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1.
Nat Immunol ; 22(2): 154-165, 2021 02.
Artículo en Inglés | MEDLINE | ID: mdl-33398185

RESUMEN

Inflammatory caspase sensing of cytosolic lipopolysaccharide (LPS) triggers pyroptosis and the concurrent release of damage-associated molecular patterns (DAMPs). Collectively, DAMPs are key determinants that shape the aftermath of inflammatory cell death. However, the identity and function of the individual DAMPs released are poorly defined. Our proteomics study revealed that cytosolic LPS sensing triggered the release of galectin-1, a ß-galactoside-binding lectin. Galectin-1 release is a common feature of inflammatory cell death, including necroptosis. In vivo studies using galectin-1-deficient mice, recombinant galectin-1 and galectin-1-neutralizing antibody showed that galectin-1 promotes inflammation and plays a detrimental role in LPS-induced lethality. Mechanistically, galectin-1 inhibition of CD45 (Ptprc) underlies its unfavorable role in endotoxin shock. Finally, we found increased galectin-1 in sera from human patients with sepsis. Overall, we uncovered galectin-1 as a bona fide DAMP released as a consequence of cytosolic LPS sensing, identifying a new outcome of inflammatory cell death.


Asunto(s)
Alarminas/metabolismo , Endotoxemia/inmunología , Galectina 1/metabolismo , Mediadores de Inflamación/metabolismo , Inflamación/inmunología , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Macrófagos/metabolismo , Proteínas de Unión a Fosfato/metabolismo , Adulto , Anciano , Anciano de 80 o más Años , Alarminas/deficiencia , Alarminas/genética , Animales , Estudios de Casos y Controles , Modelos Animales de Enfermedad , Endotoxemia/inducido químicamente , Endotoxemia/metabolismo , Endotoxemia/patología , Femenino , Galectina 1/sangre , Galectina 1/deficiencia , Galectina 1/genética , Células HeLa , Humanos , Inflamación/inducido químicamente , Inflamación/metabolismo , Inflamación/patología , Péptidos y Proteínas de Señalización Intracelular/deficiencia , Péptidos y Proteínas de Señalización Intracelular/genética , Antígenos Comunes de Leucocito/metabolismo , Lipopolisacáridos , Macrófagos/inmunología , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Persona de Mediana Edad , Necroptosis , Proteínas de Unión a Fosfato/deficiencia , Proteínas de Unión a Fosfato/genética , Células RAW 264.7 , Sepsis/sangre , Sepsis/diagnóstico , Transducción de Señal , Regulación hacia Arriba
2.
Nat Immunol ; 20(7): 835-851, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31160797

RESUMEN

How tumor cells genetically lose antigenicity and evade immune checkpoints remains largely elusive. We report that tissue-specific expression of the human long noncoding RNA LINK-A in mouse mammary glands initiates metastatic mammary gland tumors, which phenotypically resemble human triple-negative breast cancer (TNBC). LINK-A expression facilitated crosstalk between phosphatidylinositol-(3,4,5)-trisphosphate and inhibitory G-protein-coupled receptor (GPCR) pathways, attenuating protein kinase A-mediated phosphorylation of the E3 ubiquitin ligase TRIM71. Consequently, LINK-A expression enhanced K48-polyubiquitination-mediated degradation of the antigen peptide-loading complex (PLC) and intrinsic tumor suppressors Rb and p53. Treatment with LINK-A locked nucleic acids or GPCR antagonists stabilized the PLC components, Rb and p53, and sensitized mammary gland tumors to immune checkpoint blockers. Patients with programmed ccll death protein-1(PD-1) blockade-resistant TNBC exhibited elevated LINK-A levels and downregulated PLC components. Hence we demonstrate lncRNA-dependent downregulation of antigenicity and intrinsic tumor suppression, which provides the basis for developing combinational immunotherapy treatment regimens and early TNBC prevention.


Asunto(s)
Presentación de Antígeno/inmunología , Regulación Neoplásica de la Expresión Génica , Neoplasias/genética , Neoplasias/inmunología , Oncogenes , ARN Largo no Codificante/genética , Escape del Tumor/genética , Escape del Tumor/inmunología , Adenoma/genética , Adenoma/metabolismo , Animales , Línea Celular Tumoral , Proliferación Celular , Transformación Celular Neoplásica/genética , Transformación Celular Neoplásica/metabolismo , Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Modelos Animales de Enfermedad , Progresión de la Enfermedad , Humanos , Ratones , Neoplasias/metabolismo , Neoplasias/patología , Fosforilación , Receptores Acoplados a Proteínas G/antagonistas & inhibidores , Microambiente Tumoral/genética , Microambiente Tumoral/inmunología , Proteína p53 Supresora de Tumor/metabolismo , Ubiquitinación , Ensayos Antitumor por Modelo de Xenoinjerto
3.
Nature ; 606(7915): 725-731, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35676473

