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Enhancer-gene communication is dependent on topologically associating domains (TADs) and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying structures and mechanisms remain controversial. Here, we investigate a boundary that typically insulates fibroblast growth factor (FGF) oncogenes but is disrupted by DNA hypermethylation in gastrointestinal stromal tumors (GISTs). The boundary contains an array of CTCF sites that enforce adjacent TADs, one containing FGF genes and the other containing ANO1 and its putative enhancers, which are specifically active in GIST and its likely cell of origin. We show that coordinate disruption of four CTCF motifs in the boundary fuses the adjacent TADs, allows the ANO1 enhancer to contact FGF3, and causes its robust induction. High-resolution micro-C maps reveal specific contact between transcription initiation sites in the ANO1 enhancer and FGF3 promoter that quantitatively scales with FGF3 induction such that modest changes in contact frequency result in strong changes in expression, consistent with a causal relationship.
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Cromatina , Elementos de Facilitación Genéticos , Factor de Unión a CCCTC/genética , Factor de Unión a CCCTC/metabolismo , Cromatina/genética , Oncogenes , ADN/químicaRESUMEN
The orbital Hall effect1 refers to the generation of electron orbital angular momentum flow transverse to an external electric field. Contrary to the common belief that the orbital angular momentum is quenched in solids, theoretical studies2,3 predict that the orbital Hall effect can be strong and is a fundamental origin of the spin Hall effect4-7 in many transition metals. Despite the growing circumstantial evidence8-11, its direct detection remains elusive. Here we report the magneto-optical observation of the orbital Hall effect in the light metal titanium (Ti). The Kerr rotation by the orbital magnetic moment accumulated at Ti surfaces owing to the orbital Hall current is measured, and the result agrees with theoretical calculations semi-quantitatively and is supported by the orbital torque12 measurement in Ti-based magnetic heterostructures. This result confirms the orbital Hall effect and indicates that the orbital angular momentum is an important dynamic degree of freedom in solids. Moreover, this calls for renewed studies of the orbital effect on other degrees of freedom such as spin2,3,13,14, valley15,16, phonon17-19 and magnon20,21 dynamics.
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The a.c. Josephson effect predicted in 19621 and observed experimentally in 19632 as quantized 'voltage steps' (the Shapiro steps) from photon-assisted tunnelling of Cooper pairs is among the most fundamental phenomena of quantum mechanics and is vital for metrological quantum voltage standards. The physically dual effect, the a.c. coherent quantum phase slip (CQPS), photon-assisted tunnelling of magnetic fluxes through a superconducting nanowire, is envisaged to reveal itself as quantized 'current steps'3,4. The basic physical significance of the a.c. CQPS is also complemented by practical importance in future current standards, a missing element for closing the quantum metrology triangle5,6. In 2012, the CQPS was demonstrated as superposition of magnetic flux quanta in superconducting nanowires 7. However, the direct flat current steps in superconductors, the only unavailable basic effect of superconductivity to date, was unattainable due to lack of appropriate materials and challenges in circuit engineering. Here we report the direct observation of the dual Shapiro steps in a superconducting nanowire. The sharp steps are clear up to 26 GHz frequency with current values 8.3 nA and limited by the present set-up bandwidth. The current steps were theoretically predicted in small Josephson junctions 30 years ago5. However, unavoidable broadening in Josephson junctions prevents their direct experimental observation8,9. We solve this problem by placing a thin NbN nanowire in an inductive environment.
