Wpływ pseudourydylacji na stabilność transkryptu i translację

Pseudourydylacja jest najczęściej spotykaną, modyfikacją postranskrypcyjną RNA w organizmach żywych. Biologiczna rola pseudourydyny (Ψ) nie została jeszcze całkowicie poznana, jednakże sztucznie wprowadzona pseudourydyna znacząco wpływa na funkcję mRNA. Ostatnio opracowane metody pozwoliły zidentyfikować Ψ w transkryptomie człowieka i myszy. Ponadto, najnowsze badania wskazały jedną z syntaz pseudourydynowych - TRUB1 jako dominującą z syntaz, odpowiedzialną za pseudourdylację mRNA ssaków z przewidywalną specyficznością.W niniejszej pracy wykorzystano unikalną, konsensusową sekwencję TRUB1 obecną w transkrypcje foxp3 i zbadano molekularny wpływ pseudourydyny na stabilizowanie transkryptu i proces translacji.Uzyskane wyniki potwierdziły, że TRUB1 istotnie wymaga specyficznej sekwencji do wprowadzenia pseudourydyny. Bioinformatyczna analiza, dzięki której znaleziono w foxp3 3'UTR sekwencje konsensusową dla TRUB1, pozwoliła na stworzenie systemu, który wskazuje na specyficzną rolę tej modyfikacji epitranskrypcyjnej. Przeprowadzone w niniejszej pracy badania in vitro pokazują wpływ pseudourydylacji na ekspresję białka.Pseudouridylation is the most abundant type of RNA posttranscriptional modification in living organisms. The biological role of pseudouridine (Ψ) has not been completely understood, however artificial pseudouridylation dramatically affects mRNA function. Recently developed methods allowed to identify Ψ in the human and mouse transcriptome. Moreover, the new findings indicated one of site-specific pseudouridine synthases – TRUB1 as the dominant pseudouridine synthase acting on mammalian mRNA with predictable specificity. By taking advantage of unique TRUB1 consensus sequence present in the foxp3 transcript we have investigated the molecular impact of pseudouridine on transcript stability and translation. The obtained data confirmed that TRUB1 indeed requires specific sequence for pseudouridine formation. Bioinformatic prediction of TRUB1 consensus site in foxp3 3’UTR allowed to generate a system that indicates the site-specific role of this epitranscriptomic modification. These in vitro studies show the effect of pseudouridylation in protein translation

Analysis of tyrosine hydroxylase gene expression in the skin in the mouse model of psoriasis

Łuszczyca pospolita jest autoimmunologiczną chorobą, w której obecność stanu zapalnego manifestuje się w postaci zaczerwienionych zmian pokrytych łuszczącym się naskórkiem. Stwierdzono, iż katecholaminy biorą udział w modulacji odpowiedzi immunologicznej poprzez aktywację głownie receptorów β-adrenergicznych obecnych na komórkach układu immunologicznego. Katecholaminy w skórze uwalnianie są nie tylko z zakończeń nerwowych, ale także mogą być bezpośrednio syntetyzowane i uwalniane przez komórki tam obecne. Enzymem charakteryzującym obecność katecholamin w danej tkance jest hydroksylaza tyrozynowa (TH), która przeprowadza reakcję hydroksylacji tyrozyny do L-DOPA. W pracy tej został zbadany wpływ stanu zapalnego w skórze na ekspresję genu hydroksylazy tyrozynowej w mysim modelu łuszczycy.Psoriasis vulgaris is an autoimmune disease in which inflammatory skin manifests itself by reddened lesions covered with scaly epidermis. It has been shown that catecholamines participate in the modulation of the immune response by activating β-adrenergic receptors expressed on the immune cells. Catecholamines can be released not only from nerve endings, but can be also synthesized and released by the cells present in the skin. Tyrosine hydroxylase (TH) is a crucial enzyme that allows to define presence of catecholamines in any tissue. TH catalyzes the reaction in which L-tyrosine is hydroxylated to L-DOPA. This study investigated if skin inflammatory processes effects on the tyrosine hydroxylase gene expression in a mouse model of psoriasis

High-Salt Diet Induces Depletion of Lactic Acid-Producing Bacteria in Murine Gut

Dietary habits are amongst the main factors that influence the gut microbiome. Accumulating evidence points to the impact of a high-salt diet (HSD) on the composition and function of the intestinal microbiota, immune system and disease. In the present study, we thus investigated the effects of different NaCl content in the food (0.03%/sodium deficient, 0.5%/control, 4% and 10% NaCl) on the gut microbiome composition in mice. The bacterial composition was profiled using the 16S ribosomal RNA (rRNA) gene amplicon sequencing. Our results revealed that HSD led to distinct gut microbiome compositions compared to sodium-deficient or control diets. We also observed significant reduction in relative abundances of bacteria associated with immuno-competent short-chain fatty acid (SCFA) production (Bifidobacterium, Faecalibaculum, Blautia and Lactobacillus) in HSD-fed mice along with significant enrichment of Clostridia, Alistipes and Akkermansia depending on the sodium content in food. Furthermore, the predictive functional profiling of microbial communities indicated that the gut microbiota found in each category presents differences in metabolic pathways related to carbohydrate, lipid and amino acid metabolism. The presented data show that HSD cause disturbances in the ecological balance of the gastrointestinal microflora primarily through depletion of lactic acid-producing bacteria in a dose-dependent manner. These findings may have important implications for salt-sensitive inflammatory diseases