RESUMEN

Synonymous mutations in protein-coding genes do not alter protein sequences and are thus generally presumed to be neutral or nearly neutral1-5. Here, to experimentally verify this presumption, we constructed 8,341 yeast mutants each carrying a synonymous, nonsynonymous or nonsense mutation in one of 21 endogenous genes with diverse functions and expression levels and measured their fitness relative to the wild type in a rich medium. Three-quarters of synonymous mutations resulted in a significant reduction in fitness, and the distribution of fitness effects was overall similar-albeit nonidentical-between synonymous and nonsynonymous mutations. Both synonymous and nonsynonymous mutations frequently disturbed the level of mRNA expression of the mutated gene, and the extent of the disturbance partially predicted the fitness effect. Investigations in additional environments revealed greater across-environment fitness variations for nonsynonymous mutants than for synonymous mutants despite their similar fitness distributions in each environment, suggesting that a smaller proportion of nonsynonymous mutants than synonymous mutants are always non-deleterious in a changing environment to permit fixation, potentially explaining the common observation of substantially lower nonsynonymous than synonymous substitution rates. The strong non-neutrality of most synonymous mutations, if it holds true for other genes and in other organisms, would require re-examination of numerous biological conclusions about mutation, selection, effective population size, divergence time and disease mechanisms that rely on the assumption that synoymous mutations are neutral.


Asunto(s)
Genes Fúngicos , Aptitud Genética , Saccharomyces cerevisiae , Mutación Silenciosa , Secuencia de Aminoácidos , Codón sin Sentido/genética , Evolución Molecular , Genes Fúngicos/genética , Aptitud Genética/genética , Tasa de Mutación , ARN de Hongos/análisis , ARN de Hongos/biosíntesis , ARN Mensajero/análisis , ARN Mensajero/biosíntesis , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Selección Genética , Mutación Silenciosa/genética
4.
Nature ; 594(7861): 41-45, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-34079139

RESUMEN

Owing to the inevitable loss in communication channels, the distance of entanglement distribution is limited to approximately 100 kilometres on the ground1. Quantum repeaters can circumvent this problem by using quantum memory and entanglement swapping2. As the elementary link of a quantum repeater, the heralded distribution of two-party entanglement between two remote nodes has only been realized with built-in-type quantum memories3-9. These schemes suffer from the trade-off between multiplexing capacity and deterministic properties and hence hinder the development of efficient quantum repeaters. Quantum repeaters based on absorptive quantum memories can overcome such limitations because they separate the quantum memories and the quantum light sources. Here we present an experimental demonstration of heralded entanglement between absorptive quantum memories. We build two nodes separated by 3.5 metres, each containing a polarization-entangled photon-pair source and a solid-state quantum memory with bandwidth up to 1 gigahertz. A joint Bell-state measurement in the middle station heralds the successful distribution of maximally entangled states between the two quantum memories with a fidelity of 80.4 ± 2.2 per cent (±1 standard deviation). The quantum nodes and channels demonstrated here can serve as an elementary link of a quantum repeater. Moreover, the wideband absorptive quantum memories used in the nodes are compatible with deterministic entanglement sources and can simultaneously support multiplexing, which paves the way for the construction of practical solid-state quantum repeaters and high-speed quantum networks.

