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1.
Cell ; 186(1): 63-79.e21, 2023 01 05.
Artigo em Inglês | MEDLINE | ID: mdl-36608659

RESUMO

Metabolism is deeply intertwined with aging. Effects of metabolic interventions on aging have been explained with intracellular metabolism, growth control, and signaling. Studying chronological aging in yeast, we reveal a so far overlooked metabolic property that influences aging via the exchange of metabolites. We observed that metabolites exported by young cells are re-imported by chronologically aging cells, resulting in cross-generational metabolic interactions. Then, we used self-establishing metabolically cooperating communities (SeMeCo) as a tool to increase metabolite exchange and observed significant lifespan extensions. The longevity of the SeMeCo was attributable to metabolic reconfigurations in methionine consumer cells. These obtained a more glycolytic metabolism and increased the export of protective metabolites that in turn extended the lifespan of cells that supplied them with methionine. Our results establish metabolite exchange interactions as a determinant of cellular aging and show that metabolically cooperating cells can shape the metabolic environment to extend their lifespan.


Assuntos
Longevidade , Saccharomyces cerevisiae , Saccharomyces cerevisiae/metabolismo , Metionina/metabolismo , Transdução de Sinais
2.
Cell ; 186(9): 2018-2034.e21, 2023 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-37080200

RESUMO

Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library in Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global protein expression is driven by a complex interplay of (1) general biological properties, including translation rate, protein turnover, the formation of protein complexes, growth rate, and genome architecture, followed by (2) functional properties, such as the connectivity of a protein in genetic, metabolic, and physical interaction networks. Moreover, we show that functional proteomics complements current gene annotation strategies through the assessment of proteome profile similarity, protein covariation, and reverse proteome profiling. Thus, our study reveals principles that govern protein expression and provides a genome-spanning resource for functional annotation.


Assuntos
Proteoma , Proteômica , Proteômica/métodos , Proteoma/metabolismo , Genômica/métodos , Genoma , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
3.
Nat Immunol ; 23(8): 1256-1272, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35902638

RESUMO

The recombination-activating genes (RAG) 1 and 2 are indispensable for diversifying the primary B cell receptor repertoire and pruning self-reactive clones via receptor editing in the bone marrow; however, the impact of RAG1/RAG2 on peripheral tolerance is unknown. Partial RAG deficiency (pRD) manifesting with late-onset immune dysregulation represents an 'experiment of nature' to explore this conundrum. By studying B cell development and subset-specific repertoires in pRD, we demonstrate that reduced RAG activity impinges on peripheral tolerance through the generation of a restricted primary B cell repertoire, persistent antigenic stimulation and an inflammatory milieu with elevated B cell-activating factor. This unique environment gradually provokes profound B cell dysregulation with widespread activation, remarkable extrafollicular maturation and persistence, expansion and somatic diversification of self-reactive clones. Through the model of pRD, we reveal a RAG-dependent 'domino effect' that impacts stringency of tolerance and B cell fate in the periphery.


Assuntos
Linfócitos B , Proteínas de Ligação a DNA , Proteínas de Homeodomínio , Proteínas Nucleares , Diferenciação Celular , Proteínas de Ligação a DNA/deficiência , Proteínas de Ligação a DNA/genética , Proteínas de Homeodomínio/genética , Humanos , Tolerância Imunológica , Contagem de Linfócitos , Proteínas Nucleares/deficiência
4.
Nature ; 630(8015): 149-157, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38778096

RESUMO

Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions and allows the generalizability of laboratory findings to be assessed. One notable discovery made in natural isolates of Saccharomyces cerevisiae is that aneuploidy-an imbalance in chromosome copy numbers-is frequent1,2 (around 20%), which seems to contradict the substantial fitness costs and transient nature of aneuploidy when it is engineered in the laboratory3-5. Here we generate a proteomic resource and merge it with genomic1 and transcriptomic6 data for 796 euploid and aneuploid natural isolates. We find that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins-especially subunits of protein complexes-show reduced expression, but the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage compensated, and average protein levels are shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and shows the utility of exploiting the natural diversity of species to attain generalizable molecular insights into complex biological processes.


