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1.
Nucleic Acids Res ; 2024 May 30.
Artículo en Inglés | MEDLINE | ID: mdl-38813828

RESUMEN

Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species evolution. The synchronization between TFCR complexity and gene expression was assessed across species using RegulatoryScore. Additionally, an explainable machine learning model highlighted the importance of the distance between TFCR and promoter in the coordinated regulation of TFCRs on gene expression. Our results revealed the developmental and evolutionary dynamics of TFCRs during embryonic development from fish, chicken to mammals. These data provide valuable resources for exploring the relationship between transcriptional regulation and phenotypic differences during embryonic development.

2.
Opt Express ; 32(6): 9931-9945, 2024 Mar 11.
Artículo en Inglés | MEDLINE | ID: mdl-38571217

RESUMEN

The degradation and attenuation of light in underwater images impose constraints on underwater vision tasks. However, the complexity and the low real-time performance of most current image enhancement algorithms make them challenging in practical applications. To address the above issues, we propose a new lightweight framework for underwater image enhancement. We adopt the curve estimation to learn the mapping between images rather than end-to-end networks, which greatly reduces the requirement for computing resources. Firstly, a designed iterative curve with parameters is used to simulate the mapping from the raw to the enhanced image. Then, the parameters of this curve are learned with a parameter estimation network called CieNet and a set of loss functions. Experimental results demonstrate that our proposed method is superior to existing algorithms in terms of evaluating indexes and visual perception quality. Furthermore, our highly lightweight network enables it to be easily integrated into small devices, making it highly applicable. The extremely short running-time of our method facilitates real-time underwater image enhancement.

3.
Food Res Int ; 185: 114289, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38658073

RESUMEN

A food adhesive comprising tannic acid (TA) and soybean protein isolate (SPI) was developed to establish a cohesive bond between soy protein gel and simulated fat. The impact of varying TA concentrations and pH levels on the adhesive's rheology, thermal stability, chemical structure, and tensile strength were investigated. Rheological results revealed a gradual decrease in adhesive viscosity with increasing TA content. Differential scanning calorimetry (DSC) and thermal gravimetric (TG) results indicated that the stability of the adhesive improved with higher TA concentrations, reaching its peak at 0.50% TA addition. The incorporation of TA resulted in the cross-linking of amino group in unfolded SPI molecules, forming a mesh structure. However, under alkaline conditions (pH 9), adhesive viscosity and stability increased compared to the original pH. This shift was due to the disruption of the SPI colloidal charge structure, an increase in the stretching of functional groups, further unfolding of the structure, and an enhanced binding of SPI to TA. Under the initial pH conditions, SPI reacted with TA's active site to form covalent crosslinked networks and hydrogen bonds. In alkaline condition, beyond hydrogen and ionic bonding, the catechol structure was oxidized, forming an ortho-quinone that crosslinked SPI and created a denser structure. Tensile strength measurements and freeze-thaw experiments revealed that the adhesive exhibited maximum tensile strength and optimal adhesion with 0.75% TA at pH 9, providing the best overall performance. This study provides a new formulation and approach for developing plant-based meat analogues adhesives.


Asunto(s)
Polifenoles , Reología , Proteínas de Soja , Taninos , Resistencia a la Tracción , Taninos/química , Proteínas de Soja/química , Concentración de Iones de Hidrógeno , Viscosidad , Adhesivos/química , Sustitutos de la Carne
4.
Brain Behav Immun ; 117: 356-375, 2024 03.
Artículo en Inglés | MEDLINE | ID: mdl-38320681

