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1.
EMBO J ; 43(18): 3968-3999, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39103492

RESUMEN

Senescence of nondividing neurons remains an immature concept, with especially the regulatory molecular mechanisms of senescence-like phenotypes and the role of proteins associated with neurodegenerative diseases in triggering neuronal senescence remaining poorly explored. In this study, we reveal that the nucleolar polyglutamine binding protein 3 (PQBP3; also termed NOL7), which has been linked to polyQ neurodegenerative diseases, regulates senescence as a gatekeeper of cytoplasmic DNA leakage. PQBP3 directly binds PSME3 (proteasome activator complex subunit 3), a subunit of the 11S proteasome regulator complex, decreasing PSME3 interaction with Lamin B1 and thereby preventing Lamin B1 degradation and senescence. Depletion of endogenous PQBP3 causes nuclear membrane instability and release of genomic DNA from the nucleus to the cytosol. Among multiple tested polyQ proteins, ataxin-1 (ATXN1) partially sequesters PQBP3 to inclusion bodies, reducing nucleolar PQBP3 levels. Consistently, knock-in mice expressing mutant Atxn1 exhibit decreased nuclear PQBP3 and a senescence phenotype in Purkinje cells of the cerebellum. Collectively, these results suggest homologous roles of the nucleolar protein PQBP3 in cellular senescence and neurodegeneration.


Asunto(s)
Senescencia Celular , Lamina Tipo B , Complejo de la Endopetidasa Proteasomal , Animales , Humanos , Ratones , Ataxina-1/metabolismo , Ataxina-1/genética , Células HEK293 , Lamina Tipo B/metabolismo , Lamina Tipo B/genética , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética , Complejo de la Endopetidasa Proteasomal/metabolismo , Proteolisis , Células de Purkinje/metabolismo
2.
Mol Cell ; 79(6): 1024-1036.e5, 2020 09 17.
Artículo en Inglés | MEDLINE | ID: mdl-32871103

RESUMEN

Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co-transcriptional RNA folding, modification, processing, and ribosomal subunit assembly by presently unknown mechanisms. We have determined cryo-electron microscopy structures of complete Escherichia coli ribosomal RNA transcription elongation complexes, comprising RNA polymerase; DNA; RNA bearing an N-utilization-site-like anti-termination element; Nus factors A, B, E, and G; inositol mono-phosphatase SuhB; and ribosomal protein S4. Our structures and structure-informed functional analyses show that fast transcription and anti-termination involve suppression of NusA-stabilized pausing, enhancement of NusG-mediated anti-backtracking, sequestration of the NusG C-terminal domain from termination factor ρ, and the ρ blockade. Strikingly, the factors form a composite RNA chaperone around the RNA polymerase RNA-exit tunnel, which supports co-transcriptional RNA folding and annealing of distal RNA regions. Our work reveals a polymerase/chaperone machine required for biosynthesis of functional ribosomes.


Asunto(s)
ARN Polimerasas Dirigidas por ADN/genética , Chaperonas Moleculares/genética , Proteínas Ribosómicas/genética , Ribosomas/genética , Sitios de Unión/genética , Microscopía por Crioelectrón , Escherichia coli/genética , Escherichia coli/ultraestructura , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/ultraestructura , Monoéster Fosfórico Hidrolasas/genética , Monoéster Fosfórico Hidrolasas/ultraestructura , Biosíntesis de Proteínas/genética , Pliegue del ARN/genética , ARN Ribosómico/genética , ARN Ribosómico/ultraestructura , Proteínas Ribosómicas/ultraestructura , Ribosomas/ultraestructura , Factores de Elongación Transcripcional/química , Factores de Elongación Transcripcional/genética , Factores de Elongación Transcripcional/ultraestructura
3.
Nat Immunol ; 16(8): 810-8, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-26147687

RESUMEN

Foxm1 is known as a typical proliferation-associated transcription factor. Here we found that Foxm1 was essential for maintenance of the quiescence and self-renewal capacity of hematopoietic stem cells (HSCs) in vivo in mice. Reducing expression of FOXM1 also decreased the quiescence of human CD34(+) HSCs and progenitor cells, and its downregulation was associated with a subset of myelodysplastic syndrome (MDS). Mechanistically, Foxm1 directly bound to the promoter region of the gene encoding the receptor Nurr1 (Nr4a2; called 'Nurr1' here), inducing transcription, while forced expression of Nurr1 reversed the loss of quiescence observed in Foxm1-deficient cells in vivo. Thus, our studies reveal a previously unrecognized role for Foxm1 as a critical regulator of the quiescence and self-renewal of HSCs mediated at least in part by control of Nurr1 expression.


