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1.
Proc Natl Acad Sci U S A ; 116(1): 148-157, 2019 01 02.
Artículo en Inglés | MEDLINE | ID: mdl-30587589

RESUMEN

The epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC) formation are two paramount processes driving tumor progression, therapy resistance, and cancer metastasis. Recent experiments show that cells with varying EMT and CSC phenotypes are spatially segregated in the primary tumor. The underlying mechanisms generating such spatiotemporal dynamics in the tumor microenvironment, however, remain largely unexplored. Here, we show through a mechanism-based dynamical model that the diffusion of EMT-inducing signals such as TGF-ß, together with noncell autonomous control of EMT and CSC decision making via the Notch signaling pathway, can explain experimentally observed disparate localization of subsets of CSCs with varying EMT phenotypes in the tumor. Our simulations show that the more mesenchymal CSCs lie at the invasive edge, while the hybrid epithelial/mesenchymal (E/M) CSCs reside in the tumor interior. Further, motivated by the role of Notch-Jagged signaling in mediating EMT and stemness, we investigated the microenvironmental factors that promote Notch-Jagged signaling. We show that many inflammatory cytokines such as IL-6 that can promote Notch-Jagged signaling can (i) stabilize a hybrid E/M phenotype, (ii) increase the likelihood of spatial proximity of hybrid E/M cells, and (iii) expand the fraction of CSCs. To validate the predicted connection between Notch-Jagged signaling and stemness, we knocked down JAG1 in hybrid E/M SUM149 human breast cancer cells in vitro. JAG1 knockdown significantly restricted tumor organoid formation, confirming the key role that Notch-Jagged signaling can play in tumor progression. Together, our integrated computational-experimental framework reveals the underlying principles of spatiotemporal dynamics of EMT and CSCs.


Asunto(s)
Células Madre Neoplásicas/fisiología , Microambiente Tumoral/fisiología , Neoplasias de la Mama/patología , Citocinas/metabolismo , Transición Epitelial-Mesenquimal/fisiología , Femenino , Técnicas de Silenciamiento del Gen , Humanos , Células Neoplásicas Circulantes/patología , Células Madre Neoplásicas/citología , Fenotipo , Receptores Notch/metabolismo , Transducción de Señal , Factor de Crecimiento Transformador beta/metabolismo
2.
Proc Natl Acad Sci U S A ; 115(31): 8025-8030, 2018 07 31.
Artículo en Inglés | MEDLINE | ID: mdl-30012604

RESUMEN

Evidence suggests that astrocytes play key roles in structural and functional organization of neuronal circuits. To understand how astrocytes influence the physiopathology of cerebellar circuits, we cultured cells from cerebella of mice that lack the ATM gene. Mutations in ATM are causative of the human cerebellar degenerative disease ataxia-telangiectasia. Cerebellar cultures grown from Atm-/- mice had disrupted network synchronization, atrophied astrocytic arborizations, reduced autophagy levels, and higher numbers of synapses per neuron than wild-type cultures. Chimeric circuitries composed of wild-type astrocytes and Atm-/- neurons were indistinguishable from wild-type cultures. Adult cerebellar characterizations confirmed disrupted astrocyte morphology, increased GABAergic synaptic markers, and reduced autophagy in Atm-/- compared with wild-type mice. These results indicate that astrocytes can impact neuronal circuits at levels ranging from synaptic expression to global dynamics.


Asunto(s)
Astrocitos/fisiología , Enfermedades Cerebelosas/fisiopatología , Red Nerviosa/fisiopatología , Animales , Proteínas de la Ataxia Telangiectasia Mutada/genética , Proteínas de la Ataxia Telangiectasia Mutada/fisiología , Autofagia , Células Cultivadas , Ratones , Sinapsis/fisiología
3.
Phys Biol ; 14(3): 035007, 2017 05 23.
Artículo en Inglés | MEDLINE | ID: mdl-28443829