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Acute hepatitis A (AHA) involves severe CD8+ T cell-mediated liver injury. Here we showed during AHA, CD8+ T cells specific to unrelated viruses became activated. Hepatitis A virus (HAV)-infected cells produced IL-15 that induced T cell receptor (TCR)-independent activation of memory CD8+ T cells. TCR-independent activation of non-HAV-specific CD8+ T cells were detected in patients, as indicated by NKG2D upregulation, a marker of TCR-independent T cell activation by IL-15. CD8+ T cells derived from AHA patients exerted innate-like cytotoxicity triggered by activating receptors NKG2D and NKp30 without TCR engagement. We demonstrated that the severity of liver injury in AHA patients correlated with the activation of HAV-unrelated virus-specific CD8+ T cells and the innate-like cytolytic activity of CD8+ T cells, but not the activation of HAV-specific T cells. Thus, host injury in AHA is associated with innate-like cytotoxicity of bystander-activated CD8+ T cells, a result with implications for acute viral diseases.
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Linfocitos T CD8-positivos/inmunología , Citotoxicidad Inmunológica/inmunología , Hepatitis A/inmunología , Hepatopatías/inmunología , Activación de Linfocitos/inmunología , Adolescente , Adulto , Pruebas Inmunológicas de Citotoxicidad , Ensayo de Inmunoadsorción Enzimática , Femenino , Citometría de Flujo , Técnica del Anticuerpo Fluorescente , Hepatitis A/complicaciones , Humanos , Immunoblotting , Interleucina-15/metabolismo , Hígado/inmunología , Hígado/metabolismo , Hígado/patología , Hepatopatías/etiología , Masculino , Persona de Mediana Edad , Subfamilia K de Receptores Similares a Lectina de Células NK/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa , Adulto JovenRESUMEN
Many Mendelian disorders, such as Huntington's disease (HD) and spinocerebellar ataxias, arise from expansions of CAG trinucleotide repeats. Despite the clear genetic causes, additional genetic factors may influence the rate of those monogenic disorders. Notably, genome-wide association studies discovered somewhat expected modifiers, particularly mismatch repair genes involved in the CAG repeat instability, impacting age at onset of HD. Strikingly, FAN1, previously unrelated to repeat instability, produced the strongest HD modification signals. Diverse FAN1 haplotypes independently modify HD, with rare genetic variants diminishing DNA binding or nuclease activity of the FAN1 protein, hastening HD onset. However, the mechanism behind the frequent and the most significant onset-delaying FAN1 haplotype lacking missense variations has remained elusive. Here, we illustrated that a microRNA acting on 3'-UTR (untranslated region) SNP rs3512, rather than transcriptional regulation, is responsible for the significant FAN1 expression quantitative trait loci signal and allelic imbalance in FAN1 messenger ribonucleic acid (mRNA), accounting for the most significant and frequent onset-delaying modifier haplotype in HD. Specifically, miR-124-3p selectively targets the reference allele at rs3512, diminishing the stability of FAN1 mRNA harboring that allele and consequently reducing its levels. Subsequent validation analyses, including the use of antagomir and 3'-UTR reporter vectors with swapped alleles, confirmed the specificity of miR-124-3p at rs3512. Together, these findings indicate that the alternative allele at rs3512 renders the FAN1 mRNA less susceptible to miR-124-3p-mediated posttranscriptional regulation, resulting in increased FAN1 levels and a subsequent delay in HD onset by mitigating CAG repeat instability.
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Enfermedad de Huntington , MicroARNs , Humanos , Regiones no Traducidas 3'/genética , Endodesoxirribonucleasas , Exodesoxirribonucleasas/genética , Estudio de Asociación del Genoma Completo , Enfermedad de Huntington/genética , MicroARNs/genética , Enzimas MultifuncionalesRESUMEN
The most prevalent disease-causing mutation of CFTR is the deletion of Phe508 (ΔF508), which leads to defects in conventional Golgi-mediated exocytosis and cell surface expression. We report that ΔF508-CFTR surface expression can be rescued in vitro and in vivo by directing it to an unconventional GRASP-dependent secretion pathway. An integrated molecular and physiological analysis indicates that mechanisms associated with ER stress induce cell surface trafficking of the ER core-glycosylated wild-type and ΔF508-CFTR via the GRASP-dependent pathway. Phosphorylation of a specific site of GRASP and the PDZ-based interaction between GRASP and CFTR are critical for this unconventional surface trafficking. Remarkably, transgenic expression of GRASP in ΔF508-CFTR mice restores CFTR function and rescues mouse survival without apparent toxicity. These findings provide insight into how unconventional protein secretion is activated, and offer a potential therapeutic strategy for the treatment of cystic fibrosis and perhaps diseases stemming from other misfolded proteins.
