Fusobacterium and CRC
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20036 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1885680_1.fastq.gz | Fastqsanger.gz | |||
| ERR1885680_2.fastq.gz | Fastqsanger.gz | |||
| ERR1885690_1.fastq.gz | Fastqsanger.gz | |||
| ERR1885690_2.fastq.gz | Fastqsanger.gz | |||
| ERR1885700_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1000 |
Similar Datasets
Project description:To elucidate whether Fusobacterium Nucleatum(Fn) plays a role in colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of Fn treated HCT116 colorectal cancer cell lines.
2021-02-23 | GSE141805 | GEO
Project description:Fusobacterium genomic diversity in Vietnamese colorectal cancer patients
| PRJNA791829 | ENA
Project description:Colorectal cancer is the third most common malignancy and the fourth most common cause of cancer mortality worldwide. In 2008, more than one million cases were newly diagnosed, and more than 600,000 people died from the disease. Given its slow development from removable precancerous lesions and curable early stages, screening for CRC has the potential to reduce both the incidence and mortality of the disease. However, compliance with current screening methods remains poor and there is a clear need for an accurate in vitro blood test to increase participation in colorectal cancer screening. In this study, we performed genome-wide gene expression profiling of peripheral blood samples from 100 healthy controls and 100 colorectal cancer patients using PAXgeneTM technology and Affymetrix GeneChip® microarrays. We show that monitoring gene expression in blood results in distinct transcriptional profiles between the controls and cancer patients. Thus, the microarray-based blood gene expression profiling holds great promise for developing novel biomarkers for colorectal cancer detection.
2013-05-03 | E-MTAB-1532 | biostudies-arrayexpress
Project description:Genome sequences of Fusobacterium nucleatum isolates obtained from patients with colorectal cancer
| PRJDB16243 | ENA
Project description:Localization of Fusobacterium nucleatum in the placenta may be associated with pregnancy complications including preeclampsia (PE), but its specific pathobiology is unknown. Our aim was to analyze the effect of Fusobacterium nucleatum on HUVEC cells to further elucidate placental dysfunction in the context of Fusobacterium nucleatum infestation.
2024-06-08 | GSE269085 | GEO
Project description:Fusobacterium nucleatum is a Gram-negative oncobacterium that is associated with colorectal cancer. The molecular mechanisms utilized by F. nucleatum to promote colorectal tumor development have largely focused on adhesin-mediated binding to the tumor tissue and on the pro-inflammatory capacity of F. nucleatum. However, the exact manner in which F. nucleatum promotes inflammation in the tumor microenvironment and subsequent tumor promotion remains underexplored. Here, we show that both live F. nucleatum and sterile F. nucleatum-conditioned medium promote CXCL8 release from the intestinal adenocarcinoma HT-29 cell line. We determined that the pro-inflammatory response was ALPK1-dependent in both HEK293 and HT-29 cells and that the released F. nucleatum molecule had characteristics that match those of the pro-inflammatory ALPK1 ligand ADP-heptose or related heptose phosphates. In addition, not only F. nucleatum but also other Fusobacterium species such as F. varium, F. necrophorum and F. gonidiaformans promoted an ALPK1-dependent pro-inflammatory environment, indicating that ADP-heptose or related heptose phosphates secretion is a conserved feature of the Fusobacterium genus. By performing transcriptional analysis of ADP-heptose stimulated HT-29 cells, we found several inflammatory and cancer-related pathways to be differentially regulated, including DNA mismatch repair genes and the immune inhibitory receptor PD-L1. Finally, we show that stimulation of HT-29 cells with F. nucleatum resulted in an ALPK1-dependent upregulation of PD-L1. These results aid in our understanding of the mechanisms by which F. nucleatum can affect tumor development and therapy and pave the way for future therapeutic approaches.