Asunto(s)
Proliferación Celular/genética , Factores de Transcripción Forkhead/genética , Regulación de la Expresión Génica , Células Madre Hematopoyéticas/metabolismo , Animales , Células Cultivadas , Citometría de Flujo , Proteína Forkhead Box M1 , Factores de Transcripción Forkhead/metabolismo , Perfilación de la Expresión Génica , Células HEK293 , Humanos , Ratones Endogámicos C57BL , Ratones Noqueados , Ratones Transgénicos , Síndromes Mielodisplásicos/genética , Síndromes Mielodisplásicos/metabolismo , Miembro 2 del Grupo A de la Subfamilia 4 de Receptores Nucleares/genética , Miembro 2 del Grupo A de la Subfamilia 4 de Receptores Nucleares/metabolismo , Análisis de Secuencia por Matrices de Oligonucleótidos , Regiones Promotoras Genéticas/genética , Unión Proteica , Interferencia de ARN , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
4.
Cell ; 151(4): 900-911, 2012 Nov 09.
Artículo en Inglés | MEDLINE | ID: mdl-23141545

RESUMEN

Short hairpin RNA (shRNA)-induced RNAi is used for biological discovery and therapeutics. Dicer, whose normal role is to liberate endogenous miRNAs from their precursors, processes shRNAs into different biologically active siRNAs, affecting their efficacy and potential for off-targeting. We found that, in cells, Dicer induced imprecise cleavage events around the expected sites based on the previously described 5'/3' counting rules. These promiscuous noncanonical cleavages were abrogated when the cleavage site was positioned 2 nt from a bulge or loop. Interestingly, we observed that the ~1/3 of mammalian endogenous pre-miRNAs that contained such structures were more precisely processed by Dicer. Implementing a "loop-counting rule," we designed potent anti-HCV shRNAs with substantially reduced off-target effects. Our results suggest that Dicer recognizes the loop/bulge structure in addition to the ends of shRNAs/pre-miRNAs for accurate processing. This has important implications for both miRNA processing and future design of shRNAs for RNAi-based genetic screens and therapies.


Asunto(s)
ARN Interferente Pequeño/metabolismo , Ribonucleasa III/metabolismo , Animales , Secuencia de Bases , Embrión de Mamíferos/citología , Células HEK293 , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Ratones , MicroARNs , ARN Interferente Pequeño/química , Análisis de Secuencia de ARN
5.
Mol Cell ; 74(1): 143-157.e5, 2019 04 04.
Artículo en Inglés | MEDLINE | ID: mdl-30795892

RESUMEN

Bacteriophage λN protein, a model anti-termination factor, binds nascent RNA and host Nus factors, rendering RNA polymerase resistant to all pause and termination signals. A 3.7-Å-resolution cryo-electron microscopy structure and structure-informed functional analyses reveal a multi-pronged strategy by which the intrinsically unstructured λN directly modifies RNA polymerase interactions with the nucleic acids and subverts essential functions of NusA, NusE, and NusG to reprogram the transcriptional apparatus. λN repositions NusA and remodels the ß subunit flap tip, which likely precludes folding of pause or termination RNA hairpins in the exit tunnel and disrupts termination-supporting interactions of the α subunit C-terminal domains. λN invades and traverses the RNA polymerase hybrid cavity, likely stabilizing the hybrid and impeding pause- or termination-related conformational changes of polymerase. λN also lines upstream DNA, seemingly reinforcing anti-backtracking and anti-swiveling by NusG. Moreover, λN-repositioned NusA and NusE sequester the NusG C-terminal domain, counteracting ρ-dependent termination. Other anti-terminators likely utilize similar mechanisms to enable processive transcription.


Asunto(s)
Bacteriófago lambda/metabolismo , Escherichia coli/metabolismo , ARN Bacteriano/biosíntesis , Factores de Transcripción/metabolismo , Terminación de la Transcripción Genética , Proteínas Reguladoras y Accesorias Virales/metabolismo , Bacteriófago lambda/genética , Sitios de Unión , Microscopía por Crioelectrón , ARN Polimerasas Dirigidas por ADN/genética , ARN Polimerasas Dirigidas por ADN/metabolismo , Escherichia coli/genética , Escherichia coli/virología , Regulación Bacteriana de la Expresión Génica , Modelos Moleculares , Conformación de Ácido Nucleico , Unión Proteica , Conformación Proteica , ARN Bacteriano/química , ARN Bacteriano/genética , Relación Estructura-Actividad , Factores de Transcripción/química , Factores de Transcripción/genética , Proteínas Reguladoras y Accesorias Virales/química , Proteínas Reguladoras y Accesorias Virales/genética
6.
PLoS Pathog ; 20(9): e1012546, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39316625