RESUMEN

Many cell-fate decisions during embryonic development are governed by a motif comprised of two transcription factors (TFs) A and B that mutually inhibit each other and may self-activate. This motif, called as a self-activating toggle switch (SATS), can typically have three stable states (phenotypes)-two corresponding to differentiated cell fates, each of which has a much higher level of one TF than the other-[Formula: see text] or [Formula: see text]-and the third state corresponding to an 'undecided' stem-like state with similar levels of both A and B-[Formula: see text]. Furthermore, two or more SATSes can be coupled together in various topologies in different contexts, thereby affecting the coordination between multiple cellular decisions. However, two questions remain largely unanswered: (a) what governs the co-existence and relative stability of these three stable states? (b) What orchestrates the decision-making of coupled SATSes? Here, we first demonstrate that the co-existence and relative stability of the three stable states in an individual SATS can be governed by the relative strength of self-activation, external signals activating and/or inhibiting A and B, and mutual degradation between A and B. Simultaneously, we investigate the effects of these factors on the decision-making of two coupled SATSes. Our results offer novel understanding into the operating principles of individual and coupled tristable self-activating toggle switches (SATSes) regulating cellular differentiation and can yield insights into synthesizing three-way genetic circuits and understanding of cellular reprogramming.


Asunto(s)
Diferenciación Celular , Reprogramación Celular , Desarrollo Embrionario/fisiología , Redes Reguladoras de Genes , Factores de Transcripción/metabolismo , Modelos Biológicos
4.
PLoS Comput Biol ; 13(3): e1005456, 2017 03.
Artículo en Inglés | MEDLINE | ID: mdl-28362798

RESUMEN

One of the most important roles of cells is performing their cellular tasks properly for survival. Cells usually achieve robust functionality, for example, cell-fate decision-making and signal transduction, through multiple layers of regulation involving many genes. Despite the combinatorial complexity of gene regulation, its quantitative behavior has been typically studied on the basis of experimentally verified core gene regulatory circuitry, composed of a small set of important elements. It is still unclear how such a core circuit operates in the presence of many other regulatory molecules and in a crowded and noisy cellular environment. Here we report a new computational method, named random circuit perturbation (RACIPE), for interrogating the robust dynamical behavior of a gene regulatory circuit even without accurate measurements of circuit kinetic parameters. RACIPE generates an ensemble of random kinetic models corresponding to a fixed circuit topology, and utilizes statistical tools to identify generic properties of the circuit. By applying RACIPE to simple toggle-switch-like motifs, we observed that the stable states of all models converge to experimentally observed gene state clusters even when the parameters are strongly perturbed. RACIPE was further applied to a proposed 22-gene network of the Epithelial-to-Mesenchymal Transition (EMT), from which we identified four experimentally observed gene states, including the states that are associated with two different types of hybrid Epithelial/Mesenchymal phenotypes. Our results suggest that dynamics of a gene circuit is mainly determined by its topology, not by detailed circuit parameters. Our work provides a theoretical foundation for circuit-based systems biology modeling. We anticipate RACIPE to be a powerful tool to predict and decode circuit design principles in an unbiased manner, and to quantitatively evaluate the robustness and heterogeneity of gene expression.


Asunto(s)
Biología Computacional/métodos , Redes Reguladoras de Genes , Modelos Genéticos , Transición Epitelial-Mesenquimal/genética , Regulación de la Expresión Génica , Humanos , Cinética , Modelos Estadísticos , Distribución Aleatoria
5.
Cancer Res ; 77(7): 1564-1574, 2017 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-28202516

