Non-autonomous Response Research Articles

PATHOGEN APATHY RESULTING FROM SKN-1 ACTIVATION: A MARK OF RESILIENCE OR A RATTLED GUT FEELING?

Abstract Innate immunity is a key driver in promoting survival against xenobiotic stressors and hostile environments and an appropriate immune response is essential to organismal health across lifespan. Caenorhabditis elegans encounter pathogens in their natural environment and initiate cytoprotective and immune responses that can have long-lasting effects on health, even after the pathogen has been neutralized. Pseudomonas aeruginosa (PA14) is an opportunistic pathogen that is lethal to C. elegans with prolonged exposure. C. elegans employ multiple defense mechanisms to ensure survival upon exposure to pathogens to defend against the current infection and to avoid continued exposure, including activation of the key cytoprotective transcription factor SKN-1 (mammalian homologue Nrf2). Although wild type C. elegans quickly learn to avoid pathogens, our current work documents a peculiar apathy to pathogen in animals with constitutive activation of SKN-1. The outcome is surprising as the role of SKN-1 is to protect an animal from intracellular and environmental insults. This behavior is mediated by tissue specific actions of SKN-1 that initiate cell non-autonomous responses for pathogen avoidance, survival, and metabolic adaptation. Based on transcriptional signature of animals with SKN-1 activation upon exposure to PA14 we observed that the apathy behavior is independent of somatic lipid depletion, thus uncoupling these two exceptional physiological responses. Further, we define the role of neurosignalling molecules in the gut-brain axis that drive the apathy response to pathogens. Our work reveals new insights into how animals perceive pathogens in the environment and subsequently alter behavior and cellular programs to promote survival.

Both cell autonomous and non-autonomous processes modulate the association between replication timing and mutation rate

Cancer somatic mutations are the product of multiple mutational and repair processes, some of which are tightly associated with DNA replication. Mutation rates (MR) are known to be higher in late replication timing (RT) regions, but different processes can affect this association. Systematic analysis of the mutational landscape of 2787 tumors from 32 tumor types revealed that approximately one third of the tumor samples show weak association between replication timing and mutation rate. Further analyses revealed that those samples have unique mutational signatures and are enriched with mutations in genes involved in DNA replication, DNA repair and chromatin structure. Surprisingly, analysis of differentially expressed genes between weak and strong RT-MR association groups revealed that tumors with weak association are enriched with genes associated with cell–cell communication and the immune system, suggesting a non-autonomous response to DNA damage.

Intraneuronal tau aggregation induces the integrated stress response in astrocytes.

Progressive aggregation of tau protein in neurons is associated with neurodegeneration in tauopathies. Cell non-autonomous disease mechanisms in astrocytes may be important drivers of the disease process but remain largely elusive. Here, we studied cell type-specific responses to intraneuronal tau aggregation prior to neurodegeneration. To this end, we developed a fully human co-culture model of seed-independent intraneuronal tau pathology, which shows no neuron and synapse loss. Using high-content microscopy, we show that intraneuronal tau aggregation induces oxidative stress accompanied by activation of the integrated stress response specifically in astrocytes. This requires the direct co-culture with neurons and is not related to neurodegeneration or extracellular tau levels. Tau-directed antisense therapy reduced intraneuronal tau levels and aggregation and prevented the cell non-autonomous responses in astrocytes. These data identify the astrocytic integrated stress response as a novel disease mechanism activated by intraneuronal tau aggregation. In addition, our data provide the first evidence for the efficacy of tau-directed antisense therapy to target cell autonomous and cell non-autonomous disease pathways in a fully human model of tau pathology.

Foxm1 Modulates Cell Non-Autonomous Response in Zebrafish Skeletal Muscle Homeostasis.

foxm1 is a master regulator of the cell cycle, contributing to cell proliferation. Recent data have shown that this transcription factor also modulates gene networks associated with other cellular mechanisms, suggesting non-proliferative functions that remain largely unexplored. In this study, we used CRISPR/Cas9 to disrupt foxm1 in the zebrafish terminally differentiated fast-twitching muscle cells. foxm1 genomic disruption increased myofiber death and clearance. Interestingly, this contributed to non-autonomous satellite cell activation and proliferation. Moreover, we observed that Cas9 expression alone was strongly deleterious to muscle cells. Our report shows that foxm1 modulates a muscle non-autonomous response to myofiber death and highlights underreported toxicity to high expression of Cas9 in vivo.