Assuntos
Aneuploidia , Complexo de Endopeptidases do Proteassoma , Proteólise , Proteoma , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Mecanismo Genético de Compensação de Dose , Variação Genética , Complexo de Endopeptidases do Proteassoma/metabolismo , Complexo de Endopeptidases do Proteassoma/genética , Proteoma/metabolismo , Proteoma/genética , Proteômica , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Ubiquitinação , Perfilação da Expressão Gênica , Genômica
5.
Circulation ; 2024 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-39286890

RESUMO

BACKGROUND: The European Chronic Thromboembolic Pulmonary Hypertension registry (CTEPH), conducted between 2007 and 2012, reported the major impact of pulmonary endarterectomy (PEA) on the long-term survival of patients with CTEPH. Since then, 2 additional treatments for inoperable CTEPH have become available: balloon pulmonary angioplasty (BPA), and an approved oral drug therapy with the guanylate cyclase stimulator riociguat. The current registry aimed to evaluate the effect of these new therapeutic approaches in a worldwide context. METHODS: Participation in this international global registry included 34 centers in 20 countries. Between February 2015 and September 2016, 1009 newly diagnosed, consecutive patients were included and followed until September 2019. RESULTS: Overall, 605 patients (60%) underwent PEA and 185 (18%) underwent BPA; 76% of the 219 remaining patients not receiving mechanical intervention (ie, neither PEA nor BPA) were treated with pulmonary hypertension drugs. Oof patients undergoing PEA and BPA, 38% and 78% also received drugs for pulmonary hypertension, respectively. Median age at diagnosis was higher in the BPA and No PEA/BPA groups than in the PEA group: 66 and 69, respectively, versus 60 years. Pulmonary vascular resistance (PVR) was similar in all groups, with an average of 643 dynes/(s·cm-5). During an observation period (>3 years; ≤5.6 years), death was reported in 7%, 11%, and 27% of patients treated by PEA and BPA, and those receiving no mechanical intervention (P<0.001). In Kaplan-Meier analysis, 3-year survival was 94%, 92%, and 71% in the 3 groups, respectively. PEA 3-year survival improved by 5% from that observed between 2007 and 2012. There was no survival difference in patients receiving vitamin K antagonists and non-vitamin K oral anticoagulants (P=0.756). In Cox regression, reduced mortality was associated with: PEA and BPA in the global cohort; history of venous thromboembolism and lower PVR in the PEA group; lower right atrial pressure in the BPA group; and use of pulmonary hypertension drugs, oxygen therapy, and lower right atrial pressure, as well as functional class in the group receiving no mechanical intervention. CONCLUSIONS: This second international CTEPH registry reveals important improvement in patient survival since the introduction of BPA and an approved drug for pulmonary hypertension. The type of anticoagulation regimen did not influence survival. REGISTRATION: URL https://clinicaltrials.gov; Unique identifier: NCT02656238.

6.
PLoS Biol ; 20(12): e3001912, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36455053

RESUMO

The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1). Hsu1p acts as a homocysteine synthase and allows the cells to substitute for Met17p by reassimilating hydrosulfide ions leaked from met17Δ cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity to overcome sulfur limitation.


Assuntos
Cisteína Sintase , Metionina , Saccharomyces cerevisiae , Cisteína/metabolismo , Cisteína Sintase/genética , Cisteína Sintase/metabolismo , Metionina/metabolismo , Proteômica , Racemetionina , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Enxofre/metabolismo
7.
Eur Respir J ; 2024 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-39209473

RESUMO

Chronic thromboembolic pulmonary hypertension is a complication of pulmonary embolism and a treatable cause of pulmonary hypertension. The pathology is a unique combination of mechanical obstruction due to failure of clot resolution, and a variable degree of microvascular disease, that both contribute to pulmonary vascular resistance. Accordingly, multiple treatments have been developed to target the disease components. However, accurate diagnosis is often delayed. Evaluation includes high-quality imaging modalities, necessary for disease confirmation and for appropriate treatment planning. All patients with chronic thromboembolic pulmonary disease, and especially those with pulmonary hypertension, should be referred to expert centres for multidisciplinary team decision on treatment. The first decision remains assessment of operability, and the best improvement in symptoms and survival is achieved by the mechanical therapies, pulmonary endarterectomy and balloon pulmonary angioplasty. With the advances in multimodal therapies, excellent outcomes can be achieved with 3-year survival of >90%.