RESUMEN

Both exogenous gaseous and liquid forms of formaldehyde (FA) can induce depressive-like behaviors in both animals and humans. Stress and neuronal excitation can elicit brain FA generation. However, whether endogenous FA participates in depression occurrence remains largely unknown. In this study, we report that midbrain FA derived from lipopolysaccharide (LPS) is a direct trigger of depression. Using an acute depressive model in mice, we found that one-week intraperitoneal injection (i.p.) of LPS activated semicarbazide-sensitive amine oxidase (SSAO) leading to FA production from the midbrain vascular endothelium. In both in vitro and in vivo experiments, FA stimulated the production of cytokines such as IL-1ß, IL-6, and TNF-α. Strikingly, one-week microinfusion of FA as well as LPS into the midbrain dorsal raphe nucleus (DRN, a 5-HT-nergic nucleus) induced depressive-like behaviors and concurrent neuroinflammation. Conversely, NaHSO3 (a FA scavenger), improved depressive symptoms associated with a reduction in the levels of midbrain FA and cytokines. Moreover, the chronic depressive model of mice injected with four-week i.p. LPS exhibited a marked elevation in the levels of midbrain LPS accompanied by a substantial increase in the levels of FA and cytokines. Notably, four-week i.p. injection of FA as well as LPS elicited cytokine storm in the midbrain and disrupted the blood-brain barrier (BBB) by activating microglia and reducing the expression of claudin 5 (CLDN5, a protein with tight junctions in the BBB). However, the administration of 30 nm nano-packed coenzyme-Q10 (Q10, an endogenous FA scavenger), phototherapy (PT) utilizing 630-nm red light to degrade FA, and the combination of PT and Q10, reduced FA accumulation and neuroinflammation in the midbrain. Moreover, the combined therapy exhibited superior therapeutic efficacy in attenuating depressive symptoms compared to individual treatments. Thus, LPS-derived FA directly initiates depression onset, thereby suggesting that scavenging FA represents a promising strategy for depression treatment.


Asunto(s)
Depresión , Lipopolisacáridos , Humanos , Ratones , Animales , Lipopolisacáridos/farmacología , Depresión/tratamiento farmacológico , Enfermedades Neuroinflamatorias , Citocinas/metabolismo , Mesencéfalo/metabolismo , Formaldehído
5.
Cell Death Dis ; 15(1): 9, 2024 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-38182571

RESUMEN

Chromatin accessibility plays important roles in revealing the regulatory networks of gene expression, while its application in bladder cancer is yet to be fully elucidated. Chloride intracellular channel 3 (CLIC3) protein has been reported to be associated with the progression of some tumors, whereas the specific mechanism of CLIC3 in tumor remains unclear. Here, we screened for key genes in bladder cancer through the identification of transcription factor binding site clustered region (TFCR) on the basis of chromatin accessibility and TF motif. CLIC3 was identified by joint profiling of chromatin accessibility data with TCGA database. Clinically, CLIC3 expression was significantly elevated in bladder cancer and was negatively correlated with patient survival. CLIC3 promoted the proliferation of bladder cancer cells by reducing p21 expression in vitro and in vivo. Mechanistically, CLIC3 interacted with NAT10 and inhibited the function of NAT10, resulting in the downregulation of ac4C modification and stability of p21 mRNA. Overall, these findings uncover an novel mechanism of mRNA ac4C modification and CLIC3 may act as a potential therapeutic target for bladder cancer.


Asunto(s)
Neoplasias de la Vejiga Urinaria , Humanos , Canales de Cloruro/genética , Cromatina , Acetiltransferasas N-Terminal , ARN Mensajero/genética , Vejiga Urinaria , Neoplasias de la Vejiga Urinaria/genética
6.
J Am Chem Soc ; 146(2): 1563-1571, 2024 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-38141030

RESUMEN

Controllable ring-opening of polycyclic aromatic hydrocarbons plays a crucial role in various chemical and biological processes. However, breaking down aromatic covalent C-C bonds is exceptionally challenging due to their high stability and strong aromaticity. This study presents a seminal report on the precise and highly selective on-surface ring-opening of the seven-membered ring within the aromatic azulene moieties under mild conditions. The chemical structures of the resulting products were identified using bond-resolved scanning probe microscopy. Furthermore, through density functional theory calculations, we uncovered the mechanism behind the ring-opening process and elucidated its chemical driving force. The key to achieving this ring-opening process lies in manipulating the local aromaticity of the aromatic azulene moiety through strain-induced internal ring rearrangement and cyclodehydrogenation. By precisely controlling these factors, we successfully triggered the desired ring-opening reaction. Our findings not only provide valuable insights into the ring-opening process of polycyclic aromatic hydrocarbons but also open up new possibilities for the manipulation and reconstruction of these important chemical structures.

