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1.
Cell ; 187(20): 5735-5752.e25, 2024 Oct 03.
Artículo en Inglés | MEDLINE | ID: mdl-39168126

RESUMEN

Xp11 translocation renal cell carcinoma (tRCC) is a rare, female-predominant cancer driven by a fusion between the transcription factor binding to IGHM enhancer 3 (TFE3) gene on chromosome Xp11.2 and a partner gene on either chromosome X (chrX) or an autosome. It remains unknown what types of rearrangements underlie TFE3 fusions, whether fusions can arise from both the active (chrXa) and inactive X (chrXi) chromosomes, and whether TFE3 fusions from chrXi translocations account for the female predominance of tRCC. To address these questions, we performed haplotype-specific analyses of chrX rearrangements in tRCC whole genomes. We show that TFE3 fusions universally arise as reciprocal translocations and that oncogenic TFE3 fusions can arise from chrXi:autosomal translocations. Female-specific chrXi:autosomal translocations result in a 2:1 female-to-male ratio of TFE3 fusions involving autosomal partner genes and account for the female predominance of tRCC. Our results highlight how X chromosome genetics constrains somatic chrX alterations and underlies cancer sex differences.


Asunto(s)
Factores de Transcripción Básicos con Cremalleras de Leucinas y Motivos Hélice-Asa-Hélice , Carcinoma de Células Renales , Cromosomas Humanos X , Neoplasias Renales , Translocación Genética , Humanos , Carcinoma de Células Renales/genética , Carcinoma de Células Renales/patología , Femenino , Translocación Genética/genética , Cromosomas Humanos X/genética , Masculino , Factores de Transcripción Básicos con Cremalleras de Leucinas y Motivos Hélice-Asa-Hélice/genética , Factores de Transcripción Básicos con Cremalleras de Leucinas y Motivos Hélice-Asa-Hélice/metabolismo , Neoplasias Renales/genética , Neoplasias Renales/patología , Proteínas de Fusión Oncogénica/genética , Caracteres Sexuales , Haplotipos/genética
2.
Cell ; 180(1): 107-121.e17, 2020 01 09.
Artículo en Inglés | MEDLINE | ID: mdl-31866069

RESUMEN

Fibrosis can develop in most organs and causes organ failure. The most common type of lung fibrosis is known as idiopathic pulmonary fibrosis, in which fibrosis starts at the lung periphery and then progresses toward the lung center, eventually causing respiratory failure. Little is known about the mechanisms underlying the pathogenesis and periphery-to-center progression of the disease. Here we discovered that loss of Cdc42 function in alveolar stem cells (AT2 cells) causes periphery-to-center progressive lung fibrosis. We further show that Cdc42-null AT2 cells in both post-pneumonectomy and untreated aged mice cannot regenerate new alveoli, resulting in sustained exposure of AT2 cells to elevated mechanical tension. We demonstrate that elevated mechanical tension activates a TGF-ß signaling loop in AT2 cells, which drives the periphery-to-center progression of lung fibrosis. Our study establishes a direct mechanistic link between impaired alveolar regeneration, mechanical tension, and progressive lung fibrosis.


Asunto(s)
Células Madre Adultas/metabolismo , Fibrosis Pulmonar Idiopática/etiología , Alveolos Pulmonares/metabolismo , Células Madre Adultas/patología , Anciano , Células Epiteliales Alveolares/patología , Animales , Fenómenos Biomecánicos/fisiología , Femenino , Fibrosis/patología , Humanos , Fibrosis Pulmonar Idiopática/metabolismo , Fibrosis Pulmonar Idiopática/patología , Pulmón/patología , Masculino , Ratones , Persona de Mediana Edad , Alveolos Pulmonares/patología , Regeneración , Transducción de Señal , Células Madre/patología , Estrés Mecánico , Estrés Fisiológico/fisiología , Factor de Crecimiento Transformador beta/metabolismo , Proteína de Unión al GTP cdc42/genética , Proteína de Unión al GTP cdc42/metabolismo
4.
Nature ; 613(7944): 460-462, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36653563

