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1.
Brief Bioinform ; 25(1)2023 11 22.
Artículo en Inglés | MEDLINE | ID: mdl-38180830

RESUMEN

2'-O-methylation (2OM) is the most common post-transcriptional modification of RNA. It plays a crucial role in RNA splicing, RNA stability and innate immunity. Despite advances in high-throughput detection, the chemical stability of 2OM makes it difficult to detect and map in messenger RNA. Therefore, bioinformatics tools have been developed using machine learning (ML) algorithms to identify 2OM sites. These tools have made significant progress, but their performances remain unsatisfactory and need further improvement. In this study, we introduced H2Opred, a novel hybrid deep learning (HDL) model for accurately identifying 2OM sites in human RNA. Notably, this is the first application of HDL in developing four nucleotide-specific models [adenine (A2OM), cytosine (C2OM), guanine (G2OM) and uracil (U2OM)] as well as a generic model (N2OM). H2Opred incorporated both stacked 1D convolutional neural network (1D-CNN) blocks and stacked attention-based bidirectional gated recurrent unit (Bi-GRU-Att) blocks. 1D-CNN blocks learned effective feature representations from 14 conventional descriptors, while Bi-GRU-Att blocks learned feature representations from five natural language processing-based embeddings extracted from RNA sequences. H2Opred integrated these feature representations to make the final prediction. Rigorous cross-validation analysis demonstrated that H2Opred consistently outperforms conventional ML-based single-feature models on five different datasets. Moreover, the generic model of H2Opred demonstrated a remarkable performance on both training and testing datasets, significantly outperforming the existing predictor and other four nucleotide-specific H2Opred models. To enhance accessibility and usability, we have deployed a user-friendly web server for H2Opred, accessible at https://balalab-skku.org/H2Opred/. This platform will serve as an invaluable tool for accurately predicting 2OM sites within human RNA, thereby facilitating broader applications in relevant research endeavors.


Asunto(s)
Aprendizaje Profundo , ARN , Humanos , ARN/genética , Secuencia de Bases , Nucleótidos , Metilación
2.
BMC Health Serv Res ; 22(1): 1321, 2022 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-36335361

RESUMEN

BACKGROUND: Public reporting has been considered effective in reducing health care costs by mitigating information asymmetry in the market as payers have incorporated publicly available information mandates into pay-for-performance programs and value-based purchasing. Therefore, hospitals have faced increasing pressures to provide price transparency. Despite the widespread promotion of healthcare transparency, the effectiveness of public reporting has not yet been sufficiently understood. This study analyzed the impact of transparency policy and competition on hospital costs by taking the state operations of all-payer claims databases (APCDs) as a case of interest. METHODS: We employed a fixed-effects regression, which allows the generation of hospital-specific effects, in accordance with the suggestion by the Hausman test. The study samples comprise nonprofit and for-profit general acute care hospitals in the United States for 2011-2017. The finalized dataset ranges from 3547 observations in 2011 to 3405 observations in 2015 after removing missing values. RESULTS: We found that hospitals in the states with APCDs tend to bear higher average operating expenses than those without APCDs, which may indicate that states maintaining higher healthcare expenditures are more attentive to a price transparency initiative and tend to adopt APCDs. With regard to competition, the results showed that weak market competition is significantly associated with higher operating costs, supporting the traditional competition theory. However, the combined effect of APCDs and competition did not indicate a significant association with operating expenses. Further investigation showed a continued tendency for a weak intensity of competition to be linked to lower hospital operating costs in states without APCDs. For those located in non-APCD adopted states, market consolidation helped hospitals coordinate care more effectively, economize operating costs, and enjoy economies of scale due to their large size. Similar trends did not appear in APCD-adopted states except for in 2015. CONCLUSIONS: This study observed limited evidence of the impact of APCDs and market competition. Our findings suggest that states need to make multifaceted efforts to contain hospital costs, not solely depending on the rollout of cost information or market competition. Market concentration may lead to coordinated care or cost economization in some cases. Still, the existing literature also demonstrates some potentially harmful impacts of increased concentration in the healthcare market, such as inefficient use of resources, unilateral market power, and deterrence of innovation. The introduction of a price transparency tool may require additional policy actions that take market competition into consideration.


