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1.
Nature ; 631(8020): 307-312, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38898280

RESUMEN

Spin accumulation in semiconductor structures at room temperature and without magnetic fields is key to enable a broader range of optoelectronic functionality1. Current efforts are limited owing to inherent inefficiencies associated with spin injection across semiconductor interfaces2. Here we demonstrate spin injection across chiral halide perovskite/III-V interfaces achieving spin accumulation in a standard semiconductor III-V (AlxGa1-x)0.5In0.5P multiple quantum well light-emitting diode. The spin accumulation in the multiple quantum well is detected through emission of circularly polarized light with a degree of polarization of up to 15 ± 4%. The chiral perovskite/III-V interface was characterized with X-ray photoelectron spectroscopy, cross-sectional scanning Kelvin probe force microscopy and cross-sectional transmission electron microscopy imaging, showing a clean semiconductor/semiconductor interface at which the Fermi level can equilibrate. These findings demonstrate that chiral perovskite semiconductors can transform well-developed semiconductor platforms into ones that can also control spin.

2.
Nature ; 623(7986): 313-318, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37696288

RESUMEN

Metal halide perovskite solar cells (PSCs) represent a promising low-cost thin-film photovoltaic technology, with unprecedented power conversion efficiencies obtained for both single-junction and tandem applications1-8. To push PSCs towards commercialization, it is critical, albeit challenging, to understand device reliability under real-world outdoor conditions where multiple stress factors (for example, light, heat and humidity) coexist, generating complicated degradation behaviours9-13. To quickly guide PSC development, it is necessary to identify accelerated indoor testing protocols that can correlate specific stressors with observed degradation modes in fielded devices. Here we use a state-of-the-art positive-intrinsic-negative (p-i-n) PSC stack (with power conversion efficiencies of up to approximately 25.5%) to show that indoor accelerated stability tests can predict our six-month outdoor ageing tests. Device degradation rates under illumination and at elevated temperatures are most instructive for understanding outdoor device reliability. We also find that the indium tin oxide/self-assembled monolayer-based hole transport layer/perovskite interface most strongly affects our device operation stability. Improving the ion-blocking properties of the self-assembled monolayer hole transport layer increases averaged device operational stability at 50 °C-85 °C by a factor of about 2.8, reaching over 1,000 h at 85 °C and to near 8,200 h at 50 °C, with a projected 20% degradation, which is among the best to date for high-efficiency p-i-n PSCs14-17.

3.
Nature ; 611(7935): 278-283, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-36049505

RESUMEN

Perovskite solar cells (PSCs) with an inverted structure (often referred to as the p-i-n architecture) are attractive for future commercialization owing to their easily scalable fabrication, reliable operation and compatibility with a wide range of perovskite-based tandem device architectures1,2. However, the power conversion efficiency (PCE) of p-i-n PSCs falls behind that of n-i-p (or normal) structure counterparts3-6. This large performance gap could undermine efforts to adopt p-i-n architectures, despite their other advantages. Given the remarkable advances in perovskite bulk materials optimization over the past decade, interface engineering has become the most important strategy to push PSC performance to its limit7,8. Here we report a reactive surface engineering approach based on a simple post-growth treatment of 3-(aminomethyl)pyridine (3-APy) on top of a perovskite thin film. First, the 3-APy molecule selectively reacts with surface formamidinium ions, reducing perovskite surface roughness and surface potential fluctuations associated with surface steps and terraces. Second, the reaction product on the perovskite surface decreases the formation energy of charged iodine vacancies, leading to effective n-type doping with a reduced work function in the surface region. With this reactive surface engineering, the resulting p-i-n PSCs obtained a PCE of over 25 per cent, along with retaining 87 per cent of the initial PCE after over 2,400 hours of 1-sun operation at about 55 degrees Celsius in air.

