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1.
J Mol Biol ; 433(21): 167240, 2021 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-34508725

RESUMO

Receptor tyrosine kinases (RTK) bind growth factors and are critical for cell proliferation and differentiation. Their dysregulation leads to a loss of growth control, often resulting in cancer. Epidermal growth factor receptor (EGFR) is the prototypic RTK and can bind several ligands exhibiting distinct mitogenic potentials. Whereas the phosphorylation on individual EGFR sites and their roles for downstream signaling have been extensively studied, less is known about ligand-specific ubiquitination events on EGFR, which are crucial for signal attenuation and termination. We used a proteomics-based workflow for absolute quantitation combined with mathematical modeling to unveil potentially decisive ubiquitination events on EGFR from the first 30 seconds to 15 minutes of stimulation. Four ligands were used for stimulation: epidermal growth factor (EGF), heparin-binding-EGF like growth factor, transforming growth factor-α and epiregulin. Whereas only little differences in the order of individual ubiquitination sites were observed, the overall amount of modified receptor differed depending on the used ligand, indicating that absolute magnitude of EGFR ubiquitination, and not distinctly regulated ubiquitination sites, is a major determinant for signal attenuation and the subsequent cellular outcomes.


Assuntos
Fator de Crescimento Epidérmico/metabolismo , Epirregulina/metabolismo , Fator de Crescimento Semelhante a EGF de Ligação à Heparina/metabolismo , Transdução de Sinais/genética , Fator de Crescimento Transformador alfa/metabolismo , Sequência de Aminoácidos , Linhagem Celular Tumoral , Fator de Crescimento Epidérmico/química , Fator de Crescimento Epidérmico/genética , Epirregulina/química , Epirregulina/genética , Células Epiteliais/citologia , Células Epiteliais/metabolismo , Receptores ErbB/química , Receptores ErbB/genética , Receptores ErbB/metabolismo , Expressão Gênica , Fator de Crescimento Semelhante a EGF de Ligação à Heparina/química , Fator de Crescimento Semelhante a EGF de Ligação à Heparina/genética , Humanos , Ligantes , Modelos Moleculares , Mutação , Fosforilação , Conformação Proteica , Processamento de Proteína Pós-Traducional , Proteômica , Fator de Crescimento Transformador alfa/química , Fator de Crescimento Transformador alfa/genética , Ubiquitinação
2.
EMBO Mol Med ; 13(8): e14532, 2021 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-34260159

RESUMO

Since the start of 2020, the world has been upended by the pandemic caused by the severe acute respiratory coronavirus type 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). It has not only led to a tragic loss of life and terrible economic costs but has also been met with an unprecedented response of the scientific and medical communities. In an effort to better understand this viral infection, scientists around the world generated the largest surge in research in documented history for any topic (Lever & Altman, 2021). A part of this work has included the need to better understand the impact of the virus on human proteins-the key machinery of the cell-and human physiology. In their recent study, Geyer and colleagues (Geyer et al, 2021) analyzed a total of 720 proteomes from longitudinal serum samples of 31 hospitalized COVID-19 patients and control individuals with COVID-19-like symptoms but not infected with SARS-CoV-2, providing a comprehensive characterization of the plasma proteome changes along the time course of infection.


Assuntos
COVID-19 , Proteômica , Humanos , Pandemias , Proteoma , SARS-CoV-2
3.
Nat Med ; 27(4): 668-676, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33837377

RESUMO

Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2, P = 1.6 × 10-6; IFNAR2, P = 9.8 × 10-11 and IL-10RB, P = 2.3 × 10-14) using cis-expression quantitative trait loci genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared expression quantitative trait loci signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.


Assuntos
COVID-19/genética , Reposicionamento de Medicamentos , Análise da Randomização Mendeliana/métodos , SARS-CoV-2 , Enzima de Conversão de Angiotensina 2/genética , Enzima de Conversão de Angiotensina 2/fisiologia , COVID-19/tratamento farmacológico , Estudo de Associação Genômica Ampla , Humanos , Subunidade beta de Receptor de Interleucina-10/genética , Subunidade beta de Receptor de Interleucina-10/fisiologia , Locos de Características Quantitativas , Receptor de Interferon alfa e beta/genética , Receptor de Interferon alfa e beta/fisiologia
4.
ACS Omega ; 6(8): 5091-5100, 2021 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-33681549

RESUMO

Protein degradation is a key component of the regulation of gene expression and is at the center of several pathogenic processes. Proteins are regularly degraded, but there is large variation in their lifetimes, and the kinetics of protein degradation are not well understood. Many different factors can influence protein degradation rates, painting a highly complex picture. This has been partially unravelled in recent years thanks to invaluable advances in proteomics techniques. In this Mini-Review, we give a global vision of the determinants of protein degradation rates with the backdrop of the current understanding of proteolytic systems to give a contemporary view of the field.