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Proteínas Portadoras/metabolismo , Regulador de Conductancia de Transmembrana de Fibrosis Quística/metabolismo , Proteínas de la Membrana/metabolismo , Vías Secretoras , Animales , Membrana Celular/metabolismo , Retículo Endoplásmico/metabolismo , Péptidos y Proteínas de Señalización Intracelular , Ratones , Transporte de ProteínasRESUMEN
Fundamental studies of chemical reactions often consider the molecular dynamics along a reaction coordinate using a calculated or suggested potential energy surface1-5. But fully mapping such dynamics experimentally, by following all nuclear motions in a time-resolved manner-that is, the motions of wavepackets-is challenging and has not yet been realized even for the simple stereotypical bimolecular reaction6-8: A-B + C â A + B-C. Here we track the trajectories of these vibrational wavepackets during photoinduced bond formation of the gold trimer complex [Au(CN)2-]3 in an aqueous monomer solution, using femtosecond X-ray liquidography9-12 with X-ray free-electron lasers13,14. In the complex, which forms when three monomers A, B and C cluster together through non-covalent interactions15,16, the distance between A and B is shorter than that between B and C. Tracking the wavepacket in three-dimensional nuclear coordinates reveals that within the first 60 femtoseconds after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 femtoseconds to give a linear and covalently bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we map and unambiguously assign to specific normal modes using only the experimental data. In principle, more intense X-rays could visualize the motion not only of highly scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door to the direct tracking of the atomic motions involved in many chemical reactions.
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Recurrent spillovers of α- and ß-coronaviruses (CoV) such as severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome-CoV, SARS-CoV-2, and possibly human CoV have caused serious morbidity and mortality worldwide. In this study, six receptor-binding domains (RBDs) derived from α- and ß-CoV that are considered to have originated from animals and cross-infected humans were linked to a heterotrimeric scaffold, proliferating cell nuclear antigen (PCNA) subunits, PCNA1, PCNA2, and PCNA3. They assemble to create a stable mosaic multivalent nanoparticle, 6RBD-np, displaying a ring-shaped disk with six protruding antigens, like jewels in a crown. Prime-boost immunizations with 6RBD-np in mice induced significantly high Ab titers against RBD antigens derived from α- and ß-CoV and increased interferon (IFN-γ) production, with full protection against the SARS-CoV-2 wild type and Delta challenges. The mosaic 6RBD-np has the potential to induce intergenus cross-reactivity and to be developed as a pan-CoV vaccine against future CoV spillovers.
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COVID-19 , Nanopartículas , Humanos , Animales , Ratones , SARS-CoV-2 , Anticuerpos Antivirales , COVID-19/prevención & control , Anticuerpos Neutralizantes , Glicoproteína de la Espiga del Coronavirus/genéticaRESUMEN
Unlike proteins, which have a wealth of validated structural data, experimentally or computationally validated DNA origami datasets are limited. Here we present a graph neural network that can predict the three-dimensional conformation of DNA origami assemblies both rapidly and accurately. We develop a hybrid data-driven and physics-informed approach for model training, designed to minimize not only the data-driven loss but also the physics-informed loss. By employing an ensemble strategy, the model can successfully infer the shape of monomeric DNA origami structures almost in real time. Further refinement of the model in an unsupervised manner enables the analysis of supramolecular assemblies consisting of tens to hundreds of DNA blocks. The proposed model enables an automated inverse design of DNA origami structures for given target shapes. Our approach facilitates the real-time virtual prototyping of DNA origami, broadening its design space.