4.
EMBO J ; 41(6): e108016, 2022 03 15.
Artículo en Inglés | MEDLINE | ID: mdl-35191555

RESUMEN

Interferon regulatory factor 3 (IRF3)-induced type I interferon (I-IFN) production plays key roles in both antiviral and autoimmune responses. IRF3 phosphorylation, dimerization, and nuclear localization are needed for its activation and function, but the precise regulatory mechanisms remain to be explored. Here, we show that the serine/threonine kinase AKT2 interacts with IRF3 and phosphorylates it on Thr207, thereby attenuating IRF3 nuclear translocation in a 14-3-3ε-dependent manner and reducing I-IFN production. We further find that AKT2 expression is downregulated in viral-infected macrophages or in monocytes and tissue samples from systemic lupus erythematosus (SLE) patients and mouse models. Akt2-deficient mice exhibit increased I-IFN induction and reduced mortality in response to viral infection, but aggravated severity of SLE. Overexpression of AKT2 kinase-inactive or IRF3-T207A mutants in zebrafish supports that AKT2 negatively regulates I-IFN production and antiviral response in a kinase-dependent manner. This negative role of AKT2 in IRF3-induced I-IFN production suggests that AKT2 may be therapeutically targeted to differentially regulate antiviral infection and SLE.


Asunto(s)
Interferón beta/biosíntesis , Lupus Eritematoso Sistémico , Pez Cebra , Animales , Antivirales , Humanos , Lupus Eritematoso Sistémico/genética , Ratones , Fosforilación , Proteínas Serina-Treonina Quinasas , Proteínas Proto-Oncogénicas c-akt/genética , Proteínas Proto-Oncogénicas c-akt/metabolismo , Pez Cebra/metabolismo
5.
Nucleic Acids Res ; 2024 Oct 26.
Artículo en Inglés | MEDLINE | ID: mdl-39460625

RESUMEN

Liquid-liquid phase separation (LLPS) is a crucial process for the formation of biomolecular condensates such as coacervate droplets, P-bodies and stress granules, which play critical roles in many physiological and pathological processes. Increasing studies have shown that not only proteins but also RNAs play a critical role in LLPS. To host LLPS-associated RNAs, we previously developed a database named 'RPS' in 2021. In this study, we present an updated version RPS 2.0 (https://rps.renlab.cn/) to incorporate the newly generated data and to host new LLPS-associated RNAs driven by post-transcriptional regulatory mechanisms. Currently, RPS 2.0 hosts 171 301 entries of LLPS-associated RNAs in 24 different biomolecular condensates with four evidence types, including 'Reviewed', 'High-throughput (LLPS enrichment)', 'High-throughput (LLPS perturbation)' and 'Predicted', and five event types, including 'Expression', 'APA', 'AS', 'A-to-I' and 'Modification'. Additionally, extensive annotations of LLPS-associated RNAs are provided in RPS 2.0, including RNA sequence and structure features, RNA-protein/RNA-RNA interactions, RNA modifications, as well as diseases related annotations. We expect that RPS 2.0 will further promote research of LLPS-associated RNAs and deepen our understanding of the biological functions and regulatory mechanisms of LLPS.

6.
Nucleic Acids Res ; 52(17): e81, 2024 Sep 23.
Artículo en Inglés | MEDLINE | ID: mdl-39119904

RESUMEN

Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.


Asunto(s)
ADN Bacteriano , Reacción en Cadena de la Polimerasa Multiplex , Staphylococcus aureus , Reacción en Cadena de la Polimerasa Multiplex/métodos , Humanos , ADN Bacteriano/genética , Staphylococcus aureus/genética , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Colorantes Fluorescentes/química , Color , Sepsis/diagnóstico , Sepsis/genética , Sepsis/microbiología , Fluorescencia , Sensibilidad y Especificidad
7.
Bioinformatics ; 40(Suppl 2): ii120-ii127, 2024 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-39230705

RESUMEN

MOTIVATION: Learning cellular dynamics through reconstruction of the underlying cellular potential energy landscape (aka Waddington landscape) from time-series single-cell RNA sequencing (scRNA-seq) data is a current challenge. Prevailing data-driven computational methods can be hampered by the lack of physical principles to guide learning from complex data, resulting in reduced prediction accuracy and interpretability when applied to infer cell population dynamics. RESULTS: Here, we propose PI-SDE, a physics-informed neural stochastic differential equation (SDE) framework that combines the Hamilton-Jacobi (HJ) equation and neural SDE to learn cellular dynamics. Grounded in potential energy theory of biological systems, PI-SDE integrates the principle of least action by enforcing the HJ equation when reconstructing cellular potential energy function. This approach not only facilitates accurate predictions, but also improves interpretability, especially in the reconstructed potential energy landscape. Through benchmarking on two real scRNA-seq datasets, we demonstrate the importance of incorporating the HJ regularization term in dynamic inference, especially in predicting gene expression at held-out time points. Meanwhile, the learned potential energy landscape provides biologically interpretable insights into the process of cell differentiation. Our framework enhances model performance, while maintaining robustness and stability. AVAILABILITY: PI-SDE software is available at https://github.com/QiJiang-QJ/PI-SDE.


