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1.
Cell ; 187(13): 3284-3302.e23, 2024 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-38843832

RESUMEN

The cleavage of zygotes generates totipotent blastomeres. In human 8-cell blastomeres, zygotic genome activation (ZGA) occurs to initiate the ontogenesis program. However, capturing and maintaining totipotency in human cells pose significant challenges. Here, we realize culturing human totipotent blastomere-like cells (hTBLCs). We find that splicing inhibition can transiently reprogram human pluripotent stem cells into ZGA-like cells (ZLCs), which subsequently transition into stable hTBLCs after long-term passaging. Distinct from reported 8-cell-like cells (8CLCs), both ZLCs and hTBLCs widely silence pluripotent genes. Interestingly, ZLCs activate a particular group of ZGA-specific genes, and hTBLCs are enriched with pre-ZGA-specific genes. During spontaneous differentiation, hTBLCs re-enter the intermediate ZLC stage and further generate epiblast (EPI)-, primitive endoderm (PrE)-, and trophectoderm (TE)-like lineages, effectively recapitulating human pre-implantation development. Possessing both embryonic and extraembryonic developmental potency, hTBLCs can autonomously generate blastocyst-like structures in vitro without external cell signaling. In summary, our study provides key criteria and insights into human cell totipotency.


Asunto(s)
Diferenciación Celular , Empalmosomas , Animales , Humanos , Ratones , Blastocisto/metabolismo , Blastocisto/citología , Blastómeros/metabolismo , Blastómeros/citología , Reprogramación Celular , Desarrollo Embrionario/genética , Estratos Germinativos/metabolismo , Estratos Germinativos/citología , Células Madre Pluripotentes/metabolismo , Células Madre Pluripotentes/citología , Empalme del ARN , Empalmosomas/metabolismo , Células Madre Totipotentes/metabolismo , Células Madre Totipotentes/citología , Cigoto/metabolismo , Células Cultivadas , Modelos Moleculares , Estructura Terciaria de Proteína , Genoma Humano , Análisis de la Célula Individual , Factor 15 de Diferenciación de Crecimiento/química , Factor 15 de Diferenciación de Crecimiento/genética , Factor 15 de Diferenciación de Crecimiento/metabolismo , Epigenómica , Linaje de la Célula
2.
Cell ; 186(20): 4271-4288.e24, 2023 Sep 28.
Artículo en Inglés | MEDLINE | ID: mdl-37699390

RESUMEN

Endometrial decidualization connecting embryo implantation and placentation is transient but essential for successful pregnancy, which, however, is not systematically investigated. Here, we use a scStereo-seq technology to spatially visualize and define the dynamic functional decidual hubs assembled by distinct immune, endothelial, trophoblast, and decidual stromal cells (DSCs) in early pregnant mice. We unravel the DSC transdifferentiation trajectory and surprisingly discover a dual-featured type of immune-featured DSCs (iDSCs). We find that immature DSCs attract immune cells and induce decidual angiogenesis at the mesenchymal-epithelial transition hub during decidualization initiation. iDSCs enable immune cell recruitment and suppression, govern vascularization, and promote cytolysis at immune cell assembling and vascular hubs, respectively, to establish decidual homeostasis at a later stage. Interestingly, dysfunctional and spatially disordered iDSCs cause abnormal accumulation of immune cells in the vascular hub, which disrupts decidual hub specification and eventually leads to pregnancy complications in DBA/2-mated CBA/J mice.

3.
Cell ; 186(26): 5892-5909.e22, 2023 12 21.
Artículo en Inglés | MEDLINE | ID: mdl-38091994

RESUMEN

Different functional regions of brain are fundamental for basic neurophysiological activities. However, the regional specification remains largely unexplored during human brain development. Here, by combining spatial transcriptomics (scStereo-seq) and scRNA-seq, we built a spatiotemporal developmental atlas of multiple human brain regions from 6-23 gestational weeks (GWs). We discovered that, around GW8, radial glia (RG) cells have displayed regional heterogeneity and specific spatial distribution. Interestingly, we found that the regional heterogeneity of RG subtypes contributed to the subsequent neuronal specification. Specifically, two diencephalon-specific subtypes gave rise to glutamatergic and GABAergic neurons, whereas subtypes in ventral midbrain were associated with the dopaminergic neurons. Similar GABAergic neuronal subtypes were shared between neocortex and diencephalon. Additionally, we revealed that cell-cell interactions between oligodendrocyte precursor cells and GABAergic neurons influenced and promoted neuronal development coupled with regional specification. Altogether, this study provides comprehensive insights into the regional specification in the developing human brain.


