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1.
EMBO J ; 42(10): e112234, 2023 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-36970857

RESUMO

The interferon-induced transmembrane proteins (IFITM) are implicated in several biological processes, including antiviral defense, but their modes of action remain debated. Here, taking advantage of pseudotyped viral entry assays and replicating viruses, we uncover the requirement of host co-factors for endosomal antiviral inhibition through high-throughput proteomics and lipidomics in cellular models of IFITM restriction. Unlike plasma membrane (PM)-localized IFITM restriction that targets infectious SARS-CoV2 and other PM-fusing viral envelopes, inhibition of endosomal viral entry depends on lysines within the conserved IFITM intracellular loop. These residues recruit Phosphatidylinositol 3,4,5-trisphosphate (PIP3) that we show here to be required for endosomal IFITM activity. We identify PIP3 as an interferon-inducible phospholipid that acts as a rheostat for endosomal antiviral immunity. PIP3 levels correlated with the potency of endosomal IFITM restriction and exogenous PIP3 enhanced inhibition of endocytic viruses, including the recent SARS-CoV2 Omicron variant. Together, our results identify PIP3 as a critical regulator of endosomal IFITM restriction linking it to the Pi3K/Akt/mTORC pathway and elucidate cell-compartment-specific antiviral mechanisms with potential relevance for the development of broadly acting antiviral strategies.


Assuntos
Antivirais , COVID-19 , Humanos , Interferons/metabolismo , Fosfolipídeos , Fosfatidilinositol 3-Quinases/metabolismo , RNA Viral , Proteínas de Ligação a RNA/metabolismo , SARS-CoV-2/metabolismo , Internalização do Vírus , Proteínas de Membrana/metabolismo
2.
PLoS Genet ; 18(3): e1010101, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35239666

RESUMO

Glutamine analogs are potent suppressors of general glutamine metabolism with anti-cancer activity. 6-diazo-5-oxo-L-norleucine (DON) is an orally available glutamine analog which has been recently improved by structural modification for cancer treatment. Here, we explored the chemogenomic landscape of DON sensitivity using budding yeast as model organism. We identify evolutionarily conserved proteins that mediate cell resistance to glutamine analogs, namely Ura8CTPS1/2, Hpt1HPRT1, Mec1ATR, Rad53CHK1/CHK2 and Rtg1. We describe a function of Ura8 as inducible CTP synthase responding to inhibition of glutamine metabolism and propose a model for its regulation by CTP levels and Nrd1-dependent transcription termination at a cryptic unstable transcript. Disruption of the inducible CTP synthase under DON exposure hyper-activates the Mec1-Rad53 DNA damage response (DDR) pathway, which prevents chromosome breakage. Simultaneous inhibition of CTP synthase and Mec1 kinase synergistically sensitizes cells to DON, whereas CTP synthase over-expression hampers DDR mutant sensitivity. Using genome-wide suppressor screening, we identify factors promoting DON-induced CTP depletion (TORC1, glutamine transporter) and DNA breakage in DDR mutants. Together, our results identify CTP regulation and the Mec1-Rad53 DDR axis as key glutamine analog response pathways, and provide a rationale for the combined targeting of glutamine and CTP metabolism in DDR-deficient cancers.


Assuntos
Glutamina , Citidina Trifosfato , Glutamina/metabolismo
3.
J Neurochem ; 166(2): 346-366, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37303123

RESUMO

Astrocytes associate with amyloid plaques in Alzheimer's disease (AD). Astrocytes react to changes in the brain environment, including increasing concentrations of amyloid-ß (Aß). However, the precise response of astrocytes to soluble small Aß oligomers at concentrations similar to those present in the human brain has not been addressed. In this study, we exposed astrocytes to media from neurons that express the human amyloid precursor protein (APP) transgene with the double Swedish mutation (APPSwe), and which contains APP-derived fragments, including soluble human Aß oligomers. We then used proteomics to investigate changes in the astrocyte secretome. Our data show dysregulated secretion of astrocytic proteins involved in the extracellular matrix and cytoskeletal organization and increase secretion of proteins involved in oxidative stress responses and those with chaperone activity. Several of these proteins have been identified in previous transcriptomic and proteomic studies using brain tissue from human AD and cerebrospinal fluid (CSF). Our work highlights the relevance of studying astrocyte secretion to understand the brain response to AD pathology and the potential use of these proteins as biomarkers for the disease.


