MiRNA array in colorectal carcinoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE33961 | GEO | 2011/11/29
SECONDARY ACCESSION(S): PRJNA150529
REPOSITORIES: GEO
Similar Datasets
Project description:To search for potential miRNAs associated with prognosis in colorectal carcinoma, miRNA expression profiles were analyzed in patients with stage III colorectal carcinoma. miRNA expression levels were compared between long and short time survival after surgery with standard chemotherapy. Two groups of colorectal carcinoma tissues for miRNA array. Long time (L) survival (≥5 years) group and short time survival (S) (<5 years) group.
2011-11-29 | E-GEOD-33961 | biostudies-arrayexpress
Project description:REMAUS04 is a phase III trial comparing DNA array-based chemotherapy (by DLD30 score and TOP2A expression) to standard neoadjuvant chemotherapy, in patients with HER2-negative breast carcinoma not eligible for conserving surgery. We evaluated whether whole genome array approach is feasible in daily practice, and if the use of a genomic score (DLD30/TOP2A) improves chemotherapy efficacy.
2016-07-01 | GSE63471 | GEO
Project description:Colorectal cancer (CRC) has one of the highest worldwide incidences and mortality rates. Compared to surgery alone, adjuvant 5-Fluorouracil (5FU)-based chemotherapy improves 5-year overall survival (OS) in only 3-4% of stage II and 15-20% of stage III patients in unselected populations. Significant advances have been made in the molecular stratification of CRC, with the emerging Consensus Molecular Subtype (CMS) and Colorectal Cancer Intrinsic Signature (CRIS) transcriptomics-based classification systems; however, the therapeutic impact of molecular stratification has so far been limited. In an effort to identify subgroups of patients benefitting from chemotherapy, we assessed which CMS and CRIS subgroups of stage II and III CRC benefitted from adjuvant 5FU-based chemotherapy using in-house and published datasets.
2017-12-31 | GSE103479 | GEO
Project description:REMAUS04 is a phase III trial comparing DNA array-based chemotherapy (by DLD30 score and TOP2A expression) to standard neoadjuvant chemotherapy, in patients with HER2-negative breast carcinoma not eligible for conserving surgery. We evaluated whether whole genome array approach is feasible in daily practice, and if the use of a genomic score (DLD30/TOP2A) improves chemotherapy efficacy. DNA arrays were performed within 15 days after tumor biopsy. Only samples with >30% cancer cells, a RIN>6 and good cDNA quality were eligible for hybridization on arrays U133Av2.
2016-07-01 | E-GEOD-63471 | biostudies-arrayexpress
Project description:The aim of our study was to evaluate the ability of miRNA expression patterns to predict chemotherapy response in a cohort of 39 patients with metastatic colorectal carcinoma
2014-08-12 | GSE48664 | GEO
Project description:Background: Capecitabine-based adjuvant chemotherapy is the first-line treatment for patients with colorectal cancer (CRC). Although this therapy generally reduces the incidence of CRC recurrence and mortality, it can cause various chemotherapy-related adverse events (CRAEs), one of the most frequent of which is hand-foot syndrome (HFS). Most of the currently available HFS prediction markers focus on the pharmacokinetic parameters of drugs or their metabolites, yet our understanding of the biomolecular mechanism of HFS remains limited. Methods: We conducted an integrated multi-omics analysis of 63 Chinese patients with colorectal cancer (CRC) who had chemotherapy related adverse effect (CRAE) records during adjuvant chemotherapy. The metabolomic profiles for each of plasma, urine, and colorectal tissue as well as profiles for colorectal-tissue transcriptomics and genome methylation were analyzed based on samples collected before and during surgery. Results: Susceptibility to HFS was found to be associated with profibrotic changes in several aspects of cellular biochemistry and physiology, characterized by reduced nucleotide salvage (indicating potential tissue damage, elevated spermine release, increased M2 macrophage polarization, and hypermethylation of genes for collagen formation. All these aspects were found to promote fibrosis, even before patients received chemotherapeutic drugs or developed any HFS symptoms. Additionally, we developed and validated relevant biomarkers with reasonably good discrimination performance and a high AUROC (area under the receiver operating characteristic curve) value, i.e., from 0.848 to 1.000. Conclusions: Our results demonstrate that a profibrotic phenotype characterized by multi-omics variation in colorectal tissue, plasma, and urine is closely related to the susceptibility to chemotherapy-induced HFS. Our findings provide a better understanding of the molecular mechanism underlying HFS.
