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Feasibility of unbiased RNA profiling of colorectal tumors: a proof of principle.

ABSTRACT: Liquid biopsy profile which can screen for early CRC. We aimed to depict the profile of early stage CRC as well as for advanced adenomas by combination of current molecular knowledge with microarray technology, using efficient circulating free RNA purification from blood and RNA amplification technologies. Circulating free RNA profile of plasma from colorectal cancer patients, advanced adenomas and healthy colonoscopia subjects.

ORGANISM(S): Homo sapiens

PROVIDER: GSE83353 | GEO | 2016/06/15

SECONDARY ACCESSION(S): PRJNA325661

REPOSITORIES: GEO

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Feasibility of unbiased RNA profiling of colorectal tumors: a proof of principle.

Project description:Liquid biopsy profile which can screen for early CRC. We aimed to depict the profile of early stage CRC as well as for advanced adenomas by combination of current molecular knowledge with microarray technology, using efficient circulating free RNA purification from blood and RNA amplification technologies. Circulating free RNA profile of plasma from colorectal cancer patients, advanced adenomas and healthy colonoscopia subjects. Plasma was drawn from 3 healthy colonoscopia subjects, 4 adanced adenomas subjects and 3 colorectal cancer patients. Circulating free RNA was purified from plasma samples and applied on GeneChip human 1.0 ST Arrays. The 'HuGene_1_0_green_yelow_red_DATASET.xlsx' and 'probe_level_expression_matrix.txt' files contain the primary data that was used to draw the conclusions of the current study. Please note that exon-level' analysis was performed but NO probe summarization to probeset was performed, therefore both data matrices contains non-unique identifiers.

2016-06-15 | E-GEOD-83353 | biostudies-arrayexpress

Feasibility of Unbiased RNA Profiling of Colorectal Tumors: A Proof of Principle.

Project description:Despite recent advances in molecular profiling of colorectal cancer (CRC), as of yet this has not translated into an unbiased molecular liquid biopsy profile which can accurately screen for early CRC. In this study we depict the profile of early stage CRC as well as for advanced adenomas (AA) by combination of current molecular knowledge with microarray technology, using efficient circulating free plasma RNA purification from blood and RNA amplification technologies. We joined literature search with Affymetrix gene chip experimental procedure to draw the circulating free plasma RNA profile of colorectal cancer disease reflected in blood. The RNA panel was tested by two datasets comparing patients with CRC with healthy subjects and patients with AA to healthy subjects. For the CRC patient cohort (28 CRC cases vs. 41 healthy controls), the ROC analysis of the selected biomarker panel generated a sensitivity of 75% and a specificity of 93% for the detection of CRC using 8-gene classification model. For the AA patient cohort (28 subjects vs. 46 healthy controls), a sensitivity of 60% and a specificity of 87% were calculated using a 2-gene classification model. We have identified a panel of 8 plasma RNA markers as a preliminary panel for CRC detection and subset markers suitable for AA detection. Subjected to extensive clinical validation we suggest that this panel represents a feasible approach and a potential strategy for noninvasive early diagnosis, as a first-line screening test for asymptomatic, average-risk population before colonoscopy.

| S-EPMC4956030 | biostudies-literature

Real-time quantitative miRNA PCR analysis of human plasma samples; circulating miRNAs miR-34a and miR-150 associated with colorectal cancer progression

Project description:Background: Screening for the early detection of colorectal cancer is important to improve patient survival. The aim of this study was to investigate the potential of circulating cell-free miRNAs as biomarkers of CRC, and their efficiency at delineating patients with polyps and benign adenomas from normal and cancer patient groups. Methods: The expression of 667 miRNAs was assessed in a discovery set of 48 plasma samples comprising normal, polyp, adenoma, and early and advanced cancer samples. Three miRNAs (miR-34a, miR-150, and miR-923) were further examined in a validation cohort of 97 subjects divided into the same five groups, and in an independent public dataset of 40 CRC samples and paired normal tissues. Results: High levels of circulating miR-34a and low miR-150 levels distinguished groups of patients with polyps from those with advanced cancer (AUC=0.904), and low circulating miR-150 levels separated patients with adenomas from those with advanced cancer (AUC=0.875). In addition, the altered expression of miR-34a and miR-150 in an independent public dataset of forty CRC samples and paired normal tissues was confirmed. Conclusion: We identified two circulating miRNAs capable of distinguishing patient groups with different diseases of the colon from each other, and patients with advanced cancer from benign disease groups.