RESUMEN

Abnormal metabolism is a hallmark of cancer, yet its regulation remains poorly understood. Cancer cells were considered to utilize primarily glycolysis for ATP production, referred to as the Warburg effect. However, recent evidence suggests that oxidative phosphorylation (OXPHOS) plays a crucial role during cancer progression. Here we utilized a systems biology approach to decipher the regulatory principle of glycolysis and OXPHOS. Integrating information from literature, we constructed a regulatory network of genes and metabolites, from which we extracted a core circuit containing HIF-1, AMPK, and ROS. Our circuit analysis showed that while normal cells have an oxidative state and a glycolytic state, cancer cells can access a hybrid state with both metabolic modes coexisting. This was due to higher ROS production and/or oncogene activation, such as RAS, MYC, and c-SRC. Guided by the model, we developed two signatures consisting of AMPK and HIF-1 downstream genes, respectively, to quantify the activity of glycolysis and OXPHOS. By applying the AMPK and HIF-1 signatures to The Cancer Genome Atlas patient transcriptomics data of multiple cancer types and single-cell RNA-seq data of lung adenocarcinoma, we confirmed an anticorrelation between AMPK and HIF-1 activities and the association of metabolic states with oncogenes. We propose that the hybrid phenotype contributes to metabolic plasticity, allowing cancer cells to adapt to various microenvironments. Using model simulations, our theoretical framework of metabolism can serve as a platform to decode cancer metabolic plasticity and design cancer therapies targeting metabolism. Cancer Res; 77(7); 1564-74. ©2017 AACR.


Asunto(s)
Glucólisis , Neoplasias/metabolismo , Fosforilación Oxidativa , Proteínas Quinasas Activadas por AMP/fisiología , Humanos , Factor 1 Inducible por Hipoxia/fisiología , Modelos Biológicos , Neoplasias/genética , Neoplasias/terapia , Proteínas Proto-Oncogénicas c-myc/fisiología , Especies Reactivas de Oxígeno/metabolismo , Microambiente Tumoral
6.
Cancer Converg ; 1(1): 2, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-29623961

RESUMEN

BACKGROUND: The Epithelial-Mesenchymal Transition (EMT) endows epithelial-looking cells with enhanced migratory ability during embryonic development and tissue repair. EMT can also be co-opted by cancer cells to acquire metastatic potential and drug-resistance. Recent research has argued that epithelial (E) cells can undergo either a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype that typically displays collective migration, or a complete EMT to adopt a mesenchymal (M) phenotype that shows individual migration. The core EMT regulatory network - miR-34/SNAIL/miR-200/ZEB1 - has been identified by various studies, but how this network regulates the transitions among the E, E/M, and M phenotypes remains controversial. Two major mathematical models - ternary chimera switch (TCS) and cascading bistable switches (CBS) - that both focus on the miR-34/SNAIL/miR-200/ZEB1 network, have been proposed to elucidate the EMT dynamics, but a detailed analysis of how well either or both of these two models can capture recent experimental observations about EMT dynamics remains to be done. RESULTS: Here, via an integrated experimental and theoretical approach, we first show that both these two models can be used to understand the two-step transition of EMT - E→E/M→M, the different responses of SNAIL and ZEB1 to exogenous TGF-ß and the irreversibility of complete EMT. Next, we present new experimental results that tend to discriminate between these two models. We show that ZEB1 is present at intermediate levels in the hybrid E/M H1975 cells, and that in HMLE cells, overexpression of SNAIL is not sufficient to initiate EMT in the absence of ZEB1 and FOXC2. CONCLUSIONS: These experimental results argue in favor of the TCS model proposing that miR-200/ZEB1 behaves as a three-way decision-making switch enabling transitions among the E, hybrid E/M and M phenotypes.

7.
PLoS One ; 11(12): e0168805, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27997608

RESUMEN

BACKGROUND: Regulation of hepatic glucose production has been a target for antidiabetic drug development, due to its major contribution to glucose homeostasis. Previous pre-clinical study demonstrated that peripheral electrical stimulation (PES) may stimulate glucose utilization and improve hepatic insulin sensitivity. The aim of the present study was to evaluate safety, tolerability, and the glucose-lowering effect of this approach in patients with type 2 diabetes (T2DM). METHODS: Twelve patients with T2DM were recruited for an open label, interventional, randomized trial. Eleven patients underwent, in a crossover design, an active, and a no-intervention control periods, separated with a two-week washout phase. During the active period, the patients received a daily lower extremity PES treatment (1.33Hz/16Hz burst mode), for 14 days. Study endpoints included changes in glucose levels, number of hypoglycemic episodes, and other potential side effects. Endpoints were analyzed based on continuous glucose meter readings, and laboratory evaluation. RESULTS: We found that during the active period, the most significant effect was on nocturnal glucose control (P < 0.0004), as well as on pre-meal mean glucose levels (P < 0.02). The mean daily glucose levels were also decreased although it did not reach clinical significance (P = 0.07). A reduction in serum cortisol (P < 0.01) but not in insulin was also detected after 2 weeks of treatment. No adverse events were recorded. CONCLUSIONS: These results indicate that repeated PES treatment, even for a very short duration, can improve blood glucose control, possibly by suppressing hepatic glucose production. This effect may be mediated via hypothalamic-pituitary-adrenal axis modulation. TRIAL REGISTRATION: ClinicalTrials.gov NCT02727790.


