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1.
Mol Cell ; 82(18): 3333-3349.e9, 2022 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-35981542

RESUMEN

The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, c-Jun, and CTCF. While E2F/DP facilitates RB association with promoters, AP-1 recruits RB to enhancers. Although phosphorylation in CDK sites is often portrayed as releasing RB from chromatin, we show that the cell cycle redistributes RB so that it enriches at promoters in G1 and at non-promoter sites in cycling cells. RB-bound promoters include the classic E2F-targets and are similar between lineages, but RB-bound enhancers associate with different categories of genes and vary between cell types. Thus, RB has a well-preserved role controlling E2F in G1, and it targets cell-type-specific enhancers and CTCF sites when cells enter S-phase.


Asunto(s)
Cromatina , Proteína de Retinoblastoma , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Cromatina/genética , Factores de Transcripción E2F/genética , Factores de Transcripción E2F/metabolismo , Factor de Transcripción E2F1/genética , Factor de Transcripción E2F1/metabolismo , Regiones Promotoras Genéticas , Proteína de Retinoblastoma/genética , Proteína de Retinoblastoma/metabolismo , Factor de Transcripción AP-1/genética
2.
Cell ; 157(2): 472-485, 2014 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-24725412

RESUMEN

Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of familial and sporadic Parkinson's disease (PD). Elevated LRRK2 kinase activity and neurodegeneration are linked, but the phosphosubstrate that connects LRRK2 kinase activity to neurodegeneration is not known. Here, we show that ribosomal protein s15 is a key pathogenic LRRK2 substrate in Drosophila and human neuron PD models. Phosphodeficient s15 carrying a threonine 136 to alanine substitution rescues dopamine neuron degeneration and age-related locomotor deficits in G2019S LRRK2 transgenic Drosophila and substantially reduces G2019S LRRK2-mediated neurite loss and cell death in human dopamine and cortical neurons. Remarkably, pathogenic LRRK2 stimulates both cap-dependent and cap-independent mRNA translation and induces a bulk increase in protein synthesis in Drosophila, which can be prevented by phosphodeficient T136A s15. These results reveal a novel mechanism of PD pathogenesis linked to elevated LRRK2 kinase activity and aberrant protein synthesis in vivo.


Asunto(s)
Neuronas/metabolismo , Enfermedad de Parkinson/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas Ribosómicas/metabolismo , Secuencia de Aminoácidos , Animales , Drosophila melanogaster , Humanos , Proteína 2 Quinasa Serina-Treonina Rica en Repeticiones de Leucina , Datos de Secuencia Molecular , Neuronas/patología , Enfermedad de Parkinson/patología , Proteínas Ribosómicas/química
3.
Trends Genet ; 40(3): 211-212, 2024 03.
Artículo en Inglés | MEDLINE | ID: mdl-38171966

RESUMEN

The complex relationship between chromatin accessibility, transcriptional regulation, and cancer transitions presents a daunting puzzle. Terekhanova et al. created a pan-cancer epigenetic and transcriptomic atlas at single-cell resolution, yielding important insights into the underlying chromatin architecture of cancer transitions and novel discoveries with the potential to advance precision medicine.


Asunto(s)
Regulación de la Expresión Génica , Neoplasias , Humanos , Neoplasias/genética , Cromatina/genética , Transcriptoma , Epigénesis Genética/genética
4.
Cell ; 145(5): 732-44, 2011 May 27.
Artículo en Inglés | MEDLINE | ID: mdl-21620138

RESUMEN

The pyruvate kinase isoforms PKM1 and PKM2 are alternatively spliced products of the PKM2 gene. PKM2, but not PKM1, alters glucose metabolism in cancer cells and contributes to tumorigenesis by mechanisms that are not explained by its known biochemical activity. We show that PKM2 gene transcription is activated by hypoxia-inducible factor 1 (HIF-1). PKM2 interacts directly with the HIF-1α subunit and promotes transactivation of HIF-1 target genes by enhancing HIF-1 binding and p300 recruitment to hypoxia response elements, whereas PKM1 fails to regulate HIF-1 activity. Interaction of PKM2 with prolyl hydroxylase 3 (PHD3) enhances PKM2 binding to HIF-1α and PKM2 coactivator function. Mass spectrometry and anti-hydroxyproline antibody assays demonstrate PKM2 hydroxylation on proline-403/408. PHD3 knockdown inhibits PKM2 coactivator function, reduces glucose uptake and lactate production, and increases O(2) consumption in cancer cells. Thus, PKM2 participates in a positive feedback loop that promotes HIF-1 transactivation and reprograms glucose metabolism in cancer cells.