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ADN , Redes Neurales de la Computación , Conformación de Ácido Nucleico , ADN/químicaRESUMEN
Heat dissipation is a natural consequence of operating any electronic system. In nearly all computing systems, such heat is usually minimized by design and cooling. Here, we show that the temporal dynamics of internally produced heat in electronic devices can be engineered to both encode information within a single device and process information across multiple devices. In our demonstration, electronic NbOx Mott neurons, integrated on a flexible organic substrate, exhibit 18 biomimetic neuronal behaviours and frequency-based nociception within a single component by exploiting both the thermal dynamics of the Mott transition and the dynamical thermal interactions with the organic substrate. Further, multiple interconnected Mott neurons spatiotemporally communicate purely via heat, which we use for graph optimization by consuming over 106 times less energy when compared with the best digital processors. Thus, exploiting natural thermal processes in computing can lead to functionally dense, energy-efficient and radically novel mixed-physics computing primitives.
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BACKGROUND: Allergic rhinitis (AR) phenotypes in childhood are unclear. OBJECTIVES: This study sought to determine AR phenotypes and investigate their natural course and clinical and transcriptomic characteristics. METHODS: Latent class trajectory analysis was used for phenotyping AR in 1050 children from birth through 12 years using a birth cohort study. Blood transcriptome analyses were performed to define the underlying mechanisms of each phenotype. RESULTS: Five AR phenotypes were identified: early onset (n = 88, 8.4%), intermediate transient (n = 110, 10.5%), late onset (n = 209, 19.9%), very late onset (n=187, 17.8%), and never/infrequent (n = 456, 43.4%). Children with early-onset AR were associated with higher AR severity and sensitizations to foods at age 1 year and inhalants at age 3 years and asthma symptoms, but not with bronchial hyperresponsiveness (BHR). Children with late-onset AR phenotype associated with sensitizations to various foods at age 1 year but not from age 3 years, and to inhalants from age 7 years and with asthma with BHR. Children with very late-onset AR phenotype associated with sensitizations to foods throughout preschool age and to inhalants at ages 7 and 9 years and with asthma with BHR. Transcriptome analysis showed that early-onset AR was associated with viral/bacterial infection-related defense response, whereas late-onset AR was associated with T cell-related immune response. CONCLUSIONS: Early-onset AR phenotype was associated with sensitization to foods and inhalants at an early age and asthma symptoms, but not with BHR, whereas very late- and late-onset AR phenotypes were positively associated with sensitization to inhalants and asthma with BHR. Transcriptomic analyses indicated that early- and late-onset AR phenotypes had distinct underlying mechanisms related to AR as well.
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Fenotipo , Rinitis Alérgica , Transcriptoma , Humanos , Preescolar , Femenino , Masculino , Niño , Rinitis Alérgica/genética , Rinitis Alérgica/inmunología , Lactante , Recién Nacido , Cohorte de Nacimiento , Edad de Inicio , Perfilación de la Expresión Génica , Estudios de Cohortes , Asma/genética , Asma/inmunologíaRESUMEN
Immunocompromised patients with coronavirus disease 2019 were prospectively enrolled from March to November 2022 to understand the association between antibody responses and severe acute respiratory syndrome coronavirus 2 shedding. A total of 62 patients were analyzed, and the results indicated a faster decline in genomic and subgenomic viral RNA in patients with higher neutralizing and S1-specific immunoglobulin G (IgG) antibodies (both P < .001). Notably, high neutralizing antibody levels were associated with a significantly faster decrease in viable virus cultures (P = .04). Our observations suggest the role of neutralizing antibodies in prolonged virus shedding in immunocompromised patients, highlighting the potential benefits of enhancing their humoral immune response through vaccination or monoclonal antibody treatments.