Asunto(s)
Costos de Hospital , Reembolso de Incentivo , Estados Unidos , Humanos , Gastos en Salud , Bases de Datos Factuales , Hospitales
3.
Int J Mol Sci ; 23(15)2022 Aug 03.
Artículo en Inglés | MEDLINE | ID: mdl-35955780

RESUMEN

HDAC6 is overexpressed in ovarian cancer and is known to be correlated with tumorigenesis. Accordingly, ACY-241, a selective HDAC6 inhibitor, is currently under clinical trial and has been tested in combination with various drugs. HDAC8, another member of the HDAC family, has recently gained attention as a novel target for cancer therapy. Here, we evaluated the synergistic anticancer effects of PCI-34051 and ACY-241 in ovarian cancer. Among various ovarian cancer cells, PCI-34051 effectively suppresses cell proliferation in wild-type p53 ovarian cancer cells compared with mutant p53 ovarian cancer cells. In ovarian cancer cells harboring wild-type p53, PCI-34051 in combination with ACY-241 synergistically represses cell proliferation, enhances apoptosis, and suppresses cell migration. The expression of pro-apoptotic proteins is synergistically upregulated, whereas the expressions of anti-apoptotic proteins and metastasis-associated proteins are significantly downregulated in combination treatment. Furthermore, the level of acetyl-p53 at K381 is synergistically upregulated upon combination treatment. Overall, co-inhibition of HDAC6 and HDAC8 through selective inhibitors synergistically suppresses cancer cell proliferation and metastasis in p53 wild-type ovarian cancer cells. These results suggest a novel approach to treating ovarian cancer patients and the therapeutic potential in developing HDAC6/8 dual inhibitors.


Asunto(s)
Neoplasias Ováricas , Intervención Coronaria Percutánea , Línea Celular Tumoral , Femenino , Histona Desacetilasa 6/metabolismo , Inhibidores de Histona Desacetilasas/farmacología , Inhibidores de Histona Desacetilasas/uso terapéutico , Histona Desacetilasas/genética , Histona Desacetilasas/metabolismo , Humanos , Ácidos Hidroxámicos/farmacología , Indoles , Neoplasias Ováricas/tratamiento farmacológico , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Proteína p53 Supresora de Tumor/genética
4.
J Korean Med Sci ; 36(8): e58, 2021 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-33650336

RESUMEN

BACKGROUND: Human breast milk (HBM) contains optimal nutrients for infant growth. Probiotics are used to prevent disease and, when taken by the mother, they may affect infant microbiome as well as HBM. However, few studies have specifically investigated the effect of probiotic intake by the mother on HBM and infant microbiota at genus/species level. Therefore, we present a comprehensive analysis of paired HBM and infant feces (IF) microbiome samples before and after probiotic intake by HBM-producing mothers. METHODS: Lactating mothers were administered with Lactobacillus rhamnosus (n = 9) or Saccharomyces boulardii capsules (n = 9), for 2 months; or no probiotic (n = 7). Paired HBM and IF samples were collected before and after treatment and analyzed by next-generation sequencing. RESULTS: Forty-three HBM and 49 IF samples were collected and sequenced. Overall, in 43 HBM samples, 1,190 microbial species belonging to 684 genera, 245 families, 117 orders, and 56 classes were detected. In 49 IF samples, 372 microbial species belonging to 195 genera, 79 families, 42 orders, and 18 classes were identified. Eight of 20 most abundant genera in both HBM and IF samples overlapped: Streptococcus (14.42%), Lactobacillus, Staphylococcus, and Veillonella, which were highly abundant in the HBM samples; and Bifidobacterium (27.397%), Bacteroides, and Faecalibacterium, which were highly abundant in the IF samples. Several major bacterial genera and species were detected in the HBM and IF samples after probiotic treatment, illustrating complex changes in the microbiomes upon treatment. CONCLUSION: This is the first Korean microbiome study in which the effect of different probiotic intake by the mother on the microbiota in HBM and IF samples was investigated. This study provides a cornerstone to further the understanding of the effect of probiotics on the mother and infant microbiomes.


