RESUMEN

Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enhanced yeast one-hybrid (eY1H) assays to derive a comprehensive network comprising 1380 interactions between 265 TFs and 108 cytokine gene promoters. Our eY1H-derived network greatly expands the known repertoire of TF-cytokine gene interactions and the set of TFs known to regulate cytokine genes. We found an enrichment of nuclear receptors and confirmed their role in cytokine regulation in primary macrophages. Additionally, we used the eY1H-derived network as a framework to identify pairs of TFs that can be targeted with commercially-available drugs to synergistically modulate cytokine production. Finally, we integrated the eY1H data with single cell RNA-seq and phenotypic datasets to identify novel TF-cytokine regulatory axes in immune diseases and immune cell lineage development. Overall, the eY1H data provides a rich resource to study cytokine regulation in a variety of physiological and disease contexts.

Asunto(s)

Linaje de la Célula/inmunología , Citocinas/genética , Redes Reguladoras de Genes/inmunología , Linfocitos/inmunología , Regiones Promotoras Genéticas , Factores de Transcripción/genética , Linaje de la Célula/genética , Citocinas/clasificación , Citocinas/inmunología , Conjuntos de Datos como Asunto , Células Dendríticas/citología , Células Dendríticas/inmunología , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Ontología de Genes , Células HEK293 , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Linfocitos/clasificación , Linfocitos/citología , Macrófagos/citología , Macrófagos/inmunología , Anotación de Secuencia Molecular , Monocitos/citología , Monocitos/inmunología , Cultivo Primario de Células , Unión Proteica , Receptores Citoplasmáticos y Nucleares/genética , Receptores Citoplasmáticos y Nucleares/inmunología , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Análisis de la Célula Individual , Células THP-1 , Factores de Transcripción/clasificación , Factores de Transcripción/inmunología , Transcripción Genética , Técnicas del Sistema de Dos Híbridos

RESUMEN

In this Correction, the authors would like to acknowledge that the original publication of the article "A holistic view of cancer bioenergetics: mitochondrial function and respiration play fundamental roles in the development and progression of diverse tumors" [1] was supported by CPRIT (Cancer Prevention & Research Institute of Texas) Grant RP160617.

RESUMEN

Efficient delivery to the cell nucleus remains a significant challenge for many biomolecules, including anticancer drugs, proteins and DNAs. Despite numerous attempts to improve nuclear import including the use of nuclear localization signal (NLS) peptides and nanoparticle carriers, they are limited by the nanoparticle size, conjugation method, dependence on the functional nuclear import and intracellular trafficking mechanisms. To overcome these limitations, here we report that the nanomechanical force from plasmonic nanobubbles increases nuclear membrane permeability and promotes universal uptake of macromolecules into the nucleus, including macromolecules that are larger than the nuclear pore complex and would otherwise not enter the nucleus. Importantly, we show that plasmonic nanobubble-induced nanomechanical transduction significantly improves gene transfection and protein expression, compared to standard electroporation treatment alone. This novel nanomechanical transduction increases the size range and is broadly applicable for macromolecule delivery to the cell nucleus, leading to new opportunities and applications including for gene therapy and anticancer drug delivery.

Asunto(s)

Núcleo Celular/química , Técnicas de Transferencia de Gen , Sistemas Microelectromecánicos , Nanopartículas/química , Animales , Permeabilidad de la Membrana Celular , Portadores de Fármacos/química , Sistemas de Liberación de Medicamentos , Sustancias Macromoleculares/química , Ratones , Tamaño de la Partícula , Células RAW 264.7

RESUMEN

The yeast Gis1 protein is a transcriptional regulator belonging to the JMJD2/KDM4 subfamily of demethylases that contain a JmjC domain, which are highly conserved from yeast to humans. They have important functions in histone methylation, cellular signaling and tumorigenesis. Besides serving as a cofactor in many proteins, heme is known to directly regulate the activities of proteins ranging from transcriptional regulators to potassium channels. Here, we report a novel mechanism governing heme regulation of Gis1 transcriptional and histone demethylase activities. We found that two Gis1 modules, the JmjN + JmjC domain and the zinc finger (ZnF), can bind to heme specifically in vitro. In vivo functional analysis showed that the ZnF, not the JmjN + JmjC domain, promotes heme activation of transcriptional activity. Likewise, measurements of the demethylase activity of purified Gis1 proteins showed that full-length Gis1 and the JmjN + JmjC domain both possess demethylase activity. However, heme potentiates the demethylase activity of full-length Gis1, but not that of the JmjN + JmjC domain, which can confer heme activation of transcriptional activity in an unrelated protein. These results demonstrate that Gis1 represents a novel class of multi-functional heme sensing and signaling proteins, and that heme binding to the ZnF stimulates Gis1 demethylase and transcriptional activities.