Asunto(s)
Hipoxia de la Célula , Dioxigenasas/metabolismo , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Neoplasias/metabolismo , Piruvato Quinasa/metabolismo , Animales , Línea Celular Tumoral , Dioxigenasas/genética , Retroalimentación , Técnicas de Silenciamiento del Gen , Técnicas de Inactivación de Genes , Células HeLa , Humanos , Factor 1 Inducible por Hipoxia/metabolismo , Prolina Dioxigenasas del Factor Inducible por Hipoxia , Redes y Vías Metabólicas , Ratones , Elementos de Respuesta , Activación Transcripcional , Factores de Transcripción p300-CBP/metabolismo
5.
J Biol Chem ; 300(1): 105566, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38103643

RESUMEN

Macrophages play critical roles in inflammation and tissue homeostasis, and their functions are regulated by various autocrine, paracrine, and endocrine factors. We have previously shown that CTRP6, a secreted protein of the C1q family, targets both adipocytes and macrophages to promote obesity-linked inflammation. However, the gene programs and signaling pathways directly regulated by CTRP6 in macrophages remain unknown. Here, we combine transcriptomic and phosphoproteomic analyses to show that CTRP6 activates inflammatory gene programs and signaling pathways in mouse bone marrow-derived macrophages (BMDMs). Treatment of BMDMs with CTRP6 upregulated proinflammatory, and suppressed the antiinflammatory, gene expression. We also showed that CTRP6 activates p44/42-MAPK, p38-MAPK, and NF-κB signaling pathways to promote inflammatory cytokine secretion from BMDMs, and that pharmacologic inhibition of these signaling pathways markedly attenuated the effects of CTRP6. Pretreatment of BMDMs with CTRP6 also sensitized and potentiated the BMDMs response to lipopolysaccharide (LPS)-induced inflammatory signaling and cytokine secretion. Consistent with the metabolic phenotype of proinflammatory macrophages, CTRP6 treatment induced a shift toward aerobic glycolysis and lactate production, reduced oxidative metabolism, and elevated mitochondrial reactive oxygen species production in BMDMs. Importantly, in accordance with our in vitro findings, BMDMs from CTRP6-deficient mice were less inflammatory at baseline and showed a marked suppression of LPS-induced inflammatory gene expression and cytokine secretion. Finally, loss of CTRP6 in mice also dampened LPS-induced inflammation and hypothermia. Collectively, our findings suggest that CTRP6 regulates and primes the macrophage response to inflammatory stimuli and thus may have a role in modulating tissue inflammatory tone in different physiological and disease contexts.


Asunto(s)
Adipoquinas , Perfilación de la Expresión Génica , Inflamación , Lipopolisacáridos , Macrófagos , Fosfoproteínas , Proteómica , Animales , Ratones , Adipoquinas/deficiencia , Adipoquinas/genética , Adipoquinas/metabolismo , Células de la Médula Ósea/citología , Citocinas/metabolismo , Glucólisis , Hipotermia/complicaciones , Inflamación/complicaciones , Inflamación/genética , Inflamación/inmunología , Inflamación/metabolismo , Ácido Láctico/biosíntesis , Lipopolisacáridos/inmunología , Macrófagos/citología , Macrófagos/inmunología , Macrófagos/metabolismo , Ratones Endogámicos C57BL , Proteína Quinasa 1 Activada por Mitógenos/metabolismo , Proteína Quinasa 3 Activada por Mitógenos/metabolismo , FN-kappa B/metabolismo , Fosfoproteínas/análisis , Fosfoproteínas/metabolismo , Transducción de Señal , Especies Reactivas de Oxígeno/metabolismo
6.
J Am Chem Soc ; 146(15): 10655-10665, 2024 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-38564662