Asunto(s)
Glucemia/metabolismo , Diabetes Mellitus Tipo 2/sangre , Diabetes Mellitus Tipo 2/terapia , Terapia por Estimulación Eléctrica/métodos , Anciano , Estudios Cruzados , Femenino , Humanos , Hidrocortisona/sangre , Insulina/sangre , Masculino , Persona de Mediana Edad
8.
Sci Rep ; 6: 27444, 2016 06 07.
Artículo en Inglés | MEDLINE | ID: mdl-27271458

RESUMEN

Communication between and within brain regions is essential for information processing within functional networks. The current methods to determine the influence of one region on another are either based on temporal resolution, or require a predefined model for the connectivity direction. However these requirements are not always achieved, especially in fMRI studies, which have poor temporal resolution. We thus propose a new graph theory approach that focuses on the correlation influence between selected brain regions, entitled Dependency Network Analysis (DEPNA). Partial correlations are used to quantify the level of influence of each node during task performance. As a proof of concept, we conducted the DEPNA on simulated datasets and on two empirical motor and working memory fMRI tasks. The simulations revealed that the DEPNA correctly captures the network's hierarchy of influence. Applying DEPNA to the functional tasks reveals the dynamics between specific nodes as would be expected from prior knowledge. To conclude, we demonstrate that DEPNA can capture the most influencing nodes in the network, as they emerge during specific cognitive processes. This ability opens a new horizon for example in delineating critical nodes for specific clinical interventions.


Asunto(s)
Encéfalo/fisiología , Mapeo Encefálico , Humanos , Imagen por Resonancia Magnética , Memoria a Corto Plazo
9.
J R Soc Interface ; 13(118)2016 05.
Artículo en Inglés | MEDLINE | ID: mdl-27170649

RESUMEN

Metastasis can involve repeated cycles of epithelial-to-mesenchymal transition (EMT) and its reverse mesenchymal-to-epithelial transition. Cells can also undergo partial transitions to attain a hybrid epithelial/mesenchymal (E/M) phenotype that allows the migration of adhering cells to form a cluster of circulating tumour cells. These clusters can be apoptosis-resistant and possess an increased metastatic propensity as compared to the cells that undergo a complete EMT (mesenchymal cells). Hence, identifying the key players that can regulate the formation and maintenance of such clusters may inform anti-metastasis strategies. Here, we devise a mechanism-based theoretical model that links cell-cell communication via Notch-Delta-Jagged signalling with the regulation of EMT. We demonstrate that while both Notch-Delta and Notch-Jagged signalling can induce EMT in a population of cells, only Jagged-dominated Notch signalling, but not Delta-dominated signalling, can lead to the formation of clusters containing hybrid E/M cells. Our results offer possible mechanistic insights into the role of Jagged in tumour progression, and offer a framework to investigate the effects of other microenvironmental signals during metastasis.


Asunto(s)
Transición Epitelial-Mesenquimal , Proteína Jagged-1/metabolismo , Modelos Biológicos , Proteínas de Neoplasias/metabolismo , Neoplasias/metabolismo , Receptores Notch/metabolismo , Transducción de Señal , Línea Celular Tumoral , Humanos , Metástasis de la Neoplasia , Neoplasias/patología
10.
Metabolism ; 65(6): 863-73, 2016 06.
Artículo en Inglés | MEDLINE | ID: mdl-27173465

