JAMA Netw Open. 2021 Mar 1;4(3):e213233. doi: 10.1001/jamanetworkopen.2021.3233.

NO ABSTRACT

PMID:33769504 | DOI:10.1001/jamanetworkopen.2021.3233

Elife. 2021 Mar 26;10:e63642. doi: 10.7554/eLife.63642. Online ahead of print.

ABSTRACT

Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Further, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with Inflammatory Bowel Disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.

PMID:33769280 | DOI:10.7554/eLife.63642

Plant Biotechnol J. 2021 Mar 26. doi: 10.1111/pbi.13587. Online ahead of print.

ABSTRACT

Tartary buckwheat (Fagopyrum tataricum, TB) is rich in bioactive flavonoids, which have a variety of biological activities (Ghorbani, 2017). Jasmonates (JAs) are essential phytohormones, which play key roles in regulating the formation of numerous secondary metabolites, including flavonoids rutin (Zhou and Memelink, 2016; Li et al., 2019). It has been reported that JAs could induce flavonoids accumulation and identified a class of JAs-responsive R2R3-MYB TFs, such as FtMYB11, a repressor of rutin biosynthesis in TB (Zhang et al., 2018; Zhou et al., 2017). JAs leads to FtMYBs degradation by 26S proteasome pathway (Zhang et al., 2018). However, the posttranslational regulation of these FtMYBs has not been reported.

PMID:33768635 | DOI:10.1111/pbi.13587

Eur J Clin Microbiol Infect Dis. 2021 Mar 25. doi: 10.1007/s10096-021-04229-y. Online ahead of print.

ABSTRACT

Human papillomavirus (HPV) infection among men who have sex with men (MSM) in China is underreported. We performed a systematic review and meta-analysis to clarify site-specific HPV prevalence among MSM in China. We searched both English and Chinese databases for all studies published before April 1, 2020, that reported HPV prevalence among MSM in China. Random-effects meta-analysis was used to calculate summary estimates. Thirty-four articles were eligible, where 32, 5, and 2 articles reported HPV prevalence at the anus, penis, and oral cavity, respectively. The estimated prevalence of anal HPV among MSM in China was 85.1% (HIV-positive), 53.6% (HIV-negative), and 59.2% (unknown HIV status), with HPV genotypes being predominated by HPV 6, 11, 16, 18, 52, and 58. Any HPV and high-risk (HR) HPV was more common in northern China, while low-risk HPV was more common in southern China. HPV prevalence increased with age among HIV-negative MSM, from 40.5% (aged < 20 years) to 57.2% (aged ≥ 40 years). High prevalence of any HPV (HIV+: 95.1%; HIV-: 97.7%) and multiple infections (HIV+: 75.9%; HIV-: 41.7%) was found in anogenital warts among MSM. HPV is common among MSM in China. MSM living with HIV and/or anogenital warts were at disproportionate risk for HR HPV. Younger MSM were found to have a lower HPV prevalence. HPV vaccines would have prevented the majority of infections if given before sex debut. HPV at anatomical sites other than the anus, incident HPV infection, and the cost-effectiveness of HPV vaccination in this population are worth further investigation.

PMID:33768442 | DOI:10.1007/s10096-021-04229-y

Theor Appl Genet. 2021 Mar 25. doi: 10.1007/s00122-021-03809-y. Online ahead of print.

