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1.  Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge 
By recruiting the essential HIS3 gene to the GAL regulatory system and switching to a repressing glucose medium, we confronted yeast cells with a novel challenge they had not encountered before along their history in evolution.Adaptation to this challenge involved a global transcriptional response of a sizeable fraction of the genome, which relaxed on the time scale of the population adaptation, of order of 10 generations.For a large fraction of the responding genes there is no simple biological interpretation, connecting them to the specific cellular demands imposed by the novel challenge.Strikingly, repeating the experiment did not reproduce similar transcription patterns neither in the transient phase nor in the adapted state in glucose.These results suggest that physiological selection operates on the new metabolic configurations generated by the non-specific large scale transcriptional response to eventually stabilize an adaptive state.
Cells adjust their transcriptional state to accommodate environmental and genetic perturbations. Some common perturbations, such as changes in nutrient composition, elicit well-characterized transcriptional responses that can be understood by simple engineering-like design principles as satisfying specific demands imposed by the perturbation. However, cells also have the ability to adapt to novel and unforeseen challenges. This ability is central in realizing the evolvability potential of cells as they respond to dramatic genetic or environmental changes along evolution. Little is known about the mechanisms underlying such adaptations to novel challenges; in particular, the role of the transcriptional regulatory network in such adaptations has not been characterized. Genome-wide measurements have revealed that, in many cases, perturbations lead to a global transcriptional response involving a sizeable fraction of the genome (Gasch et al, 2000; Jelinsky et al, 2000; Causton et al, 2001; Ideker et al, 2001; Lai et al, 2005). Such global behavior suggests that general collective properties of the genetic network, rather than specific pre-designed pathways, determine an important part of the transcriptional response. It is not known however what fraction of genes within such massive transcriptional responses is essential to the specific cellular demands. It is also unknown whether the non-pre-designed part of the response can have a functional role in adaptation to novel challenges.
To study these questions, we confronted yeast cells with a novel challenge they had not encountered before along their history in evolution. A strain of the yeast Saccharomyces cerevisiae was engineered to recruit the gene HIS3, an essential enzyme from the histidine biosynthesis pathway (Hinnebusch, 1992), to the GAL regulatory system, responsible for galactose utilization (Stolovicki et al, 2006). The GAL system is known to be strongly repressed when the cells are exposed to glucose. Therefore, upon switching to a medium containing glucose and lacking histidine, the GAL system and with it HIS3 are highly repressed immediately following the switch and the cells encounter a severe challenge. We have recently shown that a cell population carrying this rewired genome can adapt to grow competitively in a chemostat in a medium containing pure glucose (Stolovicki et al, 2006). This adaptation occurred on a timescale of ∼10 generations; applying a stronger environmental pressure in the form of a competitive inhibitor to HIS3 (3AT) resulted in a similar adaptation albeit with a longer timescale. Figure 1 shows the dynamics of the population's cell density (blue lines, measured by OD) following a medium switch from galactose to glucose in the chemostat without (A) and with (B) 3AT. The experiments revealed that adaptation occurs on physiological timescales (much shorter than required by spontaneous random mutations), but the mechanisms underlying this adaptation have remained unclear (Stolovicki et al, 2006).
Yeast cells had not encountered recruitment of HIS3 to the GAL system along their evolutionary history, and their genome could not possibly have been selected to specifically address glucose repression of HIS3. This experiment, therefore, provides a unique opportunity to characterize the spontaneous transcriptional response during adaptation to a novel challenge and to assess the functional role of the regulatory system in this adaptation. We used DNA microarrays to measure the genome-wide expression levels at time points along the adaptation process, with and without 3AT. These measurements revealed that a sizeable fraction of the genome responded by induction or repression to the switch into glucose. Superimposed on the OD traces, Figure 1 shows the results of a clustering analysis of the expression of genes as measured by the arrays along time in the experiments. This analysis revealed two dominant clusters, each containing hundreds of genes in each experiment, which responded to the medium switch to glucose by a strong transient induction or repression followed by relaxation to steady state on the timescale of the adaptation process, ∼ 10 generations. The two clusters in each experiment show similar but opposite dynamics.
A detailed analysis of the gene content in the two clusters revealed that only a small portion of the response was induced by a change in carbon source (15% overlap between the corresponding clusters in the two experiments, with and without 3AT). Moreover, it revealed a very low overlap with the universal stress response observed for a wide range of environmental stresses (Gasch et al, 2000; Causton et al, 2001) and with the typical response to amino-acid starvation (Natarajan et al, 2001). Additionally, all known specific responses to stress in the literature are characterized by transient induction or repression with relaxation to steady state within a generation time (Gasch et al, 2000; Koerkamp et al, 2002; Wu et al, 2004), whereas in our experiments relaxation of the transcriptional response occurs over many generations. Taken together, these results show that the transcriptional response observed here is neither a metabolic response to the change in carbon source nor is it a standard response to stress or amino-acid starvation. This raises the possibility that it is a spontaneous collective response that is largely composed of genes that do not have a specific function. This possibility was tested directly by repeating the experiment with different populations and comparing their responses. This procedure revealed reproducible adaptation dynamics and steady states in terms of population density, but showed significantly different transcriptional transient responses and steady states for the two repeated experiments. Thus, a significant portion of the genes that changed their expression during the adaptation process do not have a well-defined and reproducible function in the challenging environment.
The application of a stronger environmental pressure in the form of 3AT had a dramatic effect on the global characteristics of the transcriptional response: it induced a markedly higher correlation among the hundreds of responding genes. Figure 3A compares the array data in color code for the two experiments. It is seen that the emergent pattern of transcription exhibits a higher degree of order by the introduction of high external pressure. Observation of the transcriptional patterns for specific metabolic pathways illustrates the different contributions to the correlated dynamics (Figure 3B–D). A general energetic module such as glycolysis exhibited similar patterns of induction and relaxation in experiments with and without 3AT (Figure 3B). However, in general, we found that more than one-third of the known metabolic modules (30 out of 88 modules described in KEGG) exhibited high expression correlation among their genes when the environmental pressure was high but not when it was low. As an example, Figure 3C shows the histidine biosynthesis pathway and Figure 3D the purine pathway. Note the highly ordered trajectories in the lower panels (with 3AT) compared to the disordered ones in the upper panels (no 3AT). This order extends also between genes belonging to different and even distant metabolic modules. It indicates that a global transcriptional regulatory mechanism is in operation, rather than a local specific one. Surprisingly, genes belonging to the same metabolic pathway exhibited simultaneous positively and negatively correlated dynamics. Thus, an important conclusion of this work is that the global transcriptional response to a novel challenge cannot be explained by a simple cellular or metabolic logic. This is to be expected if the response had not been specifically selected in evolution and was not pre-designed for the challenge.
Our data clearly reveal that the massive transcriptional response underlies the adaptation process to a novel challenge. The novelty of the challenge presented to the cells excludes the possibility that this response has been specifically selected toward this challenge. Thus, transcriptional regulation has dynamic properties resulting in a general massive nonspecific response to a novel perturbation. Such a response in turn allows for metabolic rearrangements, which by feeding back on transcription lead to adaptation of the cells to the unforeseen situation. The drastic change in the expression state of the cell opens multiple new metabolic pathways. Physiological selection works then on these multiple metabolic pathways to stabilize an adaptive state that causes relaxation of the perturbed expression pattern. This scenario, involving the creation of a library of possibilities and physiological selection over this library, is compatible with our understanding of a broad class of biological systems, placing the cellular metabolic/regulatory networks on the same footing as the neural or the immune systems (Gerhart and Kirschner, 1997).
Cells adjust their transcriptional state to accommodate environmental and genetic perturbations. An open question is to what extent transcriptional response to perturbations has been specifically selected along evolution. To test the possibility that transcriptional reprogramming does not need to be ‘pre-designed' to lead to an adaptive metabolic state on physiological timescales, we confronted yeast cells with a novel challenge they had not previously encountered. We rewired the genome by recruiting an essential gene, HIS3, from the histidine biosynthesis pathway to a foreign regulatory system, the GAL network responsible for galactose utilization. Switching medium to glucose in a chemostat caused repression of the essential gene and presented the cells with a severe challenge to which they adapted over approximately 10 generations. Using genome-wide expression arrays, we show here that a global transcriptional reprogramming (>1200 genes) underlies the adaptation. A large fraction of the responding genes is nonreproducible in repeated experiments. These results show that a nonspecific transcriptional response reflecting the natural plasticity of the regulatory network supports adaptation of cells to novel challenges.
doi:10.1038/msb4100147
PMCID: PMC1865588  PMID: 17453047
adaptation; cellular metabolism; expression arrays; plasticity; transcriptional response
2.  Direct Type I IFN but Not MDA5/TLR3 Activation of Dendritic Cells Is Required for Maturation and Metabolic Shift to Glycolysis after Poly IC Stimulation 
PLoS Biology  2014;12(1):e1001759.
Type I IFN signaling is indispensable for the maturation of dendritic cells (DCs) that are required to elicit an immune response, and it also controls a shift in cellular metabolism to meet the increased energy demands of DC maturation.
