Metabolic fitness of IgA+ plasma cells in the gut requires DOCK8

Dedicator of cytokinesis 8 (DOCK8) mutations lead to a primary immunodeficiency associated with recurrent gastrointestinal infections and poor antibody responses but, paradoxically, heightened IgE to food antigens, suggesting that DOCK8 is central to immune homeostasis in the gut. Using Dock8-deficient mice, we found that DOCK8 was necessary for mucosal IgA production to multiple T cell-dependent antigens, including peanut and cholera toxin. Yet DOCK8 was not necessary in T cells for this phenotype. Instead, B cell-intrinsic DOCK8 was required for maintenance of antigen-specific IgA-secreting plasma cells (PCs) in the gut lamina propria. Unexpectedly, DOCK8 was not required for early B cell activation, migration, or IgA class switching. An unbiased interactome screen revealed novel protein partners involved in metabolism and apoptosis. Dock8-deficient IgA+ B cells had impaired cellular respiration and failed to engage glycolysis appropriately. These results demonstrate that maintenance of the IgA+ PC compartment requires DOCK8 and suggest that gut IgA+ PCs have unique metabolic requirements for long-term survival in the lamina propria.

A genome-wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs

The genome is pervasively transcribed to produce a vast array of non-coding RNAs (ncRNAs). Long non-coding RNAs (lncRNAs) are transcripts of >200 nucleotides and are best known for their ability to regulate gene expression. Enhancer RNAs (eRNAs) are subclass of lncRNAs that are synthesized from enhancer regions and have also been shown to coordinate gene expression. The biological function and significance of most lncRNAs and eRNAs remain to be determined. Epithelial to mesenchymal transition (EMT) is a ubiquitous cellular process that occurs during cellular migration, homeostasis, fibrosis, and cancer-cell metastasis. EMT-transcription factors, such as SNAI1 induce a complex transcriptional program that coordinates the morphological and molecular changes associated with EMT. Such complex transcriptional programs are often subject to coordination by networks of ncRNAs and thus can be leveraged to identify novel functional ncRNA loci. Here, using a genome-wide CRISPR activation (CRISPRa) screen targeting ∼10,000 lncRNA loci we identified ncRNA loci that could either promote or attenuate EMT. We discovered a novel locus that we named SCREEM (SNAI1 cis-regulatory eRNAs expressed in monocytes). The SCREEM locus contained a cluster of eRNAs that when activated using CRISPRa induced expression of the neighboring gene SNAI1, driving concomitant EMT. However, the SCREEM eRNA transcripts themselves appeared dispensable for the induction of SNAI1 expression. Interestingly, the SCREEM eRNAs and SNAI1 were co-expressed in activated monocytes, where the SCREEM locus demarcated a monocyte-specific super-enhancer. These findings suggest a potential role for SNAI1 in monocytes. Exploration of the SCREEM-SNAI axis could reveal novel aspects of monocyte biology.

Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro

Although epithelial-mesenchymal transition (EMT) is a common feature of fibrotic lung disease, its role in fibrogenesis is controversial. Recently, aberrant basaloid cells were identified in fibrotic lung tissue as a novel epithelial cell type displaying a partial EMT phenotype. The developmental origin of these cells remains unknown. To elucidate the role of EMT in the development of aberrant basaloid cells from the bronchial epithelium, we mapped EMT-induced transcriptional changes at the population and single-cell levels. Human bronchial epithelial cells grown as submerged or air-liquid interface (ALI) cultures with or without EMT induction were analyzed by bulk and single-cell RNA-Sequencing. Comparison of submerged and ALI cultures revealed differential expression of 8,247 protein coding (PC) and 1,621 long noncoding RNA (lncRNA) genes and revealed epithelial cell-type-specific lncRNAs. Similarly, EMT induction in ALI cultures resulted in robust transcriptional reprogramming of 6,020 PC and 907 lncRNA genes. Although there was no evidence for fibroblast/myofibroblast conversion following EMT induction, cells displayed a partial EMT gene signature and an aberrant basaloid-like cell phenotype. The substantial transcriptional differences between submerged and ALI cultures highlight that care must be taken when interpreting data from submerged cultures. This work supports that lung epithelial EMT does not generate fibroblasts/myofibroblasts and confirms ALI cultures provide a physiologically relevant system to study aberrant basaloid-like cells and mechanisms of EMT. We provide a catalog of PC and lncRNA genes and an interactive browser (https://bronc-epi-in-vitro.cells.ucsc.edu/) of single-cell RNA-Seq data for further exploration of potential roles in the lung epithelium in health and lung disease.