2024-05-13 | GSE267317 | GEO
Project description:Fusobacterium nucleatum is a Gram negative oral bacterial species associated with periodontal disease progression. This species is perhaps best known for its ability to adhere to a vast array of other bacteria and eukaryotic cells. Numerous studies of F. nucleatum have examined various coaggregation partners and inhibitors, but it is largely unknown whether these interactions induce a particular genetic response. We tested coaggregation between F. nucleatum ATCC strain 25586 and various species of Streptococcus in the presence of a semi-defined growth medium containing saliva. We found that this condition could support efficient coaggregation, but surprisingly also stimulated a similar degree of autoaggregation. We further characterized the autoaggregation response, since few reports have examined this in F. nucleatum. After screening several common coaggregation inhibitors, we identified L-lysine as a competitive inhibitor of autoaggregation. We performed a microarray analysis of the planktonic vs. autoaggregated cells and found nearly 100 genes that were affected after only about 60 min. of aggregation. We tested a subset of these genes via real-time RT-PCR and confirmed the validity of the microarray results. Some of these genes were also found to be inducible in cell pellets created by centrifugation. Based upon these data, it appears that autoaggregation activates a genetic program that may be utilized for growth in a high cell density environment, such as the oral biofilm. The study aims to determine the effect of autoaggregation upon the transcriptome. The study contains 2 separate experiments that both measure dispersed (i.e. non-aggregated) vs. aggregated cells and each experiment was performed in duplicate. Samples with no added components other than medium were dispersed, samples containing 25% saliva were aggregated, and samples containing 25% saliva + 50mM L-lysine remained dispersed.
2009-10-15 | E-GEOD-18554 | biostudies-arrayexpress
Project description:Colorectal cancer (CRC) with high rate of mortality is one of the most commonly diagnosed cancers in worldwide. Advanced colorectal cancer is often accompanied by malignant proliferation of tumor cells. Further researches on colorectal cancer proliferation to find new targets and develop new therapeutic regimen are an important direction for colorectal cancer treatment. In this study, genome-wide RNAi screening was used to discover the essential genes associated with colorectal cancer cell proliferation. We found DKC1 (dyskerin pseudouridine synthase 1) promoted CRC proliferation through binding and modifying ribosomal proteins (RPL10A, RPL22L1, RPL34, RPS3) mRNA to increase the mRNAs stability and eventually increasing their expression. Besides, DKC1 is highly expressed in colorectal cancer and its aberrantly high expression is associated with poor prognosis of colorectal cancer patients. These results suggest that DKC1 could be a new therapeutic target for colorectal cancer.
2021-02-08 | PXD018103 | Pride
Project description:Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered much attention for its newly discovered prevalence in colorectal and breast cancer tissue. The growing interest in this emerging cancer-associated bacterium sharply contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. Post-transcriptional networks are also unknown, for fusobacteria lack all established small RNA-associated proteins. Here, we present high-resolution global RNA maps for two clinically relevant F. nucleatum subspecies for different growth conditions, and use these to uncover fundamental aspects of fusobacterial gene expression architecture and a previously unknown suite of noncoding RNAs. Developing a new vector for functional analysis of fusobacterial genes, we identify a conserved oxygen-induced small RNA as a post-transcriptional repressor of major porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum to colonize different compartments of the human body.
2021-05-03 | GSE161360 | GEO
Project description:At present, the function of Fusobacterium nucleosocci outer membrane vesicles under normal intestinal environmental pH conditions has been mainly studied, but there are few studies related to the function of Fusobacterium nucleosius outer membrane vesicles under cancer microenvironment pH conditions. The purpose of this study was to pioneer the comparative analysis of the composition of Fusobacterium nucleosibacterium outer membrane vesicle proteins under normal intestinal environmental pH conditions and cancer microenvironment pH conditions, and to find out the virulence factor protein of Fusobacterium nucleosocci outer membrane vesicles under cancer microenvironment pH conditions. To do this, we adjusted the initial pH of TSPC medium to around 6.0 using acidic cysteine to mimic the cancer microenvironment pH conditions. We combined ultracentrifugation and density gradient centrifugation to separate and extract Fusobacterium nucleosi's outer membrane vesicles from two pH environments, and used TMT quantitative proteomics to identify proteins in outer membrane vesicles. A total of 991 proteins were identified, compared with normal outer membrane vesicles, 306 proteins in the outer membrane vesicles in the tumor environment were up-regulated and 360 proteins were down-regulated, and some of the up-regulated proteins of the out-membrane vesicles in the tumor environment were virulence factor proteins, such as multiple pentatype autotransporters and MORN2 domain proteins, and the functions of these proteins were mainly related to adhesion and invasion. In addition, the down-regulation of enzyme levels involved in butyrate metabolism in the outer membrane vesicles of Fusobacterium nucleosionae under the condition of cancer microenvironment pH inhibits the butyric acid production capacity of Fusobacterium nucleobacteria, resulting in a decrease in butyric acid production capacity, which may promote the development of colorectal cancer. In conclusion, quantitative proteomics comparative analysis has increased our understanding of Fusobacterium nucleosom outer membrane vesicle virulence protein in the tumor environment.
2022-10-18 | PXD037520 |