Single-cell transcriptomics: a novel precision medicine technique in nephrology.

Due to the complex structure and function of the kidneys, the mechanism of kidney disease is unclear. In particular, transcriptomics approaches at the bulk level are unable to differentiate primary autonomous responses, which lead to disease development, from secondary cell non-autonomous responses. Single-cell analysis techniques can overcome the limitations inherent in the measurement of heterogeneous cell populations and clarify the central issues in kidney biology and disease pathogenesis. Single-cell sequencing helps in identifying disease-related biomarkers and pathways, stratifying patients, and deciding on appropriate treatment methods. Here we review a variety of single-cell analysis techniques and single-cell transcriptomics studies performed in the field of nephrology. Moreover, we discuss the future prospects of single-cell analysis-based precision medicine in nephrology.

Differential roles of GDF15 and FGF21 in systemic metabolic adaptation to the mitochondrial integrated stress response

SummaryPerturbation of mitochondrial proteostasis provokes cell autonomous and cell non-autonomous responses that contribute to homeostatic adaptation. Here, we demonstrate distinct metabolic effects of hepatic metabokines as cell non-autonomous factors in mice with mitochondrial OxPhos dysfunction. Liver-specific mitochondrial stress induced by a loss-of-function mutation in Crif1 (LKO) leads to aberrant oxidative phosphorylation and promotes the mitochondrial unfolded protein response. LKO mice are highly insulin sensitive and resistant to diet-induced obesity. The hepatocytes of LKO mice secrete large quantities of metabokines, including GDF15 and FGF21, which confer metabolic benefits. We evaluated the metabolic phenotypes of LKO mice with global deficiency of GDF15 or FGF21 and show that GDF15 regulates body and fat mass and prevents diet-induced hepatic steatosis, whereas FGF21 upregulates insulin sensitivity, energy expenditure, and thermogenesis in white adipose tissue. This study reveals that the mitochondrial integrated stress response (ISRmt) in liver mediates metabolic adaptation through hepatic metabokines.

Nonlinear analysis of a geared rotor system supported by fluid film journal bearings

This paper presents a novel approach for modeling and analyzing a geared rotor-bearing system including nonlinear forces in the gear set and the supporting fluid film journal bearings. The rotordynamics system model has five degrees of freedom that define the transverse displacements of the shaft-gear centerlines and the relative displacement of the gear tooth contact point. The journal bearing nonlinear forces are obtained via a solution of Reynolds equation for lubricant film pressure utilizing the finite element method. Co-existing, steady-state, autonomous and non-autonomous responses are obtained in an accurate and computationally efficient manner utilizing the multiple shooting and continuation algorithms. This yields the full manifolds of the multiple bifurcation system. Chaos is identified with maximum Lyapunov exponents, frequency spectra, Poincaré attractors, etc. The results reveal a dependence of the gear set contact conditions and system nonlinear response characteristics, i.e. jump, co-existing responses, subharmonic resonances and chaos on the choice of journal bearing parameters. The results also show that Hopf bifurcations, which occur along with oil whirl in a journal bearing system, can be attenuated by increasing the gear torque.

Transcriptional changes during hepatic ischemia-reperfusion in the rat

There are few effective targeted strategies to reduce hepatic ischemia-reperfusion (IR) injury, a contributor to poor outcomes in liver transplantation recipients. It has been proposed that IR injury is driven by the generation of reactive oxygen species (ROS). However, recent studies implicate other mediators of the injury response, including mitochondrial metabolic dysfunction. We examined changes in global gene expression after transient hepatic ischemia and at several early reperfusion times to identify potential targets that could be used to protect against IR injury. Male Wistar rats were subjected to 30 minutes of 70% partial warm ischemia followed by 0, 0.5, 2, or 6 hours of reperfusion. RNA was extracted from the reperfused and non-ischemic lobes at each time point for microarray analysis. Identification of differentially expressed genes and pathway analysis were used to characterize IR-induced changes in the hepatic transcriptome. Changes in the reperfused lobes were specific to the various reperfusion times. We made the unexpected observation that many of these changes were also present in tissue from the paired non-ischemic lobes. However, the earliest reperfusion time, 30 minutes, showed a marked increase in the expression of a set of immediate-early genes (c-Fos, c-Jun, Atf3, Egr1) that was exclusive to the reperfused lobe. We interpreted these results as indicating that this early response represented a tissue autonomous response to reperfusion. In contrast, the changes that occurred in both the reperfused and non-ischemic lobes were interpreted as indicating a non-autonomous response resulting from hemodynamic changes and/or circulating factors. These tissue autonomous and non-autonomous responses may serve as targets to ameliorate IR injury.