5.
Nature ; 592(7856): 794-798, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33854239

RESUMEN

The initiation of cell division integrates a large number of intra- and extracellular inputs. D-type cyclins (hereafter, cyclin D) couple these inputs to the initiation of DNA replication1. Increased levels of cyclin D promote cell division by activating cyclin-dependent kinases 4 and 6 (hereafter, CDK4/6), which in turn phosphorylate and inactivate the retinoblastoma tumour suppressor. Accordingly, increased levels and activity of cyclin D-CDK4/6 complexes are strongly linked to unchecked cell proliferation and cancer2,3. However, the mechanisms that regulate levels of cyclin D are incompletely understood4,5. Here we show that autophagy and beclin 1 regulator 1 (AMBRA1) is the main regulator of the degradation of cyclin D. We identified AMBRA1 in a genome-wide screen to investigate the genetic basis of  the response to CDK4/6 inhibition. Loss of AMBRA1 results in high levels of cyclin D in cells and in mice, which promotes proliferation and decreases sensitivity to CDK4/6 inhibition. Mechanistically, AMBRA1 mediates ubiquitylation and proteasomal degradation of cyclin D as a substrate receptor for the cullin 4 E3 ligase complex. Loss of AMBRA1 enhances the growth of lung adenocarcinoma in a mouse model, and low levels of AMBRA1 correlate with worse survival in patients with lung adenocarcinoma. Thus, AMBRA1 regulates cellular levels of cyclin D, and contributes to cancer development and the response of cancer cells to CDK4/6 inhibitors.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/metabolismo , Ciclina D/metabolismo , Adenocarcinoma del Pulmón/genética , Animales , División Celular , Quinasa 4 Dependiente de la Ciclina/antagonistas & inhibidores , Quinasa 4 Dependiente de la Ciclina/metabolismo , Quinasa 6 Dependiente de la Ciclina/antagonistas & inhibidores , Quinasa 6 Dependiente de la Ciclina/metabolismo , Genes Supresores de Tumor , Humanos , Neoplasias Pulmonares/genética , Ratones , Piperazinas/farmacología , Piridinas/farmacología , Células U937 , Ubiquitinación
6.
Mol Cell ; 76(3): 359-370, 2019 11 07.
Artículo en Inglés | MEDLINE | ID: mdl-31668929

RESUMEN

The engagement of programmed cell death protein 1 (PD-1; encoded by the PDCD1 gene) receptor expressed on activated T cells and its ligand, programmed death-ligand 1 (PD-L1; encoded by the CD274 gene), is a major co-inhibitory checkpoint signaling that controls T cell activities. Various types of cancers express high levels of PD-L1 and exploit PD-L1/PD-1 signaling to evade T cell immunity. Blocking the PD-L1/PD-1 pathway has consistently shown remarkable anti-tumor effects in patients with advanced cancers and is recognized as the gold standard for developing new immune checkpoint blockade (ICB) and combination therapies. However, the response rates of anti-PD-L1 have been limited in several solid tumors. Therefore, furthering our understanding of the regulatory mechanisms of PD-L1 can bring substantial benefits to patients with cancer by improving the efficacy of current PD-L1/PD-1 blockade or other ICBs. In this review, we provide current knowledge of PD-L1 regulatory mechanisms at the transcriptional, posttranscriptional, post-translational, and extracellular levels, and discuss the implications of these findings in cancer diagnosis and immunotherapy.


Asunto(s)
Antígeno B7-H1/metabolismo , Biomarcadores de Tumor/metabolismo , Neoplasias/metabolismo , Animales , Antineoplásicos Inmunológicos/uso terapéutico , Antígeno B7-H1/antagonistas & inhibidores , Antígeno B7-H1/genética , Antígeno B7-H1/inmunología , Biomarcadores de Tumor/antagonistas & inhibidores , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/inmunología , Regulación Neoplásica de la Expresión Génica , Humanos , Terapia Molecular Dirigida , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Neoplasias/inmunología , Procesamiento Proteico-Postraduccional , Procesamiento Postranscripcional del ARN , Transducción de Señal , Transcripción Genética , Escape del Tumor
7.
Mol Cell ; 75(3): 644-660.e5, 2019 08 08.
Artículo en Inglés | MEDLINE | ID: mdl-31398325

RESUMEN

Cell-cell communication via ligand-receptor signaling is a fundamental feature of complex organs. Despite this, the global landscape of intercellular signaling in mammalian liver has not been elucidated. Here we perform single-cell RNA sequencing on non-parenchymal cells isolated from healthy and NASH mouse livers. Secretome gene analysis revealed a highly connected network of intrahepatic signaling and disruption of vascular signaling in NASH. We uncovered the emergence of NASH-associated macrophages (NAMs), which are marked by high expression of triggering receptors expressed on myeloid cells 2 (Trem2), as a feature of mouse and human NASH that is linked to disease severity and highly responsive to pharmacological and dietary interventions. Finally, hepatic stellate cells (HSCs) serve as a hub of intrahepatic signaling via HSC-derived stellakines and their responsiveness to vasoactive hormones. These results provide unprecedented insights into the landscape of intercellular crosstalk and reprogramming of liver cells in health and disease.