Type I interferons (IFNs) play an important role in direct antiviral defense as well as linking the innate and adaptive immune responses. On dendritic cells (DCs), IFNs facilitate their activation and contribute to CD8+ and CD4+ T cell priming. However, the precise molecular mechanism by which IFNs regulate maturation and immunogenicity of DCs in vivo has not been studied in depth. Here we show that, after in vivo stimulation with the TLR ligand poly IC, IFNs dominate transcriptional changes in DCs. In contrast to direct TLR3/mda5 signaling, IFNs are required for upregulation of all pathways associated with DC immunogenicity. In addition, metabolic pathways, particularly the switch from oxidative phosphorylation to glycolysis, are also regulated by IFNs and required for DC maturation. These data provide evidence for a metabolic reprogramming concomitant with DC maturation and offer a novel mechanism by which IFNs modulate DC maturation.
Author Summary
Immune responses are orchestrated by a specialized cell type called dendritic cells (DCs). In order to achieve durable and robust immunity, DCs need to undergo an intricate differentiation process known as maturation. This process is poorly understood at the moment. Poly IC, which mimics viral RNA and is an agonist for the viral pattern recognition receptors (PRRs) that signal “danger” to the immune system, can induce full maturation of DCs and it has been shown that this requires type I IFN signaling. In this study we set out to examine the specific signals provided by direct PRR or IFN stimulation that are required for DC maturation. We found to our surprise that type I IFN can regulate almost all steps of the DC's maturation process without requiring direct PRR involvement. We also show that type I IFN regulates several metabolic switches essential for preservation of DC integrity: it stimulates the expression of the hypoxia-inducible factor 1α (Hif1α), which controls the metabolic shift from oxidative phosphorylation (used by resting cells to generate energy) to aerobic glycolysis, a less efficient but faster energy-producing process. This metabolic shift was required to meet increased energy demands of activated DCs and to prevent their premature death, thus sustaining an immune response to viral infection.
doi:10.1371/journal.pbio.1001759
PMCID: PMC3883643  PMID: 24409099
3.  Polyclonal B Cell Differentiation and Loss of Gastrointestinal Tract Germinal Centers in the Earliest Stages of HIV-1 Infection 
PLoS Medicine  2009;6(7):e1000107.
Studying the effects of early HIV infection on human antibody responses, M. Anthony Moody and colleagues find rapid polyclonal B cell differentiation and structural damage to gut-associated lymphoid tissue.
Background
The antibody response to HIV-1 does not appear in the plasma until approximately 2–5 weeks after transmission, and neutralizing antibodies to autologous HIV-1 generally do not become detectable until 12 weeks or more after transmission. Moreover, levels of HIV-1–specific antibodies decline on antiretroviral treatment. The mechanisms of this delay in the appearance of anti-HIV-1 antibodies and of their subsequent rapid decline are not known. While the effect of HIV-1 on depletion of gut CD4+ T cells in acute HIV-1 infection is well described, we studied blood and tissue B cells soon after infection to determine the effect of early HIV-1 on these cells.
Methods and Findings
In human participants, we analyzed B cells in blood as early as 17 days after HIV-1 infection, and in terminal ileum inductive and effector microenvironments beginning at 47 days after infection. We found that HIV-1 infection rapidly induced polyclonal activation and terminal differentiation of B cells in blood and in gut-associated lymphoid tissue (GALT) B cells. The specificities of antibodies produced by GALT memory B cells in acute HIV-1 infection (AHI) included not only HIV-1–specific antibodies, but also influenza-specific and autoreactive antibodies, indicating very early onset of HIV-1–induced polyclonal B cell activation. Follicular damage or germinal center loss in terminal ileum Peyer's patches was seen with 88% of follicles exhibiting B or T cell apoptosis and follicular lysis.
Conclusions
Early induction of polyclonal B cell differentiation, coupled with follicular damage and germinal center loss soon after HIV-1 infection, may explain both the high rate of decline in HIV-1–induced antibody responses and the delay in plasma antibody responses to HIV-1.
Please see later in the article for Editors' Summary
Editors' Summary
Background
Acquired immunodeficiency syndrome (AIDS) has killed more than 25 million people since 1981 and more than 30 million people are now infected with the human immunodeficiency virus (HIV), which causes AIDS. HIV infects and kills a type of immune system cell called CD4+ T lymphocytes. These cells are needed to maintain a vigorous immune response, so people infected with HIV eventually become susceptible to other infections and develop full-blown AIDS. However, early during HIV infection, other parts of the immune system attempt to fight off the virus. Soon after infection, immune system cells called B lymphocytes begin to produce HIV-specific antibodies (proteins that recognize viral molecules called antigens). The first antibodies to HIV usually appear two to seven weeks after infection; from about 12 weeks after infection, antibodies are made that can kill the specific HIV type responsible for the infection (neutralizing antibodies).
Why Was This Study Done?
Unfortunately, by this time, it is too late for the antibody (“humoral”) immune response to clear HIV from the body. Indeed, the humoral immune response to HIV is very slow; for most viruses, neutralizing antibodies appear within days of infection. To help them design an effective HIV vaccine, scientists need to understand how the virus delays humoral responses to HIV infection (and how it later causes the production of HIV-specific antibodies to decline). Little is known, however, about the early effects of HIV infection on B lymphocytes. These cells are born and mature in the bone marrow. “Naïve” B lymphocytes, each of which carries an antigen-specific receptor (a protein that binds to a specific antigen), then enter the blood and circulate around the body, passing through the “peripheral lymphoid organs”. Exposure to antigens in these organs, which include lymph nodes and gut-associated lymphoid tissues, activates the subset of B lymphocytes that recognize the specific antigens that are present. Finally, with the help of activated T lymphocytes, the activated B lymphocytes proliferate and change (differentiate) into antibody-secreting cells and memory B lymphocytes (which respond more quickly to antigen than naïve B lymphocytes). In this study, the researchers investigate the effects of early HIV-1 infection on B lymphocytes in blood and in gut-associated lymphoid tissues.
What Did the Researchers Do and Find?
The researchers collected blood from patients as early as 17 days after HIV-1 infection and tissue samples from the lower portion of the small intestine (a region rich in gut-associated lymphoid structures called Peyer's patches) from 47 days after infection onward. When they analyzed the B lymphocytes in these samples (which were collected during two trials organized by the US Center for HIV/AIDS Vaccine Immunology [CHAVI]), they found that HIV-1 infection rapidly induced the activation of many different B cells that recognized a variety of antigens (polyclonal activation), as well as the appearance of differentiated B cells in blood and in gut-associated lymphoid tissue. The B lymphocytes that were activated in the gut made HIV-specific antibodies but also antibodies against unrelated antigens (such as flu virus proteins). Finally, the structure of Peyer's patches was altered early in HIV-1 infection. More specifically, most of the lymphoid follicles (organized collections of lymphocytes and antigen-presenting cells) in the Peyer's patches showed signs of damage and T- and B-lymphocyte death and the number of germinal centers (regions in lymphoid follicles in which B lymphocytes proliferate) was reduced.
What Do These Findings Mean?
Although the depletion of gut-associated CD4+ T lymphocytes in early HIV-1 infection is well known, these new results demonstrate the effects of early HIV-1 infection on gut-associated and circulating B lymphocytes. The results of this study are limited by the methods used to analyze the antibodies induced by HIV infection and by only taking tissue samples from one region of the gut. Nevertheless, the findings of polyclonal B-cell activation and damage to gut-associated lymphoid follicles soon after HIV-1 infection may have implications for HIV-1 vaccine design. Specifically, these findings suggest that an effective HIV-1 vaccine will need to ensure that significant levels of neutralizing antibodies are present in people before HIV-1 infection and that other protective immune defenses are fully primed so that, in the event of HIV-1 infection, the virus can be dealt with effectively before it disables any part of the immune system.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1000107.
Information is available from the US National Institute of Allergy and Infectious Diseases on HIV infection and AIDS
HIV InSite has comprehensive information on all aspects of HIV/AIDS, including an article about how HIV-1 infection affects the immune system
Information is available from Avert, an international AIDS charity on many aspects of HIV/AIDS, including information on the stages of HIV infection, and on AIDS vaccines (in English and Spanish)
The US Center for HIV/AIDS Vaccine Immunology (CHAVI) Web site provides information on research designed to solve major problems in HIV vaccine development and design
doi:10.1371/journal.pmed.1000107
PMCID: PMC2702159  PMID: 19582166
4.  Structural Control of Metabolic Flux 
PLoS Computational Biology  2013;9(12):e1003368.
Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions. To meet the accompanying change in metabolic demands, the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state, which is characterized by reaction fluxes and metabolite concentrations. These state transitions are the effect of simultaneously manipulating fluxes through several reactions. While metabolic control analysis has provided a powerful framework for elucidating the principles governing this orchestrated action to understand metabolic control, its applications are restricted by the limited availability of kinetic information. Here, we introduce structural metabolic control as a framework to examine individual reactions' potential to control metabolic functions, such as biomass production, based on structural modeling. The capability to carry out a metabolic function is determined using flux balance analysis (FBA). We examine structural metabolic control on the example of the central carbon metabolism of Escherichia coli by the recently introduced framework of functional centrality (FC). This framework is based on the Shapley value from cooperative game theory and FBA, and we demonstrate its superior ability to assign “share of control” to individual reactions with respect to metabolic functions and environmental conditions. A comparative analysis of various scenarios illustrates the usefulness of FC and its relations to other structural approaches pertaining to metabolic control. We propose a Monte Carlo algorithm to estimate FCs for large networks, based on the enumeration of elementary flux modes. We further give detailed biological interpretation of FCs for production of lactate and ATP under various respiratory conditions.