ABSTRACT

Several stable QTL were detected using metaGWAS analysis for different agronomic and quality traits under 26 normal and heat stressed environments. Heat stress, exacerbated by global warming, has a negative influence on wheat production worldwide and climate resilient cultivars can help mitigate these impacts. Selection decisions should therefore depend on multi-environment experiments representing a range of temperatures at critical stages of development. Here, we applied a meta-genome wide association analysis (metaGWAS) approach to detect stable QTL with significant effects across multiple environments. The metaGWAS was applied to 11 traits scored in 26 trials that were sown at optimal or late times of sowing (TOS1 and TOS2, respectively) at five locations. A total of 2571 unique wheat genotypes (13,959 genotypes across all environments) were included and the analysis conducted on TOS1, TOS2 and both times of sowing combined (TOS1&2). The germplasm was genotyped using a 90 k Infinium chip and imputed to exome sequence level, resulting in 341,195 single nucleotide polymorphisms (SNPs). The average accuracy across all imputed SNPs was high (92.4%). The three metaGWAS analyses revealed 107 QTL for the 11 traits, of which 16 were detected in all three analyses and 23 were detected in TOS1&2 only. The remaining QTL were detected in either TOS1 or TOS2 with or without TOS1&2, reflecting the complex interactions between the environments and the detected QTL. Eight QTL were associated with grain yield and seven with multiple traits. The identified QTL provide an important resource for gene enrichment and fine mapping to further understand the mechanisms of gene × environment interaction under both heat stressed and unstressed conditions.

PMID:33768282 | DOI:10.1007/s00122-021-03809-y

Plant Physiol. 2021 Mar 26:kiab145. doi: 10.1093/plphys/kiab145. Online ahead of print.

ABSTRACT

Lateral roots are important to forage for nutrients due to their ability to increase the uptake area of a root system. Hence, it comes as no surprise that lateral root formation is affected by nutrients or nutrient starvation, and as such contributes to the root system plasticity. Understanding the molecular mechanisms regulating root adaptation dynamics towards nutrient availability is useful to optimize plant nutrient use efficiency. There is at present a profound, though still evolving, knowledge on lateral root pathways. Here, we aimed to review the intersection with nutrient signaling pathways to give an update on the regulation of lateral root development by nutrients, with a particular focus on nitrogen. Remarkably, it is for most nutrients not clear how lateral root formation is controlled. Only for nitrogen, one of the most dominant nutrients in the control of lateral root formation, the crosstalk with multiple key signals determining lateral root development is clearly shown. In this update, we first present a general overview of the current knowledge of how nutrients affect lateral root formation, followed by a deeper discussion on how nitrogen signaling pathways act on different lateral root-mediating mechanisms for which multiple recent studies yield insights.

PMID:33768243 | DOI:10.1093/plphys/kiab145

Expert Rev Precis Med Drug Dev. 2021;6(1):51-63. doi: 10.1080/23808993.2021.1840273. Epub 2020 Oct 28.

ABSTRACT

INTRODUCTION: In parallel to the clinical maturation of heart transplantation over the last 50 years, rejection testing has been revolutionized within the systems biology paradigm triggered by the Human Genome Project.

AREAS COVERED: We have co-developed the first FDA-cleared diagnostic and prognostic leukocyte gene expression profiling biomarker test in transplantation medicine that gained international evidence-based medicine guideline acceptance to rule out moderate/severe acute cellular cardiac allograft rejection without invasive endomyocardial biopsies. This work prompted molecular re-classification of intragraft biology, culminating in the identification of a pattern of intragraft myocyte injury, in addition to acute cellular rejection and antibody-mediated rejection. This insight stimulated research into non-invasive detection of myocardial allograft injury. The addition of a donor-organ specific myocardial injury marker based on donor-derived cell-free DNA further strengthens the non-invasive monitoring concept, combining the clinical use of two complementary non-invasive blood-based measures, host immune activity-related risk of acute rejection as well as cardiac allograft injury.

EXPERT OPINION: This novel complementary non-invasive heart transplant monitoring strategy based on leukocyte gene expression profiling and donor-derived cell-free DNA that incorporates longitudinal variability measures provides an exciting novel algorithm of heart transplant allograft monitoring. This algorithm's clinical utility will need to be tested in an appropriately designed randomized clinical trial which is in preparation.

PMID:33768160 | PMC:PMC7986584 | DOI:10.1080/23808993.2021.1840273

Mol Ther Nucleic Acids. 2021 Feb 18;24:154-163. doi: 10.1016/j.omtn.2021.02.014. eCollection 2021 Jun 4.

