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1.
Nat Methods ; 13(4): 310-8, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26901648

RESUMO

It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense.


Assuntos
Causalidade , Redes Reguladoras de Genes , Neoplasias/genética , Mapeamento de Interação de Proteínas/métodos , Software , Biologia de Sistemas , Algoritmos , Biologia Computacional , Simulação por Computador , Perfilação da Expressão Gênica , Humanos , Modelos Biológicos , Transdução de Sinais , Células Tumorais Cultivadas
2.
J Immunol ; 192(1): 358-66, 2014 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-24319262

RESUMO

Neuroinflammation occurs in acute and chronic CNS injury, including stroke, traumatic brain injury, and neurodegenerative diseases. Microglia are specialized resident myeloid cells that mediate CNS innate immune responses. Disease-relevant stimuli, such as reactive oxygen species (ROS), can influence microglia activation. Previously, we observed that p53, a ROS-responsive transcription factor, modulates microglia behaviors in vitro and in vivo, promoting proinflammatory functions and suppressing downregulation of the inflammatory response and tissue repair. In this article we describe a novel mechanism by which p53 modulates the functional differentiation of microglia both in vitro and in vivo. Adult microglia from p53-deficient mice have increased expression of the anti-inflammatory transcription factor c-Maf. To determine how p53 negatively regulates c-Maf, we examined the impact of p53 on known c-Maf regulators. MiR-155 is a microRNA that targets c-Maf. We observed that cytokine-induced expression of miR-155 was suppressed in p53-deficient microglia. Furthermore, Twist2, a transcriptional activator of c-Maf, is increased in p53-deficient microglia. We identified recognition sites in the 3' untranslated region of Twist2 mRNA that are predicted to interact with two p53-dependent microRNAs: miR-34a and miR-145. In this article, we demonstrate that miR-34a and -145 are regulated by p53 and negatively regulate Twist2 and c-Maf expression in microglia and the RAW macrophage cell line. Taken together, these findings support the hypothesis that p53 activation induced by local ROS or accumulated DNA damage influences microglia functions and that one specific molecular target of p53 in microglia is c-Maf.


Assuntos
MicroRNAs/genética , Microglia/metabolismo , Proteínas Proto-Oncogênicas c-maf/genética , Proteína Supressora de Tumor p53/metabolismo , Animais , Isquemia Encefálica/genética , Isquemia Encefálica/metabolismo , Linhagem Celular , Modelos Animais de Doenças , Regulação da Expressão Gênica , Humanos , Masculino , Camundongos , Camundongos Knockout , MicroRNAs/metabolismo , Modelos Biológicos , Fenótipo , Proteínas Proto-Oncogênicas c-maf/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Proteína Supressora de Tumor p53/genética , Proteína 1 Relacionada a Twist/genética , Proteína 1 Relacionada a Twist/metabolismo
3.
Glia ; 59(10): 1402-13, 2011 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-21598312

RESUMO

Several neurodegenerative diseases are influenced by the innate immune response in the central nervous system (CNS). Microglia have proinflammatory and subsequently neurotoxic actions as well as anti-inflammatory functions that promote recovery and repair. Very little is known about the transcriptional control of these specific microglial behaviors. We have previously shown that in HIV-associated neurocognitive disorders (HAND), the transcription factor p53 accumulates in microglia and that microglial p53 expression is required for the in vitro neurotoxicity of the HIV coat glycoprotein gp120. These findings suggested a novel function for p53 in regulating microglial activation. Here, we report that in the absence of p53, microglia demonstrate a blunted response to interferon-γ, failing to increase expression of genes associated with classical macrophage activation or secrete proinflammatory cytokines. Microarray analysis of global gene expression profiles revealed increased expression of genes associated with anti-inflammatory functions, phagocytosis, and tissue repair in p53 knockout (p53(-/-)) microglia compared with those cultured from strain matched p53 expressing (p53(+/+)) mice. We further observed that p53(-/-) microglia demonstrate increased phagocytic activity in vitro and expression of markers for alternative macrophage activation both in vitro and in vivo. In HAND brain tissue, the alternative activation marker CD163 was expressed in a separate subset of microglia than those demonstrating p53 accumulation. These data suggest that p53 influences microglial behavior, supporting the adoption of a proinflammatory phenotype, while p53 deficiency promotes phagocytosis and gene expression associated with alternative activation and anti-inflammatory functions.