Asunto(s)
Encéfalo , Transcriptoma , Humanos , Neuronas Dopaminérgicas , Neuronas GABAérgicas , Mesencéfalo , Neocórtex , Encéfalo/crecimiento & desarrollo , Encéfalo/metabolismo
4.
Cell ; 184(11): 2843-2859.e20, 2021 05 27.
Artículo en Inglés | MEDLINE | ID: mdl-33991488

RESUMEN

Since establishment of the first embryonic stem cells (ESCs), in vitro culture of totipotent cells functionally and molecularly comparable with in vivo blastomeres with embryonic and extraembryonic developmental potential has been a challenge. Here we report that spliceosomal repression in mouse ESCs drives a pluripotent-to-totipotent state transition. Using the splicing inhibitor pladienolide B, we achieve stable in vitro culture of totipotent ESCs comparable at molecular levels with 2- and 4-cell blastomeres, which we call totipotent blastomere-like cells (TBLCs). Mouse chimeric assays combined with single-cell RNA sequencing (scRNA-seq) demonstrate that TBLCs have a robust bidirectional developmental capability to generate multiple embryonic and extraembryonic cell lineages. Mechanically, spliceosomal repression causes widespread splicing inhibition of pluripotent genes, whereas totipotent genes, which contain few short introns, are efficiently spliced and transcriptionally activated. Our study provides a means for capturing and maintaining totipotent stem cells.


Asunto(s)
Células Madre Totipotentes/citología , Células Madre Totipotentes/metabolismo , Animales , Blastómeros/citología , Diferenciación Celular/genética , Línea Celular , Linaje de la Célula/genética , Embrión de Mamíferos/citología , Células Madre Embrionarias/citología , Femenino , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos ICR , Células Madre Embrionarias de Ratones/citología , Células Madre Totipotentes/fisiología
5.
Cell ; 179(5): 1160-1176.e24, 2019 11 14.
Artículo en Inglés | MEDLINE | ID: mdl-31730855

RESUMEN

Pediatric-onset colitis and inflammatory bowel disease (IBD) have significant effects on the growth of infants and children, but the etiopathogenesis underlying disease subtypes remains incompletely understood. Here, we report single-cell clustering, immune phenotyping, and risk gene analysis for children with undifferentiated colitis, Crohn's disease, and ulcerative colitis. We demonstrate disease-specific characteristics, as well as common pathogenesis marked by impaired cyclic AMP (cAMP)-response signaling. Specifically, infiltration of PDE4B- and TNF-expressing macrophages, decreased abundance of CD39-expressing intraepithelial T cells, and platelet aggregation and release of 5-hydroxytryptamine at the colonic mucosae were common in colitis and IBD patients. Targeting these pathways by using the phosphodiesterase inhibitor dipyridamole restored immune homeostasis and improved colitis symptoms in a pilot study. In summary, comprehensive analysis of the colonic mucosae has uncovered common pathogenesis and therapeutic targets for children with colitis and IBD.


Asunto(s)
Enfermedades Inflamatorias del Intestino/patología , Enfermedades Inflamatorias del Intestino/terapia , Mucosa Intestinal/patología , Antígenos CD/metabolismo , Apirasa/metabolismo , Linfocitos B/efectos de los fármacos , Linfocitos B/inmunología , Muerte Celular/efectos de los fármacos , Microambiente Celular/efectos de los fármacos , Niño , Estudios de Cohortes , Colon/patología , Células Dendríticas/efectos de los fármacos , Células Dendríticas/metabolismo , Dipiridamol/farmacología , Células Endoteliales/efectos de los fármacos , Células Endoteliales/metabolismo , Células Epiteliales/efectos de los fármacos , Células Epiteliales/metabolismo , Células Epiteliales/patología , Fibroblastos/efectos de los fármacos , Fibroblastos/metabolismo , Regulación de la Expresión Génica/efectos de los fármacos , Predisposición Genética a la Enfermedad , Homeostasis/efectos de los fármacos , Humanos , Inmunoglobulina G/sangre , Memoria Inmunológica , Inflamación/patología , Enfermedades Inflamatorias del Intestino/sangre , Enfermedades Inflamatorias del Intestino/genética , Interferón Tipo I/metabolismo , Macrófagos/efectos de los fármacos , Macrófagos/metabolismo , Metilprednisolona/farmacología , Células Mieloides/efectos de los fármacos , Células Mieloides/metabolismo
6.
Mol Cell ; 84(14): 2665-2681.e13, 2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-38955180