Assuntos
Doença de Alzheimer , Astrócitos , Humanos , Astrócitos/metabolismo , Proteômica , Secretoma , Peptídeos beta-Amiloides/metabolismo , Doença de Alzheimer/metabolismo , Precursor de Proteína beta-Amiloide/metabolismo
4.
Proc Natl Acad Sci U S A ; 117(35): 21288-21298, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32817544

RESUMO

The endoplasmic reticulum (ER) is the reservoir for calcium in cells. Luminal calcium levels are determined by calcium-sensing proteins that trigger calcium dynamics in response to calcium fluctuations. Here we report that Selenoprotein N (SEPN1) is a type II transmembrane protein that senses ER calcium fluctuations by binding this ion through a luminal EF-hand domain. In vitro and in vivo experiments show that via this domain, SEPN1 responds to diminished luminal calcium levels, dynamically changing its oligomeric state and enhancing its redox-dependent interaction with cellular partners, including the ER calcium pump sarcoplasmic/endoplasmic reticulum calcium ATPase (SERCA). Importantly, single amino acid substitutions in the EF-hand domain of SEPN1 identified as clinical variations are shown to impair its calcium-binding and calcium-dependent structural changes, suggesting a key role of the EF-hand domain in SEPN1 function. In conclusion, SEPN1 is a ER calcium sensor that responds to luminal calcium depletion, changing its oligomeric state and acting as a reductase to refill ER calcium stores.


Assuntos
Cálcio/metabolismo , Retículo Endoplasmático/metabolismo , Proteínas Sensoras de Cálcio Intracelular/metabolismo , Proteínas Musculares/metabolismo , Selenoproteínas/metabolismo , Células HeLa , Humanos , Proteínas Sensoras de Cálcio Intracelular/genética , Proteínas Musculares/genética , Oxirredução , Selenoproteínas/genética
5.
EMBO J ; 37(23)2018 12 03.
Artigo em Inglês | MEDLINE | ID: mdl-30373810

RESUMO

Focal deletions occur frequently in the cancer genome. However, the putative tumor-suppressive genes residing within these regions have been difficult to pinpoint. To robustly identify these genes, we implemented a computational approach based on non-negative matrix factorization, NMF, and interrogated the TCGA dataset. This analysis revealed a metagene signature including a small subset of genes showing pervasive hemizygous deletions, reduced expression in cancer patient samples, and nucleolar function. Amid the genes belonging to this signature, we have identified PNRC1, a nuclear receptor coactivator. We found that PNRC1 interacts with the cytoplasmic DCP1α/DCP2 decapping machinery and hauls it inside the nucleolus. PNRC1-dependent nucleolar translocation of the decapping complex is associated with a decrease in the 5'-capped U3 and U8 snoRNA fractions, hampering ribosomal RNA maturation. As a result, PNRC1 ablates the enhanced proliferation triggered by established oncogenes such as RAS and MYC These observations uncover a previously undescribed mechanism of tumor suppression, whereby the cytoplasmic decapping machinery is hauled within nucleoli, tightly regulating ribosomal RNA maturation.


Assuntos
Nucléolo Celular/metabolismo , Proliferação de Células , Neoplasias/metabolismo , Proteínas Nucleares/metabolismo , RNA Ribossômico/metabolismo , Fatores de Transcrição/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Células A549 , Nucléolo Celular/genética , Nucléolo Celular/patologia , Bases de Dados de Ácidos Nucleicos , Endorribonucleases/genética , Endorribonucleases/metabolismo , Células HeLa , Humanos , Células MCF-7 , Neoplasias/genética , Neoplasias/patologia , Proteínas Nucleares/genética , Proteínas Proto-Oncogênicas c-myc/genética , Proteínas Proto-Oncogênicas c-myc/metabolismo , RNA Neoplásico/genética , RNA Neoplásico/metabolismo , RNA Ribossômico/genética , RNA Nucleolar Pequeno/genética , RNA Nucleolar Pequeno/metabolismo , Transativadores/genética , Transativadores/metabolismo , Fatores de Transcrição/genética , Proteínas Supressoras de Tumor/genética , Proteínas ras/genética , Proteínas ras/metabolismo
6.
EMBO Rep ; 21(9): e50446, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32749065