Asunto(s)
Análisis de la Célula Individual , Análisis de la Célula Individual/métodos , Redes Neurales de la Computación , Análisis de Secuencia de ARN/métodos , Humanos , RNA-Seq/métodos , Biología Computacional/métodos , Algoritmos , Análisis de Expresión Génica de una Sola Célula
8.
Proc Natl Acad Sci U S A ; 119(42): e2213718119, 2022 10 18.
Artículo en Inglés | MEDLINE | ID: mdl-36215477

RESUMEN

Transcription factors (TFs) play critical roles in hematopoiesis, and their aberrant expression can lead to various types of leukemia. The t(8;21) leukemogenic fusion protein AML1-ETO (AE) is the most common fusion protein in acute myeloid leukemia and can enhance hematopoietic stem cell renewal while blocking differentiation. A key question in understanding AE-mediated leukemia is what determines the choice of AE to activate self-renewal genes or repress differentiation genes. Toward the resolution of this problem, we earlier showed that AE resides in the stable AETFC complex and that its components colocalize on up- or down-regulated target genes and are essential for leukemogenesis. In the current study, using biochemical and genomic approaches, we show that AE-containing complexes are heterogeneous, and that assembly of the larger AETFC (containing AE, CBFß, HEB, E2A, LYL1, LMO2, and LDB1) requires LYL1. Furthermore, we provide strong evidence that the LYL1-containing AETFC preferentially binds to active enhancers and promotes AE-dependent gene activation. Moreover, we show that coactivator CARM1 interacts with AETFC and facilitates gene activation by AETFC. Collectively, this study describes a role of oncoprotein LYL1 in AETFC assembly and gene activation by recruiting CARM1 to chromatin for AML cell survival.


Asunto(s)
Leucemia Mieloide Aguda , Proteínas de Fusión Oncogénica , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismo , Proteínas Adaptadoras de Señalización CARD , Cromatina , Subunidad alfa 2 del Factor de Unión al Sitio Principal/genética , Subunidad alfa 2 del Factor de Unión al Sitio Principal/metabolismo , Guanilato Ciclasa , Humanos , Proteínas con Homeodominio LIM/genética , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/metabolismo , Proteínas de Neoplasias/genética , Proteínas de Fusión Oncogénica/genética , Proteínas de Fusión Oncogénica/metabolismo , Proteína-Arginina N-Metiltransferasas , Activación Transcripcional
9.
Nano Lett ; 24(30): 9296-9301, 2024 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-39037306

RESUMEN

The two-dimensional (2D) honeycomb lattice has attracted intensive research interest due to the appearance of Dirac-type band structures as the consequence of two sublattices in the honeycomb structure. Introducing strong spin-orbit coupling (SOC) leads to a gap opening at the Dirac point, transforming the honeycomb lattice into a 2D topological insulator as a platform for the quantum spin Hall effect (QSHE). In this work, we realize a 2D honeycomb-structured film with tellurium, the heaviest nonradioactive element in Group VI, namely, tellurene, via molecular beam epitaxy. We revealed the gap opening of 160 meV at the Dirac point due to the strong SOC in the honeycomb-structured tellurene by angle-resolved photoemission spectroscopy. The topological edge states of tellurene are detected via scanning tunneling microscopy/spectroscopy. These results demonstrate that tellurene is a novel 2D honeycomb lattice with strong SOC, and they unambiguously prove that tellurene is a promising candidate for a room-temperature QSHE system.