RESUMEN

During implantation, embryos undergo an unpolarized-to-polarized transition to initiate postimplantation morphogenesis. However, the underlying molecular mechanism is unknown. Here, we identify a transient transcriptional activation governing embryonic morphogenesis and pluripotency transition during implantation. In naive pluripotent embryonic stem cells (ESCs), which represent preimplantation embryos, we find that the microprocessor component DGCR8 can recognize stem-loop structures within nascent mRNAs to sequester transcriptional coactivator FLII to suppress transcription directly. When mESCs exit from naive pluripotency, the ERK/RSK/P70S6K pathway rapidly activates, leading to FLII phosphorylation and disruption of DGCR8/FLII interaction. Phosphorylated FLII can bind to transcription factor JUN, activating cell migration-related genes to establish poised pluripotency akin to implanting embryos. Resequestration of FLII by DGCR8 drives poised ESCs into formative pluripotency. In summary, we identify a DGCR8/FLII/JUN-mediated transient transcriptional activation mechanism. Disruption of this mechanism inhibits naive-poised-formative pluripotency transition and the corresponding unpolarized-to-polarized transition during embryo implantation, which are conserved in mice and humans.


Asunto(s)
Implantación del Embrión , Regulación del Desarrollo de la Expresión Génica , Morfogénesis , Activación Transcripcional , Animales , Implantación del Embrión/genética , Ratones , Humanos , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/genética , Fosforilación , Células Madre Embrionarias de Ratones/metabolismo , Células Madre Embrionarias de Ratones/citología , Femenino , Proteínas Proto-Oncogénicas c-jun/metabolismo , Proteínas Proto-Oncogénicas c-jun/genética , Transducción de Señal
7.
Nature ; 601(7892): 257-262, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34937940

RESUMEN

The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea1-3. However, recent culture-independent studies have suggested that the archaeon 'Candidatus Methanoliparum' alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C≤12) were not consumed. The wide distribution of Ca. Methanoliparum4-6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.


Asunto(s)
Euryarchaeota , Hidrocarburos , Metano , Alcanos/metabolismo , Biodegradación Ambiental , Euryarchaeota/enzimología , Euryarchaeota/genética , Hidrocarburos/metabolismo , Metano/metabolismo , Oxidorreductasas/metabolismo , Filogenia
8.
Proc Natl Acad Sci U S A ; 121(7): e2315688121, 2024 Feb 13.
Artículo en Inglés | MEDLINE | ID: mdl-38315857

RESUMEN

Integrating reactive radicals into membranes that resemble biological membranes has always been a pursuit for simultaneous organics degradation and water filtration. In this research, we discovered that a radical polymer (RP) that can directly trigger the oxidative degradation of sulfamethozaxole (SMX). Mechanistic studies by experiment and density functional theory simulations revealed that peroxyl radicals are the reactive species, and the radicals could be regenerated in the presence of O2. Furthermore, an interpenetrating RP network membrane consisting of polyvinyl alcohol and the RP was fabricated to demonstrate the simultaneous filtration of large molecules in the model wastewater stream and the degradation of ~ 85% of SMX with a steady permeation flux. This study offers valuable insights into the mechanism of RP-triggered advanced oxidation processes and provides an energy-efficient solution for the degradation of organic compounds and water filtration in wastewater treatment.