RESUMEN

While Ru-catalyzed hydrogenolysis holds significant promise in converting waste polyolefins into value-added alkane fuels, a major constraint is the high cost of noble metal catalysts. In this work, we propose, for the first time, that Co-based catalysts derived from CoAl-layered double hydroxide (LDH) are alternatives for efficient polyolefin hydrogenolysis. Leveraging the chemical flexibility of the LDH platform, we reveal that metallic Co species serve as highly efficient active sites for polyolefin hydrogenolysis. Furthermore, we introduced Ni into the Co framework to tackle the issue of restricted hydrogenation ability associated with contiguous Co-Co sites. In-situ analysis indicates that the integration of Ni induces electron transfer and facilitates hydrogen spillover. This dual effect synergistically enhances the hydrogenation/desorption of olefin intermediates, resulting in a significant reduction in the yield of low-value CH4 from 27.1 to 12.6%. Through leveraging the unique properties of LDH, we have developed efficient and cost-effective catalysts for the sustainable recycling and valorization of waste polyolefin materials.

7.
Am J Hum Genet ; 108(10): 1852-1865, 2021 10 07.
Artículo en Inglés | MEDLINE | ID: mdl-34559995

RESUMEN

Genome-wide association studies (GWASs) have discovered 20 risk loci in the human genome where germline variants associate with risk of pancreatic ductal adenocarcinoma (PDAC) in populations of European ancestry. Here, we fine-mapped one such locus on chr16q23.1 (rs72802365, p = 2.51 × 10-17, OR = 1.36, 95% CI = 1.31-1.40) and identified colocalization (PP = 0.87) with aberrant exon 5-7 CTRB2 splicing in pancreatic tissues (pGTEx = 1.40 × 10-69, ßGTEx = 1.99; pLTG = 1.02 × 10-30, ßLTG = 1.99). Imputation of a 584 bp structural variant overlapping exon 6 of CTRB2 into the GWAS datasets resulted in a highly significant association with pancreatic cancer risk (p = 2.83 × 10-16, OR = 1.36, 95% CI = 1.31-1.42), indicating that it may underlie this signal. Exon skipping attributable to the deletion (risk) allele introduces a premature stop codon in exon 7 of CTRB2, yielding a truncated chymotrypsinogen B2 protein that lacks chymotrypsin activity, is poorly secreted, and accumulates intracellularly in the endoplasmic reticulum (ER). We propose that intracellular accumulation of a nonfunctional chymotrypsinogen B2 protein leads to ER stress and pancreatic inflammation, which may explain the increased pancreatic cancer risk in carriers of CTRB2 exon 6 deletion alleles.


Asunto(s)
Quimotripsina/genética , Neoplasias Pancreáticas/patología , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Eliminación de Secuencia , Estudios de Casos y Controles , Quimotripsina/antagonistas & inhibidores , Quimotripsina/metabolismo , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Neoplasias Pancreáticas/etiología , Neoplasias Pancreáticas/metabolismo
8.
J Med Virol ; 96(4): e29577, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38572977

RESUMEN

Uncovering the immune response to an inactivated SARS-CoV-2 vaccine (In-Vac) and natural infection is crucial for comprehending COVID-19 immunology. Here we conducted an integrated analysis of single-cell RNA sequencing (scRNA-seq) data from serial peripheral blood mononuclear cell (PBMC) samples derived from 12 individuals receiving In-Vac compared with those from COVID-19 patients. Our study reveals that In-Vac induces subtle immunological changes in PBMC, including cell proportions and transcriptomes, compared with profound changes for natural infection. In-Vac modestly upregulates IFN-α but downregulates NF-κB pathways, while natural infection triggers hyperactive IFN-α and NF-κB pathways. Both In-Vac and natural infection alter T/B cell receptor repertoires, but COVID-19 has more significant change in preferential VJ gene, indicating a vigorous immune response. Our study reveals distinct patterns of cellular communications, including a selective activation of IL-15RA/IL-15 receptor pathway after In-Vac boost, suggesting its potential role in enhancing In-Vac-induced immunity. Collectively, our study illuminates multifaceted immune responses to In-Vac and natural infection, providing insights for optimizing SARS-CoV-2 vaccine efficacy.