RESUMEN

BACKGROUND: The epidemic nature of type 2 diabetes mellitus (T2DM), along with the downsides of current treatments, has raised the need for therapeutic alternatives. METHODS: We studied normo-glycemic and high-fat diet (HFD), induced insulin-resistant Wistar Han rats for 2 to 3weeks. Rats received peripheral electrical stimulation (PES) treatment (2Hz/16Hz bursts, 10mA) in their hind limbs for 3min, 3 times per week. Glucose tolerance was evaluated by using a glucose tolerance test at the beginning and again at the end of the study. The effect of an acute PES treatment on metabolic rates of glucose appearance and turnover was measured by using the hyperinsulinemic-euglycemic clamp (HEGC) test. RESULTS: Repeated PES treatment significantly inhibited the progression of glucose intolerance in normal and insulin-resistant rats and prevented HFD-induced gains in body weight and fat mass. Acute treatment induced a prolonged effect on glucose turnover, as evaluated by the HEGC test. Increased hepatic glucose output was observed during the basal state (P<0.005). Under hyperinsulinemic conditions, PES improved tissue sensitivity to insulin (41.1%, P<0.01), improved suppression of hepatic glucose production (58.9±4.4% vs. 87.1±4.4%, P<0.02) and significantly elevated the rate of glycogenesis (P<0.01), compared with controls. CONCLUSIONS: The present study indicates that a noninvasive PES treatment of very short duration is sufficiently potent to stimulate glucose utilization and improve hepatic insulin sensitivity in rats. Repeated PES treatment may have a beneficial effect on HFD-induced adiposity and control of body weight.


Asunto(s)
Estimulación Eléctrica , Intolerancia a la Glucosa/metabolismo , Glucosa/metabolismo , Resistencia a la Insulina/fisiología , Insulina/metabolismo , Animales , Técnica de Clampeo de la Glucosa , Hígado/metabolismo , Masculino , Ratas , Ratas Wistar
11.
PLoS One ; 11(3): e0152487, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27031230

RESUMEN

Financial markets are partially composed of sectors dominated by external driving forces, such as commodity prices, infrastructure and other indices. We characterize the statistical properties of such sectors and present a novel model for the coupling of the stock prices and their dominating driving forces, inspired by mean reverting stochastic processes. Using the model we were able to explain the market sectors' long term behavior and estimate the coupling strength between stocks in financial markets and the sector specific driving forces. Notably, the analysis was successfully applied to the shipping market, in which the Baltic dry index (BDI), an assessment of the price of transporting the major raw materials by sea, influences the shipping financial market. We also present the analysis of other sectors-the gold mining market and the food production market, for which the model was also successfully applied. The model can serve as a general tool for characterizing the coupling between external forces and affected financial variables and therefore for estimating the risk in sectors and their vulnerability to external stress.


Asunto(s)
Mercadotecnía , Modelos Económicos
12.
PLoS Comput Biol ; 12(4): e1004883, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-27104350

RESUMEN

Neural networks, despite their highly interconnected nature, exhibit distinctly localized and gated activation. Modularity, a distinctive feature of neural networks, has been recently proposed as an important parameter determining the manner by which networks support activity propagation. Here we use an engineered biological model, consisting of engineered rat cortical neurons, to study the role of modular topology in gating the activity between cell populations. We show that pairs of connected modules support conditional propagation (transmitting stronger bursts with higher probability), long delays and propagation asymmetry. Moreover, large modular networks manifest diverse patterns of both local and global activation. Blocking inhibition decreased activity diversity and replaced it with highly consistent transmission patterns. By independently controlling modularity and disinhibition, experimentally and in a model, we pose that modular topology is an important parameter affecting activation localization and is instrumental for population-level gating by disinhibition.