6.
Mol Syst Biol ; 17(2): e10188, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33590968

RESUMO

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global threat to human health and has compromised economic stability. In addition to the development of an effective vaccine, it is imperative to understand how SARS-CoV-2 hijacks host cellular machineries on a system-wide scale so that potential host-directed therapies can be developed. In situ proteome-wide abundance and thermal stability measurements using thermal proteome profiling (TPP) can inform on global changes in protein activity. Here we adapted TPP to high biosafety conditions amenable to SARS-CoV-2 handling. We discovered pronounced temporal alterations in host protein thermostability during infection, which converged on cellular processes including cell cycle, microtubule and RNA splicing regulation. Pharmacological inhibition of host proteins displaying altered thermal stability or abundance during infection suppressed SARS-CoV-2 replication. Overall, this work serves as a framework for expanding TPP workflows to globally important human pathogens that require high biosafety containment and provides deeper resolution into the molecular changes induced by SARS-CoV-2 infection.


Assuntos
COVID-19/metabolismo , Interações Hospedeiro-Patógeno , Estabilidade Proteica , SARS-CoV-2/fisiologia , Proteínas Virais/metabolismo , Antivirais/farmacologia , COVID-19/virologia , Humanos , Proteoma , SARS-CoV-2/isolamento & purificação , SARS-CoV-2/metabolismo , Temperatura , Replicação Viral/efeitos dos fármacos
7.
Nat Genet ; 53(3): 392-402, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33589840

RESUMO

Genome-wide association studies have discovered numerous genomic loci associated with Alzheimer's disease (AD); yet the causal genes and variants are incompletely identified. We performed an updated genome-wide AD meta-analysis, which identified 37 risk loci, including new associations near CCDC6, TSPAN14, NCK2 and SPRED2. Using three SNP-level fine-mapping methods, we identified 21 SNPs with >50% probability each of being causally involved in AD risk and others strongly suggested by functional annotation. We followed this with colocalization analyses across 109 gene expression quantitative trait loci datasets and prioritization of genes by using protein interaction networks and tissue-specific expression. Combining this information into a quantitative score, we found that evidence converged on likely causal genes, including the above four genes, and those at previously discovered AD loci, including BIN1, APH1B, PTK2B, PILRA and CASS4.


Assuntos
Doença de Alzheimer/genética , Proteínas Adaptadoras de Transdução de Sinal/genética , Mapeamento Cromossômico , Proteínas do Citoesqueleto/genética , Expressão Gênica , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Desequilíbrio de Ligação , Microglia/fisiologia , Proteínas Oncogênicas/genética , Polimorfismo de Nucleotídeo Único , Mapas de Interação de Proteínas/genética , Locos de Características Quantitativas , Fatores de Risco , Tetraspaninas/genética
8.
Science ; 370(6521)2020 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-33060197

RESUMO

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.


Assuntos
COVID-19/metabolismo , Proteínas do Nucleocapsídeo de Coronavírus/metabolismo , Interações entre Hospedeiro e Microrganismos , Proteínas de Transporte da Membrana Mitocondrial/metabolismo , Mapas de Interação de Proteínas , Vírus da SARS/metabolismo , SARS-CoV-2/metabolismo , Síndrome Respiratória Aguda Grave/metabolismo , Sequência Conservada , Proteínas do Nucleocapsídeo de Coronavírus/genética , Microscopia Crioeletrônica , Humanos , Proteínas de Transporte da Membrana Mitocondrial/genética , Fosfoproteínas/genética , Fosfoproteínas/metabolismo , Conformação Proteica
9.
bioRxiv ; 2020 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-32511329

RESUMO

An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity- purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.