Asunto(s)
COVID-19 , Humanos , COVID-19/prevención & control , Vacunas contra la COVID-19 , Leucocitos Mononucleares , FN-kappa B , SARS-CoV-2 , Vacunas de Productos Inactivados , Inmunidad , Análisis de Secuencia de ARN , Anticuerpos Antivirales
9.
BMC Cancer ; 24(1): 11, 2024 Jan 02.
Artículo en Inglés | MEDLINE | ID: mdl-38166700

RESUMEN

OBJECTIVE: The aim of this study was to investigate the clinical, imaging and pathological features of extraskeletal osteosarcoma (EOS) and to improve the understanding of this disease and other similar lesions. METHODS: The data for 11 patients with pathologically confirmed extraosseous osteosarcoma, including tumour site and size and imaging and clinical manifestations, were analysed retrospectively. RESULTS: Six patients were male (60%), and 5 were female (40%); patient age ranged from 23 to 76 years (average age 47.1 years). Among the 11 patients, 7 had clear calcifications or ossification with different morphologies, and 2 patients showed a massive mature bone tumour. MRI showed a mixed-signal mass with slightly longer T1 and T2 signals in the tumour parenchyma. Enhanced CT and MRI scans showed enhancement in the parenchyma. Ten patients had different degrees of necrosis and cystic degeneration in the mass, 2 of whom were complicated with haemorrhage, and MRI showed "fluid‒fluid level" signs. Of the 11 patients, five patients survived after surgery, and no obvious recurrence or metastasis was found on imaging examination. One patient died of lung metastasis after surgery, and 2 patients with open biopsy died of disease progression. One patient died of respiratory failure 2 months after operation. 2 patients had positive surgical margins, and 1 had lung metastasis 6 months after operation and died 19 months after operation. Another patient had recurrence 2 months after surgery. CONCLUSION: The diagnosis of EOS requires a combination of clinical, imaging and histological examinations. Cystic degeneration and necrosis; mineralization is common, especially thick and lumpy mineralization. Extended resection is still the first choice for localized lesions. For patients with positive surgical margins or metastases, adjuvant chemoradiotherapy is needed.


Asunto(s)
Neoplasias Óseas , Neoplasias Pulmonares , Osteosarcoma , Neoplasias de los Tejidos Blandos , Humanos , Masculino , Femenino , Persona de Mediana Edad , Adulto Joven , Adulto , Anciano , Diagnóstico Diferencial , Márgenes de Escisión , Estudios Retrospectivos , Neoplasias de los Tejidos Blandos/patología , Imagen por Resonancia Magnética , Osteosarcoma/diagnóstico por imagen , Osteosarcoma/patología , Neoplasias Pulmonares/diagnóstico por imagen , Neoplasias Óseas/patología , Necrosis/diagnóstico
10.
PLoS Comput Biol ; 19(12): e1011671, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-38039280

RESUMEN

Prokaryotic viruses, also known as bacteriophages, play crucial roles in regulating microbial communities and have the potential for phage therapy applications. Accurate prediction of phage-host interactions is essential for understanding the dynamics of these viruses and their impacts on bacterial populations. Numerous computational methods have been developed to tackle this challenging task. However, most existing prediction models can be constrained due to the substantial number of unknown interactions in comparison to the constrained diversity of available training data. To solve the problem, we introduce a model for prokaryotic virus host prediction with graph contrastive augmentation (PHPGCA). Specifically, we construct a comprehensive heterogeneous graph by integrating virus-virus protein similarity and virus-host DNA sequence similarity information. As the backbone encoder for learning node representations in the virus-prokaryote graph, we employ LGCN, a state-of-the-art graph embedding technique. Additionally, we apply graph contrastive learning to augment the node representations without the need for additional labels. We further conducted two case studies aimed at predicting the host range of multi-species phages, helping to understand the phage ecology and evolution.