Author Summary
Insight into the functioning of metabolic control to meet changing demands is a first step in rational engineering of biological systems towards a desired behavior. Metabolic control analysis provides the means to examine the impact of change of reaction fluxes on a specific target flux based on kinetic modeling, but suffers from limitations of the kinetic approach. Here, we introduce and analyze structural metabolic control as a framework to overcome these limitations. We utilize functional centrality, a framework based on the Shapley value from cooperative game theory and flux balance analysis, to determine the contribution of individual reactions to the functions accomplished by a metabolic network. These contributions, in turn, depend on the control exerted on the remaining network. Functional centrality provides the mathematical means to gain further understanding of metabolic control. The potential applications range from facilitating strategies of rational strain design to drug target identification.
doi:10.1371/journal.pcbi.1003368
PMCID: PMC3868538  PMID: 24367246
5.  Metabolic Reprogramming towards Aerobic Glycolysis Correlates with Greater Proliferative Ability and Resistance to Metabolic Inhibition in CD8 versus CD4 T Cells 
PLoS ONE  2014;9(8):e104104.
T lymphocytes (T cells) undergo metabolic reprogramming after activation to provide energy and biosynthetic materials for growth, proliferation and differentiation. Distinct T cell subsets, however, adopt metabolic programs specific to support their needs. As CD4 T cells coordinate adaptive immune responses while CD8 T cells become cytotoxic effectors, we compared activation-induced proliferation and metabolic reprogramming of these subsets. Resting CD4 and CD8 T cells were metabolically similar and used a predominantly oxidative metabolism. Following activation CD8 T cells proliferated more rapidly. Stimulation led both CD4 and CD8 T cells to sharply increase glucose metabolism and adopt aerobic glycolysis as a primary metabolic program. Activated CD4 T cells, however, remained more oxidative and had greater maximal respiratory capacity than activated CD8 T cells. CD4 T cells were also associated with greater levels of ROS and increased mitochondrial content, irrespective of the activation context. CD8 cells were better able, however, to oxidize glutamine as an alternative fuel source. The more glycolytic metabolism of activated CD8 T cells correlated with increased capacity for growth and proliferation, along with reduced sensitivity of cell growth to metabolic inhibition. These specific metabolic programs may promote greater growth and proliferation of CD8 T cells and enhance survival in diverse nutrient conditions.
doi:10.1371/journal.pone.0104104
PMCID: PMC4121309  PMID: 25090630
6.  Down-Regulation of the Interferon Signaling Pathway in T Lymphocytes from Patients with Metastatic Melanoma 
PLoS Medicine  2007;4(5):e176.
Background
Dysfunction of the immune system has been documented in many types of cancers. The precise nature and molecular basis of immune dysfunction in the cancer state are not well defined.
Methods and Findings
To gain insights into the molecular mechanisms of immune dysfunction in cancer, gene expression profiles of pure sorted peripheral blood lymphocytes from 12 patients with melanoma were compared to 12 healthy controls. Of 25 significantly altered genes in T cells and B cells from melanoma patients, 17 are interferon (IFN)-stimulated genes. These microarray findings were further confirmed by quantitative PCR and functional responses to IFNs. The median percentage of lymphocytes that phosphorylate STAT1 in response to interferon-α was significantly reduced (Δ = 16.8%; 95% confidence interval, 0.98% to 33.35%) in melanoma patients (n = 9) compared to healthy controls (n = 9) in Phosflow analysis. The Phosflow results also identified two subgroups of patients with melanoma: IFN-responsive (33%) and low-IFN-response (66%). The defect in IFN signaling in the melanoma patient group as a whole was partially overcome at the level of expression of IFN-stimulated genes by prolonged stimulation with the high concentration of IFN-α that is achievable only in IFN therapy used in melanoma. The lowest responders to IFN-α in the Phosflow assay also showed the lowest gene expression in response to IFN-α. Finally, T cells from low-IFN-response patients exhibited functional abnormalities, including decreased expression of activation markers CD69, CD25, and CD71; TH1 cytokines interleukin-2, IFN-γ, and tumor necrosis factor α, and reduced survival following stimulation with anti-CD3/CD28 antibodies compared to controls.
Conclusions
Defects in interferon signaling represent novel, dominant mechanisms of immune dysfunction in cancer. These findings may be used to design therapies to counteract immune dysfunction in melanoma and to improve cancer immunotherapy.
Prompted by altered expression patterns of interferon-responsive genes in T and B cells, Peter Lee and colleagues find that lymphocytes from melanoma patients have defects in interferon signaling.
Editors' Summary
Background.
The immune system, in addition to fighting infections, provides one of the body's main defenses against cancer. During cancer development, normal cells acquire genetic changes that allow them to grow uncontrollably and to move around the body. Some of these changes alter the antigens (proteins recognized by the immune system) expressed on their surface. As a result, the immune system recognizes and eliminates the newly formed cancer cells. Tumors—large masses of cancer cells—occur when this immune surveillance fails. Some tumors, for example, hide from the immune system by altering the antigens they express. Others release factors that shut off the immune response. However, for many tumor types, it is not clear why immune surveillance fails during their development or why global immune suppression develops in most patients with advanced disease.
Why Was This Study Done?
Scientists want to understand the molecular basis of immune dysfunction in patients with cancer because if they knew what had gone wrong with the immune system, they might be able to repair it. Also, there is considerable interest in immunotherapy for cancer—for example, treatment with interferons (proteins made by certain immune system cells that activate other immune cells and also kill tumor cells) and the development of vaccines to stimulate antitumor immune responses. So far, immunotherapy has not been very successful, probably because of the underlying dysfunction of the immune system in patients with cancer. Understanding this dysfunction might lead to improvements in immunotherapy, so in this study the researchers have investigated the molecular mechanism responsible for immune dysfunction in patients with metastatic melanoma, a deadly form of skin cancer.
What Did the Researchers Do and Find?
The researchers purified lymphocytes (immune cells that are involved in antitumor responses) from the blood of patients with metastatic melanoma and healthy people and examined their patterns of gene expression using a technique called microarray expression profiling. CD8 T cells (which kill cells expressing foreign or altered antigens), CD4 T cells (which help other T and B lymphocytes do their jobs), and B cells (which make antibodies, proteins that recognize antigens and label cancer cells for destruction by the immune system) from patients with melanoma all expressed lower levels of 24 genes, and higher levels of one gene, than those from healthy individuals. 17 of these genes were interferon-stimulated genes, which encode proteins responsible for the effects of interferons. Therefore, the researchers checked the functional responses of patient and control lymphocytes to interferon. When interferon binds to lymphocytes, it triggers the addition of a phosphate group to the protein STAT1, which then induces changes in gene expression. STAT1 phosphorylation occurred in a lower percentage of patient lymphocytes than control lymphocytes in response to interferon-α (which is sometimes used to treat melanoma). The lymphocytes from one-third of the patients responded well to interferon-α, but those from the other patients showed little response. Furthermore, prolonged treatment with high concentrations of interferon-α partly overcame the defect in interferon signaling in patient lymphocytes. Finally, T cells from the patients failed to make the normal markers of immune cell activation or cytokines (proteins that mediate the killing of tumor cells) after exposure to activating stimuli and had reduced survival compared to control lymphocytes.
What Do These Findings Mean?
These results indicate that for patients with metastatic melanoma defects in interferon signaling are an important contributor to immune dysfunction. They also show that T cells from patients with melanoma (particularly those who respond poorly to interferon-α) have functional abnormalities that make them less likely to recognize and deal with melanoma cells. These results need confirming in many more patients, but they nevertheless represent an important step toward understanding the immune dysfunction associated with advanced melanoma and possibly other tumors. In addition, the identification of two subgroups of patients—interferon responders and poor interferon responders—may explain why only some patients with melanoma benefit from treatment with interferon-α. It might, therefore, be possible to pre-select those who would benefit from this treatment (which has some serious side effects) by examining patient lymphocytes for interferon responsiveness.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040176.
US National Cancer Institute information (in English and Spanish) for patients on the immune system and its involvement in cancer, and for patients and professionals on melanoma
American Cancer Society information for patients on immunotherapy
Cancer Research Institute (New York) web-based book on cancer and the immune system
MedlinePlus encyclopedia pages on melanoma (in English and Spanish)
Cancer Research UK patient information on melanoma, including information on immunotherapy
doi:10.1371/journal.pmed.0040176
PMCID: PMC1865558  PMID: 17488182
7.  Gene expression analyses of immune responses in Atlantic salmon during early stages of infection by salmon louse (Lepeophtheirus salmonis) revealed bi-phasic responses coinciding with the copepod-chalimus transition 
BMC Genomics  2011;12:141.
Background
The salmon louse (Lepeophtheirus salmonis Krøyer), an ectoparasitic copepod with a complex life cycle causes significant losses in salmon aquaculture. Pesticide treatments against the parasite raise environmental concerns and their efficacy is gradually decreasing. Improvement of fish resistance to lice, through biological control methods, needs better understanding of the protective mechanisms. We used a 21 k oligonucleotide microarray and RT-qPCR to examine the time-course of immune gene expression changes in salmon skin, spleen, and head kidney during the first 15 days after challenge, which encompassed the copepod and chalimus stages of lice development.
