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In recent years, the function of noncoding RNAs (ncRNAs) as regulatory molecules of cell physiology has begun to be better understood. Advances in viral molecular biology have shown that host ncRNAs, cellular factors, and virus-derived ncRNAs and their interplay are strongly disturbed during viral infections. Nevertheless, the folding of RNA virus genomes has also been identified as a critical factor in regulating canonical and non-canonical functions. Due to the influence of host ncRNAs and the structure of RNA viral genomes, complex molecular and cellular processes in infections are modulated. We propose three main categories to organize the current information about RNA-RNA interactions in some well-known human viruses. The first category shows examples of host ncRNAs associated with the immune response triggered in viral infections. Even though miRNAs introduce a standpoint, they are briefly presented to keep researchers moving forward in uncovering other RNAs. The second category outlines interactions between virus-host ncRNAs, while the third describes how the structure of the RNA viral genome serves as a scaffold for processing virus-derived RNAs. Our grouping may provide a comprehensive framework to classify ncRNA-host-cell interactions for emerging viruses and diseases. In this sense, we introduced them to organize DENV-host-cell interactions.
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Virus del Dengue , Genoma Viral , ARN no Traducido , ARN Viral , Virus del Dengue/genética , Virus del Dengue/fisiología , Humanos , ARN no Traducido/genética , ARN no Traducido/metabolismo , ARN Viral/genética , ARN Viral/metabolismo , Interacciones Huésped-Patógeno/genética , Dengue/virología , MicroARNs/genética , MicroARNs/metabolismo , AnimalesRESUMEN
In recent years, a population of small RNA fragments derived from non-coding RNAs (sfd-RNAs) has gained significant interest due to its functional and structural resemblance to miRNAs, adding another level of complexity to our comprehension of small-RNA-mediated gene regulation. Despite this, scientists need more tools to test the differential expression of sfd-RNAs since the current methods to detect miRNAs may not be directly applied to them. The primary reasons are the lack of accurate small RNA and ncRNA annotation, the multi-mapping read (MMR) placement, and the multicopy nature of ncRNAs in the human genome. To solve these issues, a methodology that allows the detection of differentially expressed sfd-RNAs, including canonical miRNAs, by using an integrated copy-number-corrected ncRNA annotation was implemented. This approach was coupled with sixteen different computational strategies composed of combinations of four aligners and four normalization methods to provide a rank-order of prediction for each differentially expressed sfd-RNA. By systematically addressing the three main problems, we could detect differentially expressed miRNAs and sfd-RNAs in dengue virus-infected human dermal microvascular endothelial cells. Although more biological evaluations are required, two molecular targets of the hsa-mir-103a and hsa-mir-494 (CDK5 and PI3/AKT) appear relevant for dengue virus (DENV) infections. Here, we performed a comprehensive annotation and differential expression analysis, which can be applied in other studies addressing the role of small fragment RNA populations derived from ncRNAs in virus infection.
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RESUMEN La Transición Epitelio-Mesénquima (EMT) es un proceso de diferenciación altamente conservado en vertebrados. Este ocurre en células epiteliales con la activación progresiva de la pérdida de la polaridad, la adquisición de motilidad individual y la capacidad invasiva a otros tejidos. La EMT es un proceso normal durante el desarrollo; no obstante, en condiciones patológicas está relacionada con la inducción de metástasis, lo cual representa una vía alterna al desarrollo de procesos oncogénicos tempranos. Aunque la EMT es activada principalmente por factores de crecimiento, también se puede desencadenar por infecciones de patógenos intracelulares mediante la activación de rutas moleculares inductoras de este proceso. Por lo tanto, una infección bacteriana o viral pueda generar predisposición al desarrollo de tumores. Nuestro interés está enfocado principalmente en caracterizar la relación virus-hospedero, y en el caso de los virus, varios ya se han descrito como inductores de la EMT. En este artículo de revisión se describen el fenómeno de la plasticidad celular y la ocurrencia detallada del proceso de EMT, los patógenos virales reportados como inductores, los mecanismos moleculares usados para ello y las vías de regulación mediante miRNAs. Por último, se discute cómo esta relación virus-hospedero puede explicar la patogénesis de la enfermedad causada por Dengue virus, favoreciendo la identificación de blancos moleculares para terapia, estrategia conocida como Antivirales dirigidos a blancos celulares o HTA (Host-targeting antivirals).