Asunto(s)
Heces/microbiología , Microbioma Gastrointestinal , Leche Humana/microbiología , Probióticos/administración & dosificación , Adulto , Bacterias/genética , Bacterias/aislamiento & purificación , Lactancia Materna , Análisis por Conglomerados , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Lactante , Lacticaseibacillus rhamnosus/fisiología , Persona de Mediana Edad , Madres , ARN Ribosómico 16S/química , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/metabolismo , Saccharomyces boulardii/fisiología , Análisis de Secuencia de ADN , Adulto Joven
5.
Biochem Biophys Res Commun ; 528(3): 478-484, 2020 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-32507602

RESUMEN

BACKGROUND: Cell division is regulated by protein kinase B (PKB)-mediated FCH domain only 1 (FCHO1) phosphorylation. METHODS: FCHO1560-571, a synthetic water-soluble peptide, was generated from the PKB substrate motif 560PPRRLRSRKVSC571 found in the human FCHO1 protein. RESULTS: In this study, we found that in vitro FCHO1560-571 inhibits cell proliferation via PKB/ERK/SMAD4 pathways in KRAS-mutated A549 lung cancer cells. In addition, FCHO1560-571, at effective doses of 15 and 30 mg/kg, significantly suppressed tumor growth and decreased the size and weight of tumors in A549-xenograft mice. CONCLUSION: These results suggest that the FCHO1560-571 peptide could be a potential therapy for lung cancer.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Neoplasias Pulmonares/tratamiento farmacológico , Proteínas de la Membrana/farmacología , Células A549 , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Animales , Proteína Quinasa CDC2/antagonistas & inhibidores , Carcinoma de Pulmón de Células no Pequeñas/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/patología , Proliferación Celular/efectos de los fármacos , Progresión de la Enfermedad , Humanos , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patología , Masculino , Proteínas de la Membrana/química , Proteínas de la Membrana/genética , Ratones , Ratones Endogámicos BALB C , Ratones Desnudos , Fragmentos de Péptidos/química , Fragmentos de Péptidos/genética , Fragmentos de Péptidos/farmacología , Proteínas Proto-Oncogénicas c-akt/antagonistas & inhibidores , Proteínas Proto-Oncogénicas c-akt/metabolismo , Proteína Smad4/metabolismo , Especificidad por Sustrato , Ensayos Antitumor por Modelo de Xenoinjerto
6.
J Insect Sci ; 20(5)2020 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-32976575

RESUMEN

Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.


Asunto(s)
Escarabajos/genética , Genoma de los Insectos , Genoma Mitocondrial , Animales , Filogenia
7.
Int J Mol Sci ; 21(23)2020 Nov 26.
Artículo en Inglés | MEDLINE | ID: mdl-33256086

RESUMEN

Glioblastoma is a type of aggressive brain tumor that grows very fast and evades surrounding normal brain, lead to treatment failure. Glioblastomas are associated with Akt activation due to somatic alterations in PI3 kinase/Akt pathway and/or PTEN tumor suppressor. Sodium meta-arsenite, KML001 is an orally bioavailable, water-soluble, and trivalent arsenical and it shows antitumoral effects in several solid tumor cells via inhibiting oncogenic signaling, including Akt and MAPK. Here, we evaluated the effect of sodium meta-arsenite, KML001, on the growth of human glioblastoma cell lines with different PTEN expression status and Akt activation, including PTEN-deficient cells (U87-MG and U251) and PTEN-positive cells (LN229). The growth-inhibitory effect of KML001 was stronger in U87-MG and U251 cells, which exhibited higher Akt activity than LN229 cells. KML001 deactivated Akt and decreased its protein levels via proteasomal degradation in U87-MG cells. KML001 upregulated mutant PTEN levels via inhibition of its proteasomal degradation. KML001 inhibited cell growth more effectively in active Akt-overexpressing LN229 cells than in mock-expressing LN229 cells. Consistent with these results, KML001 sensitized PTEN-deficient cells more strongly to growth inhibition than it did PTEN-positive cells in prostate and breast cancer cell lines. Finally, we illustrated in vivo anti-tumor effects of KML001 using an intracranial xenograft mouse model. These results suggest that KML001 could be an effective chemotherapeutic drug for the treatment of glioblastoma cancer patients with higher Akt activity and PTEN loss.