Results
Large scale and highly complex transcriptome responses were found already one day after infection (dpi). Many genes showed bi-phasic expression profiles with abrupt changes between 5 and 10 dpi (the copepod-chalimus transitions); the greatest fluctuations (up- and down-regulation) were seen in a large group of secretory splenic proteases with unknown roles. Rapid sensing was witnessed with induction of genes involved in innate immunity including lectins and enzymes of eicosanoid metabolism in skin and acute phase proteins in spleen. Transient (1-5 dpi) increase of T-cell receptor alpha, CD4-1, and possible regulators of lymphocyte differentiation suggested recruitment of T-cells of unidentified lineage to the skin. After 5 dpi the magnitude of transcriptomic responses decreased markedly in skin. Up-regulation of matrix metalloproteinases in all studied organs suggested establishment of a chronic inflammatory status. Up-regulation of putative lymphocyte G0/G1 switch proteins in spleen at 5 dpi, immunoglobulins at 15 dpi; and increase of IgM and IgT transcripts in skin indicated an onset of adaptive humoral immune responses, whereas MHCI appeared to be down-regulated.
Conclusions
Atlantic salmon develops rapid local and systemic reactions to L. salmonis, which, however, do not result in substantial level of protection. The dramatic changes observed after 5 dpi can be associated with metamorphosis of copepod, immune modulation by the parasite, or transition from innate to adaptive immune responses.
doi:10.1186/1471-2164-12-141
PMCID: PMC3062619  PMID: 21385383
8.  Transcriptional Responses of Leptospira interrogans to Host Innate Immunity: Significant Changes in Metabolism, Oxygen Tolerance, and Outer Membrane 
Background
Leptospira interrogans is the major causative agent of leptospirosis. Phagocytosis plays important roles in the innate immune responses to L. interrogans infection, and L. interrogans can evade the killing of phagocytes. However, little is known about the adaptation of L. interrogans during this process.
Methodology/Principal Findings
To better understand the interaction of pathogenic Leptospira and innate immunity, we employed microarray and comparative genomics analyzing the responses of L. interrogans to macrophage-derived cells. During this process, L. interrogans altered expressions of many genes involved in carbohydrate and lipid metabolism, energy production, signal transduction, transcription and translation, oxygen tolerance, and outer membrane proteins. Among them, the catalase gene expression was significantly up-regulated, suggesting it may contribute to resisting the oxidative pressure of the macrophages. The expressions of several major outer membrane protein (OMP) genes (e.g., ompL1, lipL32, lipL41, lipL48 and ompL47) were dramatically down-regulated (10–50 folds), consistent with previous observations that the major OMPs are differentially regulated in vivo. The persistent down-regulations of these major OMPs were validated by immunoblotting. Furthermore, to gain initial insight into the gene regulation mechanisms in L. interrogans, we re-defined the transcription factors (TFs) in the genome and identified the major OmpR TF gene (LB333) that is concurrently regulated with the major OMP genes, suggesting a potential role of LB333 in OMPs regulation.
Conclusions/Significance
This is the first report on global responses of pathogenic Leptospira to innate immunity, which revealed that the down-regulation of the major OMPs may be an immune evasion strategy of L. interrogans, and a putative TF may be involved in governing these down-regulations. Alterations of the leptospiral OMPs up interaction with host antigen-presenting cells (APCs) provide critical information for selection of vaccine candidates. In addition, genome-wide annotation and comparative analysis of TFs set a foundation for further studying regulatory networks in Leptospira spp.
Author Summary
Leptospirosis is an important tropical disease around the world, particularly in humid tropical and subtropical countries. As a major pathogen of this disease, Leptospira interrogans can be shed from the urine of reservoir hosts, survive in soil and water, and infect humans through broken skin or mucous membranes. Recently, host adaptability and immune evasion of L. interrogans to host innate immunity was partially elucidated in infection or animal models. A better understanding of the molecular mechanisms of L. interrogans in response to host innate immunity is required to learn the nature of early leptospirosis. This study focused on the transcriptome of L. interrogans during host immune cells interaction. Significant changes in energy metabolism, oxygen tolerance and outer membrane protein profile were identified as potential immune evasion strategies by pathogenic Leptospira during the early stage of infection. The major outer membrane proteins (OMPs) of L. interrogans may be regulated by the major OmpR specific transcription factor (LB333). These results provide a foundation for further studying the pathogenesis of leptospirosis, as well as identifying gene regulatory networks in Leptospira spp.
doi:10.1371/journal.pntd.0000857
PMCID: PMC2964297  PMID: 21049008
9.  Immune gene expression profiling of Proliferative Kidney Disease in rainbow trout Oncorhynchus mykiss reveals a dominance of anti-inflammatory, antibody and T helper cell-like activities 
Veterinary Research  2013;44(1):55.
The myxozoan Tetracapsuloides bryosalmonae is the causative agent of Proliferative Kidney Disease (PKD) targeting primarily the kidney of infected fish where it causes a chronic lymphoid immunopathology. Although known to be associated with suppression of some cellular aspects of innate immunity and a prominent lymphocytic hyperplasia, there remains a considerable knowledge gap in our understanding of the underlying immune mechanisms driving PKD pathogenesis. To provide further insights, the expression profiles of a panel of innate / inflammatory and adaptive immune molecules were examined in rainbow trout Oncorhynchus mykiss following a natural exposure to the parasite. Relative to controls, fish with early to advanced stages of kidney pathology exhibited up-regulation of the inflammatory cytokines interleukin (IL)-6 and IL-11, although remaining refractory towards genes indicative of macrophage activity. Antimicrobial peptides (AMPs) and anti-inflammatory markers, including cathelicidin (CATH) and IL-10 were markedly up-regulated during clinical disease. Up-regulation of adaptive immune molecules, including cell markers and antibody genes reflect the lymphocytic dominance of this disease and the likely importance of lymphocyte subsets in PKD pathogenesis. Up-regulation of T helper (TH) cell-like response genes and transcription factors implies that T. bryosalmonae may elicit a complex interplay between TH cell subsets. This work, for the first time in the study of fish-myxozoan interactions, suggests that PKD pathogenesis is shaped by an anti-inflammatory phenotype, a profound B cell / antibody response and dysregulated TH cell-like activities. A better understanding of the functional roles of fish immune cells and molecules in PKD pathogenesis may facilitate future development of control measures against this disease.
doi:10.1186/1297-9716-44-55
PMCID: PMC3733943  PMID: 23865616
10.  PPARγ Agonists in Adaptive Immunity: What Do Immune Disorders and Their Models Have to Tell Us? 
PPAR Research  2013;2013:519724.
Adaptive immunity has evolved as a very powerful and highly specialized tool of host defense. Its classical protagonists are lymphocytes of the T- and B-cell lineage. Cytokines and chemokines play a key role as effector mechanisms of the adaptive immunity. Some autoimmune and inflammatory diseases are caused by disturbance of the adaptive immune system. Recent advances in understanding the pathogenesis of autoimmune diseases have led to research on new molecular and therapeutic targets. PPARγ are members of the nuclear receptor superfamily and are transcription factors involved in lipid metabolism as well as innate and adaptive immunity. PPARγ is activated by synthetic and endogenous ligands. Previous studies have shown that PPAR agonists regulate T-cell survival, activation and T helper cell differentiation into effector subsets: Th1, Th2, Th17, and Tregs. PPARγ has also been associated with B cells. The present review addresses these issues by placing PPARγ agonists in the context of adaptive immune responses and the relation of the activation of these receptors with the expression of cytokines involved in adaptive immunity.
doi:10.1155/2013/519724
PMCID: PMC3747405  PMID: 23983678
11.  Human-Specific Evolution and Adaptation Led to Major Qualitative Differences in the Variable Receptors of Human and Chimpanzee Natural Killer Cells 
PLoS Genetics  2010;6(11):e1001192.
Natural killer (NK) cells serve essential functions in immunity and reproduction. Diversifying these functions within individuals and populations are rapidly-evolving interactions between highly polymorphic major histocompatibility complex (MHC) class I ligands and variable NK cell receptors. Specific to simian primates is the family of Killer cell Immunoglobulin-like Receptors (KIR), which recognize MHC class I and associate with a range of human diseases. Because KIR have considerable species-specificity and are lacking from common animal models, we performed extensive comparison of the systems of KIR and MHC class I interaction in humans and chimpanzees. Although of similar complexity, they differ in genomic organization, gene content, and diversification mechanisms, mainly because of human-specific specialization in the KIR that recognizes the C1 and C2 epitopes of MHC-B and -C. Humans uniquely focused KIR recognition on MHC-C, while losing C1-bearing MHC-B. Reversing this trend, C1-bearing HLA-B46 was recently driven to unprecedented high frequency in Southeast Asia. Chimpanzees have a variety of ancient, avid, and predominantly inhibitory receptors, whereas human receptors are fewer, recently evolved, and combine avid inhibitory receptors with attenuated activating receptors. These differences accompany human-specific evolution of the A and B haplotypes that are under balancing selection and differentially function in defense and reproduction. Our study shows how the qualitative differences that distinguish the human and chimpanzee systems of KIR and MHC class I predominantly derive from adaptations on the human line in response to selective pressures placed on human NK cells by the competing needs of defense and reproduction.
