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1.
Cell ; 184(13): 3452-3466.e18, 2021 06 24.
Artículo en Inglés | MEDLINE | ID: mdl-34139176

RESUMEN

Antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein prevent SARS-CoV-2 infection. However, the effects of antibodies against other spike protein domains are largely unknown. Here, we screened a series of anti-spike monoclonal antibodies from coronavirus disease 2019 (COVID-19) patients and found that some of antibodies against the N-terminal domain (NTD) induced the open conformation of RBD and thus enhanced the binding capacity of the spike protein to ACE2 and infectivity of SARS-CoV-2. Mutational analysis revealed that all of the infectivity-enhancing antibodies recognized a specific site on the NTD. Structural analysis demonstrated that all infectivity-enhancing antibodies bound to NTD in a similar manner. The antibodies against this infectivity-enhancing site were detected at high levels in severe patients. Moreover, we identified antibodies against the infectivity-enhancing site in uninfected donors, albeit at a lower frequency. These findings demonstrate that not only neutralizing antibodies but also enhancing antibodies are produced during SARS-CoV-2 infection.


Asunto(s)
Anticuerpos Monoclonales/inmunología , Anticuerpos Neutralizantes/inmunología , Anticuerpos Antivirales/inmunología , SARS-CoV-2/inmunología , Glicoproteína de la Espiga del Coronavirus/inmunología , Animales , COVID-19/inmunología , Línea Celular , Chlorocebus aethiops , Células HEK293 , Humanos , Unión Proteica/inmunología , Dominios Proteicos/inmunología , Glicoproteína de la Espiga del Coronavirus/genética , Células Vero
2.
Immunity ; 56(8): 1939-1954.e12, 2023 08 08.
Artículo en Inglés | MEDLINE | ID: mdl-37442134

RESUMEN

Lung infection during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via the angiotensin-I-converting enzyme 2 (ACE2) receptor induces a cytokine storm. However, the precise mechanisms involved in severe COVID-19 pneumonia are unknown. Here, we showed that interleukin-10 (IL-10) induced the expression of ACE2 in normal alveolar macrophages, causing them to become vectors for SARS-CoV-2. The inhibition of this system in hamster models attenuated SARS-CoV-2 pathogenicity. Genome-wide association and quantitative trait locus analyses identified a IFNAR2-IL10RB readthrough transcript, COVID-19 infectivity-enhancing dual receptor (CiDRE), which was highly expressed in patients harboring COVID-19 risk variants at the IFNAR2 locus. We showed that CiDRE exerted synergistic effects via the IL-10-ACE2 axis in alveolar macrophages and functioned as a decoy receptor for type I interferons. Collectively, our data show that high IL-10 and CiDRE expression are potential risk factors for severe COVID-19. Thus, IL-10R and CiDRE inhibitors might be useful COVID-19 therapies.


Asunto(s)
COVID-19 , Humanos , COVID-19/genética , SARS-CoV-2 , Enzima Convertidora de Angiotensina 2/genética , Interleucina-10/genética , Macrófagos Alveolares/metabolismo , Estudio de Asociación del Genoma Completo , Peptidil-Dipeptidasa A/metabolismo
3.
Immunity ; 52(3): 542-556.e13, 2020 03 17.
Artículo en Inglés | MEDLINE | ID: mdl-32187520

RESUMEN

Fibrosis is an incurable disorder of unknown etiology. Segregated-nucleus-containing atypical monocytes (SatMs) are critical for the development of fibrosis. Here we examined the mechanisms that recruit SatMs to pre-fibrotic areas. A screen based on cytokine expression in the fibrotic lung revealed that the chemokine Cxcl12, which is produced by apoptotic nonhematopoietic cells, was essential for SatM recruitment. Analyses of lung tissues at fibrosis onset showed increased expression of Rbm7, a component of the nuclear exosome targeting complex. Rbm7 deletion suppressed bleomycin-induced fibrosis and at a cellular level, suppressed apoptosis of nonhematopoietic cells. Mechanistically, Rbm7 bound to noncoding (nc)RNAs that form subnuclear bodies, including Neat1 speckles. Dysregulated expression of Rbm7 resulted in the nuclear degradation of Neat1 speckles, the dispersion of the DNA repair protein BRCA1, and the triggering of apoptosis. Thus, Rbm7 in epithelial cells plays a critical role in the development of fibrosis by regulating ncRNA decay and thereby the production of chemokines that recruit SatMs.