RESUMEN

Most structural and evolutionary properties of galaxies strongly rely on the stellar initial mass function (IMF), namely the distribution of the stellar mass formed in each episode of star formation1-4. The IMF shapes the stellar population in all stellar systems, and so has become one of the most fundamental concepts of modern astronomy. Both constant and variable IMFs across different environments have been claimed despite a large number of theoretical5-7 and observational efforts8-15. However, the measurement of the IMF in Galactic stellar populations has been limited by the relatively small number of photometrically observed stars, leading to high uncertainties12-16. Here we report a star-counting result based on approximately 93,000 spectroscopically observed M-dwarf stars, an order of magnitude more than previous studies, in the 100-300 parsec solar neighbourhood. We find unambiguous evidence of a variable IMF that depends on both metallicity and stellar age. Specifically, the stellar population formed at early times contains fewer low-mass stars compared with the canonical IMF, independent of stellar metallicities. In more recent times, however, the proportion of low-mass stars increases with stellar metallicity. The variable abundance of low-mass stars in our Milky Way establishes a powerful benchmark for models of star formation and can heavily affect results in Galactic chemical-enrichment modelling, mass estimation of galaxies and planet-formation efficiency.

5.
PLoS Biol ; 22(6): e3002647, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38900742

RESUMEN

The human brain is organized as segregation and integration units and follows complex developmental trajectories throughout life. The cortical manifold provides a new means of studying the brain's organization in a multidimensional connectivity gradient space. However, how the brain's morphometric organization changes across the human lifespan remains unclear. Here, leveraging structural magnetic resonance imaging scans from 1,790 healthy individuals aged 8 to 89 years, we investigated age-related global, within- and between-network dispersions to reveal the segregation and integration of brain networks from 3D manifolds based on morphometric similarity network (MSN), combining multiple features conceptualized as a "fingerprint" of an individual's brain. Developmental trajectories of global dispersion unfolded along patterns of molecular brain organization, such as acetylcholine receptor. Communities were increasingly dispersed with age, reflecting more disassortative morphometric similarity profiles within a community. Increasing within-network dispersion of primary motor and association cortices mediated the influence of age on the cognitive flexibility of executive functions. We also found that the secondary sensory cortices were decreasingly dispersed with the rest of the cortices during aging, possibly indicating a shift of secondary sensory cortices across the human lifespan from an extreme to a more central position in 3D manifolds. Together, our results reveal the age-related segregation and integration of MSN from the perspective of a multidimensional gradient space, providing new insights into lifespan changes in multiple morphometric features of the brain, as well as the influence of such changes on cognitive performance.


Asunto(s)
Envejecimiento , Encéfalo , Cognición , Longevidad , Imagen por Resonancia Magnética , Humanos , Adulto , Anciano , Cognición/fisiología , Adolescente , Persona de Mediana Edad , Masculino , Imagen por Resonancia Magnética/métodos , Femenino , Anciano de 80 o más Años , Niño , Encéfalo/diagnóstico por imagen , Encéfalo/fisiología , Encéfalo/crecimiento & desarrollo , Adulto Joven , Longevidad/fisiología , Envejecimiento/fisiología , Red Nerviosa/fisiología , Red Nerviosa/diagnóstico por imagen , Función Ejecutiva/fisiología
6.
Nature ; 600(7887): 54-58, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34666338

RESUMEN

The Moon has a magmatic and thermal history that is distinct from that of the terrestrial planets1. Radioisotope dating of lunar samples suggests that most lunar basaltic magmatism ceased by around 2.9-2.8 billion years ago (Ga)2,3, although younger basalts between 3 Ga and 1 Ga have been suggested by crater-counting chronology, which has large uncertainties owing to the lack of returned samples for calibration4,5. Here we report a precise lead-lead age of 2,030 ± 4 million years ago for basalt clasts returned by the Chang'e-5 mission, and a 238U/204Pb ratio (µ value)6 of about 680 for a source that evolved through two stages of differentiation. This is the youngest crystallization age reported so far for lunar basalts by radiometric dating, extending the duration of lunar volcanism by approximately 800-900 million years. The µ value of the Chang'e-5 basalt mantle source is within the range of low-titanium and high-titanium basalts from Apollo sites (µ value of about 300-1,000), but notably lower than those of potassium, rare-earth elements and phosphorus (KREEP) and high-aluminium basalts7 (µ value of about 2,600-3,700), indicating that the Chang'e-5 basalts were produced by melting of a KREEP-poor source. This age provides a pivotal calibration point for crater-counting chronology in the inner Solar System and provides insight on the volcanic and thermal history of the Moon.