Asunto(s)
Comunicación Celular/genética , Hígado/metabolismo , Enfermedad del Hígado Graso no Alcohólico/genética , Análisis de Secuencia de ARN , Animales , Reprogramación Celular/genética , Modelos Animales de Enfermedad , Células Estrelladas Hepáticas/metabolismo , Células Estrelladas Hepáticas/patología , Humanos , Ligandos , Hígado/patología , Macrófagos/metabolismo , Macrófagos/patología , Ratones , Enfermedad del Hígado Graso no Alcohólico/metabolismo , Enfermedad del Hígado Graso no Alcohólico/patología , Transducción de Señal/genética , Análisis de la Célula Individual
8.
Nature ; 588(7839): 693-698, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33177715

RESUMEN

Despite its success in achieving the long-term survival of 10-30% of treated individuals, immune therapy is still ineffective for most patients with cancer1,2. Many efforts are therefore underway to identify new approaches that enhance such immune 'checkpoint' therapy3-5 (so called because its aim is to block proteins that inhibit checkpoint signalling pathways in T cells, thereby freeing those immune cells to target cancer cells). Here we show that inhibiting PCSK9-a key protein in the regulation of cholesterol metabolism6-8-can boost the response of tumours to immune checkpoint therapy, through a mechanism that is independent of PCSK9's cholesterol-regulating functions. Deleting the PCSK9 gene in mouse cancer cells substantially attenuates or prevents their growth in mice in a manner that depends on cytotoxic T cells. It also enhances the efficacy of immune therapy that is targeted at the checkpoint protein PD1. Furthermore, clinically approved PCSK9-neutralizing antibodies synergize with anti-PD1 therapy in suppressing tumour growth in mouse models of cancer. Inhibiting PCSK9-either through genetic deletion or using PCSK9 antibodies-increases the expression of major histocompatibility protein class I (MHC I) proteins on the tumour cell surface, promoting robust intratumoral infiltration of cytotoxic T cells. Mechanistically, we find that PCSK9 can disrupt the recycling of MHC I to the cell surface by associating with it physically and promoting its relocation and degradation in the lysosome. Together, these results suggest that inhibiting PCSK9 is a promising way to enhance immune checkpoint therapy for cancer.


Asunto(s)
Inhibidores de Puntos de Control Inmunológico/farmacología , Inhibidores de Puntos de Control Inmunológico/uso terapéutico , Inmunoterapia/métodos , Neoplasias/tratamiento farmacológico , Neoplasias/inmunología , Inhibidores de PCSK9 , Receptor de Muerte Celular Programada 1/antagonistas & inhibidores , Animales , Anticuerpos Neutralizantes/inmunología , Anticuerpos Neutralizantes/farmacología , Anticuerpos Neutralizantes/uso terapéutico , Línea Celular Tumoral , Modelos Animales de Enfermedad , Femenino , Antígenos de Histocompatibilidad Clase I/inmunología , Antígenos de Histocompatibilidad Clase I/metabolismo , Humanos , Lisosomas/metabolismo , Ratones , Neoplasias/metabolismo , Neoplasias/patología , Proproteína Convertasa 9/deficiencia , Proproteína Convertasa 9/genética , Proproteína Convertasa 9/inmunología , Linfocitos T Citotóxicos/citología , Linfocitos T Citotóxicos/inmunología , Ensayos Antitumor por Modelo de Xenoinjerto
9.
Mol Cell ; 71(4): 606-620.e7, 2018 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-30118680

RESUMEN

Metformin has been reported to possess antitumor activity and maintain high cytotoxic T lymphocyte (CTL) immune surveillance. However, the functions and detailed mechanisms of metformin's role in cancer immunity are not fully understood. Here, we show that metformin increases CTL activity by reducing the stability and membrane localization of programmed death ligand-1 (PD-L1). Furthermore, we discover that AMP-activated protein kinase (AMPK) activated by metformin directly phosphorylates S195 of PD-L1. S195 phosphorylation induces abnormal PD-L1 glycosylation, resulting in its ER accumulation and ER-associated protein degradation (ERAD). Consistently, tumor tissues from metformin-treated breast cancer patients exhibit reduced PD-L1 levels with AMPK activation. Blocking the inhibitory signal of PD-L1 by metformin enhances CTL activity against cancer cells. Our findings identify a new regulatory mechanism of PD-L1 expression through the ERAD pathway and suggest that the metformin-CTLA4 blockade combination has the potential to increase the efficacy of immunotherapy.