9.
Proc Natl Acad Sci U S A ; 121(18): e2319833121, 2024 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-38648480

RESUMEN

Sirt2 is a nicotinamide adenine dinucleotide (NAD+)-dependent protein lysine deacylase that can remove both acetyl group and long-chain fatty acyl groups from lysine residues of many proteins. It was reported to affect inflammatory bowel disease (IBD) symptoms in a mouse model. However, conflicting roles were reported, with genetic knockout aggravating while pharmacological inhibition alleviating IBD symptoms. These seemingly conflicting reports cause confusion and deter further efforts in developing Sirt2 inhibitors as a potential treatment strategy for IBD. We investigated these conflicting reports and elucidated the role of Sirt2 in the mouse model of IBD. We essentially replicated these conflicting results and confirmed that Sirt2 inhibitors' protective effect is not through off-targets as two very different Sirt2 inhibitors (TM and AGK2) showed similar protection in the IBD mouse model. We believe that the differential effects of inhibitors and knockout are due to the fact that the Sirt2 inhibitors only inhibit some but not all the activities of Sirt2. This hypothesis is confirmed by the observation that a PROTAC degrader of Sirt2 did not protect mice in the IBD model, similar to Sirt2 knockout. Our study provides an interesting example where genetic knockout and pharmacological inhibition do not align and emphasizes the importance of developing substrate-dependent inhibitors. Importantly, we showed that the effect of Sirt2 inhibition in IBD is through regulating the gut epithelium barrier by inhibiting Arf6-mediated endocytosis of E-cadherin, a protein important for the intestinal epithelial integrity. This mechanistic understanding further supports Sirt2 as a promising therapeutic target for treating IBD.


Asunto(s)
Colitis , Mucosa Intestinal , Sirtuina 2 , Animales , Humanos , Ratones , Cadherinas/metabolismo , Cadherinas/genética , Colitis/inducido químicamente , Colitis/tratamiento farmacológico , Colitis/prevención & control , Modelos Animales de Enfermedad , Furanos , Enfermedades Inflamatorias del Intestino/metabolismo , Enfermedades Inflamatorias del Intestino/tratamiento farmacológico , Enfermedades Inflamatorias del Intestino/patología , Mucosa Intestinal/metabolismo , Mucosa Intestinal/efectos de los fármacos , Mucosa Intestinal/patología , Ratones Endogámicos C57BL , Ratones Noqueados , Quinolinas , Sirtuina 2/metabolismo , Sirtuina 2/antagonistas & inhibidores , Sirtuina 2/genética
10.
PLoS Genet ; 20(9): e1011151, 2024 Sep 09.
Artículo en Inglés | MEDLINE | ID: mdl-39250516

RESUMEN

Genetic studies of blood pressure (BP) traits to date have been performed on conventional measures by brachial cuff sphygmomanometer for systolic BP (SBP) and diastolic BP, integrating several physiologic occurrences. Genetic associations with central SBP (cSBP) have not been well-studied. Genetic discovery studies of BP have been most often performed in European-ancestry samples. Here, we investigated genetic associations with cSBP in a Chinese population and functionally validated the impact of a novel associated coiled-coil domain containing 93 (CCDC93) gene on BP regulation. An exome-wide association study (EWAS) was performed using a mixed linear model of non-invasive cSBP and peripheral BP traits in a Han Chinese population (N = 5,954) from Beijing, China genotyped with a customized Illumina ExomeChip array. We identified four SNP-trait associations with three SNPs, including two novel associations (rs2165468-SBP and rs33975708-cSBP). rs33975708 is a coding variant in the CCDC93 gene, c.535C>T, p.Arg179Cys (MAF = 0.15%), and was associated with increased cSBP (ß = 29.3 mmHg, P = 1.23x10-7). CRISPR/Cas9 genome editing was used to model the effect of Ccdc93 loss in mice. Homozygous Ccdc93 deletion was lethal prior to day 10.5 of embryonic development. Ccdc93+/- heterozygous mice were viable and morphologically normal, with 1.3-fold lower aortic Ccdc93 protein expression (P = 0.0041) and elevated SBP as compared to littermate Ccdc93+/+ controls (110±8 mmHg vs 125±10 mmHg, P = 0.016). Wire myography of Ccdc93+/- aortae showed impaired acetylcholine-induced relaxation and enhanced phenylephrine-induced contraction. RNA-Seq transcriptome analysis of Ccdc93+/- mouse thoracic aortae identified significantly enriched pathways altered in fatty acid metabolism and mitochondrial metabolism. Plasma free fatty acid levels were elevated in Ccdc93+/- mice (96±7mM vs 124±13mM, P = 0.0031) and aortic mitochondrial dysfunction was observed through aberrant Parkin and Nix protein expression. Together, our genetic and functional studies support a novel role of CCDC93 in the regulation of BP through its effects on vascular mitochondrial function and endothelial function.