Assuntos
Córtex Cerebral/patologia , Regulação da Expressão Gênica/genética , Microglia/metabolismo , Fenótipo , Proteína Supressora de Tumor p53/metabolismo , Análise de Variância , Animais , Antígenos CD/metabolismo , Apoptose/efeitos dos fármacos , Apoptose/genética , Linhagem Celular Transformada , Córtex Cerebral/citologia , Transtornos Cognitivos/etiologia , Transtornos Cognitivos/metabolismo , Transtornos Cognitivos/virologia , Ensaio de Imunoadsorção Enzimática/métodos , Perfilação da Expressão Gênica , Regulação da Expressão Gênica/efeitos dos fármacos , Proteína gp120 do Envelope de HIV/farmacologia , Infecções por HIV/induzido quimicamente , Ataque Isquêmico Transitório/metabolismo , Ataque Isquêmico Transitório/patologia , Masculino , Camundongos , Camundongos Knockout , Microglia/efeitos dos fármacos , Análise de Sequência com Séries de Oligonucleotídeos , Fagocitose/efeitos dos fármacos , Fatores de Tempo , Proteína Supressora de Tumor p53/deficiência , Proteína Supressora de Tumor p53/genética
4.
Cancer Cell ; 38(6): 829-843.e4, 2020 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-33157050

RESUMO

Perturbation biology is a powerful approach to modeling quantitative cellular behaviors and understanding detailed disease mechanisms. However, large-scale protein response resources of cancer cell lines to perturbations are not available, resulting in a critical knowledge gap. Here we generated and compiled perturbed expression profiles of ∼210 clinically relevant proteins in >12,000 cancer cell line samples in response to ∼170 drug compounds using reverse-phase protein arrays. We show that integrating perturbed protein response signals provides mechanistic insights into drug resistance, increases the predictive power for drug sensitivity, and helps identify effective drug combinations. We build a systematic map of "protein-drug" connectivity and develop a user-friendly data portal for community use. Our study provides a rich resource to investigate the behaviors of cancer cells and the dependencies of treatment responses, thereby enabling a broad range of biomedical applications.


Assuntos
Antineoplásicos/farmacologia , Neoplasias/metabolismo , Mapas de Interação de Proteínas/efeitos dos fármacos , Proteômica/métodos , Antineoplásicos/uso terapêutico , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Biologia Computacional , Resistencia a Medicamentos Antineoplásicos , Humanos , Terapia de Alvo Molecular , Neoplasias/tratamento farmacológico , Análise Serial de Proteínas , Interface Usuário-Computador
5.
Cell Syst ; 4(1): 73-83.e10, 2017 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-28017544

RESUMO

Signaling networks downstream of receptor tyrosine kinases are among the most extensively studied biological networks, but new approaches are needed to elucidate causal relationships between network components and understand how such relationships are influenced by biological context and disease. Here, we investigate the context specificity of signaling networks within a causal conceptual framework using reverse-phase protein array time-course assays and network analysis approaches. We focus on a well-defined set of signaling proteins profiled under inhibition with five kinase inhibitors in 32 contexts: four breast cancer cell lines (MCF7, UACC812, BT20, and BT549) under eight stimulus conditions. The data, spanning multiple pathways and comprising ∼70,000 phosphoprotein and ∼260,000 protein measurements, provide a wealth of testable, context-specific hypotheses, several of which we experimentally validate. Furthermore, the data provide a unique resource for computational methods development, permitting empirical assessment of causal network learning in a complex, mammalian setting.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Fosfoproteínas/análise , Algoritmos , Neoplasias da Mama/metabolismo , Linhagem Celular Tumoral , Simulação por Computador , Feminino , Redes Reguladoras de Genes/genética , Redes Reguladoras de Genes/fisiologia , Humanos , Modelos Biológicos , Fosforilação , Sensibilidade e Especificidade , Transdução de Sinais/fisiologia
6.
Proc Natl Acad Sci U S A ; 103(9): 3268-73, 2006 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-16492753

RESUMO

The fidelity of yeast RNA polymerase II (Pol II) was assessed in vivo with an assay in which errors in transcription of can1-100, a nonsense allele of CAN1, result in enhanced sensitivity to the toxic arginine analog canavanine. The Pol II accessory factor TFIIS has been proposed to play a role in transcript editing by stimulating the intrinsic nuclease activity of the RNA polymerase. However, deletion of DST1, the gene encoding the yeast homolog of TFIIS, had only a small effect on transcriptional fidelity, as determined by this assay. In contrast, strains containing a deletion of RPB9, which encodes a small core subunit of Pol II, were found to engage in error-prone transcription. rpb9Delta strains also had increased steady-state levels of can1-100 mRNA, consistent with transcriptional errors that decrease the normal sensitivity of the can1-100 transcript to nonsense-mediated decay, a pathway that degrades mRNAs with premature stop codons. Sequences of cDNAs from rpb9Delta strains confirmed a significantly increased occurrence of transcriptional substitutions and insertions. These results suggest that Rpb9 plays an important role in maintaining transcriptional fidelity, whereas TFIIS may serve a different primary purpose.


Assuntos
RNA Polimerase II/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Transcrição Gênica/genética , Sistemas de Transporte de Aminoácidos Básicos/genética , DNA Complementar/genética , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , RNA Polimerase II/deficiência , RNA Polimerase II/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Fatores de Elongação da Transcrição/genética , Fatores de Elongação da Transcrição/metabolismo
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