Author Summary
Natural killer (NK) cells are versatile lymphocytes that make essential contributions to immune defense and placental reproduction. Essential to NK cell development, diversification and function are variable families of surface receptors that recognize equally variable determinants of polymorphic major histocompatibility complex (MHC) class I molecules, better known as the tissue types matched in clinical organ transplantation. These ligand-receptor interactions evolve rapidly, exhibiting much species specificity and convergent evolution. Consequently, mice represent a poor model, because their receptors are so disparate from the independently evolved human counterparts that are restricted to simian primates. To identify unique and shared aspects of human NK cell biology, we have defined the genomics, population biology, and immunology of variable chimpanzee NK cell receptors and ligands to a level permitting accurate, informed comparison with the well-characterized human system. In both receptors and ligands there are dramatic, qualitative differences between humans and chimpanzees. We show these differences arose during human evolution from the last common human–chimpanzee ancestor, while the chimpanzee system remained relatively stable. That two so closely related species exhibit major differences in NK cell receptors and ligands testifies to the strong and varying selection imposed by the different demands and competing needs of defense and reproduction.
doi:10.1371/journal.pgen.1001192
PMCID: PMC2973822  PMID: 21079681
12.  Lack of Mucosal Immune Reconstitution during Prolonged Treatment of Acute and Early HIV-1 Infection 
PLoS Medicine  2006;3(12):e484.
Background
During acute and early HIV-1 infection (AEI), up to 60% of CD4+ T cells in the lamina propria of the lower gastrointestinal (GI) tract are lost as early as 2–4 wk after infection. Reconstitution in the peripheral blood during therapy with highly active antiretroviral therapy (HAART) is well established. However, the extent of immune reconstitution in the GI tract is unknown.
Methods and Findings
Fifty-four AEI patients and 18 uninfected control participants underwent colonic biopsy. Forty of the 54 AEI patients were followed after initiation of antiretroviral therapy (18 were studied longitudinally with sequential biopsies over a 3-y period after beginning HAART, and 22 were studied cross sectionally after 1–7 y of uninterrupted therapy). Lymphocyte subsets, markers of immune activation and memory in the peripheral blood and GI tract were determined by flow cytometry and immunohistochemistry. In situ hybridization was performed in order to identify persistent HIV-1 RNA expression. Of the patients studied, 70% maintained, on average, a 50%–60% depletion of lamina propria lymphocytes despite 1–7 y of HAART. Lymphocytes expressing CCR5 and both CCR5 and CXCR4 were persistently and preferentially depleted. Levels of immune activation in the memory cell population, CD45RO+ HLA-DR+, returned to levels seen in the uninfected control participants in the peripheral blood, but were elevated in the GI tract of patients with persistent CD4+ T cell depletion despite therapy. Rare HIV-1 RNA–expressing cells were detected by in situ hybridization.
Conclusions
Apparently suppressive treatment with HAART during acute and early infection does not lead to complete immune reconstitution in the GI mucosa in the majority of patients studied, despite immune reconstitution in the peripheral blood. Though the mechanism remains obscure, the data suggest that there is either viral or immune-mediated accelerated T cell destruction or, possibly, alterations in T cell homing to the GI tract. Although clinically silent over the short term, the long-term consequences of the persistence of this lesion may emerge as the HIV-1–infected population survives longer owing to the benefits of HAART.
Despite early initiation of anti-HIV therapy, loss of T cells in the gastrointestinal mucosa persisted for years in most members of a clinical cohort identified early after HIV-1 infection.
Editors' Summary
Background.
AIDS causes disease by inactivating the body's immune response against infection. The AIDS virus (HIV) is most active against the white blood cells called T lymphocytes, particularly the CD4 T lymphocytes, which recognize infection and activate other cells of the immune system to fight it. In what was formerly believed to be a gradual process, HIV infection is now known to deplete a subset of the body's CD4 lymphocytes, called memory cells, quite rapidly—over only a few days—within a few weeks after a person becomes infected with the AIDS virus. This was not known until recently because researchers were counting CD4 cells only in blood, while a majority of the memory lymphocytes are located in and around the digestive system. It is these intestinal memory lymphocytes that are rapidly wiped out, while those in the blood fall much more gradually, usually over several years. Few studies of mucosal lymphocytes have been done in humans because such studies require biopsies of the intestinal lining (mucosa).
Why Was This Study Done?
Although CD4 cells in the blood can return and remain at normal levels when HIV infection is treated with antiviral drugs, it has been unclear as to whether the mucosal CD4 cells return as well. People who begin treatment as soon as possible after becoming infected with HIV might seem to have the best chance of regaining their mucosal immunity, compared to those who wait until the CD4 cells in their blood have fallen, which is a generally accepted reason to start medication for HIV. Therefore, the researchers wanted to see whether people who start treatment early after becoming infected with HIV might experience restoration of their mucosal immunity over time and, if so, what kinds of lymphocytes would return.
What Did the Researchers Do and Find?
The researchers studied people who started treatment for HIV within a few weeks to months of becoming infected and who then remained on treatment. Some volunteers underwent biopsies of the intestinal mucosa before starting treatment and then at various points from 1 y until as long as 3 y after infection. Others volunteered for biopsy only one time, anywhere from less than 1 y to 7 y following treatment. The biopsy specimens were examined under the microscope and with a technique called flow cytometry using specific staining methods to assess their structure and functional characteristics. Results were compared to biopsies from a group of HIV-uninfected volunteers.
The researchers found that the percentage of CD4 lymphocytes dropped much lower in the intestinal mucosa than in blood during early infection and then, unlike in blood, remained low even after several years of treatment for HIV. In the microscope images, they found that mucosal CD4 cells were lost mostly from regions of active battle against invading germs, rather than from “training sites” for new CD4 cells. Over time, only 30% of the volunteers showed return of CD4 cells to normal levels in these active sites.
Unlike T lymphocytes in the blood, which tend to return to a resting state after HIV is treated, the T lymphocytes in the intestinal mucosa tended to persist in an activated state despite HIV treatment, even though only a tiny fraction of these cells were found to be infected with HIV. A high level of activation of mucosal lymphocytes soon after infection was found to predict poor restoration of mucosal CD4 cells over time.
What Do These Findings Mean?
These experiments confirm that studying easily obtained blood lymphocytes provides only a limited view of how HIV affects the immune system as a whole. The finding that immune cells of the intestinal mucosa remain depleted and over-activated for years despite antiretroviral treatment raises the concern that over time this will result in clinical problems. Fortunately, this does not appear to be the case in most people currently being treated for HIV, some for as long as 10 y, but the results of this study suggest that we should remain vigilant for gastrointestinal problems resulting from impaired immunity over time. The finding that mucosal lymphocytes do appear to return to normal levels in a minority of volunteers is of interest, and suggests that early interventions to reduce activation of intestinal T cells (such as antimicrobial or immunomodulatory treatment) might be worth investigating in those recently infected with HIV. Finally, these results suggest that a vaccine to prevent HIV may need to stimulate immune responses that can act very quickly following infection, before the bulk of lymphocytes capable of countering the infection are lost, perhaps irreversibly.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0030484.
UCSF HIV InSite includes resources on HIV immunology and vaccine development
AIDS fact sheets and brochures from the US National Institute of Allergy and Infectious Diseases
Medline Plus article on acute HIV infection from the US National Library of Medicine
doi:10.1371/journal.pmed.0030484
PMCID: PMC1762085  PMID: 17147468
13.  Metabolic switching and fuel choice during T-cell differentiation and memory development 
Immunological reviews  2012;249(1):27-42.
Summary
Clearance or control of pathogens or tumors usually requires T-cell-mediated immunity. As such, understanding the mechanisms that govern the function, maintenance, and persistence of T cells will likely lead to new treatments for controlling disease. During an immune response, T-cell development is marked by striking changes in metabolism. There is a growing appreciation that these metabolic changes underlie the capacity of T cells to perform particular functions, and this has led to a recent focus on the idea that the manipulation of cellular metabolism can be used to shape adaptive immune responses. Although interest in this area has grown in the last few years, a full understanding of the metabolic control of T-cell functions, particularly during an immune response in vivo, is still lacking. In this review, we first provide a basic overview of metabolism in T cells, and then we focus on recent studies providing new or updated insights into the regulation of metabolic pathways and how they underpin T-cell differentiation and memory T-cell development.
doi:10.1111/j.1600-065X.2012.01150.x
PMCID: PMC3645891  PMID: 22889213
T cell; metabolism; immune response
14.  The Role of Selenium in Inflammation and Immunity: From Molecular Mechanisms to Therapeutic Opportunities 
Antioxidants & Redox Signaling  2012;16(7):705-743.