7.
Cancer Gene Ther ; 31(3): 439-453, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38146007

RESUMEN

Recurrence and extraocular metastasis in advanced intraocular retinoblastoma (RB) are still major obstacles for successful treatment of Chinese children. Tuberous sclerosis complex (TSC) is a very rare, multisystemic genetic disorder characterized by hamartomatous growth. In this study, we aimed to compare genomic and epigenomic profiles with human RB or TSC using recently developed nanopore sequencing, and to identify disease-associated variations or genes. Peripheral blood samples were collected from either RB or RB/TSC patients plus their normal siblings, followed by nanopore sequencing and identification of disease-specific structural variations (SVs) and differentially methylated regions (DMRs) by a systematic biology strategy named as multiomics-based joint screening framework. In total, 316 RB- and 1295 TSC-unique SVs were identified, as well as 1072 RB- and 1114 TSC-associated DMRs, respectively. We eventually identified 6 key genes for RB for further functional validation. Knockdown of CDK19 with specific siRNAs significantly inhibited Y79 cellular proliferation and increased sensitivity to carboplatin, whereas downregulation of AHNAK2 promoted the cell growth as well as drug resistance. Those two genes might serve as potential diagnostic markers or therapeutic targets of RB. The systematic biology strategy combined with functional validation might be an effective approach for rare pediatric malignances with limited samples and challenging collection process.


Asunto(s)
Secuenciación de Nanoporos , Neoplasias de la Retina , Retinoblastoma , Esclerosis Tuberosa , Niño , Humanos , Retinoblastoma/genética , Esclerosis Tuberosa/diagnóstico , Esclerosis Tuberosa/genética , Epigenómica , Genómica , Neoplasias de la Retina/genética , Neoplasias de la Retina/patología , Quinasas Ciclina-Dependientes
8.
Opt Express ; 31(22): 36638-36655, 2023 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-38017810

RESUMEN

Due to the inconsistent absorption and scattering effects of different wavelengths of light, underwater images often suffer from color casts, blurred details, and low visibility. To address this image degradation problem, we propose a robust and efficient underwater image enhancement method named UIEOGP. It can be divided into the following three steps. First, according to the light attenuation effect presented by Lambert Beer's law, combined with the variance change after attenuation, we estimate the depth of field in the underwater image. Then, we propose a local-based color correction algorithm to address the color cast issue in underwater images, employing the statistical distribution law. Finally, drawing inspiration from the law of light propagation, we propose detail enhancement algorithms, each based on the geometric properties of circles and ellipses, respectively. The enhanced images produced by our method feature vibrant colors, improved contrast, and sharper detail. Extensive experiments show that our method outperforms current state-of-the-art methods. In further experiments, we found that our method is beneficial for downstream tasks of underwater image processing, such as the detection of keypoints and edges in underwater images.

9.
Artif Cells Nanomed Biotechnol ; 51(1): 532-546, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37948136

RESUMEN

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related death. Therefore, we intend to explore novel strategies against PDAC. The exosomes-based biomimetic nanoparticle is an appealing candidate served as a drug carrier in cancer treatment, due to its inherit abilities. In the present study, we designed dasatinib-loaded hybrid exosomes by fusing human pancreatic cancer cells derived exosomes with dasatinib-loaded liposomes, followed by characterization for particle size (119.9 ± 6.10 nm) and zeta potential (-11.45 ± 2.24 mV). Major protein analysis from western blot techniques reveal the presence of exosome marker proteins CD9 and CD81. PEGylated hybrid exosomes showed pH-sensitive drug release in acidic condition, benefiting drug delivery to acidic cancer environment. Dasatinib-loaded hybrid exosomes exhibited significantly higher uptake rates and cytotoxicity to parent PDAC cells by two-sample t-test or by one-way ANOVA analysis of variance, as compared to free drug or liposomal formulations. The results from our computational analysis demonstrated that the drug-likeness, ADMET, and protein-ligand binding affinity of dasatinib are verified successfully. Cancer derived hybrid exosomes may serve as a potential therapeutic candidate for pancreatic cancer treatment.


Asunto(s)
Carcinoma Ductal Pancreático , Exosomas , Neoplasias Pancreáticas , Humanos , Dasatinib/farmacología , Dasatinib/metabolismo , Exosomas/metabolismo , Línea Celular Tumoral , Neoplasias Pancreáticas/patología , Carcinoma Ductal Pancreático/metabolismo , Carcinoma Ductal Pancreático/patología , Liposomas/metabolismo , Neoplasias Pancreáticas
10.
Chem Sci ; 14(23): 6420-6429, 2023 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-37325150

RESUMEN

The violation of the Kasha photoemission rule in organic molecules has intrigued chemists since their discovery, being always of relevance given its connection with unique electronic properties of molecules. However, an understanding of the molecular structure-anti-Kasha property relationship in organic materials has not been well-established, possibly because of the few existing cases available, limiting their prospective exploration and ad hoc design. Here we introduce a novel strategy to design organic emitters from high excited states combining intramolecular J-coupling of anti-Kasha chromophores with the hindering of vibrationally-induced non-radiative decay channels by enforcing molecular rigidity. We apply our approach to the integration of two antiparallel azulene units bridged with one heptalene all inserted into a polycyclic conjugated hydrocarbon (PCH). With the help of quantum chemistry calculations, we identify a suitable PCH embedding structure and predict its anti-Kasha emission from the third high energy excited singlet state. Finally, steady fluorescence and transient absorption spectroscopy studies corroborate the photophysical properties in a recently synthesized chemical derivative with this pre-designed structure.

