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1.
Mol Cells ; 47(2): 100011, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38242235

RESUMEN

Online application for survival analysis (OASIS) and its update, OASIS 2, have been widely used for survival analysis in biological and medical sciences. Here, we provide a portable version of OASIS, an all-in-one offline suite, to facilitate secure survival analysis without uploading the data to online servers. OASIS portable provides a virtualized and isolated instance of the OASIS 2 webserver, operating on the users' personal computers, and enables user-friendly survival analysis without internet connection and security issues.


Asunto(s)
Internet , Análisis de Supervivencia
2.
Korean J Physiol Pharmacol ; 28(1): 73-81, 2024 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-38154966

RESUMEN

The substantia gelatinosa (SG) within the trigeminal subnucleus caudalis (Vc) is recognized as a pivotal site of integrating and modulating afferent fibers carrying orofacial nociceptive information. Although naringenin (4',5,7-thrihydroxyflavanone), a natural bioflavonoid, has been proven to possess various biological effects in the central nervous system (CNS), the activity of naringenin at the orofacial nociceptive site has not been reported yet. In this study, we explored the influence of naringenin on GABA response in SG neurons of Vc using whole-cell patch-clamp technique. The application of GABA in a bath induced two forms of GABA responses: slow and fast. Naringenin enhanced both amplitude and area under curve (AUC) of GABA-mediated responses in 57% (12/21) of tested neurons while decreasing both parameters in 33% (7/21) of neurons. The enhancing or suppressing effect of naringenin on GABA response have been observed, with enhancement occurring when the GABA response was slow, and suppression when it was fast. Furthermore, both the enhancement of slower GABA responses and the suppression of faster GABA responses by naringenin were concentration dependent. Interestingly, the nature of GABA response was also found to be sex-dependent. A majority of SG neurons from juvenile female mice exhibited slower GABA responses, whereas those from juvenile males predominantly displayed faster GABA responses. Taken together, this study indicates that naringenin plays a partial role in modulating orofacial nociception and may hold promise as a therapeutic target for treating orofacial pain, with effects that vary according to sex.

3.
Cell Rep ; 42(11): 113351, 2023 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-37910504

RESUMEN

Genome-wide association studies (GWASs) have identified numerous variants associated with polygenic traits and diseases. However, with few exceptions, a mechanistic understanding of which variants affect which genes in which tissues to modulate trait variation is lacking. Here, we present genomic analyses to explain trait heritability of blood pressure (BP) through the genetics of transcriptional regulation using GWASs, multiomics data from different tissues, and machine learning approaches. Approximately 500,000 predicted regulatory variants across four tissues explain 33.4% of variant heritability: 2.5%, 5.3%, 7.7%, and 11.8% for kidney-, adrenal-, heart-, and artery-specific variants, respectively. Variation in the enhancers involved shows greater tissue specificity than in the genes they regulate, suggesting that gene regulatory networks perturbed by enhancer variants in a tissue relevant to a phenotype are the major source of interindividual variation in BP. Thus, our study provides an approach to scan human tissue and cell types for their physiological contribution to any trait.


Asunto(s)
Estudio de Asociación del Genoma Completo , Sitios de Carácter Cuantitativo , Humanos , Sitios de Carácter Cuantitativo/genética , Presión Sanguínea/genética , Regulación de la Expresión Génica , Redes Reguladoras de Genes , Fenotipo , Polimorfismo de Nucleótido Simple/genética , Variación Genética
4.
Patterns (N Y) ; 4(6): 100736, 2023 Jun 09.
Artículo en Inglés | MEDLINE | ID: mdl-37409049

RESUMEN

Predicting cancer recurrence is essential to improving the clinical outcomes of patients with colorectal cancer (CRC). Although tumor stage information has been used as a guideline to predict CRC recurrence, patients with the same stage show different clinical outcomes. Therefore, there is a need to develop a method to identify additional features for CRC recurrence prediction. Here, we developed a network-integrated multiomics (NIMO) approach to select appropriate transcriptome signatures for better CRC recurrence prediction by comparing the methylation signatures of immune cells. We validated the performance of the CRC recurrence prediction based on two independent retrospective cohorts of 114 and 110 patients. Moreover, to confirm that the prediction was improved, we used both NIMO-based immune cell proportions and TNM (tumor, node, metastasis) stage data. This work demonstrates the importance of (1) using both immune cell composition and TNM stage data and (2) identifying robust immune cell marker genes to improve CRC recurrence prediction.