Asunto(s)
Antineoplásicos/farmacología , Antígeno B7-H1/genética , Antígeno CTLA-4/genética , Regulación Neoplásica de la Expresión Génica , Hipoglucemiantes/farmacología , Metformina/farmacología , Proteínas Quinasas Activadas por AMP/genética , Proteínas Quinasas Activadas por AMP/inmunología , Animales , Antígeno B7-H1/inmunología , Antígeno CTLA-4/inmunología , Línea Celular Tumoral , Retículo Endoplásmico/efectos de los fármacos , Retículo Endoplásmico/genética , Retículo Endoplásmico/metabolismo , Degradación Asociada con el Retículo Endoplásmico , Células Epiteliales/citología , Células Epiteliales/efectos de los fármacos , Células Epiteliales/inmunología , Femenino , Glicosilación , Humanos , Glándulas Mamarias Humanas/citología , Glándulas Mamarias Humanas/efectos de los fármacos , Glándulas Mamarias Humanas/inmunología , Melanoma Experimental/tratamiento farmacológico , Melanoma Experimental/genética , Melanoma Experimental/inmunología , Melanoma Experimental/patología , Ratones , Ratones Endogámicos NOD , Fosforilación , Serina/metabolismo , Linfocitos T Citotóxicos/citología , Linfocitos T Citotóxicos/efectos de los fármacos , Linfocitos T Citotóxicos/inmunología
10.
Proc Natl Acad Sci U S A ; 120(1): e2217476120, 2023 01 03.
Artículo en Inglés | MEDLINE | ID: mdl-36584296

RESUMEN

HIV gene expression is modulated by the combinatorial activity of the HIV transcriptional activator, Tat, host transcription factors, and chromatin remodeling complexes. To identify host factors regulating HIV transcription, we used specific single-guide RNAs and endonuclease-deficient Cas9 to perform chromatin affinity purification of the integrated HIV promoter followed by mass spectrometry. The scaffold protein, p32, also called ASF/SF2 splicing factor-associated protein, was identified among the top enriched factors present in actively transcribing HIV promoters but absent in silenced ones. Chromatin immunoprecipitation analysis confirmed the presence of p32 on active HIV promoters and its enhanced recruitment by Tat. HIV uses Tat to efficiently recruit positive transcription elongation factor b (p-TEFb) (CDK9/CCNT1) to TAR, an RNA secondary structure that forms from the first 59 bp of HIV transcripts, to enhance RNAPII transcriptional elongation. The RNA interference of p32 significantly reduced HIV transcription in primary CD4+T cells and in HIV chronically infected cells, independently of either HIV splicing or p32 anti-splicing activity. Conversely, overexpression of p32 specifically increased Tat-dependent HIV transcription. p32 was found to directly interact with Tat's basic domain enhancing Tat stability and half-life. Conversely, p32 associates with Tat via N- and C-terminal domains. Likely due its scaffold properties, p32 also promoted Tat association with TAR, p-TEFb, and RNAPII enhancing Tat-dependent HIV transcription. In sum, we identified p32 as a host factor that interacts with and stabilizes Tat protein, promotes Tat-dependent transcriptional regulation, and may be explored for HIV-targeted transcriptional inhibition.


Asunto(s)
Infecciones por VIH , VIH-1 , Humanos , Factor B de Elongación Transcripcional Positiva/genética , Factor B de Elongación Transcripcional Positiva/metabolismo , VIH-1/fisiología , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , ARN Polimerasa II/genética , ARN Polimerasa II/metabolismo , Chaperonas Moleculares/metabolismo , Infecciones por VIH/genética , Transcripción Genética , Duplicado del Terminal Largo de VIH/genética
11.
Am J Hum Genet ; 109(6): 1077-1091, 2022 06 02.
Artículo en Inglés | MEDLINE | ID: mdl-35580588

RESUMEN

Hearing loss is one of the top contributors to years lived with disability and is a risk factor for dementia. Molecular evidence on the cellular origins of hearing loss in humans is growing. Here, we performed a genome-wide association meta-analysis of clinically diagnosed and self-reported hearing impairment on 723,266 individuals and identified 48 significant loci, 10 of which are novel. A large proportion of associations comprised missense variants, half of which lie within known familial hearing loss loci. We used single-cell RNA-sequencing data from mouse cochlea and brain and mapped common-variant genomic results to spindle, root, and basal cells from the stria vascularis, a structure in the cochlea necessary for normal hearing. Our findings indicate the importance of the stria vascularis in the mechanism of hearing impairment, providing future paths for developing targets for therapeutic intervention in hearing loss.


