Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics

Introduction

Metaproteomics is a rapidly advancing field that offers unique insights into the taxonomic composition and the functional activity of microbial communities, and their effects on host physiology. Classically, data-dependent acquisition (DDA) mass spectrometry (MS) has been applied for peptide identification and quantification in metaproteomics. However, DDA-MS exhibits well-known limitations in terms of depth, sensitivity, and reproducibility. Consequently, methodological improvements are required to better characterize the protein landscape of microbiomes and their interactions with the host.

Methods

We present an optimized proteomic workflow that utilizes the information captured by Parallel Accumulation-Serial Fragmentation (PASEF) MS for comprehensive metaproteomic studies in complex fecal samples of mice.

Results and discussion

We show that implementing PASEF using a DDA acquisition scheme (DDA-PASEF) increased peptide quantification up to 5 times and reached higher accuracy and reproducibility compared to previously published classical DDA and data-independent acquisition (DIA) methods. Furthermore, we demonstrate that the combination of DIA, PASEF, and neuronal-network-based data analysis, was superior to DDA-PASEF in all mentioned parameters. Importantly, DIA-PASEF expanded the dynamic range towards low-abundant proteins and it doubled the quantification of proteins with unknown or uncharacterized functions. Compared to previous classical DDA metaproteomic studies, DIA-PASEF resulted in the quantification of up to 4 times more taxonomic units using 16 times less injected peptides and 4 times shorter chromatography gradients. Moreover, 131 additional functional pathways distributed across more and even uniquely identified taxa were profiled as revealed by a peptide-centric taxonomic-functional analysis. We tested our workflow on a validated preclinical mouse model of neuropathic pain to assess longitudinal changes in host-gut microbiome interactions associated with pain - an unexplored topic for metaproteomics. We uncovered the significant enrichment of two bacterial classes upon pain, and, in addition, the upregulation of metabolic activities previously linked to chronic pain as well as various hitherto unknown ones. Furthermore, our data revealed pain-associated dynamics of proteome complexes implicated in the crosstalk between the host immune system and the gut microbiome. In conclusion, the DIA-PASEF metaproteomic workflow presented here provides a stepping stone towards a deeper understanding of microbial ecosystems across the breadth of biomedical and biotechnological fields.

Development and validation of COEWS (COVID-19 Early Warning Score) for hospitalized COVID-19 with laboratory features: A multicontinental retrospective study

Background

The emergence of new SARS-CoV-2 variants with significant immune-evasiveness, the relaxation of measures for reducing the number of infections, the waning of immune protection (particularly in high-risk population groups), and the low uptake of new vaccine boosters, forecast new waves of hospitalizations and admission to intensive care units. There is an urgent need for easily implementable and clinically effective Early Warning Scores (EWSs) that can predict the risk of complications within the next 24-48 hr. Although EWSs have been used in the evaluation of COVID-19 patients, there are several clinical limitations to their use. Moreover, no models have been tested on geographically distinct populations or population groups with varying levels of immune protection.

Methods

We developed and validated COVID-19 Early Warning Score (COEWS), an EWS that is automatically calculated solely from laboratory parameters that are widely available and affordable. We benchmarked COEWS against the widely used NEWS2. We also evaluated the predictive performance of vaccinated and unvaccinated patients.

Results

The variables of the COEWS predictive model were selected based on their predictive coefficients and on the wide availability of these laboratory variables. The final model included complete blood count, blood glucose, and oxygen saturation features. To make COEWS more actionable in real clinical situations, we transformed the predictive coefficients of the COEWS model into individual scores for each selected feature. The global score serves as an easy-to-calculate measure indicating the risk of a patient developing the combined outcome of mechanical ventilation or death within the next 48 hr.The discrimination in the external validation cohort was 0.743 (95% confidence interval [CI]: 0.703-0.784) for the COEWS score performed with coefficients and 0.700 (95% CI: 0.654-0.745) for the COEWS performed with scores. The area under the receiver operating characteristic curve (AUROC) was similar in vaccinated and unvaccinated patients. Additionally, we observed that the AUROC of the NEWS2 was 0.677 (95% CI: 0.601-0.752) in vaccinated patients and 0.648 (95% CI: 0.608-0.689) in unvaccinated patients.