Asunto(s)
Apoptosis/inmunología , Núcleo Celular/inmunología , Exosomas/inmunología , Fibrosis Pulmonar/inmunología , Proteínas de Unión al ARN/inmunología , Animales , Apoptosis/genética , Núcleo Celular/genética , Núcleo Celular/metabolismo , Quimiocina CXCL12/inmunología , Quimiocina CXCL12/metabolismo , Exosomas/genética , Exosomas/metabolismo , Regulación de la Expresión Génica/inmunología , Células HEK293 , Humanos , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Ratones Transgénicos , Monocitos/inmunología , Monocitos/metabolismo , Células 3T3 NIH , Fibrosis Pulmonar/genética , Fibrosis Pulmonar/metabolismo , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo
4.
Hepatology ; 2023 Aug 09.
Artículo en Inglés | MEDLINE | ID: mdl-37556368

RESUMEN

BACKGROUND AND AIMS: Epigenetic plasticity is a major challenge in cancer-targeted therapy. However, the molecular basis governing this process has not yet been clearly defined. Despite the considerable success of poly(ADP-ribose) polymerase inhibitors (PARPi) in cancer therapy, the limited response to PARPi, especially in HCC, has been a bottleneck in its clinical implications. Herein, we investigated the molecular basis of the histone methyltransferase KMT5C (lysine methyltransferase 5C) that governs PARPi sensitivity and explored a potential therapeutic strategy for enhancing PARPi efficacy. APPROACH AND RESULTS: We identified KMT5C, a trimethyltransferase of H4K20, as a targetable epigenetic factor that promoted liver tumor growth in mouse de novo MYC/Trp53-/- and xenograft liver tumor models. Notably, induction of KMT5C by environmental stress was crucial for DNA repair and HCC cell survival. Mechanistically, KMT5C interacted with the pivotal component of homologous recombination repair, RAD51, and promoted RAD51/RAD54 complex formation, which was essential for the activation of dsDNA breaks repair. This effect depended on the methyltransferase activity of KMT5C. We further demonstrated that the function of KMT5C in promoting HCC progression was dependent on RAD51. Importantly, either a pharmacological inhibitor (A196) or genetic inhibition of KMT5C sensitized liver cancer cells to PARPi. CONCLUSIONS: KMT5C played a vital role in promoting liver cancer progression by activating the DNA repair response. Our results revealed a novel therapeutic approach using the KMT5C inhibitor A196, concurrent with olaparib, as a potential HCC therapy.

5.
Proc Natl Acad Sci U S A ; 118(49)2021 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-34848538

RESUMEN

Auditory transduction is mediated by chordotonal (Cho) neurons in Drosophila larvae, but the molecular identity of the mechanotransduction (MET) channel is elusive. Here, we established a whole-cell recording system of Cho neurons and showed that two transient receptor potential vanilloid (TRPV) channels, Nanchung (NAN) and Inactive (IAV), are essential for MET currents in Cho neurons. NAN and IAV form active ion channels when expressed simultaneously in S2 cells. Point mutations in the pore region of NAN-IAV change the reversal potential of the MET currents. Particularly, residues 857 through 990 in the IAV carboxyl terminus regulate the kinetics of MET currents in Cho neurons. In addition, TRPN channel NompC contributes to the adaptation of auditory transduction currents independent of its ion-conduction function. These results indicate that NAN-IAV, rather than NompC, functions as essential pore-forming subunits of the native auditory transduction channel in Drosophila and provide insights into the gating mechanism of MET currents in Cho neurons.


Asunto(s)
Proteínas de Drosophila/metabolismo , Canales Iónicos/metabolismo , Mecanotransducción Celular/fisiología , Neuronas/fisiología , Canales de Potencial de Receptor Transitorio/metabolismo , Potenciales de Acción/fisiología , Secuencia de Aminoácidos , Animales , Línea Celular , Proteínas de Drosophila/genética , Drosophila melanogaster , Fenómenos Electrofisiológicos , Regulación de la Expresión Génica , Canales Iónicos/genética , Larva , Técnicas de Placa-Clamp , Mutación Puntual , Canales de Potencial de Receptor Transitorio/genética
6.
J Transl Med ; 21(1): 255, 2023 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-37046312