Metabolic remodeling induced by mitokines in heart failure.

The prevalence rates of heart failure (HF) are greater than 10% in individuals aged >75 years, indicating an intrinsic link between aging and HF. It has been recognized that mitochondrial dysfunction contributes to the pathology of HF. Mitokines are a type of cytokines, peptides, or signaling pathways produced or activated by the nucleus or the mitochondria through cell non-autonomous responses during cellular stress. In addition to promoting the communication between the mitochondria and the nucleus, mitokines also exert a systemic regulatory effect by circulating to distant tissues. It is noteworthy that increasing evidence has demonstrated that mitokines are capable of reducing the metabolic-related HF risk factors and are associated with HF severity. Consequently, mitokines might represent a potential therapy target for HF.

CXCL13 and Its Receptor CXCR5 in Cancer: Inflammation, Immune Response, and Beyond.

It is well-established that the chemokine C-X-C motif ligand 13 (CXCL13) and its receptor, the G-protein coupled receptor (GPCR) CXCR5, play fundamental roles in inflammatory, infectious and immune responses. Originally identified as a B-cell chemoattractant, CXCL13 exerts important functions in lymphoid neogenesis, and has been widely implicated in the pathogenesis of a number of autoimmune diseases and inflammatory conditions, as well as in lymphoproliferative disorders. Current evidence also indicates that the CXCL13:CXCR5 axis orchestrates cell-cell interactions that regulate lymphocyte infiltration within the tumor microenvironment, thereby determining responsiveness to cytotoxic and immune-targeted therapies. In this review, we provide a comprehensive perspective of the involvement of CXCL13 and its receptor in cancer progression. Studies in recent years postulated novel roles for this chemokine in controlling the cancer cell phenotype, and suggest important functions in the growth and metastatic dissemination of solid tumors. Carcinogens have been found to induce CXCL13 production, and production of this chemokine within the tumor milieu has been shown to impact the proliferation, migration, and invasive properties of cancer cells. Thus, the complex networks of cellular interactions involving tumoral CXCL13 and CXCR5 integrate to promote cancer cell autonomous and non-autonomous responses, highlighting the relevance of autocrine and paracrine interactions in dictating the cancer phenotype. Dissecting the molecular and signaling events regulated by CXCL13 and how this chemokine dynamically controls the interaction between the cancer cell and the tumor microenvironment is key to identify novel effectors and therapeutic targets for cancer treatment.

Inter-Organ Growth Coordination Is Mediated by the Xrp1-Dilp8 Axis in Drosophila

How organs scale with other body parts is not mechanistically understood. We have addressed this question using the Drosophila imaginal disc model. When the growth of one disc domain is perturbed, other parts of the disc and other discs slow down their growth, maintaining proper inter-disc and intra-disc proportions. We show here that the relaxin-like Dilp8 is required for this inter-organ coordination. Our work also reveals that the stress-response transcription factor Xrp1 plays a key role upstream of dilp8 in linking organ growth status with the systemic growth response. In addition, we show that the small ribosomal subunit protein RpS12 is required to trigger Xrp1-dependent non-autonomous response. Our work demonstrates that RpS12, Xrp1, and Dilp8 form an independent regulatory module that ensures intra- and inter-organ growth coordination during development.

Hypodermal responses to protein synthesis inhibition induce systemic developmental arrest and AMPK-dependent survival in Caenorhabditis elegans

Across organisms, manipulation of biosynthetic capacity arrests development early in life, but can increase health- and lifespan post-developmentally. Here we demonstrate that this developmental arrest is not sickness but rather a regulated survival program responding to reduced cellular performance. We inhibited protein synthesis by reducing ribosome biogenesis (rps-11/RPS11 RNAi), translation initiation (ifg-1/EIF3G mutation and egl-45/EIF3A RNAi), or ribosome progression (cycloheximide treatment), all of which result in a specific arrest at larval stage 2 of C. elegans development. This quiescent state can last for weeks—beyond the normal C. elegans adult lifespan—and is reversible, as animals can resume reproduction and live a normal lifespan once released from the source of protein synthesis inhibition. The arrest state affords resistance to thermal, oxidative, and heavy metal stress exposure. In addition to cell-autonomous responses, reducing biosynthetic capacity only in the hypodermis was sufficient to drive organism-level developmental arrest and stress resistance phenotypes. Among the cell non-autonomous responses to protein synthesis inhibition is reduced pharyngeal pumping that is dependent upon AMPK-mediated signaling. The reduced pharyngeal pumping in response to protein synthesis inhibition is recapitulated by exposure to microbes that generate protein synthesis-inhibiting xenobiotics, which may mechanistically reduce ingestion of pathogen and toxin. These data define the existence of a transient arrest-survival state in response to protein synthesis inhibition and provide an evolutionary foundation for the conserved enhancement of healthy aging observed in post-developmental animals with reduced biosynthetic capacity.