RESUMO

Melanoma progression is generally associated with increased transcriptional activity mediated by the Yes-associated protein (YAP). Mechanical signals from the extracellular matrix are sensed by YAP, which then activates the expression of proliferative genes, promoting melanoma progression and drug resistance. Which extracellular signals induce mechanotransduction, and how this is mediated, is not completely understood. Here, using secretome analyses, we reveal the extracellular accumulation of amyloidogenic proteins, i.e. premelanosome protein (PMEL), in metastatic melanoma, together with proteins that assist amyloid maturation into fibrils. We also confirm the accumulation of amyloid-like aggregates, similar to those detected in Alzheimer disease, in metastatic cell lines, as well as in human melanoma biopsies. Mechanistically, beta-secretase 2 (BACE2) regulates the maturation of these aggregates, which in turn induce YAP activity. We also demonstrate that recombinant PMEL fibrils are sufficient to induce mechanotransduction, triggering YAP signaling. Finally, we demonstrate that BACE inhibition affects cell proliferation and increases drug sensitivity, highlighting the importance of amyloids for melanoma survival, and the use of beta-secretase inhibitors as potential therapeutic approach for metastatic melanoma.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal , Melanoma , Proteínas Adaptadoras de Transdução de Sinal/genética , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Proteínas Amiloidogênicas , Humanos , Mecanotransdução Celular , Melanoma/tratamento farmacológico , Melanoma/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
7.
Mol Cell ; 56(2): 193-204, 2014 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-25242146

RESUMO

The idea that stem cell therapies work only via cell replacement is challenged by the observation of consistent intercellular molecule exchange between the graft and the host. Here we defined a mechanism of cellular signaling by which neural stem/precursor cells (NPCs) communicate with the microenvironment via extracellular vesicles (EVs), and we elucidated its molecular signature and function. We observed cytokine-regulated pathways that sort proteins and mRNAs into EVs. We described induction of interferon gamma (IFN-γ) pathway in NPCs exposed to proinflammatory cytokines that is mirrored in EVs. We showed that IFN-γ bound to EVs through Ifngr1 activates Stat1 in target cells. Finally, we demonstrated that endogenous Stat1 and Ifngr1 in target cells are indispensable to sustain the activation of Stat1 signaling by EV-associated IFN-γ/Ifngr1 complexes. Our study identifies a mechanism of cellular signaling regulated by EV-associated IFN-γ/Ifngr1 complexes, which grafted stem cells may use to communicate with the host immune system.


Assuntos
Interferon gama/metabolismo , Células-Tronco Neurais/citologia , Receptores de Interferon/metabolismo , Vesículas Transportadoras/metabolismo , Células 3T3 , Animais , Transporte Biológico , Comunicação Celular , Microambiente Celular , Inflamação/imunologia , Interferon gama/biossíntese , Interferon gama/genética , Camundongos , Células-Tronco Neurais/transplante , RNA Mensageiro , Receptores de Interferon/genética , Fator de Transcrição STAT1/biossíntese , Fator de Transcrição STAT1/genética , Fator de Transcrição STAT1/metabolismo , Transdução de Sinais , Células Th1/metabolismo , Células Th2/metabolismo , Receptor de Interferon gama
8.
Cell Mol Life Sci ; 79(1): 45, 2021 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-34913092

RESUMO

PA28γ is a nuclear activator of the 20S proteasome that, unlike the 19S regulatory particle, stimulates hydrolysis of several substrates in an ATP- and ubiquitin-independent manner and whose exact biological functions and molecular mechanism of action still remain elusive. In an effort to shed light on these important issues, we investigated the stimulatory effect of PA28γ on the hydrolysis of different fluorogenic peptides and folded or denatured full-length proteins by the 20S proteasome. Importantly, PA28γ was found to dramatically enhance breakdown rates by 20S proteasomes of several naturally or artificially unstructured proteins, but not of their native, folded counterparts. Furthermore, these data were corroborated by experiments in cell lines with a nucleus-tagged myelin basic protein. Finally, mass spectrometry analysis of the products generated during proteasomal degradation of two proteins demonstrated that PA28γ does not increase, but rather decreases, the variability of peptides that are potentially suitable for MHC class I antigen presentation. These unexpected findings indicate that global stimulation of the degradation of unfolded proteins may represent a more general feature of PA28γ and suggests that this proteasomal activator might play a broader role in the pathway of protein degradation than previously believed.


Assuntos
Autoantígenos/metabolismo , Proteínas Intrinsicamente Desordenadas/metabolismo , Complexo de Endopeptidases do Proteassoma/metabolismo , Células HeLa , Humanos , Proteólise , Resposta a Proteínas não Dobradas
9.
EMBO J ; 35(14): 1504-21, 2016 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-27252488

RESUMO

Fused in sarcoma (FUS) is a ubiquitously expressed RNA-binding protein proposed to function in various RNA metabolic pathways, including transcription regulation, pre-mRNA splicing, RNA transport and microRNA processing. Mutations in the FUS gene were identified in patients with amyotrophic lateral sclerosis (ALS), but the pathomechanisms by which these mutations cause ALS are not known. Here, we show that FUS interacts with the minor spliceosome constituent U11 snRNP, binds preferentially to minor introns and directly regulates their removal. Furthermore, a FUS knockout in neuroblastoma cells strongly disturbs the splicing of minor intron-containing mRNAs, among them mRNAs required for action potential transmission and for functional spinal motor units. Moreover, an ALS-associated FUS mutant that forms cytoplasmic aggregates inhibits splicing of minor introns by trapping U11 and U12 snRNAs in these aggregates. Collectively, our findings suggest a possible pathomechanism for ALS in which mutated FUS inhibits correct splicing of minor introns in mRNAs encoding proteins required for motor neuron survival.