RESUMEN

PURPOSE: The claudin 18.2 (CLDN18.2) antigen is frequently expressed in malignant tumors, including pancreatic ductal adenocarcinoma (PDAC). Although CLDN18.2-targeted CAR-T cells demonstrated some therapeutic efficacy in PDAC patients, further improvement is needed. One of the major obstacles might be the abundant cancer-associated fibroblasts (CAFs) in the PDAC tumor microenvironment (TME). Targeting fibroblast activation protein (FAP), a vital characteristic of CAFs provides a potential way to overcome this obstacle. In this study, we explored the combined antitumor activity of FAP-targeted and CLDN18.2-targeted CAR-T cells against PDAC. METHODS: Novel FAP-targeted CAR-T cells were developed. Sequential treatment of FAP-targeted and CLDN18.2-targeted CAR-T cells as well as the corresponding mechanism were explored in immunocompetent mouse models of PDAC. RESULTS: The results indicated that the priorly FAP-targeted CAR-T cells infusion could significantly eliminate CAFs and enhance the anti-PDAC efficacy of subsequently CLDN18.2-targeted CAR-T cells in vivo. Interestingly, we observed that FAP-targeted CAR-T cells could suppress the recruitment of myeloid-derived suppressor cells (MDSCs) and promote the survival of CD8+ T cells and CAR-T cells in tumor tissue. CONCLUSION: In summary, our finding demonstrated that FAP-targeted CAR-T cells could increase the antitumor activities of sequential CAR-T therapy via remodeling TME, at least partially through inhibiting MDSCs recruitment. Sequential infusion of FAP-targeted and CLDN18.2-targeted CAR-T cells might be a feasible approach to enhance the clinical outcome of PDAC.


Asunto(s)
Carcinoma Ductal Pancreático , Células Supresoras de Origen Mieloide , Neoplasias Pancreáticas , Receptores Quiméricos de Antígenos , Animales , Ratones , Carcinoma Ductal Pancreático/terapia , Linfocitos T CD8-positivos , Línea Celular Tumoral , Células Supresoras de Origen Mieloide/metabolismo , Neoplasias Pancreáticas/terapia , Neoplasias Pancreáticas/metabolismo , Receptores Quiméricos de Antígenos/metabolismo , Serina Endopeptidasas/metabolismo , Microambiente Tumoral , Humanos , Neoplasias Pancreáticas
7.
Molecules ; 28(19)2023 Sep 28.
Artículo en Inglés | MEDLINE | ID: mdl-37836685

RESUMEN

Mpox virus (MPXV), the most pathogenic zoonotic orthopoxvirus, caused worldwide concern during the SARS-CoV-2 epidemic. Growing evidence suggests that the MPXV surface protein A29 could be a specific diagnostic marker for immunological detection. In this study, a fully synthetic phage display library was screened, revealing two nanobodies (A1 and H8) that specifically recognize A29. Subsequently, an in vitro affinity maturation strategy based on computer-aided design was proposed by building and docking the A29 and A1 three-dimensional structures. Ligand-receptor binding and molecular dynamics simulations were performed to predict binding modes and key residues. Three mutant antibodies were predicted using the platform, increasing the affinity by approximately 10-fold compared with the parental form. These results will facilitate the application of computers in antibody optimization and reduce the cost of antibody development; moreover, the predicted antibodies provide a reference for establishing an immunological response against MPXV.


Asunto(s)
COVID-19 , Anticuerpos de Dominio Único , Humanos , Anticuerpos de Dominio Único/química , Monkeypox virus , SARS-CoV-2/metabolismo , Diseño Asistido por Computadora
8.
PLoS Pathog ; 16(6): e1008308, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32574204

RESUMEN

One of the determinants for tissue tropism of hepatitis C virus (HCV) is miR-122, a liver-specific microRNA. Recently, it has been reported that interaction of miR-122 to HCV RNA induces a conformational change of the 5'UTR internal ribosome entry site (IRES) structure to form stem-loop II structure (SLII) and hijack of translating 80S ribosome through the binding of SLIII to 40S subunit, which leads to efficient translation. On the other hand, low levels of HCV-RNA replication have also been detected in some non-hepatic cells; however, the details of extrahepatic replication remain unknown. These observations suggest the possibility that miRNAs other than miR-122 can support efficient replication of HCV-RNA in non-hepatic cells. Here, we identified a number of such miRNAs and show that they could be divided into two groups: those that bind HCV-RNA at two locations (miR-122 binding sites I and II), in a manner similar to miR-122 (miR-122-like), and those that target a single site that bridges sites I and II and masking both G28 and C29 in the 5'UTR (non-miR-122-like). Although the enhancing activity of these non-hepatic miRNAs were lower than those of miR-122, substantial expression was detected in various normal tissues. Furthermore, structural modeling indicated that both miR-122-like and non-miR-122-like miRNAs not only can facilitate the formation of an HCV IRES SLII but also can stabilize IRES 3D structure in order to facilitate binding of SLIII to the ribosome. Together, these results suggest that HCV facilitates miR-122-independent replication in non-hepatic cells through recruitment of miRNAs other than miR-122. And our findings can provide a more detailed mechanism of miR-122-dependent enhancement of HCV-RNA translation by focusing on IRES tertiary structure.