Asunto(s)
Antineoplásicos/uso terapéutico , Arsenitos/uso terapéutico , Neoplasias Encefálicas/tratamiento farmacológico , Neoplasias Encefálicas/enzimología , Glioblastoma/tratamiento farmacológico , Glioblastoma/enzimología , Proteínas Proto-Oncogénicas c-akt/metabolismo , Compuestos de Sodio/uso terapéutico , Animales , Antineoplásicos/farmacología , Apoptosis/efectos de los fármacos , Arsenitos/farmacología , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/patología , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Regulación hacia Abajo/efectos de los fármacos , Activación Enzimática/efectos de los fármacos , Femenino , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Glioblastoma/genética , Glioblastoma/patología , Humanos , Ratones Endogámicos BALB C , Ratones Desnudos , Fosfohidrolasa PTEN/metabolismo , Compuestos de Sodio/farmacología , Regulación hacia Arriba/efectos de los fármacos , Ensayos Antitumor por Modelo de Xenoinjerto
8.
Lab Invest ; 99(8): 1157-1172, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-30700846

RESUMEN

Doxorubicin is a widely used DNA damage-inducing anti-cancer drug. However, its use is limited by its dose-dependent side effects, such as cardiac toxicity. Cholesterol-lowering statin drugs increase the efficacy of some anti-cancer drugs. Cholesterol is important for cell growth and a critical component of lipid rafts, which are plasma membrane microdomains important for cell signaling. 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMG-CR) is a critical enzyme in cholesterol synthesis. Here, we show that doxorubicin downregulated HMG-CR protein levels and thus reduced levels of cholesterol and lipid rafts. Cholesterol addition attenuated doxorubicin-induced cell death, and cholesterol depletion enhanced it. Reduction of HMG-CR activity by simvastatin, a statin that acts as an HMG-CR inhibitor, or by siRNA-mediated HMG-CR knockdown enhanced doxorubicin cytotoxicity. Doxorubicin-induced HMG-CR downregulation was associated with inactivation of the EGFR-Src pathway. Furthermore, a high-cholesterol-diet attenuated the anti-cancer activity of doxorubicin in a tumor xenograft mouse model. In a multivulva model of Caenorhabditis elegans expressing an active-EGFR mutant, doxorubicin decreased hyperplasia more efficiently in the absence than in the presence of cholesterol. These data indicate that EGFR/Src/HMG-CR is a new pathway mediating doxorubicin-induced cell death and that cholesterol control could be combined with doxorubicin treatment to enhance efficacy and thus reduce side effects.


Asunto(s)
Antineoplásicos/farmacología , Doxorrubicina/farmacología , Receptores ErbB/metabolismo , Hidroximetilglutaril-CoA Reductasas/metabolismo , Transducción de Señal/efectos de los fármacos , Familia-src Quinasas/metabolismo , Animales , Caenorhabditis elegans , Línea Celular Tumoral , Regulación hacia Abajo/efectos de los fármacos , Humanos , Hidroximetilglutaril-CoA Reductasas/genética , Masculino , Ratones , Ratones Endogámicos BALB C , Ratones Desnudos , Ensayos Antitumor por Modelo de Xenoinjerto
9.
Int J Mol Sci ; 20(19)2019 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-31547213

RESUMEN

Symplocarpus, a skunk cabbage genus, includes two sister groups, which are drastically different in life history traits and thermogenesis, as follows: The nonthermogenic summer flowering S. nipponicus and thermogenic early spring flowering S. renifolius. Although the molecular basis of thermogenesis and complete chloroplast genome (plastome) of thermogenic S. renifolius have been well characterized, very little is known for that of S. nipponicus. We sequenced the complete plastomes of S. nipponicus sampled from Japan and Korea and compared them with that of S. renifolius sampled from Korea. The nonthermogenic S. nipponicus plastomes from Japan and Korea had 158,322 and 158,508 base pairs, respectively, which were slightly shorter than the thermogenic plastome of S. renifolius. No structural or content rearrangements between the species pairs were found. Six highly variable noncoding regions (psbC/trnS, petA/psbJ, trnS/trnG, trnC/petN, ycf4/cemA, and rpl3/rpl22) were identified between S. nipponicus and S. renifolius and 14 hot-spot regions were also identified at the subfamily level. We found a similar total number of SSR (simple sequence repeat) motifs in two accessions of S. nipponicus sampled from Japan and Korea. Phylogenetic analysis supported the basal position of subfamily Orontioideae and the monophyly of genus Symplocarpus, and also revealed an unexpected evolutionary relationship between S. nipponicus and S. renifolius.