10.
Oncologist ; 29(8): e1061-e1072, 2024 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-38842680

RESUMEN

BACKGROUND: Patients with intrahepatic cholangiocarcinoma (ICC) are prone to recurrence and poor survival. Targeted therapy related to isocitrate dehydrogenase (IDH) is an extremely important treatment. IDH1 and IDH2 mutations are generally thought to have similar effects on the tumor landscape. However, it is doubtful whether these 2 mutations have exactly the same effects on tumor cells and the tumor microenvironment. METHODS: All collected tumor samples were subjected to simultaneous whole-exon sequencing and proteome sequencing. RESULTS: IDH1 mutations accounted for 12.2%, and IDH2 mutations accounted for 5.5%, all missense mutations. Tumors with IDH mutations had lower proportions of KRAS and TP53 mutations. Mutated genes were obviously enriched in the kinase pathway in the tumors with IDH2 mutations. The signaling pathways were mainly enriched in the activation of cellular metabolic activities and an increase of inhibitory immune cells in the tumors with IDH mutations. Moreover, tumors had unique enrichment in DNA repair in IDH1 mutants and secretion of biological molecules in IDH2 mutants. Inhibitory immune cells might be more prominent in IDH2 mutants, and the expression of immune checkpoints PVR and HLA-DQB1 was more prominent in IDH1 mutants. IDH mutants were more related to metabolism-related and inflammation-immune response clusters, and some belonged to the DNA replication and repair cluster. CONCLUSIONS: These results revealed the differential IDH1 and IDH2 mutation-related landscapes, and we have provided an important reference database to guide ICC treatment.


Asunto(s)
Neoplasias de los Conductos Biliares , Colangiocarcinoma , Isocitrato Deshidrogenasa , Mutación , Humanos , Isocitrato Deshidrogenasa/genética , Colangiocarcinoma/genética , Colangiocarcinoma/patología , Femenino , Masculino , Neoplasias de los Conductos Biliares/genética , Neoplasias de los Conductos Biliares/patología , Persona de Mediana Edad , Anciano , Adulto , Microambiente Tumoral
11.
Anal Chem ; 96(22): 9209-9217, 2024 06 04.
Artículo en Inglés | MEDLINE | ID: mdl-38769607

RESUMEN

To tackle the predicament of the traditional turn-off mechanism, exploring an activated turn-on system remains an intriguing and crucial objective in biosensing fields. Herein, a dark DNA Ag nanocluster (NC) with hairpin-structured DNA containing a six-base cytosine loop (6C loop) as a template is atypically synthesized. Intriguingly, the dark DNA Ag NCs can be lit to display strong red-emission nanoclusters. Building upon these exciting findings, an unprecedented and upgraded turn-on biosensing system [entropy-driven catalysis circuit (EDCC)-Ag NCs/graphene oxide (GO)] has been created, which employs an EDCC to precisely manipulate the conformational transition of DNA Ag NCs on the GO surface from adsorption to desorption. Benefiting from the effective quenching of GO and signal amplification capability of the EDCC, the newly developed EDCC-Ag NCs/GO biosensing system displays a high signal-to-background (S/B) ratio (26-fold) and sensitivity (limit of detection as low as 0.4 pM). Meanwhile, it has good specificity, excellent stability, and reliability in both buffer and biological samples. To the best of our knowledge, it is the first example that adopts an EDCC to precisely modulate the configuration transformation of DNA Ag NCs on the GO surface to obtain a biosensor with low background, strong fluorescence, high contrast, and sensitivity. This exciting finding may provide a new route to fabricate a novel turn-on biosensor based on hairpin-templated DNA Ag NCs in the optical imaging and bioanalytical fields.


Asunto(s)
Técnicas Biosensibles , ADN , Grafito , Nanopartículas del Metal , Plata , Propiedades de Superficie , Grafito/química , Plata/química , Técnicas Biosensibles/métodos , ADN/química , Nanopartículas del Metal/química , Catálisis , Entropía , Humanos
12.
Small ; : e2403717, 2024 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-39046075