Stress signaling between organs in metazoa.

Many organisms have developed a robust ability to adapt and survive in the face of environmental perturbations that threaten the integrity of their genome, proteome, or metabolome. Studies in multiple model organisms have shown that, in general, when exposed to stress, cells activate a complex prosurvival signaling network that includes immune and DNA damage response genes, chaperones, antioxidant enzymes, structural proteins, metabolic enzymes, and noncoding RNAs. The manner of activation runs the gamut from transcriptional induction of genes to increased stability of transcripts to posttranslational modification of important biosynthetic proteins within the stressed tissue. Superimposed on these largely autonomous effects are nonautonomous responses in which the stressed tissue secretes peptides and other factors that stimulate tissues in different organs to embark on processes that ultimately help the organism as a whole cope with stress. This review focuses on the mechanisms by which tissues in one organ adapt to environmental challenges by regulating stress responses in tissues of different organs.

Dally Proteoglycan Mediates the Autonomous and Nonautonomous Effects on Tissue Growth Caused by Activation of the PI3K and TOR Pathways.

How cells acquiring mutations in tumor suppressor genes outcompete neighboring wild-type cells is poorly understood. The phosphatidylinositol 3-kinase (PI3K)–phosphatase with tensin homology (PTEN) and tuberous sclerosis complex (TSC)-target of rapamycin (TOR) pathways are frequently activated in human cancer, and this activation is often causative of tumorigenesis. We utilized the Gal4-UAS system in Drosophila imaginal primordia, highly proliferative and growing tissues, to analyze the impact of restricted activation of these pathways on neighboring wild-type cell populations. Activation of these pathways leads to an autonomous induction of tissue overgrowth and to a remarkable nonautonomous reduction in growth and proliferation rates of adjacent cell populations. This nonautonomous response occurs independently of where these pathways are activated, is functional all throughout development, takes place across compartments, and is distinct from cell competition. The observed autonomous and nonautonomous effects on tissue growth rely on the up-regulation of the proteoglycan Dally, a major element involved in modulating the spreading, stability, and activity of the growth promoting Decapentaplegic (Dpp)/transforming growth factor β(TGF-β) signaling molecule. Our findings indicate that a reduction in the amount of available growth factors contributes to the outcompetition of wild-type cells by overgrowing cell populations. During normal development, the PI3K/PTEN and TSC/TOR pathways play a major role in sensing nutrient availability and modulating the final size of any developing organ. We present evidence that Dally also contributes to integrating nutrient sensing and organ scaling, the fitting of pattern to size.

Multiple mechanisms generate Lorentzian and 1/fα power spectra in daily stream-flow time series

Power-law scaling is an ubiquitous feature of the power spectrum of streamflow on the daily to monthly timescales where the spectrum is most strongly affected by hydrologic catchment-scale processes. Numerous mechanistic explanations for the emergence of this power-law scaling have been proposed. This study employs empirical spectra obtained for eight river basins in the South Eastern US and synthetic spectra generated from a range of proposed mechanisms to explore these explanations. The empirical analysis suggested that streamflow spectra were characterized by multiple power-law scaling regimes with high-frequency exponents α in the range −1 to −5. In the studied basins, α tended to increase with drainage area. The power-law generating mechanisms analyzed included linear and nonlinear catchment water balance arguments, power-law recession behavior, autonomous and non-autonomous responses of channel hydraulics and the n-fold convolution of linear reservoirs underpinning Dooge or Nash hydrographs. Of these mechanisms, only n-fold convolutions with n=2 or 3 generated power spectra with features that were consistent with the empirical cases. If the effects of daily streamflow sampling on truncating power spectra were considered, then the trends in α with drainage area were also consistent with this mechanism. Generalizing the linear convolution approach to a network of reservoirs with randomly distributed parameters preserved the features of the power spectrum and maintained consistency with empirical spectra.