Asunto(s)
Bacteriófagos , Células Procariotas , Ecología , Especificidad del Huésped , Aprendizaje
11.
Wound Repair Regen ; 32(3): 279-291, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38353052

RESUMEN

Pressure ulcer (PU) is a worldwide problem that is difficult to address because of the related inflammatory response, local hypoxia, and repeated ischaemia/reperfusion, causing great suffering and financial burden to patients. Traditional Chinese medicine turtle plate powder can treat skin trauma, but its composition is complex and inconvenient to use. Here, we combined cholesterol myristate (S8) with berberine (BBR), with anti-inflammatory and antibacterial effects, as a drug and used hydroxypropyl methylcellulose and polyvinylpyrrolidone K30 as carriers to construct a novel film-forming polymeric solution (S8 + BBR FFPS), comprehensively study its reparative effect on PU and explore the potential mechanism in rat PU models. The results showed that S8 + BBR FFPS inhibits excessive inflammatory response, promotes re-epithelialization, and promotes hair follicle growth during the healing process of PU, which may be related to the activation of the Wnt/ß-catenin signalling pathway by S8 + BBR FFPS to mediate hair follicle stem cell proliferation and maintain skin homeostasis. Therefore, S8 + BBR FFPS may be a potential candidate for the treatment of chronic skin injury, and its association with the Wnt/ß-catenin signalling pathway may provide new ideas to guide the design of biomaterial-based wound dressings for chronic wound repair.


Asunto(s)
Berberina , Modelos Animales de Enfermedad , Úlcera por Presión , Ratas Sprague-Dawley , Vía de Señalización Wnt , Cicatrización de Heridas , Animales , Úlcera por Presión/tratamiento farmacológico , Berberina/farmacología , Berberina/uso terapéutico , Ratas , Cicatrización de Heridas/efectos de los fármacos , Vía de Señalización Wnt/efectos de los fármacos , Masculino , Polímeros/farmacología , Proliferación Celular/efectos de los fármacos
12.
Environ Sci Technol ; 58(16): 7032-7044, 2024 Apr 23.
Artículo en Inglés | MEDLINE | ID: mdl-38602351

RESUMEN

High-elevation mountains have experienced disproportionately rapid warming, yet the effect of warming on the lateral export of terrestrial carbon to rivers remains poorly explored and understood in these regions. Here, we present a long-term data set of dissolved inorganic carbon (DIC) and a more detailed, short-term data set of DIC, δ13CDIC, and organic carbon from two major rivers of the Qinghai-Tibetan Plateau, the Jinsha River (JSR) and the Yalong River (YLR). In the higher-elevation JSR with ∼51% continuous permafrost coverage, warming (>3 °C) and increasing precipitation coincided with substantially increased DIC concentrations by 35% and fluxes by 110%. In the lower-elevation YLR with ∼14% continuous permafrost, such increases did not occur despite a comparable extent of warming. Riverine concentrations of dissolved and particulate organic carbon increased with discharge (mobilization) in both rivers. In the JSR, DIC concentrations transitioned from dilution (decreasing concentration with discharge) in earlier, colder years to chemostasis (relatively constant concentration) in later, warmer years. This changing pattern, together with lighter δ13CDIC under high discharge, suggests that permafrost thawing boosts DIC production and export via enhancing soil respiration and weathering. These findings reveal the predominant role of warming in altering carbon lateral export by escalating concentrations and fluxes and modifying export patterns.