Asunto(s)
Modelos Neurológicos , Red Nerviosa/fisiología , Animales , Bioingeniería , Comunicación Celular/fisiología , Células Cultivadas , Biología Computacional , Simulación por Computador , Fenómenos Electrofisiológicos , Técnicas In Vitro , Neuronas/fisiología , Ratas , Transmisión Sináptica/fisiología
13.
PLoS One ; 11(4): e0154196, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27105224

RESUMEN

The rapid increase of wealth inequality in the past few decades is one of the most disturbing social and economic issues of our time. Studying its origin and underlying mechanisms is essential for policy aiming to control and even reverse this trend. In that context, controlling the distribution of income, using income tax or other macroeconomic policy instruments, is generally perceived as effective for regulating the wealth distribution. We provide a theoretical tool, based on the realistic modeling of wealth inequality dynamics, to describe the effects of personal savings and income distribution on wealth inequality. Our theoretical approach incorporates coupled equations, solved using iterated maps to model the dynamics of wealth and income inequality. Notably, using the appropriate historical parameter values we were able to capture the historical dynamics of wealth inequality in the United States during the course of the 20th century. It is found that the effect of personal savings on wealth inequality is substantial, and its major decrease in the past 30 years can be associated with the current wealth inequality surge. In addition, the effect of increasing income tax, though naturally contributing to lowering income inequality, might contribute to a mild increase in wealth inequality and vice versa. Plausible changes in income tax are found to have an insignificant effect on wealth inequality, in practice. In addition, controlling the income inequality, by progressive taxation, for example, is found to have a very small effect on wealth inequality in the short run. The results imply, therefore, that controlling income inequality is an impractical tool for regulating wealth inequality.


Asunto(s)
Algoritmos , Impuesto a la Renta/estadística & datos numéricos , Renta/estadística & datos numéricos , Modelos Económicos , Factores Socioeconómicos , Cuenta Bancaria/estadística & datos numéricos , Cuenta Bancaria/tendencias , Humanos , Renta/tendencias , Impuesto a la Renta/tendencias , Estados Unidos
14.
Proc Natl Acad Sci U S A ; 113(11): E1555-64, 2016 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-26929325

RESUMEN

The immunoproteasome plays a key role in generation of HLA peptides for T cell-mediated immunity. Integrative genomic and proteomic analysis of non-small cell lung carcinoma (NSCLC) cell lines revealed significantly reduced expression of immunoproteasome components and their regulators associated with epithelial to mesenchymal transition. Low expression of immunoproteasome subunits in early stage NSCLC patients was associated with recurrence and metastasis. Depleted repertoire of HLA class I-bound peptides in mesenchymal cells deficient in immunoproteasome components was restored with either IFNγ or 5-aza-2'-deoxycytidine (5-aza-dC) treatment. Our findings point to a mechanism of immune evasion of cells with a mesenchymal phenotype and suggest a strategy to overcome immune evasion through induction of the immunoproteasome to increase the cellular repertoire of HLA class I-bound peptides.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/inmunología , Carcinoma de Pulmón de Células no Pequeñas/mortalidad , Neoplasias Pulmonares/inmunología , Neoplasias Pulmonares/mortalidad , Complejo de la Endopetidasa Proteasomal/genética , Adulto , Anciano , Anciano de 80 o más Años , Antígenos CD/inmunología , Antígenos CD/metabolismo , Cadherinas/inmunología , Cadherinas/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/patología , Línea Celular Tumoral , Supervivencia sin Enfermedad , Transición Epitelial-Mesenquimal/genética , Femenino , Regulación Neoplásica de la Expresión Génica , Antígenos HLA/metabolismo , Humanos , Neoplasias Pulmonares/patología , Masculino , Persona de Mediana Edad , Complejo de la Endopetidasa Proteasomal/inmunología , Factor de Transcripción STAT3/genética , Factor de Transcripción STAT3/inmunología , Serina-Treonina Quinasas TOR/genética , Serina-Treonina Quinasas TOR/inmunología
15.
Oncotarget ; 7(19): 27067-84, 2016 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-27008704