[The influence of diet on mental health]

The influence of nutritional factors on brain metabolism and the course of mental illness are increasingly being addressed in international research. It is a matter of discussion whether dietary habits, e.g., the amount of fish or vegetables, have an effect on the incidence of certain illnesses. Furthermore an optimized or supplemented diet could offer therapeutic possibilities; one example is the role of polyunsaturated fatty acids as an add-on therapy in affective disorders. The limitations of psychopharmacotherapy (drug interactions, side effects, noncompliance) underline the theoretical and practical relevance of nutrition in mental illness, the more so as mentally ill patients (especially when demented, anorectic, depressed, or schizophrenic) are at higher risk of malnutrition anyway. Even if the therapeutic evidence is still limited and the effects may be relatively weak, nutritional assessment and an optimized diet can be recommended for every patient.

The monoterpene terpinolene from the oil of Pinus mugo L. in concert with alpha-tocopherol and beta-carotene effectively prevents oxidation of LDL

Antioxidants from several nutrients, e.g. vitamin E, beta-carotene, or flavonoids, inhibit the oxidative modification of low-density lipoproteins. This protective effect could possibly retard atherogenesis and in consequence avoid coronary heart diseases. Some studies have shown a positive effect of those antioxidants on cardiovascular disease. Another class of naturally occurring antioxidants are terpenoids, which are found in essential oils. The essential oil of Pinus mugo and the contained monoterpene terpinolene effectively prevent low-density lipoprotein (LDL)-oxidation. In order to test the mechanism by which terpinolene protects LDL from oxidation, LDL from human blood plasma enriched in terpinolene was isolated. In this preparation not only the lipid part of LDL is protected against copper-induced oxidation--as proven by following the formation of conjugated dienes, but also the oxidation of the protein part is inhibited, since loss of tryptophan fluorescence is strongly delayed. This inhibition is due to a retarded oxidation of intrinsic carotenoids of LDL, and not, as in the case of some flavonoids, attributable to a protection of intrinsic alpha-tocopherol. These results are in agreement with our previous results, which showed the same effects for a monoterpene from lemon oil, i.e. gamma-terpinene.

Terpenoids as Plant Antioxidants

Plant antioxidants are composed of a broad variety of different substances like ascorbic acid and tocopherols, polyphenolic compounds, or terpenoids. They perform several important functions in plants and humans (e.g., carotenoids function as accessory pigments for light harvesting and provide photoprotection and pigmentation in plants). Monoterpenes and diterpenes, which are the main components of essential oils, act as allelopathic agents, attractants in plant-plant or plant-pathogen/herbivore interactions or repellants. For humans, carotenoids play an important role for health, carotenoids with provitamin A activity are important for vision; other carotenoids influence the human immune function and gap-junctional communication (GJC). Additionally, their antioxidative capacity is believed to be responsible for the health promoting properties of fruits and vegetables. Three main ways of antioxidant action of carotenoids have been detected until now (i.e., quenching of singlet oxygen, hydrogen transfer, or electron transfer). These mechanisms and investigation of antioxidant activity in vitro are discussed in detail. The monoterpenes limonene and perillyl alcohol may be promising substances in cancer therapy. Several investigations have studied the antioxidant activity of monoterpenes and diterpenes or essential oils in vitro. Results as well as the action of a newly discovered, very effective antioxidant (i.e., gamma-terpinene) are discussed. An important point when assessing the antioxidant activity of plant antioxidants is to consider their interaction with other antioxidants. Especially combinations of hydrophilic and lipophilic antioxidants may exert synergistic effects, as has been shown for rutin in combination with gamma-terpinene, lutein, or lycopene.

