Cross-regulatory Mechanisms Research Articles

Metabolic Responses to Redox Stress in Vascular Cells.

Significance: Redox stress underlies numerous vascular disease mechanisms. Metabolic adaptability is essential for vascular cells to preserve energy and redox homeostasis. Recent Advances: Single-cell technologies and multiomic studies demonstrate significant metabolic heterogeneity among vascular cells in health and disease. Increasing evidence shows that reductive or oxidative stress can induce metabolic reprogramming of vascular cells. A recent example is intracellular L-2-hydroxyglutarate accumulation in response to hypoxic reductive stress, which attenuates the glucose flux through glycolysis and mitochondrial respiration in pulmonary vascular cells and provides protection against further reductive stress. Critical Issues: Regulation of cellular redox homeostasis is highly compartmentalized and complex. Vascular cells rely on multiple metabolic pathways, but the precise connectivity among these pathways and their regulatory mechanisms is only partially defined. There is also a critical need to understand better the cross-regulatory mechanisms between the redox system and metabolic pathways as perturbations in either systems or their cross talk can be detrimental. Future Directions: Future studies are needed to define further how multiple metabolic pathways are wired in vascular cells individually and as a network of closely intertwined processes given that a perturbation in one metabolic compartment often affects others. There also needs to be a comprehensive understanding of how different types of redox perturbations are sensed by and regulate different cellular metabolic pathways with specific attention to subcellular compartmentalization. Lastly, integration of dynamic changes occurring in multiple metabolic pathways and their cross talk with the redox system is an important goal in this multiomics era.

Genetic Network between Leaf Senescence and Plant Immunity: Crucial Regulatory Nodes and New Insights.

Leaf senescence is an essential physiological process that is accompanied by the remobilization of nutrients from senescent leaves to young leaves or other developing organs. Although leaf senescence is a genetically programmed process, it can be induced by a wide variety of biotic and abiotic factors. Accumulating studies demonstrate that senescence-associated transcription factors (Sen-TFs) play key regulatory roles in controlling the initiation and progression of leaf senescence process. Interestingly, recent functional studies also reveal that a number of Sen-TFs function as positive or negative regulators of plant immunity. Moreover, the plant hormone salicylic acid (SA) and reactive oxygen species (ROS) have been demonstrated to be key signaling molecules in regulating leaf senescence and plant immunity, suggesting that these two processes share similar or common regulatory networks. However, the interactions between leaf senescence and plant immunity did not attract sufficient attention to plant scientists. Here, we review the regulatory roles of SA and ROS in biotic and abiotic stresses, as well as the cross-talks between SA/ROS and other hormones in leaf senescence and plant immunity, summarize the transcriptional controls of Sen-TFs on SA and ROS signal pathways, and analyze the cross-regulation between senescence and immunity through a broad literature survey. In-depth understandings of the cross-regulatory mechanisms between leaf senescence and plant immunity will facilitate the cultivation of high-yield and disease-resistant crops through a molecular breeding strategy.

JAK-STAT Signaling: A Double-Edged Sword of Immune Regulation and Cancer Progression.

Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling mediates almost all immune regulatory processes, including those that are involved in tumor cell recognition and tumor-driven immune escape. Antitumor immune responses are largely driven by STAT1 and STAT2 induction of type I and II interferons (IFNs) and the downstream programs IFNs potentiate. Conversely, STAT3 has been widely linked to cancer cell survival, immunosuppression, and sustained inflammation in the tumor microenvironment. The discovery of JAK-STAT cross-regulatory mechanisms, post-translational control, and non-canonical signal transduction has added a new level of complexity to JAK-STAT governance over tumor initiation and progression. Endeavors to better understand the vast effects of JAK-STAT signaling on antitumor immunity have unearthed a wide range of targets, including oncogenes, miRNAs, and other co-regulatory factors, which direct specific phenotypical outcomes subsequent to JAK-STAT stimulation. Yet, the rapidly expanding field of therapeutic developments aimed to resolve JAK-STAT aberrations commonly reported in a multitude of cancers has been marred by off-target effects. Here, we discuss JAK-STAT biology in the context of immunity and cancer, the consequences of pathway perturbations and current therapeutic interventions, to provide insight and consideration for future targeting innovations.

An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms.