7.
Am J Pathol ; 2024 Aug 31.
Artículo en Inglés | MEDLINE | ID: mdl-39222908

RESUMEN

The vaginal epithelium plays pivotal roles in host defense against pathogen invasion, contributing to the maintenance of an acidic microenvironment within the vaginal lumen through the activity of acid-base transport proteins. However, the precise defense mechanisms of the vaginal epithelium after a bacterial infection remain incompletely understood. This study showed that bacterial lipopolysaccharide (LPS) potentiated net proton efflux by up-regulating the expression of Na+-H+ exchanger 1 (NHE1) without affecting other acid-base transport proteins in vaginal epithelial cells. Pharmacologic inhibition or genetic knockdown of Toll-like receptor-4 and the extracellular signal-regulated protein kinase signaling pathway effectively counteracted the up-regulation of NHE1 and the enhanced proton efflux triggered by LPS in vaginal epithelial cells. In vivo studies revealed that LPS administration led to luminal acidification through the up-regulation of NHE1 expression in the rat vagina. Moreover, inhibition of NHE exhibited an impaired defense against acute bacterial infection in the rat vagina. These findings collectively indicate the active involvement of vaginal epithelial cells in facilitating luminal acidification during acute bacterial infection, offering potential insights into the treatment of bacterial vaginosis.

8.
Plant Cell ; 34(11): 4274-4292, 2022 10 27.
Artículo en Inglés | MEDLINE | ID: mdl-35929087

RESUMEN

Lipid droplets (LDs) are evolutionarily conserved organelles that serve as hubs of cellular lipid and energy metabolism in virtually all organisms. Mobilization of LDs is important in light-induced stomatal opening. However, whether and how LDs are involved in stomatal development remains unknown. We show here that Arabidopsis thaliana LIPID DROPLETS AND STOMATA 1 (LDS1)/RABC1 (At1g43890) encodes a member of the Rab GTPase family that is involved in regulating LD dynamics and stomatal morphogenesis. The expression of RABC1 is coordinated with the different phases of stomatal development. RABC1 targets to the surface of LDs in response to oleic acid application in a RABC1GEF1-dependent manner. RABC1 physically interacts with SEIPIN2/3, two orthologues of mammalian seipin, which function in the formation of LDs. Disruption of RABC1, RABC1GEF1, or SEIPIN2/3 resulted in aberrantly large LDs, severe defects in guard cell vacuole morphology, and stomatal function. In conclusion, these findings reveal an aspect of LD function and uncover a role for lipid metabolism in stomatal development in plants.


Asunto(s)
Proteínas de Arabidopsis , Arabidopsis , Animales , Arabidopsis/metabolismo , Gotas Lipídicas/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Metabolismo de los Lípidos/genética , Mamíferos/metabolismo
9.
Mol Psychiatry ; 29(7): 1980-1989, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38351174

RESUMEN

Individuals with depression have the highest lifetime prevalence of suicide attempts (SA) among mental illnesses. Numerous neuroimaging studies have developed biomarkers from task-related neural activation in depressive patients with SA, but the findings are inconsistent. Empowered by the contemporary interconnected view of depression as a neural system disorder, we sought to identify a specific brain circuit utilizing published heterogeneous neural activations. We systematically reviewed all published cognitive and emotional task-related functional MRI studies that investigated differences in the location of neural activations between depressive patients with and without SA. We subsequently mapped an underlying brain circuit functionally connecting to each experimental activation using a large normative connectome database (n = 1000). The identified SA-related functional network was compared to the network derived from the disease control group. Finally, we decoded this convergent functional connectivity network using microscale transcriptomic and chemo-architectures, and macroscale psychological processes. We enrolled 11 experimental tasks from eight studies, including depressive patients with SA (n = 147) and without SA (n = 196). The heterogeneous SA-related neural activations localized to the somato-cognitive action network (SCAN), exhibiting robustness to little perturbations and specificity for depression. Furthermore, the SA-related functional network was colocalized with brain-wide gene expression involved in inflammatory and immunity-related biological processes and aligned with the distribution of the GABA and noradrenaline neurotransmitter systems. The findings demonstrate that the SA-related functional network of depression is predominantly located at the SCAN, which is an essential implication for understanding depressive patients with SA.


