Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer (miRNA)
Ontology highlight
ABSTRACT:
ORGANISM(S): Human alphaherpesvirus 1 Rattus norvegicus Betapolyomavirus hominis Mus musculus Human gammaherpesvirus 8 JC polyomavirus Betapolyomavirus macacae Homo sapiens human gammaherpesvirus 4 Human immunodeficiency virus 1 Human betaherpesvirus 5
PROVIDER: GSE41012 | GEO | 2015/09/30
SECONDARY ACCESSION(S): PRJNA175535
REPOSITORIES: GEO
Similar Datasets
Project description:Global gene profile of TNM-specific sequence design and integrated network-based bioinformatic analysis in 20 Colorectal cancer patients(n=5 for each TNM stage) are carried out to find the dynamic gene expression pattern specific to TNM stage. microRNA microrray experiment of the same samples were also performed. Two different platform of microarray data were analyzed together to uncover the potential biomarker for progression of colorectal cancer.
2015-09-30 | GSE41011 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2015-09-30 | GSE41015 | GEO
Project description:Matrix metalloproteinase-2 (MMP-2) plays a role in cell migration and invasion that involve degradation of extracellular matrix proteins as well as vascular remodeling. Increased expression of MMP-2 has often been observed in the tumors of colorectal cancer (CRC) patients. In order to unveil the perturbed proteomic signal during MMP-2-induced cancer progression, we analyzed MMP-2 dependent secretome change in HCT116 cancer cells by stable isotopic labeling with amino acids in cell culture (SILAC), together with the plasma proteome profile of CRC patients by label-free quantification according to disease progression from TNM stage I to IV. We also analyzed public database of CRC tissue proteome deposited by Clinical Proteomic Tumor Analysis Consortium (NCI/NIH). As a strategy for integrating the multi-layered proteomes, we first performed unsupervised hierarchical clustering on plasma and tissue proteomes according to TNM stage, and then Fisher’s exact test to find out which clusters were significantly represented by the secretome decreased by more than 1.5-fold upon MMP-2 knock down. The resultant cluster included CD9-ITGB1-ITGA7 protein complex as well as MMP-2. The proteins included in this cluster were mostly related to cell-cell communications and cell motility, and showed remarkable increased expression in tissue and plasma upon disease progression from TNM I to II. MMP-2 induced activation of FAK phospho-signaling in an activity-dependent manner. With the comparative and integrative multi-layered proteomic analysis, we suggest that high invasiveness featured in the disease progression of colorectal cancer with increased secretion of MMP-2 is because MMP-2 activates FAK signaling through CD9-integrin complex and consequently induces positive feedback of MMP-2 upregulation.
2021-08-26 | PXD018304 | Pride
Project description:MicroRNAs (miRNAs) are intrinsic regulators in the various cellular processes, and their abnormalities are considered to be involved in the onset of human disorders, including cancer. Circulating miRNA is focused as new cancer biomarker however it is regarded that circulating RNA are released not only from tumor but also by various pathways. Recently, exosomes, small membrane vesicles, have been a major interest in cancer research field, because of their unique biological properties. Exosomes are secreted from various cells and the components (Lipids, mRNAs, miRNAs and proteins) reflect origin of the cells secreting them. Identification of exosomal miRNAs from cancer cells is expected to provide useful biomarkers of cancer. To identify specific exosomal miRNAs as candidate biomarkers for colorectal cancer, we profiled exosomal miRNAs in sera of colon cancer patients (n=88) at various TNM stages (I to IV) and healthy controls (n=11) and selected significantly higher microRNAs in serum exosomes of colorectal cancer patients than that of healthy controls. Moreover, we tried to detect their serum exosome levels of using samples from patients after surgical resection of primary tumors (n=24). Serum exosomes were prepared by step-wise ultra-centrifugation methods in 24 colorectal cancer patients (age; 35-65) after surgical resection of primary tumor (TNM stage I; n=6, stage II; n=5, stage IIIa; n=5, stage IIIb; n=5, stage IV; n=3) .Exosome fraction was mixed with Trizol-LS reagent (Invitrogen), and aqueous phase was collected by adding chloroform. After addition of ethanol to the aqueous phase, it was placed on to an RNeasy mini spin column (Qiagen) for the purification of total RNAs. The total RNAs were analyzed by Agilent Human miRNA V3 Microarray (G4470C) according to the manufacturer's instructions.