Abstract
Dietary selenium (]Se), mainly through its incorporation into selenoproteins, plays an important role in inflammation and immunity. Adequate levels of Se are important for initiating immunity, but they are also involved in regulating excessive immune responses and chronic inflammation. Evidence has emerged regarding roles for individual selenoproteins in regulating inflammation and immunity, and this has provided important insight into mechanisms by which Se influences these processes. Se deficiency has long been recognized to negatively impact immune cells during activation, differentiation, and proliferation. This is related to increased oxidative stress, but additional functions such as protein folding and calcium flux may also be impaired in immune cells under Se deficient conditions. Supplementing diets with above-adequate levels of Se can also impinge on immune cell function, with some types of inflammation and immunity particularly affected and sexually dimorphic effects of Se levels in some cases. In this comprehensivearticle, the roles of Se and individual selenoproteins in regulating immune cell signaling and function are discussed. Particular emphasis is given to how Se and selenoproteins are linked to redox signaling, oxidative burst, calcium flux, and the subsequent effector functions of immune cells. Data obtained from cell culture and animal models are reviewed and compared with those involving human physiology and pathophysiology, including the effects of Se levels on inflammatory or immune-related diseases including anti-viral immunity, autoimmunity, sepsis, allergic asthma, and chronic inflammatory disorders. Finally, the benefits and potential adverse effects of intervention with Se supplementation for various inflammatory or immune disorders are discussed. Antioxid. Redox Signal. 16, 705–743.
I. Introduction
II. Bioactive Forms of Se and Their Effects
III. Incorporation of Dietary Se into Selenoproteins
IV. The Selenoprotein Family
A. An overview of selenoproteins
B. Selenoprotein functions
1. Glutathione peroxidases
2. Thioredoxin reductases
3. Deiodinases
4. Selenoprotein P
5. Selenoproteins K and S
6. Other selenoprotein family members
C. The hierarchy of selenoprotein expression
V. Selenoprotein Expression in Immune Tissues and Cells
A. Tissue and cellular distribution under physiological conditions
B. Selenoprotein expression in immune cells and tissues in response to Se changes
C. The selenoproteomic response during immune cell activation
VI. Se and Redox Signaling in Immune Cells
A. An overview
B. Types of ROS important for immune cell signaling
C. Se levels related to the production of ROS in immune cells
D. Se levels related to calcium and redox signaling in immune cells
1. H2O2 as a secondary messenger in leukocyte activation
2. The relationship between Ca2+ flux and oxidative burst
3. The effects of Se intake on Ca2+ flux and redox signaling in T cells
4. Se related to calcium and redox signaling in phagocytes
5. A novel link between Selk and the calpain/calpastatin system
VII. Se and Immune Cell Effector Functions
A. T helper cell differentiation
1. Se and T helper differentiation
2. Regulatory T helper cells
3. Epigenetic poising in naive T helper cells
B. B cell function and antibody production
C. Adherence and migration of leukocytes
1. Expression of adherence molecules
2. Migration
D. Se and eicosinoid synthesis in macrophages
E. Phagocytosis
F. Inflammation linked to ER stress
VIII. Linkages Between Se and Human Disease
A. Se supplementation to boost anti-viral immunity
1. Se levels can affect the virus itself
2. Human immunodeficiency virus 1/acquired immune deficiency syndrome
3. Influenza viruses
4. Poliovirus
B. Critical illness stress-induced immune suppression
C. Systemic inflammatory response syndrome
D. Intestinal inflammation and food-borne illnesses
E. Allergies and asthma
1. Epidemiology
2. Mouse models of allergic asthma
3. Intervention with Se supplementation for patients with asthma
F. Cystic fibrosis
G. Autoimmunity
H. Se supplementation and aging immunity
I. Lymphedema
J. Se supplementation and inflammation associated with diabetes
IX. Can Se Supplementation Be Targeted to the Immune System?
X. Information Gaps and Future Directions
doi:10.1089/ars.2011.4145
PMCID: PMC3277928  PMID: 21955027
15.  The Intercellular Metabolic Interplay between Tumor and Immune Cells 
Functional and effective immune response requires a metabolic rewiring of immune cells to meet their energetic and anabolic demands. Beyond this, the availability of extracellular and intracellular metabolites may serve as metabolic signals interconnecting with cellular signaling events to influence cellular fate and immunological function. As such, tumor microenvironment represents a dramatic example of metabolic derangement, where the highly metabolic demanding tumor cells may compromise the function of some immune cells by competing nutrients (a form of intercellular competition), meanwhile may support the function of other immune cells by forming a metabolic symbiosis (a form of intercellular collaboration). It has been well known that tumor cells harness immune system through information exchanges that are largely attributed to soluble protein factors and intercellular junctions. In this review, we will discuss recent advance on tumor metabolism and immune metabolism, as well as provide examples of metabolic communications between tumor cells and immune system, which may represent a novel mechanism of conveying tumor-immune privilege.
doi:10.3389/fimmu.2014.00358
PMCID: PMC4112791  PMID: 25120544
metabolism; tumor; tumor immunity; antagonism; symbiosis
16.  HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology 
We present HepatoNet1, a manually curated large-scale metabolic network of the human hepatocyte that encompasses >2500 reactions in six intracellular and two extracellular compartments.Using constraint-based modeling techniques, the network has been validated to replicate numerous metabolic functions of hepatocytes corresponding to a reference set of diverse physiological liver functions.Taking the detoxification of ammonia and the formation of bile acids as examples, we show how these liver-specific metabolic objectives can be achieved by the variable interplay of various metabolic pathways under varying conditions of nutrients and oxygen availability.
The liver has a pivotal function in metabolic homeostasis of the human body. Hepatocytes are the principal site of the metabolic conversions that underlie diverse physiological functions of the liver. These functions include provision and homeostasis of carbohydrates, amino acids, lipids and lipoproteins in the systemic blood circulation, biotransformation, plasma protein synthesis and bile formation, to name a few. Accordingly, hepatocyte metabolism integrates a vast array of differentially regulated biochemical activities and is highly responsive to environmental perturbations such as changes in portal blood composition (Dardevet et al, 2006). The complexity of this metabolic network and the numerous physiological functions to be achieved within a highly variable physiological environment necessitate an integrated approach with the aim of understanding liver metabolism at a systems level. To this end, we present HepatoNet1, a stoichiometric network of human hepatocyte metabolism characterized by (i) comprehensive coverage of known biochemical activities of hepatocytes and (ii) due representation of the biochemical and physiological functions of hepatocytes as functional network states. The network comprises 777 metabolites in six intracellular (cytosol, endoplasmic reticulum and Golgi apparatus, lysosome, mitochondria, nucleus, and peroxisome) and two extracellular compartments (bile canaliculus and sinusoidal space) and 2539 reactions, including 1466 transport reactions. It is based on the manual evaluation of >1500 original scientific research publications to warrant a high-quality evidence-based model. The final network is the result of an iterative process of data compilation and rigorous computational testing of network functionality by means of constraint-based modeling techniques. We performed flux-balance analyses to validate whether for >300 different metabolic objectives a non-zero stationary flux distribution could be established in the network. Figure 1 shows one such functional flux mode associated with the synthesis of the bile acid glycochenodeoxycholate, one important hepatocyte-specific physiological liver function. Besides those pathways directly linked to the synthesis of the bile acid, the mevalonate pathway and the de novo synthesis of cholesterol, the flux mode comprises additional pathways such as gluconeogenesis, the pentose phosphate pathway or the ornithine cycle because the calculations were routinely performed on a minimal set of exchangeable metabolites, that is all reactants were forced to be balanced and all exportable intermediates had to be catabolized into non-degradable end products. This example shows how HepatoNet1 under the challenges of limited exchange across the network boundary can reveal numerous cross-links between metabolic pathways traditionally perceived as separate entities. For example, alanine is used as gluconeogenic substrate to form glucose-6-phosphate, which is used in the pentose phosphate pathway to generate NADPH. The glycine moiety for bile acid conjugation is derived from serine. Conversion of ammonia into non-toxic nitrogen compounds is one central homeostatic function of hepatocytes. Using the HepatoNet1 model, we investigated, as another example of a complex metabolic objective dependent on systemic physiological parameters, how the consumption of oxygen, glucose and palmitate is affected when an external nitrogen load is converted in varying proportions to the non-toxic nitrogen compounds: urea, glutamine and alanine. The results reveal strong dependencies between the available level of oxygen and the substrate demand of hepatocytes required for effective ammonia detoxification by the liver.