Asunto(s)
Encéfalo , Cognición , Conectoma , Depresión , Imagen por Resonancia Magnética , Humanos , Imagen por Resonancia Magnética/métodos , Conectoma/métodos , Depresión/fisiopatología , Encéfalo/fisiopatología , Encéfalo/metabolismo , Cognición/fisiología , Femenino , Masculino , Adulto , Intento de Suicidio/psicología , Red Nerviosa/fisiopatología , Red Nerviosa/metabolismo , Red Nerviosa/diagnóstico por imagen , Ideación Suicida , Trastorno Depresivo Mayor/fisiopatología , Trastorno Depresivo Mayor/metabolismo , Vías Nerviosas/fisiopatología , Mapeo Encefálico/métodos
10.
Nucleic Acids Res ; 51(D1): D1179-D1187, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36243959

RESUMEN

Transcriptome-wide association studies (TWASs), as a practical and prevalent approach for detecting the associations between genetically regulated genes and traits, are now leading to a better understanding of the complex mechanisms of genetic variants in regulating various diseases and traits. Despite the ever-increasing TWAS outputs, there is still a lack of databases curating massive public TWAS information and knowledge. To fill this gap, here we present TWAS Atlas (https://ngdc.cncb.ac.cn/twas/), an integrated knowledgebase of TWAS findings manually curated from extensive literature. In the current implementation, TWAS Atlas collects 401,266 high-quality human gene-trait associations from 200 publications, covering 22,247 genes and 257 traits across 135 tissue types. In particular, an interactive knowledge graph of the collected gene-trait associations is constructed together with single nucleotide polymorphism (SNP)-gene associations to build up comprehensive regulatory networks at multi-omics levels. In addition, TWAS Atlas, as a user-friendly web interface, efficiently enables users to browse, search and download all association information, relevant research metadata and annotation information of interest. Taken together, TWAS Atlas is of great value for promoting the utility and availability of TWAS results in explaining the complex genetic basis as well as providing new insights for human health and disease research.


Asunto(s)
Sitios de Carácter Cuantitativo , Transcriptoma , Humanos , Transcriptoma/genética , Estudio de Asociación del Genoma Completo/métodos , Fenotipo , Bases del Conocimiento , Polimorfismo de Nucleótido Simple , Predisposición Genética a la Enfermedad
11.
BMC Bioinformatics ; 25(1): 282, 2024 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-39198740

RESUMEN

BACKGROUND: Thermostability is a fundamental property of proteins to maintain their biological functions. Predicting protein stability changes upon mutation is important for our understanding protein structure-function relationship, and is also of great interest in protein engineering and pharmaceutical design. RESULTS: Here we present mutDDG-SSM, a deep learning-based framework that uses the geometric representations encoded in protein structure to predict the mutation-induced protein stability changes. mutDDG-SSM consists of two parts: a graph attention network-based protein structural feature extractor that is trained with a self-supervised learning scheme using large-scale high-resolution protein structures, and an eXtreme Gradient Boosting model-based stability change predictor with an advantage of alleviating overfitting problem. The performance of mutDDG-SSM was tested on several widely-used independent datasets. Then, myoglobin and p53 were used as case studies to illustrate the effectiveness of the model in predicting protein stability changes upon mutations. Our results show that mutDDG-SSM achieved high performance in estimating the effects of mutations on protein stability. In addition, mutDDG-SSM exhibited good unbiasedness, where the prediction accuracy on the inverse mutations is as well as that on the direct mutations. CONCLUSION: Meaningful features can be extracted from our pre-trained model to build downstream tasks and our model may serve as a valuable tool for protein engineering and drug design.


