Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

Metabolism is a major regulator of immune cell function, but it remains difficult to study the metabolic status of individual cells. Here, we present Compass, an algorithm to characterize cellular metabolic states based on single-cell RNA sequencing and flux balance analysis. We applied Compass to associate metabolic states with T helper 17 (Th17) functional variability (pathogenic potential) and recovered a metabolic switch between glycolysis and fatty acid oxidation, akin to known Th17/regulatory T cell (Treg) differences, which we validated by metabolic assays. Compass also predicted that Th17 pathogenicity was associated with arginine and downstream polyamine metabolism. Indeed, polyamine-related enzyme expression was enhanced in pathogenic Th17 and suppressed in Treg cells. Chemical and genetic perturbation of polyamine metabolism inhibited Th17 cytokines, promoted Foxp3 expression, and remodeled the transcriptome and epigenome of Th17 cells toward a Treg-like state. In vivo perturbations of the polyamine pathway altered the phenotype of encephalitogenic T cells and attenuated tissue inflammation in CNS autoimmunity.

Targeting nucleotide metabolism as the nexus of viral infections, cancer, and the immune response

Virus-infected cells and cancers share metabolic commonalities that stem from their insatiable need to replicate while evading the host immune system. These similarities include hijacking signaling mechanisms that induce metabolic rewiring in the host to up-regulate nucleotide metabolism and, in parallel, suppress the immune response. In both cancer and viral infections, the host immune cells and, specifically, lymphocytes augment nucleotide synthesis to support their own proliferation and effector functions. Consequently, established treatment modalities targeting nucleotide metabolism against cancers and virally infected cells may result in restricted immune response. Encouragingly, following the introduction of immunotherapy against cancers, multiple studies improved our understanding for improving antigen presentation to the immune system. We propose here that understanding the immune consequences of targeting nucleotide metabolism against cancers may be harnessed to optimize therapy against viral infections.

In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity

Cellular metabolism is a major regulator of immune response, but it is difficult to study the metabolic status of an individual immune cell using current technologies. Here, we present Compass, an algorithm to characterize the metabolic landscape of single cells in silico based on single-cell RNA-Seq and flux balance analysis. We used Compass to study the landscape of metabolic heterogeneity in Th17 cells and search for novel metabolic regulators of their inflammatory function. In central carbon metabolism, Compass predicted a metabolic switch between glycolysis and fatty acid oxidation that mirrors the Th17 vs. Treg phenotype, which we validated through transcriptomic, metabolic and functional assays. The TCA cycle was predicted to break at two points, both of which have been independently identified by other groups in M1 macrophage polarization. Surprisingly, and contrary to common immunometabolic understanding, Compass predicted that glycolysis too was divided into functional modules, and that one of them supported an anti-inflammatory phenotype. We validate the paradoxical prediction and demonstrate that inhibition of this module promotes a pro-inflammatory transcriptional program in Th17 cells, resulting in neuroinflammation in an adoptive transfer model of autoimmune disease. In conclusion, Compass is a widely applicable algorithm to characterize metabolic states at single cell resolution. It allows associating cellular metabolic states with effector functions and detection of metabolic targets that regulate effector phenotypes. We expect it to become a widely used tool with the increasing availability of single-cell RNA-Seq data, spurred by efforts such as the human cell atlas.

Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation

Naive T cell stimulation activates anabolic metabolism to fuel the transition from quiescence to growth and proliferation. Here we show that naive CD4(+) T cell activation induces a unique program of mitochondrial biogenesis and remodeling. Using mass spectrometry, we quantified protein dynamics during T cell activation. We identified substantial remodeling of the mitochondrial proteome over the first 24 hr of T cell activation to generate mitochondria with a distinct metabolic signature, with one-carbon metabolism as the most induced pathway. Salvage pathways and mitochondrial one-carbon metabolism, fed by serine, contribute to purine and thymidine synthesis to enable T cell proliferation and survival. Genetic inhibition of the mitochondrial serine catabolic enzyme SHMT2 impaired T cell survival in culture and antigen-specific T cell abundance in vivo. Thus, during T cell activation, mitochondrial proteome remodeling generates specialized mitochondria with enhanced one-carbon metabolism that is critical for T cell activation and survival.

Mitochondrial metabolism in T cell activation and senescence: a mini-review

The aging immune system is unable to optimally respond to pathogens and generate long-term immunological memory against encountered antigens. Amongst the immune components most affected by aging are T lymphocytes. T lymphocytes are cells of the cell-mediated immune system, which can recognize microbial antigens and either directly kill infected cells or support the maturation and activation of other immune cells. When activated, T cells undergo a metabolic switch to accommodate their changing needs at every stage of the immune response. Here we review the different aspects of metabolic regulation of T cell activation, focusing on the emerging role of mitochondrial metabolism, and discuss changes that may contribute to age-related decline in T cell potency. Better understanding of the role of mitochondrial metabolism in immune cell function could provide insights into mechanisms of immune senescence with the potential for developing novel therapeutic approaches to improve immune responses in aged individuals.

CNS-specific immunity at the choroid plexus shifts toward destructive Th2 inflammation in brain aging

The adaptive arm of the immune system has been suggested as an important factor in brain function. However, given the fact that interactions of neurons or glial cells with T lymphocytes rarely occur within the healthy CNS parenchyma, the underlying mechanism is still a mystery. Here we found that at the interface between the brain and blood circulation, the epithelial layers of the choroid plexus (CP) are constitutively populated with CD4(+) effector memory cells with a T-cell receptor repertoire specific to CNS antigens. With age, whereas CNS specificity in this compartment was largely maintained, the cytokine balance shifted in favor of the T helper type 2 (Th2) response; the Th2-derived cytokine IL-4 was elevated in the CP of old mice, relative to IFN-γ, which decreased. We found this local cytokine shift to critically affect the CP epithelium, triggering it to produce the chemokine CCL11 shown to be associated with cognitive dysfunction. Partial restoration of cognitive ability in aged mice, by lymphopenia-induced homeostasis-driven proliferation of memory T cells, was correlated with restoration of the IL-4:IFN-γ ratio at the CP and modulated the expression of plasticity-related genes at the hippocampus. Our data indicate that the cytokine milieu at the CP epithelium is affected by peripheral immunosenescence, with detrimental consequences to the aged brain. Amenable to immunomodulation, this interface is a unique target for arresting age-related cognitive decline.

Brain homeostasis is maintained by "danger" signals stimulating a supportive immune response within the brain's borders

An organism's behavior is determined by the way it senses and perceives the surrounding environment, and by its responses to these stimuli. The major factors known to affect the behavioral response to an event are genetic background, environmental factors, and past experiences, and their imprinting on the relevant brain circuits. Recently, circulating immune cells were introduced as novel players into this system. It was proposed that the brain and circulating immune cells engage in a continuous dialogue that takes place within the brain's territory, though outside the parenchyma (occurring within the brain's borders - the choroid plexi, the brain meninges and the cerebrospinal fluid (CSF)). The cytokines secreted by activated leukocytes residing at the borders were shown to affect neurotrophic factors production within the parenchyma. Here, we suggest that such a dialogue is stimulated at the brain's borders, upon need, by a "danger" signal that originates in the parenchyma in response to any destabilizing event, and discuss the potential role of reactive oxygen species (ROS) in transmitting this signal. Accordingly, a failure to restore balance is likely to lead to aberrant responses to subsequent events. This view thus supports the contention that circulating immune cells are required to maintain the brain's balanced activity and suggests a novel mechanism whereby the surveying immune cells are sensing the brain's status and needs.

Thymic involution, a co-morbidity factor in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a devastating disease, characterized by extremely rapid loss of motor neurons. Our studies over the last decade have established CD4(+) T cells as important players in central nervous system maintenance and repair. Those results, together with recent findings that CD4(+) T cells play a protective role in mouse models of ALS, led us to the current hypothesis that in ALS, a rapid T-cell malfunction may develop in parallel to the motor neuron dysfunction. Here, we tested this hypothesis by assessing thymic function, which serves as a measure of peripheral T-cell availability, in an animal model of ALS (mSOD1 [superoxide dismutase] mice; G93A) and in human patients. We found a significant reduction in thymic progenitor-cell content, and abnormal thymic histology in 3-4-month-old mSOD1 mice. In ALS patients, we found a decline in thymic output, manifested in the reduction in blood levels of T-cell receptor rearrangement excision circles, a non-invasive measure of thymic function, and demonstrated a restricted T-cell repertoire. The morbidity of the peripheral immune cells was also manifested in the increase of pro-apoptotic BAX/BCXL2 expression ratio in peripheral blood mononuclear cells (PBMCs) of these patients. In addition, gene expression screening in the same PBMCs, revealed in the ALS patients a reduction in key genes known to be associated with T-cell activity, including: CD80, CD86, IFNG and IL18. In light of the reported beneficial role of T cells in animal models of ALS, the present observation of thymic dysfunction, both in human patients and in an animal model, might be a co-pathological factor in ALS, regardless of the disease aetiology. These findings may lead to the development of novel therapeutic approaches directed at overcoming the thymic defect and T-cell deficiency.

Age-dependent spatial memory loss can be partially restored by immune activation

Aging is often associated with a decline in hippocampus-dependent spatial memory. Here, we show that functional cell-mediated immunity is required for the maintenance of hippocampus-dependent spatial memory. Sudden imposition of immune compromise in young mice caused spatial memory impairment, whereas immune reconstitution reversed memory deficit in immune-deficient mice. Analysis of hippocampal gene expression suggested that immune-dependent spatial memory performance was associated with the expression of insulin-like growth factor (Igf1) and of genes encoding proteins related to presynaptic activity (Syt10, Cplx2). We further showed that memory loss in aged mice could be attributed to age-related attenuation of the immune response and could be reversed by immune system activation. Homeostatic-driven proliferation of lymphocytes, which expands the existing T cell repertoire, restored spatial memory deficits in aged mice. Thus, our results identify a novel function of the immune system in the maintenance of spatial memory and suggest an original approach for arresting or reversing age-associated memory loss.