Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment

Neutrophils rapidly respond to inflammation and infection, but to which degree their functional trajectories after mobilization from the bone marrow are shaped within the circulation remains vague. Experimental limitations have so far hampered neutrophil research in human disease. Here, using innovative fixation and single-cell-based toolsets, we profile human and murine neutrophil transcriptomes and proteomes during steady state and bacterial infection. We find that peripheral priming of circulating neutrophils leads to dynamic shifts dominated by conserved up-regulation of antimicrobial genes across neutrophil substates, facilitating pathogen containment. We show the TLR4/NF-κB signaling-dependent up-regulation of canonical neutrophil activation markers like CD177/NB-1 during acute inflammation, resulting in functional shifts in vivo. Blocking de novo RNA synthesis in circulating neutrophils abrogates these plastic shifts and prevents the adaptation of antibacterial neutrophil programs by up-regulation of distinct effector molecules upon infection. These data underline transcriptional plasticity as a relevant mechanism of functional neutrophil reprogramming during acute infection to foster bacterial containment within the circulation.

Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation

Maladaptive, non-resolving inflammation contributes to chronic inflammatory diseases such as atherosclerosis. Because macrophages remove necrotic cells, defective macrophage programs can promote chronic inflammation with persistent tissue injury. Here, we investigated the mechanisms sustaining vascular macrophages. Intravital imaging revealed a spatiotemporal macrophage niche across vascular beds alongside mural cells (MCs)-pericytes and smooth muscle cells. Single-cell transcriptomics, co-culture, and genetic deletion experiments revealed MC-derived expression of the chemokines CCL2 and MIF, which actively preserved macrophage survival and their homeostatic functions. In atherosclerosis, this positioned macrophages in viable plaque areas, away from the necrotic core, and maintained a homeostatic macrophage phenotype. Disruption of this MC-macrophage unit via MC-specific deletion of these chemokines triggered detrimental macrophage relocalizing, exacerbated plaque necrosis, inflammation, and atheroprogression. In line, CCL2 inhibition at advanced stages of atherosclerosis showed detrimental effects. This work presents a MC-driven safeguard toward maintaining the homeostatic vascular macrophage niche.

Self-sustaining IL-8 loops drive a prothrombotic neutrophil phenotype in severe COVID-19

Neutrophils provide a critical line of defense in immune responses to various pathogens, inflicting self-damage upon transition to a hyperactivated, procoagulant state. Recent work has highlighted proinflammatory neutrophil phenotypes contributing to lung injury and acute respiratory distress syndrome (ARDS) in patients with coronavirus disease 2019 (COVID-19). Here, we use state-of-the art mass spectrometry-based proteomics and transcriptomic and correlative analyses as well as functional in vitro and in vivo studies to dissect how neutrophils contribute to the progression to severe COVID-19. We identify a reinforcing loop of both systemic and neutrophil intrinsic IL-8 (CXCL8/IL-8) dysregulation, which initiates and perpetuates neutrophil-driven immunopathology. This positive feedback loop of systemic and neutrophil autocrine IL-8 production leads to an activated, prothrombotic neutrophil phenotype characterized by degranulation and neutrophil extracellular trap (NET) formation. In severe COVID-19, neutrophils directly initiate the coagulation and complement cascade, highlighting a link to the immunothrombotic state observed in these patients. Targeting the IL-8-CXCR-1/-2 axis interferes with this vicious cycle and attenuates neutrophil activation, degranulation, NETosis, and IL-8 release. Finally, we show that blocking IL-8-like signaling reduces severe acute respiratory distress syndrome of coronavirus 2 (SARS-CoV-2) spike protein-induced, human ACE2-dependent pulmonary microthrombosis in mice. In summary, our data provide comprehensive insights into the activation mechanisms of neutrophils in COVID-19 and uncover a self-sustaining neutrophil-IL-8 axis as a promising therapeutic target in severe SARS-CoV-2 infection.

Vascular neutrophilic inflammation and immunothrombosis distinguish severe COVID-19 from influenza pneumonia

OBJECTIVE

Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can lead to severe pneumonia, but also thrombotic complications and non-pulmonary organ failure. Recent studies suggest intravascular neutrophil activation and subsequent immune cell-triggered immunothrombosis as a central pathomechanism linking the heterogenous clinical picture of coronavirus disease 2019 (COVID-19). We sought to study whether immunothrombosis is a pathognomonic factor in COVID-19 or a general feature of (viral) pneumonia, as well as to better understand its upstream regulation.