Asunto(s)
Mutación , Estabilidad Proteica , Proteínas , Proteínas/química , Proteínas/genética , Proteínas/metabolismo , Mioglobina/química , Mioglobina/genética , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/química , Proteína p53 Supresora de Tumor/metabolismo , Biología Computacional/métodos , Aprendizaje Profundo , Aprendizaje Automático Supervisado , Bases de Datos de Proteínas , Conformación Proteica
12.
Glia ; 72(3): 504-528, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-37904673

RESUMEN

Retinal degeneration, characterized by Müller cell gliosis and photoreceptor apoptosis, is considered an early event in diabetic retinopathy (DR). Our previous study proposed that GMFB may mediate diabetic retinal degeneration. This study identified GMFB as a sensitive and functional gliosis marker for DR. Compared to the wild type (WT) group, Gmfb knockout (KO) significantly improved visual function, attenuated gliosis, reduced the apoptosis of neurons, and decreased the mRNA levels of tumor necrosis factor α (Tnf-α) and interleukin-1ß (Il-1ß) in diabetic retinas. Tgf-ß3 was enriched by hub genes using RNA sequencing in primary WT and KO Müller cells. Gmfb KO significantly upregulated the transforming growth factor (TGF)-ß3 protein level via the AKT pathway. The protective effect of TGF-ß3 in the vitreous resulted in significantly improved visual function and decreased the number of apoptotic cells in the diabetic retina. The protection of Gmfb KO in primary Müller cells against high glucose (HG)-induced photoreceptor apoptosis was partially counteracted by TGF-ß3 antibody and administration of TGFBR1/2 inhibitors. Nuclear receptor subfamily 3 group C member 1 (NR3C1) binds to the promoter region of Gmfb and regulates Gmfb mRNA at the transcriptional level. NR3C1 was increased in the retinas of early diabetic rats but decreased in the retinas of late diabetic rats. N'-[(1E)-(3-Methoxyphenyl)Methylene]-3-Methyl-1H-Pyrazole-5-Carbohydrazide (DS-5) was identified as an inhibitor of GMFB, having a protective role in DR. We demonstrated that GMFB/AKT/TGF-ß3 mediated early diabetic retinal degeneration in diabetic rats. This study provides a novel therapeutic strategy for treating retinal degeneration in patients with DR.


Asunto(s)
Diabetes Mellitus Experimental , Retinopatía Diabética , Degeneración Retiniana , Humanos , Ratas , Animales , Degeneración Retiniana/patología , Células Ependimogliales/metabolismo , Estreptozocina/toxicidad , Proteínas Proto-Oncogénicas c-akt/metabolismo , Factor de Crecimiento Transformador beta3/efectos adversos , Factor de Crecimiento Transformador beta3/metabolismo , Diabetes Mellitus Experimental/inducido químicamente , Diabetes Mellitus Experimental/metabolismo , Diabetes Mellitus Experimental/patología , Gliosis/patología , Retina/metabolismo , Retinopatía Diabética/patología , ARN Mensajero/metabolismo
13.
Lab Invest ; : 102134, 2024 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-39307311

RESUMEN

Alcoholic liver disease (ALD) caused by chronic alcohol abuse involves complex processes from steatosis to fibrosis, cirrhosis, and hepatocellular carcinoma, posing a global health issue. Bromodomain protein 4 (BRD4) typically serves as a "reader" modulating the functions of transcription factors involved in various biological processes and disease progression. However, the specific mechanisms underlying alcoholic liver injury remain unclear. Here, we detected aberrant BRD4 expression in the alcohol-induced ALD mouse model of chronic and binge ethanol feeding developed by the National Institute on Alcohol Abuse and Alcoholism (NIAAA model), consistent with the in vitro results in Aml-12 mouse hepatocytes. Blocking and inhibiting BRD4 restored the impaired autophagic flux and lysosomal functions in alcohol-treated Aml-12 cells, whereas BRD4 overexpression reduced the expression levels of autophagy marker and lysosomal genes. Furthermore, mouse BRD4 knockdown, mediated by a short hairpin RNA carried by the adeno-associated virus serotype 8, significantly attenuated the alcohol-induced hepatocyte damage, including lipid deposition and inflammatory cell infiltration. Mechanistically, BRD4 overexpression in alcoholic liver injury inhibited the expression of sirtuin (SIRT)-1 in Aml-12 cells. Chromatin immunoprecipitation and dual-luciferase reporter assays revealed that BRD4 functions as a transcription factor and suppressor, actively binding to the SIRT1 promoter region and inhibiting its transcription. SIRT1 activated autophagy, which was suppressed in alcoholic liver injury via Beclin1 deacetylation. In conclusion, our study revealed that BRD4 negatively regulated the SIRT1/Beclin1 axis and that its deficiency alleviated alcohol-induced liver injury in mice, thus providing a new strategy for ALD treatment.