10.
Nature ; 583(7816): 459-468, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32353859

RESUMO

A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.


Assuntos
Betacoronavirus/efeitos dos fármacos , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/metabolismo , Reposicionamento de Medicamentos , Terapia de Alvo Molecular , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/metabolismo , Mapas de Interação de Proteínas , Proteínas Virais/metabolismo , Animais , Antivirais/classificação , Antivirais/farmacologia , Betacoronavirus/genética , Betacoronavirus/metabolismo , Betacoronavirus/patogenicidade , COVID-19 , Chlorocebus aethiops , Clonagem Molecular , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/virologia , Avaliação Pré-Clínica de Medicamentos , Células HEK293 , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Humanos , Imunidade Inata , Espectrometria de Massas , Pandemias , Pneumonia Viral/imunologia , Pneumonia Viral/virologia , Ligação Proteica , Biossíntese de Proteínas/efeitos dos fármacos , Domínios Proteicos , Mapeamento de Interação de Proteínas , Receptores sigma/metabolismo , SARS-CoV-2 , Proteínas Ligases SKP Culina F-Box/metabolismo , Células Vero , Proteínas Virais/genética
11.
Nucleic Acids Res ; 48(5): 2544-2563, 2020 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-32016395

RESUMO

The evolution of gene expression regulation has contributed to species differentiation. The 3' untranslated regions (3'UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3'UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3'UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3'UTR of orthologous genes and demonstrated that 3'UTR sequence variations affect protein production. This suggested that species-specific functional 3'UTRs might be specifically selected during evolution. 3'UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3'UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3'UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3'UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.


Assuntos
Regiões 3' não Traduzidas/genética , Evolução Molecular , Regulação Bacteriana da Expressão Gênica , Staphylococcus/genética , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sequência de Bases , Elementos de DNA Transponíveis/genética , Rearranjo Gênico/genética , Genes Bacterianos , Hemólise , Nucleotídeos/genética , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Ovinos , Especificidade da Espécie
12.
Gigascience ; 9(1)2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31942620

RESUMO

BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked. FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.


Assuntos
Decapodiformes/genética , Genoma , Genômica , Animais , Evolução Biológica , Cromatografia Líquida , Biologia Computacional/métodos , Elementos de DNA Transponíveis , Perfilação da Expressão Gênica , Genômica/métodos , Anotação de Sequência Molecular , Família Multigênica , RNA não Traduzido , Espectrometria de Massas em Tandem , Transcriptoma , Sequenciamento Completo do Genoma
13.
Genome Res ; 30(1): 127-137, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31831592

RESUMO

Bone marrow-derived mesenchymal stem cells (MSCs) differentiate into osteoblasts upon stimulation by signals present in their niche. Because the global signaling cascades involved in the early phases of MSCs osteoblast (OB) differentiation are not well-defined, we used quantitative mass spectrometry to delineate changes in human MSCs proteome and phosphoproteome during the first 24 h of their OB lineage commitment. The temporal profiles of 6252 proteins and 15,059 phosphorylation sites suggested at least two distinct signaling waves: one peaking within 30 to 60 min after stimulation and a second upsurge after 24 h. In addition to providing a comprehensive view of the proteome and phosphoproteome dynamics during early MSCs differentiation, our analyses identified a key role of serine/threonine protein kinase D1 (PRKD1) in OB commitment. At the onset of OB differentiation, PRKD1 initiates activation of the pro-osteogenic transcription factor RUNX2 by triggering phosphorylation and nuclear exclusion of the histone deacetylase HDAC7.


Assuntos
Diferenciação Celular , Células-Tronco Mesenquimais/citologia , Células-Tronco Mesenquimais/metabolismo , Osteoblastos/citologia , Osteoblastos/metabolismo , Fosfoproteínas/metabolismo , Proteoma , Proteômica , Humanos , Filogenia , Proteômica/métodos
14.
Syst Med (New Rochelle) ; 2(1): 1-9, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31119214