APPROACH AND RESULTS

By comparing histopathological specimens of SARS-CoV-2 with influenza-affected lungs, we show that vascular neutrophil recruitment, NETosis, and subsequent immunothrombosis are typical features of severe COVID-19, but less prominent in influenza pneumonia. Activated neutrophils were typically found in physical association with monocytes. To explore this further, we combined clinical data of COVID-19 cases with comprehensive immune cell phenotyping and bronchoalveolar lavage fluid scRNA-seq data. We show that a HLADRlow CD9low monocyte population expands in severe COVID-19, which releases neutrophil chemokines in the lungs, and might in turn explain neutrophil expansion and pulmonary recruitment in the late stages of severe COVID-19.

CONCLUSIONS

Our data underline an innate immune cell axis causing vascular inflammation and immunothrombosis in severe SARS-CoV-2 infection.

SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing

The MinION sequencer by Oxford Nanopore Technologies turns DNA and RNA sequencing into a routine task in biology laboratories or in field research. For downstream analysis it is required to have a sufficient amount of target reads. Especially prokaryotic or bacteriophagic sequencing samples can contain a significant amount of off-target sequences in the processed sample, stemming from human DNA/RNA contamination, insufficient rRNA depletion, or remaining DNA/RNA from other organisms (e.g. host organism from bacteriophage cultivation). Such impurity, contamination and off-targets (ICOs) block read capacity, requiring to sequence deeper. In comparison to second-generation sequencing, MinION sequencing allows to reuse its chip after a (partial) run. This allows further usage of the same chip with more sample, even after adjusting the library preparation to reduce ICOs. The earlier a sample's ICOs are detected, the better the sequencing chip can be conserved for future use. Here we present sequ-into, a low-resource and user-friendly cross-platform tool to detect ICO sequences from a predefined ICO database in samples early during a MinION sequencing run. The data provided by sequ-into empowers the user to quickly take action to preserve sample material and chip capacity. sequ-into is available from https://github.com/mjoppich/sequ-into.

From command-line bioinformatics to bioGUI

Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface only. Providing a graphical user interface (GUI) for bioinformatics applications is one step toward routinely making CL-only applications available to more scientists and, thus, toward a more effective interdisciplinary work. With our bioGUI framework we address two main problems of using CL bioinformatics applications: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using CL tools which, however, could well support them in their research. With bioGUI install modules and templates, installing and using CL tools is made possible for most scientists-even on Windows, due to bioGUI's support for Windows Subsystem for Linux. In addition, bioGUI templates can easily be created, making the bioGUI framework highly rewarding for developers. From the bioGUI repository it is possible to download, install and use bioinformatics tools with just a few clicks.

Using Context-Sensitive Text Mining to Identify miRNAs in Different Stages of Atherosclerosis

790 human and mouse micro-RNAs (miRNAs) are involved in diseases. More than 26,428 miRNA–gene interactions are annotated in humans and mice. Most of these interactions are posttranscriptional regulations: miRNAs bind to the messenger RNAs (mRNAs) of genes and induce their degradation, thereby reducing the gene expression of target genes. For atherosclerosis, 667 miRNA–gene interactions for 124 miRNAs and 343 genes have been identified and described in numerous publications. Some interactions were observed through high-throughput experiments, others were predicted using bioinformatic methods, and some were determined by targeted experiments. Several reviews collect knowledge on miRNA–gene interactions in (specific aspects of) atherosclerosis.

Here, we use our bioinformatics resource (atheMir) to give an overview of miRNA–gene interactions in the context of atherosclerosis. The interactions are based on public databases and context-based text mining of 28 million PubMed abstracts. The miRNA–gene interactions are obtained from more than 10,000 publications, of which more than 1,000 are in a cardiovascular disease context (266 in atherosclerosis). We discuss interesting miRNA–gene interactions in atherosclerosis, grouped by specific processes in different cell types and six phases of atherosclerotic progression. All evidence is referenced and easily accessible: Relevant interactions are provided by atheMir as supplementary tables for further evaluation and, for example, for the subsequent data analysis of high-throughput measurements as well as for the generation and validation of hypotheses. The atheMir approach has several advantages: (1) the evidence is easily accessible, (2) regulatory interactions are uniformly available for subsequent high-throughput data analysis, and (3) the resource can incrementally be updated with new findings.