14.
Mol Cancer ; 23(1): 165, 2024 Aug 13.
Artículo en Inglés | MEDLINE | ID: mdl-39138527

RESUMEN

BACKGROUND: Overexpression of receptor tyrosine kinase-like orphan receptor 1 (ROR1) contributes to cancer cell proliferation, survival and migration, playing crucial roles in tumor development. ROR1 has been proposed as a potential therapeutic target for cancer treatment. This study aimed to develop novel humanized ROR1 monoclonal antibodies and investigate their anti-tumor effects. METHODS: ROR1 expression in tumor tissues and cell lines was analyzed by immunohistochemistry and flow cytometry. Antibodies from mouse hybridomas were humanized by the complementarity-determining region (CDR) grafting technique. Surface plasmon resonance spectroscopy, ELISA assay and flow cytometry were employed to characterize humanized antibodies. In vitro cellular assay and in vivo mouse experiment were conducted to comprehensively evaluate anti-tumor activity of these antibodies. RESULTS: ROR1 exhibited dramatically higher expression in lung adenocarcinoma, liver cancer and breast cancer, and targeting ROR1 by short-hairpin RNAs significantly inhibited proliferation and migration of cancer cells. Two humanized ROR1 monoclonal antibodies were successfully developed, named h1B8 and h6D4, with high specificity and affinity to ROR1 protein. Moreover, these two antibodies effectively suppressed tumor growth in the lung cancer xenograft mouse model, c-Myc/Alb-cre liver cancer transgenic mouse model and MMTV-PyMT breast cancer mouse model. CONCLUSIONS: Two humanized monoclonal antibodies targeting ROR1, h1B8 and h6D4, were successfully developed and exhibited remarkable anti-tumor activity in vivo.


Asunto(s)
Anticuerpos Monoclonales Humanizados , Proliferación Celular , Receptores Huérfanos Similares al Receptor Tirosina Quinasa , Ensayos Antitumor por Modelo de Xenoinjerto , Receptores Huérfanos Similares al Receptor Tirosina Quinasa/metabolismo , Receptores Huérfanos Similares al Receptor Tirosina Quinasa/antagonistas & inhibidores , Receptores Huérfanos Similares al Receptor Tirosina Quinasa/inmunología , Animales , Humanos , Ratones , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Anticuerpos Monoclonales Humanizados/farmacología , Anticuerpos Monoclonales Humanizados/uso terapéutico , Femenino , Movimiento Celular/efectos de los fármacos , Neoplasias/tratamiento farmacológico , Neoplasias/inmunología , Neoplasias/patología , Neoplasias/terapia , Neoplasias/metabolismo , Ratones Transgénicos , Modelos Animales de Enfermedad , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/patología , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/inmunología
15.
Funct Integr Genomics ; 24(5): 173, 2024 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-39320434

RESUMEN

Septic cardiomyopathy is a secondary myocardial injury caused by sepsis. N6-methyl-adenosine (m6A) modification is involved in the pathological progression of septic cardiomyopathy; however, the pathological mechanism remains unclear. In this study, we identified the overall m6A modification pattern in septic myocardial injury and determined its potential interactions with differentially expressed genes (DEGs). A sepsis mouse model exhibiting septic symptoms and myocardial tissue damage was induced by lipopolysaccharide (LPS). LPS-induced septic myocardial tissues and control myocardial tissues were subjected to methylated RNA immunoprecipitation sequencing and RNA sequencing to screen for differentially expressed m6A peaks and DEGs. We identified 859 significantly m6A-modified genes in septic myocardial tissues, including 432 upregulated and 427 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to explore the biological importance of differentially expressed m6A methylated genes and DEGs. Differentially expressed m6A methylated genes were enriched in immune- and inflammation-related pathways. Conjoint analysis revealed co-expression of differentially expressed m6A genes and DEGs, including genes that were upregulated or downregulated and those showing opposite trends. High expression of m6A-related genes (WTAP and IGF2BP2), interleukin-17, and interleukin-17 pathway-related genes (MAPK11 and TRAF3IP2) was verified using reverse transcription-quantitative PCR. We confirmed the presence of m6A modification of the transcriptome and m6A-mediated gene expression in septic myocardial tissues.


