Tissue and blood microRNA array profiles of colorectal cancer patients
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ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE39845 | GEO | 2013/12/30
SECONDARY ACCESSION(S): PRJNA171850
REPOSITORIES: GEO
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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).
2013-12-30 | E-GEOD-39845 | biostudies-arrayexpress
Project description:Association studies have linked alterations of blood-derived circulating microRNAs (ci-miRNAs) with colorectal cancer (CRC). However, questions remain about the specificity of these abundance variations as biomarkers and their effects on the haematogenous spread of metastatic CRC (mCRC).
2021-07-17 | GSE180202 | GEO
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
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.
2013-01-11 | GSE25609 | GEO
Project description:Purpose: Preoperative 5-fluorouracil (5-FU) based radiochemotherapy (RCT) represents the standard treatment for locally advanced rectal cancer. Both, tumor response and progression vary considerably. MicroRNAs represent master regulators of gene expression, and may therefore contribute to this heterogeneity. Results: Thirty-six miRNAs were identified to significantly correlate with sensitivity of CRC cell lines to RCT (q < 0.05). This list included miR320a as most significantly correlated as well as other miRNAs involved in the MAPK-, TGF- and Wnt-pathway. Importantly, transfection of selected miRNAs (let7g, miR-132, miR-224, miR-320a and miR-429) each induced a shift of sensitivity (p<0.00001). Moreover, high expression of miR-224 was associated with a poor prognosis in rectal cancer patients (p=0.043). Experimental design: Genome-wide microRNA (miRNA) profiling was performed from 12 colorectal cancer (CRC) cell lines. To establish an in vitro signature of radiochemosensitivity, these profiles were correlated to the individual sensitivities of each cell line to 5-FU and radiation. The functional relevance of selected miRNAs was validated by transfecting miRNA-mimics into SW480 cells, followed by treatment with 5-FU and radiation. 12 Samples with 3 replicates each.
2013-09-01 | E-GEOD-40976 | biostudies-arrayexpress
Project description:Colorectal cancer is the 3rd commonly diagnosed cancer (10.2%) and 2nd cause of cancer death (9.2%) in all cancers.There will be estimated 1.8 million new colorectal cancer cases and 0.9 million colorectal cancer deaths in 20181. As the 5th incidence rates and mortality rates cancer in china, colorectal cancer incidence rates has increased from 1990 to 20112,3. CRC is concidered as a muti-step progress diseases4, patients with precursors lesions and early stage CRC can get great benefit from surgical treatment, colonoscope can detect visiable early dieases but not suitable for large-scale screening5, because of the poor sensitivity or specificity, blood carcinoembryonic antigen(CEA)6,7 and fecal blood testing(FOBT)8 provide limited help. There is no standard biomarker predicting CRC lymph node and liver metastasis4, although It’s very valuable for patients and docter before and after surgery9. Liver is the main site for colorectal cancer metastasis10, hepatic resection is the only treatment and successful for CRC-LM11, Unfortunately, over 50% of patients who get hepatic resection develop recurrences11, since then it’s hlepful to find biomarkers for monitoring CRC metastasis, blood CEA has been accepted as indicator of CRC progress12, in current study, we aim to explore a more convient and presion way for monitoring CRC metastasis.
2022-03-15 | PXD032291 |
Project description:The purpose of this study is to identify miRNAs involved in the pathology of colorectal cancer (CRC) liver metastasis and investigate their underlying mechanisms. A total of 39 miRNAs were identified to be differentially expressed between 16 primary CRC tissues with liver metastases and 16 CRC tissues without liver metastases from 32 patients by Affymetric miRNA microarrays. 16 coloretcal cancer tissues with liver metastasis and 16 colorectal cancer tissues without liver metastasis were included in this study for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the differentially expressed miRNAs between colorectal cancer tissues with and without liver metastasis.
2013-12-10 | E-GEOD-53159 | biostudies-arrayexpress
Project description:Aberrant DNA hypermethylation of CpG islands occurs frequently throughout the genome in human colorectal cancer (CRC). A genome-scale DNA hypermethylation analysis technique using plasma is attractive for the noninvasive early detection of CRC. The methylated CpG tandems amplification and sequencing (MCTA-Seq) method was applied to plasma samples from 147 CRC patients and 134 controls in which 5 from the CRC patients and 2 from the control subjects failed to pass a quality control value and were excluded from further analysis. The capacity of the method for discriminating CRC and hepatocellular carcinoma (HCC) was assessed. We identified many DNA methylation markers including known (e.g., SEPT9 and IKZF1) and novel (e.g., EMBP1, KCNQ5 and CHST11) CpG islands for detecting CRC in blood. A panel of 80 markers significantly discriminated early stage CRC and controls with a sensitivity of 78% and a specificity of 90%. This method can efficiently distinguish between early stage CRC and HCC. MCTA-Seq is a promising method for the noninvasive detection of CRC that also shows great potential for identifying the tissue of origin of cancer.