Asunto(s)
Araceae , ADN de Plantas/genética , Genoma de Plastidios , Filogenia , Araceae/clasificación , Araceae/genética , Japón , Corea (Geográfico) , Especificidad de la Especie
10.
Biochem Biophys Res Commun ; 495(1): 594-600, 2018 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-29128360

RESUMEN

Autophagy is a biological recycling process via the self-digestion of organelles, proteins, and lipids for energy-consuming differentiation and homeostasis. The Golgi serves as a donor of the double-membraned phagophore for autophagosome assembly. In addition, recent studies have demonstrated that pulmonary and hepatic fibrosis is accompanied by autophagy. However, the relationships among Golgi function, autophagy, and fibrosis are unclear. Here, we show that the deletion of GOLGA2, encoding a cis-Golgi protein, induces autophagy with Golgi disruption. The induction of autophagy leads to fibrosis along with the reduction of subcellular lipid storage (lipid droplets and lamellar bodies) by autophagy in the lung and liver. GOLGA2 knockout mice clearly demonstrated fibrosis features such as autophagy-activated cells, densely packed hepatocytes, increase of alveolar macrophages, and decrease of alveolar surfactant lipids (dipalmitoylphosphatidylcholine). Therefore, we confirmed the associations among Golgi function, fibrosis, and autophagy. Moreover, GOLGA2 knockout mice may be a potentially valuable animal model for studying autophagy-induced fibrosis.


Asunto(s)
Autoantígenos/metabolismo , Autofagia , Cirrosis Hepática/metabolismo , Hígado/metabolismo , Pulmón/metabolismo , Proteínas de la Membrana/metabolismo , Fibrosis Pulmonar/metabolismo , Animales , Gotas Lipídicas/metabolismo , Hígado/patología , Cirrosis Hepática/patología , Pulmón/patología , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Fibrosis Pulmonar/patología
11.
Cell Commun Signal ; 16(1): 29, 2018 06 11.
Artículo en Inglés | MEDLINE | ID: mdl-29890989

RESUMEN

TRIO and F-actin-binding protein (TRIOBP) also referred to as Tara, was originally isolated as a cytoskeleton remodeling protein. TRIOBP-1 is important for regulating F-actin filament reorganization. TRIOBP variants are broadly classified as variant-1 or - 4 and do not share exons. TRIOBP variant-5 contains all exons. Earlier studies indicated that TRIOBP-4/5 mutation is a pivotal element of autosomal recessive nonsyndromic hearing loss. However, recent studies provide clues that TRIOBP variants are associated with other human diseases including cancer and brain diseases. In this review, recent functional studies focusing on TRIOBP variants and its possible disease models are described.


Asunto(s)
Enfermedad , Proteínas de Microfilamentos/metabolismo , Encéfalo/metabolismo , Variación Genética , Pérdida Auditiva/metabolismo , Humanos , Proteínas de Microfilamentos/genética , Neoplasias/metabolismo
12.
Cancer Cell Int ; 17: 87, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-29033691

RESUMEN

BACKGROUND: Glioblastoma is the most common and aggressive brain tumor associated with a poor prognosis. Plant homeodomain finger protein 20 (PHF20) is highly expressed in primary human gliomas and its expression is associated with tumor grade. However, the molecular mechanism by which PHF20 regulates glioblastoma remains poorly understood. METHODS: Genome wide gene expression analysis was performed to identify differentially expressed genes (DEGs) in U87 cells with PHF20 gene knockdown. Gene ontology (GO) and pathway enrichment analyses were performed to investigate the functions and pathways of DEGs. Pathway-net and signal-net analyses were conducted to identify the key genes and pathways related to PHF20. RESULTS: Expression of 540 genes, including FEN1 and CCL3, were significantly altered upon PHF20 gene silencing. GO analysis results showed that DEGs were significantly enriched in small molecule metabolic and apoptotic processes. Pathway analysis indicated that DEGs were mainly involved in cancer and metabolic pathways. The MAPK, apoptosis and p53 signaling pathways were identified as the hub pathways in the pathway network, while PLCB1, NRAS and PIK3 s were hub genes in the signaling network. CONCLUSIONS: Our findings indicated that PHF20 is a pivotal upstream regulator. It affects the occurrence and development of glioma by regulating a series of tumor-related genes, such as FEN1, CCL3, PLCB1, NRAS and PIK3s, and activation of apoptosis signaling pathways. Therefore, PHF20 might be a novel biomarker for early diagnosis, and a potential target for glioblastoma therapies.