13.
Environ Res ; 257: 119251, 2024 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-38815714

RESUMEN

The bioavailable diverse dissolved organic matter (DOM) present in glacial meltwater significantly contributes to downstream carbon cycling in mountainous regions. However, the comprehension of molecular-level characteristics of riverine DOM, from tributary to downstream and their fate in glacier-fed desert rivers remains limited. Herein, we employed spectroscopic and high-resolution mass spectrometry techniques to study both optical and molecular-level characteristics of DOM in the Tarim River catchment, northwest China. The results revealed that the DOC values in the downstream were higher than those in the tributaries, yet they remained comparable to those found in other glacier-fed streams worldwide. Five distinct components were identified using EEM-PARAFAC analysis in both tributary and downstream samples. The dominance of three protein-like components in tributary samples, contrasting with a higher presence of humic-like components in downstream samples, which implied that the dilution and alterations of the glacier DOM signature and overprinting with terrestrial-derived DOM. Molecular composition revealed that thousands of compounds with higher molecular weight and increased aromaticity were transformed, generated and introduced from terrestrial inputs during downstream transportation. The twofold rise in polycyclic aromatic and polyphenolic compounds observed downstream compared to tributaries indicated a greater influx of terrestrial organic matter introduced into the downstream during water transportation. The study suggests that the glacier-sourced DOM experienced minimal photodegradations, with limited influence from human activities, while also being shaped by terrestrial inputs during its transit in the alpine-arid region. This unique scenario offers valuable insights into comprehending the fate of DOM originating from glacial meltwater in arid mountainous regions.


Asunto(s)
Cubierta de Hielo , Ríos , China , Ríos/química , Cubierta de Hielo/química , Monitoreo del Ambiente/métodos , Compuestos Orgánicos/análisis , Contaminantes Químicos del Agua/análisis , Sustancias Húmicas/análisis , Espectrometría de Masas , Clima Desértico
14.
Angew Chem Int Ed Engl ; 63(12): e202315922, 2024 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-38287420

RESUMEN

Breaking the D4h symmetry in the square-planar M-N4 configuration of macrocycle molecular catalysts has witnessed enhanced electrocatalytic activity, but at the expense of electrochemical stability. Herein, we hypothesize that the lability of the active Cu-N3 motifs in the N-confused copper (II) tetraphenylporphyrin (CuNCP) could be overcome by applying pulsed potential electrolysis (PPE) during electrocatalytic carbon dioxide reduction. We find that applying PPE can indeed enhance the CH4 selectivity on CuNCP by 3 folds to reach the partial current density of 170 mA cm-2 at >60 % Faradaic efficiency (FE) in flow cell. However, combined ex situ X-ray diffraction (XRD), transmission electron microscope (TEM), and in situ X-ray absorption spectroscopy (XAS), infrared (IR), Raman, scanning electrochemical microscopy (SECM) characterizations reveal that, in a prolonged time scale, the decomplexation of CuNCP is unavoidable, and the promoted water dissociation under high anodic bias with lowered pH and enriched protons facilitates successive hydrogenation of *CO on the irreversibly reduced Cu nanoparticles, leading to the improved CH4 selectivity. As a key note, this study signifies the adaption of electrolytic protocol to the catalyst structure for tailoring local chemical environment towards efficient CO2 reduction.

15.
J Am Chem Soc ; 145(1): 224-233, 2023 Jan 11.
Artículo en Inglés | MEDLINE | ID: mdl-36562472

RESUMEN

Two-phase transformation reaction is ubiquitous in solid-state electrochemistry; however, it usually involves inferior structure rearrangement upon extraction and insertion of large-sized Na+, thus leading to severe local strain, cracks, and capacity decay in sodium-ion batteries (SIBs). Here, a homeostatic solid solution reaction is reported in the layered cathode material P'2-Na0.653Ni0.081Mn0.799Ti0.120O2 during sodiation and desodiation. It is induced by the synergistic incorporation of Ni and Ti for the reinforced O(2p)-Mn(3d-eg*) hybridization, which leads to mitigated Jahn-Teller distortion of MnO6 octahedra, contracted transition-metal oxide slabs, and enlarged Na layer spacings. The thermodynamically favorable solid solution pathway rewards the SIBs with excellent cycling stability (87.2% capacity retention after 500 cycles) and rate performance (100.5 mA h g-1 at 2500 mA g-1). The demonstrated reaction pathway will open a new avenue for rational designing of cathode materials for SIBs and beyond.