Asunto(s)
Regulación Viral de la Expresión Génica , Hepacivirus/fisiología , MicroARNs/metabolismo , Biosíntesis de Proteínas , ARN Viral , Proteínas Virales/biosíntesis , Replicación Viral/fisiología , Regiones no Traducidas 5' , Línea Celular Tumoral , Humanos , MicroARNs/genética , ARN Viral/biosíntesis , ARN Viral/genética , Proteínas Virales/genética
9.
Nucleic Acids Res ; 47(W1): W5-W10, 2019 07 02.
Artículo en Inglés | MEDLINE | ID: mdl-31062021

RESUMEN

Here, we describe a web server that integrates structural alignments with the MAFFT multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based Database of Aligned Structural Homologs (DASH), which provides structural alignments at the domain and chain levels for all proteins in the Protein Data Bank (PDB), and can be queried interactively or by a simple REST-like API. MAFFT-DASH integration can be invoked with a single flag on either the web (https://mafft.cbrc.jp/alignment/server/) or command-line versions of MAFFT. In our benchmarks using 878 cases from the BAliBase, HomFam, OXFam, Mattbench and SISYPHUS datasets, MAFFT-DASH showed 10-20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in comparison to a reference alignment. When MAFFT alignments were supplemented with homologous sequences, further improvement was observed. Potential applications of DASH beyond MSA enrichment include functional annotation through detection of remote homology and assembly of template libraries for homology modeling.


Asunto(s)
Secuencia de Aminoácidos/genética , Proteínas/genética , Alineación de Secuencia/métodos , Programas Informáticos , Algoritmos , Bases de Datos de Proteínas , Humanos , Análisis de Secuencia de Proteína/métodos , Análisis de Secuencia de ARN , Homología de Secuencia
10.
Adv Exp Med Biol ; 1349: 371-385, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-35138623

RESUMEN

The ability of living organisms to detect mechanical force originates from mechanotransduction ion channels, which convert membrane tension into electrical or chemical signals that are transmitted to the brain. A variety of studies on touch and sound perception in both vertebrates and invertebrates have broadened our understanding of mechanotransduction and identified promising candidates for mechanotransduction ion channels. Here, we discussed the physiological properties of mechanotransduction ion channels in hearing and touch, the identification of their molecular entities, and recent structural studies providing insights to their gating mechanisms in force sensing. We present an updated review of the evidence supporting several candidates, including NOMPC, Brv1, and TMC channels, as mechanotransduction ion channels and highlight their qualifications satisfying the specific criteria proposed for a mechanotransducer.


Asunto(s)
Percepción del Tacto , Tacto , Animales , Audición , Canales Iónicos/metabolismo , Mecanotransducción Celular
11.
Eur J Immunol ; 48(4): 593-604, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29244194

RESUMEN

AT-rich interactive domain-containing protein 5a (Arid5a) is an RNA-binding protein (RBP) required for autoimmunity via stabilization of interleukin-6 (Il6) and signal transducer and activator of transcription 3 (STAT3) mRNAs. However, the roles of Arid5a in Th17 cells and its association with autoimmunity remain unknown. Here, we show that the levels of Arid5a and OX40 are correlated in CD4+ T cells under Th17 conditions in an IL-6-dependent manner. Lack of Arid5a in T cells reduced OX40 expression levels and repressed IL-17 production in response to OX40 ligation. Arid5a stabilized OX40 mRNA by recognizing the alternative decay element (ADE)-like stem-loop (SL) in the 3' untranslated region (3'UTR). Interestingly, Arid5a impaired the RNA-destabilizing functions of Regnase-1 and Roquin-1 on OX40 ADE-like SL. In EAE, Arid5a-deficient mice exhibited resistance to EAE, with reduced OX40 expression in CD4+ T cells, and the number of CD4+ CD45+ T cells was decreased in CNS. Furthermore, ameliorated EAE was induced by adoptive transfer of Arid5a-/- encephalitogenic CD4+ T cells expressing less OX40 mRNA and producing less IL-17. In conclusion, our findings indicate that the Arid5a/OX40 axis in CD4+ T cells may have important implications in pathogenesis of autoimmune diseases such as EAE.