11.
Nature ; 586(7829): 434-439, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-33029007

RESUMEN

Cysteine palmitoylation (S-palmitoylation) is a reversible post-translational modification that is installed by the DHHC family of palmitoyltransferases and is reversed by several acyl protein thioesterases1,2. Although thousands of human proteins are known to undergo S-palmitoylation, how this modification is regulated to modulate specific biological functions is poorly understood. Here we report that the key T helper 17 (TH17) cell differentiation stimulator, STAT33,4, is subject to reversible S-palmitoylation on cysteine 108. DHHC7 palmitoylates STAT3 and promotes its membrane recruitment and phosphorylation. Acyl protein thioesterase 2 (APT2, also known as LYPLA2) depalmitoylates phosphorylated STAT3 (p-STAT3) and enables it to translocate to the nucleus. This palmitoylation-depalmitoylation cycle enhances STAT3 activation and promotes TH17 cell differentiation; perturbation of either palmitoylation or depalmitoylation negatively affects TH17 cell differentiation. Overactivation of TH17 cells is associated with several inflammatory diseases, including inflammatory bowel disease (IBD). In a mouse model, pharmacological inhibition of APT2 or knockout of Zdhhc7-which encodes DHHC7-relieves the symptoms of IBD. Our study reveals not only a potential therapeutic strategy for the treatment of IBD but also a model through which S-palmitoylation regulates cell signalling, which might be broadly applicable for understanding the signalling functions of numerous S-palmitoylation events.


Asunto(s)
Diferenciación Celular , Colitis/inmunología , Colitis/patología , Lipoilación , Factor de Transcripción STAT3/química , Factor de Transcripción STAT3/metabolismo , Células Th17/citología , Células Th17/inmunología , Acetiltransferasas/deficiencia , Acetiltransferasas/genética , Acetiltransferasas/metabolismo , Aciltransferasas/antagonistas & inhibidores , Aciltransferasas/metabolismo , Animales , Membrana Celular/metabolismo , Núcleo Celular/metabolismo , Colitis/tratamiento farmacológico , Colitis/metabolismo , Modelos Animales de Enfermedad , Femenino , Células HEK293 , Humanos , Enfermedades Inflamatorias del Intestino/metabolismo , Enfermedades Inflamatorias del Intestino/patología , Masculino , Ratones , Transporte de Proteínas , Células Th17/metabolismo , Tioléster Hidrolasas/antagonistas & inhibidores , Tioléster Hidrolasas/metabolismo , Regulación hacia Arriba
12.
Proc Natl Acad Sci U S A ; 120(15): e2221980120, 2023 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-37023128

RESUMEN

Aqueous zinc-ion batteries are emerging as one of the most promising large-scale energy storage systems due to their low cost and high safety. However, Zn anodes often encounter the problems of Zn dendrite growth, hydrogen evolution reaction, and formation of by-products. Herein, we developed the low ionic association electrolytes (LIAEs) by introducing 2, 2, 2-trifluoroethanol (TFE) into 30 m ZnCl2 electrolyte. Owing to the electron-withdrawing effect of -CF3 groups in TFE molecules, in LIAEs, the Zn2+ solvation structures convert from larger aggregate clusters into smaller parts and TFE will construct H-bonds with H2O in Zn2+ solvation structure simultaneously. Consequently, ionic migration kinetics are significantly enhanced and the ionization of solvated H2O is effectively suppressed in LIAEs. As a result, Zn anodes in LIAE display a fast plating/stripping kinetics and high Coulombic efficiency of 99.74%. The corresponding full batteries exhibit an improved comprehensive performance such as high-rate capability and long cycling life.