8.
PLoS Biol ; 19(12): e3001468, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34860829

RESUMO

The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken-egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a "metabolism first" theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network.


Assuntos
Cisteína/metabolismo , Ferro/metabolismo , Ribosemonofosfatos/metabolismo , Aminoácidos/metabolismo , Catálise , Cisteína/química , Evolução Molecular , Glucose/metabolismo , Glicólise/fisiologia , Ferro/química , Espectroscopia de Ressonância Magnética/métodos , Redes e Vias Metabólicas/fisiologia , Origem da Vida , Via de Pentose Fosfato/genética , Via de Pentose Fosfato/fisiologia
9.
Thromb J ; 22(1): 42, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38773510

RESUMO

BACKGROUND: This study aimed to evaluate the association of antiphospholipid antibodies (aPL) and conventional markers of coagulation with ischemic and bleeding risk in patients with atrial fibrillation (AF) undergoing percutaneous coronary intervention (PCI). METHODS: In this prospective two-center observational cohort study, patients with AF and an indication for oral anticoagulation (OAC) were enrolled after PCI. Blood was drawn on day 1-3 after PCI. Dilute Russell's viper venom time was used to determine lupus anticoagulant (LA) in OAC-free plasma. Anti-cardiolipin (aCL) IgG, IgM, and anti-ß2-Glycoprotein 1 (aß2GP1) IgG were analyzed by enzyme-linked immunosorbent assay (ELISA). Fibrinogen (FIB), d-dimer, and prothrombin fragment 1 and 2 (PF 1 + 2) were measured in citrated plasma. The primary ischemic outcome was time to major adverse cardiovascular events (MACE; death, myocardial infarction, or stroke) assessed at 6 months. Bleeding was defined according to International Society on Thrombosis and Haemostasis. RESULTS: 158 patients were enrolled between May 2020 and May 2021 on day 1-3 after PCI. The median age was 78 years (interquartile range [IQR] 72-82), 111 (70%) were male, and 39 (25%) presented with acute coronary syndrome. D-dimer was elevated in 74 (47%) patients, FIB was increased in 40 (25%) and PF1 + 2 in 68 (43%) patients. 32 (20%) patients had ≥ 1 antiphospholipid antibody elevated (aPL; LA: 19 [12%], aCL: 14 [9%], aß2GP1: 2 [1%]). The presence of aPL was neither significantly associated with MACE (HR 1.46, 95% CI [0.39-5.49], p = 0.579), nor bleeding (HR 1.07 [0.30-3.84], p = 0.917). Elevated d-dimer was significantly associated with higher risk for MACE (HR 5.06 [1.09-23.41], p = 0.038) and major bleeding (HR 7.04 [1.58-31.47], p = 0.011). Elevated D-dimer increased the predictive capacity of HAS-BLED for major bleedings (HAS-BLED: AUC 0.71 [0.60-0.83] vs. HAS-BLED + d-dimer: AUC 0.79 [0.70-0.88]; p = 0.025). Increased levels of FIB were associated with higher risk for MACE (HR 3.65 [1.11-11.96], p = 0.033). CONCLUSION: Biomarkers of coagulation might be suitable to assess ischemic and bleeding risk in patients with AF following PCI.