11.
J Am Chem Soc ; 145(27): 14912-14921, 2023 Jul 12.
Artículo en Inglés | MEDLINE | ID: mdl-37338220

RESUMEN

Incorporating heteroatoms, such as nitrogen, oxygen, and/or sulfur atoms, into cycloarenes can effectively regulate their molecular geometries and (opto)electronic properties. However, the rarity of cycloarenes and heterocycloarenes limits the further exploitation of their applications. Herein, we designed and synthesized the first examples of boron and nitrogen (BN)-doped cycloarenes (BN-C1 and BN-C2) via one-pot intramolecular electrophilic borylation of imine-based macrocycles. BN-C2 adopts a bowl-shaped conformation, while BN-C1 possesses a planar geometry. Accordingly, the solubility of BN-C2 was significantly improved by replacing two hexagons in BN-C1 with two N-pentagons, due to the creation of distortions away from planarity. Various experiments and theoretical calculations were carried out for heterocycloarenes BN-C1 and BN-C2, demonstrating that the incorporated BN bonds diminish the aromaticity of 1,2-azaborine units and their adjacent benzenoid rings but preserve the dominant aromatic properties of pristine kekulene. Importantly, when two additional electron-rich nitrogen atoms were introduced, the highest occupied molecular orbital energy level of BN-C2 was elaborately lifted compared with that of BN-C1. As a result, the energy-level alignment of BN-C2 with the work function of the anode and the perovskite layer was suitable. Therefore, for the first time, heterocycloarene (BN-C2) was explored as a hole-transporting layer in inverted perovskite solar cell devices, in which the power conversion efficiency reached 14.4%.

12.
Genome Biol ; 24(1): 90, 2023 04 24.
Artículo en Inglés | MEDLINE | ID: mdl-37095580

RESUMEN

BACKGROUND: DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation. RESULTS: Here, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation. CONCLUSIONS: Our study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.


Asunto(s)
Cromatina , Reparación del ADN , ADN , Roturas del ADN de Doble Cadena , Proteínas de Unión al ADN/metabolismo
13.
Biotechnol Lett ; 45(5-6): 679-687, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-37071383

RESUMEN

OBJECTIVES: To better understand the unique inhibitory behavior of a non-natural cofactor preferred formaldehyde dehydrogenase (FalDH) mutant 9B2. RESULTS: We described our serendipitous observation that 9B2 was reversibly inhibited by residual imidazole introduced during protein preparation, while the wild-type enzyme was not sensitive to imidazole. Kinetic analysis showed that imidazole was a competitive inhibitor of formaldehyde with a Ki of 16 µM and an uncompetitive inhibitor of Nicotinamide Cytosine Dinucleotide for 9B2, indicating that formaldehyde and imidazole were combined in the same position. Molecular docking results of 9B2 showed that imidazole could favorably bind very close to the nicotinamide moiety of the cofactor, where formaldehyde was expected to reside for catalysis, which was in line with a competitive inhibition. CONCLUSION: The mutant 9B2 can be competitively inhibited by imidazole, suggesting that cautions should be taken to evaluate activities as protein mutants might attain unexpected sensitivity to a component in buffers for purification or activity assays.


Asunto(s)
Formaldehído , Imidazoles , Cinética , Simulación del Acoplamiento Molecular , Imidazoles/farmacología , Niacinamida
14.
Angew Chem Int Ed Engl ; 62(10): e202217124, 2023 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-36511094

RESUMEN

Incorporating non-hexagonal rings into polycyclic conjugated hydrocarbons (PCHs) can significantly affect their electronic and optoelectronic properties and chemical reactivities. Here, we report the first bottom-up synthesis of a dicyclohepta[a,g]heptalene-embedded PCH (1) with four continuous heptagons, which are arranged in a "Z" shape. Compared with its structural isomer bischrysene 1 R with only hexagonal rings, compound 1 presents a distinct antiaromatic character, especially the inner heptalene core, which possesses clear antiaromatic nature. In addition, PCH 1 exhibits a narrower highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gap than its benzenoid contrast 1 R, as verified by experimental measurements and theoretical calculations. Our work reported herein not only provides a new way to synthesize novel PCHs with non-alternant topologies but also offers the possibility to tune their electronic and optical properties.