DataSheet_1_Dissecting the role of CSF2RB expression in human regulatory T cells.pdf

Colony stimulating factor 2 receptor subunit beta (CSF2RB; CD131) is the common subunit of the type I cytokine receptors for granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin (IL)-3 and IL-5. Interestingly, FOXP3+ regulatory T cells (Tregs), which play a pivotal role in prevention of autoimmunity have been demonstrated to highly overexpress CSF2RB and genome-wide association studies (GWAS) identified CSF2RB as being linked to autoimmune diseases like multiple sclerosis (MS). However, the exact biological role of CD131 in human Tregs has not been defined yet. Here we investigated CD131 importance on Treg phenotype and function in a broad range of in vitro studies. Although we could not recognize a specific function of CSF2RB; CD131 in human Tregs, our data show that CD131 expression is vastly restricted to Tregs even under stimulatory conditions, indicating that CD131 could aid as a potential marker to identify Treg subpopulations from pools of activated CD4+ T cells. Importantly, our analysis further demonstrate the overexpression of CSF2RB in Tregs of patients with autoimmune diseases like MS and systemic lupus erythematosus (SLE) in comparison to healthy controls, thereby indicating that CSF2RB expression in Tregs could serve as a potential novel biomarker for disease.</p

Impact of High Salt-Intake on a Natural Gut Ecosystem in <i>Wildling</i> Mice

The mammalian holobiont harbors a complex and interdependent mutualistic gut bacterial community. Shifts in the composition of this bacterial consortium are known to be a key element in host health, immunity and disease. Among many others, dietary habits are impactful drivers for a potential disruption of the bacteria–host mutualistic interaction. In this context, we previously demonstrated that a high-salt diet (HSD) leads to a dysbiotic condition of murine gut microbiota, characterized by a decrease or depletion of well-known health-promoting gut bacteria. However, due to a controlled and sanitized environment, conventional laboratory mice (CLM) possess a less diverse gut microbiota compared to wild mice, leading to poor translational outcome for gut microbiome studies, since a reduced gut microbiota diversity could fail to depict the complex interdependent networks of the microbiome. Here, we evaluated the HSD effect on gut microbiota in CLM in comparison to wildling mice, which harbor a natural gut ecosystem more closely mimicking the situation in humans. Mice were treated with either control food or HSD and gut microbiota were profiled using amplicon-based methods targeting the 16S ribosomal gene. In line with previous findings, our results revealed that HSD induced significant loss of alpha diversity and extensive modulation of gut microbiota composition in CLM, characterized by the decrease in potentially beneficial bacteria from Firmicutes phylum such as the genera Lactobacillus, Roseburia, Tuzzerella, Anaerovorax and increase in Akkermansia and Parasutterella. However, HSD-treated wildling mice did not show the same changes in terms of alpha diversity and loss of Firmicutes bacteria as CLM, and more generally, wildlings exhibited only minor shifts in the gut microbiota composition upon HSD. In line with this, 16S-based functional analysis suggested only major shifts of gut microbiota ecological functions in CLM compared to wildling mice upon HSD. Our findings indicate that richer and wild-derived gut microbiota is more resistant to dietary interventions such as HSD, compared to gut microbiota of CLM, which may have important implications for future translational microbiome research

Table_1_Dissecting the role of CSF2RB expression in human regulatory T cells.pdf

Colony stimulating factor 2 receptor subunit beta (CSF2RB; CD131) is the common subunit of the type I cytokine receptors for granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin (IL)-3 and IL-5. Interestingly, FOXP3+ regulatory T cells (Tregs), which play a pivotal role in prevention of autoimmunity have been demonstrated to highly overexpress CSF2RB and genome-wide association studies (GWAS) identified CSF2RB as being linked to autoimmune diseases like multiple sclerosis (MS). However, the exact biological role of CD131 in human Tregs has not been defined yet. Here we investigated CD131 importance on Treg phenotype and function in a broad range of in vitro studies. Although we could not recognize a specific function of CSF2RB; CD131 in human Tregs, our data show that CD131 expression is vastly restricted to Tregs even under stimulatory conditions, indicating that CD131 could aid as a potential marker to identify Treg subpopulations from pools of activated CD4+ T cells. Importantly, our analysis further demonstrate the overexpression of CSF2RB in Tregs of patients with autoimmune diseases like MS and systemic lupus erythematosus (SLE) in comparison to healthy controls, thereby indicating that CSF2RB expression in Tregs could serve as a potential novel biomarker for disease.</p

Exploring the microbiome analysis and visualization landscape

Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them