Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1040478 | ENA |
REPOSITORIES: ENA
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Project description:Ulcerative colitis is a chronic inflammatory disorder for which a definitive cure is still missing. This is characterized by an overwhelming inflammatory milieu in the colonic tract where a composite set of immune and non-immune cells orchestrate its pathogenesis. Over the last years, a growing body of evidence has been pinpointing gut virome dysbiosis as underlying its progression. Nonetheless, its role during the early phases of chronic inflammation is far from being fully defined. Here we show the gut virome-associated Hepatitis B virus protein X, most likely acquired after an event of zoonotic spillover, to be associated with the early stages of ulcerative colitis and to induce colonic inflammation in mice. It acts as a transcriptional regulator in epithelial cells, provoking barrier leakage and altering mucosal immunity at the level of both innate and adaptive immunity. This study paves the way to the comprehension of the aetiopathogenesis of intestinal inflammation and encourages further investigations of the virome as a trigger also in other scenarios. Moreover, it provides a brand-new standpoint that looks at the virome as a target for tailored treatments, blocking the early phases of chronic inflammation and possibly leading to better disease management.
2023-02-20 | GSE204665 | GEO
Project description:Necrotizing enterocolitis (NEC) is a severe intestinal disorder connected to a gut microbiota dysbiosis. Approximately 7-8% of very low birth weight (VLBW) infants are diagnosed with NEC with mortality rates reaching 20-50%. Fecal virome transfer (FVT) is an approach where the bacteria-free fecal fraction from a healthy donor is administered to a patient with a GM dysbiosis. FVT contains e.g. bacteriophages, eukaryotic viruses, and metabolites. Oral administered FVT from healthy milk-fed term pigs shows promising potential in preventing NEC in the preterm piglet model. However, efficacy and safety are inconsistent between experiments. In the current study, we aim to explore methods of creating reproducible FVT-like treatments and test if these act preventive against NEC and possess minimal side effects in the preterm piglet model. Using cesarean-delivered, formula-fed preterm pigs, we compare the NEC preventive effect of native donor fecal virome (nFV) with: 1) a defined bacteriophage cocktail targeting NEC-associated bacteria; and 2) a chemostat fecal virome propagation with lactose as the major carbohydrate source (cFV), and 3) chemostat fecal virome propagation with lactose and milk oligosaccharides (cFV-OS). All methods will be compared to control treatment with SM buffer (SM).
2026-08-01 | GSE250234 | GEO
Project description:Virological research has traditionally focused on individual viruses or viral families. Advances in DNA synthesis now allow large-scale construction of individual gene products, enabling systematic exploration of the virome. Here, we developed a barcoded library of ~12,000 viral open reading frames (vORFs) from 513 viral species, which we leveraged to agnostically identify regulators of cellular proliferation and the innate and adaptive immune responses. Using this platform, we identified hundreds of viral regulators of cellular proliferation, class I MHC antigen presentation, and interferon signaling. Integrating results across these screens revealed unique phenotypic profiles and functional vORF modules, allowing the in-depth characterization of two previously uncharacterized viral proteins, MC162R and YLDV 151R, which impair class I MHC antigen presentation and IFN signaling, respectively. Together, the viral ORFeome provides a scalable framework for dissecting viral protein function across the breadth of the virome.
2026-09-07 | PXD077768 | Pride
Project description:Virological research has traditionally focused on individual viruses or viral families. Advances in DNA synthesis now allow large-scale construction of individual gene products, enabling systematic exploration of the virome. Here, we developed a barcoded library of ~12,000 viral open reading frames (vORFs) from 513 viral species, which we leveraged to agnostically identify regulators of cellular proliferation and the innate and adaptive immune responses. Using this platform, we identified hundreds of viral regulators of cellular proliferation, class I MHC antigen presentation, and interferon signaling. Integrating results across these screens revealed unique phenotypic profiles and functional vORF modules, allowing the in-depth characterization of two previously uncharacterized viral proteins, MC162R and YLDV 151R, which impair class I MHC antigen presentation and IFN signaling, respectively. Together, the viral ORFeome provides a scalable framework for dissecting viral protein function across the breadth of the virome.
2026-09-07 | PXD077896 | Pride
Project description:Virological research has traditionally focused on individual viruses or viral families. Advances in DNA synthesis now allow large-scale construction of individual gene products, enabling systematic exploration of the virome. Here, we developed a barcoded library of ~12,000 viral open reading frames (vORFs) from 513 viral species, which we leveraged to agnostically identify regulators of cellular proliferation and the innate and adaptive immune responses. Using this platform, we identified hundreds of viral regulators of cellular proliferation, class I MHC antigen presentation, and interferon signaling. Integrating results across these screens revealed unique phenotypic profiles and functional vORF modules, allowing the in-depth characterization of two previously uncharacterized viral proteins, MC162R and YLDV 151R, which impair class I MHC antigen presentation and IFN signaling, respectively. Together, the viral ORFeome provides a scalable framework for dissecting viral protein function across the breadth of the virome.
2026-09-07 | PXD077910 | Pride
Project description:Despite considerable speculation for the role of cytosine (DNA) methylation in biological and molecular processes in insects, direct functional tests are lacking. Here we provide evidence for the functional role of the maintenance DNA methyltransferase 1 (Dnmt1) in an insect using experimental manipulation. Through RNA interference (RNAi) we successfully post-transcriptionally knocked down Dnmt1 in ovarian tissue of the hemipteran Oncopeltus fasciatus (the large milkweed bug). Individuals depleted for dnmt1, and subsequently DNA methylation, failed to reproduce. Manipulating the levels of DNA methylation did not result in changes in overall gene expression. Furthermore, reductions in levels of DNA methylation at transposable elements (TEs) did not lead to large-scale reactivation of TE transcription. Despite the lack of a causal relationship between reduced DNA methylation and gene expression in the tissue we surveyed, eggs were inviable revealing an important function of DNA methylation in O. fasciatus. Our work provides direct experimental evidence for a functional role of Dnmt1 and DNA methylation in insects and presents O. fasciatus as a tractable model for further exploration of the function of DNA methylation in other tissues and life history circumstances for insects.
2018-07-05 | GSE109199 | GEO