Nuclear factor kappa B (NFκB) is a transcription factor that controls inflammation and cell survival. In clinical histology, elevated NFκB activity is a hallmark of poor prognosis in inflammatory disease and cancer, and may be the result of a combination of diverse micro-environmental constituents. While previous quantitative studies of NFκB focused on its signaling dynamics in single cells, we address here how multiple stimuli may combine to control tissue level NFκB activity. We present a novel, simplified model of NFκB (SiMoN) that functions as an NFκB activity calculator. We demonstrate its utility by exploring how type I and type II interferons modulate NFκB activity in macrophages. Whereas, type I IFNs potentiate NFκB activity by inhibiting translation of IκBα and by elevating viral RNA sensor (RIG-I) expression, type II IFN amplifies NFκB activity by increasing the degradation of free IκB through transcriptional induction of proteasomal cap components (PA28). Both cross-regulatory mechanisms amplify NFκB activation in response to weaker (viral) inducers, while responses to stronger (bacterial or cytokine) inducers remain largely unaffected. Our work demonstrates how the NFκB calculator can reveal distinct mechanisms of crosstalk on NFκB activity in interferon-containing microenvironments.

A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types.

Models of the development and early progression of colorectal cancer are based upon understanding the cycle of stem cell turnover, proliferation, differentiation and death. Existing crypt compartmental models feature a linear pathway of cell types, with little regulatory mechanism. Previous work has shown that there are perturbations in the enteroendocrine cell population of macroscopically normal crypts, a compartment not included in existing models. We show that existing models do not adequately recapitulate the dynamics of cell fate pathways in the crypt. We report the progressive development, iterative testing and fitting of a developed compartmental model with additional cell types, and which includes feedback mechanisms and cross-regulatory mechanisms between cell types. The fitting of the model to existing data sets suggests a need to invoke cross-talk between cell types as a feature of colon crypt cycle models.

GATA-3 regulation and stability in T helper type 2 cells (P1310)

Abstract GATA-3 and T-bet, the key transcription factors of T helper type 1 and type 2 cells, respectively, are specifically upregulated during differentiation of naive Th cells in response to antigen and cytokine signals. GATA-3 expression increases in response to IL-4/STAT6 signaling, whereas T-bet is induced by the IL-12/STAT4 and IFN-y/STAT1 pathways. GATA-3 and T-bet subsequently induce lineage-specific gene expression. Here, we study the regulation of GATA-3 in Th2 cells as well as the interactions between the Th1 and Th2 signaling pathways using time-resolved dose-response experiments and mathematical modeling. We measured the dose response of GATA-3, T-bet and pSTAT1/4/6 to IL-4 and IL-12 in vitro during differentiation and fitted mathematical models to the data. GATA-3 expression was graded and depended on the cytokines’ concentrations. The activation of STAT6 downstream of IL-4 and STAT4 downstream of IL-12 was stronger and longer-lasting with higher cytokine concentrations. We discovered several cross-regulatory mechanisms between the Th1 and Th2 pathways. Furthermore, the different amounts of GATA-3 reached in vitro were stably maintained in vivo for 30 days after transfer into naive mice, suggesting a cell-intrinsic mechanism allowing quantitative memory of GATA-3 expression in resting Th2 cells. Our results provide insight into the molecular mechanisms that underlie the induction and maintenance of Th2 cell differentiation.

The Plasticity of Regulatory T Cell Function

Regulatory T cells (T(regs)) can suppress a wide variety of cell types, in diverse organ sites and inflammatory conditions. Whereas T(regs) possess multiple suppressive mechanisms, the number required for maximal function is unclear. Furthermore, whether any interrelationship or cross-regulatory mechanisms exist to orchestrate and control their utilization is unknown. In this study, we assessed the functional capacity of T(regs) lacking the ability to secrete both IL-10 and IL-35, which individually are required for maximal T(reg) activity. Surprisingly, IL-10/IL-35 double-deficient T(regs) were fully functional in vitro and in vivo. Loss of IL-10 and IL-35 was compensated for by a concurrent increase in cathepsin E (Ctse) expression, enhanced TRAIL (Tnfsf10) expression, and soluble TRAIL release, rendering IL-10/IL-35 double-deficient T(regs) functionally dependent on TRAIL in vitro and in vivo. Lastly, whereas C57BL/6 T(regs) are normally IL-10/IL-35 dependent, BALB/c T(regs), which express high levels of cathepsin E and enhanced TRAIL expression, are partially TRAIL dependent by default. These data reveal that cross-regulatory pathways exist that control the utilization of suppressive mechanisms, thereby providing T(reg) functional plasticity.