2014-04-01 | E-GEOD-40246 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are intrinsic regulators in the various cellular processes, and their abnormalities are considered to be involved in the onset of human disorders, including cancer. Circulating miRNA is focused as new cancer biomarker however it is regarded that circulating RNA are released not only from tumor but also by various pathways. Recently, exosomes, small membrane vesicles, have been a major interest in cancer research field, because of their unique biological properties. Exosomes are secreted from various cells and the components (Lipids, mRNAs, miRNAs and proteins) reflect origin of the cells secreting them. Identification of exosomal miRNAs from cancer cells is expected to provide useful biomarkers of cancer. To identify specific exosomal miRNAs as candidate biomarkers for colorectal cancer, we profiled exosomal miRNAs in sera of colon cancer patients (n=88) at various TNM stages (I to IV) and healthy controls (n=11) and selected significantly higher microRNAs in serum exosomes of colorectal cancer patients than that of healthy controls. Moreover, we tried to detect their serum exosome levels of using samples from patients after surgical resection of primary tumors (n=24). Serum exosomes were prepared by step-wise ultra-centrifugation methods in 11 healthy controls and 88 colorectal cancer patients with various TNM stages (I; n=20, stage II; n=20, stage IIIa; n=20, stage IIIb: n=16, stage IV; n=12) (age; 35-65) .Exosome fraction was mixed with Trizol-LS reagent (Invitrogen), and aqueous phase was collected by adding chloroform. After addition of ethanol to the aqueous phase, it was placed on to an RNeasy mini spin column (Qiagen) for the purification of total RNAs. The total RNAs were analyzed by Agilent Human miRNA V3 Microarray (G4470C) according to the manufacturer's instructions.
2014-04-01 | E-GEOD-39833 | biostudies-arrayexpress
Project description:In order to search for circRNA differentially expressed in colorectal cancer tissues and adjacent normal tissues, the cancer tissues and adjacent normal tissues of 3 patients with colorectal cancer(TNM:ⅡB) were selected for circRNA microarray detection. Differentially expressed circRNAs were screened.Then qRT-PCR was used to verify.
2022-04-27 | GSE197991 | GEO
Project description:Colorectal cancer molecular signatures derived from omics data can be employed to stratify CRC patients and aid decisions about therapies or evaluate prognostic outcome. However, molecular biomarkers for identification of patients at increased risk of disease relapse are currently lacking. Here, we present a comprehensive multi-omics analysis of a Danish colorectal cancer tumor cohort composed of 412 biopsies from tumors of 371 patients diagnosed at TNM stage II or III. From mass spectrometry-based patient proteome profiles, we classified the tumors into four molecular subtypes, including a mesenchymal-like subtype. As the mesenchymal-rich tumors are known to represent the most invasive and metastatic phenotype, we focused on the protein signature defining this subtype to evaluate their potential as relapse risk markers. Among signature-specific proteins, we followed-up Caveolae-Associated Protein-1 (CAVIN1) and demonstrated its role in tumor progression in a 3D in vitro model of colorectal cancer. Compared to previous omics analyses of CRC, our multi-omics classification provided deeper insights into EMT in cancer cells with stronger correlations with risk of relapse.