RESUMO

Introduction: Drug-resistant infections are becoming increasingly frequent worldwide, causing hundreds of thousands of deaths annually. This is partly due to the very limited set of protein drug targets known for human-infecting viral genomes. The eleven influenza virus proteins, for instance, exploit host cell factors for replication and suppression of the antiviral immune responses. A systems medicine approach to identify relevant and druggable host factors would dramatically expand therapeutic options. Therapeutic target identification, however, has hitherto relied on static molecular networks, whereas in reality the interactome, in particular during an infection, is subject to constant change. Methods: We developed time-course network enrichment (TiCoNE), an expert-centered approach for discovering temporal response pathways. In the first stage of TiCoNE, time-series expression data is clustered in a human-augmented manner to identify groups of biological entities with coherent temporal responses. Throughout this process, the expert can add, remove, merge, or split temporal patterns. The resulting groups can then be mapped to an interaction network to identify enriched pathways and to analyze cross-talk enrichments and depletions between groups. Finally, temporal response groups of two experiments can be intersected, to identify condition-variant response patterns that represent promising drug-target candidates. Results: We applied TiCoNE to human gene expression data for influenza A virus infection and rhino virus infection, respectively. We then identified coherent temporal response patterns and employed our cross-talk analysis to establish two potential timelines of systems-level host responses for either infection. Next, we compared the two phenotypes and unraveled condition-variant temporal groups interacting on a networks level. The highest-ranking ones we then validated via literature search and wet-lab experiments. This not only confirmed many of our candidates as previously known, but we also identified phospholipid scramblase 1 (encoded by PLSCR1) as a previously not recognized host factor that is essential for influenza A virus infection. Conclusion: With TiCoNE we developed a novel approach for conjointly analyzing molecular networks with time-series expression data and demonstrated its power by identifying temporal drug-targets. We provide proof-of-concept that not only novel targets can be identified using our approach, but also that anti-infective drug target discovery can be enhanced by investigating temporal molecular networks of the host in response to viral infection.

15.
Nat Struct Mol Biol ; 25(7): 631-640, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29967540

RESUMO

Ubiquitination is a post-translational modification (PTM) that is essential for balancing numerous physiological processes. To enable delineation of protein ubiquitination at a site-specific level, we generated an antibody, denoted UbiSite, recognizing the C-terminal 13 amino acids of ubiquitin, which remain attached to modified peptides after proteolytic digestion with the endoproteinase LysC. Notably, UbiSite is specific to ubiquitin. Furthermore, besides ubiquitination on lysine residues, protein N-terminal ubiquitination is readily detected as well. By combining UbiSite enrichment with sequential LysC and trypsin digestion and high-accuracy MS, we identified over 63,000 unique ubiquitination sites on 9,200 proteins in two human cell lines. In addition to uncovering widespread involvement of this PTM in all cellular aspects, the analyses reveal an inverse association between protein N-terminal ubiquitination and acetylation, as well as a complete lack of correlation between changes in protein abundance and alterations in ubiquitination sites upon proteasome inhibition.


Assuntos
Lisina/química , Ubiquitina/imunologia , Ubiquitina/metabolismo , Ubiquitinação , Especificidade de Anticorpos , Sítios de Ligação , Linhagem Celular , Humanos , Células Jurkat , Espectrometria de Massas , Proteoma/química , Proteoma/metabolismo , Ubiquitina/química
16.
J Proteome Res ; 17(1): 296-304, 2018 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-29091453

RESUMO

Modulation of protein activities by reversible post-translational modifications (PTMs) is a major molecular mechanism involved in the control of virtually all cellular processes. One of these PTMs is ubiquitination, which regulates key processes including protein degradation, cell cycle, DNA damage repair, and signal transduction. Because of its importance for numerous cellular functions, ubiquitination has become an intense topic of research in recent years, and proteomics tools have greatly facilitated the identification of many ubiquitination targets. Taking advantage of the StUbEx strategy for exchanging the endogenous ubiquitin with an epitope-tagged version, we created a modified system, StUbEx PLUS, which allows precise mapping of ubiquitination sites by mass spectrometry. Application of StUbEx PLUS to U2OS cells treated with proteasomal inhibitors resulted in the identification of 41 589 sites on 7762 proteins, which thereby revealed the ubiquitous nature of this PTM and demonstrated the utility of the approach for comprehensive ubiquitination studies at site-specific resolution.