ABSTRACT Epithelial-to-Mesenchymal Transition (EMT) is a highly conserved dedifferentiation process in vertebrates. This process occurs in epithelial cells activating progressive loss of cell polarity, acquisition of individual motility and invasive capacity to other tissues. EMT is a normal process during development process, however, in pathological conditions is related to the induction of metastasis, which represents an alternative path to the development of early oncogenic processes. Although, EMT is mainly activated by growth factors, it can also be triggered by intracellular-pathogen-infections by activating molecular pathways that induce this process. Therefore, a bacterial or viral infection may generate predisposition to the development of tumors. Our interest is mainly focused on characterizing the host-virus relationship, and in the case of viruses, several have already been described as EMT inductors. In this review, phenomenon of cellular plasticity, detailed occurrence of the EMT, viral pathogens reported as inducers, the molecular mechanisms, and the regulatory pathways through miRNAs are described. Finally, we discuss how this host-virus relationship may explain the pathogenesis of the disease caused by Dengue virus, favoring the identification of molecular targets for therapy, a strategy known as Host-Targeting Antivirals (HTA).
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RESUMEN El diseño eficiente de compuestos aprovechando las características estructurales de las moléculas y la búsqueda eficiente de dianas terapéuticas, ha proporcionado herramientas efectivas en la investigación de nuevos tratamientos cuando esta se enfoca en mecanismos celulares de la enfermedad. Los cambios fenotípicos producidos por la interacción in vitro entre molécula-diana, pueden controlarse cuantitativamente mediante imagenología de células vivas. Para garantizar una interacción adecuada, es necesario considerar diferentes elementos cruciales: 1. Las características estructurales y la dinámica molecular del compuesto a evaluar. 2. La relevancia del blanco para la fisiopatología de interés. Sin embargo, el desconocimiento del panorama general en el descubrimiento de fármacos, desde problemáticas estructurales y celulares, ha enlentecido la búsqueda de nuevos tratamientos. Esta revisión descriptiva de tema presenta algunos aspectos estructurales importantes para la caracterización de compuestos como candidatos terapéuticos, y aproximaciones experimentales para desarrollo de sistemas celulares. Los tópicos discutidos se enfocan en la monitorización por imagenología de células vivas y así mismo proporcionamos ejemplos relevantes. La monitorización de efectos fenotípicos producidos por interacciones entre candidato químico y blanco terapéutico en un sistema celular puede favorecer la búsqueda eficiente de moléculas potencialmente terapéuticas.
SUMMARY The efficient compounds' design taking advantage of the molecule's structural characteristics and efficient search for therapeutic targets has provided effective tools for the research of new treatments when this is focused on disease cellular mechanisms. Phenotypic changes produced by in vitro interaction between molecules and targets can be monitored quantitatively by live cell imaging. To guarantee adequate interaction, it is necessary to consider different crucial elements: 1. Structural characteristics and molecular dynamics of the evaluated compound. 2. Target relevance for the concern physiopathology. However, overview's ignorance of the drug discovery, from structural and cellular problems, has slowed the new treatments research. This literature review presents some important structural aspects for compounds' characterization as therapeutic candidates and experimental approaches for cellular systems development. Subjects discussed are focused on live cell imaging and we also provide relevant examples. Phenotypic monitoring of interactions' produced effects between the chemical candidate and therapeutic target in a cellular system can favor the efficient search of potentially therapeutic molecules.
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BACKGROUND Viruses can modulate intracellular signalling pathways to complete their infectious cycle. Among these, the PI3K/Akt pathway allows prolonged survival of infected cells that favours viral replication. GSK3β, a protein kinase downstream of PI3K/Akt, gets inactivated upon activation of the PI3K/Akt pathway, and its association with viral infections has been recently established. In this study, the role of GSK3β during Dengue virus-2 (DENV-2) infection was investigated. METHODS GSK3β participation in the DENV-2 replication process was evaluated with pharmacological and genetic inhibition during early [0-12 h post-infection (hpi)], late (12-24 hpi), and 24 hpi in Huh7 and Vero cells. We assessed the viral and cellular processes by calculating the viral titre in the supernatants, In-Cell Western, western blotting and fluorescence microscopy. RESULTS Phosphorylation of GSK3β-Ser9 was observed at the early stages of infection; neither did treatment with small molecule inhibitors nor pre-treatment prior to viral infection of GSK3β reduce viral titres of the supernatant at these time points. However, a decrease in viral titres was observed in cells infected and treated with the inhibitors much later during viral infection. Consistently, the infected cells at this stage displayed plasma membrane damage. Nonetheless, these effects were not elicited with the use of genetic inhibitors of GSK3β. CONCLUSIONS The results suggest that GSK3β participates at the late stages of the DENV replication cycle, where viral activation may promote apoptosis and release of viral particles.