15.
Environ Res ; 216(Pt 4): 114808, 2023 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-36379237

RESUMEN

Crystal plane regulation, defect engineering, and element doping can effectively solve the problems of large band gaps, poor light absorption, and fast recombination of BiOCl. In this work, iodine-doped BiOCl (I/BiOCl) nanowafers with abundant (110) crystal planes and oxygen vacancies (OV) were prepared by a simple hydrothermal method and assessed for pollutant photodegradation. I/BiOCl with a molar ratio of I to Cl of 0.6 (I0.6/BiOCl) degraded under visible light 95.8% of the toxic dye rhodamine B and 85.1% of the persistent antibiotic tetracycline in 5 and 10 min, respectively. In comparison, unmodified BiOCl photodegraded only between 42.0% and 48.2% of these critical water pollutants. Furthermore, I0.6/BiOCl was highly stable with most of its photocatalytic activity remaining after 4 cycles. Three reasons explain the excellent photodegradation properties of I0.6/BiOCl. First, the doped photocatalyst grew abundant (110) crystal planes, which inhibits the recombination of photogenerated electron-hole pairs. Second, the large quantity of OV present in I0.6/BiOCl increased active sites for reactive oxygen species generation, improved photogenerated charge separation, and pollutants adsorption. Lastly, I0.6/BiOCl had a modified electronic band structure enhancing light absorption. Overall, these results describe a promising photocatalyst capable of degrading efficiently major pollutants with different structures.


Asunto(s)
Contaminantes Ambientales , Yodo , Fotólisis , Oxígeno , Tetraciclina , Antibacterianos
16.
Chemosphere ; 311(Pt 2): 137000, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36309057

RESUMEN

Developing highly efficient heterostructured photocatalysts with robust redox ability is of great significance to wastewater purification. Herein, a novel Z-scheme AgI/Sb2WO6 heterojunction was successfully constructed via a chemical-precipitation method. The Z-scheme system can serve as a highly efficient photocatalyst for degradation of organic pollutants in water. Under visible light illumination, the degradation efficiency of rhodamine B and tetracycline over the optimal Z-scheme heterojunction can achieve 95% in 12 min and 80% in 8 min, which is 10.8 and 11.4 times higher than that over single Sb2WO6, respectively. Interestingly, low amounts of Ag0 can be generated and attached on the surface of Sb2WO6 during the photocatalytic process, further enhancing the photocatalytic activity of the Z-scheme heterojunction. Based on theoretical calculations, the interfacial internal electric field (IEF) can facilitate the photoexcited electrons at the conduction band (CB) of AgI to consume the photoexcited holes at the valence band (VB) of Sb2WO6, which greatly promotes the Z-scheme charge transfer path. Quenching experiments and electron spin resonance analyses demonstrate superoxide radicals play a major role in the photocatalytic reactions. The concept of constructing a Z-scheme heterojunction photocatalyst with efficient interfacial charge transfer shall provide a design guide for wastewater purification.


Asunto(s)
Electrones , Contaminantes Ambientales , Teoría Funcional de la Densidad , Luz , Iluminación
17.
Environ Sci Technol ; 56(24): 18008-18017, 2022 12 20.
Artículo en Inglés | MEDLINE | ID: mdl-36480705

RESUMEN

Photo-Fenton-like reaction based on oxalic acid (OA) activation is a promising method for the fast degradation of pollutants due to the low cost and safety. Hence, the magnetic recyclable greigite (Fe3S4) with the exposed {011} facet (FS-011) was prepared using a facile one-pot hydrothermal method and activated OA under visible light irradiation for pollutant removal, in which the removal efficiency values of FS-011 for metronidazole (MNZ) and hexavalent chromium were 2.02 and 1.88 times higher than that of Fe3S4 with the exposed {112} facet, respectively. Density functional theory calculations revealed that OA was more easily adsorbed by the {011} facet of Fe3S4 than by the {112} facet, and the in situ-generated H2O2 preferred to diffuse away from the active sites of the {011} facet of Fe3S4 than from that of the {112} facet, which was conducive to the continuous adsorption and efficient activation of OA. Moreover, the analyses of Fukui index and dual descriptor confirmed the degradation mechanism that the imidazole ring of MNZ was easy to be attacked by electrophilic species, while the amino group of MNZ was easy to be attacked by nucleophilic species. These findings deeply analyzed the mechanism of enhanced OA activation by facet engineering and consolidated the theoretical basis for practical application of Fenton-like reactions.


