Similar Datasets
Project description:Role of ILC in bladder infection
| PRJNA731515 | ENA
Project description:Urinary tract infections (UTI) are common and recurrent. Both host genetics and UTI history impact susceptibility to recurrent UTI (rUTI) in women and in animal models. To identify shared patterns of host response that correlate with susceptibility, we investigated bladder inflammatory and transcriptional kinetics in acute and rUTI models. We found that TNFɑ signaling kinetics differed with mouse strain and infection history. Mice resistant to severe UTI/rUTI displayed a robust TNFɑ-dependent inflammation during the first 6 hours of acute cystitis, which waned by 24 hours; mice that are susceptible varied in their early responses but were prone to severe inflammation at 24 hours post-infection. Depletion of TNFɑ in an rUTI model revealed that early TNFɑ signaling promoted colonization resistance via exfoliation of infected bladder cells, but prolonged TNFɑ signaling exacerbated inflammation, thereby worsening infection. Host genetics and disease history impacts susceptibility by regulating the kinetics of a common TNFɑ pathway.
2019-07-21 | GSE117532 | GEO
Project description:The anaerobic actinobacterium Gardnerella was first isolated from the bladder by suprapubic aspiration more than fifty years ago. Since then, Gardnerella has been increasingly recognized as a common and often abundant member of the female urinary microbiome (urobiome). Some studies even suggest that the presence of Gardnerella is associated with urological disorders in women. We recently reported that inoculation of Gardnerella into the bladders of mice results in urothelial exfoliation. Here we performed whole bladder RNA-seq in our mouse model to identify additional host pathways involved in the response to Gardnerella bladder exposure. The transcriptional response to Gardnerella reflected the urothelial turnover that is a consequence of exfoliation, while also illustrating the activation pathways involved in inflammation and immunity. Additional timed exposure experiments in mice provided further evidence of a potentially clinically relevant consequence of bladder exposures to Gardnerella -- increased susceptibility to subsequent UTI caused by uropathogenic Escherichia coli. Together these data provide a broader picture of the bladder response to Gardnerella and lay the groundwork for future studies examining the impact of Gardnerella on bladder health.
2022-05-20 | GSE203195 | GEO
Project description:Uropathogenic Escherichia coli (UPEC) are the most common cause of urinary tract infection (UTI). UPEC normally reside in the intestine, and during establishment of UTI, it undergoes metabolic adaptations, first to urine and then upon tissue invasion to the bladder cell interior. In order to understand these adaptations, we used quantitative proteomic profiling to characterize protein expression of UPEC strain UTI89 growing in human urine and when inside J82 bladder cells. In order to facilitate detection of UPEC proteins over the excess amount of eukaryotic proteins in bladder cells, we developed a method where proteins from UTI89 grown in MOPS and urine was spiked-in to enhance detection of bacterial proteins. More than 2000 E. coli proteins were detected. During growth in urine, proteins associated with iron acquisition and several amino acid uptake and biosynthesis systems, in particular arginine metabolism, were significantly upregulated. During growth in J82 cells, proteins related to iron uptake and arginine metabolisms were upregulated together with proteins involved in sulphur compound turnover. Results suggested that UPEC experience a richer environment in bladder cells compared to urine. There was no direct correlation between upregulated proteins and proteins reported to be essential for infections, showing that upregulation during growth does not signify that the proteins are essential for growth under a condition.
2022-06-09 | PXD032049 | Pride
Project description:Single cell RNAseq of human ILCs to investigate potential heterogeneity within ILC subsets
2019-07-01 | GSE114396 | GEO
Project description:Dissection and FACS cell sorting techniques were used to isolate the superficial, intermediate and basal cell types from the bladder urothelium of adult female mice following UTI infections, and their controls. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific noncoding RNAs.
2017-09-30 | GSE85491 | GEO
Project description:In order to determine the dependency of mature tissue-resident ILCs on combinations of synergistic and antagonising Transcription Factors (TFs), we generated mice with conditional deletions of RORc, RORa and Tbx21 driven from the Id2 allele, utilizing a tamoxifen inducible Cre-recombinase in combination with a tdRFP allele to report Cre-excision (Id2creERT2 x ROSAtdRFP). RFP+ small intestinal ILCs were sorted from the lamina propria digests (gated as CD45+, Lineage negative, CD90+ CD127+, tdRFP+ - see manuscript for full methodological details), from control mice or mice containing loxP flanked alleles for RORc, RORc and RORa or RORc and Tbx21. Four samples of sort-purified ILCs were then subjected to 10X single cell sequencing; - Id2creERT2 - Id2idRORc - Id2idRORc/RORa - Id2idRORc/Tbx21
2021-09-23 | E-MTAB-9795 | biostudies-arrayexpress
Project description:Innate lymphoid cells (ILCs) are highly plastic immune cells that have been separated into 3 main subsets, characterized by distinct phenotypic and functional profiles. Using single cell approaches, heightened heterogeneity of mouse ILCs has been recently appreciated, imprinted by tissue signals that shape their transcriptome and epigenome. Intra-subset diversity has also been observed in human ILCs. However, combined transcriptomic and epigenetic analyses of single ILCs in humans are lacking. Here we show high transcriptional and epigenetic heterogeneity among human circulating ILCs in healthy individuals. We describe phenotypically distinct subclusters within main circulating ILC populations. We show diverse chromatin accessibility within main ILC subsets, compatible with differentially poised states. We validate the use of this healthy donor-based analysis as resource dataset to infer ILC changes occurring in disease conditions. Overall, our work provides new insights in the complex human ILC biology. We anticipate our work to be a starting point to facilitate hypothesis-driven studies in patients, without the need to perform single cell OMICs using precious patients’ material
2023-09-01 | GSE225167 | GEO
Project description:Innate lymphoid cells (ILCs) are highly plastic immune cells that have been separated into 3 main subsets, characterized by distinct phenotypic and functional profiles. Using single cell approaches, heightened heterogeneity of mouse ILCs has been recently appreciated, imprinted by tissue signals that shape their transcriptome and epigenome. Intra-subset diversity has also been observed in human ILCs. However, combined transcriptomic and epigenetic analyses of single ILCs in humans are lacking. Here we show high transcriptional and epigenetic heterogeneity among human circulating ILCs in healthy individuals. We describe phenotypically distinct subclusters within main circulating ILC populations. We show diverse chromatin accessibility within main ILC subsets, compatible with differentially poised states. We validate the use of this healthy donor-based analysis as resource dataset to infer ILC changes occurring in disease conditions. Overall, our work provides new insights in the complex human ILC biology. We anticipate our work to be a starting point to facilitate hypothesis-driven studies in patients, without the need to perform single cell OMICs using precious patients’ material
2023-09-01 | GSE225168 | GEO
Project description:Anti CD90 was used to deplete ILCs in RAG mice at point of iniation of DSS colitis in Rag mice. After 6 days the Macrophages were sorted from the colon and compared by using RNASeq to mice in which ILCs had not been repleted but still had colitus induced.
2020-07-17 | GSE135492 | GEO