Asunto(s)
Autoinmunidad/inmunología , Proteínas de Unión al ADN/metabolismo , Glicoproteínas de Membrana/genética , Factor de Transcripción STAT3/inmunología , Células Th17/inmunología , Factores de Transcripción/metabolismo , Factores de Necrosis Tumoral/genética , Traslado Adoptivo , Animales , Autoinmunidad/genética , Línea Celular , Encefalomielitis Autoinmune Experimental/inmunología , Encefalomielitis Autoinmune Experimental/patología , Células HEK293 , Humanos , Interleucina-17/biosíntesis , Interleucina-6/inmunología , Secuencias Invertidas Repetidas/genética , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Ligando OX40 , Interferencia de ARN , ARN Mensajero/genética , ARN Interferente Pequeño/genética , Proteínas de Unión al ARN/metabolismo , Ribonucleasas/genética , Factor de Transcripción STAT3/genética , Ubiquitina-Proteína Ligasas/genética
12.
Nucleic Acids Res ; 45(5): 2687-2703, 2017 03 17.
Artículo en Inglés | MEDLINE | ID: mdl-28168301

RESUMEN

The AT-rich interactive domain-containing protein 5a (Arid5a) plays a critical role in autoimmunity by regulating the half-life of Interleukin-6 (IL-6) mRNA. However, the signaling pathways underlying Arid5a-mediated regulation of IL-6 mRNA stability are largely uncharacterized. Here, we found that during the early phase of lipopolysaccharide (LPS) stimulation, NF-κB and an NF-κB-triggered IL-6-positive feedback loop activate Arid5a gene expression, increasing IL-6 expression via stabilization of the IL-6 mRNA. Subsequently, mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP-1) promotes translocation of AU-rich element RNA-binding protein 1 (AUF-1) from the nucleus to the cytoplasm, where it destabilizes Arid5a mRNA by binding to AU-rich elements in the 3΄ UTR. This results in downregulation of IL-6 mRNA expression. During the late phase of LPS stimulation, p38 MAPK phosphorylates Arid5a and recruits the WW domain containing E3 ubiquitin protein ligase 1 (WWP1) to its complex, which in turn ubiquitinates Arid5a in a K48-linked manner, leading to its degradation. Inhibition of Arid5a phosphorylation and degradation increases production of IL-6 mRNA. Thus, our data demonstrate that LPS-induced NF-κB and MAPK signaling are required to control the regulation of the IL-6 mRNA stabilizing molecule Arid5a. This study therefore substantially increases our understanding of the mechanisms by which IL-6 is regulated.


Asunto(s)
Proteínas de Unión al ADN/metabolismo , Interleucina-6/genética , Sistema de Señalización de MAP Quinasas , FN-kappa B/metabolismo , Estabilidad del ARN , Receptor Toll-Like 4/metabolismo , Factores de Transcripción/metabolismo , Regiones no Traducidas 3' , Animales , Células Cultivadas , Proteínas de Unión al ADN/biosíntesis , Proteínas de Unión al ADN/genética , Fosfatasa 1 de Especificidad Dual/metabolismo , Ribonucleoproteína Nuclear Heterogénea D0 , Ribonucleoproteína Heterogénea-Nuclear Grupo D/metabolismo , Interleucina-6/metabolismo , Ratones , Ratones Endogámicos C57BL , ARN Mensajero/metabolismo , Factor de Transcripción STAT3/metabolismo , Factores de Transcripción/biosíntesis , Factores de Transcripción/genética , Ubiquitina-Proteína Ligasas/metabolismo , Ubiquitinación , Regulación hacia Arriba , Proteínas Quinasas p38 Activadas por Mitógenos/metabolismo
13.
Nucleic Acids Res ; 42(15): 10086-98, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25063293

RESUMEN

Increasing awareness of the importance of protein-RNA interactions has motivated many approaches to predict residue-level RNA binding sites in proteins based on sequence or structural characteristics. Sequence-based predictors are usually high in sensitivity but low in specificity; conversely structure-based predictors tend to have high specificity, but lower sensitivity. Here we quantified the contribution of both sequence- and structure-based features as indicators of RNA-binding propensity using a machine-learning approach. In order to capture structural information for proteins without a known structure, we used homology modeling to extract the relevant structural features. Several novel and modified features enhanced the accuracy of residue-level RNA-binding propensity beyond what has been reported previously, including by meta-prediction servers. These features include: hidden Markov model-based evolutionary conservation, surface deformations based on the Laplacian norm formalism, and relative solvent accessibility partitioned into backbone and side chain contributions. We constructed a web server called aaRNA that implements the proposed method and demonstrate its use in identifying putative RNA binding sites.