5.
Neuroscience ; 521: 89-101, 2023 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-37142181

RESUMEN

Inhibitory neurotransmitters such as gamma-aminobutyric acid (GABA) and glycine are known to be abundant in the substantia gelatinosa (SG) of the trigeminal subnucleus caudalis (Vc). Thus, it has been recognized as an initial synaptic site for regulating orofacial nociceptive stimuli. Honokiol, a principal active ingredient derived from the bark of Magnolia officinalis, has been exploited in traditional remedies with multiple biological effects, including anti-nociception on humans. However, the anti-nociceptive mechanism of honokiol on SG neurons of the Vc remains fully elusive. In this study, effects of honokiol on SG neurons of the Vc in mice were investigated using the whole-cell patch-clamp method. In a concentration-dependent manner, honokiol significantly enhanced frequencies of spontaneous postsynaptic currents (sPSCs) that were independent of action potential generation. Notably, honokiol-induced increase in the frequency of sPSCs was attributed to the release of inhibitory neurotransmitters through both glycinergic and GABAergic pre-synaptic terminals. Furthermore, higher concentration of honokiol induced inward currents that were noticeably attenuated in the presence of picrotoxin (a GABAA receptor antagonist) or strychnine (a glycine receptor antagonist). Honokiol also exhibited potentiation effect on glycine- and GABAA receptor-mediated responses. In inflammatory pain model, the increase in frequency of spontaneous firing on SG neurons induced by formalin was significantly inhibited by the application of honokiol. Altogether, these findings indicate that honokiol might directly affect SG neurons of the Vc to facilitate glycinergic and GABAergic neurotransmissions and modulate nociceptive synaptic transmission against pain. Consequently, the inhibitory effect of honokiol in the central nociceptive system contributes to orofacial pain management.


Asunto(s)
Receptores de GABA-A , Sustancia Gelatinosa , Humanos , Animales , Ratones , Neuronas , Transmisión Sináptica , Glicina , Neurotransmisores/farmacología , Dolor
6.
Nat Commun ; 14(1): 2229, 2023 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-37076491

RESUMEN

Expression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). Efforts to maximize their accuracy are ongoing. Using 240 glomerular (GLOM) and 311 tubulointerstitial (TUBE) micro-dissected samples from human kidney biopsies, we discovered 5371 GLOM and 9787 TUBE genes with at least one variant significantly associated with expression (eGene) by incorporating kidney single-nucleus open chromatin data and transcription start site distance as an "integrative prior" for Bayesian statistical fine-mapping. The use of an integrative prior resulted in higher resolution eQTLs illustrated by (1) smaller numbers of variants in credible sets with greater confidence, (2) increased enrichment of partitioned heritability for GWAS of two kidney traits, (3) an increased number of variants colocalized with the GWAS loci, and (4) enrichment of computationally predicted functional regulatory variants. A subset of variants and genes were validated experimentally in vitro and using a Drosophila nephrocyte model. More broadly, this study demonstrates that tissue-specific eQTL maps informed by single-nucleus open chromatin data have enhanced utility for diverse downstream analyses.