Conclusions

The COEWS score predicts death or MV within the next 48 hr based on routine and widely available laboratory measurements. The extensive external validation, its high performance, its ease of use, and its positive benchmark in comparison with the widely used NEWS2 position COEWS as a new reference tool for assisting clinical decisions and improving patient care in the upcoming pandemic waves.

Funding

University of Vienna.

COVID-19 vaccines reduce mortality in hospitalized patients with oxygen requirements: Differences between vaccine subtypes. A multicontinental cohort study

The aim of this study was to analyze whether the coronavirus disease 2019 (COVID-19) vaccine reduces mortality in patients with moderate or severe COVID-19 disease requiring oxygen therapy. A retrospective cohort study, with data from 148 hospitals in both Spain (111 hospitals) and Argentina (37 hospitals), was conducted. We evaluated hospitalized patients for COVID-19 older than 18 years with oxygen requirements. Vaccine protection against death was assessed through a multivariable logistic regression and propensity score matching. We also performed a subgroup analysis according to vaccine type. The adjusted model was used to determine the population attributable risk. Between January 2020 and May 2022, we evaluated 21,479 COVID-19 hospitalized patients with oxygen requirements. Of these, 338 (1.5%) patients received a single dose of the COVID-19 vaccine and 379 (1.8%) were fully vaccinated. In vaccinated patients, mortality was 20.9% (95% confidence interval [CI]: 17.9-24), compared to 19.5% (95% CI: 19-20) in unvaccinated patients, resulting in a crude odds ratio (OR) of 1.07 (95% CI: 0.89-1.29; p = 0.41). However, after considering the multiple comorbidities in the vaccinated group, the adjusted OR was 0.73 (95% CI: 0.56-0.95; p = 0.02) with a population attributable risk reduction of 4.3% (95% CI: 1-5). The higher risk reduction for mortality was with messenger RNA (mRNA) BNT162b2 (Pfizer) (OR 0.37; 95% CI: 0.23-0.59; p < 0.01), ChAdOx1 nCoV-19 (AstraZeneca) (OR 0.42; 95% CI: 0.20-0.86; p = 0.02), and mRNA-1273 (Moderna) (OR 0.68; 95% CI: 0.41-1.12; p = 0.13), and lower with Gam-COVID-Vac (Sputnik) (OR 0.93; 95% CI: 0.6-1.45; p = 0.76). COVID-19 vaccines significantly reduce the probability of death in patients suffering from a moderate or severe disease (oxygen therapy).

Development and evaluation of a machine learning-based in-hospital COVID-19 disease outcome predictor (CODOP): A multicontinental retrospective study

New SARS-CoV-2 variants, breakthrough infections, waning immunity, and sub-optimal vaccination rates account for surges of hospitalizations and deaths. There is an urgent need for clinically valuable and generalizable triage tools assisting the allocation of hospital resources, particularly in resource-limited countries. We developed and validate CODOP, a machine learning-based tool for predicting the clinical outcome of hospitalized COVID-19 patients. CODOP was trained, tested and validated with six cohorts encompassing 29223 COVID-19 patients from more than 150 hospitals in Spain, the USA and Latin America during 2020-22. CODOP uses 12 clinical parameters commonly measured at hospital admission for reaching high discriminative ability up to 9 days before clinical resolution (AUROC: 0·90-0·96), it is well calibrated, and it enables an effective dynamic risk stratification during hospitalization. Furthermore, CODOP maintains its predictive ability independently of the virus variant and the vaccination status. To reckon with the fluctuating pressure levels in hospitals during the pandemic, we offer two online CODOP calculators, suited for undertriage or overtriage scenarios, validated with a cohort of patients from 42 hospitals in three Latin American countries (78-100% sensitivity and 89-97% specificity). The performance of CODOP in heterogeneous and geographically disperse patient cohorts and the easiness of use strongly suggest its clinical utility, particularly in resource-limited countries.

