Human feces metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12256 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR330103.fastq.gz | Fastqsanger.gz | |||
| DRR330104.fastq.gz | Fastqsanger.gz | |||
| DRR330105.fastq.gz | Fastqsanger.gz | |||
| DRR330106.fastq.gz | Fastqsanger.gz | |||
| DRR330107.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 45 |
Similar Datasets
Project description:Early detection of recurrence by using specific biomarkers is still a clinically unmet need although methodologies for monitoring tumor markers, cell-free DNA and circulating tumor cells have been established for decades. Because recurrence is developed from metastatic or dormant cancer cells that are under immune surveillance, alteration in the population and function of immune cells may promote recurrence. In this study, we utilized an animal model to imitate breast tumor recurrence after surgical resection and investigated the abundance and gene expression profile of immune cells by using two NanoString Panels. Our results showed that myeloid-derived-suppressor cells (MDSC) were significantly increased during recurrence. Comparison of our NanoString data with a single-cell RNA sequencing dataset of MDSC in another spontaneous breast cancer model identified colony-stimulating factor 3 receptor (Csf3r)-positive MDSC as a potential marker to predict tumor recurrence. In vitro experiments demonstrated that Csf3R+ MDSC exhibited enhanced ROS levels and stronger T cell suppression ability. Furthermore, these findings were validated in two published PBMC databases.
2024-08-18 | GSE223028 | GEO
Project description:Early detection of recurrence by using specific biomarkers is still a clinically unmet need although methodologies for monitoring tumor markers, cell-free DNA and circulating tumor cells have been established for decades. Because recurrence is developed from metastatic or dormant cancer cells that are under immune surveillance, alteration in the population and function of immune cells may promote recurrence. In this study, we utilized an animal model to imitate breast tumor recurrence after surgical resection and investigated the abundance and gene expression profile of immune cells by using two NanoString Panels. Our results showed that myeloid-derived-suppressor cells (MDSC) were significantly increased during recurrence. Comparison of our NanoString data with a single-cell RNA sequencing dataset of MDSC in another spontaneous breast cancer model identified colony-stimulating factor 3 receptor (Csf3r)-positive MDSC as a potential marker to predict tumor recurrence. In vitro experiments demonstrated that Csf3R+ MDSC exhibited enhanced ROS levels and stronger T cell suppression ability. Furthermore, these findings were validated in two published PBMC databases.
2024-08-18 | GSE223025 | GEO
Project description:Samples were taken from colorectal cancers in surgically resected specimens in 36 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting recurrence. Keywords: repeat Thirty-six colorectal cancer patients who had undergone surgical resection of colorectal cancer were studied. In all patients, curative resection was performed and no patients had any distant metastasis at the time of operation (stage III patients). Among the 36 patients, 23 patients did not develop recurrence. On the other hand, 13 patients developed rucurrence such as liver metastases, lung metastases and distant lymph node metastases. The median follow up period was 4.5 years.
2010-08-31 | E-GEOD-4526 | biostudies-arrayexpress
Project description:We carried out comprehensive analysis for the miRNA profiling of primary tumor and metastatic lesion which seems to be source of circulating miRNA. We picked up two patients who treated with primary tumor resection initially and received chemotherapy followed by surgical resection of liver metastasis. The total miRNA was isolated from frozen tissue specimens. SurePrint G3 Human miRNA microarray kit Rel.21.0 (Agilent Technologies) contains 2549 human microRNA probes. As previously reported, hsa-miR200c revealed specifically high expression in metastatic sites at both two cases. In two colorectal cancer patients, the frozen primary tumor, normal mucosa and liver-metastatic lesion were analyzed by microRNA microarray.
2015-09-19 | E-GEOD-73178 | biostudies-arrayexpress
Project description:The aim of our study was to identify a microRNA signature to predict the recurrence in stage II & III CRC patients who were treated with FOLFOX-based adjuvant chemotherapy after curative resection of tumors. We performed small RNA sequencing in 71 FFPE surgical specimens, and discovered differentially expressed microRNAs in patients who developed recurrence. Thereafter, selected microRNA biomarkers were validated in independent cohort using qRT-PCR assay.