10.
Br J Anaesth ; 2024 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-38177005

RESUMO

BACKGROUND: Anaesthesia contributes substantially to the environmental impact of healthcare. To reduce the ecological footprint of anaesthesia, a set of sustainability interventions was implemented in the University Hospital Zurich, Switzerland. This study evaluates the environmental and economic implications of these interventions. METHODS: This was a single-centre retrospective observational study. We analysed the environmental impact and financial implications of changes in sevoflurane, desflurane, propofol, and plastic consumption over 2 yr (April 2021 to March 2023). The study included pre-implementation, implementation, and post-implementation phases. RESULTS: After implementation of sustainability measures, desflurane use was eliminated, there was a decrease in the consumption of sevoflurane from a median (inter-quartile range) of 25 (14-39) ml per case to 11 (6-22) ml per case (P<0.0001). Propofol consumption increased from 250 (150-721) mg per case to 743 (370-1284) mg per case (P<0.0001). Use of plastics changed: in the first quarter analysed, two or more infusion syringes were used in 62% of cases, compared with 74% of cases in the last quarter (P<0.0001). Two or more infusion lines were used in 58% of cases in the first quarter analysed, compared with 68% of cases in the last quarter (P<0.0001). This resulted in an 81% reduction in overall environmental impact from 3 (0-7) to 1 (0-3) CO2 equivalents in kg per case (P<0.0001). The costs during the final study phase were 11% lower compared with those in the initial phase: from 25 (13-41) to 21 (14-31) CHF (Swiss francs) per case (P<0.0001). CONCLUSIONS: Implementing sustainable anaesthesia interventions can significantly reduce the environmental impact and cost of anaesthesia.

11.
J Thromb Thrombolysis ; 57(3): 361-369, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38347374

RESUMO

High on-clopidogrel platelet reactivity (HPR) associates with ischemic risk in patients after percutaneous intervention (PCI). This study aimed to evaluate the association of HPR as assessed by multiple electrode aggregometry (MEA) with ischemic, thromboembolic, and bleeding risk in patients with atrial fibrillation (AF) undergoing PCI. Patients with AF and an indication for oral anticoagulation (OAC) were included in this prospective cohort study on day 1-3 after PCI. Platelet aggregation [U] was analyzed by MEA. HPR and low platelet reactivity (LPR) were defined as ADP-induced aggregation ≥ 46 U and ≤ 18 U, respectively. TRAP-6-induced aggregation reference was 94-156 U. The primary outcome was time to all-cause death, myocardial infarction, or stroke at 6 months. The secondary outcome was time to non-major clinically relevant bleedings or major bleedings. 159 patients were enrolled between May 2020 and May 2021. The median age was 78 years (interquartile range 72-82) and 111 (70%) were male. Median ADP- and TRAP-induced aggregation were 12 (6-17) and 49 (35-68) U, respectively. 147 (93%) patients had a low overall aggregability. HPR was detected in 2 patients (1%) and 125 (79%) had LPR. ADP-induced aggregation did not significantly associate with the primary outcome (r = 0.081, p = 0.309) but correlated inversely with bleeding risk (r = - 0.201, p = 0.011). HPR status as assessed by MEA among patients with AF after PCI was rare and overall aggregability was low. Conventional cut-off values for HPR might be inappropriate for these patients. ADP-induced aggregation might be helpful to identify patients at risk for bleeding.


Assuntos
Fibrilação Atrial , Fragmentos de Peptídeos , Intervenção Coronária Percutânea , Humanos , Masculino , Idoso , Feminino , Clopidogrel/farmacologia , Agregação Plaquetária , Inibidores da Agregação Plaquetária/efeitos adversos , Fibrilação Atrial/tratamento farmacológico , Fibrilação Atrial/complicações , Intervenção Coronária Percutânea/efeitos adversos , Estudos Prospectivos , Projetos Piloto , Plaquetas , Hemorragia/induzido quimicamente , Resultado do Tratamento
12.
Eur Heart J ; 44(29): 2659-2671, 2023 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-37470202

RESUMO

The current treatment algorithm for chronic thromboembolic pulmonary hypertension (CTEPH) as depicted in the 2022 European Society of Cardiology (ESC)/European Respiratory Society (ERS) guidelines on the diagnosis and treatment of pulmonary hypertension (PH) includes a multimodal approach of combinations of pulmonary endarterectomy (PEA), balloon pulmonary angioplasty (BPA) and medical therapies to target major vessel pulmonary vascular lesions, and microvasculopathy. Today, BPA of >1700 patients has been reported in the literature from centers in Asia, the US, and also Europe; many more patients have been treated outside literature reports. As BPA becomes part of routine care of patients with CTEPH, benchmarks for safe and effective care delivery become increasingly important. In light of this development, the ESC Working Group on Pulmonary Circulation and Right Ventricular Function has decided to publish a document that helps standardize BPA to meet the need of uniformity in patient selection, procedural planning, technical approach, materials and devices, treatment goals, complications including their management, and patient follow-up, thus complementing the guidelines. Delphi methodology was utilized for statements that were not evidence based. First, an anatomical nomenclature and a description of vascular lesions are provided. Second, treatment goals and definitions of complete BPA are outlined. Third, definitions of complications are presented which may be the basis for a standardized reporting in studies involving BPA. The document is intended to serve as a companion to the official ESC/ERS guidelines.