Type-I IFN Signaling Suppresses an Excessive IFN-γ Response and Thus Prevents Lung Damage and Chronic Inflammation During Pneumocystis (PC) Clearance in CD4 T Cell-Competent Mice

Immune-reconstitution after highly active antiretroviral therapy (HAART) is often incomplete, and some HIV-infected individuals fail to regenerate type-I interferon (IFN)-producing pDCs. We recently demonstrated that during Pneumocystis (PC) infection in CD4 T cell-competent mice the absence of type-I IFN signaling results in chronic pulmonary inflammation and fibrosis despite clearance. Because the mechanisms involved are poorly understood, we further characterized the role of type-I IFN signaling in immune responses to PC. We show that type-I IFN signaling around day 7 postinfection is critical to the outcome of inflammation. Microarray analysis of pulmonary CD11c(+) cells revealed that at day 7 post infection, wild-type cells up-regulated type-I IFN-responsive genes as well as SOCS1, which is a critical negative-regulator of type-I IFN and IFN-gamma signaling. This was associated with an eosinophilic lung inflammation, PC clearance, and complete restitution. However, pulmonary CD11c(+) cells from IFNAR(-/-) mice demonstrated increased tumor necrosis factor (TNF)-alpha production and lacked SOCS1-induction at day 7. This was followed by a transient lymphocytic and IFN-gamma response before switching to a chronic eosinophilic inflammation of the lung. Early neutralization of TNF-alpha did not prevent chronic inflammation in IFNAR(-/-) mice, but treatment with an anti-IFN-gamma antibody did. We propose that during PC lung infection type-I IFNs induce SOCS1-associated regulatory mechanisms, which prevent excessive IFN-gamma-mediated responses that cause chronic lung damage. Therefore, partial immune-reconstitution in AIDS, attributable to reduced type-I IFN actions, might disrupt regulatory aspects of inflammation, causing unexplained chronic pulmonary complications as seen in some patients during HAART.

Modification of the innate immune function of dendritic cells by allergen-specific immunotherapy

Modification of the innate immune function of dendritic cells by allergen-specific immunotherapy

Antagonistic factors control the unproductive splicing of SC35 terminal intron

Alternative splicing is regulated in part by variations in the relative concentrations of a variety of factors, including serine/arginine-rich (SR) proteins. The SR protein SC35 self-regulates its expression by stimulating unproductive splicing events in the 3′ untranslated region of its own pre-mRNA. Using various minigene constructs containing the terminal retained intron and flanking exons, we identified in the highly conserved last exon a number of exonic splicing enhancer elements responding specifically to SC35, and showed an inverse correlation between affinity of SC35 and enhancer strength. The enhancer region, which is included in a long stem loop, also contains repressor elements, and is recognized by other RNA-binding proteins, notably hnRNP H protein and TAR DNA binding protein (TDP-43). Finally, in vitro and in cellulo experiments indicated that hnRNP H and TDP-43 antagonize the binding of SC35 to the terminal exon and specifically repress the use of SC35 terminal 3′ splice site. Our study provides new information about the molecular mechanisms of SC35-mediated splicing activation. It also highlights the existence of a complex network of self- and cross-regulatory mechanisms between splicing regulators, which controls their homeostasis and offers many ways of modulating their concentration in response to the cellular environment.

GABAergic Differentiation Induced by Mash1 Is Compromised by the bHLH Proteins Neurogenin2, NeuroD1, and NeuroD2

During forebrain development, Mash1 directs gamma-aminobutyric acid (GABA)ergic neuron differentiation ventrally in the ganglionic eminences. Repression of Mash1 in the cortex is necessary to prevent the formation of GABAergic interneurons. Negative regulation of Mash1 has been attributed to members of the Neurogenin family; the genetic ablation of Neurogenin2 (Ngn2) leads to the derepression of Mash1 and the formation of ectopic GABAergic neurons in the cortex. We have developed an in vitro system to clarify the importance of NeuroD proteins in the Mash1 regulatory pathway. Using a neurosphere culture system, we show that the downstream effectors of the Ngn2 pathway NeuroD1 and NeuroD2 can abrogate GABAergic differentiation directed by Mash1. The ectopic expression of either of these genes in Mash1-expressing cells derived from the lateral ganglionic eminence, independently downregulate Mash1 expression without affecting expression of distal less homeodomain genes. This results in a complete loss of the GABAergic phenotype. Moreover, we demonstrate that ectopic expression of Mash1 in cortical progenitors is sufficient to phenocopy the loss of Ngn2 and strongly enhances ectopic GABAergic differentiation. Collectively, our results define the compensatory and cross-regulatory mechanisms that exist among basic helix-loop-helix transcription factors during neuronal fate specification.