Synergistic inhibition of low-density lipoprotein oxidation by rutin, gamma-terpinene, and ascorbic acid

Low-density lipoprotein (LDL) oxidation may play a significant role in atherogenesis. Flavonoids are well-known for their excellent antioxidative capacity in various model systems, therefore we examined the behaviour of rutin, a quercetin-3-rutinosid, in the copper-mediated LDL oxidation. Rutin alone has been shown to protect LDL against oxidation. Furthermore we investigated the combination of rutin with a hydrophilic (ascorbate) and a lipophilic antioxidant (gamma-terpinene) in copper-mediated LDL oxidation. In both cases we found a synergistic effect on lag phase prolongation. To elucidate whether this effect mainly depends on the copper chelating ability of rutin we examined its reaction in more detail. Although inhibiting the oxidation of alpha-linolenic acid in the "rose bengal system" no direct influence of a copper-rutin-complex was determined. We conclude that a redox active copper-rutin-complex is still able to initiate the LDL oxidation but may prevent copper from a reaction at the binding sites of apoB-100. The synergistic effect in preventing LDL oxidation is due to this trapping of copper in a complex in the case of ascorbate. The synergistic action of rutin and gamma-terpinene can be explained by different distribution of rutin and gamma-terpinene in, and around the LDL-particle, respectively.

Antioxidative effects of lemon oil and its components on copper induced oxidation of low density lipoprotein

Oxidation of low density lipoprotein (LDL) has been implicated in atherogenesis since several years. Therefore many researchers are looking for potent antioxidants which are able to inhibit LDL-oxidation and thus lower the risk for atherosclerosis. In particular several flavonoids have been investigated for their antioxidant capacity and it was shown that many factors influence the ability of flavonoids to retard LDL-oxidation, among others their lipophilic character. Since essential oils and some of their components which are highly lipophilic, have been shown to possess antioxidant properties, their effects on copper-induced LDL-oxidation were analysed. Plasma was incubated with different terpenoid substances and subsequently the LDL was isolated. It could be demonstrated that the terpenoids were enriched in LDL after incubation with plasma. To follow the kinetics of copper induced LDL-oxidation formation of conjugated dienes as well as loss of tryptophan fluorescence were measured. Furthermore the antioxidants alpha-tocopherol, beta-carotene and lycopene were quantified in LDL. It could be shown that particularly lemon oil and one of its components, gamma-terpinene, are efficiently slowing down the oxidation of LDL. This effect is independent of alpha-tocopherol stability in LDL, whereas the loss of carotenoids during oxidation is strongly retarded.

Protein fold class prediction: new methods of statistical classification

Feed forward neural networks are compared with standard and new statistical classification procedures for the classification of proteins. We applied logistic regression, an additive model and projection pursuit regression from the methods based on a posterior probabilities; linear, quadratic and a flexible discriminant analysis from the methods based on class conditional probabilities, and the K-nearest-neighbors classification rule. Both, the apparent error rate obtained with the training sample (n = 143) and the test error rate obtained with the test sample (n = 125) and the 10-fold cross validation error were calculated. We conclude that some of the standard statistical methods are potent competitors to the more flexible tools of machine learning.

Antioxidant properties of essential oils. Possible explanations for their anti-inflammatory effects

Pathogenesis and symptoms of inflammatory processes are accompanied and/or initiated by the production of reactive oxygen species (ROS). The effects of essential oils on these processes have been studied with the aid of biochemical model reactions simulating these pathological events. It can be shown that Myrtol Standardized and Eucalyptus oil ameliorate inflammatory processes by interacting with aggressive oxygen radicals of the OH.-type and interfere with leukocyte activation. These activities partially allow attenuation of oxidative attack and damage introduced by infections or environmental impacts.