2025-03-17 | PXD056331 | Pride
Project description:With ever-increasing incidence and high metastatic potential, cutaneous melanoma is the deadliest skin cancer. Risk prediction based on the Tumor-Node-Metastasis (TNM) staging system has medium accuracy with intermediate IIB-IIIB stages, as roughly 25% of patients with low-medium-grade TNM, and hence a favorable prognostic, undergo an aggressive disease with short survival and around 15% of deaths arise from metastases of thin, low-risk lesions. Therefore, reliable prognostic biomarkers are required. We used genomic and clinical information of melanoma patients from the TCGA-SKCM cohort and two GEO studies for discovery and validation of potential biomarkers, respectively. Neither mutation nor overexpression of major melanoma driver genes provided significant prognostic information. Conversely, expression of MGRN1 and the melanocyte-specific genes MLANA, PMEL, and TYRP1 provided a simple 4-gene signature identifying with high-sensitivity (>80%), low-medium TNM patients with adverse outcomes. Transcriptomic analysis of tumors with this signature, or from low-medium-grade TNM patients with poor outcomes, revealed comparable dysregulation of an inflammatory response, cell cycle progression, and DNA damage/repair programs. A functional analysis of MGRN1- knockout cells confirmed these molecular features. Therefore, the simple MGRN1-MLANAPMEL- TYRP1 combination of biomarkers complemented TNM staging prognostic accuracy and pointed to the dysregulation of immunological responses and genomic stability as determinants of a melanoma outcome.
2025-09-14 | GSE305457 | GEO
Project description:Purpose: The goal of this experiment was to identify differentially expressed miRNAs between colon cancer patients with and without metachronous metastases. Background: Colon cancer prognosis and treatment are currently based on a classification system still showing large heterogeneity in clinical outcome, especially in TNM-stages II-III. Prognostic biomarkers for metastasis risk are warranted, as development of distant recurrent disease mainly accounts for the high lethality rates of colon cancer. MicroRNAs have been proposed as potential biomarkers for cancer. Furthermore, a verified standard for normalization of the amount of input material in PCR-based relative quantification of miRNA expression is lacking. Methods: A selection of frozen tumor specimens from two independent patient cohorts with TNM-stage II-III microsatellite stable primary adenocarcinomas were used for laser capture microdissection. Next-generation sequencing was performed on small RNAs isolated from colorectal tumors from the Dutch cohort (N=50). Differential expression analysis, comparing in metastasized- and non-metastasized tumors, identified prognostic microRNAs. Validation was performed on colon tumors from the German cohort (N=43) using qPCR. Results: MiR-25-3p and miR-339-5p were identified and validated as independent prognostic markers and used to construct a multivariate nomogram for metastasis risk prediction. The nomogram showed good probability prediction in validation. Additionally, we recommend combination of miR-16-5p and miR-26a-5p as standard for normalization in qPCR of colon cancer tissue-derived microRNA expression. Conclusions: In this international study, we identified and validated an miRNA classifier in primary cancers, and propose a nomogram capable of predicting metastasis risk in microsatellite stable TNM-stage II-III colon cancer.
2014-11-08 | GSE63119 | GEO
Project description:Colorectal cancer (CRC) is a common malignant gastrointestinal cancer. Efforts for preventive and personalized medicine have intensified in the last decade with attention to novel forms of biomarkers. In the present study, microRNA and genetic analyses were performed in tandem for differential transcriptome profiling between primary tumors with or without nodes or distant metastases. Serial Test Cluster (STC) analysis demonstrated that 20 genes and two microRNAs showed distinctive expression patterns associated with the tumor, node, and metastasis (TNM) stage. The selected target genes were characterized by GO and Pathway analysis. A microRNA-target gene network analysis showed that miR-429 resided in the center of the network, indicating that miR-429 might serve important roles in the development of CRC. Real-time PCR and tissue microarrays showed that miR-429 had a dynamic expression pattern during the CRC progression stage, and was significantly downregulated in stage II and stage III clinical progression. The low expression of miR-429 was correlated with poor prognosis for CRC. Taken together, miR-429 warrant further clinical translation research as a candidate biomarker for CRC prognosis. Additional downstream targets and attendant gene function also need to be discerned to design a sound critical path to personalized medicine for persons susceptible to, or diagnosed with CRC.
| S-EPMC3903170 | biostudies-literature