Asunto(s)
Sordera , Pérdida Auditiva , Animales , Cóclea , Estudio de Asociación del Genoma Completo , Pérdida Auditiva/genética , Humanos , Ratones , Estría Vascular
12.
Brief Bioinform ; 24(3)2023 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-37088980

RESUMEN

Immunofluorescence patterns of anti-nuclear antibodies (ANAs) on human epithelial cell (HEp-2) substrates are important biomarkers for the diagnosis of autoimmune diseases. There are growing clinical requirements for an automatic readout and classification of ANA immunofluorescence patterns for HEp-2 images following the taxonomy recommended by the International Consensus on Antinuclear Antibody Patterns (ICAP). In this study, a comprehensive collection of HEp-2 specimen images covering a broad range of ANA patterns was established and manually annotated by experienced laboratory experts. By utilizing a supervised learning methodology, an automatic immunofluorescence pattern classification framework for HEp-2 specimen images was developed. The framework consists of a module for HEp-2 cell detection and cell-level feature extraction, followed by an image-level classifier that is capable of recognizing all 14 classes of ANA immunofluorescence patterns as recommended by ICAP. Performance analysis indicated an accuracy of 92.05% on the validation dataset and 87% on an independent test dataset, which has surpassed the performance of human examiners on the same test dataset. The proposed framework is expected to contribute to the automatic ANA pattern recognition in clinical laboratories to facilitate efficient and precise diagnosis of autoimmune diseases.


Asunto(s)
Anticuerpos Antinucleares , Enfermedades Autoinmunes , Humanos , Técnica del Anticuerpo Fluorescente , Anticuerpos Antinucleares/análisis , Enfermedades Autoinmunes/diagnóstico , Células Epiteliales , Aprendizaje Automático Supervisado
13.
Brief Bioinform ; 25(1)2023 11 22.
Artículo en Inglés | MEDLINE | ID: mdl-38205966

RESUMEN

Multi-omics data integration is a complex and challenging task in biomedical research. Consensus clustering, also known as meta-clustering or cluster ensembles, has become an increasingly popular downstream tool for phenotyping and endotyping using multiple omics and clinical data. However, current consensus clustering methods typically rely on ensembling clustering outputs with similar sample coverages (mathematical replicates), which may not reflect real-world data with varying sample coverages (biological replicates). To address this issue, we propose a new consensus clustering with missing labels (ccml) strategy termed ccml, an R protocol for two-step consensus clustering that can handle unequal missing labels (i.e. multiple predictive labels with different sample coverages). Initially, the regular consensus weights are adjusted (normalized) by sample coverage, then a regular consensus clustering is performed to predict the optimal final cluster. We applied the ccml method to predict molecularly distinct groups based on 9-omics integration in the Karolinska COSMIC cohort, which investigates chronic obstructive pulmonary disease, and 24-omics handprint integrative subgrouping of adult asthma patients of the U-BIOPRED cohort. We propose ccml as a downstream toolkit for multi-omics integration analysis algorithms such as Similarity Network Fusion and robust clustering of clinical data to overcome the limitations posed by missing data, which is inevitable in human cohorts consisting of multiple data modalities. The ccml tool is available in the R language (https://CRAN.R-project.org/package=ccml, https://github.com/pulmonomics-lab/ccml, or https://github.com/ZhoulabCPH/ccml).


Asunto(s)
Asma , Multiómica , Adulto , Humanos , Consenso , Análisis por Conglomerados , Algoritmos , Asma/genética
14.
Brief Bioinform ; 25(1)2023 11 22.
Artículo en Inglés | MEDLINE | ID: mdl-38221905

RESUMEN

BACKGROUND: Portal vein thrombosis (PVT) is a significant issue in cirrhotic patients, necessitating early detection. This study aims to develop a data-driven predictive model for PVT diagnosis in chronic hepatitis liver cirrhosis patients. METHODS: We employed data from a total of 816 chronic cirrhosis patients with PVT, divided into the Lanzhou cohort (n = 468) for training and the Jilin cohort (n = 348) for validation. This dataset encompassed a wide range of variables, including general characteristics, blood parameters, ultrasonography findings and cirrhosis grading. To build our predictive model, we employed a sophisticated stacking approach, which included Support Vector Machine (SVM), Naïve Bayes and Quadratic Discriminant Analysis (QDA). RESULTS: In the Lanzhou cohort, SVM and Naïve Bayes classifiers effectively classified PVT cases from non-PVT cases, among the top features of which seven were shared: Portal Velocity (PV), Prothrombin Time (PT), Portal Vein Diameter (PVD), Prothrombin Time Activity (PTA), Activated Partial Thromboplastin Time (APTT), age and Child-Pugh score (CPS). The QDA model, trained based on the seven shared features on the Lanzhou cohort and validated on the Jilin cohort, demonstrated significant differentiation between PVT and non-PVT cases (AUROC = 0.73 and AUROC = 0.86, respectively). Subsequently, comparative analysis showed that our QDA model outperformed several other machine learning methods. CONCLUSION: Our study presents a comprehensive data-driven model for PVT diagnosis in cirrhotic patients, enhancing clinical decision-making. The SVM-Naïve Bayes-QDA model offers a precise approach to managing PVT in this population.