2022-11-16 | GSE217978 | GEO
Project description:While we and others have uncovered and validated several genomic predictors for metastatic recurrences, a molecular or genomic predictor that can reliably identify high-risk patients for late de novo recurrence has not been firmly established. We analyzed previously reported gene expression data from human livers that underwent partial hepatectomy or transplantation, which were representative physiological conditions that trigger liver regeneration signals. We generated gene expression data from tumor and matched non-tumor surrounding tissues of 72 hepatocellular carcinoma (HCC) patients who underwent surgical resection as the primary treatment. We used these gene expression data to develop a new prognostification model for recurrence of HCC after surgery. We generated gene expression data from tumor and matched non-tumor surrounding tissues of 72 HCC patients who underwent surgical resection as the primary treatment.
2014-11-03 | E-GEOD-39791 | biostudies-arrayexpress
Project description:Background: The presence of vascular invasion (VI) in pathology specimens has been widely described as closely linked to poor outcome in hepatocellular carcinoma (HCC) patients after tumor resection. Previous attempts have been conducted to achieve molecular markers or signatures to predict HCC recurrence in HCC. Here, we aim to develop a diagnostic model combining clinical and genomic variables able to detect the presence of VI prior to surgery and link it to survival estimation. Methods: Seventy-nine HCV related HCC samples from patients that underwent surgical resection as a treatment for HCC were subjected to Genome-wide gene expression profiling and a predictive model of vascular invasion was constructed. The model was tested in an independent-validation set of 153 fixed tissue samples of resected HCC. Quantitative RTPCR and inmunohistochemistry were performed in HCC samples to test a potential biomarker. Results: A 39-gene signature was able to accurately (72%) identify vascular invasion in HCC patients treated with resection. A model including tumor size and the signature is able to predict presence of VI with 85% accuracy in HCV-related HCC patients, and is able to exclude VI in up to 87% cases in HCC from all etiologies. Conclusions: Using the VI gene signature together with tumor size, VI can be successfully detected in HCC patients. The diagnostic model, integrated in a previously reported survival chart is able to provide an estimated survival for selected cases. Clinical implications of this fact are relevant to provide objective data to further apply expanded indication of curative treatments in HCC. Gene-expression profiling was performed using formalin-fixed, paraffin-embedded hepatocellular carcinoma tissues obtained at the time of surgical resection.
2011-07-30 | E-GEOD-20017 | biostudies-arrayexpress
Project description:Treatment of glioblastoma with anti-CSF-1R immunotherapy, radiotherapy, or surgical tumor resection were found to all induce a fibrotic response to treatment, which was highly associated with tumor recurrence. To investigate the drivers of fibrotic treatment response we performed multi-omic analysis of the glioblastoma microenvironment following treatment with anti-CSF-1R immunotherapy. Studies consisted of mass spectrometry proteomic analysis, single cell transcriptomics, and high-dimensional spatial analysis. These data identified a protective spatial niche that supported tumor cell survival following treatment, ultimately leading to tumor recurrence. Therapeutic inhibition of fibrotic treatment response blocked the formation of this niche, and significantly improved survival in anti-CSF-1R preclinical trials
2024-08-12 | PXD041689 | Pride
Project description:Surgical resection is the major clinical intervention for Stage III colorectal cancer (CRC) currently. However, as much as 30.8% of the patients who had ever taken curative resection came out of recurrence eventually. Therefore, to facilitate formulating effective treatment plans, there is an intense demand for Stage III CRC post-surgical prognostic biomarkers. In this study, we identified total 146 differentially expressed proteins (DEPs) associated with poor prognosis in Stage III CRC patients with TMT-based quantitative mass spectrometry (MS). In these DEPs, the protein expression level of R-Ras and Transgelin were tested with immunohistochemistry (IHC) of 192 individual specimens. Further Kaplan-Meier analysis revealed that the level of R-Ras and Transgelin is associated with patients’ 5-year overall survival (OS) and disease-free survival (DFS) significantly, and multivariate Cox-regression analyses revealed that R-Ras and Transgelin are independent prognostic factors for OS and DFS respectively. In conclusion, our study presents that R-Ras and Transgelin are potential post-surgical prognostic biomarkers of Stage III CRC.
2016-06-20 | PXD002903 | 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