Class IA PI3Ks regulate subcellular and functional dynamics of IDO1

Knowledge of a protein's spatial dynamics at the subcellular level is key to understanding its function(s), interactions, and associated intracellular events. Indoleamine 2,3-dioxygenase 1 (IDO1) is a cytosolic enzyme that controls immune responses via tryptophan metabolism, mainly through its enzymic activity. When phosphorylated, however, IDO1 acts as a signaling molecule in plasmacytoid dendritic cells (pDCs), thus activating genomic effects, ultimately leading to long-lasting immunosuppression. Whether the two activities-namely, the catalytic and signaling functions-are spatially segregated has been unclear. We found that, under conditions favoring signaling rather than catabolic events, IDO1 shifts from the cytosol to early endosomes. The event requires interaction with class IA phosphoinositide 3-kinases (PI3Ks), which become activated, resulting in full expression of the immunoregulatory phenotype in vivo in pDCs as resulting from IDO1-dependent signaling events. Thus, IDO1's spatial dynamics meet the needs for short-acting as well as durable mechanisms of immune suppression, both under acute and chronic inflammatory conditions. These data expand the theoretical basis for an IDO1-centered therapy in inflammation and autoimmunity.

Loss of Phosphatidylinositol 3-Kinase Activity in Regulatory T Cells Leads to Neuronal Inflammation

Class I PI3K enzymes are critical for the maintenance of effective immunity. In T cells, PI3Kα and PI3Kδ are activated by the TCR and costimulatory receptors, whereas PI3Kγ is activated by G protein-coupled chemokine receptors. PI3Kδ is a key regulator of regulatory T (Treg) cell function. PI3K isoform-selective inhibitors are in development for the treatment of diseases associated with immune dysregulation, including chronic inflammatory conditions, cancer, and autoimmune diseases. Idelalisib (PI3Kδ), alpelisib (PI3Kα), duvelisib (PI3Kδ/γ), and copanlisib (pan-PI3K) have recently been approved for use in cancer treatment. Although effective, these therapies often have severe side effects associated with immune dysregulation and, in particular, loss of Treg cells. Therefore, it is important to gain a better understanding of the relative contribution of different PI3K isoforms under homeostatic and inflammatory conditions. Experimental autoimmune encephalitis is a mouse model of T cell-driven CNS inflammation, in which Treg cells play a key protective role. In this study, we show that PI3Kδ is required to maintain normal Treg cell development and phenotype under homeostatic conditions but that loss of PI3Kδ alone in Treg cells does not lead to autoimmunity. However, combined loss of PI3Kα and PI3Kδ signaling resulted in increased experimental autoimmune encephalitis disease severity. Moreover, mice lacking PI3Kα and PI3Kδ in Treg cells developed spontaneous peripheral nerve inflammation. These results show a key role for PI3K signaling in Treg cell-mediated protection against CNS inflammation.

Targeting PI3Kδ function for amelioration of murine chronic graft-versus-host disease

Chronic graft-versus-host disease (cGVHD) is a leading cause of morbidity and mortality following allotransplant. Activated donor effector T cells can differentiate into pathogenic T helper (Th)-17 cells and germinal center (GC)-promoting T follicular helper (Tfh) cells, resulting in cGVHD. Phosphoinositide-3-kinase-δ (PI3Kδ), a lipid kinase, is critical for activated T cell survival, proliferation, differentiation, and metabolism. We demonstrate PI3Kδ activity in donor T cells that become Tfh cells is required for cGVHD in a nonsclerodermatous multiorgan system disease model that includes bronchiolitis obliterans (BO), dependent upon GC B cells, Tfhs, and counterbalanced by T follicular regulatory cells, each requiring PI3Kδ signaling for function and survival. Although B cells rely on PI3Kδ pathway signaling and GC formation is disrupted resulting in a substantial decrease in Ig production, PI3Kδ kinase-dead mutant donor bone marrow-derived GC B cells still supported BO cGVHD generation. A PI3Kδ-specific inhibitor, compound GS-649443, that has superior potency to idelalisib while maintaining selectivity, reduced cGVHD in mice with active disease. In a Th1-dependent and Th17-associated scleroderma model, GS-649443 effectively treated mice with active cGVHD. These data provide a foundation for clinical trials of US Food and Drug Administration (FDA)-approved PI3Kδ inhibitors for cGVHD therapy in patients.

PI3Kδ hyper-activation promotes development of B cells that exacerbate Streptococcus pneumoniae infection in an antibody-independent manner

Streptococcus pneumoniae is a major cause of pneumonia and a leading cause of death world-wide. Antibody-mediated immune responses can confer protection against repeated exposure to S. pneumoniae, yet vaccines offer only partial protection. Patients with Activated PI3Kδ Syndrome (APDS) are highly susceptible to S. pneumoniae. We generated a conditional knock-in mouse model of this disease and identify a CD19+B220- B cell subset that is induced by PI3Kδ signaling, resides in the lungs, and is correlated with increased susceptibility to S. pneumoniae during early phases of infection via an antibody-independent mechanism. We show that an inhaled PI3Kδ inhibitor improves survival rates following S. pneumoniae infection in wild-type mice and in mice with activated PI3Kδ. These results suggest that a subset of B cells in the lung can promote the severity of S. pneumoniae infection, representing a potential therapeutic target.

Multi-tissue DNA methylation age predictor in mouse

Background

DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing process. It has also not been shown whether this epigenetic clock is unique to humans or conserved in the more experimentally tractable mouse.