Asunto(s)
Proteínas de Unión al ARN/química , Algoritmos , Aminoácidos/química , Inteligencia Artificial , Sitios de Unión , Modelos Moleculares , Unión Proteica , Estructura Secundaria de Proteína , ARN/química , ARN/metabolismo , Proteínas de Unión al ARN/metabolismo , Análisis de Secuencia de Proteína , Programas Informáticos , Homología Estructural de Proteína
14.
Anal Biochem ; 472: 52-61, 2015 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-25479604

RESUMEN

RNA-LIM is a procedure that can analyze various pseudo-potentials describing the affinity between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce a coarse-grained estimate of the structure of the ssRNA at the protein interface. The search algorithm works by evolving an ssRNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. Optimal routes are found by application of a set of minimal "limiting" restraints derived jointly from (i) selective sampling of the ribonucleotide amino acid affinity pseudo-potential data, (ii) limited surface path exploration by prior determination of surface arc lengths, and (iii) RNA structural specification obtained from a statistical potential gathered from a library of experimentally determined ssRNA structures. We describe the general approach using a NAST (Nucleic Acid Simulation Tool)-like approximation of the ssRNA chain and a generalized pseudo-potential reflecting the location of nucleic acid binding residues. Minimum and maximum performance indicators of the methodology are established using both synthetic data, for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded, and a representative real case, where the RNA binding sites are predicted by the amplified antisense RNA (aaRNA) method. Some potential uses and extensions of the routine are discussed. RNA-LIM analysis programs along with detailed instructions for their use are available on request from the authors.


Asunto(s)
Modelos Químicos , Conformación de Ácido Nucleico , ARN sin Sentido/química , Proteínas de Unión al ARN/química , Programas Informáticos
15.
Nucleic Acids Res ; 40(3): 972-80, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-21976727

RESUMEN

What physical mechanism leads to organization of a highly condensed and confined circular chromosome? Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains. The experimentally observed high precision of separate subcellular positioning of loci (located on different chromosomal domains) in Escherichia coli naturally emerges as a result of entropic demixing of such chromosomal loops. We propose one possible mechanism for organizing these domains: regulatory control defined by the underlying E. coli gene regulatory network requires the colocalization of transcription factor genes and target genes. Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their compression due to the confining geometry induces an effective nucleoid filament-type of structure. Thus, we propose that the physical structure of the chromosome is a direct result of regulatory interactions. To reproduce the observed precise ordering of the chromosome, we estimate that the domain sizes are distributed between 10 and 700 kb, in agreement with the size of topological domains identified in the context of DNA supercoiling.


Asunto(s)
Cromosomas Bacterianos/química , ADN Bacteriano/química , Escherichia coli/genética , Redes Reguladoras de Genes , Regulación Bacteriana de la Expresión Génica , Modelos Genéticos , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
16.
Food Chem X ; 21: 101183, 2024 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-38357371

RESUMEN

Aldehydes are the strongest and most abundant aromatic compounds in Kung Pao Chicken. However, the perceptual interactions between these aldehydes are not fully understood. Therefore, the flavor contribution of nine key aldehydes was estimated by determining thresholds. Except for benzaldehyde, the thresholds of all aldehydes measured in tasteless chicken matrices (TM) were significantly larger than their comparable values in water. Based on these results, the perceptual interactions of nine aldehydes were evaluated using S-curves and σ-τ plots. The interactions indicated that 31 of their 36 binary mixtures exhibited additive effects, three had masking effects, while two had synergistic effects. Recombination experiments showed that the addition of aldehydes lowered the odor threshold of aldehyde reconstitution (AR), thereby enhancing the aroma intensity of AR. These findings contribute to a better understanding of Kung Pao Chicken's aroma and can be used to improve its aroma quality.