Asunto(s)
Vena Porta , Trombosis de la Vena , Humanos , Vena Porta/patología , Factores de Riesgo , Teorema de Bayes , Medicina de Precisión , Cirrosis Hepática/complicaciones , Cirrosis Hepática/diagnóstico , Fibrosis , Trombosis de la Vena/complicaciones , Trombosis de la Vena/diagnóstico
15.
Blood ; 142(23): 2002-2015, 2023 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-37738460

RESUMEN

Acute myeloid leukemia (AML) with TP53 mutation is one of the most lethal cancers and portends an extremely poor prognosis. Based on in silico analyses of druggable genes and differential gene expression in TP53-mutated AML, we identified pololike kinase 4 (PLK4) as a novel therapeutic target and examined its expression, regulation, pathogenetic mechanisms, and therapeutic potential in TP53-mutated AML. PLK4 expression was suppressed by activated p53 signaling in TP53 wild-type AML and was increased in TP53-mutated AML cell lines and primary samples. Short-term PLK4 inhibition induced DNA damage and apoptosis in TP53 wild-type AML. Prolonged PLK4 inhibition suppressed the growth of TP53-mutated AML and was associated with DNA damage, apoptosis, senescence, polyploidy, and defective cytokinesis. A hitherto undescribed PLK4/PRMT5/EZH2/H3K27me3 axis was demonstrated in both TP53 wild-type and mutated AML, resulting in histone modification through PLK4-induced PRMT5 phosphorylation. In TP53-mutated AML, combined effects of histone modification and polyploidy activated the cGAS-STING pathway, leading to secretion of cytokines and chemokines and activation of macrophages and T cells upon coculture with AML cells. In vivo, PLK4 inhibition also induced cytokine and chemokine expression in mouse recipients, and its combination with anti-CD47 antibody, which inhibited the "don't-eat-me" signal in macrophages, synergistically reduced leukemic burden and prolonged animal survival. The study shed important light on the pathogenetic role of PLK4 and might lead to novel therapeutic strategies in TP53-mutated AML.


Asunto(s)
Histonas , Leucemia Mieloide Aguda , Animales , Ratones , Histonas/metabolismo , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/metabolismo , Mutación , Metilación , Nucleotidiltransferasas/metabolismo , Leucemia Mieloide Aguda/patología , Inmunidad , Poliploidía
16.
Mol Ther ; 32(5): 1461-1478, 2024 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-38414246

RESUMEN

Osteoarthritis (OA) is an age-related or post-traumatic degenerative whole joint disease characterized by the rupture of articular cartilage homeostasis, the regulatory mechanisms of which remain elusive. This study identifies the essential role of heterogeneous nuclear ribonucleoprotein K (hnRNPK) in maintaining articular cartilage homeostasis. Hnrnpk expression is markedly downregulated in human and mice OA cartilage. The deletion of Hnrnpk effectively accelerates the development of post-traumatic and age-dependent OA in mice. Mechanistically, the KH1 and KH2 domain of Hnrnpk bind and degrade the mRNA of WWC1. Hnrnpk deletion increases WWC1 expression, which in turn leads to the activation of Hippo signaling and ultimately aggravates OA. In particular, intra-articular injection of LPA and adeno-associated virus serotype 5 expressing WWC1 RNA interference ameliorates cartilage degeneration induced by Hnrnpk deletion, and intra-articular injection of adeno-associated virus serotype 5 expressing Hnrnpk protects against OA. Collectively, this study reveals the critical roles of Hnrnpk in inhibiting OA development through WWC1-dependent downregulation of Hippo signaling in chondrocytes and defines a potential target for the prevention and treatment of OA.


Asunto(s)
Cartílago Articular , Condrocitos , Ribonucleoproteína Heterogénea-Nuclear Grupo K , Vía de Señalización Hippo , Osteoartritis , Proteínas Serina-Treonina Quinasas , Transducción de Señal , Animales , Humanos , Masculino , Ratones , Cartílago Articular/metabolismo , Cartílago Articular/patología , Condrocitos/metabolismo , Dependovirus/genética , Modelos Animales de Enfermedad , Regulación de la Expresión Génica , Ribonucleoproteína Heterogénea-Nuclear Grupo K/metabolismo , Ribonucleoproteína Heterogénea-Nuclear Grupo K/genética , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Péptidos y Proteínas de Señalización Intracelular/genética , Osteoartritis/metabolismo , Osteoartritis/genética , Osteoartritis/etiología , Osteoartritis/patología , Osteoartritis/terapia , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas Serina-Treonina Quinasas/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo
17.
Nucleic Acids Res ; 51(W1): W560-W568, 2023 07 05.
Artículo en Inglés | MEDLINE | ID: mdl-37224539