Revealing Nonlinear Dynamics Phenomena in Mooring Due to Slowly-Varying Drift

The effects of slowly-varying wave drift forces on the nonlinear dynamics of mooring systems have been studied extensively in the past 30 years. It has been concluded that slowly-varying wave drift may resonate with mooring system natural frequencies. In recent work, we have shown that this resonance phenomenon is only one of several possible nonlinear dynamic interactions between slowly-varying wave drifts and mooring systems. We were able to reveal new phenomena, based on the design methodology developed at the University of Michigan for autonomous mooring systems, and treating slowly-varying wave drift as an external time-varying force in systematic simulations. This methodology involves exhaustive search regarding the nonautonomous excitation, however, and approximations in defining response bifurcations. In this paper, a new approach is developed, based on the harmonic balance method, where the response to the slowly-varying wave drift spectrum is modeled by limit cycles of frequency, estimated from a limited number of simulations. Thus, it becomes possible to rewrite the nonautonomous system as autonomous and reveal stability properties of the nonautonomous response. Catastrophe sets of the symmetric principal equilibrium, serving as design charts, define regions in the design space where the trajectories of the mooring system are asymptotically stable, limit cycles, or nonperiodic. This methodology reveals and proves that mooring systems subjected to slowly-varying wave drift exhibit many nonlinear phenomena, which lead to motions with amplitudes two to three orders of magnitude larger than those resulting from linear resonance. A turret mooring system (TMS) is used to demonstrate the harmonic balance methodology developed. The produced catastrophe sets are then compared with numerical results obtained from systematic simulations of the TMS dynamics.

A dp53-Dependent Mechanism Involved in Coordinating Tissue Growth in Drosophila

Author SummaryThe coordination of growth within and between organs contributes to the generation of functionally integrated structures and well-proportioned animals and plants. Though these issues have fascinated biologists for centuries, the responsible molecular mechanisms remain largely uncharacterized. In this work, we have used the Drosophila wing primordium to show that adjacent cell populations grow and proliferate in a coordinated manner. By reducing growth rates in specific territories within the developing wing, we showed that the tissue responds as a whole and that in adjacent cell populations the growth and cell cycle rates are concomitantly reduced, thus maintaining tissue proportions and normal wing shape. Interestingly, we show that the Drosophila tumour suppressor protein dp53 and apoptotic machinery play a key role in coordinating this tissue-wide response. Both growth and proliferation rates are regulated in a coordinated and non-autonomous manner by the activity of dp53, whilst the apoptotic pathway has a specific and non-autonomous role in regulating cell proliferation rates. Our studies describe a novel mechanism for regulating tissue growth in developing organs that may ultimately be relevant for other processes involving coordination of growth, such as tissue renewal, regeneration, and cancer.

The biophysical stage of radiation carcinogenesis.

The dependence of the induction of cancer on the absorbed dose of ionizing radiations has been specified in terms of increasing complexity. The first notion of simple proportionality (the "linear hypothesis") is now frequently replaced with a dependence of both the first and second powers of the dose (the "linear-quadratic model"), which implies proportionality at low doses only. Microdosimetric considerations, in particular the theory of dual radiation action, would be in accord with this relation if tumors were to arise from single cells as the result of a transformation that is autonomous (i.e., depends only on the radiation received by the cell). In this case, it must be expected that the linear portion of the dose-effect curve is dose rate independent, but that the quadratic component may decrease with decreasing dose rate because of repair during the interval between two events (energy depositions by individual particles). Various data appeared to be in agreement with this picture. However, it was shown some time ago that the dose-incidence relation of some neoplasms indicates a non-autonomous response because of departure from a linear dependence when the mean number of events in cells is much less than one in neutron irradiations. Another discrepancy is the repeated observation that reduction of dose rate, while resulting in the expected lessening of the effectiveness of low-LET radiation, increases the effectiveness of neutrons (especially in the case of oncogenic cell transformation). As will be shown, it is possible to account for this phenomenon, although at this point the limitations of the available data make the explanation semi-quantitative and therefore still somewhat hypothetical. However, it should be noted that it does not even require a nonautonomous response and thus is at least an example of the complexities that can arise in the earliest (biophysical) stage of radiation carcinogenesis.