17.
Cancer Lett ; 595: 217006, 2024 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-38823763

RESUMEN

Driver genomic mutations in tumors define specific molecular subtypes that display distinct malignancy competence, therapeutic resistance and clinical outcome. Although TP53 mutation has been identified as the most common mutation in hepatocellular carcinoma (HCC), current understanding on the biological traits and therapeutic strategies of this subtype has been largely unknown. Here, we reveal that fatty acid ß oxidation (FAO) is remarkable repressed in TP53 mutant HCC and which links to poor prognosis in HCC patients. We further demonstrate that carnitine palmitoyltransferase 1 (CPT1A), the rate-limiting enzyme of FAO, is universally downregulated in liver tumor tissues, and which correlates with poor prognosis in HCC and promotes HCC progression in the de novo liver tumor and xenograft tumor models. Mechanically, hepatic Cpt1a loss disrupts lipid metabolism and acetyl-CoA production. Such reduction in acetyl-CoA reduced histone acetylation and epigenetically reprograms branched-chain amino acids (BCAA) catabolism, and leads to the accumulation of cellular BCAAs and hyperactivation of mTOR signaling. Importantly, we reveal that genetic ablation of CPT1A renders TP53 mutant liver cancer mTOR-addicted and sensitivity to mTOR inhibitor AZD-8055 treatment. Consistently, Cpt1a loss in HCC directs tumor cell therapeutic response to AZD-8055. CONCLUSION: Our results show genetic evidence for CPT1A as a metabolic tumor suppressor in HCC and provide a therapeutic approach for TP53 mutant HCC patients.


Asunto(s)
Carcinoma Hepatocelular , Carnitina O-Palmitoiltransferasa , Neoplasias Hepáticas , Mutación , Proteína p53 Supresora de Tumor , Humanos , Carnitina O-Palmitoiltransferasa/genética , Carnitina O-Palmitoiltransferasa/metabolismo , Carnitina O-Palmitoiltransferasa/antagonistas & inhibidores , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/metabolismo , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/tratamiento farmacológico , Neoplasias Hepáticas/patología , Neoplasias Hepáticas/metabolismo , Animales , Ratones , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/patología , Carcinoma Hepatocelular/tratamiento farmacológico , Carcinoma Hepatocelular/metabolismo , Aminoácidos de Cadena Ramificada/metabolismo , Línea Celular Tumoral , Serina-Treonina Quinasas TOR/metabolismo , Serina-Treonina Quinasas TOR/genética , Ensayos Antitumor por Modelo de Xenoinjerto , Metabolismo de los Lípidos/genética , Transducción de Señal , Acetilcoenzima A/metabolismo , Regulación Neoplásica de la Expresión Génica , Masculino
18.
J Immunother Cancer ; 12(6)2024 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-38908854

RESUMEN

BACKGROUND AND AIMS: The immunosuppressive tumor microenvironment (TME) plays an essential role in cancer progression and immunotherapy response. Despite the considerable advancements in cancer immunotherapy, the limited response to immune checkpoint blockade (ICB) therapies in patients with hepatocellular carcinoma (HCC) remains a major challenge for its clinical implications. Here, we investigated the molecular basis of the protein O-fucosyltransferase 1 (POFUT1) that drives HCC immune evasion and explored a potential therapeutic strategy for enhancing ICB efficacy. METHODS: De novo MYC/Trp53-/- liver tumor and the xenograft tumor models were used to evaluate the function of POFUT1 in immune evasion. Biochemical assays were performed to elucidate the underlying mechanism of POFUT1-mediated immune evasion. RESULTS: We identified POFUT1 as a crucial promoter of immune evasion in liver cancer. Notably, POFUT1 promoted HCC progression and inhibited T-cell infiltration in the xenograft tumor and de novo MYC/Trp53-/- mouse liver tumor models. Mechanistically, we demonstrated that POFUT1 stabilized programmed death ligand 1 (PD-L1) protein by preventing tripartite motif containing 21-mediated PD-L1 ubiquitination and degradation independently of its protein-O-fucosyltransferase activity. In addition, we further demonstrated that PD-L1 was required for the tumor-promoting and immune evasion effects of POFUT1 in HCC. Importantly, inhibition of POFUT1 could synergize with anti-programmed death receptor 1 therapy by remodeling TME in the xenograft tumor mouse model. Clinically, POFUT1 high expression displayed a lower response rate and worse clinical outcome to ICB therapies. CONCLUSIONS: Our findings demonstrate that POFUT1 functions as a novel regulator of tumor immune evasion and inhibition of POFUT1 may be a potential therapeutic strategy to enhance the efficacy of immune therapy in HCC.