Asunto(s)
Estudio de Asociación del Genoma Completo , Enfermedades Renales , Humanos , Estudio de Asociación del Genoma Completo/métodos , Teorema de Bayes , Enfermedades Renales/genética , Genómica , Cromatina/genética , Polimorfismo de Nucleótido Simple , Predisposición Genética a la Enfermedad/genética
7.
Proc Natl Acad Sci U S A ; 119(51): e2212810119, 2022 12 20.
Artículo en Inglés | MEDLINE | ID: mdl-36508674

RESUMEN

Chromatin accessibility assays are central to the genome-wide identification of gene regulatory elements associated with transcriptional regulation. However, the data have highly variable quality arising from several biological and technical factors. To surmount this problem, we developed a sequence-based machine learning method to evaluate and refine chromatin accessibility data. Our framework, gapped k-mer SVM quality check (gkmQC), provides the quality metrics for a sample based on the prediction accuracy of the trained models. We tested 886 DNase-seq samples from the ENCODE/Roadmap projects to demonstrate that gkmQC can effectively identify "high-quality" (HQ) samples with low conventional quality scores owing to marginal read depths. Peaks identified in HQ samples are more accurately aligned at functional regulatory elements, show greater enrichment of regulatory elements harboring functional variants, and explain greater heritability of phenotypes from their relevant tissues. Moreover, gkmQC can optimize the peak-calling threshold to identify additional peaks, especially for rare cell types in single-cell chromatin accessibility data.


Asunto(s)
Cromatina , Secuencias Reguladoras de Ácidos Nucleicos , Cromatina/genética , Secuencias Reguladoras de Ácidos Nucleicos/genética , Análisis de Secuencia de ADN/métodos , Regulación de la Expresión Génica , Genoma
8.
iScience ; 25(11): 105392, 2022 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-36345336

RESUMEN

Predicting colorectal cancer recurrence after tumor resection is crucial because it promotes the administration of proper subsequent treatment or management to improve the clinical outcomes of patients. Several clinical or molecular factors, including tumor stage, metastasis, and microsatellite instability status, have been used to assess the risk of recurrence, although their predictive ability is limited. Here, we predicted colorectal cancer recurrence based on cellular deconvolution of bulk tumors into two distinct immune cell states: cancer-associated (tumor-infiltrating immune cell-like) and noncancer-associated (peripheral blood mononuclear cell-like). Prediction model performed significantly better when immune cells were deconvoluted into two states rather than a single state, suggesting that the difference in cancer recurrence was better explained by distinct states of immune cells. It indicates the importance of distinguishing immune cell states using cellular deconvolution to improve the prediction of colorectal cancer recurrence.

9.
Front Endocrinol (Lausanne) ; 13: 939699, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36387844

RESUMEN

It has been reported that reactive oxygen species (ROS) derived from oxygen molecule reduction can interfere with the cross-talk between the hypothalamic-pituitary-gonadal (HPG) axis and other endocrine axes, thus affecting fertility. Furthermore, ROS have been linked to GnRH receptor signaling in gonadotropes involved in gonadotropin release. There has been evidence that ROS can interfere with the HPG axis and gonadotropin release at various levels. However, the direct effect of ROS on gonadotropin-releasing hormone (GnRH) neuron remains unclear. Thus, the objective of this study was to determine the effect of hydrogen peroxide (H2O2), an ROS source, on GnRH neuronal excitabilities in transgenic GnRH-green fluorescent protein-tagged mice using the whole-cell patch-clamp electrophysiology. In adults, H2O2 at high concentrations (mM level) hyperpolarized most GnRH neurons tested, whereas low concentrations (pM to µM) caused slight depolarization. In immature GnRH neurons, H2O2 exposure induced excitation. The sensitivity of GnRH neurons to H2O2 was increased with postnatal development. The effect of H2O2 on adult female GnRH neurons was found to be estrous cycle-dependent. Hyperpolarization mediated by H2O2 persisted in the presence of tetrodotoxin, a voltage-gated Na+ channel blocker, and amino-acids receptor blocking cocktail containing blockers for the ionotropic glutamate receptors, glycine receptors, and GABAA receptors, indicating that H2O2 could act on GnRH neurons directly. Furthermore, glibenclamide, an ATP-sensitive K+ (KATP) channel blocker, completely blocked H2O2-mediated hyperpolarization. Increasing endogenous H2O2 by inhibiting glutathione peroxidase decreased spontaneous activities of most GnRH neurons. We conclude that ROS can act as signaling molecules for regulating GnRH neuron's excitability and that adult GnRH neurons are sensitive to increased ROS concentration. Results of this study demonstrate that ROS have direct modulatory effects on the HPG axis at the hypothalamic level to regulate GnRH neuron's excitabilities.