RESUMEN

Epithelial-to-Mesenchymal Transition (EMT) and its reverse - Mesenchymal to Epithelial Transition (MET) - are hallmarks of cellular plasticity during embryonic development and cancer metastasis. During EMT, epithelial cells lose cell-cell adhesion and gain migratory and invasive traits either partially or completely, leading to a hybrid epithelial/mesenchymal (hybrid E/M) or a mesenchymal phenotype respectively. Mesenchymal cells move individually, but hybrid E/M cells migrate collectively as observed during gastrulation, wound healing, and the formation of tumor clusters detected as Circulating Tumor Cells (CTCs). Typically, the hybrid E/M phenotype has largely been tacitly assumed to be transient and 'metastable'. Here, we identify certain 'phenotypic stability factors' (PSFs) such as GRHL2 that couple to the core EMT decision-making circuit (miR-200/ZEB) and stabilize hybrid E/M phenotype. Further, we show that H1975 lung cancer cells can display a stable hybrid E/M phenotype and migrate collectively, a behavior that is impaired by knockdown of GRHL2 and another previously identified PSF - OVOL. In addition, our computational model predicts that GRHL2 can also associate hybrid E/M phenotype with high tumor-initiating potential, a prediction strengthened by the observation that the higher levels of these PSFs may be predictive of poor patient outcome. Finally, based on these specific examples, we deduce certain network motifs that can stabilize the hybrid E/M phenotype. Our results suggest that partial EMT, i.e. a hybrid E/M phenotype, need not be 'metastable', and strengthen the emerging notion that partial EMT, but not necessarily a complete EMT, is associated with aggressive tumor progression.


Asunto(s)
Células Epiteliales/metabolismo , Transición Epitelial-Mesenquimal/genética , Regulación Neoplásica de la Expresión Génica , Células Madre Mesenquimatosas/metabolismo , Línea Celular Tumoral , Movimiento Celular/genética , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Humanos , MicroARNs/genética , MicroARNs/metabolismo , Fenotipo , Interferencia de ARN , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Homeobox 1 de Unión a la E-Box con Dedos de Zinc/genética , Homeobox 1 de Unión a la E-Box con Dedos de Zinc/metabolismo
16.
Sci Rep ; 6: 21037, 2016 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-26876008

RESUMEN

Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations, and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer.


Asunto(s)
Redes Reguladoras de Genes , Modelos Teóricos , Secuencias Reguladoras de Ácidos Nucleicos/genética , Simulación por Computador , Dinámicas no Lineales
17.
Trends Microbiol ; 24(4): 257-269, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26822253

RESUMEN

Microorganisms use collective migration to cross barriers and reach new habitats, and the ability to form motile swarms offers a competitive advantage. Traditionally, dispersal by microbial swarm propagation has been studied in monoculture. Microorganisms can facilitate other species' dispersal by forming multispecies swarms, with mutual benefits. One party (the transporter) moves a sessile partner (the cargo). This results in asymmetric associations ranging from temporary marriages of convenience to long-term fellow travellers. In the context of the 'microbial market', the parties offer very different services in exchange. We discuss bacteria transporting bacteria, eukaryotic microorganisms moving bacteria, and bacteria facilitating the spread of eukaryotes - and ask what the benefits are, the methods of study, and the consequences of multispecies, swarming logistics networks.


Asunto(s)
Fenómenos Fisiológicos Bacterianos , Ecosistema , Bacterias , Microbiología Ambiental , Flagelos/fisiología , Consorcios Microbianos , Interacciones Microbianas , Modelos Biológicos
18.
Sci Rep ; 5: 17379, 2015 Dec 02.
Artículo en Inglés | MEDLINE | ID: mdl-26627083

RESUMEN

Cellular plasticity during cancer metastasis is a major clinical challenge. Two key cellular plasticity mechanisms -Epithelial-to-Mesenchymal Transition (EMT) and Mesenchymal-to-Amoeboid Transition (MAT) - have been carefully investigated individually, yet a comprehensive understanding of their interconnections remains elusive. Previously, we have modeled the dynamics of the core regulatory circuits for both EMT (miR-200/ZEB/miR-34/SNAIL) and MAT (Rac1/RhoA). We now extend our previous work to study the coupling between these two core circuits by considering the two microRNAs (miR-200 and miR-34) as external signals to the core MAT circuit. We show that this coupled circuit enables four different stable steady states (phenotypes) that correspond to hybrid epithelial/mesenchymal (E/M), mesenchymal (M), amoeboid (A) and hybrid amoeboid/mesenchymal (A/M) phenotypes. Our model recapitulates the metastasis-suppressing role of the microRNAs even in the presence of EMT-inducing signals like Hepatocyte Growth Factor (HGF). It also enables mapping the microRNA levels to the transitions among various cell migration phenotypes. Finally, it offers a mechanistic understanding for the observed phenotypic transitions among different cell migration phenotypes, specifically the Collective-to-Amoeboid Transition (CAT).