Tryptophan usage by Helicobacter pylori differs among strains

Because of its association with severe gastric pathologies, including gastric cancer, Helicobacter pylori has been subject of research for more than 30 years. Its capacity to adapt and survive in the human stomach can be attributed to its genetic flexibility. Its natural competence and its capacity to turn genes on and off allows H. pylori to adapt rapidly to the changing conditions of its host. Because of its genetic variability, it is difficult to establish the uniqueness of each strain obtained from a human host. The methods considered to-date to deliver the best result for differentiation of strains are Rapid Amplification of Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis. While RAPD analysis is cost-effective, it requires a stable genome for its reliability. MLST and WGS are optimal for strain identification, however, they require analysis of data at the bioinformatics level. Using the StainFree method, which modifies tryptophan residues on proteins using 2, 2, 2, - trichloroethanol (TCE), we observed a strain specific pattern of tryptophan in 1D acrylamide gels. In order to establish the effectiveness of tryptophan fingerprinting for strain identification, we compared the graphic analysis of tryptophan-labelled bands in the gel images with MLST results. Based on this, we find that tryptophan banding patterns can be used as an alternative method for the differentiation of H. pylori strains. Furthermore, investigating the origin for these differences, we found that H. pylori strains alters the number and/or position of tryptophan present in several proteins at the genetic code level, with most exchanges taking place in membrane- and cation-binding proteins, which could be part of a novel response of H. pylori to host adaptation.

Determination of dichlorobenzidine-hemoglobin adducts by GC/MS-NCI

A method based on gas chromatography/mass spectrometry-negative ion chemical ionization detection (GC/MS-NCI) was developed for the determination of 3,3'-dichlorobenzidine (DCB)-hemoglobin adducts. Adducts were released from hemoglobin by mild alkaline hydrolysis and determined by GC/MS-NCI after extraction and derivatization with heptafluorobutyric anhydride (HFBA). 2,2'-DCB was used as internal standard and the recovery of the diarylamine derivatives in the overall procedure was 65-88%. The limit of detection attained was below 0.1 ng/g hemoglobin for DCB as well as for the metabolite N-acetyl-3,3'-dichlorobenzidine (acDCB). The method was shown to be linear up to 150 ng/g hemoglobin. In the NCI mass spectra of the HFB derivatives the dominant ion is (M-HF)-. Due to the presence of two chlorines in the diarylamines, the characteristic ratio of 1.5 for m/z 624 to 626 (for diHFB-DCB and diHFB-2,2'-DCB) and m/z 470 to 472 (for HFB-acDCB) can be observed and used for identification. The method was applied to the determination of DCB-hemoglobin adducts formed in young female Wistar rats after treatment for 4 weeks with 0.006%, 0.0012% or 0.00024% DCB via the drinking water. Two adducts were detectable by GC/MS-NCI after alkaline hydrolysis of hemoglobin samples, extraction and derivatization. The structure of these adducts could be assigned to DCB and acDCB by co-chromatography with the synthetic standards and by the presence of the characteristic ion (M-HF)-. Assessment of the time dependence of hemoglobin adduct formation during subchronic treatment with DCB revealed an increase in adduct levels during weeks 1-3. After this time adduct levels essentially remained constant. In hemoglobin samples isolated from animals treated for 4 weeks with DCB a dose-proportional increase in the total amount DCB- and acDCB-hemoglobin adducts from 8.1 ng DCB/g hemoglobin at 0.3 mg/kg body weight per day (0.00024% in drinking water) to 159.9 ng DCB/g hemoglobin at 5.8 mg/kg body weight per day (0.006% in drinking water) was observed. The ratio of the DCB adduct to the acDCB adduct was strongly dose dependent. At low DCB doses the acDCB- and DCB adducts were formed at similar levels, whereas at high DCB doses the DCB adduct was predominant.

Lack of bioavailability of dichlorobenzidine form diarylide azo pigments: molecular dosimetry for hemoglobin and DNA adducts