13.
J Biol Chem ; 300(2): 105591, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38141769

RESUMEN

Long noncoding RNAs (lncRNAs) are specifically expressed in different diseases and regulate disease progression. To explore the functions of rheumatoid arthritis (RA)-specific lncRNA, we determined the lncRNA expression profile of fibroblast-like synoviocytes (FLS) obtained from patients with RA and osteoarthritis (OA) using a LncRNA microarray and identified up-regulated LncNFYB in RA as a potential therapeutic target. Using gain- and loss-of-function studies, LncNFYB was proven to promote FLS proliferation and cell cycle progress but not affect their invasion, migration, and apoptotic abilities. Further investigation discovered that LncRNA could combine with annexin A2 (ANXA2) and enhance the level of phospho-ANXA2 (Tyr24) in the plasma membrane area, which induced the activation of ERK1/2 to promote proliferation. These findings provide new insights into the biological functions of LncNFYB on modification of FLS, which may be exploited for the therapy of RA.


Asunto(s)
Anexina A2 , Artritis Reumatoide , Sistema de Señalización de MAP Quinasas , ARN Largo no Codificante , Sinoviocitos , Humanos , Anexina A2/genética , Anexina A2/metabolismo , Artritis Reumatoide/genética , Artritis Reumatoide/metabolismo , Artritis Reumatoide/fisiopatología , Proliferación Celular/genética , Células Cultivadas , Activación Enzimática/genética , Fibroblastos/citología , Fibroblastos/metabolismo , Perfilación de la Expresión Génica , Osteoartritis/genética , Osteoartritis/metabolismo , Osteoartritis/fisiopatología , Fosforilación/genética , Unión Proteica/genética , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Sinoviocitos/citología , Sinoviocitos/metabolismo
14.
Bioinformatics ; 40(6)2024 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-38897656

RESUMEN

MOTIVATION: Predicting protein-ligand binding affinity is crucial in new drug discovery and development. However, most existing models rely on acquiring 3D structures of elusive proteins. Combining amino acid sequences with ligand sequences and better highlighting active sites are also significant challenges. RESULTS: We propose an innovative neural network model called DEAttentionDTA, based on dynamic word embeddings and a self-attention mechanism, for predicting protein-ligand binding affinity. DEAttentionDTA takes the 1D sequence information of proteins as input, including the global sequence features of amino acids, local features of the active pocket site, and linear representation information of the ligand molecule in the SMILE format. These three linear sequences are fed into a dynamic word-embedding layer based on a 1D convolutional neural network for embedding encoding and are correlated through a self-attention mechanism. The output affinity prediction values are generated using a linear layer. We compared DEAttentionDTA with various mainstream tools and achieved significantly superior results on the same dataset. We then assessed the performance of this model in the p38 protein family. AVAILABILITY AND IMPLEMENTATION: The resource codes are available at https://github.com/whatamazing1/DEAttentionDTA.


Asunto(s)
Redes Neurales de la Computación , Unión Proteica , Proteínas , Ligandos , Proteínas/química , Proteínas/metabolismo , Secuencia de Aminoácidos , Programas Informáticos , Sitios de Unión , Biología Computacional/métodos , Bases de Datos de Proteínas
15.
Bioinformatics ; 40(1)2024 01 02.
Artículo en Inglés | MEDLINE | ID: mdl-38058211

RESUMEN

MOTIVATION: Pediatric kidney disease is a widespread, progressive condition that severely impacts growth and development of children. Chronic kidney disease is often more insidious in children than in adults, usually requiring a renal biopsy for diagnosis. Biopsy evaluation requires copious examination by trained pathologists, which can be tedious and prone to human error. In this study, we propose an artificial intelligence (AI) method to assist pathologists in accurate segmentation and classification of pediatric kidney structures, named as AI-based Pediatric Kidney Diagnosis (APKD). RESULTS: We collected 2935 pediatric patients diagnosed with kidney disease for the development of APKD. The dataset comprised 93 932 histological structures annotated manually by three skilled nephropathologists. APKD scored an average accuracy of 94% for each kidney structure category, including 99% in the glomerulus. We found strong correlation between the model and manual detection in detected glomeruli (Spearman correlation coefficient r = 0.98, P < .001; intraclass correlation coefficient ICC = 0.98, 95% CI = 0.96-0.98). Compared to manual detection, APKD was approximately 5.5 times faster in segmenting glomeruli. Finally, we show how the pathological features extracted by APKD can identify focal abnormalities of the glomerular capillary wall to aid in the early diagnosis of pediatric kidney disease. AVAILABILITY AND IMPLEMENTATION: https://github.com/ChunyueFeng/Kidney-DataSet.