Asunto(s)
Hormona Liberadora de Gonadotropina , Peróxido de Hidrógeno , Animales , Ratones , Femenino , Hormona Liberadora de Gonadotropina/metabolismo , Peróxido de Hidrógeno/farmacología , Especies Reactivas de Oxígeno , Neuronas/metabolismo , Ratones Transgénicos , Receptores de GABA-A , Adenosina Trifosfato/farmacología
10.
Nucleic Acids Res ; 50(4): 1849-1863, 2022 02 28.
Artículo en Inglés | MEDLINE | ID: mdl-35137181

RESUMEN

Mouse models have been engineered to reveal the biological mechanisms of human diseases based on an assumption. The assumption is that orthologous genes underlie conserved phenotypes across species. However, genetically modified mouse orthologs of human genes do not often recapitulate human disease phenotypes which might be due to the molecular evolution of phenotypic differences across species from the time of the last common ancestor. Here, we systematically investigated the evolutionary divergence of regulatory relationships between transcription factors (TFs) and target genes in functional modules, and found that the rewiring of gene regulatory networks (GRNs) contributes to the phenotypic discrepancies that occur between humans and mice. We confirmed that the rewired regulatory networks of orthologous genes contain a higher proportion of species-specific regulatory elements. Additionally, we verified that the divergence of target gene expression levels, which was triggered by network rewiring, could lead to phenotypic differences. Taken together, a careful consideration of evolutionary divergence in regulatory networks could be a novel strategy to understand the failure or success of mouse models to mimic human diseases. To help interpret mouse phenotypes in human disease studies, we provide quantitative comparisons of gene expression profiles on our website (http://sbi.postech.ac.kr/w/RN).


Asunto(s)
Evolución Molecular , Redes Reguladoras de Genes , Animales , Humanos , Ratones , Fenotipo , Especificidad de la Especie , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
11.
Nat Prod Res ; 36(22): 5788-5792, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-35086401

RESUMEN

Although a number of studies have reported that resveratrol has analgesic effects, the direct effect of resveratrol on substantia gelatinosa (SG) neurons of the trigeminal subnucleus caudalis (Vc) involved in orofacial nociceptive transmission has not been clearly examined. Thus, the objective of this study was to investigate effects of resveratrol on SG neurons of Vc in mice using a whole-cell patch-clamp technique. Resveratrol (500 µM) induced repeatable inward currents without desensitisation. Resveratrol-induced inward currents were shown in a concentration-dependent manner. Resveratrol-induced responses were sustained in the presence of tetrodotoxin, 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), and DL-2-Amino-5-phosphonovaleric acid (DL-AP5). However, resveratrol-induced inward currents were suppressed in the presence of picrotoxin and strychnine. These results indicate that resveratrol can directly act on SG neurons of Vc with possible inhibitory effects on SG neurons through activation of GABAA receptors and/or glycine receptors. Thus, resveratrol can be a potential therapeutic for orofacial pain modulation.


Asunto(s)
Receptores de Glicina , Sustancia Gelatinosa , Ratones , Animales , Resveratrol/farmacología , Neuronas , Ácido gamma-Aminobutírico
12.
Front Endocrinol (Lausanne) ; 13: 1059255, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36699037