RESUMEN

Pseudorabies virus (PRV) infection causes systemic inflammatory responses and inflammatory damages in infected animals, which are associated with the activation of inflammasome and pyroptosis in infected tissues. Here, we identified a critical function of PRV non-structural protein UL4 that enhanced ASC-dependent inflammasome activation to promote pyroptosis. Whereas, the deficiency of viral UL4 was able to reduce ASC-dependent inflammasome activation and the occurrences of pyroptosis. Mechanistically, the 132-145 aa of UL4 permitted its translocation from the nucleus to the cytoplasm to interact with cytoplasmic ASC to promote the activation of NLRP3 and AIM2 inflammasome. Further research showed that UL4 promoted the phosphorylation levels of SYK and JNK to enhance the ASC phosphorylation, which led to the increase of ASC oligomerization, thus promoting the activation of NLRP3 and AIM2 inflammasome and enhanced GSDMD-mediated pyroptosis. In vivo experiments further showed that PRV UL4 (132DVAADAAAEAAAAE145) mutated strain (PRV-UL4mut) infection did not lead to a significant decrease in viral titers at 12 h. p. i, but it induced lower levels of IL-1ß, IL-18, and GSDMD-NT, which led to an alleviated inflammatory infiltration and pathological damage in the lungs and brains, and a lower death rate compared with wild-type PRV strain infection. Taken together, our findings unravel that UL4 is an important viral regulator to manipulate the inflammasome signaling and pyroptosis of host cells to promote the pathogenicity of PRV, which might be further exploited as a new target for live attenuated vaccines or therapeutic strategies against pseudorabies in the future.


Asunto(s)
Proteínas Adaptadoras de Señalización CARD , Herpesvirus Suido 1 , Inflamasomas , Inflamación , Seudorrabia , Piroptosis , Animales , Inflamasomas/metabolismo , Inflamasomas/inmunología , Ratones , Herpesvirus Suido 1/inmunología , Inflamación/metabolismo , Seudorrabia/virología , Seudorrabia/metabolismo , Seudorrabia/inmunología , Seudorrabia/patología , Proteínas Adaptadoras de Señalización CARD/metabolismo , Proteínas Virales/metabolismo , Proteínas Virales/genética , Ratones Endogámicos C57BL
7.
PLoS Pathog ; 20(6): e1012305, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38905309

RESUMEN

PoRVA and PEDV coinfections are extremely common in clinical practice. Although coinfections of PoRVA and PEDV are known to result in increased mortality, the underlying mechanism remains unknown. Here, we found that PoRVA infection promoted PEDV infection in vivo and in vitro and that PoRVA G9P[23] (RVA-HNNY strain) enhanced PEDV replication more significantly than did PoRVA G5P[7] (RVA-SXXA strain). Metabolomic analysis revealed that RVA-HNNY more efficiently induced an increase in the intracellular glutamine content in porcine small intestinal epithelial cells than did RVA-SXXA, which more markedly promoted ATP production to facilitate PEDV replication, whereas glutamine deprivation abrogated the effect of PoRVA infection on promoting PEDV replication. Further studies showed that PoRVA infection promoted glutamine uptake by upregulating the expression of the glutamine transporter protein SLC1A5. In SLC1A5 knockout cells, PoRVA infection neither elevated intracellular glutamine nor promoted PEDV replication. During PoRVA infection, the activity and protein expression levels of glutamine catabolism-related enzymes (GLS1 and GLUD1) were also significantly increased promoting ATP production through glutamine anaplerosis into the TCA cycle. Consistent with that, siRNAs or inhibitors of GLS1 and GLUD1 significantly inhibited the promotion of PEDV replication by PoRVA. Notably, RVA-HNNY infection more markedly promoted SLC1A5, GLS1 and GLUD1 expression to more significantly increase the uptake and catabolism of glutamine than RVA-SXXA infection. Collectively, our findings illuminate a novel mechanism by which PoRVA infection promotes PEDV infection and reveal that the modulation of glutamine uptake is key for the different efficiencies of PoRVA G9P[23] and PoRVA G5P[7] in promoting PEDV replication.


Asunto(s)
Glutamina , Virus de la Diarrea Epidémica Porcina , Replicación Viral , Glutamina/metabolismo , Animales , Replicación Viral/fisiología , Porcinos , Virus de la Diarrea Epidémica Porcina/fisiología , Infecciones por Coronavirus/metabolismo , Infecciones por Coronavirus/virología , Enfermedades de los Porcinos/metabolismo , Chlorocebus aethiops
8.
PLoS Pathog ; 20(2): e1012014, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38394330