Asunto(s)
Antígeno B7-H1 , Fucosiltransferasas , Inmunoterapia , Neoplasias Hepáticas , Fucosiltransferasas/metabolismo , Fucosiltransferasas/genética , Neoplasias Hepáticas/inmunología , Neoplasias Hepáticas/tratamiento farmacológico , Humanos , Ratones , Animales , Antígeno B7-H1/metabolismo , Inmunoterapia/métodos , Carcinoma Hepatocelular/inmunología , Carcinoma Hepatocelular/tratamiento farmacológico , Carcinoma Hepatocelular/patología , Escape del Tumor , Microambiente Tumoral , Evasión Inmune , Línea Celular Tumoral
19.
Adv Sci (Weinh) ; 11(6): e2306156, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38062916

RESUMEN

Acute lung injury (ALI) is a severe respiratory disease with a high mortality rate. The integrity of the pulmonary endothelial barrier influences the development and prognosis of ALI. Therefore, it has become an important target for ALI treatment. Extracellular vesicles (EVs) are promising nanotherapeutic agents against ALI. Herein, endothelium-derived engineered extracellular vesicles (eEVs) that deliver microRNA-125b-5p (miRNA-125b) to lung tissues exerting a protective effect on endothelial barrier integrity are reported. eEVs that are modified with lung microvascular endothelial cell-targeting peptides (LET) exhibit a prolonged retention time in lung tissues and targeted lung microvascular endothelial cells in vivo and in vitro. To improve the efficacy of the EVs, miRNA-125b is loaded into EVs. Finally, LET-EVs-miRNA-125b is constructed. The results show that compared to the EVs, miRNA-125b, and EVs-miRNA-125b, LET-EVs-miRNA-125b exhibit the most significant treatment efficacy in ALI. Moreover, LET-EVs-miRNA-125b is found to have an important protective effect on endothelial barrier integrity by inhibiting cell apoptosis, promoting angiogenesis, and protecting intercellular junctions. Sequencing analysis reveals that LET-EVs-miRNA-125b downregulates early growth response-1 (EGR1) levels, which may be a potential mechanism of action. Taken together, these findings suggest that LET-EVs-miRNA-125b can treat ALI by protecting the endothelial barrier integrity.


Asunto(s)
Lesión Pulmonar Aguda , Vesículas Extracelulares , MicroARNs , Humanos , Células Endoteliales , Pulmón , MicroARNs/genética , Lesión Pulmonar Aguda/terapia , Endotelio
20.
Ying Yong Sheng Tai Xue Bao ; 34(1): 221-228, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36799397

RESUMEN

To screen out phosphorus solubilizing strains that can adapt to cold climate in Qinghai Province, Bacillus mucilaginosus, B. megaterium, B. cereus, Streptomyces violovariabilis, S. cinnamofuscus, and S. flavoagglomeratus were screened with solid plate medium as the primary and liquid medium as the secondary screening, with calcium phosphate, lecithin, and phytic acid as the single source of phosphorus. By comprehensively comparing the size of phosphate solubilizing circle in the solid plate medium and the soluble phosphorus content in the liquid medium, three strains of phosphate solubilizing bacteria with good phosphate solubilizing effects were screened, S. violovariabilis, S. cinnamofuscus, and B. mucilaginosus. The three phosphate solubilizing bacteria were made into liquid ino-culants, and the small rapeseed pot experiment was carried out with two soils with different fertilities in a cold climate in September. Compared with the control, plant height, fresh weight, root length, and root weight of rapes in high-fertility cultivated soil increased by 35.5%, 191.0%, 26.2%, and 282.7%, while plant phosphorus absorption, total phosphorus and available phosphorus contents in the rhizosphere soil increased by 968.9%, 5.1%, and 2.1%, respectively. In low-fertility soil, plant height and fresh weight was increased by 45.8% and 61.3%, root length and weight was decreased by 2.6% and 4.4%, while plant phosphorus absorption and the contents of total P and available P in rhizosphere soil were increased by 91.5 %, 29.1%, and 213.7%, respectively. The effect of the other two inoculants treatments was less significant than S. violovariabilis. Therefore, S. violovariabilis was the phosphate solubilizing strain suitable for the cold climate in Qinghai.


Asunto(s)
Brassica napus , Fósforo Dietético , Fósforo , Fosfatos , Suelo , Microbiología del Suelo
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