Gene Regulation in Continuous Cultures: A Unified Theory for Bacteria and Yeasts

During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially (diauxie) or simultaneously. The ubiquity of these growth patterns suggests that they may be driven by a universal mechanism common to all microbial species. Recently, we showed that a minimal model accounting only for enzyme induction and dilution, the two processes that occur in all microbes, explains the phenotypes observed in batch cultures of various wild-type and mutant/recombinant cells (Narang and Pilyugin in J. Theor. Biol. 244:326-348, 2007). Here, we examine the extension of the minimal model to continuous cultures. We show that: (1) Several enzymatic trends, attributed entirely to cross-regulatory mechanisms, such as catabolite repression and inducer exclusion, can be quantitatively explained by enzyme dilution. (2) The bifurcation diagram of the minimal model for continuous cultures, which classifies the substrate consumption pattern at any given dilution rate and feed concentrations, provides a precise explanation for the empirically observed correlations between the growth patterns in batch and continuous cultures. (3) Numerical simulations of the model are in excellent agreement with the data. The model captures the variation of the steady state substrate concentrations, cell densities, and enzyme levels during the single- and mixed-substrate growth of bacteria and yeasts at various dilution rates and feed concentrations. This variation is well approximated by simple analytical expressions that furnish deep physical insights. (4) Since the minimal model describes the behavior of the cells in the absence of cross-regulatory mechanisms, it provides a rigorous framework for quantifying the effect of these mechanisms. We illustrate this by analyzing several data sets from the literature.

Cross-regulatory mechanisms in hormone signaling

Recent studies suggest that hormones act through a web of interacting responses rather than through isolated linear pathways. This signal integration architecture may be one mechanism for increasing the specificity of outcomes in different cellular contexts. Several common themes for cross-regulation between pathways can be observed. Here, we propose a classification scheme for different levels of signaling pathway cross-regulation. This scheme is based on which parts of the individual pathways are acting as information conduits between pathways. Examples from the recent plant hormone biology literature are used to illustrate the different modes of interaction.

Crosstalk via the NF-κB signaling system

The nuclear factor kappaB (NF-κB) family of transcription factors consists of 15 possible dimers whose activity is controlled by a family of inhibitor proteins, known as IκBs. A variety of cellular stimuli, many of them transduced by members of the tumor necrosis factor receptor (TNFR) superfamily, induce degradation of IκBs to activate an overlapping subset of NF-κB dimers. However, generation and stimulus-responsive activation of NF-κB dimers are intimately linked via various cross-regulatory mechanisms that allow crosstalk between different signaling pathways through the NF-κB signaling system. In this review, we summarize these mechanisms and discuss physiological and pathological consequences of crosstalk between apparently distinct inflammatory and developmental signals. We argue that a systems approach will be valuable for understanding questions of specificity and emergent properties of highly networked cellular signaling systems.

Generation and Activation of Multiple Dimeric Transcription Factors within the NF-κB Signaling System

The NF-kappaB signaling pathway regulates the activity of multiple dimeric transcription factors that are generated from five distinct monomers. The availabilities of specific dimers are regulated during cell differentiation and organ development and determine the cell's responsiveness to inflammatory or developmental signals. An altered dimer distribution is a hallmark of many chronic diseases. Here, we reveal that the cellular processes that generate different NF-kappaB dimers are highly connected through multiple cross-regulatory mechanisms. First, we find that steady-state expression of RelB is regulated by the canonical pathway and constitutive RelA activity. Indeed, synthesis control of RelB is the major determinant of noncanonical NF-kappaB dimer activation. Second, processing, not synthesis, of p100 and p105 is mechanistically linked via competitive dimerization with a limited pool of RelA and RelB. This homeostatic cross-regulatory mechanism determines the availability of the p50- and p52-containing dimers and also of the noncanonical IkappaB p100. Our results inform a wiring diagram to delineate NF-kappaB dimer formation that emphasizes that inflammatory and developmental signaling cannot be considered separately but are highly interconnected.