RESUMEN

The mechanism of genome DNA replication in circular single-stranded DNA viruses is currently a mystery, except for the fact that it undergoes rolling-circle replication. Herein, we identified SUMOylated porcine nucleophosmin-1 (pNPM1), which is previously reported to be an interacting protein of the viral capsid protein, as a key regulator that promotes the genome DNA replication of porcine single-stranded DNA circovirus. Upon porcine circovirus type 2 (PCV2) infection, SUMO2/3 were recruited and conjugated with the K263 site of pNPM1's C-terminal domain to SUMOylate pNPM1, subsequently, the SUMOylated pNPM1 were translocated in nucleoli to promote the replication of PCV2 genome DNA. The mutation of the K263 site reduced the SUMOylation levels of pNPM1 and the nucleolar localization of pNPM1, resulting in a decrease in the level of PCV2 DNA replication. Meanwhile, the mutation of the K263 site prevented the interaction of pNPM1 with PCV2 DNA, but not the interaction of pNPM1 with PCV2 Cap. Mechanistically, PCV2 infection increased the expression levels of Ubc9, the only E2 enzyme involved in SUMOylation, through the Cap-mediated activation of ERK signaling. The upregulation of Ubc9 promoted the interaction between pNPM1 and TRIM24, a potential E3 ligase for SUMOylation, thereby facilitating the SUMOylation of pNPM1. The inhibition of ERK activation could significantly reduce the SUMOylation levels and the nucleolar localization of pNPM1, as well as the PCV2 DNA replication levels. These results provide new insights into the mechanism of circular single-stranded DNA virus replication and highlight NPM1 as a potential target for inhibiting PCV2 replication.


Asunto(s)
Infecciones por Circoviridae , Circovirus , Enfermedades de los Porcinos , Porcinos , Animales , Circovirus/genética , Circovirus/metabolismo , ADN de Cadena Simple/genética , ADN de Cadena Simple/metabolismo , Nucleofosmina , Sumoilación , Infecciones por Circoviridae/genética , Infecciones por Circoviridae/metabolismo , Replicación Viral/fisiología , ADN Viral/genética , ADN Viral/metabolismo
9.
Nature ; 582(7813): 501-505, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32541968

RESUMEN

Quantum key distribution (QKD)1-3 is a theoretically secure way of sharing secret keys between remote users. It has been demonstrated in a laboratory over a coiled optical fibre up to 404 kilometres long4-7. In the field, point-to-point QKD has been achieved from a satellite to a ground station up to 1,200 kilometres away8-10. However, real-world QKD-based cryptography targets physically separated users on the Earth, for which the maximum distance has been about 100 kilometres11,12. The use of trusted relays can extend these distances from across a typical metropolitan area13-16 to intercity17 and even intercontinental distances18. However, relays pose security risks, which can be avoided by using entanglement-based QKD, which has inherent source-independent security19,20. Long-distance entanglement distribution can be realized using quantum repeaters21, but the related technology is still immature for practical implementations22. The obvious alternative for extending the range of quantum communication without compromising its security is satellite-based QKD, but so far satellite-based entanglement distribution has not been efficient23 enough to support QKD. Here we demonstrate entanglement-based QKD between two ground stations separated by 1,120 kilometres at a finite secret-key rate of 0.12 bits per second, without the need for trusted relays. Entangled photon pairs were distributed via two bidirectional downlinks from the Micius satellite to two ground observatories in Delingha and Nanshan in China. The development of a high-efficiency telescope and follow-up optics crucially improved the link efficiency. The generated keys are secure for realistic devices, because our ground receivers were carefully designed to guarantee fair sampling and immunity to all known side channels24,25. Our method not only increases the secure distance on the ground tenfold but also increases the practical security of QKD to an unprecedented level.

10.
Nature ; 586(7830): 572-577, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32726802

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a respiratory disease called coronavirus disease 2019 (COVID-19), the spread of which has led to a pandemic. An effective preventive vaccine against this virus is urgently needed. As an essential step during infection, SARS-CoV-2 uses the receptor-binding domain (RBD) of the spike protein to engage with the receptor angiotensin-converting enzyme 2 (ACE2) on host cells1,2. Here we show that a recombinant vaccine that comprises residues 319-545 of the RBD of the spike protein induces a potent functional antibody response in immunized mice, rabbits and non-human primates (Macaca mulatta) as early as 7 or 14 days after the injection of a single vaccine dose. The sera from the immunized animals blocked the binding of the RBD to ACE2, which is expressed on the cell surface, and neutralized infection with a SARS-CoV-2 pseudovirus and live SARS-CoV-2 in vitro. Notably, vaccination also provided protection in non-human primates to an in vivo challenge with SARS-CoV-2. We found increased levels of RBD-specific antibodies in the sera of patients with COVID-19. We show that several immune pathways and CD4 T lymphocytes are involved in the induction of the vaccine antibody response. Our findings highlight the importance of the RBD domain in the design of SARS-CoV-2 vaccines and provide a rationale for the development of a protective vaccine through the induction of antibodies against the RBD domain.