Asunto(s)
Inteligencia Artificial , Insuficiencia Renal Crónica , Adulto , Humanos , Niño , Riñón/diagnóstico por imagen , Riñón/patología , Insuficiencia Renal Crónica/patología
16.
Plant Physiol ; 2024 Sep 09.
Artículo en Inglés | MEDLINE | ID: mdl-39250752

RESUMEN

Colletotrichum brevisporum is an important fungal pathogen that causes anthracnose and has led to serious postharvest losses of papaya (Carica papaya L.) fruit in recent years. WRKY transcription factors play vital roles in regulating plant resistance to pathogens, but their functions in papaya anthracnose resistance need further exploration. In this study, we identified a WRKY transcription factor, CpWRKY50, which belongs to the WRKY IIc subfamily. During infection with C. brevisporum, expression of CpWRKY50 in anthracnose-resistant papaya cultivars was significantly higher than that in susceptible cultivars. CpWRKY50 was induced by methyl jasmonate, and CpWRKY50 localized in the nucleus. In yeast, full-length CpWRKY50 had transactivation activity, but CpWRKY50 variants truncated at the N or C termini did not. CpWRKY50 positively regulated papaya resistance to C. brevisporum, as demonstrated by transient overexpression of CpWRKY50 in papaya and heterologous expression of CpWRKY50 in tomato. Moreover, endogenous jasmonic acid (JA) and JA-isoleucine levels in the fruits of transgenic tomato OE lines were higher than in wild type both before and after inoculation with C. brevisporum, indicating that increased CpWRKY50 expression promotes JA accumulation. Furthermore, our results revealed CpWRKY50 directly binds to W-box motifs (TTGACC) in the promoters of two JA signaling-related genes, CpMYC2 and pathogenesis-related 4 CpPR4, thereby activating their expression. Our data support that CpWRKY50 positively regulates anthracnose resistance in papaya by promoting JA signaling. These results broaden our understanding of papaya disease resistance mechanisms and will facilitate the genetic improvement of papaya through molecular breeding.

17.
Stem Cells ; 2024 Sep 12.
Artículo en Inglés | MEDLINE | ID: mdl-39269318

RESUMEN

Transplanted mesenchymal stem cells (MSCs) can significantly aid in repairing spinal cord injuries (SCI) by migrating to and settling at the injury site. However, this process is typically inefficient, as only a small fraction of MSCs successfully reach the target lesion area. During SCI, the increased expression and secretion of hepatocyte growth factor (HGF) act as a chemoattractant that guides MSC migration. Nonetheless, the precise mechanisms by which HGF influences MSC migration are not fully understood. This study focused on unraveling the molecular pathways that drive MSC migration towards the SCI site in response to HGF. It was found that HGF can activate ß-catenin signaling in MSCs either by phosphorylating LRP6 or by suppressing GSK3ß phosphorylation through the AKT and ERK1/2 pathways, or by enhancing the expression and nuclear translocation of TCF4. This activation leads to elevated Nedd9 expression, which promotes focal adhesion formation and F-actin polymerization, facilitating chemotactic migration. Transplanting MSCs during peak HGF expression in injured tissues substantially improves nerve regeneration, reduces scarring, and enhances hind limb mobility. Additionally, prolonging HGF release can further boost MSC migration and engraftment, thereby amplifying regenerative outcomes. However, inhibiting HGF/Met or interfering with ß-catenin or Nedd9 signaling significantly impairs MSC engraftment, obstructing tissue repair and functional recovery. Together, these findings provide a theoretical basis and practical strategy for MSC transplantation therapy in SCI, highlighting the specific molecular mechanisms by which HGF regulates ß-catenin signaling in MSCs, ultimately triggering their chemotactic migration.

