Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA103039 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression data from early stage CRC patients' tumors [Affymetrix]
| PRJNA323569 | ENA
Project description:Expression data from early stage CRC patients' tumors [Agilent]
| PRJNA323568 | ENA
Project description:Expression data from early stage CRC patients' tumors [NanoString-Test]
| PRJNA323566 | ENA
Project description:Expression data from early stage CRC patients' tumors [NanoString-Design]
| PRJNA323567 | ENA
Project description:Colorectal cancer (CRC) is currently the third leading cause of cancer related mortality in the world. U.S. Food and Drug Administration-approval circulating tumor markers, including carcinoembryonic antigen, carbohydrate antigen (CA) 19-9 and CA125, were used as prognostic biomarker of CRC that attributed to low sensitivity in diagnosis of CRC. Therefore, our purpose is to develop a novel strategy for novel clinical biomarker for early CRC diagnosis. We used mass spectrometry (MS) methods such as nanoLC-MS/MS, targeted LC-MS/MS, and stable iso-tope-labeled multiple reaction monitoring (MRM) MS coupled to machine learning algorithms and logistic regression to analyze plasma samples from patients with early-stage CRC, late-stage CRC, and healthy controls (HCs).
2021-07-29 | PXD024997 | Pride
Project description:Metastasis is the major cause of cancer mortality. Up to 25% of early stage sporadic colorectal cancer (CRC) patients succumb to metastasis after curative surgery. We used microarrays to detail gene expression and identified a metastasis-prone signature for early stage CRC. Keywords: RNA expression Tumors from age- and ethnicity-matched 70 patients and biopsies from 12 healthy controls were used. We aimed to find a metastasis-prone signature for early stage CRC by genome-wide expression profiling of age- and ethnicity-matched patients and healthy controls using the Affymetrix U133 Plus 2 array.
2010-02-15 | E-GEOD-9348 | biostudies-arrayexpress
Project description:Extracellular vesicles (EVs) are valuable sources for the discovery of useful cancer biomarkers. This study explores the potential usefulness of tumor cell-derived EV membrane proteins as plasma biomarkers for early detection of colorectal cancer (CRC). EVs were isolated from the culture supernatants of four CRC cell lines by ultracentrifugation, and their protein profiles were analyzed by LC-MS/MS. Bioinformatics analysis of identified proteins revealed 518 EV membrane proteins in common among at least three CRC cell lines. We next used accurate in-clusion mass screening (AIMS) in parallel with iTRAQ-based quantitative proteomic analysis to highlight candidate proteins and validated their presence in pooled plasma-generated EVs from 30 healthy controls and 30 CRC patients. From these, we chose 14 potential EV-derived targets for further quantification by targeted MS assay in a separate individual cohort comprising of 73 CRC and 80 healthy subjects. Quantitative analyses revealed significant increases in ADAM10, CD59 and TSPAN9 levels (2.19- to 5.26-fold, p <0.0001) in plasma EVs from CRC patients, with AUC values of 0.83, 0.95 and 0.87, respectively. Higher EV CD59 levels were significantly corre-lated with distant metastasis (p = 0.0475), and higher EV TSPAN9 levels were significantly asso-ciated with lymph node metastasis (p = 0.0011), distant metastasis at diagnosis (p = 0.0104) and higher TNM stage (p = 0.0065). A two-marker panel consisting of CD59 and TSPAN9 outper-formed the conventional marker CEA in discriminating CRC and stage I/II CRC patients from healthy controls, with AUC values of 0.98 and 0.99, respectively. Our results identify EV mem-brane proteins in common among CRC cell lines and altered plasma EV protein profiles in CRC patients, and suggest plasma EV CD59 and TSPAN9 as a novel biomarker panel for detecting early-stage CRC.
2023-03-11 | PXD038871 | Pride
Project description:Transcriptional profiling of Homo sapiens inflammatory skin diseases (whole skin biospies): Psoriasis (Pso), vs Atopic Dermatitis (AD) vs Lichen planus (Li), vs Contact Eczema (KE), vs Healthy control (KO) In recent years, different genes and proteins have been highlighted as potential biomarkers for psoriasis, one of the most common inflammatory skin diseases worldwide. However, most of these markers are not psoriasis-specific but also found in other inflammatory disorders. We performed an unsupervised cluster analysis of gene expression profiles in 150 psoriasis patients and other inflammatory skin diseases (atopic dermatitis, lichen planus, contact eczema, and healthy controls). We identified a cluster of IL-17/TNFα-associated genes specifically expressed in psoriasis, among which IL-36γ was the most outstanding marker. In subsequent immunohistological analyses IL-36γ was confirmed to be expressed in psoriasis lesions only. IL-36γ peripheral blood serum levels were found to be closely associated with disease activity, and they decreased after anti-TNFα-treatment. Furthermore, IL-36γ immunohistochemistry was found to be a helpful marker in the histological differential diagnosis between psoriasis and eczema in diagnostically challenging cases. These features highlight IL-36γ as a valuable biomarker in psoriasis patients, both for diagnostic purposes and measurement of disease activity during the clinical course. Furthermore, IL-36γ might also provide a future drug target, due to its potential amplifier role in TNFα- and IL-17 pathways in psoriatic skin inflammation. In recent years, different genes and proteins have been highlighted as potential biomarkers for psoriasis, one of the most common inflammatory skin diseases worldwide. However, most of these markers are not psoriasis-specific but also found in other inflammatory disorders. We performed an unsupervised cluster analysis of gene expression profiles in 150 psoriasis patients and other inflammatory skin diseases (atopic dermatitis, lichen planus, contact eczema, and healthy controls). We identified a cluster of IL-17/TNFα-associated genes specifically expressed in psoriasis, among which IL-36γ was the most outstanding marker. In subsequent immunohistological analyses IL-36γ was confirmed to be expressed in psoriasis lesions only. IL-36γ peripheral blood serum levels were found to be closely associated with disease activity, and they decreased after anti-TNFα-treatment. Furthermore, IL-36γ immunohistochemistry was found to be a helpful marker in the histological differential diagnosis between psoriasis and eczema in diagnostically challenging cases. These features highlight IL-36γ as a valuable biomarker in psoriasis patients, both for diagnostic purposes and measurement of disease activity during the clinical course. Furthermore, IL-36γ might also provide a future drug target, due to its potential amplifier role in TNFα- and IL-17 pathways in psoriatic skin inflammation.
2014-12-02 | GSE63741 | GEO
Project description:Background Early cancer detection has the potential to significantly improve treatment outcomes and survival rates. This study investigates the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) as biomarkers for early-stage colorectal cancer (CRC) detection in cell-free DNA (cfDNA). Methods We analyzed cfDNA from 37 treatment-naive CRC patients and 32 healthy controls using duet evoC 6-base whole genome sequencing (A, C, T, G, 5mC, 5hmC). We then built CRC classifiers using differentially methylated regions identified in stage IV CRC tissue samples. We compared the performance of models using 5mC-only, 5hmC-only, modified cytosine, or 5mC and 5hmC features. Results Here we show that models combining measurements of 5mC and 5hmC significantly enhance diagnostic accuracy (AUC = 0.95) compared to traditional approaches that conflate these markers (modified C, AUC = 0.66). Notably, of all the DMRs considered, almost half show an increase in 5hmC at stage I and a corresponding decrease in 5mC at stage IV, suggesting that 5hmC can effectively track regions undergoing demethylation during tumor development. Conclusions These results support the hypothesis that distinguishing between 5mC and 5hmC improves the sensitivity of liquid biopsy tests for early-stage cancer detection.
2025-12-02 | GSE311517 | GEO