Asunto(s)
Anticuerpos Antivirales/inmunología , Betacoronavirus/inmunología , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/prevención & control , Pandemias/prevención & control , Neumonía Viral/inmunología , Neumonía Viral/prevención & control , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/inmunología , Vacunas Virales/inmunología , Animales , Anticuerpos Neutralizantes/inmunología , COVID-19 , Vacunas contra la COVID-19 , Humanos , Macaca mulatta/inmunología , Macaca mulatta/virología , Ratones , Ratones Endogámicos BALB C , Ratones Endogámicos C57BL , Modelos Animales , Modelos Moleculares , Dominios Proteicos , SARS-CoV-2 , Suero/inmunología , Bazo/citología , Bazo/inmunología , Linfocitos T/inmunología , Vacunación
11.
PLoS Comput Biol ; 20(1): e1011759, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38181051

RESUMEN

Abrupt changes in system states and dynamical behaviors are often observed in natural systems; such phenomena, named regime shifts, are explained as transitions between alternative steady states (more generally, attractors). Various methods have been proposed to detect regime shifts from time series data, but a generic detection method with theoretical linkage to underlying dynamics is lacking. Here, we provide a novel method named Nested-Library Analysis (NLA) to retrospectively detect regime shifts using empirical dynamic modeling (EDM) rooted in theory of attractor reconstruction. Specifically, NLA determines the time of regime shift as the cutting point at which sequential reduction of the library set (i.e., the time series data used to reconstruct the attractor for forecasting) optimizes the forecast skill of EDM. We illustrate this method on a chaotic model of which changing parameters present a critical transition. Our analysis shows that NLA detects the change point in the model system and outperforms existing approaches based on statistical characteristics. In addition, NLA empirically detected a real-world regime shift event revealing an abrupt change of Pacific Decadal Oscillation index around the mid-1970s. Importantly, our method can be easily generalized to various systems because NLA is equation-free and requires only a single time series.


Asunto(s)
Dinámicas no Lineales , Estudios Retrospectivos
12.
Cell Mol Life Sci ; 81(1): 133, 2024 Mar 13.
Artículo en Inglés | MEDLINE | ID: mdl-38472560

RESUMEN

Acute lung injury (ALI) is a common clinical syndrome, which often results in pulmonary edema and respiratory distress. It has been recently reported that phosphatidylethanolamine binding protein 4 (PEBP4), a basic cytoplasmic protein, has anti-inflammatory and hepatoprotective effects, but its relationship with ALI remains undefined so far. In this study, we generated PEBP4 knockout (KO) mice to investigate the potential function of PEBP4, as well as to evaluate the capacity of alveolar fluid clearance (AFC) and the activity of phosphatidylinositide 3-kinases (PI3K)/serine-theronine protein kinase B (PKB, also known as AKT) signaling pathway in lipopolysaccharide (LPS)-induced ALI mice models. We found that PEBP4 deficiency exacerbated lung pathological damage and edema, and increased the wet/dry weight ratio and total protein concentration of bronchoalveolar lavage fluid (BALF) in LPS-treated mice. Meanwhile, PEBP4 KO promoted an LPS-induced rise in the pulmonary myeloperoxidase (MPO) activity, serum interleuin (IL)-1ß, IL-6, and tumor necrosis factor (TNF)-α levels, and pulmonary cyclooxygenase-2 (COX-2) expression. Mechanically, PEBP4 deletion further reduced the protein expression of Na+ transport markers, including epithelial sodium channel (ENaC)-α, ENaC-γ, Na,K-ATPase α1, and Na,K-ATPase ß1, and strengthened the inhibition of PI3K/AKT signaling in LPS-challenged mice. Furthermore, we demonstrated that selective activation of PI3K/AKT with 740YP or SC79 partially reversed all of the above effects caused by PEBP4 KO in LPS-treated mice. Altogether, our results indicated the PEBP4 deletion has a deterioration effect on LPS-induced ALI by impairing the capacity of AFC, which may be achieved through modulating the PI3K/AKT pathway.


Asunto(s)
Lesión Pulmonar Aguda , Lipopolisacáridos , Animales , Ratones , Lesión Pulmonar Aguda/inducido químicamente , Lipopolisacáridos/farmacología , Pulmón/metabolismo , Fosfatidilinositol 3-Quinasas/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Transducción de Señal , ATPasa Intercambiadora de Sodio-Potasio/metabolismo , ATPasa Intercambiadora de Sodio-Potasio/farmacología , ATPasa Intercambiadora de Sodio-Potasio/uso terapéutico , Factor de Necrosis Tumoral alfa/metabolismo
13.
Am J Respir Crit Care Med ; 210(4): 444-454, 2024 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-38422478