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Anticuerpos Neutralizantes , Anticuerpos Antivirales , COVID-19 , Huésped Inmunocomprometido , Inmunoglobulina G , SARS-CoV-2 , Esparcimiento de Virus , Humanos , COVID-19/inmunología , COVID-19/virología , SARS-CoV-2/inmunología , Anticuerpos Antivirales/sangre , Anticuerpos Antivirales/inmunología , Masculino , Estudios Prospectivos , Femenino , Persona de Mediana Edad , Anticuerpos Neutralizantes/sangre , Anticuerpos Neutralizantes/inmunología , Inmunoglobulina G/sangre , Inmunoglobulina G/inmunología , Anciano , ARN Viral , Adulto , Formación de Anticuerpos/inmunologíaRESUMEN
The preparation of high-sulfur content organosulfur polymers has generated considerable interest as an emerging area in polymer science that has been driven by advances in the inverse vulcanization polymerization of elemental sulfur with organic comonomers. While numerous new inverse vulcanized polysulfides have been made over the past decade, insights into the mechanism of inverse vulcanization and structural characterization of the high-sulfur-content copolymers remain limited in scope. Furthermore, the exploration of new molecular architectures for organic comonomer synthesis remains an important frontier to enhance the properties of these new polymeric materials. In the current report, the first detailed study on the synthesis and inverse vulcanization of polycyclic rigid comonomers derived from norbornadiene was conducted, affording a quantitative assessment of polymer microstructure for these organopolysulfides and insights into the inverse vulcanization polymerization mechanism for this class of monomers. In particular, a stereoselective synthesis of the endo-exo norbornadiene cyclopentadiene adduct (Stillene) was achieved, which enabled direct comparison with the known exo-exo norbornadiene dimer (NBD2) previously used for inverse vulcanization. Reductive degradation of these sulfur copolymers and detailed structural analysis of the recovered sulfurated organic fragments revealed that remarkable exo-stereospecificity was achieved in the inverse vulcanization of elemental sulfur with both these polycyclic dienyl comonomers, which correlated to the robust thermomechanical properties associated with organopolysulfides made from NBD2 previously. Melt processing and molding of these sulfur copolymers were conducted to fabricate free-standing plastic lenses for long-wave infrared thermal imaging.
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The cluster-based body-centered-cubic superlattice (cBCC SL) represents one of the most complicated structures among reported nanocrystal assemblies, comprised of 72 truncated tetrahedral quantum dots per unit cell. Our previous report revealed that truncated tetrahedral quantum dots within cBCC SLs possessed highly controlled translational and orientational order owing to an unusual energetic landscape based on the balancing of entropic and enthalpic contributions during the assembly process. However, the cBCC SL's structural transformability and mechanical properties, uniquely originating from such complicated nanostructures, have yet to be investigated. Herein, we report that cBCC SLs can undergo dynamic transformation to face-centered-cubic SLs in response to post-assembly molecular exposure. We monitored the dynamic transformation process using in situ synchrotron-based small-angle X-ray scattering, revealing a dynamic transformation involving multiple steps underpinned by interactions between incoming molecules and TTQDs' surface ligands. Furthermore, our mechanistic study demonstrated that the precise configuration of TTQDs' ligand molecules in cBCC SLs was key to their high structural transformability and unique jelly-like soft mechanical properties. While ligand molecular configurations in nanocrystal SLs are often considered minor features, our findings emphasize their significance in controlling weak van der Waals interactions between nanocrystals within assembled SLs, leading to previously unremarked superstructural transformability and unique mechanical properties. Our findings promote a facile route toward further creation of soft materials, nanorobotics, and out-of-equilibrium assemblies based on nanocrystal building blocks.