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Animales , Replicación Viral/fisiología , Virus del Dengue/enzimología , Glucógeno Sintasa Quinasas/antagonistas & inhibidores , Glucógeno Sintasa Quinasas/fisiología , Fosforilación/fisiología , Transducción de Señal , Western Blotting , Apoptosis/fisiología , Aedes/citología , Línea Celular Tumoral , Microscopía FluorescenteRESUMEN
RESUMEN La quinasa dependiente de ciclina 5 (CDK5) regula diversas funciones en neuronas, células endoteliales y epiteliales, entre ellas la dinámica del citoesqueleto. Así mismo, se ha reportado que componentes del citoesqueleto, tales como, filamentos de actina y microtúbulos juegan un rol importante durante la infección por el virus dengue (DENV). El objetivo del presente trabajo fue evaluar por dos métodos, inhibición química y silenciamiento génico, la participación de CDK5 durante la infección por DENV-2. La actividad antiviral de roscovitina fue evaluada usando ensayos de Unidades Formadoras de Placa (PFU). La eficiencia de transfección y el silenciamiento de CDK5, empleando miARNs artificiales, se determinó por citometría de flujo. El efecto sobre la proteína de envoltura viral y elementos del citoesqueleto se evidenció mediante microscopia avanzada de fluorescencia y análisis de imágenes. Roscovitina mostró actividad antiviral en etapas pre y post-infectivas en una forma dependiente de la dosis. El tratamiento con roscovitina y miRCDK5 mostró ser efectivo reduciendo la cantidad de CDK5 en células no infectadas. En células infectadas y transfectadas con miRCDK5, así como tratadas con el inhibidor, se observó una reducción significativa de la proteína de envoltura viral; sin embargo, no se encontró reducción significativa de CDK5. Además, el tratamiento con roscovitina indujo cambios celulares morfológicos evidentes en células infectadas. Los resultados indican la potencial participación de CDK5 durante la infección por DENV-2, posiblemente mediando la traducción proteica o la replicación del genoma viral a través de la regulación de la dinámica del citoesqueleto. Se requieren datos adicionales para esclarecer la mecanística del fenómeno usando métodos alternativos.
ABSTRACT Cyclin-Dependent Kinase 5 (CDK5) regulates several functions in neurons, endothelial, and epithelial cells, including the cytoskeleton dynamics. Likewise, it has been reported that some cytoskeleton elements, such as actin filaments and microtubules, play an essential role during Dengue virus (DENV) infection. This work aimed to evaluate the role of CDK5 during DENV-2 infection by two methods, chemical inhibition, and gene silencing. The antiviral activity of roscovitine was evaluated using Plaque Forming Units (PFU) assay. The transfection efficiency and knockdown of CDK5, using artificial miRNAs, was carried out by flow cytometry. The effect on the viral envelope protein and cytoskeleton elements was evidenced by advanced fluorescence microscopy and image analysis. Roscovitine showed antiviral activity in pre and post-infection stages in a dose-dependent manner. Treatment with roscovitine and miRCDK5 decrease the amount of CDK5 in uninfected cells. In cells infected and transfected with miRCDK5, as well as treated with the inhibitor, a significant reduction of the viral envelope protein was observed; however, no significant reduction of CDK5 was found. Also, evident morphological cellular changes were observed during the treatment with roscovitine in infected cells. The results indicate the potential participation of CDK5 during DENV-2 infection, possibly mediating protein translation or replication of the viral genome through the cytoskeletal dynamics regulation. Additional data are required to clarify the mechanistic of these phenomena using alternative methods.
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Abstract INTRODUCTION: In this study, we aimed to identify DENV-2 subtypes in Aedes aegypti pools collected between 2011 and 2017 in a rural area of Northern Cordoba, Colombia ("La Balsa"). METHODS: RT-PCR was performed to analyze the capsid/pre-membrane region (C-PrM). Sequencing and phylogenetic bayesian inference using reference DENV-2 sequences were performed. RESULTS: Twelve pools that tested positive for DENV-2 were characterized based on the C-PrM region and grouped under the Asian/American clade. CONCLUSIONS: This study is the first to report the DENV-2 Asian-American subtype in a rural area of Cordoba region, which is associated with severe dengue and local epidemics.