RESUMEN

Rationale: Distinguishing connective tissue disease-associated interstitial lung disease (CTD-ILD) from idiopathic pulmonary fibrosis (IPF) can be clinically challenging. Objectives: To identify proteins that separate and classify patients with CTD-ILD and those with IPF. Methods: Four registries with 1,247 patients with IPF and 352 patients with CTD-ILD were included in analyses. Plasma samples were subjected to high-throughput proteomics assays. Protein features were prioritized using recursive feature elimination to construct a proteomic classifier. Multiple machine learning models, including support vector machine, LASSO (least absolute shrinkage and selection operator) regression, random forest, and imbalanced Random Forest, were trained and tested in independent cohorts. The validated models were used to classify each case iteratively in external datasets. Measurements and Main Results: A classifier with 37 proteins (proteomic classifier 37 [PC37]) was enriched in the biological process of bronchiole development and smooth muscle proliferation and immune responses. Four machine learning models used PC37 with sex and age score to generate continuous classification values. Receiver operating characteristic curve analyses of these scores demonstrated consistent areas under the curve of 0.85-0.90 in the test cohort and 0.94-0.96 in the single-sample dataset. Binary classification demonstrated 78.6-80.4% sensitivity and 76-84.4% specificity in the test cohort and 93.5-96.1% sensitivity and 69.5-77.6% specificity in the single-sample classification dataset. Composite analysis of all machine learning models confirmed 78.2% (194 of 248) accuracy in the test cohort and 82.9% (208 of 251) in the single-sample classification dataset. Conclusions: Multiple machine learning models trained with large cohort proteomic datasets consistently distinguished CTD-ILD from IPF. Many of the identified proteins are involved in immune pathways. We further developed a novel approach for single-sample classification, which could facilitate honing the differential diagnosis of ILD in challenging cases and improve clinical decision making.


Asunto(s)
Enfermedades Pulmonares Intersticiales , Aprendizaje Automático , Proteómica , Humanos , Enfermedades Pulmonares Intersticiales/sangre , Enfermedades Pulmonares Intersticiales/diagnóstico , Femenino , Masculino , Proteómica/métodos , Persona de Mediana Edad , Anciano , Fibrosis Pulmonar Idiopática/sangre , Fibrosis Pulmonar Idiopática/diagnóstico , Diagnóstico Diferencial , Enfermedades del Tejido Conjuntivo/sangre , Enfermedades del Tejido Conjuntivo/diagnóstico , Biomarcadores/sangre
14.
Proc Natl Acad Sci U S A ; 119(46): e2122121119, 2022 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-36343245

RESUMEN

The in vivo mechanisms underlying dominant syndromes caused by mutations in SRY-Box Transcription Factor 9 (SOX9) and SOX10 (SOXE) transcription factors, when they either are expressed alone or are coexpressed, are ill-defined. We created a mouse model for the campomelic dysplasia SOX9Y440X mutation, which truncates the transactivation domain but leaves DNA binding and dimerization intact. Here, we find that SOX9Y440X causes deafness via distinct mechanisms in the endolymphatic sac (ES)/duct and cochlea. By contrast, conditional heterozygous Sox9-null mice are normal. During the ES development of Sox9Y440X/+ heterozygotes, Sox10 and genes important for ionic homeostasis are down-regulated, and there is developmental persistence of progenitors, resulting in fewer mature cells. Sox10 heterozygous null mutants also display persistence of ES/duct progenitors. By contrast, SOX10 retains its expression in the early Sox9Y440X/+ mutant cochlea. Later, in the postnatal stria vascularis, dominant interference by SOX9Y440X is implicated in impairing the normal cooperation of SOX9 and SOX10 in repressing the expression of the water channel Aquaporin 3, thereby contributing to endolymphatic hydrops. Our study shows that for a functioning endolymphatic system in the inner ear, SOX9 regulates Sox10, and depending on the cell type and target gene, it works either independently of or cooperatively with SOX10. SOX9Y440X can interfere with the activity of both SOXE factors, exerting effects that can be classified as haploinsufficient/hypomorphic or dominant negative depending on the cell/gene context. This model of disruption of transcription factor partnerships may be applicable to congenital deafness, which affects ∼0.3% of newborns, and other syndromic disorders.


Asunto(s)
Sordera , Oído Interno , Factor de Transcripción SOX9 , Factores de Transcripción SOXE , Animales , Ratones , Sordera/metabolismo , Oído Interno/metabolismo , Audición/genética , Homeostasis , Ratones Noqueados , Factor de Transcripción SOX9/genética , Factor de Transcripción SOX9/metabolismo , Factores de Transcripción SOXE/genética , Factores de Transcripción SOXE/metabolismo
15.
Chem Soc Rev ; 53(18): 9306-9343, 2024 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-39143951

RESUMEN

Cellulose, as the most abundant natural polymer on Earth, has long captured researchers' attention due to its high strength and modulus. Nevertheless, transferring its exceptional mechanical properties to macroscopic 2D and 3D materials poses numerous challenges. This review provides an overview of the research progress in the development of strong cellulose-based materials using both the "bottom-up" and "top-down" approaches. In the "bottom-up" strategy, various forms of regenerated cellulose-based materials and nanocellulose-based high-strength materials assembled by different methods are discussed. Under the "top-down" approach, the focus is on the development of reinforced cellulose-based materials derived from wood, bamboo, rattan and straw. Furthermore, a brief overview of the potential applications fordifferent types of strong cellulose-based materials is given, followed by a concise discussion on future directions.