16.
Am J Transplant ; 23(3): 336-352, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36695693

RESUMEN

Acute rejection (AR) is an important factor that leads to poor prognosis after liver transplantation (LT). Macrophage M1-polarization is an important mechanism in AR development. MicroRNAs play vital roles in disease regulation; however, their effects on macrophages and AR remain unclear. In this study, rat models of AR were established following LT, and macrophages and peripheral blood mononuclear cells were isolated from rats and humans, respectively. We found miR-449a expression to be significantly reduced in macrophages and peripheral blood mononuclear cells. Overexpression of miR-449a not only inhibited the M1-polarization of macrophages in vitro but also improved the AR of transplant in vivo. The mechanism involved inhibiting the noncanonical nuclear factor-kappaB (NF-κB) pathway. We identified procollagen-lysine1,2-oxoglutarate5-dioxygenase 1 (PLOD1) as a target gene of miR-449a, which could reverse miR-449a's inhibition of macrophage M1-polarization, amelioration of AR, and inhibition of the NF-κB pathway. Overall, miR-449a inhibited the NF-κB pathway in macrophages through PLOD1 and also inhibited the M1-polarization of macrophages, thus attenuating AR after LT. In conclusion, miR-449a and PLOD1 may be new targets for the prevention and mitigation of AR.


Asunto(s)
Trasplante de Hígado , MicroARNs , Animales , Humanos , Ratas , Leucocitos Mononucleares/metabolismo , Macrófagos/metabolismo , MicroARNs/genética , FN-kappa B/metabolismo , Procolágeno/metabolismo , Procolágeno/farmacología
17.
Biochem Biophys Res Commun ; 656: 86-96, 2023 05 14.
Artículo en Inglés | MEDLINE | ID: mdl-36958259

RESUMEN

The abnormal immune response mediated by malignant melanoma is related to PD1. Paeonol has pharmacological antitumor activity. Previous studies have indicated that paeonol induces tumor cell apoptosis, but its underlying mechanism in tumor immunity remains unknown. In this study, malignant melanoma was established in normal and thymectomized mice to determine the important role of the thymus in the antitumor effects of paeonol. Paeonol-treated thymocytes were cocultured with melanoma cell spheres to further evaluate the regulatory role of thymocytes in tumor immune dysfunction. Studies have shown that PD1 may be targeted by miR-139-5p. Our results revealed that tumor-induced thymic atrophy was significantly accompanied by high PD1 expression and low miR-139-5p expression. Interestingly, paeonol significantly reversed thymic atrophy and largely protected thymocytes against low PD1 expression and high miR-139-5p expression. Dual-luciferase assays indicated that miR-139-5p interacted with the 3' untranslated region (3'-UTR) of PD1. These results showed that paeonol alleviates PD1-mediated antitumor immunity by reducing miR-139-5p expression and demonstrated a novel mechanism for melanoma immunotherapy.


Asunto(s)
Melanoma , MicroARNs , Animales , Ratones , Regulación hacia Arriba , MicroARNs/genética , MicroARNs/metabolismo , Línea Celular Tumoral , Melanoma/tratamiento farmacológico , Melanoma/genética , Melanoma/patología , Apoptosis , Proliferación Celular , Regulación Neoplásica de la Expresión Génica , Melanoma Cutáneo Maligno
18.
Clin Proteomics ; 20(1): 56, 2023 Dec 05.
Artículo en Inglés | MEDLINE | ID: mdl-38053024

RESUMEN

BACKGROUND: Cell surface proteins perform critical functions related to immune response, signal transduction, cell-cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite several enrichment methods exploiting their biochemical and biophysical properties. METHODS: Here, we report a novel method for enrichment of proteins localized to cell surface. We developed this new approach designated surface Biotinylation Site Identification Technology (sBioSITe) by adapting our previously published method for direct identification of biotinylated peptides. In this strategy, the primary amine groups of lysines on proteins on the surface of live cells are first labeled with biotin, and subsequently, biotinylated peptides are enriched by anti-biotin antibodies and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS: By direct detection of biotinylated lysines from PC-3, a prostate cancer cell line, using sBioSITe, we identified 5851 peptides biotinylated on the cell surface that were derived from 1409 proteins. Of these proteins, 533 were previously shown or predicted to be localized to the cell surface or secreted extracellularly. Several of the identified cell surface markers have known associations with prostate cancer and metastasis including CD59, 4F2 cell-surface antigen heavy chain (SLC3A2) and adhesion G protein-coupled receptor E5 (CD97). Importantly, we identified several biotinylated peptides derived from plectin and nucleolin, both of which are not annotated in surface proteome databases but have been shown to have aberrant surface localization in certain cancers highlighting the utility of this method. CONCLUSIONS: Detection of biotinylation sites on cell surface proteins using sBioSITe provides a reliable method for identifying cell surface proteins. This strategy complements existing methods for detection of cell surface expressed proteins especially in discovery-based proteomics approaches.

