver metastasis (LM) colorectal cancer (CRC). The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in human and xenogratfs derived samples. Raw data were processed using R minfi package. The main goal of this study is to develop a methylation-based classifier and predictor for metastatic CRC (mCRC), in order to find specific patients stratification for anti-EGFR targeted therapy (cetuximab) and bring the promise to shed new light on the role of methylation in driving colorectal cancer progression in different groups of patients.

2023-01-31 | GSE208713 | GEO

Lipopolysaccharide-regulated secretion of soluble and vesicle-based colorectal cancer cell proteins

Project description:Colorectal cancer (CRC), among the major cancer types in western world is responsible for 10% of cancer related deaths, often due to late detection when the tumor has already spread out of the colon. Surgery is the mainstay curative treatment for CRC. Nevertheless, between 15-30% of stage II and III patients develop hepatic metastasis within 5 years. Paradoxically, tumor surgery can contribute to the metastatic process, due to inflammatory mediator release in response to surgery, which promotes the metastatic ability of cancer cells. During surgery, bacterial products, such as LPS, from commensal bacteria translocate across the bowel wall, reach systemic circulation and induce an inflammatory response through to the activation of the Nuclear Factor-ĸB (NF-ĸB) pathway. Inflammation promotes malignant transformation by inducing chromosomal and microsatellite instability or CpG island methylation [14], but its direct effect on cancer cells and contribution to metastasis development remains to be elucidated. In this experiment we mimic the perioperative microenvironment where bacterial products get in contact with CRC cancer cells. We assessed the identity of the secreted proteins, including those released through extracellular vesicles (EV), of six CRC cell lines once exposed to lipopolysaccharide (LPS).

2022-02-28 | PXD011611 | Pride

Genomic Signatures Reveal DNA Damage Response Deficiency in Brain Metastases of Colorectal Cancer

Project description:We performed RNA-Seq on primary colorectal cancer (CRC) tissues and brain metastatic tissues from two CRC patients. Differential expression analysis was conducted to find genes associated with brain metastasis.

2019-06-06 | GSE132226 | GEO

Proteomics and liquid biopsy characterization of human EMT-related metastasis in colorectal cancer

Project description:Tumor cells undergo epithelial-mesenchymal transition (EMT), however, there is a room of disagreement in role of EMT heterogeneity to colorectal cancer metastasis (mCRC) evolution. To uncover new EMT-related metastasis proteins and pathways, we addressed the EMT status in colorectal cancer liver metastasis patient-derived CTCs to identify proteins that promote their distant metastasis. And then, we performed a comparative proteomic analysis in matched pairs of primary tumor tissues, adjacent mucosa tissues and liver metastases tissues. By integrative analysis we show that, unstable Epithelial/Mesenchymal (E/M)-type CTCs had the strongest liver metastases formation ability and the proportion of E/M-type CTCs correlated with distant metastases. Using an optimized proteomic workflow including data independent acquisition (DIA) and parallel reaction monitoring (PRM), we identified novel EMT-related protein cluster (e.g., GNG2, COL6A1, COL6A2, DCN, COL6A3, LAMB2, TNXB, CAVIN1) and well-described (e.g., KRAS and ERBB2) core protein level changes in EMT-related metastasis progression, and the proteomic data indicate KRAS, ERBB2, COL6A1 and CAVIN1 are promising EMT-related metastatic biomarker candidates. This study contributes to catch on EMT in CRC metastasis and in favor of heterogeneous EMT phenotypes as a key piece for tumor outcome and treatment. We further propose that therapies targeting this aggressive subset (E/M-type) of CTCs and related protein may be worthy of exploration as potential suppressors of metastatic evolution

2022-05-09 | PXD033788 |

Epigenomic reprogramming of therapy-resistant circulating tumor cells in colon cancer

Project description:Therapy resistance is a major limitation for treatment efficacy in colorectal cancer. Circulating tumor cells (CTCs) and epigenetic modifications, such as DNA methylation, are involved in the development of acquired resistance during treatment. The aim of this work was to characterize the DNA methylation landscape of colon CTCs during cancer progression and the development of therapy resistance. We analyzed nine permanent colon CTC-derived cell lines, which were collected at baseline (CTC-MCC-41) and during treatment and cancer progression (CTC-MCC-41.4 and CTC-MCC-41.5 [A-G]) from peripheral blood samples of a patient with metastatic colon cancer. The DNA methylome of these nine CTC lines was analyzed by EPIC arrays.

2023-12-13 | GSE239549 | GEO

Differential regulation of extracellular matrix proteins in three recurrent liver metastases of a single patient with colorectal cancer

Project description:Colorectal cancer (CRC) patients suffer from the second highest mortality among all cancer entities. In half of all CRC patients, colorectal cancer liver metastases (CRLM) can be observed. Metastatic colorectal cancer is associated with poor overall survival and limited treatment options. Even after successful surgical resection of the primary tumor, metachronous liver metastases occur in one out of eight cases. The only available curative intended treatment is hepatic resection, but metachronous CRLM frequently recur after approximately one year. In this study, we performed a proteome analysis of three recurrent liver metastases of a single CRC patient by mass spectrometry. Despite surgical resection of the primary CRC and adjuvant chemotherapy plus cetuximab treatment, the patient developed three metachronous CRLM which occurred consecutively after 9, 21 and 31 months. We identified a set of 1,132 proteins expressed in the three metachronous CRLM, of which 481 were differentially regulated, including 81 proteins that were associated with the extracellular matrix (ECM). 56 ECM associated proteins were identified as upregulated in the third metastasis, 26 (46%) of which were previously described as negative prognostic markers in CRC, including tenascin C, nidogen 1, fibulin1 and vinculin. These data may reflect an ascending trend of malignancy from the first to the third metachronous colorectal cancer liver metastasis. Additionally, the results indicate different ECM phenotypes for recurrent metachronous metastasis, associated with different grades of malignancy and highlights the importance of individual analysis of molecular features in different, consecutive metastatic events in a single patient.

2021-09-09 | PXD020109 | Pride

Partial hepatectomy accelerates colorectal metastasis by priming a prometastatic niche in the liver

Project description:Despite being the standard of care for patients with Stage IV colorectal cancer (CRC), the effects of a resection of liver metastasis on the metastatic disease are poorly understood. To elucidate the influence of surgical metastasectomies on metastasized CRC, we investigated the cellular and molecular effects of partial hepatectomy in a mouse model of orthograde CRC liver metastasis.

2024-06-02 | GSE253251 | GEO

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