RESUMEN

Objective: Polycystic ovarian syndrome (PCOS) is a heterogeneous endocrine disorder in reproductive-age women, characterized by the accretion of small cystic follicles in the ovary associated with chronic anovulation and overproduction of androgens. Ovarian function in all mammals is controlled by gonadotropin-releasing hormone (GnRH) neurons, which are the central regulator of the hypothalamic-pituitary-gonadal (HPG) axis. However, the impact on the neurotransmitter system regulating GnRH neuronal function in the letrozole-induced PCOS mouse model remains unclear. Methods: In this study, we compared the response of various neurotransmitters and neurosteroids regulating GnRH neuronal activities between letrozole-induced PCOS and normal mice via electrophysiological techniques. Results: Response to neurotransmitter systems like GABAergic, glutamatergic and kisspeptinergic were suppressed in letrozole-fed compared to normal mice. In addition, neurosteroids tetrahydrodeoxycorticosterone (THDOC) and 4,5,6,7-tetrahydroisoxazolo[5,4-c] pyridine-3-ol (THIP) mediated response on GnRH neurons were significantly smaller on letrozole-fed mice compared to normal mice. Furthermore, we also found that letrozole-fed mice showed irregularity in the estrous cycle, increased body weight, and anovulation in female mice. Conclusion: These findings suggest that PCOS is an endocrine disorder that may directly affect the neurotransmitter system regulating GnRH neuronal activity at the hypothalamic level and impact reproductive physiology.


Asunto(s)
Anovulación , Neuroesteroides , Síndrome del Ovario Poliquístico , Animales , Femenino , Humanos , Ratones , Hormona Liberadora de Gonadotropina , Letrozol , Neuronas , Neurotransmisores , Síndrome del Ovario Poliquístico/inducido químicamente , Transmisión Sináptica
13.
Sci Adv ; 7(49): eabj8156, 2021 Dec 03.
Artículo en Inglés | MEDLINE | ID: mdl-34860542

RESUMEN

The Golgi apparatus plays a central role in trafficking cargoes such as proteins and lipids. Defects in the Golgi apparatus lead to various diseases, but its role in organismal longevity is largely unknown. Using a quantitative proteomic approach, we found that a Golgi protein, MON-2, was up-regulated in long-lived Caenorhabditis elegans mutants with mitochondrial respiration defects and was required for their longevity. Similarly, we showed that DOP1/PAD-1, which acts with MON-2 to traffic macromolecules between the Golgi and endosome, contributed to the longevity of respiration mutants. Furthermore, we demonstrated that MON-2 was required for up-regulation of autophagy, a longevity-associated recycling process, by activating the Atg8 ortholog GABARAP/LGG-1 in C. elegans. Consistently, we showed that mammalian MON2 activated GABARAPL2 through physical interaction, which increased autophagic flux in mammalian cells. Thus, the evolutionarily conserved role of MON2 in trafficking between the Golgi and endosome is an integral part of autophagy-mediated longevity.

14.
Am J Chin Med ; 49(6): 1437-1448, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34247560

RESUMEN

Linalool, a major odorous constituent in essential oils extracted from lavender, is known to have a wide range of physiological effects on humans including pain management. The substantia gelatinosa (SG) of the trigeminal subnucleus caudalis (Vc) is involved in transmission of orofacial nociceptive responses through thin myelinated A[Formula: see text] and unmyelinated C primary afferent fibers. Up to date, the orofacial antinociceptive mechanism of linalool concerning SG neurons of the Vc has not been completely clarified yet. To fill this knowledge gap, whole-cell patch-clamp technique was used in this study to examine how linalool acted on SG neurons of the Vc in mice. Under a high chloride pipette solution, non-desensitizing and repeatable linalool-induced inward currents were preserved in the presence of tetrodotoxin (a voltage-gated Na[Formula: see text]channel blocker), CNQX (a non-NMDA glutamate receptor antagonist), and DL-AP5 (an NMDA receptor antagonist). However, linalool-induced inward currents were partially suppressed by picrotoxin (a GABA[Formula: see text] receptor antagonist) or strychnine (a glycine receptor antagonist). These responses were almost blocked in the presence of picrotoxin and strychnine. It was also found that linalool exhibited potentiation with GABA- and glycine-induced responses. Taken together, these data show that linalool has GABA- and glycine-mimetic effects, suggesting that it can be a promising target molecule for orofacial pain management by activating inhibitory neurotransmission in the SG area of the Vc.


