Similar Datasets
Project description:The Piedmont study is a prospectively designed retrospective evaluation of a new 48-gene antifolate response signature (AF-PRS) in patients with locally advanced/metastatic NS-NSCLC treated with pemetrexed-containing platinum doublet chemotherapy (PMX-PDC). The study tested the hypothesis that the AF-PRS selects for patients with NS-NSCLC that preferentially respond to PMX-PDC, with a goal of providing clinical support for AF-PRS as potential diagnostic test. Overall, 53% of patients were AF-PRS(+), which was associated with extended PFS, but not OS, vs. AF-PRS(-) (16.6 vs. 6.6 mo; p = 0.025). In patients who were Stage I-III patients at time of treatment, PFS, but not OS, was further extended in AF-PRS(+) vs. AF-PRS(-) (36.2 vs. 9.3 mo; p = 0.03). A complete response (CR) to therapy was noted in 14 of 95 patients. AF-PRS(+) preferentially selected a majority (79%) of CRs, which were evenly split between patients Stage I-III (6 of 7) and Stage IV (5 of 7) at time of treatment. AF-PRS identified a significant population of patients with extended survival and/or clinical response following PMX-PDC treatment. AF-PRS may be a useful diagnostic test for patients indicated for systemic chemotherapy, especially when determining the optimal PDC regimen for locally advanced disease.
2023-05-23 | GSE232569 | GEO
Project description:Plasmacytoid dendritic cells (pDC) are the main source of type I interferon (IFN) during viral infections. Their other functions are debated, due to a lack of tools to identify and target them in vivo without affecting pDC-like cells and transitional DC (tDC), which harbor overlapping phenotypes and transcriptomes but a higher efficacy for T cell activation. To overcome this bottleneck, we designed, generated and validated a pDC-Tomato reporter mouse. We bred pDC-Tomato with Zbtb46 GFP mice to yield the he ZeST mouse strain that enabled transcriptomic profiling of all splenic DC types, by single cell RNA sequencing, both at steady state and during the course of the infection with mouse cytomegalovirus (MCMV). Analyses of the transcriptomic dataset unraveled diverging activation of pDC-like cells vs tDC during the infection. This dataset and the associated specific gene modules will be useful to delineate the physiological functions of pDC versus other DC types.
2023-01-26 | GSE196720 | GEO
Project description:Intramammary infections of two common non-aureus staphylococci
| PRJEB60227 | ENA
Project description: Not available
| S-EPMC10770246 | biostudies-literature
Project description:The healthy intestine mounts immune responses to microbiota to maintain homeostasis, which includes basal production of interferon cytokines. Previous work showed that Type III Interferon (IFN-λ) stimulates localized pockets of interferon-stimulated genes (ISGs) in the adult mouse intestinal epithelium at homeostasis that provide preemptive protection from viral pathogens. Here, we demonstrate that a major source of homeostatic IFN-λ production in the intestine is a population of epithelium-associated plasmacytoid dendritic cells (pDC). These pDC are recruited to the intestine by bacterial microbiota colonization, and pDC depletion or bone marrow reconstitution with IFN-λ-deficient pDC results in reduced homeostatic ISGs in the intestinal epithelium. Notably, intestinal pDC preferentially produce IFN-λ over Type I IFNs whereas splenic pDC produce more Type I IFNs. Comparison of splenic and intestinal pDC reveal tissue-specific changes in gene expression and genomic accessibility, including evidence of response to transforming growth factor beta (TGF-β) in the intestine. Isolated gut pDC produce more IFN-λ that splenic pDC upon stimulation, and pre-treatment of a human pDC cell line with TGF-β results in enhanced production of IFN-λ upon stimulation. This study implicates pDC as important sources of homeostatic IFN-λ in the intestine and defines the role of barrier cytokine TGF-β in regulating IFN types produced by pDC upon stimulation. Reprogramming of recruited pDC by tissue cytokines may have important implications for balancing effective antimicrobial responses with damaging inflammation at barrier tissues.
2026-02-13 | GSE304884 | GEO
Project description:Non-targeted detection of the microbial composition using high-throughput sequencing
| PRJEB53921 | ENA
Project description:Targeted sequencing of plasma-derived vs. urinary cfDNA from patients with triple negative breast cancer
| PRJEB52592 | ENA
Project description:DNA metabarcoding data for: Opportunistic vs selective feeding strategies of zooplankton under changing environmental conditions
| PRJEB52087 | ENA
Project description:Here we confirm an essential requirement for the BCL11A transcription factor in fetal pDC development, and for the first time demonstrate this lineage specific requirement in the adult organism. Genome-wide analyses of BCL11A DNA binding and expression revealed that BCL11A regulates transcription of E2-2 and other pDC differentiation modulators including ID2 and MTG16. Our results identify BCL11A as an essential, lineage-specific factor that regulates pDC development. ChIP sequenicng was performed for a transcription factor of BCL11A in Cal1 cell line. Input was sequenced and used as a control.
2014-02-15 | E-GEOD-55043 | biostudies-arrayexpress
Project description:Prostate cancer (PCa) growth depends on de novo lipogenesis controlled by the mitochondrial pyruvate dehydrogenase complex (PDC). In this study, we identified lysine methyltransferase (KMT)9 as a novel regulator of PDC activity. KMT9 is localized in mitochondria of PCa cells, but not in mitochondria of other tumor cell types. Mitochondrial KMT9 regulates PDC activity by monomethylation of its subunit dihydrolipoamide transacetylase (DLAT) at lysine 596. Depletion of KMT9 compromises PDC activity, de novo lipogenesis, and PCa cell proliferation, which can be rescued with exogenous KMT9 targeted to mitochondria. Similarly, comparable defects caused by DLAT depletion can be rescued with exogenous DLAT, but not with a methylation-defective DLAT mutant. Concomitant chemical inhibition of de novo lipogenesis and KMT9 depletion more efficiently impair PCa cell proliferation than either treatment alone. Importantly, KMT9 controls PDC activity, de novo lipogenesis, and tumor growth in a PCa mouse model. Finally, in human patients, levels of mitochondrial KMT9 and DLAT K596me1 correlate with Gleason grade. Together, we present a novel mechanism of PDC regulation and the first example of a histone methyltransferase with nuclear and mitochondrial functions. The exceptional dependency on mitochondrial KMT9 allows to develop novel therapeutic strategies to fight PCa.
2024-12-03 | PXD053942 | Pride