Assuntos
Esclerose Lateral Amiotrófica/patologia , Íntrons , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Splicing de RNA , Proteína FUS de Ligação a RNA/genética , Proteína FUS de Ligação a RNA/metabolismo , Linhagem Celular , Humanos
10.
Anal Chem ; 92(13): 8874-8882, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32501676

RESUMO

Metabolomics and lipidomics studies are becoming increasingly popular but available tools for automated data analysis are still limited. The major issue in untargeted metabolomics is linked to the lack of efficient ranking methods allowing accurate identification of metabolites. Herein, we provide a user-friendly open-source software, named SMfinder, for the robust identification and quantification of small molecules. The software introduces an MS2 false discovery rate approach, which is based on single spectral permutation and increases identification accuracy. SMfinder can be efficiently applied to shotgun and targeted analysis in metabolomics and lipidomics without requiring extensive in-house acquisition of standards as it provides accurate identification by using available MS2 libraries in instrument independent manner. The software, downloadable at www.ifom.eu/SMfinder, is suitable for untargeted, targeted, and flux analysis.


Assuntos
Lipidômica/métodos , Metabolômica/métodos , Interface Usuário-Computador , Isótopos de Carbono/química , Isótopos de Carbono/metabolismo , Linhagem Celular Tumoral , Humanos , Lipídeos/análise , Metaboloma
11.
Proc Natl Acad Sci U S A ; 113(41): E6219-E6227, 2016 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-27671648

RESUMO

Cells in the tumor microenvironment may be reprogrammed by tumor-derived metabolites. Cholesterol-oxidized products, namely oxysterols, have been shown to favor tumor growth directly by promoting tumor cell growth and indirectly by dampening antitumor immune responses. However, the cellular and molecular mechanisms governing oxysterol generation within tumor microenvironments remain elusive. We recently showed that tumor-derived oxysterols recruit neutrophils endowed with protumoral activities, such as neoangiogenesis. Here, we show that hypoxia inducible factor-1a (HIF-1α) controls the overexpression of the enzyme Cyp46a1, which generates the oxysterol 24-hydroxycholesterol (24S-HC) in a pancreatic neuroendocrine tumor (pNET) model commonly used to study neoangiogenesis. The activation of the HIF-1α-24S-HC axis ultimately leads to the induction of the angiogenic switch through the positioning of proangiogenic neutrophils in proximity to Cyp46a1+ islets. Pharmacologic blockade or genetic inactivation of oxysterols controls pNET tumorigenesis by dampening the 24S-HC-neutrophil axis. Finally, we show that in some human pNET samples Cyp46a1 transcripts are overexpressed, which correlate with the HIF-1α target VEGF and with tumor diameter. This study reveals a layer in the angiogenic switch of pNETs and identifies a therapeutic target for pNET patients.


Assuntos
Transformação Celular Neoplásica/metabolismo , Hidroxicolesteróis/metabolismo , Tumores Neuroendócrinos/etiologia , Tumores Neuroendócrinos/metabolismo , Neoplasias Pancreáticas/etiologia , Neoplasias Pancreáticas/metabolismo , Animais , Transformação Celular Neoplásica/genética , Colestanotriol 26-Mono-Oxigenase/genética , Colestanotriol 26-Mono-Oxigenase/metabolismo , Colesterol 24-Hidroxilase , Citocinas/metabolismo , Modelos Animais de Doenças , Progressão da Doença , Ativação Enzimática , Feminino , Imunofluorescência , Proteínas Ativadoras de GTPase/genética , Proteínas Ativadoras de GTPase/metabolismo , Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Imuno-Histoquímica , Masculino , Camundongos , Camundongos Transgênicos , Neovascularização Patológica/genética , Tumores Neuroendócrinos/patologia , Neoplasias Pancreáticas/patologia , Fator A de Crescimento do Endotélio Vascular/genética , Fator A de Crescimento do Endotélio Vascular/metabolismo
12.
J Neurochem ; 145(3): 245-257, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29315582

RESUMO

Peripheral myelin protein 22 (PMP22) is a component of compact myelin in the peripheral nervous system. The amount of PMP22 in myelin is tightly regulated, and PMP22 over or under-expression cause Charcot-Marie-Tooth 1A (CMT1A) and Hereditary Neuropathy with Pressure Palsies (HNPP). Despite the importance of PMP22, its function remains largely unknown. It was reported that PMP22 interacts with the ß4 subunit of the laminin receptor α6ß4 integrin, suggesting that α6ß4 integrin and laminins may contribute to the pathogenesis of CMT1A or HNPP. Here we asked if the lack of α6ß4 integrin in Schwann cells influences myelin stability in the HNPP mouse model. Our data indicate that PMP22 and ß4 integrin may not interact directly in myelinating Schwann cells, however, ablating ß4 integrin delays the formation of tomacula, a characteristic feature of HNPP. In contrast, ablation of integrin ß4 worsens nerve conduction velocities and non-compact myelin organization in HNPP animals. This study demonstrates that indirect interactions between an extracellular matrix receptor and a myelin protein influence the stability and function of myelinated fibers.


Assuntos
Artrogripose/metabolismo , Neuropatia Hereditária Motora e Sensorial/metabolismo , Integrina alfa6beta4/metabolismo , Células de Schwann/metabolismo , Animais , Artrogripose/patologia , Neuropatia Hereditária Motora e Sensorial/patologia , Camundongos , Camundongos Knockout , Proteínas da Mielina/metabolismo , Bainha de Mielina/metabolismo , Bainha de Mielina/patologia , Células de Schwann/patologia
13.
Cereb Cortex ; 27(3): 2226-2248, 2017 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-27005990

RESUMO

Alterations in the balance of inhibitory and excitatory synaptic transmission have been implicated in the pathogenesis of neurological disorders such as epilepsy. Eukaryotic elongation factor 2 kinase (eEF2K) is a highly regulated, ubiquitous kinase involved in the control of protein translation. Here, we show that eEF2K activity negatively regulates GABAergic synaptic transmission. Indeed, loss of eEF2K increases GABAergic synaptic transmission by upregulating the presynaptic protein Synapsin 2b and α5-containing GABAA receptors and thus interferes with the excitation/inhibition balance. This cellular phenotype is accompanied by an increased resistance to epilepsy and an impairment of only a specific hippocampal-dependent fear conditioning. From a clinical perspective, our results identify eEF2K as a potential novel target for antiepileptic drugs, since pharmacological and genetic inhibition of eEF2K can revert the epileptic phenotype in a mouse model of human epilepsy.


Assuntos
Quinase do Fator 2 de Elongação/metabolismo , Epilepsia/enzimologia , Neurônios/enzimologia , Transmissão Sináptica/fisiologia , Animais , Células Cultivadas , Córtex Cerebral/efeitos dos fármacos , Córtex Cerebral/enzimologia , Córtex Cerebral/patologia , Condicionamento Psicológico/fisiologia , Modelos Animais de Doenças , Quinase do Fator 2 de Elongação/antagonistas & inibidores , Quinase do Fator 2 de Elongação/genética , Epilepsia/patologia , Medo/fisiologia , Hipocampo/efeitos dos fármacos , Hipocampo/enzimologia , Hipocampo/patologia , Camundongos Endogâmicos C57BL , Camundongos Knockout , Inibição Neural/efeitos dos fármacos , Inibição Neural/fisiologia , Neurônios/efeitos dos fármacos , Neurônios/patologia , Ratos Sprague-Dawley , Receptores de GABA-A/metabolismo , Sinapsinas/genética , Sinapsinas/metabolismo , Transmissão Sináptica/efeitos dos fármacos , Ácido gama-Aminobutírico/metabolismo
14.
Nucleic Acids Res ; 44(18): 8786-8798, 2016 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-27407105

RESUMO

In eukaryotic cells the CDC7/DBF4 kinase, also known as DBF4-dependent kinase (DDK), is required for the firing of DNA replication origins. CDC7 is also involved in replication stress responses and its depletion sensitises cells to drugs that affect fork progression, including Topoisomerase 2 poisons. Although CDC7 is an important regulator of cell division, relatively few substrates and bona-fide CDC7 phosphorylation sites have been identified to date in human cells. In this study, we have generated an active recombinant CDC7/DBF4 kinase that can utilize bulky ATP analogues. By performing in vitro kinase assays using benzyl-thio-ATP, we have identified TOP2A as a primary CDC7 substrate in nuclear extracts, and serine 1213 and serine 1525 as in vitro phosphorylation sites. We show that CDC7/DBF4 and TOP2A interact in cells, that this interaction mainly occurs early in S-phase, and that it is compromised after treatment with CDC7 inhibitors. We further provide evidence that human DBF4 localises at centromeres, to which TOP2A is progressively recruited during S-phase. Importantly, we found that CDC7/DBF4 down-regulation, as well S1213A/S1525A TOP2A mutations can advance the timing of centromeric TOP2A recruitment in S-phase. Our results indicate that TOP2A is a novel DDK target and have important implications for centromere biology.


Assuntos
Antígenos de Neoplasias/metabolismo , Proteínas de Ciclo Celular/metabolismo , Centrômero/genética , Centrômero/metabolismo , DNA Topoisomerases Tipo II/metabolismo , Proteínas de Ligação a DNA/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas de Ciclo Celular/antagonistas & inibidores , Replicação do DNA , Humanos , Fosforilação , Proteínas de Ligação a Poli-ADP-Ribose , Ligação Proteica , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Origem de Replicação , Fase S
15.
J Proteome Res ; 16(4): 1719-1727, 2017 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-28282139

RESUMO

In global proteomic analysis, it is estimated that proteins span from millions to less than 100 copies per cell. The challenge of protein quantitation by classic shotgun proteomic techniques relies on the presence of missing values in peptides belonging to low-abundance proteins that lowers intraruns reproducibility affecting postdata statistical analysis. Here, we present a new analytical workflow MvM (missing value monitoring) able to recover quantitation of missing values generated by shotgun analysis. In particular, we used confident data-dependent acquisition (DDA) quantitation only for proteins measured in all the runs, while we filled the missing values with data-independent acquisition analysis using the library previously generated in DDA. We analyzed cell cycle regulated proteins, as they are low abundance proteins with highly dynamic expression levels. Indeed, we found that cell cycle related proteins are the major components of the missing values-rich proteome. Using the MvM workflow, we doubled the number of robustly quantified cell cycle related proteins, and we reduced the number of missing values achieving robust quantitation for proteins over ∼50 molecules per cell. MvM allows lower quantification variance among replicates for low abundance proteins with respect to DDA analysis, which demonstrates the potential of this novel workflow to measure low abundance, dynamically regulated proteins.


Assuntos
Proteínas de Ciclo Celular/isolamento & purificação , Peptídeos/isolamento & purificação , Proteoma/genética , Proteômica , Proteínas de Ciclo Celular/genética , Peptídeos/genética , Espectrometria de Massas em Tandem
16.
Hum Mol Genet ; 24(7): 1843-55, 2015 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-25452428

RESUMO

Selenoprotein N (SEPN1) is a broadly expressed resident protein of the endoplasmic reticulum (ER) whose loss-of-function inexplicably leads to human muscle disease. We found that SEPN1 levels parallel those of endoplamic reticulum oxidoreductin 1 (ERO1), an ER protein thiol oxidase, and that SEPN1's redox activity defends the ER from ERO1-generated peroxides. Moreover, we have defined the redox-regulated interactome of SEPN1 and identified the ER calcium import SERCA2 pump as a redox-partner of SEPN1. SEPN1 enhances SERCA2 activity by reducing luminal cysteines that are hyperoxidized by ERO1-generated peroxides. Cells lacking SEPN1 are hypersensitive to ERO1 overexpression and conspicuously defective in ER calcium re-uptake. After being muscle-transduced with an adeno-associated virus driving ERO1α, SEPN1 knockout mice unmasks a myopathy that resembles the dense core disease due to human mutations in SEPN1, whereas the combined attenuation of ERO1α and SEPN1 enhances cell fitness. These observations reveal the involvement of SEPN1 in ER redox and calcium homeostasis and that an ERO1 inhibitor, restoring redox-dependent calcium homeostasis, may ameliorate the myopathy of SEPN1 deficiency.


Assuntos
Retículo Endoplasmático/metabolismo , Proteínas Musculares/metabolismo , Músculo Esquelético/metabolismo , Doenças Musculares/metabolismo , ATPases Transportadoras de Cálcio do Retículo Sarcoplasmático/metabolismo , Selenoproteínas/metabolismo , Animais , Cisteína/metabolismo , Retículo Endoplasmático/genética , Humanos , Camundongos , Camundongos Knockout , Proteínas Musculares/genética , Músculo Esquelético/patologia , Doenças Musculares/genética , Doenças Musculares/patologia , Oxirredução , Oxirredutases/genética , Oxirredutases/metabolismo , Peróxidos/metabolismo , ATPases Transportadoras de Cálcio do Retículo Sarcoplasmático/genética , Selenoproteínas/genética
17.
J Neuroinflammation ; 13(1): 232, 2016 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-27590826

RESUMO

BACKGROUND: Neural stem cells (NSCs) display tissue trophic and immune modulatory therapeutic activities after transplantation in central nervous system disorders. The intercellular interplay between stem cells and target immune cells is increased in NSCs exposed to inflammatory cues. Here, we hypothesize that inflammatory cytokine signalling leads to metabolic reprogramming of NSCs regulating some of their immune modulatory effects. METHODS: NSC lines were prepared from the subventricular zone (SVZ) of 7-12-week-old mice. Whole secretome-based screening and analysis of intracellular small metabolites was performed in NSCs exposed to cocktails of either Th1-like (IFN-γ, 500 U/ml; TNF-α, 200 U/ml; IL-1ß, 100 U/ml) or Th2-like (IL-4, IL-5 and IL-13; 10 ng/ml) inflammatory cytokines for 16 h in vitro. Isotopologues distribution of arginine and downstream metabolites was assessed by liquid chromatography/mass spectrometry in NSCs incubated with U-(13)C6 L-arginine in the presence or absence of Th1 or Th2 cocktails (Th1 NSCs or Th2 NSCs). The expression of arginase I and II was investigated in vitro in Th1 NSCs and Th2 NSCs and in vivo in the SVZ of mice with experimental autoimmune encephalomyelitis, as prototypical model of Th1 cell-driven brain inflammatory disease. The effects of the inflammatory cytokine signalling were studied in NSC-lymph node cells (LNC) co-cultures by flow cytometry-based analysis of cell proliferation following pan-arginase inhibition with N(ω)-hydroxy-nor-arginine (nor-NOHA). RESULTS: Cytokine-primed NSCs showed significantly higher anti-proliferative effect in co-cultures vs. control NSCs. Metabolomic analysis of intracellular metabolites revealed alteration of arginine metabolism and increased extracellular arginase I activity in cytokine-primed NSCs. Arginase inhibition by nor-NOHA partly rescued the anti-proliferative effects of cytokine-primed NSCs. CONCLUSIONS: Our work underlines the use of metabolic profiling as hypothesis-generating tools that helps unravelling how stem cell-mediated mechanisms of tissue restoration become affected by local inflammatory responses. Among different therapeutic candidates, we identify arginase signalling as novel metabolic determinant of the NSC-to-immune system communication.


Assuntos
Arginina/metabolismo , Citocinas/metabolismo , Fatores Imunológicos/metabolismo , Células-Tronco Neurais/imunologia , Células-Tronco Neurais/metabolismo , Animais , Arginase/metabolismo , Proliferação de Células/efeitos dos fármacos , Células Cultivadas , Técnicas de Cocultura , Colorimetria , Citocinas/farmacologia , Modelos Animais de Doenças , Encefalomielite Autoimune Experimental/metabolismo , Encefalomielite Autoimune Experimental/patologia , Feminino , Ventrículos Laterais/citologia , Metabolômica , Camundongos , Células-Tronco Neurais/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos , Linfócitos T/efeitos dos fármacos , Linfócitos T/imunologia , Linfócitos T/metabolismo
18.
Mol Cell ; 32(1): 81-95, 2008 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-18851835

RESUMO

RBM5/Luca-15/H37 is a gene frequently inactivated in lung cancers and overexpressed in breast tumors. Its protein product has been detected in prespliceosomal complexes and modulates cell proliferation and Fas-mediated apoptosis. We report that RBM5 is a component of complexes involved in 3' splice site recognition and regulates alternative splicing of apoptosis-related genes, including the Fas receptor, switching between isoforms with antagonistic functions in programmed cell death. In contrast with classical mechanisms of splicing regulation, RBM5 does not affect early events of splice site recognition that lead to Fas exon 6 definition. Instead, RBM5 inhibits the transition between prespliceosomal complexes assembled around exon 6 to mature spliceosomes assembled on the flanking introns and promotes sequence-specific pairing of the distal splice sites. An OCRE domain important for RBM5 function contacts components of the U4/5/6 tri-snRNP, consistent with the idea that RBM5 modulates splice site pairing after prespliceosome assembly and exon definition.


Assuntos
Proteínas de Ciclo Celular/metabolismo , Proteínas de Ligação a DNA/metabolismo , Sítios de Splice de RNA , Proteínas de Ligação a RNA/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Receptor fas/genética , Processamento Alternativo , Apoptose/genética , Sequência de Bases , Proteína Reguladora de Apoptosis Semelhante a CASP8 e FADD/genética , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/genética , DNA/genética , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Éxons , Genes Supressores de Tumor , Células HeLa , Humanos , Técnicas In Vitro , Íntrons , Dados de Sequência Molecular , Proteínas Nucleares/metabolismo , Estrutura Terciária de Proteína , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Ribonucleoproteína Nuclear Pequena U5/metabolismo , Ribonucleoproteínas/metabolismo , Fator de Processamento U2AF , Proteínas Supressoras de Tumor/química , Proteínas Supressoras de Tumor/genética
19.
Nucleic Acids Res ; 42(13): 8433-48, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24939902

RESUMO

The proliferating cell nuclear antigen (PCNA) protein serves as a molecular platform recruiting and coordinating the activity of factors involved in multiple deoxyribonucleic acid (DNA) transactions. To avoid dangerous genome instability, it is necessary to prevent excessive retention of PCNA on chromatin. Although PCNA functions during DNA replication appear to be regulated by different post-translational modifications, the mechanism regulating PCNA removal and degradation after nucleotide excision repair (NER) is unknown. Here we report that CREB-binding protein (CBP), and less efficiently p300, acetylated PCNA at lysine (Lys) residues Lys13,14,77 and 80, to promote removal of chromatin-bound PCNA and its degradation during NER. Mutation of these residues resulted in impaired DNA replication and repair, enhanced the sensitivity to ultraviolet radiation, and prevented proteolytic degradation of PCNA after DNA damage. Depletion of both CBP and p300, or failure to load PCNA on DNA in NER deficient cells, prevented PCNA acetylation and degradation, while proteasome inhibition resulted in accumulation of acetylated PCNA. These results define a CBP and p300-dependent mechanism for PCNA acetylation after DNA damage, linking DNA repair synthesis with removal of chromatin-bound PCNA and its degradation, to ensure genome stability.


Assuntos
Proteína de Ligação a CREB/metabolismo , Reparo do DNA , Antígeno Nuclear de Célula em Proliferação/metabolismo , Fatores de Transcrição de p300-CBP/metabolismo , Acetilação , Proteína de Ligação a CREB/química , Células Cultivadas , Cromatina/metabolismo , DNA/biossíntese , Dano ao DNA , Replicação do DNA , DNA Polimerase Dirigida por DNA/metabolismo , Humanos , Mutação , Antígeno Nuclear de Célula em Proliferação/genética
20.
Mol Cell Proteomics ; 12(12): 3948-61, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-24045696

RESUMO

Intracellular pathogens contribute to a significant proportion of infectious diseases worldwide. The successful strategy of evading the immune system by hiding inside host cells is common to all the microorganism classes, which exploit membrane microdomains, enriched in cholesterol and sphingolipids, to invade and colonize the host cell. These assemblies, with distinct biochemical properties, can be isolated by means of flotation in sucrose density gradient centrifugation because they are insoluble in nonionic detergents at low temperature. We analyzed the protein and lipid contents of detergent-resistant membranes from erythrocytes infected by Plasmodium falciparum, the most deadly human malaria parasite. Proteins associated with membrane microdomains of trophic parasite blood stages (trophozoites) include an abundance of chaperones, molecules involved in vesicular trafficking, and enzymes implicated in host hemoglobin degradation. About 60% of the identified proteins contain a predicted localization signal suggesting a role of membrane microdomains in protein sorting/trafficking. To validate our proteomic data, we raised antibodies against six Plasmodium proteins not characterized previously. All the selected candidates were recovered in floating low-density fractions after density gradient centrifugation. The analyzed proteins localized either to internal organelles, such as the mitochondrion and the endoplasmic reticulum, or to exported membrane structures, the parasitophorous vacuole membrane and Maurer's clefts, implicated in targeting parasite proteins to the host erythrocyte cytosol or surface. The relative abundance of cholesterol and phospholipid species varies in gradient fractions containing detergent-resistant membranes, suggesting heterogeneity in the lipid composition of the isolated microdomain population. This study is the first report showing the presence of cholesterol-rich microdomains with distinct properties and subcellular localization in trophic stages of Plasmodium falciparum.


Assuntos
Membrana Eritrocítica/química , Microdomínios da Membrana/química , Plasmodium falciparum/genética , Proteoma/genética , Proteínas de Protozoários/genética , Trofozoítos/metabolismo , Anticorpos/química , Centrifugação com Gradiente de Concentração , Colesterol/química , Cisteína Endopeptidases/genética , Cisteína Endopeptidases/metabolismo , Detergentes/química , Membrana Eritrocítica/parasitologia , Técnica Indireta de Fluorescência para Anticorpo , Expressão Gênica , Interações Hospedeiro-Parasita , Humanos , Membranas Intracelulares/química , Microdomínios da Membrana/parasitologia , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Anotação de Sequência Molecular , Fosfolipídeos/química , Plasmodium falciparum/química , Plasmodium falciparum/metabolismo , Transporte Proteico , Proteoma/metabolismo , Proteínas de Protozoários/metabolismo , Trofozoítos/química
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