RESUMEN

In organic-inorganic hybrid devices, fine interfacial controls by organic components directly affect the device performance. However, fabrication of uniformed interfaces using π-conjugated molecules remains challenging due to facile aggregation by their strong π-π interaction. In this report, a π-conjugated scaffold insulated by covalently linked permethylated α-cyclodextrin moiety with an azido group is synthesized for surface Huisgen cycloaddition on metal oxides. Fourier-transformed infrared (FT-IR) spectroscopy and X-ray photoelectron spectroscopy confirm the successful immobilization of the insulated azido scaffold on ZnO nanowire array surfaces. Owing to the highly independent immobilization, the scaffold allows rapid and complete conversion of the surface azido group in Huisgen cycloaddition reactions with ethynyl-terminated molecules, as confirmed by FT-IR spectroscopy monitoring. Cyclic voltammetry analysis of modified indium tin oxide substrates shows the positive effects of cyclic insulation toward suppression of intermolecular interaction between molecules introduced by the surface Huisgen cycloaddition reactions. The utility of the scaffold for heterogeneous catalysis is demonstrated in electrocatalytic selective O2 reduction to H2O2 with cobalt(II) chlorin modified fluorine doped tin oxide electrode and photocatalytic H2 generation with iridium(III) dye-sensitized Pt-loaded TiO2 nanoparticle. These results highlight the potential of the insulated azido scaffold for a stepwise functionalization process, enabling precise and well-defined hybrid interfaces.

13.
Biol Reprod ; 110(3): 450-464, 2024 Mar 13.
Artículo en Inglés | MEDLINE | ID: mdl-38035769

RESUMEN

Adenosylhomocysteinase (AHCY), a key enzyme in the methionine cycle, is essential for the development of embryos and the maintenance of mouse embryonic stem cells (mESCs). However, the precise underlying mechanism of Ahcy in regulating pluripotency remains unclear. As the only enzyme that can hydrolyze S-adenosylhomocysteine in mammals, AHCY plays a critical role in the metabolic homeostasis, epigenetic remodeling, and transcriptional regulation. Here, we identified Ahcy as a direct target of OCT4 and unveiled that AHCY regulates the self-renewal and differentiation potency of mESCs through multiple mechanisms. Our study demonstrated that AHCY is required for the metabolic homeostasis of mESCs. We revealed the dual role of Ahcy in both transcriptional activation and inhibition, which is accomplished via the maintenance of H3K4me3 and H3K27me3, respectively. We found that Ahcy is required for H3K4me3-dependent transcriptional activation in mESCs. We also demonstrated that AHCY interacts with polycomb repressive complex 2 (PRC2), thereby maintaining the pluripotency of mESCs by sustaining the H3K27me3-regulated transcriptional repression of related genes. These results reveal a previously unrecognized OCT4-AHCY-PRC2 axis in the regulation of mESCs' pluripotency and provide insights into the interplay between transcriptional factors, cellular metabolism, chromatin dynamics and pluripotency regulation.


Asunto(s)
Histonas , Células Madre Embrionarias de Ratones , Animales , Ratones , Adenosilhomocisteinasa/genética , Adenosilhomocisteinasa/metabolismo , Diferenciación Celular , Histonas/metabolismo , Mamíferos/metabolismo , Células Madre Embrionarias de Ratones/metabolismo , Complejo Represivo Polycomb 2/genética
14.
Plant Biotechnol J ; 22(8): 2333-2347, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38600703

RESUMEN

Sterols have long been associated with diverse fields, such as cancer treatment, drug development, and plant growth; however, their underlying mechanisms and functions remain enigmatic. Here, we unveil a critical role played by a GmNF-YC9-mediated CCAAT-box transcription complex in modulating the steroid metabolism pathway within soybeans. Specifically, this complex directly activates squalene monooxygenase (GmSQE1), which is a rate-limiting enzyme in steroid synthesis. Our findings demonstrate that overexpression of either GmNF-YC9 or GmSQE1 significantly enhances soybean stress tolerance, while the inhibition of SQE weakens this tolerance. Field experiments conducted over two seasons further reveal increased yields per plant in both GmNF-YC9 and GmSQE1 overexpressing plants under drought stress conditions. This enhanced stress tolerance is attributed to the reduction of abiotic stress-induced cell oxidative damage. Transcriptome and metabolome analyses shed light on the upregulation of multiple sterol compounds, including fucosterol and soyasaponin II, in GmNF-YC9 and GmSQE1 overexpressing soybean plants under stress conditions. Intriguingly, the application of soybean steroids, including fucosterol and soyasaponin II, significantly improves drought tolerance in soybean, wheat, foxtail millet, and maize. These findings underscore the pivotal role of soybean steroids in countering oxidative stress in plants and offer a new research strategy for enhancing crop stress tolerance and quality from gene regulation to chemical intervention.