Compensational regulation of bHLH transcription factors in the postnatal development of BETA2/NeuroD1-null retina

The bHLH transcriptional factor BETA2/NeuroD1 is essential for the survival of photoreceptor cells in the retina. Although this gene is expressed throughout the retina, BETA2/NeuroD1 knockout mice show photoreceptor cell degeneration only in the outer nuclear layer of the retina; other retinal neurons are not affected. Previous studies on retina explants lacking three bHLH genes revealed that retinal neurons in the inner nuclear layer require multiple bHLH genes for their differentiation and survival. However, single- or double-gene mutations show no or a lesser degree of abnormalities during eye development, likely because of compensation or cooperative regulation among those genes. Because not all null mice survive until the retina is fully organized, no direct evidence of this concept has been reported. To understand the regulatory mechanisms between bHLH factors in retinal development, we performed a detailed analysis of BETA2/NeuroD1 knockout mice. BETA2/NeuroD1 was expressed in all 3 layers of the mouse retina, including all major types of neurons. In addition, a null mutation of BETA2/NeuroD1 resulted in up-regulation of other bHLH genes, Mash1, Neurogenin2, and Math3, in the inner nuclear layer. Our data suggest that compensatory and cross regulatory mechanisms exist among the bHLH factors during retinal development.

Molecular and cellular control of T1/T2 immunity at the interface between antimicrobial defense and immune pathology.

The immune system evolved to rapidly recognize infectious threats and promptly mobilize cellular effectors to the infection site. Establishment of a robust T1-type immunity is a prerequisite for effective defense against most viruses and intracellular bacteria. However, accumulating evidence shows that T1 and T2 responses during such infections are not mutually exclusive. A possibility may be that the dual T1-T2 nature of antiviral immune responses is merely a byproduct of less than perfect crossregulatory mechanisms. Herein, we discuss molecular and cellular mechanisms of T-cell differentiation along with recent evidence supporting the hypothesis that rather than representing an epiphenomenon, coinduction of virus-specific T2 cells plays a significant homeostatic role. Thus, molecular pathways that regulate IL-4 production during influenza virus infection monitor T1-mediated immune responses in vital organs such as lungs and prevent immune pathology that may otherwise interfere with recovery from disease. Such evidence suggests that coinduction of T2 immunity maintains immune homeostasis during T1-mediated defense reactions. Finally, we outline implications on the earlier concept of T1/T2 dichotomy, supporting a model in which these two subsets, rather than being mutually antagonistic, together facilitate the recovery from infection.

Utilization of thyroid transcription factor-1 immunostaining in the diagnosis of lung tumors.

AbstractTranscription factors play a crucial role in the determination and maintenance of differentiated cellular phenotype and their activity is considered to constitute the main switch to regulate gene expression (1). Based on their localization and expression, transcription factors have been subdivided into two major groups: ubiquitous and tissue-specific. Tissue-specific transcription factors are those that present in a few cell types and are involved in the regulation of genes expressed only in those cells. Thyroid transcription factor-1 (TTF-1) is a 38-kDa homeodomain containing nuclear transcription protein of the Nkx2 gene family. It consists of a single polypeptide of 371 amino acids that is encoded by a single locus (2). TTF-1 is expressed in the epithelial cells of the thyroid, lung, and diencephalon during early embryogenesis (3–5). After birth, its expression is mostly maintained in the follicular and parafollicular C-cells of the thyroid and in bronchioalveolar cells. In the thyroid, TTF-1 activates the transcription of thyroglobulin, thyroperoxidase, and sodium-iodine transport protein (6–8). In the lung, TTF-1 stimulates the synthesis of surfactant proteins A (9), B (10,11), and C (12), and Clara cell secretory protein (13) through the binding of the corresponding gene promoter enhancers. TTF-1 gene expression is regulated in respiratory epithelial cells at the transcriptional and posttranscriptional levels (14) by means of cross-regulatory mechanisms involving hepatocyte nuclear factor 3, Oct-1 protein, GATA-6, and calreticulin (15–17). KeywordsSmall Cell CarcinomaMerkel Cell CarcinomaPulmonary AdenocarcinomaRespiratory Epithelial CellAtypical CarcinoidThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Osteoprotegerin Is a Receptor for the Cytotoxic Ligand TRAIL

TRAIL is a tumor necrosis factor-related ligand that induces apoptosis upon binding to its death domain-containing receptors, DR4 and DR5. Two additional TRAIL receptors, TRID/DcR1 and DcR2, lack functional death domains and function as decoy receptors for TRAIL. We have identified a fifth TRAIL receptor, namely osteoprotegerin (OPG), a secreted tumor necrosis factor receptor homologue that inhibits osteoclastogenesis and increases bone density in vivo. OPG-Fc binds TRAIL with an affinity of 3.0 nM, which is slightly weaker than the interaction of TRID-Fc or DR5-Fc with TRAIL. OPG inhibits TRAIL-induced apoptosis of Jurkat cells. Conversely, TRAIL blocks the anti-osteoclastogenic activity of OPG. These data suggest potential cross-regulatory mechanisms by OPG and TRAIL.