RESUMEN

Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression heterogeneities in diverse cell types underlying homeostasis, development and pathological states. However, the loss of spatial information hinders its applications in deciphering spatially related features, such as cell-cell interactions in a spatial context. Here, we present STellaris (https://spatial.rhesusbase.com), a web server aimed to rapidly assign spatial information to scRNA-seq data based on their transcriptomic similarity with public spatial transcriptomics (ST) data. STellaris is founded on 101 manually curated ST datasets comprising 823 sections across different organs, developmental stages and pathological states from humans and mice. STellaris accepts raw count matrix and cell type annotation of scRNA-seq data as the input, and maps single cells to spatial locations in the tissue architecture of properly matched ST section. Spatially resolved information for intercellular communications, such as spatial distance and ligand-receptor interactions (LRIs), are further characterized between annotated cell types. Moreover, we also expanded the application of STellaris in spatial annotation of multiple regulatory levels with single-cell multiomics data, using the transcriptome as a bridge. STellaris was applied to several case studies to showcase its utility of adding value to the ever-growing scRNA-seq data from a spatial perspective.


Asunto(s)
Perfilación de la Expresión Génica , Programas Informáticos , Animales , Humanos , Ratones , Computadores , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Transcriptoma
18.
Proc Natl Acad Sci U S A ; 119(21): e2119765119, 2022 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-35594392

RESUMEN

SignificanceQuantum coherence has a fundamentally different origin for nonidentical and identical particles since for the latter a unique contribution exists due to indistinguishability. Here we experimentally show how to exploit, in a controllable fashion, the contribution to quantum coherence stemming from spatial indistinguishability. Our experiment also directly proves, on the same footing, the different role of particle statistics (bosons or fermions) in supplying coherence-enabled advantage for quantum metrology. Ultimately, our results provide insights toward viable quantum-enhanced technologies based on tunable indistinguishability of identical building blocks.

19.
J Am Chem Soc ; 146(23): 16222-16228, 2024 Jun 12.
Artículo en Inglés | MEDLINE | ID: mdl-38778012

RESUMEN

The crystal structure of a material is essentially determined by the nature of its chemical bonding. Consequently, the atomic coordination intimately correlates with the degree of ionicity or covalency of the material. Based on this principle, materials with similar chemical compositions can be successfully categorized into different coordination groups. However, counterexamples have recently emerged in complex ternary compounds. For instance, covalent IB-IIIA-VIA2 compounds, such as AgInS2, prefer a tetrahedrally coordinated structure (TCS), while ionic IA-VA-VIA2 compounds, such as NaBiS2, would favor an octahedrally coordinated structure (OCS). One naturally expects that IB-VA-VIA2 compounds with intermediate ionicity or covalency, such as AgBiS2, should then have a mix-coordinated structure (MCS) consisting of covalent AgS4 tetrahedra and ionic BiS6 octahedra. Surprisingly, only the experimental presence of the OCS was observed for AgBiS2. To resolve this puzzle, we perform first-principles studies of the phase stabilities of ternary compounds at finite temperatures. We find that AgBiS2 indeed prefers MCS at the ground state, in agreement with the typical expectation, but under experimental synthesis conditions, disordered OCS becomes energetically more favorable because of its low mixing energy and high configurational entropy. Our work elucidates the critical role of configurational disorder in stabilizing chemically unfavorable coordination, providing a rigorous rationale for the anomalous coordination preference in IB-VA-VIA2 compounds.

20.
J Am Chem Soc ; 146(22): 15393-15402, 2024 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-38767283

RESUMEN

Quinone-based electrodes using carbonyl redox reactions are promising candidates for aqueous energy storage due to their high theoretical specific capacity and high-rate performance. However, the proton storage manners and their influences on the electrochemical performance of quinone are still not clear. Herein, we reveal that proton storage could determine the products of the enol conversion and the electrochemical stability of the organic electrode. Specifically, the protons preferentially coordinated with the prototypical pyrene-4,5,9,10-tetraone (PTO) cathode, and increasing the proton concentration in the electrolyte can improve its working potentials and cycling stability by tailoring the enol conversion reaction. We also found that exploiting Al2(SO4)3 as a pH buffer can increase the energy density of the Zn||PTO batteries from 242.8 to 284.6 Wh kg-1. Our research has a guiding significance for emphasizing proton storage of organic electrodes based on enol conversion reactions and improving their electrochemical performance.

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