Asunto(s)
Glycine max , Estrés Fisiológico , Glycine max/genética , Glycine max/fisiología , Glycine max/metabolismo , Estrés Fisiológico/genética , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Plantas Modificadas Genéticamente , Esteroides/metabolismo , Sequías , Productos Agrícolas/genética , Productos Agrícolas/metabolismo , Proteínas de Plantas/metabolismo , Proteínas de Plantas/genética
15.
J Virol ; 97(11): e0122623, 2023 Nov 30.
Artículo en Inglés | MEDLINE | ID: mdl-37861337

RESUMEN

IMPORTANCE: Although a virus can regulate many cellular responses to facilitate its replication by interacting with host proteins, the host can also restrict virus infection through these interactions. In the present study, we showed that the host eukaryotic translation elongation factor 1 alpha (eEF1A), an essential protein in the translation machinery, interacted with two proteins of a fish rhabdovirus, Siniperca chuatsi rhabdovirus (SCRV), and inhibited virus infection via two different mechanisms: (i) inhibiting the formation of crucial viral protein complexes required for virus transcription and replication and (ii) promoting the ubiquitin-proteasome degradation of viral protein. We also revealed the functional regions of eEF1A that are involved in the two processes. Such a host protein inhibiting a rhabdovirus infection in two ways is rarely reported. These findings provided new information for the interactions between host and fish rhabdovirus.


Asunto(s)
Enfermedades de los Peces , Proteínas de Peces , Factor 1 de Elongación Peptídica , Infecciones por Rhabdoviridae , Rhabdoviridae , Animales , Peces , Factor 1 de Elongación Peptídica/genética , Factor 1 de Elongación Peptídica/metabolismo , Rhabdoviridae/fisiología , Infecciones por Rhabdoviridae/metabolismo , Infecciones por Rhabdoviridae/veterinaria , Proteínas Virales/genética , Proteínas Virales/metabolismo , Proteínas de Peces/metabolismo , Enfermedades de los Peces/metabolismo
16.
Brief Bioinform ; 23(6)2022 11 19.
Artículo en Inglés | MEDLINE | ID: mdl-36259363

RESUMEN

Robust strategies to identify patients at high risk for tumor metastasis, such as those frequently observed in intrahepatic cholangiocarcinoma (ICC), remain limited. While gene/protein expression profiling holds great potential as an approach to cancer diagnosis and prognosis, previously developed protocols using multiple diagnostic signatures for expression-based metastasis prediction have not been widely applied successfully because batch effects and different data types greatly decreased the predictive performance of gene/protein expression profile-based signatures in interlaboratory and data type dependent validation. To address this problem and assist in more precise diagnosis, we performed a genome-wide integrative proteome and transcriptome analysis and developed an ensemble machine learning-based integration algorithm for metastasis prediction (EMLI-Metastasis) and risk stratification (EMLI-Prognosis) in ICC. Based on massive proteome (216) and transcriptome (244) data sets, 132 feature (biomarker) genes were selected and used to train the EMLI-Metastasis algorithm. To accurately detect the metastasis of ICC patients, we developed a weighted ensemble machine learning method based on k-Top Scoring Pairs (k-TSP) method. This approach generates a metastasis classifier for each bootstrap aggregating training data set. Ten binary expression rank-based classifiers were generated for detection of metastasis separately. To further improve the accuracy of the method, the 10 binary metastasis classifiers were combined by weighted voting based on the score from the prediction results of each classifier. The prediction accuracy of the EMLI-Metastasis algorithm achieved 97.1% and 85.0% in proteome and transcriptome datasets, respectively. Among the 132 feature genes, 21 gene-pair signatures were developed to establish a metastasis-related prognosis risk-stratification model in ICC (EMLI-Prognosis). Based on EMLI-Prognosis algorithm, patients in the high-risk group had significantly dismal overall survival relative to the low-risk group in the clinical cohort (P-value < 0.05). Taken together, the EMLI-ICC algorithm provides a powerful and robust means for accurate metastasis prediction and risk stratification across proteome and transcriptome data types that is superior to currently used clinicopathological features in patients with ICC. Our developed algorithm could have profound implications not just in improved clinical care in cancer metastasis risk prediction, but also more broadly in machine-learning-based multi-cohort diagnosis method development. To make the EMLI-ICC algorithm easily accessible for clinical application, we established a web-based server for metastasis risk prediction (http://ibi.zju.edu.cn/EMLI/).