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Anti-programmed death-ligand 1 (PD-L1) Ab-based therapies have demonstrated potential for treating metastatic urothelial cancer with high PD-L1 expression. Urinary exosomes are promising biomarkers for liquid biopsy, but urine's high variability requires normalization for accurate analysis. This study proposes using the PD-L1/Alix ratio to normalize exosomal PD-L1 signal intensity with Alix, an internal exosomal protein less susceptible to heterogeneity concerns than surface protein markers. Extracellular vesicles were isolated using ExoDisc and characterized using various methods, including ExoView to analyze tetraspanins, PD-L1, and Alix on individual exosomes. On-disc ELISA was used to evaluate PD-L1 and Alix-normalized PD-L1 in 15 urothelial cancer patients during the initial treatment cycle with Tecentriq. Results showed that Alix signal range was relatively uniform, whereas tetraspanin marker intensity varied for individual exosome particles. On-disc ELISA was more reliable for detecting exosomal PD-L1 expression than standard plate ELISA-based measurement. Using exosomal Alix expression for normalization is a more reliable approach than conventional methods for monitoring patient status. Overall, the study provides a practical and reliable method for detecting exosomal PD-L1 in urine samples from patients with urothelial cancer.
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Antígeno B7-H1 , Biomarcadores de Tumor , Exosomas , Humanos , Exosomas/metabolismo , Antígeno B7-H1/orina , Biomarcadores de Tumor/orina , Proteínas de Ciclo Celular/orina , Ensayo de Inmunoadsorción Enzimática/métodos , Masculino , Neoplasias de la Vejiga Urinaria/orina , Neoplasias de la Vejiga Urinaria/patología , Femenino , Anciano , Persona de Mediana Edad , Neoplasias Urológicas/orina , Neoplasias Urológicas/patología , Biopsia Líquida/métodosRESUMEN
BACKGROUND & AIMS: Ultrasound (US) is recommended for HCC surveillance in high-risk patients but has limited performance in detecting early-stage HCC. We aimed to compare the diagnostic performance of biannual US and annual non-contrast abbreviated magnetic resonance imaging (NC-AMRI) as HCC surveillance modalities in high-risk patients. METHODS: This prospective, multicenter cohort study enrolled participants with an estimated annual risk of HCC greater than 5% between October 2015 and April 2017. Participants underwent six rounds of HCC surveillance at 6-month intervals, with both US and NC-AMRI at rounds 1, 3, and 5, and only US at rounds 2, 4, and 6. The sensitivity, diagnostic yield (DY), and false referral rate (FRR) for HCC detection by US and NC-AMRI were compared. RESULTS: In total, 208 participants underwent 980 US and 516 NC-AMRI examinations during 30 months of follow-up. Among them, 34 HCCs were diagnosed in 31 participants, with 20 (64.5%) classified as very early-stage and 11 (35.5%) as early-stage HCC. The sensitivity of annual NC-AMRI (71.0%, 22/31) was marginally higher than that of biannual US (45.2%, 14/31; p = 0.077). NC-AMRI showed a significantly higher DY than US (4.26% vs. 1.43%, p <0.001), with a similar FRR (2.91% vs. 3.06%, p = 0.885). A simulation of alternating US and NC-AMRI at 6-month intervals yielded a sensitivity of 83.9% (26/31), significantly exceeding that of biannual US (p = 0.006). CONCLUSIONS: Annual NC-AMRI showed a marginally higher sensitivity than biannual US for HCC detection in high-risk patients. The DY of annual NC-AMRI was significantly higher than that of biannual US, without increasing the FRR. Thus, alternating US and NC-AMRI at 6-month intervals could be an optimal surveillance strategy for high-risk patients. IMPACT AND IMPLICATIONS: Current guidelines permit the use of magnetic resonance imaging (MRI) as a surveillance tool for hepatocellular carcinoma in patients in whom ultrasonography (US) is inadequate. However, the specific indications, imaging sequences, and intervals for MRI surveillance remain unclear. In our study, we found that annual non-contrast abbreviated MRI exhibited marginally higher sensitivity and significantly better diagnostic yield than biannual US in patients at high risk of hepatocellular carcinoma. Alternating US and non-contrast abbreviated MRI at 6-month intervals led to significantly improved sensitivity compared to biannual US, making it a potentially optimal surveillance strategy for high-risk patients. GOV IDENTIFIER: NCT02551250.