Assuntos
Sítios de Ligação , Peptídeos/isolamento & purificação , Ubiquitina/metabolismo , Ubiquitinação , Linhagem Celular , Humanos , Espectrometria de Massas , Peptídeos/metabolismo , Processamento de Proteína Pós-Traducional
17.
Mol Cell Proteomics ; 16(8): 1433-1446, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28572092

RESUMO

Cylindromatosis tumor suppressor protein (CYLD) is a deubiquitinase, best known as an essential negative regulator of the NFkB pathway. Previous studies have suggested an involvement of CYLD in epidermal growth factor (EGF)-dependent signal transduction as well, as it was found enriched within the tyrosine-phosphorylated complexes in cells stimulated with the growth factor. EGF receptor (EGFR) signaling participates in central cellular processes and its tight regulation, partly through ubiquitination cascades, is decisive for a balanced cellular homeostasis. Here, using a combination of mass spectrometry-based quantitative proteomic approaches with biochemical and immunofluorescence strategies, we demonstrate the involvement of CYLD in the regulation of the ubiquitination events triggered by EGF. Our data show that CYLD regulates the magnitude of ubiquitination of several major effectors of the EGFR pathway by assisting the recruitment of the ubiquitin ligase Cbl-b to the activated EGFR complex. Notably, CYLD facilitates the interaction of EGFR with Cbl-b through its Tyr15 phosphorylation in response to EGF, which leads to fine-tuning of the receptor's ubiquitination and subsequent degradation. This represents a previously uncharacterized strategy exerted by this deubiquitinase and tumors suppressor for the negative regulation of a tumorigenic signaling pathway.


Assuntos
Enzima Desubiquitinante CYLD/metabolismo , Receptores ErbB/metabolismo , Proteólise , Proteínas Proto-Oncogênicas c-cbl/metabolismo , Ubiquitinação , Cromatografia Líquida , Enzima Desubiquitinante CYLD/genética , Células HeLa , Humanos , Fosforilação , Proteômica , Espectrometria de Massas em Tandem , Tirosina/metabolismo
18.
J Proteome Res ; 14(8): 3348-61, 2015 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-26074025

RESUMO

Muscle stem cells, or satellite cells, play an important role in the maintenance and repair of muscle tissue and have the capacity to proliferate and differentiate in response to physiological or environmental changes. Although they have been extensively studied, the key regulatory steps and the complex temporal protein dynamics accompanying the differentiation of primary human muscle cells remain poorly understood. Here, we demonstrate the advantages of applying a MS-based quantitative approach, stable isotope labeling by amino acids in cell culture (SILAC), for studying human myogenesis in vitro and characterize the fine-tuned changes in protein expression underlying the dramatic phenotypic conversion of primary mononucleated human muscle cells during in vitro differentiation to form multinucleated myotubes. Using an exclusively optimized triple encoding SILAC procedure, we generated dynamic expression profiles during the course of myogenic differentiation and quantified 2240 proteins, 243 of which were regulated. These changes in protein expression occurred in sequential waves and underlined vast reprogramming in key processes governing cell fate decisions, i.e., cell cycle withdrawal, RNA metabolism, cell adhesion, proteolysis, and cytoskeletal organization. In silico transcription factor target analysis demonstrated that the observed dynamic changes in the proteome could be attributed to a cascade of transcriptional events involving key myogenic regulatory factors as well as additional regulators not yet known to act on muscle differentiation. In addition, we created of a dynamic map of the developing myofibril, providing valuable insights into the formation and maturation of the contractile apparatus in vitro. Finally, our SILAC-based quantitative approach offered the possibility to follow the expression profiles of several muscle disease-associated proteins simultaneously and therefore could be a valuable resource for future studies investigating pathogenesis of degenerative muscle disorders as well as assessing new therapeutic strategies.


Assuntos
Diferenciação Celular , Fibras Musculares Esqueléticas/metabolismo , Proteoma/metabolismo , Proteômica/métodos , Células Satélites de Músculo Esquelético/metabolismo , Aminoácidos/metabolismo , Western Blotting , Células Cultivadas , Cromatografia Líquida , Análise por Conglomerados , Humanos , Imuno-Histoquímica , Recém-Nascido , Marcação por Isótopo/métodos , Cinética , Fibras Musculares Esqueléticas/citologia , Proteoma/classificação , Células Satélites de Músculo Esquelético/citologia , Espectrometria de Massas por Ionização por Electrospray , Espectrometria de Massas em Tandem , Fatores de Tempo
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