Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

Messner, Christoph B.; Demichev, Vadim; Wendisch, Daniel; Michalick, Laura; White, Matthew; Freiwald, Anja; Textoris-Taube, Kathrin; Vernardis, Spyros; Egger, Anna-Sophia; Kreidl, Marco; Ludwig, Daniela; Kilian, Christiane; Agostini, Federica; Zelezniak, Aleksej; Thibeault, Charlotte; Pfeiffer, Moritz; Hippenstiel, Stefan; Hocke, Andreas C.; Kalle, Christof von; Campbell, Archie; Hayward, Caroline; Porteous, David J.; Marioni, Riccardo E.; Langenberg, Claudia; Lilley, Kathryn S.; Kuebler, Wolfgang M.; Mülleder, Michael; Drosten, Christian; Suttorp, Norbert; Witzenrath, Martin; Kurth, Florian; Sander, Leif Erik; Ralser, Markus

doi:10.1016/j.cels.2020.05.012

Cited by 466 publications

(732 citation statements)

References 100 publications

(137 reference statements)

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“…As a result, eight upstream regulators that regulate 28 DEPs were discovered; of these, six regulators were increased and remaining two regulators were decreased. One of the most significant regulators is IL-6, and the immune response triggered by it is activated in severe COVID-19 patients, as reported in previous publications [5,6,23,24]. In addition to IL-6, IL-1B and tumor necrosis factor (TNF) are the major components of the cytokine storm commonly observed in severe COVID-19 patients [25].…”

Section: Functional Characteristics Distinguish the Severe Covid-19 Gmentioning

confidence: 82%

“…Furthermore, these MS-based proteomic workflows for biomarker discovery and profiling are well established [3]. However, only two studies have presently applied proteomics to the serum of COVID-19 patients with moderate proteome depth [5,6]. Therefore, detailed understanding of the in-depth proteome of plasma or serum is necessary to develop prognostic or predictive protein markers.…”

Section: Introductionmentioning

confidence: 99%

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In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients

Park

Kim

et al. 2020

Preprint

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over ten million patients worldwide. Although most coronavirus disease 2019 (COVID-19) patients have a good prognosis, some develop severe illness. Markers that define disease severity or predict clinical outcome need to be urgently developed as the mortality rate in critical cases is approximately 61.5%. In the present study, we performed in-depth proteome profiling of undepleted plasma from eight COVID-19 patients. Quantitative proteomic analysis using the BoxCar method revealed that 91 out of 1,222 quantified proteins were differentially expressed depending on the severity of COVID-19. Importantly, we found 76 proteins, previously not reported, which could be novel prognostic biomarker candidates. Our plasma proteome signatures captured the host response to SARS-CoV-2 infection, thereby highlighting the role of neutrophil activation, complement activation, platelet function, and T cell suppression as well as proinflammatory factors upstream and downstream of interleukin-6, interleukin-1B, and tumor necrosis factor. Consequently, this study supports the development of blood biomarkers and potential therapeutic targets to aid clinical decision-making and subsequently improve prognosis of COVID-19.

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Section: Functional Characteristics Distinguish the Severe Covid-19 Gmentioning

confidence: 82%

Section: Introductionmentioning

confidence: 99%

In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients

Park

Kim

et al. 2020

Preprint

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“…Severe cases are marked by progression into the lower airways and alveoli. Here, it manifests as an atypical form of acute respiratory distress syndrome (ARDS) characterized by good lung compliance measurements 7,8 , and elevated levels of coagulation markers such as D-dimers 9 , and pro-inflammatory markers in the blood 10 . Autopsy reports show numerous microvascular thrombi in the lungs of deceased patients together with evidence of the intracellular presence of the virus in vascular cells 11,12 .…”

Section: Introductionmentioning

confidence: 99%

Rapid endothelial infection, endothelialitis and vascular damage characterise SARS-CoV-2 infection in a human lung-on-chip model