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Carcinoma Hepatocelular , Neoplasias Hepáticas , Imagen por Resonancia Magnética , Ultrasonografía , Humanos , Neoplasias Hepáticas/diagnóstico por imagen , Neoplasias Hepáticas/diagnóstico , Neoplasias Hepáticas/epidemiología , Carcinoma Hepatocelular/diagnóstico por imagen , Carcinoma Hepatocelular/diagnóstico , Carcinoma Hepatocelular/epidemiología , Imagen por Resonancia Magnética/métodos , Imagen por Resonancia Magnética/estadística & datos numéricos , Femenino , Masculino , Ultrasonografía/métodos , Ultrasonografía/estadística & datos numéricos , Estudios Prospectivos , Persona de Mediana Edad , Anciano , Detección Precoz del Cáncer/métodos , Sensibilidad y EspecificidadRESUMEN
PURPOSE: Patients with STAT1 gain-of-function (GOF) mutations often exhibit autoimmune features. The JAK1/2 inhibitor ruxolitinib can be administered to alleviate autoimmune symptoms; however, it is unclear how immune cells are molecularly changed by ruxolitinib treatment. Then, we aimed to investigate the trnscriptional and epigenetic status of immune cells before and after ruxolitinib treatment in a patient with STAT1 GOF. METHODS: A patient with a heterozygous STAT1 GOF variant (p.Ala267Val), exhibiting autoimmune features, was treated with ruxolitinib, and peripheral blood mononuclear cells (PBMCs) were longitudinally collected. PBMCs were transcriptionally analyzed by single-cell cellular indexing of the transcriptomes and epitopes by sequencing (CITE-seq), and epigenetically analyzed by assay of transposase-accessible chromatin sequencing (ATAC-seq). RESULTS: CITE-seq analysis revealed that before treatment, the patient's PBMCs exhibited aberrantly activated inflammatory features, especially IFN-related features. In particular, monocytes showed high expression levels of a subset of IFN-stimulated genes (ISGs). Ruxolitinib treatment substantially downregulated aberrantly overexpressed ISGs, and improved autoimmune features. However, epigenetic analysis demonstrated that genetic regions of ISGs-e.g., STAT1, IRF1, MX1, and OAS1-were highly accessible even after ruxolitinib treatment. When ruxolitinib was temporarily discontinued, the patient's autoimmune features were aggravated, which is in line with sustained epigenetic abnormality. CONCLUSIONS: In a patient with STAT1 GOF, ruxolitinib treatment improved autoimmune features and downregulated aberrantly overexpressed ISGs, but did not correct epigenetic abnormality of ISGs.
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Mutación con Ganancia de Función , Pirazoles , Factor de Transcripción STAT1 , Humanos , Mutación con Ganancia de Función/genética , Leucocitos Mononucleares/metabolismo , Nitrilos/farmacología , Pirazoles/farmacología , Pirimidinas/farmacología , Factor de Transcripción STAT1/genéticaRESUMEN
BACKGROUND & AIMS: Intrahepatic cholangiocarcinomas (iCCs) are characterized by their rarity, difficult diagnosis, and overall poor prognosis. The iCC molecular classification for developing precision medicine strategies was investigated. METHODS: Comprehensive genomic, transcriptomic, proteomic, and phosphoproteomic analyses were performed on treatment-naïve tumor samples from 102 patients with iCC who underwent surgical resection with curative intent. An organoid model was constructed for testing therapeutic potential. RESULTS: Three clinically supported subtypes (stem-like, poorly immunogenic, and metabolism) were identified. NCT-501 (aldehyde dehydrogenase 1 family member A1 [ALDH1A1] inhibitor) exhibited synergism with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. The oncometabolite dysregulations were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype harbors the non-T-cell tumor infiltration. Integrated multiomics analysis not only reproduced the 3 subtypes but also showed heterogeneity in iCC. CONCLUSIONS: This large-scale proteogenomic analysis provides information beyond that obtained with genomic analysis, allowing the functional impact of genomic alterations to be discerned. These findings may assist in the stratification of patients with iCC and in developing rational therapeutic strategies.