Asunto(s)
Monoterpenos Acíclicos/farmacología , Glicina/metabolismo , Manejo del Dolor/métodos , Sustancia Gelatinosa/efectos de los fármacos , Transmisión Sináptica/efectos de los fármacos , Núcleo Caudal del Trigémino/efectos de los fármacos , Ácido gamma-Aminobutírico/metabolismo , Animales , Modelos Animales de Enfermedad , Femenino , Masculino , Ratones
15.
Int J Mol Sci ; 22(8)2021 Apr 09.
Artículo en Inglés | MEDLINE | ID: mdl-33918982

RESUMEN

Lithium (Li+) salt is widely used as a therapeutic agent for treating neurological and psychiatric disorders. Despite its therapeutic effects on neurological and psychiatric disorders, it can also disturb the neuroendocrine axis in patients under lithium therapy. The hypothalamic area contains GABAergic and glutamatergic neurons and their receptors, which regulate various hypothalamic functions such as the release of neurohormones, control circadian activities. At the neuronal level, several neurotransmitter systems are modulated by lithium exposure. However, the effect of Li+ on hypothalamic neuron excitability and the precise action mechanism involved in such an effect have not been fully understood yet. Therefore, Li+ action on hypothalamic neurons was investigated using a whole-cell patch-clamp technique. In hypothalamic neurons, Li+ increased the GABAergic synaptic activities via action potential independent presynaptic mechanisms. Next, concentration-dependent replacement of Na+ by Li+ in artificial cerebrospinal fluid increased frequencies of GABAergic miniature inhibitory postsynaptic currents without altering their amplitudes. Li+ perfusion induced inward currents in the majority of hypothalamic neurons independent of amino-acids receptor activation. These results suggests that Li+ treatment can directly affect the hypothalamic region of the brain and regulate the release of various neurohormones involved in synchronizing the neuroendocrine axis.


Asunto(s)
Neuronas GABAérgicas/efectos de los fármacos , Neuronas GABAérgicas/metabolismo , Litio/farmacología , Células Piramidales/efectos de los fármacos , Células Piramidales/metabolismo , Sinapsis/efectos de los fármacos , Sinapsis/metabolismo , Animales , Humanos , Hipotálamo/metabolismo , Hipotálamo/patología , Potenciales Postsinápticos Inhibidores/efectos de los fármacos , Técnicas de Placa-Clamp , Área Preóptica/efectos de los fármacos , Área Preóptica/metabolismo , Receptores de Aminoácidos/metabolismo , Transmisión Sináptica/efectos de los fármacos
16.
Physiol Plant ; 172(3): 1422-1438, 2021 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-31828796

RESUMEN

ABCG subfamily proteins are highly enriched in terrestrial plants. Many of these proteins secrete secondary metabolites that repel or inhibit pathogens. To establish why the ABCG subfamily proteins proliferated extensively during evolution, we constructed phylogenetic trees from a broad range of eukaryotic organisms. ABCG proteins were massively duplicated in land plants and in oomycetes, a group of agronomically important plant pathogens, which prompted us to hypothesize that plant and pathogen ABCGs coevolved. Supporting this hypothesis, full-size ABCGs in host plants (Arabidopsis thaliana and Glycine max) and their pathogens (Hyaloperonospora arabidopsidis and Phytophthora sojae, respectively) had similar divergence times and patterns. Furthermore, generalist pathogens with broad ranges of host plants have diversified more ABCGs than their specialist counterparts. The hypothesis was further tested using an example pair of ABCGs that first diverged during multiplication in a host plant and its pathogen: AtABCG31 of A. thaliana and HpaP802307 of H. arabidopsidis. AtABCG31 expression was activated following infection with H. arabidopsidis, and disrupting AtABCG31 led to increased susceptibility to H. arabidopsidis. Together, our results suggest that ABCG genes in plants and their oomycete pathogens coevolved in an arms race, to extrude secondary metabolites involved in the plant's defense response against pathogens.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Oomicetos , Transportador de Casetes de Unión a ATP, Subfamilia G , Análisis por Conglomerados , Interacciones Huésped-Patógeno , Filogenia , Enfermedades de las Plantas/genética
17.
Aging Cell ; 19(12): e13279, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33274583