Results

We have generated a comprehensive set of genome-scale base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages. Many CpG sites show significant tissue-independent correlations with age which allowed us to develop a multi-tissue predictor of age in the mouse. Our model, which estimates age based on DNA methylation at 329 unique CpG sites, has a median absolute error of 3.33 weeks and has similar properties to the recently described human epigenetic clock. Using publicly available datasets, we find that the mouse clock is accurate enough to measure effects on biological age, including in the context of interventions. While females and males show no significant differences in predicted DNA methylation age, ovariectomy results in significant age acceleration in females. Furthermore, we identify significant differences in age-acceleration dependent on the lipid content of the diet.

Conclusions

Here we identify and characterise an epigenetic predictor of age in mice, the mouse epigenetic clock. This clock will be instrumental for understanding the biology of ageing and will allow modulation of its ticking rate and resetting the clock in vivo to study the impact on biological age.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1203-5) contains supplementary material, which is available to authorized users.

Targeting PI3K signaling to ameliorate chronic graft versus host disease

The phosphoinositide 3-kinase (PI3K) pathway is a key signaling pathway necessary for T cell activation, differentiation and metabolism. T effector cells rely on increased PI3K signaling to fuel glycolysis for their metabolic needs, while T regulatory cells downregulate PI3K and favor lipid oxidation. The metabolic processes of lymphocytes modulating chronic graft versus host disease (cGVHD) have remained largely unexamined and represent a novel therapeutic strategy for this disease. Here, we investigated the role of PI3K signaling in a murine model of cGVHD that is etiologically linked to up regulated germinal centers (GCs) and characterized by multisystem organ disease; including fibrosis of the lung, which results in pulmonary dysfunction. We hypothesized that inhibition of PI3K signaling would alter the activation and/or function of GC-facilitating T follicular helper (TFH) cells resulting in lessened disease. The findings in this study are that mice treated with a PI3Kd inhibitor had decreased pulmonary dysfunction similar to that of the control, non-cGVHD mice. The frequencies of splenic TFH cells as well as GC B cells were decreased by a PI3K delta inhibitor compared to non-treated cGVHD controls. In a similar manner, mice that received PI3K kinase delta dead Tregs also had decreased TFH frequency as well as reduced pulmonary dysfunction. Our results indicate the differential requirement for signaling through PI3K delta and suggest that targeting this pathway may be a potential new therapy for treatment of cGVHD. Additional studies are required to validate the potential therapeutic use.

Neocortical glial cell numbers in human brains

Stereological cell counting was applied to post-mortem neocortices of human brains from 31 normal individuals, age 18-93 years, 18 females (average age 65 years, range 18-93) and 13 males (average age 57 years, range 19-87). The cells were differentiated in astrocytes, oligodendrocytes, microglia and neurons and counting were done in each of the four lobes. The study showed that the different subpopulations of glial cells behave differently as a function of age; the number of oligodendrocytes showed a significant 27% decrease over adult life and a strong correlation to the total number of neurons while the total astrocyte number is constant through life; finally males have a 28% higher number of neocortical glial cells and a 19% higher neocortical neuron number than females. The overall total number of neocortical neurons and glial cells was 49.3 billion in females and 65.2 billion in males, a difference of 24% with a high biological variance. These numbers can serve as reference values in quantitative studies of the human neocortex.

Spatial distribution of human neocortical neurons and glial cells according to sex and age measured by the saucer method

A new stereological probe, the saucer, was used for estimating three-dimensional (3D) spatial distributions of particles around particles. The advantages of the saucer include that the measurements and the results are in 3D and the size and design of the probe enables the investigator to sample a proportion of a suitable size to have a reasonable relationship between workload and the information obtained. In this paper the method is used on vertical sections to investigate the spatial distribution of astrocytes, oligodendrocytes, microglial cells, endothelial cells and secondary neurons around primary neurons in the human neocortex (divided into frontal-, temporal-, parietal- and occipital cortex) of young and old subjects free of neurological or psychological disease to test if age and gender has any influence on the cell distribution in human neocortex. Plots of the spatial distribution of the densities of all cell types did not show any difference between women and men and no difference between brains of young and old subjects. Thus it is concluded that in this small study the spatial distribution of the densities of the different types of cells in brains from individuals free of neurological disorders was independent of age and gender.

No change in neuron numbers in the dentate nucleus of patients with schizophrenia estimated with a new stereological method--the smooth fractionator

The dentate nucleus is phylogenetically the most recent nucleus in the cerebellum. Owing to its connections to the thalamus and the prefrontal cortex it may be involved in the symptomathology in schizophrenia and other psychiatric illnesses. In this stereological study we implemented the smooth fractionator, which combines the unbiased principles of the optical fractionator with a new and more efficient sampling strategy to the dentate nucleus. The smooth fractionator represents the most efficient sampling strategy described so far in stereology, in terms of reducing the sampling variance and thus increasing the efficiency. It is the first application of the smooth fractionator to human brain tissue and presents estimations of total number of neurons in the dentate nuclei of eight patients with schizophrenia compared to eight control persons. The total number of neurons in the dentate nucleus was estimated to 3.36 x 10(6) in subjects with schizophrenia, which was not statistically significant different from 3.65 x 10(6) in control subjects (P = 0.63). The advantages and disadvantages of the smooth fractionator method are discussed and its precision in practical application is estimated.

Histological changes of the dopaminergic nigrostriatal system in aging

Although the maximum human lifespan has not increased in recent history, average life expectancy has risen dramatically since the beginning of the last century. Lengthening of lifespan has little merit if the quality of life is not preserved. In the elderly, the decline in memory and cognitive abilities is of great concern, as is motor weakening, which increases with age. The dopaminergic system mediates some aspects of manual dexterity, in addition to cognition and emotion, and may be especially vulnerable to aging. Therefore, the aging of this system has both clinical and vocational aspects. This review includes studies quantitating age-related changes of the nigrostriatal system, with emphasis on the use of stereological methods, and provides tables of stereological studies performed in the nigrostriatal system.