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Animales , Filogenia , Aedes/virología , Dengue/virología , Virus del Dengue/clasificación , Virus del Dengue/genética , Mosquitos Vectores/virología , Serotipificación , Teorema de Bayes , Colombia/epidemiología , Dengue Grave , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Dengue/epidemiología , Virus del Dengue/aislamiento & purificación , SerogrupoRESUMEN
Arboviruses belonging to the genera Flavivirus and Alphavirus were detected in mosquitoes in a rural area of San Bernardo del Viento (Córdoba, Colombia). A total of 22,180 mosquitoes were collected, sorted into 2,102 pools, and tested by generic/nested reverse transcription-polymerase chain reaction. Venezuelan equine encephalitis virus, dengue virus, West Nile virus, St. Louis encephalitis virus, yellow fever virus, and Culex flavivirus were detected and identified by sequencing. The detection of arboviral pathogens in this zone represents possible circulation and indicates a human health risk, demonstrating the importance of virological surveillance activities.
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Humanos , Animales , Femenino , Alphavirus/genética , Culicidae/virología , Flavivirus/genética , Alphavirus/clasificación , Alphavirus/aislamiento & purificación , Región del Caribe , Colombia , Flavivirus/clasificación , Filogenia , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Población RuralRESUMEN
Objetivo: Describir las manifestaciones clínicas y hallazgos de laboratorio de una serie de casos febriles agudos con diagnóstico presuntivo de infección por el virus dengue. en Quindío (Colombia). Materiales y métodos: Se realizó un estudio de corte transversal, en pacientes con sospecha clínica de dengue en el periodo comprendido entre enero y agosto de 2013, en algunos centros hospitalarios del departamento del Quindío. Se tomaron muestras de sangre para diagnóstico de dengue, leptospira, malaria, hepatitis B, y rickettsiosis. Como pruebas confirmatorias para dengue se realizó aislamiento viral en células C6/36HT y serotipificación para dengue por RTPCR; pruebas de función hepática, cuadro hemático y niveles de citocinas. Resultados: Se caracterizaron 149 casos, de los cuales el 43% presentaron infección por dengue, 4% leptospira, 6,8% rickettsias, un caso de malaria y uno de hepatitis B. En 5 casos se logró el aislamiento del DENV2 y DENV3. Mediante la RT-PCR, se evidenció cocirculación de serotipos 2, 3, 4. Se encontró que las enzimas AST/ALT, el conteo de plaquetas, la erupción y el dolor abdominal fueron marcadores característicos de la infección por dengue, mientras la ictericia y el dolor lumbar se correlacionaron con la leptospirosis. Los valores de citocinas mostraron que la IL-10, TNF α variaron significativamente en casos con dengue frente a otros diagnósticos, y la IL-17 a presentó diferencias significativas en individuos con dengue grave. Conclusiones: El dengue se confirmó como causa etiológica importante de síndrome febril icterohemorrágico en el departamento del Quindío, pero la leptospirosis y la rickettsiosis tienen también una participación importante. Sin embargo, en el 44% de los casos fueron catalogados como síndrome febril indeterminado.
Objective: To characterise the clinical and laboratory findings on a series of febrile cases with a presumptive diagnosis of dengue virus infection in Quindío, Colombia. Materials and methods: This study was conducted from January to July 2013. Blood samples were obtained from patients suspected of dengue virus infection from Quindío department hospitals. These samples were tested for dengue, leptospira, malaria, hepatitis B and rickettsiosis. To confirm dengue infection, we performed viral isolation in C6/36HT cells and dengue serotyping by RT-PCR; liver function tests, complete blood counts and cytokine levels. Results: Of 149 cases, 43% were infected by dengue, 4% leptospira, 6.8% rickettsia, one case of malaria and one case of hepatitis b. We obtained 5 clinical isolates of DENV2 and DENV3 that evidenced co-circulation of serotypes 2, 3, and 4. We found that AST/ALT levels, platelet count, rash and abdominal pain were good markers of infection by dengue, while jaundice and lumbar pain suggested leptospirosis. Cytokine levels revealed that IL-10, TNF a varied significantly in dengue compared with other diagnostics and that IL-17 α showed significant differences in individuals with severe dengue. Conclusions: Dengue was confirmed as an important aetiology of acute febrile icterohaemorrhagic syndrome in Quindío, but leptospirosis and rickettsia also play an important role. However, 44% of the cases were classified as undetermined febrile syndrome.