13.
Korean J Physiol Pharmacol ; 21(3): 279-286, 2017 May.
Artículo en Inglés | MEDLINE | ID: mdl-28461769

RESUMEN

The root bark extract of Aralia taibaiensis is used traditionally for the treatment of diabetes mellitus in China. The total saponin extracted from Aralia Taibaiensis (sAT) has effective combined antihyperglycemic and hypolipidemic activities in experimental type 2 diabetic rats. However, the active compounds have not yet been fully investigated. In the present study, we examined effects of twelve triterpenoid saponins on AMP-activated protein kinase (AMPK) activation, and found that compound 28-O-ß-D-glucopyranosyl ester (AT12) significantly increased phosphorylation of AMPK and Acetyl-CoA carboxylase (ACC). AT12 effectively decreased blood glucose, triglyceride (TG), free fatty acid (FFA) and low density lipoprotein-cholesterol (LDL-C) levels in the rat model of type 2 diabetes mellitus (T2DM). The mechanism by which AT12 activated AMPK was subsequently investigated. Intracellular ATP level and oxygen consumption were significantly reduced by AT12 treatment. The findings suggested AT12 was a novel AMPK activator, and could be useful for the treatment of metabolic diseases.

14.
Genome Res ; 23(7): 1109-17, 2013 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-23737375

RESUMEN

Microsatellite instability (MSI) is a critical mechanism that drives genetic aberrations in cancer. To identify the entire MS mutation, we performed the first comprehensive genome- and transcriptome-wide analyses of mutations associated with MSI in Korean gastric cancer cell lines and primary tissues. We identified 18,377 MS mutations of five or more repeat nucleotides in coding sequences and untranslated regions of genes, and discovered 139 individual genes whose expression was down-regulated in association with UTR MS mutation. In addition, we found that 90.5% of MS mutations with deletions in gene regions occurred in UTRs. This analysis emphasizes the genetic diversity of MSI-H gastric tumors and provides clues to the mechanistic basis of instability in microsatellite unstable gastric cancers.


Asunto(s)
Pueblo Asiatico/genética , Estudio de Asociación del Genoma Completo , Inestabilidad de Microsatélites , Mutación , Neoplasias Gástricas/genética , Transcriptoma , Línea Celular Tumoral , Mutación del Sistema de Lectura , Regulación Neoplásica de la Expresión Génica , Frecuencia de los Genes , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Repeticiones de Microsatélite , Procesamiento Postranscripcional del ARN , Estabilidad del ARN , República de Corea , Eliminación de Secuencia , Regiones no Traducidas
15.
Nature ; 464(7287): 367-73, 2010 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-20237561

RESUMEN

Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.


Asunto(s)
Cromosomas Fúngicos/genética , Fusarium/genética , Fusarium/patogenicidad , Genoma Fúngico/genética , Genómica , Evolución Molecular , Fusarium/clasificación , Interacciones Huésped-Parásitos/genética , Familia de Multigenes/genética , Fenotipo , Filogenia , Proteoma/genética , Análisis de Secuencia de ADN , Sintenía/genética , Virulencia/genética
16.
Chemotherapy ; 61(6): 304-12, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27100100

RESUMEN

BACKGROUND: Mitochondria have emerged as a major target for anticancer therapy because of their critical role in cancer cell survival. Our preliminary works have suggested that dihydroergotamine tartrate (DHE), an antimigraine agent, may have effects on mitochondria. METHODS: We examined the effect of DHE on the survival of several lung cancer cells and confirmed that DHE suppressed diverse lung cancer cell growth effectively. To confirm whether such effects of DHE would be associated with mitochondria, A549 cells were employed for the evaluation of several important parameters, such as membrane potential, reactive oxygen species (ROS) generation, apoptosis, ATP production and autophagy. RESULTS: DHE decreased membrane permeability, increased ROS generation as well as apoptosis, and disturbed ATP production. Eventually, mitophagy was activated for damaged mitochondria. CONCLUSION: Taken together, our findings demonstrate that DHE induces lung cancer cell death by the induction of apoptosis and mitophagy, thus suggesting that DHE can be developed as an anti-lung cancer therapeutic agent.