The hypothetical release of 3,3'-dichlorobenzidine (DCB) from two insoluble azo pigments and from a soluble azo dye was investigated in female Wistar rats for a 4 week treatment with 0.2% (w/w) Colour Index Pigment 13 (PY13) or 0.2% (w/w) Colour Index Pigment Yellow 17 (PY17) in the diet or 0.06% (w/v) Colour Index Direct Red 46 (DR46) in the drinking water. Steady-state DCB-hemoglobin adduct levels were determined by GC/MS with negative chemical ionization as well as DCB-DNA adduct levels in the liver by (32)P-postlabelling and compared with the respective adduct levels obtained in animals after treatment for 4 weeks with 0.00024, 0.0012 or 0.006% (w/v) DCB in the drinking water. A dose-proportional increase in adduct levels from 8.1 ng/g hemoglobin and 2.6 ng/g DNA (relative adduct level, RAL, 3.3x10(-9)) to 160 ng/g hemoglobin and 45.4 ng/g DNA (RAL 56.1x10(-9)) was observed in the DCB-treated rats. In rats treated with DR46 total adduct levels of 17.7 ng/g hemoglobin and 5.2 ng/g DNA (RAL 6.4x10(-9))were determined. No hemoglobin of DNA adducts were found in rats treated with PY17 in the diet, at a limit of detection of 0.1 ng/g hemoglobin and 0.08 ng/g DNA (RAL 0.1x10(-9)). In animals treated with PY13 in the diet no adducts or only minimal amounts slightly above the limit of detection could be identified. Taking into consideration that PY13 was contaminated with 0.02% of the respective soluble monoazo compound, it is concluded that the small amounts of DCB detected have been released from the contaminating soluble monoazo compound and not from insoluble PY13. The results of the present study demonstrate the lack of bioavailability of DCB from the diarylide azo pigments PY17 and PY13.

Single-step, quantitative derivatization of amino, carboxyl, and hydroxyl groups in iodothyronine amino acids with ethanolic pivalic anhydride containing 4-dimethylaminopyridine

Reaction of thyroxine with ethanol and pivalic anhydride in the presence of 4-dimethylaminopyridine quantitatively forms N,O-dipivalyl thyroxine ethyl ester. Other iodothyronines react similarly and the procedure is moisture insensitive. Apparently this reaction is successful, in contrast to similar procedures reported for the derivatization of alpha-amino acids, because it overcomes the problem in other procedures of irreversible side reactions arising from an oxazolone intermediate.

Electrophore-labeling and alkylation of standards of nucleic acid pyrimidine bases for analysis by gas chromatography with electron-capture detection

The pyrimidine bases cytosine, uracil and thymine, along with some analogues, are electrophore-labeled either with pentafluorobenzoyl chloride (PFBC), pentafluorophenylsulfonyl chloride (PPSC), or heptafluorobutyric anhydride. Subsequent alkylation is most successful for PFB-cytosine, PPS-uracil, and PPS-thymine. These same alkylated compounds also have the highest aqueous stability and respond most strongly by gas chromatography-electron-capture detection. One of these derivatives, determined to be N4-PFB-1,3-dimethylcytosine by authentic synthesis, and its 5-methyl analogue, can be detected with good precision down to the 100-fg level. Poor reproducibility is encountered at the 10-fg level.

Release tags: a new class of analytical reagents

Release tags are novel compounds made up of three molecular groups: "signal," "release," and "reactivity." The signal group is the detected part of the tag, the release group provides a site for specific covalent cleavage, and the reactivity group attaches the tag to a substance of interest. The general purpose of release tags is to function as molecular labels, analogous to radioisotopes. Release tags also extend the applicability of gas-phase electrophores as signal groups to the analysis of nonvolatile substances. These electrophores are measured with high sensitivity and specificity by gas chromatography with electron-capture detection (GC-ECD). Because extensive multiplicity is potentially available with GC-ECD electrophores, many analogous but distinctive release tags can be used simultaneously as labels in a given assay. In this paper, we use N-pentafluorobenzoylmethionylglycine-N-hydroxysuccinimide ester, our first GC-ECD release tag, to determine thyroxin in serum by a method called "labeling analysis," which involves the principle of isotope-derivative analysis.

Release tags: a new class of analytical reagents

Release tags are novel compounds made up of three molecular groups: "signal," "release," and "reactivity." The signal group is the detected part of the tag, the release group provides a site for specific covalent cleavage, and the reactivity group attaches the tag to a substance of interest. The general purpose of release tags is to function as molecular labels, analogous to radioisotopes. Release tags also extend the applicability of gas-phase electrophores as signal groups to the analysis of nonvolatile substances. These electrophores are measured with high sensitivity and specificity by gas chromatography with electron-capture detection (GC-ECD). Because extensive multiplicity is potentially available with GC-ECD electrophores, many analogous but distinctive release tags can be used simultaneously as labels in a given assay. In this paper, we use N-pentafluorobenzoylmethionylglycine-N-hydroxysuccinimide ester, our first GC-ECD release tag, to determine thyroxin in serum by a method called "labeling analysis," which involves the principle of isotope-derivative analysis.