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Humanos , Masculino , Femenino , Dengue , Virus del Dengue , Laboratorios , Recuento de Plaquetas , Rickettsia , Infecciones por Rickettsia , Virus , Recuento de Células Sanguíneas , Serotipificación , Citocinas , Colombia , Dengue Grave , Fiebre/complicaciones , Infecciones , Leptospirosis , MétodosRESUMEN
Saint Louis encephalitis virus (SLEV) is a member of the Japanese-encephalitis virus serocomplex of the genus Flavivirus. SLEV is broadly distributed in the Americas and the Caribbean Islands, where it is usually transmitted by mosquitoes of the genus Culex and primarily to birds and mammalian-hosts. Humans are occasionally infected by the virus and are dead-end hosts. SLEV causes encephalitis in temperate regions, while in tropical regions of the Americas, several human cases and a wide biological diversity of SLEV-strains have been reported. The phylogenetic analysis of the envelope (E) protein genes indicated eight-genotypes of SLEV with geographic overlap. The present paper describes the genotyping of two SLEV viruses detected in mosquito-pools collected in northern Colombia (department of Cordoba). We used reverse transcription-polymerase chain reaction to amplify a fragment of theE-gene to confirm the virus identity and completeE-gene sequencing for phylogenetic analysis and genotyping of the two-SLEV viruses found circulating in Córdoba. This is the first report of SLEV genotype IV in Colombia (Córdoba) in mosquitoes from a region of human inhabitation, implicating the risk of human disease due to SLEV infection. Physicians should consider SLEV as a possible aetiology for undiagnosed febrile and neurologic syndromes among their patients who report exposure to mosquito-bites.
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Animales , Humanos , Culicidae/virología , Virus de la Encefalitis de San Luis/genética , Proteínas del Envoltorio Viral/genética , Colombia , Secuencia de Consenso , Código de Barras del ADN Taxonómico , Monitoreo Epidemiológico , Virus de la Encefalitis de San Luis/clasificación , Genotipo , Filogenia , Polimorfismo Genético/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Alineación de SecuenciaRESUMEN
El interés en la detección, identificación, y caracterización funcional de los pequeños RNAs no codificantes (sRNAs), ha generado la necesidad de optimizar las metodologías comúnmente usadas en su detección, la reacción en cadena de la polimerasa cuantitativa (RT-qPCR) y Northern blot, con el fin de que sean más sensibles y específicas. A pesar de la baja sensibilidad del Northern blot, esta metodología continúa siendo de uso común en la detección de sRNAs porque permite detectar el RNA pequeño así como a sus precursores, razón por la cual se usa como una metodología complementaria en este tipo de investigaciones. En este trabajo se describe la implementación de un nuevo protocolo para Northern blot no radioactivo, con modificaciones dirigidas a mejorar su sensibilidad y especificidad. El diseños de la sonda con la tecnología LNA, el marcaje de esta con Digoxigenina y por último la fijación del RNA a la membrana mediante 1-Ethyl-3-(-3-dimethylaminopropyl) carboniimide (EDC) y finalmente se discuten los fundamentos teóricos de estos cambios.
The interest in detection, identification and functional characterization of small non-coding RNAs (snRNAs), has generated the need to optimize the methodologies commonly used in its detection in specificity and sensitivity, The Quantitative reverse transcription PCR (RT-qPCR) and Northern blot. Even though the low sensitivity of Northern blot, this method continues to be commonly used in the sRNAs, because its capacity to detect the sRNA and its precursor, which is the reason why Northern blot is used as complementary method in this sort of Research. This work describes the implementation of an innovative non-radioactive Northern blot protocol, with modifications that improving the sensibility and specificity, with the discussion of the theoretical foundations of such modifications.
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Este artículo es una aproximación multidisciplinar, basada en los fundamentos de la teoría del caos, evolución del cerebro humano y la sistemática filogenética, para intentar contribuir al estudio del cerebro humano en condiciones normales y patológicas, evaluando la posible utilidad de esas disquisiciones en la cotidianidad de la docencia y práctica psiquiátricas. Se expone aquí que el funcionamiento cerebral se puede entender mejor desde la perspectiva de la dinámica no lineal e indeterminista de la teoría del caos, la cual permite una aproximación a fenómenos tan complejos como el origen de la inteligencia, el afecto y la enfermedad mental. Finalmente, se plantea que la metodología de la filogenética puede ser una herramienta útil que aportaría elementos para la nosología de las enfermedades mentales y eventualmente ayudaría a una comprensión más integral de éstas...