Assuntos
Angioplastia com Balão , Cardiologia , Hipertensão Pulmonar , Embolia Pulmonar , Humanos , Hipertensão Pulmonar/etiologia , Hipertensão Pulmonar/terapia , Hipertensão Pulmonar/diagnóstico , Embolia Pulmonar/complicações , Embolia Pulmonar/terapia , Embolia Pulmonar/diagnóstico , Circulação Pulmonar , Função Ventricular Direita , Angioplastia com Balão/métodos , Artéria Pulmonar/cirurgia , Doença Crônica
13.
J Allergy Clin Immunol ; 151(4): 922-925, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36463978

RESUMO

BACKGROUND: Although previous studies described the production of IgG antibodies in a subgroup of patients with common variable immunodeficiency (CVID) following messenger RNA vaccinations with BNT162b2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (CVID responders), the functionality of these antibodies in terms of avidity as measured by the dissociation rate constant (kdis) and the antibody response to booster immunization has not been studied. OBJECTIVE: We sought to analyze in CVID responders and healthy individuals, the avidity of anti-SARS-CoV-2 serum antibodies and their neutralization capacity as measured by surrogate virus-neutralizing antibodies in addition to IgG-, IgM-, and IgA-antibody levels and the response of circulating (peripheral blood) follicular T-helper cells after a third vaccination with BNT162b2 SARS-CoV-2 messenger RNA vaccine. METHODS: Binding IgG, IgA, and IgM serum levels were analyzed by ELISA in patients with CVID responding to the primary vaccination (CVID responders, n = 10) and healthy controls (n = 41). The binding avidity of anti-spike antibodies was investigated using biolayer interferometry in combination with biotin-labeled receptor-binding-domain of SARS-CoV-2 spike protein and streptavidin-labeled sensors. Antigen-specific recall T-cell responses were assessed by measuring activation-induced markers by flow cytometry. RESULTS: After the third vaccination with BNT162b2, IgG-, IgM-, and IgA-antibody levels, surrogate virus-neutralizing antibody levels, and antibody avidity were lower in CVID responders than in healthy controls. In contrast, anti-SARS-CoV-2 spike protein avidity was comparable in CVID responders and healthy individuals following primary vaccination. Follicular T-helper cell response to booster vaccination in CVID responders was significantly reduced when compared with that in healthy individuals. CONCLUSIONS: Impaired affinity maturation during booster response provides new insight into CVID pathophysiology.


Assuntos
COVID-19 , Imunodeficiência de Variável Comum , Humanos , Vacina BNT162 , Formação de Anticorpos , COVID-19/prevenção & controle , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus , Vacinas contra COVID-19 , Anticorpos Bloqueadores , Anticorpos Antivirais , Imunoglobulina A , Imunoglobulina M
14.
Proteomics ; : e2200220, 2023 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-38012370

RESUMO

How cells regulate protein levels is a central question of biology. Over the past decades, molecular biology research has provided profound insights into the mechanisms and the molecular machinery governing each step of the gene expression process, from transcription to protein degradation. Recent advances in transcriptomics and proteomics have complemented our understanding of these fundamental cellular processes with a quantitative, systems-level perspective. Multi-omic studies revealed significant quantitative, kinetic and functional differences between the genome, transcriptome and proteome. While protein levels often correlate with mRNA levels, quantitative investigations have demonstrated a substantial impact of translation and protein degradation on protein expression control. In addition, protein-level regulation appears to play a crucial role in buffering protein abundances against undesirable mRNA expression variation. These findings have practical implications for many fields, including gene function prediction and precision medicine.

15.
Proteomics ; 23(7-8): e2200013, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36349817

RESUMO

There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.