Oxygen demand is highest if nitrogen is exclusively transformed into urea. At lower fluxes into urea, an intriguing pattern for oxygen demand is predicted: oxygen demand attains a minimum if the nitrogen load is directed to urea, glutamine and alanine with relative fluxes of 0.17, 0.43 and 0.40, respectively (Figure 2A). Oxygen demand in this flux distribution is four times lower than for the maximum (100% urea) and still 77 and 33% lower than using alanine and glutamine as exclusive nitrogen compounds, respectively. This computationally predicted tendency is consistent with the notion that the zonation of ammonia detoxification, that is the preferential conversion of ammonia to urea in periportal hepatocytes and to glutamine in perivenous hepatocytes, is dictated by the availability of oxygen (Gebhardt, 1992; Jungermann and Kietzmann, 2000). The decreased oxygen demand in flux distributions using higher proportions of glutamine or alanine is accompanied by increased uptake of the substrates glucose and palmitate (Figure 2B). This is due to an increased demand of energy and carbon for the amidation and transamination of glutamate and pyruvate to discharge nitrogen in the form of glutamine and alanine, respectively. In terms of both scope and specificity, our model bridges the scale between models constructed specifically to examine distinct metabolic processes of the liver and modeling based on a global representation of human metabolism. The former include models for the interdependence of gluconeogenesis and fatty-acid catabolism (Chalhoub et al, 2007), impairment of glucose production in von Gierke's and Hers' diseases (Beard and Qian, 2005) and other processes (Calik and Akbay, 2000; Stucki and Urbanczik, 2005; Ohno et al, 2008). The hallmark of these models is that each of them focuses on a small number of reactions pertinent to the metabolic function of interest embedded in a customized representation of the principal pathways of central metabolism. HepatoNet1, currently, outperforms liver-specific models computationally predicted (Shlomi et al, 2008) on the basis of global reconstructions of human metabolism (Duarte et al, 2007; Ma and Goryanin, 2008). In contrast to either of the aforementioned modeling scales, HepatoNet1 provides the combination of a system-scale representation of metabolic activities and representation of the cell type-specific physical boundaries and their specific transport capacities. This allows for a highly versatile use of the model for the analysis of various liver-specific physiological functions. Conceptually, from a biological system perspective, this type of model offers a large degree of comprehensiveness, whereas retaining tissue specificity, a fundamental design principle of mammalian metabolism. HepatoNet1 is expected to provide a structural platform for computational studies on liver function. The results presented herein highlight how internal fluxes of hepatocyte metabolism and the interplay with systemic physiological parameters can be analyzed with constraint-based modeling techniques. At the same time, the framework may serve as a scaffold for complementation of kinetic and regulatory properties of enzymes and transporters for analysis of sub-networks with topological or kinetic modeling methods.
We present HepatoNet1, the first reconstruction of a comprehensive metabolic network of the human hepatocyte that is shown to accomplish a large canon of known metabolic liver functions. The network comprises 777 metabolites in six intracellular and two extracellular compartments and 2539 reactions, including 1466 transport reactions. It is based on the manual evaluation of >1500 original scientific research publications to warrant a high-quality evidence-based model. The final network is the result of an iterative process of data compilation and rigorous computational testing of network functionality by means of constraint-based modeling techniques. Taking the hepatic detoxification of ammonia as an example, we show how the availability of nutrients and oxygen may modulate the interplay of various metabolic pathways to allow an efficient response of the liver to perturbations of the homeostasis of blood compounds.
doi:10.1038/msb.2010.62
PMCID: PMC2964118  PMID: 20823849
computational biology; flux balance; liver; minimal flux
17.  Activated lymphocytes as a metabolic model for carcinogenesis 
Metabolic reprogramming is a key event in tumorigenesis to support cell growth, and cancer cells frequently become both highly glycolytic and glutamine dependent. Similarly, T lymphocytes (T cells) modify their metabolism after activation by foreign antigens to shift from an energetically efficient oxidative metabolism to a highly glycolytic and glutamine-dependent metabolic program. This metabolic transition enables T cell growth, proliferation, and differentiation. In both activated T cells and cancer cells metabolic reprogramming is achieved by similar mechanisms and offers similar survival and cell growth advantages. Activated T cells thus present a useful model with which to study the development of tumor metabolism. Here, we review the metabolic similarities and distinctions between activated T cells and cancer cells, and discuss both the common signaling pathways and master metabolic regulators that lead to metabolic rewiring. Ultimately, understanding how and why T cells adopt a cancer cell-like metabolic profile may identify new therapeutic strategies to selectively target tumor metabolism or inflammatory immune responses.
doi:10.1186/2049-3002-1-5
PMCID: PMC3834493  PMID: 24280044
Cancer; Lymphocyte; Metabolism; Aerobic glycolysis
18.  Early Origins of Adult Disease: Approaches for Investigating the Programmable Epigenome in Humans, Nonhuman Primates, and Rodents 
ILAR Journal  2012;53(3-4):306-321.
According to the developmental origins of health and disease hypothesis, in utero experiences reprogram an individual for immediate adaptation to gestational perturbations, with the sequelae of later-in-life risk of metabolic disease. An altered gestational milieu with resultant adult metabolic disease has been observed in instances of both in utero constraint (e.g., from famine or uteroplacental insufficiency) and overt caloric abundance (e.g., from a maternal high-fat, caloric-dense diet). The commonality of the adult metabolic phenotype begs the question of how diverse in utero experiences (i.e., reprogramming events) converge on common metabolic pathways and how the memory of these events is maintained across the lifespan. We and others have investigated the molecular mechanisms underlying fetal programming and observed that epigenetic modifications to the fetal and placental epigenome accompany these reprogramming events. Based on several lines of emerging data in human and nonhuman primates, it is now felt that modified epigenetic signature—and the histone code in particular—underlies alterations in postnatal gene expression and metabolic pathways central to accurate functioning and maintenance of health. Because of the tissue lineage specificity of many of these modifications, nonhuman primates serve as an apt model system for the capacity to recapitulate human gene expression and regulation during development. This review summarizes recent epigenetic advances using rodent and primate (both human and nonhuman) models during in utero development and contributing to adult diseases later in life.
doi:10.1093/ilar.53.3-4.306
PMCID: PMC3747760  PMID: 23744969
behavioral epigenetics; developmental origins of health and disease (DOHaD); environmental epigenetics; microbiome; nonhuman primate (NHP)
19.  PFK1 Glycosylation Is a Key Regulator of Cancer Cell Growth and Central Metabolic Pathways 
Science (New York, N.Y.)  2012;337(6097):975-980.
Cancer cells need to meet the metabolic demands of rapid cell growth within a continually changing microenvironment. Genetic mechanisms for reprogramming cellular metabolism toward proliferative, pro-survival pathways are well-reported. However, post-translational mechanisms, which would enable more rapid, reversible adaptations of cellular metabolism in response to protein signaling or environmental sensing systems, are less well understood. Here we demonstrate that the post-translational modification O-linked β-N-acetylglucosamine (O-GlcNAc) is a key metabolic regulator of glucose metabolism. O-GlcNAc is dynamically induced at Ser529 of phosphofructokinase 1 (PFK1) in response to hypoxia. Glycosylation inhibits PFK1 activity and redirects the flux of glucose from glycolysis through the pentose phosphate pathway (PPP), thereby conferring a selective growth advantage to cancer cells. Blocking glycosylation of PFK1 at Ser529 reduced cancer cell proliferation in vitro and impaired tumor formation in vivo. These studies reveal an unexpected mechanism for the regulation of metabolic enzymes and pathways, and pinpoint a new therapeutic approach for combating cancer.
doi:10.1126/science.1222278
PMCID: PMC3534962  PMID: 22923583
20.  P5 - Evaluation of Immunological Reactivity to Metal Components in Patients with Prosthesis Device 
In recent years, the development of innovative biomaterials and surgical techniques has led to a progressive increase in joint replacement arthroplasty procedures.
It is well known that all implant metals, in contact with biological fluids, undergo electrochemical and mechanical corrosion, releasing metallic particles that may induce toxic responses and local or systemic inflammatory reactions.
Several studies have demonstrated a possible relationship between particulate wear debris and symptoms of dermatitis and urticaria, but there is no evidence of a direct correlation between wear severity and immune response.
Published results show that the immune reaction changes with individual immunomodulatory status.
The aim of this study was to analyse the proliferative response in the presence of proper stimuli, and to identify possible modifications in the production of a wide range of cytokines, as potential biological markers for early diagnosis of aseptic loosening.
Methods:
This study analyses the immune response of potentially allergic patients undergoing joint replacement arthroplasty, patients with painful prosthetic joints or joint instability, and subjects without any implants, serving as controls.
In vivo assessment of metal sensitivity includes a standard patch test for hypersensitivity reactions.
Accordingly, a standard patch test for in vivo assessment of metal hypersensitivity reaction, based on the level of allergic response of the skin, was performed.
Blood samples were collected after obtaining informed consent.
Activated lymphocyte proliferation was assessed by counting [3H]-thymidine uptake (3H-TdR).
Peripheral blood mononuclear cells, isolated from heparinised blood samples using standard density gradient centrifugation, were resuspended in RPMI1640 culture medium supplemented with foetal calf serum, L-glutamine, penicillin/streptomycin, and (cultured) incubated at 37°C in 5% CO2, in the presence and absence of scalar concentrations (from 1 to 0.01mM) of chromium, nickel, titanium, cobalt and molybdenum.
Phytohaemagglutinin, a polyclonal mitogen which activates lymphocytes proliferation, was used as positive control. Cells were pulsed for the last 12 hours of culture with 1 μCi of 3H-TdR.
Lymphocyte proliferation, measured in CPM (counts per minutes), was assessed by scintillation counting of incorporated radioactivity; the results were expressed as stimulation index (SI).
Cytokine production in PBMC supernatants was analysed using Luminex LabMAP assay, which measures the concentrations of multiple analytes in the same sample.
Results and Conclusions:
Results of metal sensitivity testing show that: chromium and nickel at concentrations of 0.1 mM significantly enhanced proliferation of PBMCsisolated from samples of patients submitted to joint replacements, compared with controls.Patients with allergic reactions showed an increased proliferative response to high concentration of nickel.No proliferative response was found in normal control subjects.None of the patients analysed to date showed reactivity to titanium.
The analysis of lymphocyte culture supernatants showed the constant production of chemotactic cytokines, such as IL-8 and MIP1 α and β.
