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.
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.
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).
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.
Project description:The objective is to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases. The identification of new less invasive biomarkers is necessary to improve the detection and prognostic outcome of respiratory pathological processes. The measurement of miRNA expression through less invasive techniques such as plasma and serum have been suggested to analysis of several lung malignancies including lung cancer. These studies are assuming a common deregulated miRNA expression both in blood and lung tissue. The present study aimed to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases. we have compared circulating plasma miRNA with the bronchoalveolar cell fraction-derived miRNA patterns from 10 patients with several lung disease using a RT-qPCR assay.
Project description:microRNAs (miRNAs) are short, non-coding RNA molecules that act as regulators of gene expression. Circulating blood miRNAs offer great potential as cancer biomarkers. The objective of the study was to correlate the differential expression of miRNAs in tissue and blood in the identification of biomarkers for early detection of colorectal cancer (CRC). miRNA biomarker discovery via miRNA array profiling using paired cancer tissues (n = 30) and blood samples (CRC, n = 42; control, n = 18).
Project description:The plasma levels of tissue-specific microRNAs can be used as prognostic and diagnostic biomarkers for chronic and acute diseases. Thereby, the combination of diverse miRNAs into biomarker signatures using multivariate statistics seems especially powerful in view to tissue and condition specific miRNA shedding into the plasma. Although Next-Generation Sequencing (NGS) technology enables to analyse circulating microRNAs on a genome-scale level, it suffers from potential biases (e.g. adapter ligation bias) and lacks absolute transcript quantitation. In order to develop a robust NGS discovery assay for genome-scale quantitation of circulating microRNAs we first evaluated the sensitivity, repeatability and ligation bias of four commercially available small RNA library preparation protocols. The protocol from RealSeq Biosciences was selected based on its performance and usability, and coupled with a novel panel of exogenous small RNA spike-in controls to enable absolute quantitation and ensure comparability of data across independent NGS experiments. The established MicroRNA Next-Generation-Sequencing Discovery Assay (miND) was validated for its relative accuracy, precision, analytical measurement range and sequencing bias and was considered fit-for-purpose for microRNA biomarker discovery. Summarized, all these criteria were met and thus our analytical platform is considered fit-for-purpose for microRNA biomarker discovery from plasma, serum, cerebrospinal fluid (CSF), synovial fluid (SF), or extracellular vesicles (EV) extracted from cell culture medium in the setting of any diagnostic, prognostic or patient stratification need.
Project description:Liver cancer is one of the most lethal cancers worldwide. Liquid biopsy provides a noninvasive approach in detecting and monitoring cancer biomarkers to overcome current limitations associated with tissue biopsies, comprising the analysis of circulating tumor-derived material. In this study, we profiled plasma cell-free RNA-seq to identify recurrently dysregulated RNA biomarkers for the liquid biopsy of cancer.
Project description:Circulating tumor cells (CTCs) are the subject of several translational studies and clinical trials because their examination could offer an insight into tumor progression and clinical outcomes. Circulating tumor microemboli (CTM) are clusters of CTCs that have been described as malignant entities for over 50 years, although a comprehensive characterization of these cells is still lacking. Contrary to current consensus, we demonstrate that CTM isolated from colorectal cancer patients are not cancerous, but represent a discrete population of tumor-derived endothelial cells. CTM express epithelial and mesenchymal markers that are consistent with previous reports on circulating tumor cell phenotyping. However, they do not mirror the genetic variations of matching tumors. Transcriptome analysis of single-CTM reveals that these structures exhibit an endothelial phenotype, with further results supporting a tumor-derived endothelial lineage. CTM are widespread in blood sampled from preoperative cancer patients but not in healthy donors, suggesting CTM count as a potential biomarker of interest for colorectal cancer. CTM should not be confused with bona fide circulating epithelial tumor cells. The characterization of tumor derived endothelial cell clusters (TECCs) is likely of high diagnostic value, and may provide direct information about the underlying tumor vasculature at the time of diagnosis, during treatment and the course of the disease.