2015-03-20 | GSE67075 | GEO

Methylation analysis of serum cfDNA pooled samples for the discovery of non-invasive biomarkers for colorectal cancer

Project description:We explored the differential methylation patterns found in cfDNA between no neoplasia (NN; individuals with no colorectal findings, benign pathologies and non-advanced adenomas) and patients with advanced neoplasia (AN; advanced adenomas and colorectal cancer) using pooled samples, for the discovery of non-invasive methylation biomarkers for CRC screening. cfDNA was extracted from serum samples and methylation measurements were assessed with the Infinium MethylationEPIC BeadChip. Data was mainly preprocessed and analyzed with R/Bioconductor packages.

2023-10-01 | GSE186381 | GEO

Plasma microRNA profiling by microarray elucidates several candidate biomarkers for colorectal cancer screening

Project description:MicroRNAs (miRNAs) are small non-coding RNA molecules which function as negative gene regulators. The tissue expression profile of miRNAs shows great promise as a novel biomarker for diagnosis of cancer and other diseases. In addition, some recent reports have demonstrated that are present in human serum and plasma which could make them an ideal non-invasive biomarker for diagnosis of cancer. The aim of this study is to analyze the value/efficacy of the expression profile of plasma miRNAs in differentiating between patients with advanced adenomas and CRC and healthy individuals. The microRNA profiling study comprises serum plasmas from 20 Control, 21 colorectal cancer,20 advanced adenomas.The study also include some samples from patients after treatment.

2013-01-11 | E-GEOD-25609 | biostudies-arrayexpress

Plasma microRNA profiling by microarray elucidates several candidate biomarkers for colorectal cancer screening

2013-01-11 | GSE25609 | GEO

Novel stool-based protein biomarkers for improved colorectal cancer screening

Project description:Fecal immunochemical tests (FIT) detecting hemoglobin in stool are widely used for non-invasive colorectal cancer (CRC) screening, but their sensitivity leaves room for improvement. Our aim is to identify novel protein biomarkers in stool that outperform or complement hemoglobin in detecting CRCs and advanced adenomas (AAs). Stool samples (one series of 12 CRCs and 10 controls, and a second series of 81 CRCs, 40 AAs, 43 non-advanced adenomas and 129 controls) were analyzed by mass-spectrometry and searched for human proteins. Classification and regression tree and logistic regression analyses were performed to identify protein combinations that differentiated CRCs and/or AAs from controls. Antibody-based assays for four selected proteins were performed on an independent series of FIT samples (14 CRCs, 16 AAs, 18 non-advanced adenomas and 24 controls) Results: In total, 834 human proteins were identified, of which 29 were significantly enriched in CRCs versus controls in both stool sample series. Combinations of four proteins reached sensitivities of 80% and 45% for detecting CRCs and AAs, at 95% specificity, which was higher than hemoglobin alone.

2020-05-26 | PXD007767 | Pride

Double-tiled DNA microarrays -- proof of principle

Project description:We have developed a double-tiling method that effectively doubles the number of sequences on a microarray, and with these arrays we confirm that our design can be utilized quickly and easily. Keywords: testing novel microarray design

2006-10-23 | GSE5721 | GEO

Pre-clinical proof of principle for orally delivered Th17 antagonist miniproteins

Project description:Interleukin (IL)-23 and IL-17 are well-validated therapeutic targets in autoinflammatory diseases. Antibodies targeting IL-23 and IL-17 have shown clinical efficacy but are limited by high costs, safety risks, lack of sustained efficacy, and poor patient convenience as they require parenteral administration. Here, we present designed miniproteins inhibiting IL-23R and IL-17 with antibody-like, low picomolar affinities at a fraction of the molecular size. The minibinders potently block cell signaling in vitro and are extremely stable, enabling oral administration and low-cost manufacturing. The orally administered IL-23R minibinder shows efficacy better than a clinical anti-IL-23 antibody in mouse colitis and has a favorable pharmacokinetics (PK) and biodistribution profile in rats. This work demonstrates that orally administered de novo-designed minibinders can reach a therapeutic target past the gut epithelial barrier. With high potency, gut stability, and straightforward manufacturability, de novo-designed minibinders are a promising modality for oral biologics.

2024-06-26 | GSE263250 | GEO

LncRNA ITGB8-AS1 functions as a ceRNA to promote colorectal cancer growth and migration through integrin-mediated focal adhesion signaling

Project description:ITGB8-AS1 functions as a ceRNA to regulate cell proliferation and tumor growth of colorectal cancer (CRC) via regulating focal adhesion signaling. Targeting ITGB8-AS1 is effective in suppressing CRC cell growth and tumor growth. Elevated plasma levels of ITGB8-AS1 was detected in advanced-stage CRC. Thus, ITGB8-AS1 could serve as a potential therapeutic target and circulating biomarker in CRC.

2023-11-28 | GSE162297 | GEO

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