Asunto(s)
Apoptosis/efectos de los fármacos , Dihidroergotamina/farmacología , Mitofagia/efectos de los fármacos , Células A549 , Adenosina Trifosfato/metabolismo , Antineoplásicos/farmacología , Western Blotting , Línea Celular Tumoral , Citometría de Flujo , Humanos , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patología , Potencial de la Membrana Mitocondrial/efectos de los fármacos , Microscopía Electrónica de Transmisión , Microscopía Fluorescente , Mitocondrias/efectos de los fármacos , Mitocondrias/metabolismo , Especies Reactivas de Oxígeno/metabolismo
17.
Nat Genet ; 39(4): 561-5, 2007 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-17353894

RESUMEN

Rapid translation of genome sequences into meaningful biological information hinges on the integration of multiple experimental and informatics methods into a cohesive platform. Despite the explosion in the number of genome sequences available, such a platform does not exist for filamentous fungi. Here we present the development and application of a functional genomics and informatics platform for a model plant pathogenic fungus, Magnaporthe oryzae. In total, we produced 21,070 mutants through large-scale insertional mutagenesis using Agrobacterium tumefaciens-mediated transformation. We used a high-throughput phenotype screening pipeline to detect disruption of seven phenotypes encompassing the fungal life cycle and identified the mutated gene and the nature of mutation for each mutant. Comparative analysis of phenotypes and genotypes of the mutants uncovered 202 new pathogenicity loci. Our findings demonstrate the effectiveness of our platform and provide new insights on the molecular basis of fungal pathogenesis. Our approach promises comprehensive functional genomics in filamentous fungi and beyond.


Asunto(s)
Genoma Fúngico , Magnaporthe/genética , Factores de Virulencia/genética , Factores de Virulencia/fisiología , Agrobacterium tumefaciens/genética , Mapeo Cromosómico , Cromosomas Fúngicos , Genes Fúngicos/fisiología , Genotipo , Modelos Biológicos , Organismos Modificados Genéticamente , Fenotipo , Factores de Virulencia/aislamiento & purificación
18.
PLoS Pathog ; 9(6): e1003350, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23762023

RESUMEN

Because most efforts to understand the molecular mechanisms underpinning fungal pathogenicity have focused on studying the function and role of individual genes, relatively little is known about how transcriptional machineries globally regulate and coordinate the expression of a large group of genes involved in pathogenesis. Using quantitative real-time PCR, we analyzed the expression patterns of 206 transcription factor (TF) genes in the rice blast fungus Magnaporthe oryzae under 32 conditions, including multiple infection-related developmental stages and various abiotic stresses. The resulting data, which are publicly available via an online platform, provided new insights into how these TFs are regulated and potentially work together to control cellular responses to a diverse array of stimuli. High degrees of differential TF expression were observed under the conditions tested. More than 50% of the 206 TF genes were up-regulated during conidiation and/or in conidia. Mutations in ten conidiation-specific TF genes caused defects in conidiation. Expression patterns in planta were similar to those under oxidative stress conditions. Mutants of in planta inducible genes not only exhibited sensitive to oxidative stress but also failed to infect rice. These experimental validations clearly demonstrated the value of TF expression patterns in predicting the function of individual TF genes. The regulatory network of TF genes revealed by this study provides a solid foundation for elucidating how M. oryzae regulates its pathogenesis, development, and stress responses.