18.
J Pathol ; 262(2): 175-188, 2024 02.
Artículo en Inglés | MEDLINE | ID: mdl-37946610

RESUMEN

Neuropilin-2 (NRP2) is a multifunctional protein engaged in the regulation of angiogenesis, lymphangiogenesis, axon guidance, and tumor metastasis, but its function in colitis remains unclear. Here, we found that NRP2 was an inflammation-sensing protein rapidly and dramatically induced in myeloid cells, especially in macrophages, under inflammatory contexts. NRP2 deficiency in myeloid cells exacerbated dextran sulfate sodium salt-induced experimental colitis by promoting polarization of M1 macrophages and colon injury. Mechanistically, NRP2 could be induced via NF-κB activation by TNF-α in macrophages, but exerted an inhibitory effect on NF-κB signaling, forming a negative feedback loop with NF-κB to sense and alleviate inflammation. Deletion of NRP2 in macrophages broke this negative feedback circuit, leading to NF-κB overactivation, inflammatory exacerbation, and more severe colitis. Collectively, these findings reveal inflammation restriction as a role for NRP2 in macrophages under inflammation contexts and suggest that NRP2 in macrophages may relieve inflammation in inflammatory bowel disease. © 2023 The Pathological Society of Great Britain and Ireland.


Asunto(s)
Colitis , FN-kappa B , Humanos , Animales , Ratones , FN-kappa B/metabolismo , Neuropilina-2/genética , Neuropilina-2/metabolismo , Colitis/patología , Inflamación/patología , Macrófagos/patología , Sulfato de Dextran/toxicidad , Sulfato de Dextran/metabolismo , Ratones Endogámicos C57BL , Modelos Animales de Enfermedad
19.
Rev Med Virol ; 34(5): e2575, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39160646

RESUMEN

Neurotropic viral infections pose a significant challenge due to their ability to target the central nervous system and cause severe neurological complications. Traditional antiviral therapies face limitations in effectively treating these infections, primarily due to the blood-brain barrier, which restricts the delivery of therapeutic agents to the central nervous system. Nanoparticle-based therapies have emerged as a promising approach to overcome these challenges. Nanoparticles offer unique properties that facilitate drug delivery across biological barriers, such as the blood-brain barrier, and can be engineered to possess antiviral activities.


Asunto(s)
Antivirales , Barrera Hematoencefálica , Enfermedades Virales del Sistema Nervioso Central , Nanopartículas , Humanos , Nanopartículas/química , Antivirales/uso terapéutico , Antivirales/farmacología , Animales , Barrera Hematoencefálica/efectos de los fármacos , Enfermedades Virales del Sistema Nervioso Central/tratamiento farmacológico , Enfermedades Virales del Sistema Nervioso Central/virología , Sistemas de Liberación de Medicamentos , Virosis/tratamiento farmacológico , Virosis/virología
20.
J Immunol ; 210(8): 1098-1107, 2023 04 15.
Artículo en Inglés | MEDLINE | ID: mdl-36881861

RESUMEN

Cyclic GMP-AMP synthase (cGAS), as a cytosolic DNA sensor, plays a crucial role in antiviral immunity, and its overactivation induces excess inflammation and tissue damage. Macrophage polarization is critically involved in inflammation; however, the role of cGAS in macrophage polarization during inflammation remains unclear. In this study, we demonstrated that cGAS was upregulated in the LPS-induced inflammatory response via the TLR4 pathway, and cGAS signaling was activated by mitochondria DNA in macrophages isolated from C57BL/6J mice. We further demonstrated that cGAS mediated inflammation by acting as a macrophage polarization switch, which promoted peritoneal macrophages and the bone marrow-derived macrophages to the inflammatory phenotype (M1) via the mitochondrial DNA-mTORC1 pathway. In vivo studies verified that deletion of Cgas alleviated sepsis-induced acute lung injury by promoting macrophages to shift from the M1 phenotype to the M2 phenotype. In conclusion, our study demonstrated that cGAS mediated inflammation by regulating macrophage polarization through the mTORC1 pathway, and it further provided a potential therapeutic strategy for inflammatory diseases, especially sepsis-induced acute lung injury.


Asunto(s)
Lesión Pulmonar Aguda , Macrófagos , Diana Mecanicista del Complejo 1 de la Rapamicina , Nucleotidiltransferasas , Sepsis , Animales , Ratones , ADN Mitocondrial/metabolismo , Inflamación , Macrófagos/metabolismo , Ratones Endogámicos C57BL , Nucleotidiltransferasas/genética , Nucleotidiltransferasas/metabolismo , Fenotipo , Diana Mecanicista del Complejo 1 de la Rapamicina/metabolismo
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