Monoclonal antibody blockade of the human Eag1 potassium channel function exerts antitumor activity

The potassium channel ether à go-go has been directly linked to cellular proliferation and transformation, although its physiologic role(s) are as of yet unknown. The specific blockade of human Eag1 (hEag1) may not only allow the dissection of the role of the channel in distinct physiologic processes, but because of the implication of hEag1 in tumor biology, it may also offer an opportunity for the treatment of cancer. However, members of the potassium channel superfamily are structurally very similar to one another, and it has been notoriously difficult to obtain specific blockers for any given channel. Here, we describe and validate the first rational design of a monoclonal antibody that selectively inhibits a potassium current in intact cells. Specifically blocking hEag1 function using this antibody inhibits tumor cell growth both in vitro and in vivo. Our data provide a proof of concept that enables the generation of functional antagonistic monoclonal antibodies against ion channels with therapeutic potential. The particular antibody described here, as well as the technique developed to make additional functional antibodies to Eag1, makes it possible to evaluate the potential of the channel as a target for cancer therapy.

Different relevance of inactivation and F468 residue in the mechanisms of hEag1 channel blockage by astemizole, imipramine and dofetilide

The relevance of a point mutation at the C-terminal end of the S6 helix (F468) and the introduction of C-type inactivation in the blockage of hEag1 channels by astemizole, imipramine and dofetilide was tested. C-type inactivation decreased block by astemizole and dofetilide but not imipramine, suggesting different binding sites in the channel. F468C mutation increased IC(50) for astemizole and imipramine but in contrast to HERG channels, only slightly for dofetilide. Together with measurements on recovery of blocking, our observations indicate that the mechanism of hEag1 blockage by each of these drugs is different, and suggest relevant structural differences between hEag1 and HERG channels.

Specificity of TRH receptor coupling to G-proteins for regulation of ERG K+ channels in GH3 rat anterior pituitary cells

The identity of the G-protein coupling thyrotropin-releasing hormone (TRH) receptors to rat ether-à-go-go related gene (r-ERG) K+ channel modulation was studied in situ using perforated-patch clamped adenohypophysial GH(3) cells and dominant-negative variants (Galpha-QL/DN) of G-protein alpha subunits. Expression of dominant-negative Galpha(q/11) that minimizes the TRH-induced Ca2+ signal had no effect on r-ERG current inhibition elicited by the hormone. In contrast, the introduction of dominant-negative variants of Galpha13 and the small G-protein Rho caused a significant loss of the inhibitory effect of TRH on r-ERG. A strong reduction of this TRH effect was also obtained in cells expressing either dominant-negative Galpha(s) or transducin alpha subunits, an agent known to sequester free G-protein betagamma dimers. As a further indication of specificity of the dominant-negative effects, only the dominant-negative variants of Galpha13 and Rho (but not Galpha(s)-QL/DN or Galpha(t)) were able to reduce the TRH-induced shifts of human ERG (HERG) activation voltage dependence in HEK293 cells permanently expressing HERG channels and TRH receptors. Our results demonstrate that whereas the TRH receptor uses a G(q/11) protein for transducing the Ca2+ signal during the initial response to TRH, this G-protein is not involved in the TRH-induced inhibition of endogenous r-ERG currents in pituitary cells. They also identify G(s) (or a G(s)-like protein) and G13 as important contributors to the hormonal effect in these cells and suggest that betagamma dimers released from these proteins may participate in modulation of ERG currents triggered by TRH.

Role of BK potassium channels shaping action potentials and the associated [Ca(2+)](i) oscillations in GH(3) rat anterior pituitary cells

Measurements of electrical activity and intracellular Ca(2+) levels were performed in perforated-patch clamped GH(3) cells to determine the contribution of large-conductance calcium-activated K(+) (BK) channels to action potential repolarization and size of the associated Ca(2+) oscillations. By examining the dependence of action potential (AP) duration on extracellular Ca(2+) levels in the presence and the absence of the specific BK channel blocker paxilline, it is observed that plateau-like action potentials are associated to low densities of paxilline-sensitive currents. Extracellular Ca(2+) increases or paxilline additions are not able to largely modify action potential duration in cells showing a reduced expression of BK currents. Furthermore, specific blockade of these currents with paxilline systematically elongates AP duration, but only under conditions in which short APs and/or prominent BK currents recorded under voltage-clamp mode are present in the same cells. Our data indicate that in GH(3) cells, BK channels act primarily ending the action potential and suggest that by contributing to fine-tuning cellular electrical properties and hence intracellular Ca(2+) variations, BK channels may play an important role on time- and cell-dependent modulation of physiological outputs in adenohypophyseal cells.