Asunto(s)
Movimiento Celular , Transición Epitelial-Mesenquimal , Modelos Biológicos , Neoplasias/metabolismo , Animales , Humanos , MicroARNs/genética , MicroARNs/metabolismo , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neoplasias/genética , Neoplasias/patología , ARN Neoplásico/genética , ARN Neoplásico/metabolismo
19.
Restor Neurol Neurosci ; 33(6): 943-51, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26484702

RESUMEN

PURPOSE: Recent clinical studies present convincing evidence that hyperbaric oxygen therapy (HBOT) may be the coveted neurotherapeutic method for brain repair. One of the most interesting ways in which HBOT can induce neuroplasticity is angiogenesis. The objective in this study was to assess the neurotherapeutic effect of HBOT in post TBI patients using brain perfusion imaging and clinical cognitive functions. METHODS: Retrospective analysis of patients suffering from chronic neuro-cognitive impairment from TBI treated with HBOT. The HBOT protocol included 60 daily HBOT sessions, 5 days per week. All patients had pre and post HBOT objective computerized cognitive tests (NeuroTrax) and brain perfusion MRI. RESULTS: Ten post-TBI patients were treated with HBOT with mean of 10.3±3.2 years after their injury. After HBOT, whole-brain perfusion analysis showed significantly increased cerebral blood flow and cerebral blood volume. Clinically, HBOT induced significant improvement in the global cognitive scores (p = 0.007). The most prominent improvements were seen in information processing speed, visual spatial processing and motor skills indices. CONCLUSION: HBOT may induce cerebral angiogenesis, which improves perfusion to the chronic damage brain tissue even months to years after the injury.


Asunto(s)
Encéfalo/fisiopatología , Oxigenoterapia Hiperbárica/métodos , Neovascularización Fisiológica/fisiología , Síndrome Posconmocional/fisiopatología , Síndrome Posconmocional/terapia , Adulto , Volumen Sanguíneo/fisiología , Circulación Cerebrovascular/fisiología , Enfermedad Crónica , Trastornos del Conocimiento/etiología , Trastornos del Conocimiento/fisiopatología , Trastornos del Conocimiento/terapia , Femenino , Humanos , Angiografía por Resonancia Magnética , Masculino , Pruebas Neuropsicológicas , Síndrome Posconmocional/psicología , Flujo Sanguíneo Regional/fisiología , Estudios Retrospectivos , Resultado del Tratamiento
20.
Sci Rep ; 5: 13538, 2015 Sep 04.
Artículo en Inglés | MEDLINE | ID: mdl-26337223

RESUMEN

Metastasis is the major cause for cancer patients' death, and despite all the recent advances in cancer research it is still mostly incurable. Understanding the mechanisms that are involved in the migration of the cells in a complex environment is a key step towards successful anti-metastatic treatment. Using experimental data-based modeling, we focus on the fundamentals of metastatic invasion: motility, invasion, proliferation and metabolism, and study how they may be combined to maximize the cancer's ability to metastasize. The modeled cells' performance is measured by the number of cells that succeed in migration in a maze, which mimics the extracellular environment. We show that co-existence of different cell clones in the tumor, as often found in experiments, optimizes the invasive ability in a frequently-changing environment. We study the role of metabolism and stimulation by growth factors, and show that metabolism plays a crucial role in the metastatic process and should therefore be targeted for successful treatment.


Asunto(s)
Matriz Extracelular/metabolismo , Modelos Biológicos , Invasividad Neoplásica , Neoplasias Experimentales/fisiopatología , Neoplasias Experimentales/secundario , Microambiente Tumoral , Animales , Movimiento Celular , Proliferación Celular , Simulación por Computador , Metabolismo Energético , Humanos , Proteínas de Neoplasias/metabolismo , Neoplasias Experimentales/patología
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