Assuntos
Proteômica , Biologia de Sistemas , Humanos , Proteômica/métodos , Proteínas/análise , Espectrometria de Massas/métodos , Software
16.
Kidney Int ; 104(1): 74-89, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-36924892

RESUMO

Previous studies have identified a unique Treg population, which expresses the Th17 characteristic transcription factor RORγt. These RORγt+ Tregs possess enhanced immunosuppressive capacity, which endows them with great therapeutic potential. However, as a caveat, they are also capable of secreting pro-inflammatory IL-17A. Since the sum function of RORγt+ Tregs in glomerulonephritis (GN) remains unknown, we studied the effects of their absence. Purified CD4+ T cell populations, containing or lacking RORγt+ Tregs, were transferred into immunocompromised RAG1 knockout mice and the nephrotoxic nephritis model of GN was induced. Absence of RORγt+ Tregs significantly aggravated kidney injury, demonstrating overall kidney-protective properties. Analyses of immune responses showed that RORγt+ Tregs were broadly immunosuppressive with no preference for a particular type of T cell response. Further characterization revealed a distinct functional and transcriptional profile, including enhanced production of IL-10. Expression of the chemokine receptor CCR6 marked a particularly potent subset, whose absence significantly worsened GN. As an underlying mechanism, we found that chemokine CCL20 acting through receptor CCR6 signaling mediated expansion and activation of RORγt+ Tregs. Finally, we also detected an increase of CCR6+ Tregs in kidney biopsies, as well as enhanced secretion of chemokine CCL20 in 21 patients with anti-neutrophil cytoplasmic antibody associated GN compared to that of 31 healthy living donors, indicating clinical relevance. Thus, our data characterize RORγt+ Tregs as anti-inflammatory mediators of GN and identify them as promising target for Treg directed therapies.


Assuntos
Glomerulonefrite , Membro 3 do Grupo F da Subfamília 1 de Receptores Nucleares , Camundongos , Animais , Membro 3 do Grupo F da Subfamília 1 de Receptores Nucleares/genética , Membro 3 do Grupo F da Subfamília 1 de Receptores Nucleares/metabolismo , Linfócitos T Reguladores , Quimiocina CCL20/genética , Quimiocina CCL20/metabolismo , Rim/patologia , Camundongos Knockout , Células Th17 , Receptores CCR6/genética , Receptores CCR6/metabolismo
17.
Nat Methods ; 17(1): 41-44, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31768060

RESUMO

We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.


Assuntos
Ensaios de Triagem em Larga Escala/métodos , Espectrometria de Massas/métodos , Redes Neurais de Computação , Proteoma/análise , Proteômica/métodos , Software , Zea mays/metabolismo , Células HeLa , Humanos , Especificidade da Espécie
18.
Crit Care ; 27(1): 254, 2023 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-37381008

RESUMO

Medical technology innovation has improved patient monitoring in perioperative and intensive care medicine and continuous improvement in the technology is now a central focus in this field. Because data density increases with the number of parameters captured by patient-monitoring devices, its interpretation has become more challenging. Therefore, it is necessary to support clinicians in managing information overload while improving their awareness and understanding about the patient's health status. Patient monitoring has almost exclusively operated on the single-sensor-single-indicator principle-a technology-centered way of presenting data in which specific parameters are measured and displayed individually as separate numbers and waves. An alternative is user-centered medical visualization technology, which integrates multiple pieces of information (e.g., vital signs), derived from multiple sensors into a single indicator-an avatar-based visualization-that is a meaningful representation of the real-world situation. Data are presented as changing shapes, colors, and animation frequencies, which can be perceived, integrated, and interpreted much more efficiently than other formats (e.g., numbers). The beneficial effects of these technologies have been confirmed in computer-based simulation studies; visualization technologies improved clinicians' situation awareness by helping them effectively perceive and verbalize the underlying medical issue, while improving diagnostic confidence and reducing workload. This review presents an overview of the scientific results and the evidence for the validity of these technologies.