RESUMEN

Endothelial dysfunction is one of the main age-related arterial phenotypes responsible for cardiovascular disease (CVD) in older adults. This endothelial dysfunction results from decreased bioavailability of nitric oxide (NO) arising downstream of endothelial oxidative stress. In this study, we investigated the protective effect of anthocyanins and the underlying mechanism in rat thoracic aorta and human vascular endothelial cells in aging models. In vitro, cyanidin-3-rutinoside (C-3-R) and cyanidin-3-glucoside (C-3-G) inhibited the d-galactose (d-gal)-induced senescence in human endothelial cells, as indicated by reduced senescence-associated-ß-galactosidase activity, p21, and p16INK4a . Anthocyanins blocked d-gal-induced reactive oxygen species (ROS) formation and NADPH oxidase activity. Anthocyanins reversed d-gal-mediated inhibition of endothelial nitric oxide synthase (eNOS) serine phosphorylation and SIRT1 expression, recovering NO level in endothelial cells. Also, SIRT1-mediated eNOS deacetylation was shown to be involved in anthocyanin-enhanced eNOS activity. In vivo, anthocyanin-rich mulberry extract was administered to aging rats for 8 weeks. In vivo, mulberry extract alleviated endothelial senescence and oxidative stress in the aorta of aging rats. Consistently, mulberry extract also raised serum NO levels, increased phosphorylation of eNOS, increased SIRT1 expression, and reduced nitrotyrosine in aortas. The eNOS acetylation was higher in the aging group and was restored by mulberry extract treatment. Similarly, SIRT1 level associated with eNOS decreased in the aging group and was restored in aging plus mulberry group. These findings indicate that anthocyanins protect against endothelial senescence through enhanced NO bioavailability by regulating ROS formation and reducing eNOS uncoupling.


Asunto(s)
Envejecimiento/fisiología , Antocianinas/farmacología , Endotelio Vascular/efectos de los fármacos , Endotelio Vascular/fisiopatología , Óxido Nítrico Sintasa de Tipo III/metabolismo , Animales , Aorta Torácica/efectos de los fármacos , Aorta Torácica/fisiopatología , Senescencia Celular/efectos de los fármacos , Células Endoteliales de la Vena Umbilical Humana , Humanos , Masculino , Morus/química , Óxido Nítrico/biosíntesis , Estrés Oxidativo/efectos de los fármacos , Extractos Vegetales/farmacología , Ratas , Ratas Sprague-Dawley , Sirtuina 1/metabolismo , Desacopladores/farmacología
18.
Nat Commun ; 11(1): 5485, 2020 10 30.
Artículo en Inglés | MEDLINE | ID: mdl-33127883

RESUMEN

Cancer patient classification using predictive biomarkers for anti-cancer drug responses is essential for improving therapeutic outcomes. However, current machine-learning-based predictions of drug response often fail to identify robust translational biomarkers from preclinical models. Here, we present a machine-learning framework to identify robust drug biomarkers by taking advantage of network-based analyses using pharmacogenomic data derived from three-dimensional organoid culture models. The biomarkers identified by our approach accurately predict the drug responses of 114 colorectal cancer patients treated with 5-fluorouracil and 77 bladder cancer patients treated with cisplatin. We further confirm our biomarkers using external transcriptomic datasets of drug-sensitive and -resistant isogenic cancer cell lines. Finally, concordance analysis between the transcriptomic biomarkers and independent somatic mutation-based biomarkers further validate our method. This work presents a method to predict cancer patient drug responses using pharmacogenomic data derived from organoid models by combining the application of gene modules and network-based approaches.