Asunto(s)
Contaminantes Ambientales , Ácido Oxálico , Peróxido de Hidrógeno , Teoría Funcional de la Densidad , Luz , Metronidazol , Catálisis
18.
Commun Biol ; 5(1): 1400, 2022 12 21.
Artículo en Inglés | MEDLINE | ID: mdl-36543858

RESUMEN

Posttranscriptional modification plays an important role in key embryonic processes. Adenosine-to-inosine RNA editing, a common example of such modifications, is widespread in human adult tissues and has various functional impacts and clinical consequences. However, whether it persists in a consistent pattern in most human embryos, and whether it supports embryonic development, are poorly understood. To address this problem, we compiled the largest human embryonic editome from 2,071 transcriptomes and identified thousands of recurrent embryonic edits (>=50% chances of occurring in a given stage) for each early developmental stage. We found that these recurrent edits prefer exons consistently across stages, tend to target genes related to DNA replication, and undergo organized loss in abnormal embryos and embryos from elder mothers. In particular, these recurrent edits are likely to enhance maternal mRNA clearance, a possible mechanism of which could be introducing more microRNA binding sites to the 3'-untranslated regions of clearance targets. This study suggests a potentially important, if not indispensable, role of RNA editing in key human embryonic processes such as maternal mRNA clearance; the identified editome can aid further investigations.


Asunto(s)
Edición de ARN , ARN Mensajero Almacenado , Humanos , Desarrollo Embrionario/genética , Exones , ARN/metabolismo , ARN Mensajero Almacenado/metabolismo
19.
Nat Commun ; 13(1): 5506, 2022 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-36127339

RESUMEN

Chemoresistance limits its clinical implementation for pancreatic ductal adenocarcinoma (PDAC). We previously generated an EGFR/HER2 targeted conjugate, dual-targeting ligand-based lidamycin (DTLL), which shows a highly potent antitumor effect. To overcome chemoresistance in PDAC, we aim to study DTLL efficacy when combined with gemcitabine and explore its mechanisms of action. DTLL in combination with gemcitabine show a superior inhibitory effect on the growth of gemcitabine-resistant/sensitive tumors. DTLL sensitizes gemcitabine efficacy via distinct action mechanisms mediated by mothers against decapentaplegic homolog 4 (SMAD4). It not only prevents neoplastic proliferation via ATK/mTOR blockade and NF-κB impaired function in SMAD4-sufficient PDACs, but also restores SMAD4 bioactivity to trigger downstream NF-κB-regulated signaling in SMAD4-deficient tumors and to overcome chemoresistance. DTLL seems to act as a SMAD4 module that normalizes its function in PDAC, having a synergistic effect in combination with gemcitabine. Our findings provide insight into a rational SMAD4-directed precision therapy in PDAC.


Asunto(s)
Carcinoma Ductal Pancreático , Neoplasias Pancreáticas , Aminoglicósidos , Carcinoma Ductal Pancreático/tratamiento farmacológico , Carcinoma Ductal Pancreático/genética , Carcinoma Ductal Pancreático/patología , Línea Celular Tumoral , Desoxicitidina/análogos & derivados , Enediinos , Receptores ErbB , Humanos , Ligandos , FN-kappa B/metabolismo , Neoplasias Pancreáticas/tratamiento farmacológico , Neoplasias Pancreáticas/patología , Proteína Smad4/genética , Serina-Treonina Quinasas TOR , Gemcitabina , Neoplasias Pancreáticas
20.
Genome Res ; 2022 Aug 17.
Artículo en Inglés | MEDLINE | ID: mdl-35977841

RESUMEN

During early mammalian embryo development, different epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code in a spatiotemporal manner remains difficult to analyze, markedly limiting scientific and clinical research. Here, we present dbEmbryo, an integrated and interactive multi-omics database for human and mouse early embryos. dbEmbryo integrates data on gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as "multi-omics visualization," "Gene&Peak annotation," "ZGA gene cluster," "cis-regulation," "synergistic regulation," "promoter signal enrichment," and "3D genome." Users can retrieve gene expression and epigenetic profile patterns to analyze synergistic changes across different early embryo developmental stages. We showed the uniqueness of dbEmbryo among extant databases containing data on early embryo development and provided an overview. Using dbEmbryo, we obtained a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.

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