Thacker

Sharma

Dhar

et al. 2020

Preprint

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Background: Severe manifestations of COVID-19 include hypercoagulopathies and systemic endothelialitis. The underlying dynamics of vascular damage, and whether it is a direct consequence of endothelial infection or an indirect consequence of immune cell-mediated cytokine storms is unknown. This is in part because in vitro infection models are typically monocultures of epithelial cells or fail to recapitulate vascular physiology. Methods: We establish a vascularised lung-on-chip infection model consisting of a co-culture of primary human alveolar epithelial (epithelial) cells and human lung microvascular endothelial (endothelial) cells, with the optional addition of CD14+ macrophages to the epithelial side. This model was used to study the dynamics of viral replication and host responses to a low dose infection of SARS-CoV-2 of the epithelial layer. Findings: SARS-CoV-2 inoculation does not lead to a productive amplification of infectious virions. However, both genomic and antisense viral RNA can be found in endothelial cells within 1-day post infection (dpi) and persist upnto 3 dpi. This generates an NF-KB-mediated inflammatory response typified by IL-6 secretion and signalling coupled with a weak antiviral interferon response, even in the absence of immune cells. Endothelial inflammation leads to a progressive loss of barrier integrity, a subset of cells also shows a transient hyperplasic phenotype. Administration of Tocilizumab slows the loss of barrier integrity but does not reduce the occurrence of the latter. Interpretation: Endothelial infection can occur through basolateral transmission from infected epithelial cells at the air-liquid interface. SARS-CoV-2 mediated inflammation occurs despite the lack of rapid viral replication and is transient in epithelial cells but persistent in endothelial cells. Infected endothelial cells might be a key source of circulating IL-6 in COVID-19 patients. Vascular damage occurs independently of immune-cell mediated cytokine storms, whose effect would only exacerbate the damage. Funding: Core support from EPFL.

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“…Automatization and 96-well plate based sample processing allow the preparation of hundreds of samples per day and reduce batch effects, that otherwise are a challenge in large-scale and longitudinal experiments [6][7][8][9][10][11][12] . Further, fast, efficient and robust chromatographic separations have been achieved by replacing nanoflow LC, as traditionally used in proteomics 13,14 , with setups that use higher flow-rates.…”

Section: Introductionmentioning

confidence: 99%

“…More recently, we have introduced proteome experiments that make use of high-flow liquid chromatography (800 µl/min). In 5 minute chromatographic gradients, these allowed up to 180 proteome injections/day on a single LC-MS instrument, while increasing robustness, cost-efficacy and quantification precision in longitudinal proteome experiments 10 . In addition, the development of algorithms that enable the efficient deconvolution of complex spectra as resulting from fast chromatographic measurements is still an ongoing process, but several major steps have been achieved recently, and have increased proteomic depth as well as quantification precision in conjunction with the fast chromatographic experiments [20][21][22][23] .…”

Section: Introductionmentioning

confidence: 99%

Scanning SWATH acquisition enables high-throughput proteomics with chromatographic gradients as fast as 30 seconds

Messner

Demichev

Bloomfield

et al. 2019

Preprint

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Rapidly emerging applications in data-driven biology and personalised medicine call for the development of fast and reliable proteomic methods. However, the use of fast chromatographic gradients is limited by the mass spectrometers' sampling rate and signal interferences. Here we present scanningSWATH, a data-independent acquisition method, in which the DIA-typical stepwise windowed acquisition is replaced by continuous scanning with the first quadrupole.ScanningSWATH enables ultra-fast duty cycles as well as to assign precursor masses to the MS2 fragment traces. Furthermore, we have implemented the support for scanningSWATH in DIA-NN, a fully-automated software suite designed to deconvolute fast DIA experiments, which corrects for signal interferences. We show that the combination of scanningSWATH and DIA-NN enables the efficient application of high-flow liquid chromatography (800 µL/min flow rate) to proteomics. High-flow scanningSWATH increases proteomic sample throughput to the minute-scale, while the use of high-flow chromatography hardware improves reliability and robustness. Benchmarking on yeast and human cell lysates, we demonstrate that the proteomic depth achieved with five-minute high-flow scanningSWATH gradients is comparable to that obtained with several times slower nano-and microflow chromatographic gradients, even if compared to most recent studies that used microflow-SWATH or Evosep-DIA methods. The combination of scanningSWATH, advanced data processing, and industry-standard high-flow LC hardware paves a way for a new generation of cheaper and highly consistent proteomic methods. These allow the recording of hundreds of precise quantitative proteomes per day on a single instrument.

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Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

Cited by 466 publications

References 100 publications

In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients

In-depth blood proteome profiling analysis revealed distinct functional characteristics of plasma proteins between severe and non-severe COVID-19 patients

Rapid endothelial infection, endothelialitis and vascular damage characterise SARS-CoV-2 infection in a human lung-on-chip model

Scanning SWATH acquisition enables high-throughput proteomics with chromatographic gradients as fast as 30 seconds

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