Asunto(s)

Hemo/metabolismo , Histona Demetilasas/metabolismo , Histona Demetilasas con Dominio de Jumonji/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Transducción de Señal , Transcripción Genética , Activación Enzimática , Histona Demetilasas/genética , Histona Demetilasas con Dominio de Jumonji/genética , Unión Proteica , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética

RESUMEN

Recent experimental evidence increasingly shows that the dysregulation of cellular bioenergetics is associated with a wide array of common human diseases, including cancer, neurological diseases and diabetes. Respiration provides a vital source of cellular energy for most eukaryotic cells, particularly high energy demanding cells. However, the understanding of how respiration is globally regulated is very limited. Interestingly, recent evidence suggests that Swi3 is an important regulator of respiration genes in yeast. In this report, we performed an array of biochemical and genetic experiments and computational analysis to directly evaluate the function of Swi3 and its human homologues in regulating respiration. First, we showed, by computational analysis and measurements of oxygen consumption and promoter activities, that Swi3, not Swi2, regulates genes encoding functions involved in respiration and oxygen consumption. Biochemical analysis showed that the levels of mitochondrial respiratory chain complexes were substantially increased in Δswi3 cells, compared with the parent cells. Additionally, our data showed that Swi3 strongly affects haem/oxygen-dependent activation of respiration gene promoters whereas Swi2 affects only the basal, haem-independent activities of these promoters. We found that increased expression of aerobic expression genes is correlated with increased oxygen consumption and growth rates in Δswi3 cells in air. Furthermore, using computational analysis and RNAi knockdown, we showed that the mammalian Swi3 BAF155 and BAF170 regulate respiration in HeLa cells. Together, these experimental and computational data demonstrated that Swi3 and its mammalian homologues are key regulators in regulating respiration.

Asunto(s)

Proteínas Nucleares/genética , Respiración/genética , Proteínas de Saccharomyces cerevisiae/genética , Factores de Transcripción/genética , Adenosina Trifosfatasas , Secuencia de Aminoácidos/genética , Animales , Cromatina/genética , Proteínas de Unión al ADN/genética , Metabolismo Energético/genética , Células HeLa , Humanos , Consumo de Oxígeno/genética , Regiones Promotoras Genéticas , Saccharomyces cerevisiae/genética , Homología de Secuencia de Aminoácido

RESUMEN

Since Otto Warburg made the first observation that tumor cells exhibit altered metabolism and bioenergetics in the 1920s, many scientists have tried to further the understanding of tumor bioenergetics. Particularly, in the past decade, the application of the state-of the-art metabolomics and genomics technologies has revealed the remarkable plasticity of tumor metabolism and bioenergetics. Firstly, a wide array of tumor cells have been shown to be able to use not only glucose, but also glutamine for generating cellular energy, reducing power, and metabolic building blocks for biosynthesis. Secondly, many types of cancer cells generate most of their cellular energy via mitochondrial respiration and oxidative phosphorylation. Glutamine is the preferred substrate for oxidative phosphorylation in tumor cells. Thirdly, tumor cells exhibit remarkable versatility in using bioenergetics substrates. Notably, tumor cells can use metabolic substrates donated by stromal cells for cellular energy generation via oxidative phosphorylation. Further, it has been shown that mitochondrial transfer is a critical mechanism for tumor cells with defective mitochondria to restore oxidative phosphorylation. The restoration is necessary for tumor cells to gain tumorigenic and metastatic potential. It is also worth noting that heme is essential for the biogenesis and proper functioning of mitochondrial respiratory chain complexes. Hence, it is not surprising that recent experimental data showed that heme flux and function are elevated in non-small cell lung cancer (NSCLC) cells and that elevated heme function promotes intensified oxygen consumption, thereby fueling tumor cell proliferation and function. Finally, emerging evidence increasingly suggests that clonal evolution and tumor genetic heterogeneity contribute to bioenergetic versatility of tumor cells, as well as tumor recurrence and drug resistance. Although mutations are found only in several metabolic enzymes in tumors, diverse mutations in signaling pathways and networks can cause changes in the expression and activity of metabolic enzymes, which likely enable tumor cells to gain their bioenergetic versatility. A better understanding of tumor bioenergetics should provide a more holistic approach to investigate cancer biology and therapeutics. This review therefore attempts to comprehensively consider and summarize the experimental data supporting our latest view of cancer bioenergetics.