2019-05-31 | GSE124600 | GEO
Project description:To establish a genomewide miRNA profile of colorectal cancer-derived induced pluripotent cancer cell lines (CRC-iPC). CRC-iPC clones and two parental cell lines were subjected to miRNA microarray analysis using SurePrint Human MiRNA Microarray Release 21.0 (Agilent). In order to identify the differentially-expressed miRNAs after OSKM-reprogramming, the miRNA expression of CRC-iPCs was relatively compared to that of parental colorectal cancer cell lines. Using a stringent selection criteria of log2(fold change) (FC) ≥ 2.0 or < -2.0 and p-value < 0.05, a total of 102 statistically significant differentially-expressed miRNAs were identified. Amongst the 102 miRNAs, 50 miRNAs were down-regulated and 52 miRNAs were up-regulated. Four miRNAs (miR-362-5p, miR-532-3p, miR-125b-5p, and miR199a-3p) were randomly selected for validation by quantitative real-time PCR, the results were consistent with that of the microarray results. To establish a genomewide miRNA profile of colorectal cancer-derived induced pluripotent cancer cell lines (CRC-iPC). CRC-iPC clones and two parental cell lines were subjected to miRNA microarray analysis using SurePrint Human MiRNA Microarray Release 21.0 (Agilent). In order to identify the differentially-expressed miRNAs after OSKM-reprogramming, the miRNA expression of CRC-iPCs was relatively compared to that of parental colorectal cancer cell lines. Using a stringent selection criteria of log2(fold change) (FC) ≥ 2.0 or < -2.0 and p-value < 0.05, a total of 102 statistically significant differentially-expressed miRNAs were identified. Amongst the 102 miRNAs, 50 miRNAs were down-regulated and 52 miRNAs were up-regulated. Four miRNAs (miR-362-5p, miR-532-3p, miR-125b-5p, and miR199a-3p) were randomly selected for validation by quantitative real-time PCR, the results were consistent with that of the microarray results.
2018-07-31 | GSE87280 | GEO
Project description:Abstract: Altered expression of microRNAs (miRNAs) is associated with development and progression of various human cancers by regulating the translation of oncogenes and tumor suppressor genes. In colorectal cancer (CRC), these regulators complement the Vogelstein multi-step model of pathogenesis and have the potential of becoming a novel class of tumor biomarkers and therapeutic targets. Using QRT-PCR, we measured the expression of 621 mature miRNAs in 40 CRCs and their paired normal tissues and identified 23 significantly deregulated miRNAs. We subsequently evaluated their association with clinical characteristics of the samples and presence of alterations in the molecular markers of CRC progression. Expression levels of miR-31 were correlated with CA19-9 and miR-18a, miR-21 and miR-31 were associated with mutations in APC gene. To investigate the downstream regulation of the differentially expressed miRNAs identified we integrated putative mRNA target predictions with the results of a meta-analysis of seven public gene expression datasets of normal and tumor samples of CRC patients. Many of the CRC deregulated miRNAs computationally map to targets involved in pathways related to progression. Here one promising candidate pair (miR-1 and MET) was studied and functionally validated. We show that miR-1 can have a tumor suppressor function in CRC by directly down-regulating MET oncogene both at RNA and protein level and that re-expression of miR-1 leads to MET driven reduction of cell proliferation and motility, identifying the miR-1 down-modulation as one of the events that could enhance CRC progression. Note: Each sample has the following information: Type - tissue type (T : Tumor or N: Normal), Patient - patient identifier, Stage - tumor stage (I - IV), Status - disease status at last check-up (ED: evident disease, NED: non-evident disease), CEA - carcinoembryonic antigen (continuous), CA199 - carbohydrate antigen 19-9 (continuous), APC - mutation status of APC gene (0: wild-type, 1: mutated), KRAS - mutation status of KRAS gene (0: wild-type, 1: mutated), chr18qLOH - LOH status of 18q (0: no LOH, 1: LOH), TP53 - mutation status of TP53 gene (0: wild-type, 1: mutated). Tumor and normal counter-parts of 40 colorectal cancer patients (10 of each Stage I to IV) where profiled using TaqMan(r) Array Human MicroRNA A+B Cards v2.0
2012-02-22 | E-GEOD-28364 | biostudies-arrayexpress