Asunto(s)
Neoplasias de los Conductos Biliares , Colangiocarcinoma , Humanos , Proteoma , Algoritmos , Colangiocarcinoma/genética , Aprendizaje Automático , Neoplasias de los Conductos Biliares/genética , Conductos Biliares Intrahepáticos/patología , Medición de Riesgo
17.
Clin Chem ; 70(6): 830-840, 2024 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-38581343

RESUMEN

BACKGROUND: Microsatellite instability (MSI) indicates DNA mismatch repair deficiency in certain types of cancer, such as colorectal cancer. The current gold standard technique, PCR-capillary electrophoresis (CE), requires matching normal samples and specialized instrumentation. We developed VarTrace, a rapid and low-cost quantitative PCR (qPCR) assay, to evaluate MSI using solely the tumor sample DNA, obviating the requirement for matching normal samples. METHODS: One hundred and one formalin-fixed paraffin-embedded (FFPE) tumor samples were tested using VarTrace and compared with the Promega OncoMate assay utilizing PCR-CE. Tumor percentage limit of detection was evaluated on contrived samples derived from clinical high MSI (MSI-H) samples. Analytical sensitivity, specificity, limit of detection, and input requirements were assessed using synthetic commercial reference standards. RESULTS: VarTrace successfully analyzed all 101 clinical FFPE samples, demonstrating 100% sensitivity and 98% specificity compared to OncoMate. It detected MSI-H with 97% accuracy down to 10% tumor. Analytical studies using synthetic samples showed a limit of detection of 5% variant allele frequency and a limit of input of 0.5 ng. CONCLUSIONS: This study validates VarTrace as a swift, accurate, and economical assay for MSI detection in samples with low tumor percentages without the need for matching normal DNA. VarTrace's capacity for highly sensitive MSI analysis holds potential for enhancing the efficiency of clinical work flows and broadening the availability of this test.


Asunto(s)
Inestabilidad de Microsatélites , Humanos , Adhesión en Parafina , Neoplasias/genética , Neoplasias/diagnóstico , Reacción en Cadena de la Polimerasa Multiplex/métodos , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/diagnóstico , Sensibilidad y Especificidad , Electroforesis Capilar/métodos , Formaldehído , ADN de Neoplasias/genética , Límite de Detección , Reacción en Cadena de la Polimerasa/métodos
18.
Phys Rev Lett ; 133(11): 116403, 2024 Sep 13.
Artículo en Inglés | MEDLINE | ID: mdl-39332001

RESUMEN

Electronic orders such as charge density wave (CDW) and superconductivity raise exotic physics and phenomena as evidenced in recently discovered kagome superconductors and transition metal chalcogenides. In most materials, CDW induces a weak, perturbative effect, manifested as shadow bands, minigaps, resistivity kinks, etc. Here we demonstrate a unique example-transition metal tetratellurides TaTe_{4}, in which the CDW order dominates the electronic structure and transport properties. Using angle-resolved photoemission spectroscopy, we found that the band structure of CDW TaTe_{4} is characterized by small, bulk electron pockets. Density functional theory analyses reveal their CDW origin from the folding of the original, large Fermi pockets. Importantly, the CDW induced pockets result in prominent frequencies in the quantum oscillation of the magnetoresistance. Satisfactory agreements are reached between results from photoemission spectroscopy, density functional theory, and quantum oscillation, concerning the shape, size, location, and angle dependence of the CDW pockets. Our results underline transition metal tetratellurides as an outstanding example for exploring the interplay between CDW, pressure induced superconductivity, and potential topological states under strong field.