Asunto(s)
Adenosina , Miocardio , Sepsis , Animales , Ratones , Sepsis/genética , Sepsis/metabolismo , Miocardio/metabolismo , Miocardio/patología , Metilación , Adenosina/metabolismo , Adenosina/análogos & derivados , Masculino , Cardiomiopatías/genética , Cardiomiopatías/metabolismo , Transcriptoma , Ratones Endogámicos C57BL , Lipopolisacáridos
16.
Biochem Biophys Res Commun ; 690: 149284, 2024 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-38006801

RESUMEN

The inhibition of BRD4 bromodomain is an effective therapeutic strategy for a variety of diseases in which BRD4 are implicated. Herein, we identified a small-molecule BRD4 inhibitor hit named compound 3 using high-throughput screening. The 1.6 Å resolution co-crystal structure confirmed that the compound occupies the KAc recognition pockets of BRD4 by forming key hydrogen bonds with Asn140 and engaging in hydrophobic interactions, thus impedes the binding of acetylated lysine to BRD4. These findings suggest compound 3 can be a lead compound to develop a structurally novel BRD4 inhibitors.


Asunto(s)
Proteínas de Ciclo Celular , Proteínas Nucleares , Proteínas Nucleares/metabolismo , Proteínas de Ciclo Celular/metabolismo , Factores de Transcripción/metabolismo , Ensayos Analíticos de Alto Rendimiento , Dominios Proteicos , Relación Estructura-Actividad
17.
Biochem Biophys Res Commun ; 690: 149285, 2024 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-37995454

RESUMEN

Multidrug-resistant Pseudomonas aeruginosa is a common pathogen that causes topical infections following burn injuries. Antimicrobial photodynamic therapy (aPDT) has emerged as a promising approach for treating antibiotic-resistant bacterial infections. The objective of this study was to evaluate the aPDT efficacy of aloe-emodin (AE), which is a photosensitizer extracted from traditional Chinese herbs, on antibiotic-sensitive and antibiotic-resistant P. aeruginosa in vitro. In this study, we confirmed the effectiveness of AE-mediated aPDT against both standard and MDR P. aeruginosa, explored the effects of irradiation time and AE concentration on bacterial survival in AE-mediated aPDT, and observed the structural damage of P. aeruginosa by using transmission electron microscope. Our results showed that neither AE nor light irradiation alone caused cytotoxic effects on P. aeruginosa. However, AE-mediated aPDT effectively inactivated both antibiotic-sensitive and antibiotic-resistant P. aeruginosa. The transmission electron microscope investigation showed that aPDT mediated by AE primarily caused damage to the cytoplasm and cell membrane. Our findings suggest that AE is a photosensitizer in the aPDT of MDR P. aeruginosa-caused topical infections following burn injuries. Future investigations will concentrate on the safety and efficacy of AE-mediated aPDT in animal models and clinical trials.


Asunto(s)
Aloe , Antiinfecciosos , Quemaduras , Emodina , Fotoquimioterapia , Animales , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Pseudomonas aeruginosa , Fármacos Fotosensibilizantes/farmacología , Fármacos Fotosensibilizantes/uso terapéutico , Fármacos Fotosensibilizantes/química , Emodina/farmacología , Fotoquimioterapia/métodos , Antiinfecciosos/farmacología , Quemaduras/tratamiento farmacológico
18.
Small ; : e2406179, 2024 Sep 02.
Artículo en Inglés | MEDLINE | ID: mdl-39221682

RESUMEN

For BixSb2- xTe3 (BST) in thermoelectric field, the element ratio is easily influenced by the chemical environment, deviating from the stoichiometric ratio and giving rise to various intrinsic defects. In P-type polycrystalline BST, SbTe and BiTe are the primary forms of defects. Defect engineering is a crucial strategy for optimizing the electrical transport performance of Bi2Te3-based materials, but achieving synchronous improvement of thermal performance is challenging. In this study, mesoporous SiO2 is utilized to successfully mitigate the adverse impacts of vacancy defects, resulting in an enhancement of the electrical transport performance and a pronounced reduction in thermal conductivity. Crystal and the microstructure of the continuous modulation contribute to the effective phonon-electronic decoupling. Ultimately, the peak zT of Bi0.4Sb1.6Te3/0.8 wt% SiO2 (with a pore size of 4 nm) nanocomposites reaches as high as 1.5 at 348 K, and a thermoelectric conversion efficiency of 6.6% is achieved at ΔT = 222.7 K. These results present exciting possibilities for the realization of defect regulation in porous materials and hold reference significance for other material systems.