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Neoplasias de los Conductos Biliares , Colangiocarcinoma , Proteogenómica , Humanos , Proteómica , Pronóstico , Colangiocarcinoma/genética , Colangiocarcinoma/cirugía , Colangiocarcinoma/metabolismo , Conductos Biliares Intrahepáticos/patología , Neoplasias de los Conductos Biliares/patologíaRESUMEN
Hypoxia is a representative tumor characteristic associated with malignant progression in clinical patients. Engineered in vitro models have led to significant advances in cancer research, allowing for the investigation of cells in physiological environments and the study of disease mechanisms and processes with enhanced relevance. In this study, we propose a U-shape pillar strip for a 3D cell-lumped organoid model (3D-COM) to study the effects of hypoxia on lung cancer in a high-throughput manner. We developed a U-pillar strip that facilitates the aggregation of PDCs mixed with an extracellular matrix to make the 3D-COM in 384-plate array form. The response to three hypoxia-activated prodrugs was higher in the 3D-COM than in the 2D culture model. The protein expression of hypoxia-inducible factor 1 alpha (HIF-1α) and HIF-2α, which are markers of hypoxia, was also higher in the 3D-COM than in the 2D culture. The results show that 3D-COM better recapitulated the hypoxic conditions of lung cancer tumors than the 2D culture. Therefore, the U-shape pillar strip for 3D-COM is a good tool to study the effects of hypoxia on lung cancer in a high-throughput manner, which can efficiently develop new drugs targeting hypoxic tumors.
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Ensayos Analíticos de Alto Rendimiento , Neoplasias Pulmonares , Organoides , Humanos , Neoplasias Pulmonares/patología , Neoplasias Pulmonares/metabolismo , Organoides/metabolismo , Organoides/patología , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Hipoxia de la Célula , Técnicas de Cultivo Tridimensional de Células , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico/metabolismoRESUMEN
BACKGROUND: We investigated the association between exercise habits before or after thyroidectomy and incident type 2 diabetes mellitus (T2DM) in patients with thyroid cancer. METHODS: An observational cohort study of 69,526 thyroid cancer patients who underwent thyroidectomy for the treatment of thyroid cancer between 2010 and 2016 was performed using the Korean National Health Information Database. Regular exercise was defined as mid-term or vigorous exercise at least 1 day in a week based on a self-reported questionnaire. Patients were divided into four groups according to exercise habits before and after thyroidectomy: persistent non-exercisers, new exercisers, exercise dropouts, and exercise maintainers. RESULTS: During a median follow-up of 4.5 years, 2,720 (3.91%) patients developed T2DM. The incidence of T2DM per 1,000 person years was lower in patients who performed regular exercise before or after thyroidectomy than in persistent non-exercisers (10.77 in persistent non-exerciser group, 8.28 in new exerciser group, 8.59 in exercise dropout group, and 7.61 in exercise maintainer group). Compared with the persistent non-exerciser group, the new exerciser group (hazard ratio [HR] 0.87, 95% confidence interval [CI] 0.78-0.97), the exercise dropout group (HR 0.81, 95% CI 0.72-0.91), and the exercise maintainer group (HR 0.84, 95% CI 0.76-0.93) had lower risks of incident T2DM. Exercising < 1,500 MET-minutes/week in the exercise maintainer group was associated with a lower risk of incident T2DM compared with persistent non-exercisers (< 500: HR 0.80, 95% CI 0.67-0.96, P = 0.002; 500 to < 1,000: HR 0.81, 95% CI 0.71-0.93, P < 0.001; 1,000 to < 1,500: HR 0.81, 95% CI 0.69-0.94, P < 0.001). CONCLUSIONS: Regular exercise before or after thyroidectomy was associated with a lower risk of incident T2DM in patients with thyroid cancer.