Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 6 de 6
Filtrar
1.
Cell ; 184(26): 6243-6261.e27, 2021 12 22.
Artículo en Inglés | MEDLINE | ID: mdl-34914922

RESUMEN

COVID-19-induced "acute respiratory distress syndrome" (ARDS) is associated with prolonged respiratory failure and high mortality, but the mechanistic basis of lung injury remains incompletely understood. Here, we analyze pulmonary immune responses and lung pathology in two cohorts of patients with COVID-19 ARDS using functional single-cell genomics, immunohistology, and electron microscopy. We describe an accumulation of CD163-expressing monocyte-derived macrophages that acquired a profibrotic transcriptional phenotype during COVID-19 ARDS. Gene set enrichment and computational data integration revealed a significant similarity between COVID-19-associated macrophages and profibrotic macrophage populations identified in idiopathic pulmonary fibrosis. COVID-19 ARDS was associated with clinical, radiographic, histopathological, and ultrastructural hallmarks of pulmonary fibrosis. Exposure of human monocytes to SARS-CoV-2, but not influenza A virus or viral RNA analogs, was sufficient to induce a similar profibrotic phenotype in vitro. In conclusion, we demonstrate that SARS-CoV-2 triggers profibrotic macrophage responses and pronounced fibroproliferative ARDS.


Asunto(s)
COVID-19/patología , COVID-19/virología , Fibrosis Pulmonar Idiopática/patología , Fibrosis Pulmonar Idiopática/virología , Macrófagos/patología , Macrófagos/virología , SARS-CoV-2/fisiología , Antígenos CD/metabolismo , Antígenos de Diferenciación Mielomonocítica/metabolismo , COVID-19/diagnóstico por imagen , Comunicación Celular , Estudios de Cohortes , Fibroblastos/patología , Regulación de la Expresión Génica , Humanos , Fibrosis Pulmonar Idiopática/diagnóstico por imagen , Fibrosis Pulmonar Idiopática/genética , Células Madre Mesenquimatosas/patología , Fenotipo , Proteoma/metabolismo , Receptores de Superficie Celular/metabolismo , Síndrome de Dificultad Respiratoria/diagnóstico por imagen , Síndrome de Dificultad Respiratoria/patología , Síndrome de Dificultad Respiratoria/virología , Tomografía Computarizada por Rayos X , Transcripción Genética
2.
J Proteome Res ; 21(6): 1575-1587, 2022 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-35608653

RESUMEN

Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, the vast majority of known sites is not assigned to any protein kinase. Assigning changes in the phosphoproteome to the activity of individual kinases therefore remains a key challenge. A recent large-scale study systematically identified in vitro substrates for most human protein kinases. Here, we reprocessed and filtered these data to generate an in vitro Kinase-to-Phosphosite database (iKiP-DB). We show that iKiP-DB can accurately predict changes in kinase activity in published phosphoproteomic data sets for both well-studied and poorly characterized kinases. We apply iKiP-DB to a newly generated phosphoproteomic analysis of SARS-CoV-2 infected human lung epithelial cells and provide evidence for coronavirus-induced changes in host cell kinase activity. In summary, we show that iKiP-DB is widely applicable to facilitate the functional analysis of phosphoproteomic data sets.


Asunto(s)
COVID-19 , Fosfoproteínas , Humanos , Fosfoproteínas/metabolismo , Fosforilación , Proteínas Quinasas/genética , Proteínas Quinasas/metabolismo , SARS-CoV-2
3.
PLoS Comput Biol ; 17(11): e1009515, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34735429

RESUMEN

Very high risk neuroblastoma is characterised by increased MAPK signalling, and targeting MAPK signalling is a promising therapeutic strategy. We used a deeply characterised panel of neuroblastoma cell lines and found that the sensitivity to MEK inhibitors varied drastically between these cell lines. By generating quantitative perturbation data and mathematical modelling, we determined potential resistance mechanisms. We found that negative feedbacks within MAPK signalling and via the IGF receptor mediate re-activation of MAPK signalling upon treatment in resistant cell lines. By using cell-line specific models, we predict that combinations of MEK inhibitors with RAF or IGFR inhibitors can overcome resistance, and tested these predictions experimentally. In addition, phospho-proteomic profiling confirmed the cell-specific feedback effects and synergy of MEK and IGFR targeted treatment. Our study shows that a quantitative understanding of signalling and feedback mechanisms facilitated by models can help to develop and optimise therapeutic strategies. Our findings should be considered for the planning of future clinical trials introducing MEKi in the treatment of neuroblastoma.