Chromium and nickel significantly modulated production of cytokines, such as IL-8, MIP1 α and β MCP-1, RANTES and PDGF-BB, in patients with joint implants compared with control group.
Some patients showed the presence of cytokines with regulatory activity on cell differentiation and growth, such as IL-2, and the presence of pro-inflammatory macrophage-derived cytokines, such as IL-1.
These preliminary results suggest that there is different involvement of specific cytokines and chemokines responsible for inflammatory reactions, related to different individual responses.
PMCID: PMC3213797
21.  Metabolic reprogramming and metabolic dependency in T cells 
Immunological reviews  2012;249(1):14-26.
Summary
Upon activation, quiescent naive T cells undergo a growth phase followed by massive clonal expansion and differentiation that are essential for appropriate immune defense and regulation. Accumulation of cell biomass during the initial growth and rapid proliferation during the expansion phase is associated with dramatically increased bioenergetic and biosynthetic demands. This not only requires a metabolic rewiring during the transition between resting and activation, but also ‘addicts’ active T cells to certain metabolic pathways in ways that naive and memory T cells are not. We consider such addiction in terms of the biological effects of deprivation of metabolic substrates or inhibition of specific pathways in T cells. In this review, we illustrate the relevant metabolic pathways revealed by recent metabolic flux analysis and discuss the consequences of metabolic intervention on specific metabolic pathways in T lymphocytes.
doi:10.1111/j.1600-065X.2012.01155.x
PMCID: PMC3422760  PMID: 22889212
metabolism; T lymphocytes; T-cell activation
22.  Development of a Bovine Ileal Cannulation Model To Study the Immune Response and Mechanisms of Pathogenesis of Paratuberculosis▿  
An ileal cannulation model was developed in conjunction with a flow cytometric assay to gain a better understanding of the mechanisms of immunopathogenesis of Johne's disease caused by Mycobacterium avium subsp. paratuberculosis. Initial studies with calves showed that M. avium subsp. paratuberculosis DNA is detectable by PCR in ileal biopsies during the first months following experimental infection. Inflammatory lesions were not detected on endoscopic evaluation up to 8 months postexperimental infection. M. avium subsp. paratuberculosis DNA was detected in multiple tissues at necropsy 8 months postinfection. Examination of the activation status of epithelial lymphocytes from the jejunum and ileum from infected and control animals at necropsy revealed that none of the major subsets of lymphocytes (NK, CD2+, and CD2− γδ T lymphocytes, or CD4 and CD8 αβ T lymphocytes) expressed activation molecules CD25, CD26, CD71, ACT1, or ACT16. Subsets of CD4 and CD8 T lymphocytes from control and infected animals expressed CD26. The majority of CD4 and CD8 T lymphocytes expressed CD45R0, the memory T-lymphocyte marker. An immune response to M. avium subsp. paratuberculosis was detected by 3 months postinfection, dominated by a strong proliferative response of CD4 memory T lymphocytes. The findings indicate an immune response develops following initial exposure to M. avium subsp. paratuberculosis that controls but does not eliminate the pathogen. This persistence of M. avium subsp. paratuberculosis possibly leads to erosion and dysregulation of protective immunity at later time points postinfection. Continuous access to the ileum offers an opportunity to elucidate the cellular and molecular events leading to immune dysregulation and development of chronic inflammatory ileitis.
doi:10.1128/CVI.00347-08
PMCID: PMC2668272  PMID: 19225077
23.  Manipulating the bioenergetics of alloreactive T cells causes their selective apoptosis and arrests graft versus host disease 
Science Translational Medicine  2011;3(67):67ra8.
Cells generate ATP by glycolysis and by oxidative phosphorylation (OXPHOS) (1, 2). Despite the importance of having sufficient ATP available for the energy-dependent processes involved in immune activation, little is known about the metabolic adaptations that occur in vivo to meet the increased demand for ATP in activated and proliferating lymphocytes. We found that bone marrow (BM) cells proliferating after bone marrow transplantation (BMT) increased aerobic glycolysis but not OXPHOS, while T cells proliferating in response to alloantigens during graft versus host disease (GVHD) increased both aerobic glycolysis and OXPHOS. Metabolomic analysis of alloreactive T cells showed an accumulation of acylcarnitines consistent with changes in fatty acid oxidation. Alloreactive T cells also exhibited a hyperpolarized mitochondrial membrane potential (ΔΨm), increased superoxide production and decreased antioxidant levels, whereas proliferating BM cells did not. Bz-423, a novel small molecule inhibitor of the mitochondrial F1F0-ATPase, selectively increased superoxide and induced the apoptosis of alloreactive T cells, which arrested established GVHD in several BMT models without affecting hematopoietic engraftment or lymphocyte reconstitution. These findings challenge the current paradigm that activated T cells meet their increased demands for ATP though aerobic glycolysis, and identify the possibility that bioenergetic and redox characteristics can be selectively exploited as a novel therapeutic strategy for immune disorders.
doi:10.1126/scitranslmed.3001975
PMCID: PMC3364290  PMID: 21270339
24.  Resveratrol analogue HS-1793 induces the modulation of tumor-derived T cells 
Recent advances in the understanding of the mechanisms responsible for tumor progression suggest the possibility to control cancer growth, not only through chemotherapy-induced cancer cell destruction, but also by stimulating anticancer immunity. However, immune tolerance against tumor antigens disturbs diverse forms of immunotherapy. One of the most potent and well-studied tumor-induced immunosuppressive phenotypes found in the tumor microenvironment is the regulatory subpopulation cells (CD4+CD25+FoxP3+ Treg cells). Among the great number of natural agents derived from plants and potentially useful for application in the complementary therapy of cancer, resveratrol is gaining attention for its immunomodulating properties in breast cancer, since the ineffectiveness of numerous immunotherapy strategies may be related, in part, to their negative effects on Treg cells. The present study was undertaken to examine whether HS-1793, a synthetic resveratrol analogue free from the restriction of the metabolic instability and high dose requirement of resveratrol, shows a direct effect on immune responses by enhancing lymphocyte proliferation or an immunomodulatory effect by inducing changes in the Treg cell population in FM3A breast tumor-bearing mice. Although HS-1793 had no direct immunostimulatory effect, it dose-dependently decreased IL-2 secretion and increased IL-4 secretion of concanavalin A-stimulated lymphocytes from tumor-bearing mice, which suggest that HS-1793 may induce changes in the subpopulations of tumor-derived T lymphocytes. The CD4+CD25+ cell population from tumor-bearing mice decreased after HS-1793 treatment in a dose-dependent manner, while the CD4+ T cell population remained unchanged. FoxP3+-expressing cells among the CD4+CD25+ population showed a similar pattern. In contrast, the CD8+ T cell population as well as the interferon (IFN)-γ-expressing CD8+ T cell population and IFN-γ secretion of splenocytes from tumor-bearing mice were significantly upregulated by HS-1793 treatment. These results suggest that HS-1793 induces the modulation of tumor-derived T lymphocytes, particulary having a suppressive effect on the Treg cell population, likely contributing to enhanced tumor-specific cytotoxic T lymphocyte responses and CD4+ T cells involving antitumor immunity. Therefore, HS-1793 may serve as a promising adjuvant therapeutic reagent in breast cancer immunotherapy.
doi:10.3892/etm.2012.472
PMCID: PMC3438654  PMID: 22969934
resveratrol analogue; HS-1793; regulatory T cell; FoxP3; interferon-γ
25.  Role of Innate Lymphocytes in Infection and Inflammation 
Cooperation between the innate and adaptive immune responses is critical for enabling protective immunity against various invading microbes. Distinct types of effector T cells have different functions in adaptive immune responses. Th1 cells play important roles in the control of intracellular bacteria by producing IFN-γ to activate macrophages and in anti-viral immunity by producing IFN-γ and activating cytotoxic T lymphocytes. Th2 cell-derived cytokines are important in activating mast cells, eosinophils, and goblet cells in anti-helminth immunity. Th17 cells are pivotal for the inflammatory response mediated by neutrophils, which resists extracellular bacterial infection. In all cases, it is critical that the innate immune responses limit the growth and expansion of invading microbes until antigen-specific adaptive immune responses are established. Recent studies have identified multiple subsets in innate lymphocytes corresponding to previously defined Th subsets. Classical natural killer cells, RORγ+ lymphoid tissue inducer-related cells, and Th2-type innate lymphocytes play distinct roles in innate immune responses by producing Th1, Th17, and Th2 cytokines, respectively. Cooperation between innate lymphocytes and antigen-specific T and B cells are likely important in protective immunity against distinct types of microbes. The most recently identified subset is the RORγ-independent Lin−Thy-1+IL-7R+GATA3+ innate lymphocyte subset such as natural helper (NH) cell, which is Id2- and IL-7-dependent. This population produces Th2 cytokines, most notably IL-5 and IL-13, and plays a major role in innate immune responses during anti-helminth immunity. In addition, these cells are likely involved in the pathophysiology of some types of allergic diseases. We summarize here current knowledge regarding various innate lymphocyte subsets. In particular, we focus on the Th2-type innate lymphocyte subset.
doi:10.3389/fimmu.2012.00101
PMCID: PMC3346161  PMID: 22783250
Th2 cytokine; natural helper cell; fat-associated lymphoid cluster; nuocyte; innate helper type 2; helminth; asthma; allergic inflammation

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