2021-08-27 | GSE171550 | GEO
Project description:Approximately two decades ago, Vogelstein and Fearon proposed the adenoma-carcinoma sequence of sporadic CRC development and illustrated the accumulation of genetic alterations during the stepwise progression, thereby providing a guideline for clinical practice. Although the detection and excision of precancerous lesions could prevent colorectal cancer and reduce mortality, 6% of adenomas will ultimately develop into colorectal cancer. Thus, this genetic model for colorectal tumorigenesis may not completely reflect the complex essence of the disease and whether the mode of initiation of the events in the multistep progression affects the outcome of CRC is still unknown. In this study, mRNA and miRNA expression profiling was performed with human colorectal tissues, including normal mucosa, adenoma and adenocarcinoma. Then, an integrated approach was adopted to establish the regulatory interaction networks that were correlated with colorectal carcinogenesis. Finally, a 55-gene signature whose expression was down-regulated in precancerous lesions compared to normal tissue was identified as a potential early indicator of CRC survival. The results suggested that genes related to immunity and homeostasis played a critical role in protection against adenoma initiation and that the altered molecular events that influence colorectal cancer prognosis may be set in an early, precancerous stage. Four types of human colorectal tissues were selected by colonoscopic resection or colorectal surgery, including 15 normal mucosae, 39 low-grade adenomas (mild or moderate atypical hyperplasia), 20 high-grade adenomas (severe atypical hyperplasia or carcinoma in situ) and 33 adenocarcinomas. MicroRNA expression profiling analysis of these samples was performed on Agilent 8Ã16K Human miRNA Microarray V3 (G4470C).
2015-10-16 | E-GEOD-41655 | biostudies-arrayexpress
Project description:The human miRNA profiles of esophageal squamous cell carcinoma are rarely reported. Surgically removed human ESCC tissues and matched normal esophageal epithelial tissues (5cm away from tumor) were collected to make an Agilent microarray. Three paired of human ESCC tissues and normal controls were collected. All patients have no radiotherapy or chemotherapy before surgery. None of these three patients have distant metastasis.
2015-08-07 | E-GEOD-59973 | biostudies-arrayexpress
Project description:The aim of our study was to evaluate the ability of miRNA expression patterns to predict chemotherapy response in a cohort of 39 patients with metastatic colorectal carcinoma To define miRNA signature, samples were obtained from tumor tissue samples of 39 patients . Patients were divided into responders or non-responders according to tresponse treatment with a chemotherapy regimen that included fluoropyrimidines and either oxaliplatin or irinotecan .Tumor response was evaluated by conventional methods according to the standard RECIST 1.0 criteria: a complete response (CR) was defined as the disappearance of all measurable and evaluable evidence of disease; a partial response (PR) was defined as a > 30% decrease in the sum of the longest diameters of target lesions; stable disease (SD) was considered if the tumor burden decreased less than 30% or increased less than 20%; and progressive disease (PD) was indicated by a >20% increase in the sum of the longest diameters of target lesions or the appearance of any new lesion. Patients were classified according to best response to chemotherapy in two groups: those that achieved an objective response (Responders [R]: CR + PR) and those that did not (Non-responders [NR]: SD + PD). Mature human miRNA expression was detected and quantified using the TaqMan® Low Density Arrays (TLDA). The Human MicroRNA Card Set v2.0 array is a two card set containing a total of 384 TaqMan® MicroRNA Assays per card to enable accurate quantification of 667 human microRNAs, all catalogued in the miRBase database. Expression of target miRNAs was normalized in relation to the expression of MammU6. Cycle threshold (Ct) values were calculated using the SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. Relative quantification of miRNA expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)).
2014-08-12 | E-GEOD-48664 | biostudies-arrayexpress
Project description:Approximately two decades ago, Vogelstein and Fearon proposed the adenoma-carcinoma sequence of sporadic CRC development and illustrated the accumulation of genetic alterations during the stepwise progression, thereby providing a guideline for clinical practice. Although the detection and excision of precancerous lesions could prevent colorectal cancer and reduce mortality, 6% of adenomas will ultimately develop into colorectal cancer. Thus, this genetic model for colorectal tumorigenesis may not completely reflect the complex essence of the disease and whether the mode of initiation of the events in the multistep progression affects the outcome of CRC is still unknown. In this study, mRNA and miRNA expression profiling was performed with human colorectal tissues, including normal mucosa, adenoma and adenocarcinoma. Then, an integrated approach was adopted to establish the regulatory interaction networks that were correlated with colorectal carcinogenesis. Finally, a 55-gene signature whose expression was down-regulated in precancerous lesions compared to normal tissue was identified as a potential early indicator of CRC survival. The results suggested that genes related to immunity and homeostasis played a critical role in protection against adenoma initiation and that the altered molecular events that influence colorectal cancer prognosis may be set in an early, precancerous stage. Four types of human colorectal tissues were selected by colonoscopic resection or colorectal surgery, including 12 normal mucosae, 21 low-grade adenomas (mild or moderate atypical hyperplasia), 30 high-grade adenomas (severe atypical hyperplasia or carcinoma in situ) and 25 adenocarcinomas. Gene expression profiling analysis of these samples was performed using Agilent 4x44K human whole genome gene expression microarray (G4112F).
2015-10-16 | E-GEOD-41657 | biostudies-arrayexpress