Asunto(s)
Antineoplásicos/uso terapéutico , Neoplasias Colorrectales/tratamiento farmacológico , Aprendizaje Automático , Organoides/metabolismo , Neoplasias de la Vejiga Urinaria/tratamiento farmacológico , Vejiga Urinaria/metabolismo , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Línea Celular Tumoral , Cisplatino/uso terapéutico , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Desarrollo de Medicamentos/métodos , Fluorouracilo/uso terapéutico , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes/efectos de los fármacos , Humanos , Organoides/efectos de los fármacos , Mapas de Interacción de Proteínas/efectos de los fármacos , Transcriptoma , Vejiga Urinaria/efectos de los fármacos , Neoplasias de la Vejiga Urinaria/genética , Neoplasias de la Vejiga Urinaria/metabolismo
19.
Nat Commun ; 11(1): 4367, 2020 08 31.
Artículo en Inglés | MEDLINE | ID: mdl-32868763

RESUMEN

Invariant natural killer T (iNKT), mucosal-associated invariant T (MAIT), and γδ T cells are innate T cells that acquire memory phenotype in the thymus and share similar biological characteristics. However, how their effector differentiation is developmentally regulated is still unclear. Here, we identify analogous effector subsets of these three innate T cell types in the thymus that share transcriptional profiles. Using single-cell RNA sequencing, we show that iNKT, MAIT and γδ T cells mature via shared, branched differentiation rather than linear maturation or TCR-mediated instruction. Simultaneous TCR clonotyping analysis reveals that thymic maturation of all three types is accompanied by clonal selection and expansion. Analyses of mice deficient of TBET, GATA3 or RORγt and additional in vivo experiments corroborate the predicted differentiation paths, while human innate T cells from liver samples display similar features. Collectively, our data indicate that innate T cells share effector differentiation processes in the thymus.


Asunto(s)
Diferenciación Celular , Inmunidad Innata , Linfocitos T/metabolismo , Timo/inmunología , Animales , Células Cultivadas , Selección Clonal Mediada por Antígenos , Humanos , Hígado/citología , Hígado/inmunología , Activación de Linfocitos , Ratones , Células T Invariantes Asociadas a Mucosa/metabolismo , Células T Asesinas Naturales/metabolismo , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Células Th17/metabolismo , Timo/citología
20.
Int J Mol Sci ; 21(17)2020 Aug 20.
Artículo en Inglés | MEDLINE | ID: mdl-32825350

RESUMEN

Melatonin, a pineal gland secretion, is an amphiphilic neurohormone involved in the biological and physiologic regulation of bodily functions. Numerous studies have shown the effects of melatonin on the release of gonadotropins and their actions at one or several levels of the hypothalamic-pituitary-gonadal axis. However, direct melatonin action on gonadotropin-releasing hormone (GnRH) neurons and its mechanism of action remain unclear. Here, plasma melatonin levels were measured and the effect of melatonin on GnRH neurons was assessed using brain slice patch clamp techniques. The plasma melatonin levels in prepubertal mice were higher than those in the adults. Melatonin itself did not change the firing activity of GnRH neurons. Interestingly, the kainate receptor-mediated responses but not the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)- and N-methyl-D-aspartic acid (NMDA)-induced responses were suppressed by melatonin in both the voltage clamp and current clamp modes. The inhibitory effects of the kainate-induced response by melatonin tended to increase with higher melatonin concentrations and persisted in the presence of tetrodotoxin, a voltage-sensitive Na+ channel blocker, or luzindole, a non-selective melatonin receptor antagonist. However, the response was completely abolished by pretreatment with pertussis toxin. These results suggest that melatonin can regulate GnRH neuronal activities in prepubertal mice by partially suppressing the excitatory signaling mediated by kainate receptors through pertussis toxin-sensitive G-protein-coupled receptors.


Asunto(s)
Hormona Liberadora de Gonadotropina/metabolismo , Melatonina/farmacología , Neuronas/fisiología , Receptores de Ácido Kaínico/metabolismo , Animales , Encéfalo/efectos de los fármacos , Agonistas de Aminoácidos Excitadores , Femenino , Proteínas Fluorescentes Verdes/genética , Proteínas Fluorescentes Verdes/metabolismo , Ácido Kaínico/farmacología , Masculino , Melatonina/sangre , Ratones Endogámicos C57BL , Ratones Transgénicos , N-Metilaspartato/farmacología , Neuronas/efectos de los fármacos , Toxina del Pertussis/farmacología , Pubertad , Ácido alfa-Amino-3-hidroxi-5-metil-4-isoxazol Propiónico/farmacología
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