Asunto(s)
Proteínas Fúngicas/metabolismo , Regulación Fúngica de la Expresión Génica/fisiología , Magnaporthe/metabolismo , Magnaporthe/patogenicidad , Estrés Oxidativo/fisiología , Factores de Transcripción/metabolismo , Transcripción Genética/fisiología , Proteínas Fúngicas/genética , Perfilación de la Expresión Génica/métodos , Magnaporthe/genética , Mutación , Oryza/microbiología , Enfermedades de las Plantas/microbiología , Factores de Transcripción/genética
19.
J Korean Med Sci ; 30(2): 167-72, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25653488

RESUMEN

The correlation between serum anti-tuberculosis (TB) drug levels and the drug-induced hepatotoxicity (DIH) remains unclear. The purpose of this study was to investigate whether anti-TB DIH is associated with basal serum drug levels. Serum peak levels of isoniazid (INH), rifampicin (RMP), pyrazinamide (PZA), and ethambutol (EMB) were analyzed in blood samples 2 hr after the administration of anti-TB medication. Anti-TB DIH and mild liver function test abnormality were diagnosed on the basis of laboratory and clinical criteria. Serum anti-TB drug levels and other clinical factors were compared between the hepatotoxicity and non-hepatotoxicity groups. A total of 195 TB patients were included in the study, and the data were analyzed retrospectively. Seventeen (8.7%) of the 195 patients showed hepatotoxicity, and the mean aspartate aminotransferase/alanine aminotransferase levels in the hepatotoxicity group were 249/249 IU/L, respectively. Among the 17 patients with hepatotoxicity, 12 showed anti-TB DIH. Ten patients showed PZA-related hepatotoxicity and 2 showed INH- or RMP-related hepatotoxicity. However, intergroup differences in the serum levels of the 4 anti-TB drugs were not statistically significant. Basal serum drug concentration was not associated with the risk anti-TB DIH in patients being treated with the currently recommended doses of first-line anti-TB treatment drugs.


Asunto(s)
Antituberculosos/sangre , Enfermedad Hepática Inducida por Sustancias y Drogas/sangre , Hígado/patología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Alanina Transaminasa/sangre , Antituberculosos/efectos adversos , Antituberculosos/uso terapéutico , Aspartato Aminotransferasas/sangre , Etambutol/efectos adversos , Etambutol/sangre , Etambutol/uso terapéutico , Femenino , Humanos , Isoniazida/efectos adversos , Isoniazida/sangre , Isoniazida/uso terapéutico , Pruebas de Función Hepática , Masculino , Persona de Mediana Edad , Pirazinamida/efectos adversos , Pirazinamida/sangre , Pirazinamida/uso terapéutico , Estudios Retrospectivos , Rifampin/efectos adversos , Rifampin/sangre , Rifampin/uso terapéutico , Tuberculosis Pulmonar/tratamiento farmacológico , Adulto Joven
20.
Diabetologia ; 57(2): 383-91, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24190582

RESUMEN

AIMS/HYPOTHESIS: Genome-wide association studies have revealed an association of the transcription factor ETS variant gene 5 (ETV5) with human obesity. However, its role in glucose homeostasis and energy balance is unknown. METHODS: Etv5 knockout (KO) mice were monitored weekly for body weight (BW) and food intake. Body composition was measured at 8 and 16 weeks of age. Glucose metabolism was studied, and glucose-stimulated insulin secretion was measured in vivo and in vitro. RESULTS: Etv5 KO mice are smaller and leaner, and have a reduced BW and lower fat mass than their wild-type controls on a chow diet. When exposed to a high-fat diet, KO mice are resistant to diet-induced BW gain. Despite a greater insulin sensitivity, KO mice have profoundly impaired glucose tolerance associated with impaired insulin secretion. Morphometric analysis revealed smaller islets and a reduced beta cell size in the pancreatic islets of Etv5 KO mice. Knockdown of ETV5 in an insulin-secreting cell line or beta cells from human donors revealed intact mitochondrial and Ca(2+) channel activity, but reduced insulin exocytosis. CONCLUSION/INTERPRETATION: This work reveals a critical role for ETV5 in specifically regulating insulin secretion both in vitro and in vivo.


Asunto(s)
Péptido C/metabolismo , Proteínas de Unión al ADN/metabolismo , Exocitosis/fisiología , Glucosa/metabolismo , Homeostasis/fisiología , Insulina/metabolismo , Factores de Transcripción/metabolismo , Animales , Composición Corporal , Peso Corporal , Dieta Alta en Grasa , Ingestión de Alimentos , Estudio de Asociación del Genoma Completo , Prueba de Tolerancia a la Glucosa , Resistencia a la Insulina , Secreción de Insulina , Ratones , Ratones Noqueados
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