Asunto(s)
Retroalimentación , Modelos Biológicos , Neuroblastoma/metabolismo , Transducción de Señal , Línea Celular Tumoral , Resistencia a Antineoplásicos/efectos de los fármacos , Ensayos de Selección de Medicamentos Antitumorales , Humanos , Sistema de Señalización de MAP Quinasas , Neuroblastoma/tratamiento farmacológico , Inhibidores de Proteínas Quinasas/farmacología , Receptor IGF Tipo 1/metabolismo , Receptor IGF Tipo 2/metabolismo
4.
Cell Mol Life Sci ; 78(7): 3525-3542, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33469705

RESUMEN

Metastasis Associated in Colon Cancer 1 (MACC1) is a novel prognostic, predictive and causal biomarker for tumor progression and metastasis in many cancer types, including colorectal cancer. Besides its clinical value, little is known about its molecular function. Its similarity to SH3BP4, involved in regulating uptake and recycling of transmembrane receptors, suggests a role of MACC1 in endocytosis. By exploring the MACC1 interactome, we identified the clathrin-mediated endocytosis (CME)-associated proteins CLTC, DNM2 and AP-2 as MACC1 binding partners. We unveiled a MACC1-dependent routing of internalized transferrin receptor towards recycling. Elevated MACC1 expression caused also the activation and internalization of EGFR, a higher rate of receptor recycling, as well as earlier and stronger receptor activation and downstream signaling. These effects are limited by deletion of CME-related protein interaction sites in MACC1. Thus, MACC1 regulates CME and receptor recycling, causing increased growth factor-mediated downstream signaling and cell proliferation. This novel mechanism unveils potential therapeutic intervention points restricting MACC1-driven metastasis.


Asunto(s)
Clatrina/metabolismo , Neoplasias Colorrectales/patología , Endocitosis , Regulación Neoplásica de la Expresión Génica , Receptores de Transferrina/metabolismo , Transactivadores/metabolismo , Animales , Apoptosis , Biomarcadores de Tumor/metabolismo , Proliferación Celular , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Receptores ErbB/genética , Receptores ErbB/metabolismo , Humanos , Ratones , Proteoma/análisis , Proteoma/metabolismo , Receptores de Transferrina/genética , Transactivadores/genética , Células Tumorales Cultivadas , Ensayos Antitumor por Modelo de Xenoinjerto
5.
Nucleic Acids Res ; 45(21): 12195-12213, 2017 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-28981749

RESUMEN

The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type-specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking. By combining chromatin immunoprecipitation (ChIP) with mass spectrometry, we investigated cis-regulatory regions in macrophages to comprehensively identify histone marks specifically associated with enhancers, and to profile their dynamics after transcriptional activation elicited by an inflammatory stimulation. The intersection of the proteomics data with ChIP-seq and RNA-seq analyses revealed the existence of novel subpopulations of enhancers, marked by specific histone modification signatures: specifically, H3K4me1/K36me2 marks transcribed enhancers, while H3K4me1/K36me3 and H3K4me1/K79me2 combinations mark distinct classes of intronic enhancers. Thus, our MS analysis of functionally distinct genomic regions revealed the combinatorial code of histone modifications, highlighting the potential of proteomics in addressing fundamental questions in epigenetics.


Asunto(s)
Cromatina/metabolismo , Código de Histonas , Macrófagos/metabolismo , Animales , Línea Celular , Elementos de Facilitación Genéticos , Genoma , Histonas/metabolismo , Intrones , Lipopolisacáridos/farmacología , Macrófagos/efectos de los fármacos , Espectrometría de Masas , Ratones , Proteómica , Transcripción Genética
6.
iScience ; 24(3): 102151, 2021 Mar 19.
Artículo en Inglés | MEDLINE | ID: mdl-33585804

RESUMEN

Detailed knowledge of the molecular biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is crucial for understanding of viral replication, host responses, and disease progression. Here, we report gene expression profiles of three SARS-CoV- and SARS-CoV-2-infected human cell lines. SARS-CoV-2 elicited an approximately two-fold higher stimulation of the innate immune response compared to SARS-CoV in the human epithelial cell line Calu-3, including induction of miRNA-155. Single-cell RNA sequencing of infected cells showed that genes induced by virus infections were broadly upregulated, whereas interferon beta/lambda genes, a pro-inflammatory cytokines such as IL-6, were expressed only in small subsets of infected cells. Temporal analysis suggested that transcriptional activities of interferon regulatory factors precede those of nuclear factor κB. Lastly, we identified heat shock protein 90 (HSP90) as a protein relevant for the infection. Inhibition of the HSP90 activity resulted in a reduction of viral replication and pro-inflammatory cytokine expression in primary human airway epithelial cells.

SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA