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1.
J Am Soc Mass Spectrom ; 31(10): 2013-2024, 2020 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-32880453

RESUMO

As corona virus disease 2019 (COVID-19) is a rapidly growing public health crisis across the world, our knowledge of meaningful diagnostic tests and treatment for severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is still evolving. This novel coronavirus disease COVID-19 can be diagnosed using RT-PCR, but inadequate access to reagents, equipment, and a nonspecific target has slowed disease detection and management. Precision medicine, individualized patient care, requires suitable diagnostics approaches to tackle the challenging aspects of viral outbreaks where many tests are needed in a rapid and deployable approach. Mass spectrometry (MS)-based technologies such as proteomics, glycomics, lipidomics, and metabolomics have been applied in disease outbreaks for identification of infectious disease agents such as virus and bacteria and the molecular phenomena associated with pathogenesis. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) is widely used in clinical diagnostics in the United States and Europe for bacterial pathogen identification. Paper spray ionization mass spectrometry (PSI-MS), a rapid ambient MS technique, has recently open a new opportunity for future clinical investigation to diagnose pathogens. Ultra-high-pressure liquid chromatography coupled high-resolution mass spectrometry (UHPLC-HRMS)-based metabolomics and lipidomics have been employed in large-scale biomedical research to discriminate infectious pathogens and uncover biomarkers associated with pathogenesis. PCR-MS has emerged as a new technology with the capability to directly identify known pathogens from the clinical specimens and the potential to identify genetic evidence of undiscovered pathogens. Moreover, miniaturized MS offers possible applications with relatively fast, highly sensitive, and potentially portable ways to analyze for viral compounds. However, beneficial aspects of these rapidly growing MS technologies in pandemics like COVID-19 outbreaks has been limited. Hence, this perspective gives a brief of the existing knowledge, current challenges, and opportunities for MS-based techniques as a promising avenue in studying emerging pathogen outbreaks such as COVID-19.


Assuntos
Infecções por Coronavirus/etiologia , Lipidômica/métodos , Espectrometria de Massas/métodos , Metabolômica/métodos , Pneumonia Viral/etiologia , Proteômica/métodos , Cromatografia Líquida de Alta Pressão , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Glicômica/métodos , Humanos , Pandemias , Reação em Cadeia da Polimerase , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
2.
BMC Bioinformatics ; 21(1): 376, 2020 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-32867673

RESUMO

BACKGROUND: Two-dimensional gel electrophoresis (2-DGE) is a commonly used tool for proteomic analysis. This gel-based technique separates proteins in a sample according to their isoelectric point and molecular weight. 2-DGE images often present anomalies due to the acquisition process, such as: diffuse and overlapping spots, and background noise. This study proposes a joint pre-processing framework that combines the capabilities of nonlinear filtering, background correction and image normalization techniques for pre-processing 2-DGE images. Among the most important, joint nonlinear diffusion filtering, adaptive piecewise histogram equalization and multilevel thresholding were evaluated using both synthetic data and real 2-DGE images. RESULTS: An improvement of up to 46% in spot detection efficiency was achieved for synthetic data using the proposed framework compared to implementing a single technique of either normalization, background correction or filtering. Additionally, the proposed framework increased the detection of low abundance spots by 20% for synthetic data compared to a normalization technique, and increased the background estimation by 67% compared to a background correction technique. In terms of real data, the joint pre-processing framework reduced the false positives up to 93%. CONCLUSIONS: The proposed joint pre-processing framework outperforms results achieved with a single approach. The best structure was obtained with the ordered combination of adaptive piecewise histogram equalization for image normalization, geometric nonlinear diffusion (GNDF) for filtering, and multilevel thresholding for background correction.


Assuntos
Eletroforese em Gel Bidimensional/métodos , Bases de Dados de Proteínas , Humanos , Processamento de Imagem Assistida por Computador , Proteínas/análise , Proteômica/métodos , Razão Sinal-Ruído
3.
Internist (Berl) ; 61(10): 1094-1105, 2020 Oct.
Artigo em Alemão | MEDLINE | ID: mdl-32897404

RESUMO

BACKGROUND: The early detection and treatment of diabetic nephropathy (DN) is of crucial importance as patients with diabetes mellitus represent the largest proportion of patients on dialysis, with the highest morbidity and mortality. Currently, the first clinical sign of incipient DN is microalbuminuria, but its precision is not optimal. Many studies now report that proteins and peptides are new biomarkers in urine that primarily depict the pathophysiology of DN and thus allow for improved diagnosis of DN. OBJECTIVES: The presentation of new concepts for the early detection and treatment of DN for better patient management. MATERIAL AND METHODS: A systematic literature search was carried out. RESULTS: Many potential markers have been described in the search for new biomarkers to diagnose DN by urinary proteome analysis. However, many of these studies were not meaningful due to the small number of samples. This limitation led to inadequate validation of proteins that could not be confirmed as markers. However, the diagnostic benefit of CKD 273, a multimarker of 273 protein fragments, was sustainably demonstrated for the early diagnosis of DN. This multi-marker shows significant advantages in the precision of diagnosis and prognosis compared to albuminuria. Furthermore, many of its peptide markers map the molecular pathophysiology of DN. CONCLUSIONS: Clinical urinary proteome analysis shows great benefits and is already an appropriate tool for the early detection of incipient DN.


Assuntos
Diabetes Mellitus Tipo 2 , Nefropatias Diabéticas/diagnóstico , Nefropatias Diabéticas/urina , Proteoma/análise , Proteômica/métodos , Albuminúria/diagnóstico , Albuminúria/urina , Biomarcadores/sangue , Diabetes Mellitus Tipo 1/complicações , Diabetes Mellitus Tipo 1/urina , Diabetes Mellitus Tipo 2/complicações , Diabetes Mellitus Tipo 2/urina , Diagnóstico Precoce , Humanos
4.
BMC Bioinformatics ; 21(Suppl 13): 386, 2020 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-32938388

RESUMO

BACKGROUND: In the field of computational biology, analyzing complex data helps to extract relevant biological information. Sample classification of gene expression data is one such popular bio-data analysis technique. However, the presence of a large number of irrelevant/redundant genes in expression data makes a sample classification algorithm working inefficiently. Feature selection is one such high-dimensionality reduction technique that helps to maximize the effectiveness of any sample classification algorithm. Recent advances in biotechnology have improved the biological data to include multi-modal or multiple views. Different 'omics' resources capture various equally important biological properties of entities. However, most of the existing feature selection methodologies are biased towards considering only one out of multiple biological resources. Consequently, some crucial aspects of available biological knowledge may get ignored, which could further improve feature selection efficiency. RESULTS: In this present work, we have proposed a Consensus Multi-View Multi-objective Clustering-based feature selection algorithm called CMVMC. Three controlled genomic and proteomic resources like gene expression, Gene Ontology (GO), and protein-protein interaction network (PPIN) are utilized to build two independent views. The concept of multi-objective consensus clustering has been applied within our proposed gene selection method to satisfy both incorporated views. Gene expression data sets of Multiple tissues and Yeast from two different organisms (Homo Sapiens and Saccharomyces cerevisiae, respectively) are chosen for experimental purposes. As the end-product of CMVMC, a reduced set of relevant and non-redundant genes are found for each chosen data set. These genes finally participate in an effective sample classification. CONCLUSIONS: The experimental study on chosen data sets shows that our proposed feature-selection method improves the sample classification accuracy and reduces the gene-space up to a significant level. In the case of Multiple Tissues data set, CMVMC reduces the number of genes (features) from 5565 to 41, with 92.73% of sample classification accuracy. For Yeast data set, the number of genes got reduced to 10 from 2884, with 95.84% sample classification accuracy. Two internal cluster validity indices - Silhouette and Davies-Bouldin (DB) and one external validity index Classification Accuracy (CA) are chosen for comparative study. Reported results are further validated through well-known biological significance test and visualization tool.


Assuntos
Algoritmos , Análise por Conglomerados , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Proteômica/métodos , Humanos
5.
PLoS One ; 15(9): e0238381, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32881942

RESUMO

Small fructans improve plant tolerance for cold stress. However, the underlying molecular mechanisms are poorly understood. Here, we have demonstrated that the small fructan tetrasaccharide nystose improves the cold stress tolerance of primary rice roots. Roots developed from seeds soaked in nystose showed lower browning rate, higher root activity, and faster growth compared to seeds soaked in water under chilling stress. Comparative proteomics analysis of nystose-treated and control roots identified a total of 497 differentially expressed proteins. GO classification and KEGG pathway analysis documented that some of the upregulated differentially expressed proteins were implicated in the regulation of serine/threonine protein phosphatase activity, abscisic acid-activated signaling, removal of superoxide radicals, and the response to oxidative stress and defense responses. Western blot analysis indicated that nystose promotes the growth of primary rice roots by increasing the level of RSOsPR10, and the cold stress-induced change in RSOsPR10levelis regulated by jasmonate, salicylic acid, and abscisic acid signaling pathways in rice roots. Furthermore, OsMKK4-dependentmitogen-activated protein kinase signaling cascades may be involved in the nystose-induced cold tolerance of primary rice roots. Together, these results indicate that nystose acts as an immunostimulator of the response to cold stress by multiple signaling pathways.


Assuntos
Resposta ao Choque Frio/efeitos dos fármacos , Oligossacarídeos/farmacologia , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Proteômica/métodos , Transdução de Sinais/efeitos dos fármacos , Ácido Abscísico/metabolismo , Cromatografia Líquida de Alta Pressão , Resposta ao Choque Frio/genética , Ciclopentanos/metabolismo , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Oryza/efeitos dos fármacos , Oryza/crescimento & desenvolvimento , Oxilipinas/metabolismo , Fenótipo , Proteínas de Plantas/genética , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/metabolismo , Ácido Salicílico/metabolismo , Transdução de Sinais/genética , Espectrometria de Massas em Tandem
6.
Proc Natl Acad Sci U S A ; 117(37): 23182-23190, 2020 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-32873645

RESUMO

Enzyme turnover numbers (k cats) are essential for a quantitative understanding of cells. Because k cats are traditionally measured in low-throughput assays, they can be inconsistent, labor-intensive to obtain, and can miss in vivo effects. We use a data-driven approach to estimate in vivo k cats using metabolic specialist Escherichia coli strains that resulted from gene knockouts in central metabolism followed by metabolic optimization via laboratory evolution. By combining absolute proteomics with fluxomics data, we find that in vivo k cats are robust against genetic perturbations, suggesting that metabolic adaptation to gene loss is mostly achieved through other mechanisms, like gene-regulatory changes. Combining machine learning and genome-scale metabolic models, we show that the obtained in vivo k cats predict unseen proteomics data with much higher precision than in vitro k cats. The results demonstrate that in vivo k cats can solve the problem of inconsistent and low-coverage parameterizations of genome-scale cellular models.


Assuntos
Escherichia coli/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Técnicas de Inativação de Genes/métodos , Genoma/genética , Cinética , Aprendizado de Máquina , Modelos Biológicos , Proteômica/métodos
7.
PLoS One ; 15(9): e0237975, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32960892

RESUMO

The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.


Assuntos
Ecologia , Genômica/métodos , Metabolômica/métodos , Metagenômica/métodos , Doenças das Plantas/etiologia , Plantas/imunologia , Proteômica/métodos , Microbiota , Plantas/metabolismo , Biologia de Sistemas
8.
Hypertension ; 76(5): 1526-1536, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32981365

RESUMO

ACE2 (angiotensin-converting enzyme 2) is a key component of the renin-angiotensin-aldosterone system. Yet, little is known about the clinical and biologic correlates of circulating ACE2 levels in humans. We assessed the clinical and proteomic correlates of plasma (soluble) ACE2 protein levels in human heart failure. We measured plasma ACE2 using a modified aptamer assay among PHFS (Penn Heart Failure Study) participants (n=2248). We performed an association study of ACE2 against ≈5000 other plasma proteins measured with the SomaScan platform. Plasma ACE2 was not associated with ACE inhibitor and angiotensin-receptor blocker use. Plasma ACE2 was associated with older age, male sex, diabetes mellitus, a lower estimated glomerular filtration rate, worse New York Heart Association class, a history of coronary artery bypass surgery, and higher pro-BNP (pro-B-type natriuretic peptide) levels. Plasma ACE2 exhibited associations with 1011 other plasma proteins. In pathway overrepresentation analyses, top canonical pathways associated with plasma ACE2 included clathrin-mediated endocytosis signaling, actin cytoskeleton signaling, mechanisms of viral exit from host cells, EIF2 (eukaryotic initiation factor 2) signaling, and the protein ubiquitination pathway. In conclusion, in humans with heart failure, plasma ACE2 is associated with various clinical factors known to be associated with severe coronavirus disease 2019 (COVID-19), including older age, male sex, and diabetes mellitus, but is not associated with ACE inhibitor and angiotensin-receptor blocker use. Plasma ACE2 protein levels are prominently associated with multiple cellular pathways involved in cellular endocytosis, exocytosis, and intracellular protein trafficking. Whether these have a causal relationship with ACE2 or are relevant to novel coronavirus-2 infection remains to be assessed in future studies.


Assuntos
Infecções por Coronavirus/epidemiologia , Surtos de Doenças/estatística & dados numéricos , Progressão da Doença , Insuficiência Cardíaca/enzimologia , Insuficiência Cardíaca/fisiopatologia , Peptidil Dipeptidase A/sangue , Pneumonia Viral/epidemiologia , Centros Médicos Acadêmicos , Análise de Variância , Biomarcadores/metabolismo , Estudos de Coortes , Infecções por Coronavirus/prevenção & controle , Feminino , Humanos , Modelos Lineares , Masculino , Pessoa de Meia-Idade , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Prognóstico , Modelos de Riscos Proporcionais , Proteômica/métodos , Estudos Retrospectivos , Sensibilidade e Especificidade , Índice de Gravidade de Doença , Estados Unidos
9.
Nat Commun ; 11(1): 4894, 2020 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-32994400

RESUMO

Identification of the complete set of translated genes of viruses is important to understand viral replication and pathogenesis as well as for therapeutic approaches to control viral infection. Here, we use chemical proteomics, integrating bio-orthogonal non-canonical amino acid tagging and high-resolution mass spectrometry, to characterize the newly synthesized herpes simplex virus 1 (HSV-1) proteome in infected cells. In these infected cells, host cellular protein synthesis is shut-off, increasing the chance to preferentially detect viral proteomes. We identify nine previously cryptic orphan protein coding sequences whose translated products are expressed in HSV-1-infected cells. Functional characterization of one identified protein, designated piUL49, shows that it is critical for HSV-1 neurovirulence in vivo by regulating the activity of virally encoded dUTPase, a key enzyme that maintains accurate DNA replication. Our results demonstrate that cryptic orphan protein coding genes of HSV-1, and probably other large DNA viruses, remain to be identified.


Assuntos
Encefalite por Herpes Simples/virologia , Herpesvirus Humano 1/patogenicidade , Pirofosfatases/metabolismo , Proteínas Virais/metabolismo , Fatores de Virulência/metabolismo , Animais , Encéfalo/patologia , Encéfalo/virologia , Chlorocebus aethiops , Replicação do DNA , Modelos Animais de Doenças , Encefalite por Herpes Simples/patologia , Feminino , Genes Virais/genética , Células HEK293 , Células HeLa , Herpesvirus Humano 1/genética , Humanos , Camundongos , Biossíntese de Proteínas , Proteômica/métodos , Células Vero , Proteínas Virais/genética , Fatores de Virulência/genética , Replicação Viral
10.
Anticancer Res ; 40(10): 5509-5516, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32988874

RESUMO

BACKGROUND/AIM: Extracellular vesicles (EVs) can mediate drug resistance within the tumor microenvironment by delivering bioactive molecules, including proteins. Here, we performed a comparative proteomic analysis of EVs secreted by A549 lung cancer cells and their cisplatin-resistant counterparts in order to identify proteins involved in drug resistance. MATERIALS AND METHODS: Cells were co-cultivated using a transwell system to evaluate EV exchange. EVs were isolated by ultracentrifugation and analyzed using microscopy and nanoparticle tracking. EV proteome was analyzed by mass spectrometry. RESULTS: EV-mediated communication was observed between co-cultured A549 and A549/CDDP cells. EVs isolated from both cells were mainly exosome-like structures. Extracellular matrix components, cell adhesion proteins, complement factors, histones, proteasome subunits and membrane transporters were found enriched in the EVs released by cisplatin-resistant cells. CONCLUSION: Proteins identified in this work may have a relevant role in modulating the chemosensitivity of the recipient cells and could represent useful biomarkers to monitor cisplatin response in lung cancer.


Assuntos
Biomarcadores Tumorais/genética , Cisplatino/farmacologia , Neoplasias Pulmonares/tratamento farmacológico , Proteoma/genética , Células A549 , Cisplatino/efeitos adversos , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/genética , Exossomos/efeitos dos fármacos , Exossomos/genética , Vesículas Extracelulares/genética , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Espectrometria de Massas , Proteômica/métodos , Microambiente Tumoral/efeitos dos fármacos
11.
J Chromatogr A ; 1628: 461443, 2020 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-32822982

RESUMO

Sodium dodecyl sulfate (SDS) in proteomics samples needs to be removed and estimated prior to mass spectrometry (MS)-based analysis and to avoid MS ion-source contamination. Here, we describe an organic solvent free method to remove SDS using a simple apparatus that mainly consists of an agarose gel inside a 1 mL plastic micropipette tip and a voltage power supply with electrodes. A small volume of sample (e.g., 50 µL) is loaded on top of the gel and then voltage (cathode at the sample side) is applied with an acidic solution at the other end of the micropipette tip. Within 25 min, SDS was removed (e.g., ≥99% SDS in 3.5 mM SDS) and the peptides were retained in the sample solution. The strategy was compared to the commercially available and expensive Pierce spin column for the removal of SDS and recovery of peptides from a digested bovine serum albumin sample.


Assuntos
Técnicas de Química Analítica/métodos , Técnicas Eletroquímicas , Proteômica/métodos , Dodecilsulfato de Sódio/isolamento & purificação , Eletroforese em Gel de Poliacrilamida , Espectrometria de Massas , Peptídeos/química , Soroalbumina Bovina/química , Dodecilsulfato de Sódio/química
12.
Nat Commun ; 11(1): 3903, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32764543

RESUMO

Top-down mass spectrometry (MS)-based proteomics provides a comprehensive analysis of proteoforms to achieve a proteome-wide understanding of protein functions. However, the MS detection of low-abundance proteins from blood remains an unsolved challenge due to the extraordinary dynamic range of the blood proteome. Here, we develop an integrated nanoproteomics method coupling peptide-functionalized superparamagnetic nanoparticles (NPs) with top-down MS for the enrichment and comprehensive analysis of cardiac troponin I (cTnI), a gold-standard cardiac biomarker, directly from serum. These NPs enable the sensitive enrichment of cTnI (<1 ng/mL) with high specificity and reproducibility, while simultaneously depleting highly abundant proteins such as human serum albumin (>1010 more abundant than cTnI). We demonstrate that top-down nanoproteomics can provide high-resolution proteoform-resolved molecular fingerprints of diverse cTnI proteoforms to establish proteoform-pathophysiology relationships. This scalable and reproducible antibody-free strategy can generally enable the proteoform-resolved analysis of low-abundance proteins directly from serum to reveal previously unachievable molecular details.


Assuntos
Análise Química do Sangue/métodos , Proteínas Sanguíneas/análise , Espectrometria de Massas/métodos , Proteômica/métodos , Troponina I/sangue , Biomarcadores/sangue , Humanos , Nanopartículas de Magnetita/química , Nanopartículas de Magnetita/ultraestrutura , Nanotecnologia , Processamento de Proteína Pós-Traducional , Proteoma/análise , Reprodutibilidade dos Testes , Albumina Sérica Humana/análise
13.
Sensors (Basel) ; 20(15)2020 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-32752043

RESUMO

Coronaviruses have received global concern since 2003, when an outbreak caused by SARS-CoV emerged in China. Later on, in 2012, the Middle-East respiratory syndrome spread in Saudi Arabia, caused by MERS-CoV. Currently, the global crisis is caused by the pandemic SARS-CoV-2, which belongs to the same lineage of SARS-CoV. In response to the urgent need of diagnostic tools, several lab-based and biosensing techniques have been proposed so far. Five main areas have been individuated and discussed in terms of their strengths and weaknesses. The cell-culture detection and the microneutralization tests are still considered highly reliable methods. The genetic screening, featuring the well-established Real-time polymerase chain reaction (RT-PCR), represents the gold standard for virus detection in nasopharyngeal swabs. On the other side, immunoassays were developed, either by screening/antigen recognition of IgM/IgG or by detecting the whole virus, in blood and sera. Next, proteomic mass-spectrometry (MS)-based methodologies have also been proposed for the analysis of swab samples. Finally, virus-biosensing devices were efficiently designed. Both electrochemical immunosensors and eye-based technologies have been described, showing detection times lower than 10 min after swab introduction. Alternative to swab-based techniques, lateral flow point-of-care immunoassays are already commercially available for the analysis of blood samples. Such biosensing devices hold the advantage of being portable for on-site testing in hospitals, airports, and hotspots, virtually without any sample treatment or complicated lab precautions.


Assuntos
Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Sistemas Automatizados de Assistência Junto ao Leito , Anticorpos Antivirais/sangue , Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Betacoronavirus/metabolismo , Técnicas Biossensoriais/métodos , Infecções por Coronavirus/virologia , Humanos , Imunoensaio/métodos , Pandemias , Pneumonia Viral/virologia , Proteômica/métodos , RNA Viral/análise , RNA Viral/metabolismo , Reação em Cadeia da Polimerase em Tempo Real/métodos
14.
Nat Commun ; 11(1): 3793, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32732981

RESUMO

Reproducible research is the bedrock of experimental science. To enable the deployment of large-scale proteomics, we assess the reproducibility of mass spectrometry (MS) over time and across instruments and develop computational methods for improving quantitative accuracy. We perform 1560 data independent acquisition (DIA)-MS runs of eight samples containing known proportions of ovarian and prostate cancer tissue and yeast, or control HEK293T cells. Replicates are run on six mass spectrometers operating continuously with varying maintenance schedules over four months, interspersed with ~5000 other runs. We utilise negative controls and replicates to remove unwanted variation and enhance biological signal, outperforming existing methods. We also design a method for reducing missing values. Integrating these computational modules into a pipeline (ProNorM), we mitigate variation among instruments over time and accurately predict tissue proportions. We demonstrate how to improve the quantitative analysis of large-scale DIA-MS data, providing a pathway toward clinical proteomics.


Assuntos
Espectrometria de Massas/métodos , Proteoma/análise , Proteômica/métodos , Biomarcadores Tumorais/análise , Linhagem Celular Tumoral , Feminino , Células HEK293 , Humanos , Masculino , Neoplasias Ovarianas , Neoplasias da Próstata , Reprodutibilidade dos Testes , Saccharomyces cerevisiae
15.
Nat Commun ; 11(1): 4065, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792501

RESUMO

Identification of post-translationally or chemically modified peptides in mass spectrometry-based proteomics experiments is a crucial yet challenging task. We have recently introduced a fragment ion indexing method and the MSFragger search engine to empower an open search strategy for comprehensive analysis of modified peptides. However, this strategy does not consider fragment ions shifted by unknown modifications, preventing modification localization and limiting the sensitivity of the search. Here we present a localization-aware open search method, in which both modification-containing (shifted) and regular fragment ions are indexed and used in scoring. We also implement a fast mass calibration and optimization method, allowing optimization of the mass tolerances and other key search parameters. We demonstrate that MSFragger with mass calibration and localization-aware open search identifies modified peptides with significantly higher sensitivity and accuracy. Comparing MSFragger to other modification-focused tools (pFind3, MetaMorpheus, and TagGraph) shows that MSFragger remains an excellent option for fast, comprehensive, and sensitive searches for modified peptides in shotgun proteomics data.


Assuntos
Peptídeos/química , Algoritmos , Animais , Bases de Dados de Proteínas , Humanos , Espectrometria de Massas , Proteômica/métodos
16.
Nat Commun ; 11(1): 4111, 2020 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-32807776

RESUMO

Mutational inactivation of VHL is the earliest genetic event in the majority of clear cell renal cell carcinomas (ccRCC), leading to accumulation of the HIF-1α and HIF-2α transcription factors. While correlative studies of human ccRCC and functional studies using human ccRCC cell lines have implicated HIF-1α as an inhibitor and HIF-2α as a promoter of aggressive tumour behaviours, their roles in tumour onset have not been functionally addressed. Herein we show using an autochthonous ccRCC model that Hif1a is essential for tumour formation whereas Hif2a deletion has only minor effects on tumour initiation and growth. Both HIF-1α and HIF-2α are required for the clear cell phenotype. Transcriptomic and proteomic analyses reveal that HIF-1α regulates glycolysis while HIF-2α regulates genes associated with lipoprotein metabolism, ribosome biogenesis and E2F and MYC transcriptional activities. HIF-2α-deficient tumours are characterised by increased antigen presentation, interferon signalling and CD8+ T cell infiltration and activation. Single copy loss of HIF1A or high levels of HIF2A mRNA expression correlate with altered immune microenvironments in human ccRCC. These studies reveal an oncogenic role of HIF-1α in ccRCC initiation and suggest that alterations in the balance of HIF-1α and HIF-2α activities can affect different aspects of ccRCC biology and disease aggressiveness.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Carcinoma de Células Renais/metabolismo , Carcinoma de Células Renais/patologia , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Neoplasias Renais/metabolismo , Neoplasias Renais/patologia , Células 3T3 , Animais , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Western Blotting , Linfócitos T CD8-Positivos/metabolismo , Carcinoma de Células Renais/genética , Linhagem Celular Tumoral , Proliferação de Células/genética , Proliferação de Células/fisiologia , Regulação Neoplásica da Expressão Gênica/genética , Regulação Neoplásica da Expressão Gênica/fisiologia , Humanos , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Imuno-Histoquímica , Inflamação/genética , Inflamação/metabolismo , Neoplasias Renais/genética , Espectrometria de Massas , Camundongos , Proteômica/métodos , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de RNA , Microambiente Tumoral/genética , Microambiente Tumoral/fisiologia
17.
Nat Commun ; 11(1): 4110, 2020 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-32807790

RESUMO

Hutchinson-Gilford Progeria Syndrome (HGPS) is a premature aging disease in children that leads to early death. Smooth muscle cells (SMCs) are the most affected cells in HGPS individuals, although the reason for such vulnerability remains poorly understood. In this work, we develop a microfluidic chip formed by HGPS-SMCs generated from induced pluripotent stem cells (iPSCs), to study their vulnerability to flow shear stress. HGPS-iPSC SMCs cultured under arterial flow conditions detach from the chip after a few days of culture; this process is mediated by the upregulation of metalloprotease 13 (MMP13). Importantly, double-mutant LmnaG609G/G609GMmp13-/- mice or LmnaG609G/G609GMmp13+/+ mice treated with a MMP inhibitor show lower SMC loss in the aortic arch than controls. MMP13 upregulation appears to be mediated, at least in part, by the upregulation of glycocalyx. Our HGPS-SMCs chip represents a platform for developing treatments for HGPS individuals that may complement previous pre-clinical and clinical treatments.


Assuntos
Metaloproteinase 13 da Matriz/metabolismo , Miócitos de Músculo Liso/metabolismo , Animais , Biotecnologia/métodos , Doenças Cardiovasculares/metabolismo , Feminino , Frequência Cardíaca/efeitos dos fármacos , Células-Tronco Pluripotentes Induzidas/citologia , Células-Tronco Pluripotentes Induzidas/efeitos dos fármacos , Células-Tronco Pluripotentes Induzidas/metabolismo , Lamina Tipo A/genética , Lamina Tipo A/metabolismo , Masculino , Inibidores de Metaloproteinases de Matriz/farmacologia , Camundongos , Camundongos Mutantes , Miócitos de Músculo Liso/efeitos dos fármacos , Progéria/metabolismo , Progéria/patologia , Proteômica/métodos
18.
PLoS One ; 15(8): e0236679, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32760087

RESUMO

The Drosophila shaggy gene (sgg, GSK-3) encodes multiple protein isoforms with serine/threonine kinase activity and is a key player in diverse developmental signalling pathways. Currently it is unclear whether different Sgg proteoforms are similarly involved in signalling or if different proteoforms have distinct functions. We used CRISPR/Cas9 genome engineering to tag eight different Sgg proteoform classes and determined their localization during embryonic development. We performed proteomic analysis of the two major proteoform classes and generated mutant lines for both of these for transcriptomic and phenotypic analysis. We uncovered distinct tissue-specific localization patterns for all of the tagged proteoforms we examined, most of which have not previously been characterised directly at the protein level, including one proteoform initiating with a non-standard codon. Collectively, this suggests complex developmentally regulated splicing of the sgg primary transcript. Further, affinity purification followed by mass spectrometric analyses indicate a different repertoire of interacting proteins for the two major proteoforms we examined, one with ubiquitous expression (Sgg-PB) and one with nervous system specific expression (Sgg-PA). Specific mutation of these proteoforms shows that Sgg-PB performs the well characterised maternal and zygotic segmentations functions of the sgg locus, while Sgg-PA mutants show adult lifespan and locomotor defects consistent with its nervous system localisation. Our findings provide new insights into the role of GSK-3 proteoforms and intriguing links with the GSK-3α and GSK-3ß proteins encoded by independent vertebrate genes. Our analysis suggests that different proteoforms generated by alternative splicing are likely to perform distinct functions.