19.
Blood ; 138(6): 452-463, 2021 08 12.
Artículo en Inglés | MEDLINE | ID: mdl-33728448

RESUMEN

Current prognostic scoring systems based on clinicopathologic variables are inadequate in predicting the survival and treatment response of extranodal natural killer/T-cell lymphoma (ENKTL) patients undergoing nonanthracyline-based treatment. We aimed to construct a classifier based on single-nucleotide polymorphisms (SNPs) for improving predictive accuracy and guiding clinical decision making. Data from 722 patients with ENKTL from international centers were analyzed. A 7-SNP-based classifier was constructed using LASSO Cox regression in the training cohort (n = 336) and further validated in the internal testing cohort (n = 144) and in 2 external validation cohorts (n = 142 and n = 100). The 7-SNP-based classifier showed good prognostic predictive efficacy in the training cohort and the 3 validation cohorts. Patients with high- and low-risk scores calculated by the classifier exhibited significantly different progression-free survival (PFS) and overall survival (OS) (all P < .001). The 7-SNP-based classifier was further proved to be an independent prognostic factor by multivariate analysis, and its predictive accuracy was significantly better than clinicopathological risk variables. Application of the 7-SNP-based classifier was not affected by sample types. Notably, chemotherapy combined with radiotherapy significantly improved PFS and OS vs radiotherapy alone in high-risk Ann Arbor stage I patients, whereas there was no statistical difference between the 2 therapeutic modalities among low-risk patients. A nomogram was constructed comprising the classifier and clinicopathological variables; it showed remarkably better predictive accuracy than either variable alone. The 7-SNP-based classifier is a complement to existing risk-stratification systems in ENKTL, which could have significant implications for clinical decision making for patients with ENKTL.


Asunto(s)
Linfoma Extranodal de Células NK-T , Polimorfismo de Nucleótido Simple , Supervivencia sin Enfermedad , Femenino , Humanos , Linfoma Extranodal de Células NK-T/genética , Linfoma Extranodal de Células NK-T/mortalidad , Linfoma Extranodal de Células NK-T/radioterapia , Masculino , Persona de Mediana Edad , Tasa de Supervivencia
20.
Soft Matter ; 19(33): 6329-6340, 2023 Aug 23.
Artículo en Inglés | MEDLINE | ID: mdl-37564036

RESUMEN

By using a large enough number of particles and implementing a parallel algorithm on the CUDA platform, we have performed brute-force molecular dynamics simulations to study the template-induced heterogeneous crystallization in charged colloids. Six kinds of templates, whose patterns include the planes of fcc(100), fcc(110), fcc(111), bcc(100), bcc(110) and bcc(111), have been implanted into the middle of the simulation box. Except the fcc(111) template, whose structure benefits not only fcc but also hcp crystals resulting in a similar behavior to homogeneous crystallization, bcc-type templates favor the formation of bcc crystals and bcc-like precursors while fcc-type templates favor the formation of fcc crystals and fcc-like precursors. Therefore, for fcc(100) and fcc(110) templates, heterogeneous crystallization will definitely result in a fcc crystallite. However, the results of heterogeneous crystallization that are induced by bcc-type templates are subtly different at different state points. At the state points where the interaction strength of charged colloids is weak and the fcc phase is thermodynamically stable, the bcc crystals formed with the promotion of bcc-type templates are not stable so as to tend to transform into fcc or hcp crystals. When the interaction strength of charged colloids is high, the predominant bcc crystals formed with the promotion of bcc-type templates can always persist within the time scale of simulation although not bcc but fcc crystals are thermodynamically stable.

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