Relevance of the proximal domain in the amino-terminus of HERG channels for regulation by a phospholipase C-coupled hormone receptor

We used Xenopus oocytes co-expressing thyrotropin-releasing hormone (TRH) receptors and human ether-a-go-go-related gene (HERG) K+ channel variants carrying different amino-terminal modifications to check the relevance of the proximal domain for hormonal regulation of the channel. Deletion of the whole proximal domain (Delta 138-373) eliminates TRH-induced modifications in activation and deactivation parameters. TRH effects on activation are also suppressed with channels lacking the second half of the proximal domain or only residues 326-373. However, normal responses to TRH are obtained with Delta 346-373 channels. Thus, whereas residues 326-345 are required for the hormonal modulation of HERG activation, different proximal domain sequences contribute to set HERG gating characteristics and its regulation by TRH.

Influence of amino-terminal structures on kinetic transitions between several closed and open states in human erg K+ channels

Gating kinetics of human ether-a-go-go (eag)-related gene (HERG) K+ channel expressed in Xenopus oocytes was studied using non-inactivating channel variants carrying different structural modifications in the amino terminus. A kinetics model was elaborated to describe the behavior of full-length channels, that includes at least three open states besides the three closed states previously proposed. Deletion of the HERG-specific proximal domain (HERG D138-373) accelerated all individual forward transitions between closed states. Whereas relatively large amplitude depolarizations were required to drive full-length HERG channels to more distal open states, these were reached more easily in channels without proximal domain. Alteration of the initial eag/PAS domain by introduction of a short amino-acid sequence at the beginning of the amino terminus did not alter transitions between closed states, but prevented the channels from reaching the farthest open states that determine slower deactivation rates. This indicates that the presence of specific amino-terminal structures can be correlated with the occurrence of distinctive molecular transitions. It also demonstrates that both proximal and eag/PAS domains in the amino terminus contribute to set the gating characteristics of HERG channels.

Correlation between electrical activity and intracellular Ca2+ oscillations in GH3 rat anterior pituitary cells

Simultaneous measurements of electrical activity and intracellular Ca(2+) levels were performed in perforated-patch current-clamped individual GH3 cells. Both in cells showing brief (<100 ms) and long action potentials (APs), we found a good correlation between the averaged intracellular Ca2+ concentration ([Ca2+]i) and AP frequency, but not between the mean [Ca2+]i and AP duration. Nevertheless, the magnitude of spontaneous Ca2+ oscillations was highly dependent on the size and duration of the APs. The decay of the Ca2+ transients was not slowed when the size of the oscillations was varied either spontaneously or after elongation of the AP with the K+ channel blocker tetraethyl ammonium. Furthermore, the recovery from Ca2+ loads similar to those induced by the APs was slightly retarded after treatment of the cells with intracellular store Ca2+-ATPase inhibitors. Among previous results showing that caffeine-induced [Ca2+]i increases are secondary to electrical activity enhancements in GH3 cells, these data indicate that the Ca2+ entry triggered via APs is the primary determinant of the [Ca2+]i variations, and that Ca2+-induced Ca2+ release has a minor contribution to Ca2+ oscillations recorded during spontaneous activity. They also point to modulation of electrical activity patterns as a crucial factor regulating spontaneous [Ca2+]i signalling, and hence pituitary cell functions in response to physiological secretagogues.

Differential effects of amino-terminal distal and proximal domains in the regulation of human erg K(+) channel gating

The participation of amino-terminal domains in human ether-a-go-go (eag)-related gene (HERG) K(+) channel gating was studied using deleted channel variants expressed in Xenopus oocytes. Selective deletion of the HERG-specific sequence (HERG Delta138-373) located between the conserved initial amino terminus (the eag or PAS domain) and the first transmembrane helix accelerates channel activation and shifts its voltage dependence to hyperpolarized values. However, deactivation time constants from fully activated states and channel inactivation remain almost unaltered after the deletion. The deletion effects are equally manifested in channel variants lacking inactivation. The characteristics of constructs lacking only about half of the HERG-specific domain (Delta223-373) or a short stretch of 19 residues (Delta355-373) suggest that the role of this domain is not related exclusively to its length, but also to the presence of specific sequences near the channel core. Deletion-induced effects are partially reversed by the additional elimination of the eag domain. Thus the particular combination of HERG-specific and eag domains determines two important HERG features: the slow activation essential for neuronal spike-frequency adaptation and maintenance of the cardiac action potential plateau, and the slow deactivation contributing to HERG inward rectification.