19.
BMC Cancer ; 24(1): 924, 2024 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-39080615

RESUMEN

BACKGROUND: With advances in endoscopic submucosal dissection (ESD) technique, an increasing number of the Chinese population are being diagnosed with early gastric cancers (EGCs) at gastric angulus. However, the relationship between gastric angulus and EGCs remains obscure. OBJECTIVES: We aimed to unveil the unreported location characteristics of gastric angulus in Chinese EGC patients and the correlation between the degree of submucosal fibrosis and ESD outcomes. METHODS: We retrospectively reviewed the medical records of EGC patients treated with ESD from January 2010 to March 2023. We retrospectively investigated and analyzed 740 EGC patients using multiple analyses. RESULTS: Following gastric antrum (53.1%), the gastric angulus (21.8%) emerged as the second-most prevalent site for EGCs. It had highest incidence of severe submucosal fibrosis and ulceration than the other parts. Multivariate analysis showed independent associations of submucosal fibrosis at the angulus with ulceration (OR: 3.714, 95% CI: 1.041-13.249), procedure duration (OR: 1.037, 95% CI: 1.014-1.061), and perforation complication (OR: 14.611, 95% CI: 1.626-131.277) (all P < 0.05). CONCLUSIONS: The gastric angulus demonstrates the highest incidence of severe submucosal fibrosis and ulceration for EGCs identified by ESD. This condition is linked to unfavorable outcomes, typically increased perforation risks and prolonged operation duration. Therefore, meticulous dissection is crucial for patients with EGCs in the gastric angulus.


Asunto(s)
Resección Endoscópica de la Mucosa , Mucosa Gástrica , Neoplasias Gástricas , Humanos , Neoplasias Gástricas/cirugía , Neoplasias Gástricas/patología , Masculino , Femenino , Resección Endoscópica de la Mucosa/métodos , Persona de Mediana Edad , China/epidemiología , Estudios Retrospectivos , Anciano , Mucosa Gástrica/cirugía , Mucosa Gástrica/patología , Resultado del Tratamiento , Fibrosis
20.
BMC Cancer ; 24(1): 985, 2024 Aug 09.
Artículo en Inglés | MEDLINE | ID: mdl-39123182

RESUMEN

BACKGROUND: In China, both percutaneous microwave/radiofrequency ablation liver partition plus portal vein embolization (PALPP) and transarterial chemoembolization (TACE) plus portal vein embolization (PVE) have been utilized in planned hepatectomy. However, there is a lack of comparative studies on the effectiveness of these two techniques for cases with insufficient future liver remnant (FLR). METHODS: Patients were categorized into either the PALPP group or the TACE + PVE group. Clinical data, including FLR growth rate, complications, secondary resection rate, and overall survival rate, were compared and analyzed for both groups retrospectively. RESULTS: Between December 2014 and October 2021, a total of 29 patients underwent TACE + PVE (n = 12) and PALPP (n = 17). In the TACE + PVE group, 7 patients successfully underwent two-stage hepatectomy, while in the PALPP group, 13 patients underwent the procedure (two-stage resection rate: 58.3% vs. 76.5%, P = 0.42). There were no significant differences in postoperative complications of one-stage procedures (11.8% vs. 8.3%, P > 0.05) and second-stage resection complication (0% vs. 46.2%, P = 0.05) between the TACE + PVE and PALPP groups. However, the PALPP group demonstrated a shorter time to FLR volume growth for second-stage resection (18.5 days vs. 66 days, P = 0.001) and KGR (58.5 ml/week vs. 7.7 ml/week, P = 0.001). CONCLUSIONS: Compared with TACE + PVE, PALPP results in a more significant increase in FLR volume and a higher rate of two-stage resection without increasing postoperative complications.


Asunto(s)
Carcinoma Hepatocelular , Quimioembolización Terapéutica , Hepatectomía , Neoplasias Hepáticas , Microondas , Vena Porta , Ablación por Radiofrecuencia , Humanos , Hepatectomía/métodos , Masculino , Femenino , Persona de Mediana Edad , Neoplasias Hepáticas/terapia , Neoplasias Hepáticas/cirugía , Quimioembolización Terapéutica/métodos , Ablación por Radiofrecuencia/métodos , Microondas/uso terapéutico , Estudios Retrospectivos , Carcinoma Hepatocelular/terapia , Carcinoma Hepatocelular/cirugía , Anciano , Adulto , Hígado/cirugía , Hígado/irrigación sanguínea , Embolización Terapéutica/métodos , Resultado del Tratamiento , Complicaciones Posoperatorias/etiología , Complicaciones Posoperatorias/epidemiología , Tasa de Supervivencia , China/epidemiología , Terapia Combinada
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