19.
Brief Bioinform ; 23(3)2022 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-35368074

RESUMEN

Computational methods have been widely applied to resolve various core issues in drug discovery, such as molecular property prediction. In recent years, a data-driven computational method-deep learning had achieved a number of impressive successes in various domains. In drug discovery, graph neural networks (GNNs) take molecular graph data as input and learn graph-level representations in non-Euclidean space. An enormous amount of well-performed GNNs have been proposed for molecular graph learning. Meanwhile, efficient use of molecular data during training process, however, has not been paid enough attention. Curriculum learning (CL) is proposed as a training strategy by rearranging training queue based on calculated samples' difficulties, yet the effectiveness of CL method has not been determined in molecular graph learning. In this study, inspired by chemical domain knowledge and task prior information, we proposed a novel CL-based training strategy to improve the training efficiency of molecular graph learning, called CurrMG. Consisting of a difficulty measurer and a training scheduler, CurrMG is designed as a plug-and-play module, which is model-independent and easy-to-use on molecular data. Extensive experiments demonstrated that molecular graph learning models could benefit from CurrMG and gain noticeable improvement on five GNN models and eight molecular property prediction tasks (overall improvement is 4.08%). We further observed CurrMG's encouraging potential in resource-constrained molecular property prediction. These results indicate that CurrMG can be used as a reliable and efficient training strategy for molecular graph learning. Availability: The source code is available in https://github.com/gu-yaowen/CurrMG.


Asunto(s)
Redes Neurales de la Computación , Programas Informáticos , Curriculum , Descubrimiento de Drogas , Modelos Moleculares
20.
J Transl Med ; 22(1): 302, 2024 03 24.
Artículo en Inglés | MEDLINE | ID: mdl-38521921

RESUMEN

BACKGROUND: Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by fluctuating muscle weakness. Despite the availability of established therapies, the management of MG symptoms remains suboptimal, partially attributed to lack of efficacy or intolerable side-effects. Therefore, new effective drugs are warranted for treatment of MG. METHODS: By employing an analytical framework that combines Mendelian randomization (MR) and colocalization analysis, we estimate the causal effects of blood druggable expression quantitative trait loci (eQTLs) and protein quantitative trait loci (pQTLs) on the susceptibility of MG. We subsequently investigated whether potential genetic effects exhibit cell-type specificity by utilizing genetic colocalization analysis to assess the interplay between immune-cell-specific eQTLs and MG risk. RESULTS: We identified significant MR results for four genes (CDC42BPB, CD226, PRSS36, and TNFSF12) using cis-eQTL genetic instruments and three proteins (CTSH, PRSS8, and CPN2) using cis-pQTL genetic instruments. Six of these loci demonstrated evidence of colocalization with MG susceptibility (posterior probability > 0.80). We next undertook genetic colocalization to investigate cell-type-specific effects at these loci. Notably, we identified robust evidence of colocalization, with a posterior probability of 0.854, linking CTSH expression in TH2 cells and MG risk. CONCLUSIONS: This study provides crucial insights into the genetic and molecular factors associated with MG susceptibility, singling out CTSH as a potential candidate for in-depth investigation and clinical consideration. It additionally sheds light on the immune-cell regulatory mechanisms related to the disease. However, further research is imperative to validate these targets and evaluate their feasibility for drug development.


Asunto(s)
Predisposición Genética a la Enfermedad , Miastenia Gravis , Humanos , Multiómica , Estudio de Asociación del Genoma Completo , Miastenia Gravis/genética , Sitios de Carácter Cuantitativo/genética , Polimorfismo de Nucleótido Simple/genética
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