Assuntos
Proteínas de Drosophila/fisiologia , Drosophila melanogaster/metabolismo , Quinase 3 da Glicogênio Sintase/fisiologia , Animais , Proteínas de Drosophila/genética , Quinase 3 da Glicogênio Sintase/genética , Isoenzimas/fisiologia , Proteômica/métodos
19.
PLoS One ; 15(8): e0237181, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32813697

RESUMO

Multidrug-resistant Vibrio parahaemolyticus has become a significant public health concern. The development of effective drugs and vaccines against Vibrio parahaemolyticus is the current research priority. Thus, we aimed to find out effective drug and vaccine targets using a comprehensive genome-based analysis. A total of 4822 proteins were screened from V. parahaemolyticus proteome. Among 16 novel cytoplasmic proteins, 'VIBPA Type II secretion system protein L' and 'VIBPA Putative fimbrial protein Z' were subjected to molecular docking with 350 human metabolites, which revealed that Eliglustat, Simvastatin and Hydroxocobalamin were the top drug molecules considering free binding energy. On the contrary, 'Sensor histidine protein kinase UhpB' and 'Flagellar hook-associated protein of 25 novel membrane proteins were subjected to T-cell and B-cell epitope prediction, antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking analysis to generate the most immunogenic epitopes. Three subunit vaccines were constructed by the combination of highly antigenic epitopes along with suitable adjuvant, PADRE sequence and linkers. The designed vaccine constructs (V1, V2, V3) were analyzed by their physiochemical properties and molecular docking with MHC molecules- results suggested that the V1 is superior. Besides, the binding affinity of human TLR-1/2 heterodimer and construct V1 could be biologically significant in the development of the vaccine repertoire. The vaccine-receptor complex exhibited deformability at a minimum level that also strengthened our prediction. The optimized codons of the designed construct was cloned into pET28a(+) vector of E. coli strain K12. However, the predicted drug molecules and vaccine constructs could be further studied using model animals to combat V. parahaemolyticus associated infections.


Assuntos
Vacinas Bacterianas/imunologia , Descoberta de Drogas/métodos , Genoma Bacteriano , Vibrioses/tratamento farmacológico , Vibrioses/prevenção & controle , Vibrio parahaemolyticus/genética , Vibrio parahaemolyticus/imunologia , Biologia Computacional/métodos , Farmacorresistência Bacteriana Múltipla/genética , Epitopos de Linfócito B/imunologia , Epitopos de Linfócito T/imunologia , Escherichia coli K12/genética , Humanos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Mapas de Interação de Proteínas , Proteoma/genética , Proteômica/métodos , Vacinas de Subunidades/imunologia , Vibrioses/microbiologia
20.
Nat Protoc ; 15(9): 2956-2979, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32737464

RESUMO

Bottom-up mass spectrometry-based proteomics relies on protein digestion and peptide purification. The application of such methods to broadly available clinical samples such as formalin-fixed and paraffin-embedded (FFPE) tissues requires reversal of chemical crosslinking and the removal of reagents that are incompatible with mass spectrometry. Here, we describe in detail a protocol that combines tissue disruption by ultrasonication, heat-induced antigen retrieval and two alternative methods for efficient detergent removal to enable quantitative proteomic analysis of limited amounts of FFPE material. To show the applicability of our approach, we used hepatocellular carcinoma (HCC) as a model system. By combining the described protocol with laser-capture microdissection, we were able to quantify the intra-tumor heterogeneity of a tumor specimen on the proteome level using a single slide with tissue of 10-µm thickness. We also demonstrate broader applicability to other tissues, including human gallbladder and heart. The procedure described in this protocol can be completed within 8 d.


Assuntos
Formaldeído , Espectrometria de Massas , Inclusão em Parafina , Proteômica/métodos , Fixação de Tecidos , Carcinoma Hepatocelular/patologia , Humanos , Neoplasias Hepáticas/patologia
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