Assuntos
Unidades de Terapia Intensiva , Monitorização Fisiológica , Tecnologia , Humanos , Monitorização Fisiológica/tendências , Tecnologia/tendências , Segurança do Paciente , Medicina Perioperatória , Conscientização
19.
J Thromb Thrombolysis ; 55(1): 134-140, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36344849

RESUMO

Results from multiple electrode aggregometry (MEA) may vary according to pre-analytic factors. This study aimed to analyze the association of time from blood draw to MEA in patients undergoing percutaneous coronary intervention (PCI). In this observational single-center cohort study, platelet aggregation (aggregation units, U) was quantified by MEA (Multiplate Analyzer) after stimulation with adenosine diphosphate (ADP; final concentration [Fc] 6.4 µM), thrombin receptor activating peptide (TRAP; Fc 32 µM), or arachidonic acid (AA; Fc 0.5 mM) in patients treated with ASA and clopidogrel following PCI. High on-clopidogrel platelet reactivity (HPR) was defined as ADP-induced platelet aggregation ≥ 46 U. The manufacturer recommends performing the analysis within 30-180 min after blood draw. Patients were grouped according to the time from blood draw to MEA: 30-180 min, < 30 min, or > 180 min. Platelet function of 273 patients with coronary artery disease undergoing PCI with dual antiplatelet therapy was analyzed. The median age was 72 years (interquartile range, IQR 62-79) and 179 (66%) were male. Median ADP-, TRAP-, and AA-induced aggregation was 25 (IQR 18-36) U, 79 (IQR 63-96) U, and 12 (IQR 7-18) U, respectively. For those analyzed within 30-180 min from blood draw, no significant correlation of time from blood draw to MEA was observed 1) ADP (r = - 0.04, p = 0.51); 2) TRAP (r = - 0.06, p = 0.32); 3) AA (r = - 0.03, p = 0.67). In patients undergoing percutaneous coronary intervention and treated with dual antiplatelet therapy, the time from blood draw to multiple electrode aggregometry does not correlate with ADP- induced aggregation when the measurement occurred within the recommended time interval of 30-180 min after blood draw.


Assuntos
Intervenção Coronária Percutânea , Inibidores da Agregação Plaquetária , Humanos , Masculino , Idoso , Feminino , Inibidores da Agregação Plaquetária/farmacologia , Inibidores da Agregação Plaquetária/uso terapêutico , Clopidogrel/farmacologia , Ticlopidina , Estudos de Coortes , Plaquetas , Agregação Plaquetária , Testes de Função Plaquetária/métodos , Difosfato de Adenosina/farmacologia , Eletrodos
20.
Artigo em Inglês | MEDLINE | ID: mdl-37643729

RESUMO

BACKGROUND: Balloon pulmonary angioplasty (BPA) is a promising interventional treatment for inoperable chronic thromboembolic pulmonary hypertension (CTEPH). Evidence in favor of BPA is growing, but long-term data remain scarce. The Cambridge Pulmonary Hypertension Outcome Review (CAMPHOR) is validated for the assessment of patients with pulmonary hypertension within three domains: symptoms, activity, and quality of life (QoL). The aim of the present study was to evaluate the long-term effects of BPA on these domains in patients with inoperable CTEPH. METHODS: Between March 2014 and August 2019, technically inoperable patients with target lesions for BPA were included in this prospective, observational study. CAMPHOR scores were compared between baseline (before the first BPA) and 6 months after the last intervention and also for scores assessed at annual follow-ups. RESULTS: A total of 152 patients had completed a full series of BPA interventions and a 28 (interquartile range [IQR]: 26-32) week follow-up. Further follow-up assessments including the CAMPHOR score were performed 96 (IQR: 70-117) weeks, 178 (IQR: 156-200) weeks, and 250 (IQR: 237-275) weeks after the last intervention. From baseline to the last follow-up, CAMPHOR scores for symptoms, activity, and QoL improved from 9 (IQR: 6-14) to 3 (IQR: 0-9) (p < 0.001), 8 (IQR: 5-12) to 4 (IQR: 2-8) (p < 0.001), and 5 (IQR: 2-9) to 1 (IQR: 0-5) (p < 0.001). CONCLUSION: BPA leads to long-lasting, significant improvement of symptoms, physical capacity, and QoL in inoperable CTEPH patients.

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