16.
Nano Lett ; 24(26): 8107-8116, 2024 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-38888223

RESUMEN

The integration of sonodynamic therapy (SDT) with cuproptosis for targeted cancer treatment epitomizes a significant advancement in oncology. Herein, we present a dual-responsive therapeutic system, "CytoNano", which combines a cationic liposome infused with copper-nitride nanoparticles and oxygen-rich perfluorocarbon (Lip@Cu3N/PFC-O2), all enveloped in a biomimetic coating of neutrophil membrane and acid-responsive carboxymethylcellulose. CytoNano leverages the cellular mimicry of neutrophils and acid-responsive materials, enabling precise targeting of tumors and their acidic microenvironment. This strategic design facilitates the targeted release of Lip@Cu3N/PFC-O2 within the tumor, enhancing cancer cell uptake and mitochondrial localization. Consequently, it amplifies the therapeutic efficacy of both Cu3N-driven SDT and cuproptosis while preserving healthy tissues. Additionally, CytoNano's ultrasound responsiveness enhances intratumoral oxygenation, overcoming physiological barriers and initiating a combined sonodynamic-cuproptotic effect that induces multiple cell death pathways. Thus, we pioneer a biomimetic approach in precise sonodynamic cuproptosis, revolutionizing cancer therapy.


Asunto(s)
Mitocondrias , Terapia por Ultrasonido , Humanos , Mitocondrias/metabolismo , Mitocondrias/efectos de los fármacos , Animales , Terapia por Ultrasonido/métodos , Ratones , Línea Celular Tumoral , Neoplasias/terapia , Neoplasias/patología , Nanopartículas/química , Materiales Biomiméticos/química , Materiales Biomiméticos/farmacología , Cobre/química , Cobre/farmacología , Liposomas/química , Fluorocarburos/química , Biomimética/métodos , Oxígeno/química
17.
J Cell Mol Med ; 28(18): e70103, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39334527

RESUMEN

Colorectal cancer (CRC) represents a significant malignancy within the digestive system, characterized by high incidence and mortality rates. In recent years, molecular targeted therapy has been introduced as a supplementary strategy in CRC management, complementing traditional modalities such as surgery, radiation and chemotherapy. The identification of novel therapeutic targets for CRC remains critically important. Ferroptosis, a unique form of programmed cell death distinct from apoptosis and necrosis, is characterized by cellular damage resulting from iron-induced lipid peroxidation, leading to cell death. This study utilizes a combination of bioinformatics analysis and clinical specimen validation to demonstrate that the long non-coding RNA (lncRNA) ALMS1-IT1 is significantly upregulated in CRC tissues and strongly associated with ferroptosis. Through a series of experimental investigations, we have determined that ALMS1-IT1 negatively regulates ferroptosis in CRC cells, thereby promoting cancer growth and metastasis, acting as an oncogenic factor. Furthermore, we explored the molecular interactions of ALMS1-IT1, revealing its role in activating STAT3 protein phosphorylation. This activation enhances the immune evasion capabilities of CRC cells. Rescue experiments indicated that STAT3 activation is essential for ALMS1-IT1's suppression of ferroptosis, immune evasion and oncogenic behaviour in CRC. Our findings underscore the critical biological role of ALMS1-IT1 in the progression of CRC and suggest its potential as a target for drug development.


Asunto(s)
Neoplasias Colorrectales , Ferroptosis , Regulación Neoplásica de la Expresión Génica , ARN Largo no Codificante , Factor de Transcripción STAT3 , Ferroptosis/genética , Humanos , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Neoplasias Colorrectales/metabolismo , ARN Largo no Codificante/genética , Factor de Transcripción STAT3/metabolismo , Factor de Transcripción STAT3/genética , Línea Celular Tumoral , Animales , Ratones , Proliferación Celular , Evasión Inmune
18.
Circulation ; 148(21): 1691-1704, 2023 11 21.
Artículo en Inglés | MEDLINE | ID: mdl-37850394

