Cryptosporidium Infection and Human Colorectal Cancer
Ontology highlight
ABSTRACT:
DISEASE(S): Cryptosporidiosis,Colon Cancer,Colonic Neoplasms
PROVIDER: 2334959 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:Cryptosporidium parvum has been reported to induce digestive adenocarcinoma in a rodent model of chronic cryptosporidiosis. In the current study, the transcriptomes of C. parvum infected ileo-caecal regions of mice developing tumours were analysed to identifie potential genes involved in development of cancer
2021-12-29 | GSE188591 | GEO
Project description:The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary, California, and considered an indicator of ecosystem health. The experimental combination of molecular biomarkers with higher level condition indicators may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by contaminant exposure. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. We have developed and applied a delta smelt microarray in order to screen for probable candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses are presented along with quantitative Polymerase Chain Reaction (qPCR) assessments measuring effects upon neuromuscular, digestive and immune responses in delta smelt exposed to copper. Differences in sensitivity were measured between juvenile and larval delta smelt (LC¬5096h= 25.2 and 80.4 ?g/L Cu2+ respectively). Swimming velocity declined with higher exposure concentrations in a dose-dependent manner, though were not statistically significant to controls. Genes encoding for aspartoacylase (ASPA), hemopexin, alpha-actin and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whilst downregulation of tumor necrosis factor indicated a probable compromised immune system.
2010-08-18 | GSE23238 | GEO
Project description:The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary, California, and considered an indicator of ecosystem health. The experimental combination of molecular biomarkers with higher level condition indicators may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by contaminant exposure. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. We have developed and applied a delta smelt microarray in order to screen for probable candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses are presented along with quantitative Polymerase Chain Reaction (qPCR) assessments measuring effects upon neuromuscular, digestive and immune responses in delta smelt exposed to copper. Differences in sensitivity were measured between juvenile and larval delta smelt (LC¬5096h= 25.2 and 80.4 ?g/L Cu2+ respectively). Swimming velocity declined with higher exposure concentrations in a dose-dependent manner, though were not statistically significant to controls. Genes encoding for aspartoacylase (ASPA), hemopexin, alpha-actin and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whilst downregulation of tumor necrosis factor indicated a probable compromised immune system. We utilized 3 replicates for exposed samples and 3 replicates for controls, both of which were hybridized to a reference pool. Each replicate contained 4 pooled larval delta smelt. The Reference pool consisted of delta smelt samples from this experiment and a number of prior tests. No dye swaps were performed due to limited material. Supplementary file linked below reports candidate differentially expressed cDNAs. Data represented as filtered, normalized, Log-2 Alexa (547/555) ratios.
2010-08-18 | E-GEOD-23238 | biostudies-arrayexpress
Project description:Seminal plasma proteins are recently reported to play a significant role on semen quality. The proteomic analysis of seminal plasma is a promising investigation for enhancing the reproductive biology of male Asian elephant, their poor semen quality was stated as a considerable cause of population decline. The aim of this study was to explore seminal plasma proteins of Asian elephant and their probable function as a fundamental information for further examination on fertility problem in this species.
2023-06-29 | PXD039856 | JPOST Repository
Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization.
2011-05-01 | GSE25575 | GEO
Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization.
2011-05-01 | GSE25572 | GEO
Project description:Pancreatic ductal adenocarcinoma (PDAC) originates from normal pancreatic ducts where digestive juice is regularly produced. It remains unclear how PDAC can escape auto-digestion by digestive enzymes. Here we show that human PDAC tumor cells use gasdermin E (GSDME), a pore-forming protein upon caspase 3 cleavage, to mediate the digestive resistance. We find that GSDME facilitates the expression of mucins 1 and 13 in pancreatic tumor cells, which forms a barrier to prevent chymotrypsin-mediated destruction. Inoculation of GSDME-/- PDAC cells results in subcutaneous but not orthotopic tumor formation in mice. Either inhibiting or knocking out MUC1 or MUC13 abrogates orthotopic PDAC growth in NOD-SCID mice. Mechanistically, GSDME interacts with and transports transcription factor YBX1 into the nucleus where YBX1 directly promotes mucin expression. This GSDME-YBX1-mucin axis is also confirmed in PDAC patients. These findings uncover a unique survival mechanism of PDAC cells in pancreatic microenvironments, thus providing a potential target for PDAC treatment.
2022-05-20 | PXD030879 | Pride
Project description:Symbiotic bacteria inhabiting the distal human gut have evolved under intense pressure to utilize complex carbohydrates, predominantly plant cell wall glycans abundant in our diets. These substrates are recalcitrant to depolymerization by digestive enzymes encoded in the human genome, but are efficiently targeted by some of the ~103-104 bacterial species that inhabit this niche. These species augment our comparatively narrow carbohydrate digestive capacity by unlocking otherwise unusable sugars and fermenting them into host-absorbable forms, such as short-chain fatty acids. We used phenotype profiling, whole-genome transcriptional analysis and molecular genetic approaches to investigate complex glycan utilization by two fully sequenced and closely related human gut symbionts: Bacteroides thetaiotaomicron and Bacteroides ovatus. Together these species target all of the common glycosidic linkages found in the plant cell wall, as well as host polysaccharides, but each species exhibits a unique ‘glycan niche’: in vitro B. thetaiotaomicron targets plant cell wall pectins in addition to linkages contained in host N- and O-glycans; B. ovatus uniquely targets hemicellulosic polysaccharides along with several pectins, but is deficient in host glycan utilization. Growth of Bacteroides thetaiotaomicron in vitro in minimal medium plus different purified complex glycans. Observation of increased gene expression was used to determine genes that are involved in metabolism of each glycan. Two biological replicates each.
2011-05-01 | E-GEOD-25572 | biostudies-arrayexpress
Project description:Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.
2021-07-28 | GSE136940 | GEO
Project description:Purpose: Mutations in TP53 induce autoantibody immune responses in a subset of cancer patients, which have been proposed as biomarkers for early detection. Here, we investigate the association of p53 specific autoantibodies with multiple tumor subtypes and determine the association with p53 mutation status and epitope specificity. Experimental Design: IgG p53 autoantibodies (p53-AAb), were quantified in 412 serum saples using a programmable ELISA assay from patients with serous ovarian, pancreatic adenocarcinoma, and breast cancer. To determine if patients generated mutation specific autoantibodies we designed a panel of the most relevant 51 p53 point mutant proteins, to be displayed on custom programmable protein microarrays. To determine the epitope specificity we displayed 12 overlapping tiling fragments and 38 N- and C-terminal deletions spanning the length of the wild-type p53 proteins. Results: We detected p53-AAb with sensitivities of 58.8% (ovarian), 22% (pancreatic), 32% (triple negative breast cancer), and 10.2% (HER2+ breast cancer) at 94% specificity. Sera with p53-AAb contained broadly-reactive autoantibodies to 51 displayed p53 mutant proteins, demonstrating a polyclonal response to common epitopes. All p53-AAb displayed broad polyclonal immune response to both continuous and discontinuous epitopes at the N- and C-terminus as well as the DNA binding domain. Conclusion and clinical relevance: In this comprehensive analysis, mutations in tumor p53 induce strong, polyclonal autoantibodies with broadly reactive epitope specificity. The immunoreactivity was compared between 60 pancreactic ductal adenocarcinoma cases and 63 benign pancreatic disease controls against 52 unique mutant p53 and 379 human proteins that were printed on microscope slides. [Contributor] Arizona State University
2016-06-01 | E-GEOD-77949 | biostudies-arrayexpress