Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA207669 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of tumor-educated changes in peripheral blood monocytes at the gene expression level. We analyzed if gene expression in monocytes of patients with colorectal cancer is differential from those of healthy volunteers and found a diagnostic signature that allowed to accurately discriminate patients with colorectal cancer from healthy individuals. Peripheral blood monocytes from 93 distinct individuals are profiled on 8 beadchips. The individuals belong to one of three groups: healthy volunteers (38), patients with non-metastatic colorectal cancer (27) or patients with metastatic colorectal cancer (28).
2015-04-02 | E-GEOD-47756 | biostudies-arrayexpress
Project description:Analysis of tumor-educated changes in peripheral blood monocytes at the gene expression level. We analyzed if gene expression in monocytes of patients with colorectal cancer is differential from those of healthy volunteers and found a diagnostic signature that allowed to accurately discriminate patients with colorectal cancer from healthy individuals.
2015-04-02 | GSE47756 | GEO
Project description:DNA modifications such as 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression, and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here genome-wide 5hmC profiling in circulating cell-free DNA (cfDNA) and paired tumor/adjacent tissues collected from a cohort of 90 healthy individuals and 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver, or thyroid cancer. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-specific epigenetic signatures in cfDNA were identified in different cancers. 5hmC-based biomarkers demonstrated highly accurate predictive value for patients with colorectal and gastric cancers versus healthy controls, superior to conventional biomarkers, and comparable to epigenetic biomarkers from tissue biopsies. This new strategy could lead to the development of an effective blood-based, minimally-invasive cancer diagnosis and prognosis approach.
2017-09-05 | GSE89570 | GEO
Project description:Cervical cancer is a global public health subject as it affects women in the reproductive ages, and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50% mortality rate. Poor awareness and access to effective diagnosis have led to this enormous disease burden, calling for point-of-care, minimally invasive diagnosis methods. Here, an end-to-end quantitative approach for a new kind of diagnosis has been developed, comprising identification of optimal biomarkers, design of the sensor, and simulation of the diagnostic circuit. Using miRNA expression data in the public domain, we identified circulating miRNA biomarkers specific to cervical cancer using multi-tier screening. Synthetic riboregulators called toehold switches specific for the biomarker panel were then designed. To predict the dynamic range of toehold switches for use in genetic circuits as biosensors, we developed a generic grammar of these switches, and built a multivariate linear regression model using thermodynamic features derived from RNA secondary structure and interaction. The model yielded predictions of toehold efficacy with an adjusted R2 = 0.59. Reaction kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA biomarkers. Simulations showed a linear response between 10nM and 100nM before saturation. Our study demonstrates an end-to-end workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic signatures that would be increasingly important in today’s world. The approach has the potential to direct experimental efforts and minimise costs. All resources are provided open-source (https://github.com/igem2019) under GNU GPLv3 licence.
2022-05-05 | MODEL2107150001 | BioModels
Project description:Breast cancer patients have increased risk of myocardial infarction (MI), but whether these events impact cancer pathogenesis is not known. In mouse models of breast cancer, MI increased circulating Ly6Chigh monocytes and their recruitment to tumors, accelerating cancer progression and metastasis. Analysis of the bone marrow reservoir revealed that MI epigenetically reprogrammed Ly6Chigh monocytes to an immunosuppressive phenotype that was maintained in monocytes in the circulation and tumor at the transcriptional level. Depletion of Ly6Chigh monocytes abrogated MI-induced cancer progression and increased activated cytotoxic T cells in the tumor. In early-stage breast cancer patients, post-diagnosis incident cardiovascular events, such as MI, increased the risk of recurrence and cancer-specific mortality, highlighting the clinical relevance of our findings. Collectively, our results indicate that MI induces cross-disease communication that accelerates breast cancer progression.
2020-06-11 | GSE147929 | GEO
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:DNA Methylation Biomarkers for Noninvasive Diagnosis of Colorectal Cancer
| PRJNA185764 | ENA
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).
2014-04-01 | GSE40246 | GEO
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).
2014-04-01 | GSE39833 | GEO
Project description:The goal of this study was to determine if blood circulating monocytes of metastatic breast cancer patient would express a different activation profile compared to healthy donors, in order to use this specific changesas biomarkers to monitor then response to therapy
2017-02-09 | GSE70404 | GEO