RESUMEN

BACKGROUND: Hypercontractility and arrhythmia are key pathophysiologic features of hypertrophic cardiomyopathy (HCM), the most common inherited heart disease. ß-Adrenergic receptor antagonists (ß-blockers) are the first-line therapy for HCM. However, ß-blockers commonly selected for this disease are often poorly tolerated in patients, where heart-rate reduction and noncardiac effects can lead to reduced cardiac output and fatigue. Mavacamten, myosin ATPase inhibitor recently approved by the US Food and Drug Administration, has demonstrated the ability to ameliorate hypercontractility without lowering heart rate, but its benefits are so far limited to patients with left ventricular (LV) outflow tract obstruction, and its effect on arrhythmia is unknown. METHODS: We screened 21 ß-blockers for their impact on myocyte contractility and evaluated the antiarrhythmic properties of the most promising drug in a ventricular myocyte arrhythmia model. We then examined its in vivo effect on LV function by hemodynamic pressure-volume loop analysis. The efficacy of the drug was tested in vitro and in vivo compared with current therapeutic options (metoprolol, verapamil, and mavacamten) for HCM in an established mouse model of HCM (Myh6R403Q/+ and induced pluripotent stem cell (iPSC)-derived cardiomyocytes from patients with HCM (MYH7R403Q/+). RESULTS: We identified that carvedilol, a ß-blocker not commonly used in HCM, suppresses contractile function and arrhythmia by inhibiting RyR2 (ryanodine receptor type 2). Unlike metoprolol (a ß1-blocker), carvedilol markedly reduced LV contractility through RyR2 inhibition, while maintaining stroke volume through α1-adrenergic receptor inhibition in vivo. Clinically available carvedilol is a racemic mixture, and the R-enantiomer, devoid of ß-blocking effect, retains the ability to inhibit both α1-receptor and RyR2, thereby suppressing contractile function and arrhythmias without lowering heart rate and cardiac output. In Myh6R403Q/+ mice, R-carvedilol normalized hyperdynamic contraction, suppressed arrhythmia, and increased cardiac output better than metoprolol, verapamil, and mavacamten. The ability of R-carvedilol to suppress contractile function was well retained in MYH7R403Q/+ iPSC-derived cardiomyocytes. CONCLUSIONS: R-enantiomer carvedilol attenuates hyperdynamic contraction, suppresses arrhythmia, and at the same time, improves cardiac output without lowering heart rate by dual blockade of α1-adrenergic receptor and RyR2 in mouse and human models of HCM. This combination of therapeutic effects is unique among current therapeutic options for HCM and may particularly benefit patients without LV outflow tract obstruction.


Asunto(s)
Cardiomiopatía Hipertrófica , Metoprolol , Humanos , Ratones , Animales , Carvedilol/farmacología , Carvedilol/uso terapéutico , Metoprolol/uso terapéutico , Canal Liberador de Calcio Receptor de Rianodina/metabolismo , Cardiomiopatía Hipertrófica/complicaciones , Cardiomiopatía Hipertrófica/tratamiento farmacológico , Arritmias Cardíacas/tratamiento farmacológico , Arritmias Cardíacas/metabolismo , Antagonistas Adrenérgicos beta/farmacología , Antagonistas Adrenérgicos beta/uso terapéutico , Miocitos Cardíacos/metabolismo , Verapamilo/uso terapéutico , Receptores Adrenérgicos/metabolismo
19.
BMC Genomics ; 25(1): 142, 2024 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-38317084

RESUMEN

Whole-exome sequencing (WES) is widely used to diagnose complex genetic diseases and rare conditions. The implementation of a robust and effective quality control system for sample identification and tracking throughout the WES process is essential. We established a multiplex panel that included 22 coding single-nucleotide polymorphism (cSNP) loci. The personal identification and paternity identification abilities of the panel were evaluated, and a preliminary validation of the practical feasibility of the panel was conducted in a clinical WES case. These results indicate that the cSNP panel could be a useful tool for sample tracking in WES.


Asunto(s)
Exoma , Polimorfismo de Nucleótido Simple , Humanos , Secuenciación del Exoma , Pruebas Genéticas/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos
20.
J Am Chem Soc ; 2024 Sep 26.
Artículo en Inglés | MEDLINE | ID: mdl-39324803

RESUMEN

C3H6 is a crucial building block for many chemicals, yet separating it from other C3 hydrocarbons presents a significant challenge. Herein, we report a hydrolytically stable Cu4I4-triazolate metal-organic framework (MOF) (JNU-9-CH3) featuring 1D channels decorated with readily accessible iodine and nitrogen atoms from Cu4I4 clusters and triazolate linkers, respectively. The exposed iodine and nitrogen atoms allow for cooperative binding of C3 hydrocarbons, as evidenced by in situ single-crystal crystallography and Raman spectroscopy studies. As a result, JNU-9-CH3 exhibits substantially stronger binding affinity for C3H4, CH2═C═CH2, and C3H8 than that for C3H6. Breakthrough experiments confirm its ability to directly separate C3H6 (≥99.99%) from C3H4/CH2═C═CH2/C3H8/C3H6 mixtures at varying ratios and flow rates. Overall, we illustrate the cooperative binding of C3 hydrocarbons in a Cu4I4-triazolate MOF and its highly efficient C3H6 purification from quaternary C3 mixtures. The study highlights the potential of MOF adsorbents with metal-iodide clusters for cooperative bindings and hydrocarbon separations.

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