ABSTRACT

The study of transcriptional regulation is still difficult yet fundamental in molecular biology research. Recent research has shown that the double helix structure of nucleotides plays an important role in improving the accuracy and interpretability of transcription factor binding sites (TFBSs). Although several computational methods have been designed to take both DNA sequence and DNA shape features into consideration simultaneously, how to design an efficient model is still an intractable topic. In this paper, we proposed a hybrid convolutional recurrent neural network (CNN/RNN) architecture, CRPTS, to predict TFBSs by combining DNA sequence and DNA shape features. The novelty of our proposed method relies on three critical aspects: (1) the application of a shared hybrid CNN and RNN has the ability to efficiently extract features from large-scale genomic sequences obtained by high-throughput technology; (2) the common patterns were found from DNA sequences and their corresponding DNA shape features; (3) our proposed CRPTS can capture local structural information of DNA sequences without completely relying on DNA shape data. A series of comprehensive experiments on 66 in vitro datasets derived from universal protein binding microarrays (uPBMs) shows that our proposed method CRPTS obviously outperforms the state-of-the-art methods.

PMID:33767912 | PMC:PMC7972936 | DOI:10.1016/j.omtn.2021.02.014

Front Microbiol. 2021 Mar 9;12:598180. doi: 10.3389/fmicb.2021.598180. eCollection 2021.

ABSTRACT

While the root-associated microbiome is typically less diverse than the surrounding soil due to both plant selection and microbial competition for plant derived resources, it typically retains considerable complexity, harboring many hundreds of distinct bacterial species. Here, we report a time-dependent deviation from this trend in the rhizospheres of field grown sorghum. In this study, 16S rRNA amplicon sequencing was used to determine the impact of nitrogen fertilization on the development of the root-associated microbiomes of 10 sorghum genotypes grown in eastern Nebraska. We observed that early rhizosphere samples exhibit a significant reduction in overall diversity due to a high abundance of the bacterial genus Pseudomonas that occurred independent of host genotype in both high and low nitrogen fields and was not observed in the surrounding soil or associated root endosphere samples. When clustered at 97% identity, nearly all the Pseudomonas reads in this dataset were assigned to a single operational taxonomic unit (OTU); however, exact sequence variant (ESV)-level resolution demonstrated that this population comprised a large number of distinct Pseudomonas lineages. Furthermore, single-molecule long-read sequencing enabled high-resolution taxonomic profiling revealing further heterogeneity in the Pseudomonas lineages that was further confirmed using shotgun metagenomic sequencing. Finally, field soil enriched with specific carbon compounds recapitulated the increase in Pseudomonas, suggesting a possible connection between the enrichment of these Pseudomonas species and a plant-driven exudate profile.

PMID:33767674 | PMC:PMC7985074 | DOI:10.3389/fmicb.2021.598180

Nat Genet. 2021 Mar 25. doi: 10.1038/s41588-021-00806-1. Online ahead of print.

ABSTRACT

Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. However, the cellular origin of neuroblastoma has yet to be defined. Here we studied the single-cell transcriptomes of neuroblastomas and normal human developing adrenal glands at various stages of embryonic and fetal development. We defined normal differentiation trajectories from Schwann cell precursors over intermediate states to neuroblasts or chromaffin cells and showed that neuroblastomas transcriptionally resemble normal fetal adrenal neuroblasts. Importantly, neuroblastomas with varying clinical phenotypes matched different temporal states along normal neuroblast differentiation trajectories, with the degree of differentiation corresponding to clinical prognosis. Our work highlights the roles of oncogenic MYCN and loss of TFAP2B in blocking differentiation and may provide the basis for designing therapeutic interventions to overcome differentiation blocks.

PMID:33767450 | DOI:10.1038/s41588-021-00806-1

Nat Rev Microbiol. 2021 Mar 25. doi: 10.1038/s41579-021-00537-4. Online ahead of print.

ABSTRACT

Cross-species gene transfer is often associated with bacteria, which have evolved several mechanisms that facilitate horizontal DNA exchange. However, the increased availability of whole-genome sequences has revealed that fungal species also exchange DNA, leading to intertwined lineages, blurred species boundaries or even novel species. In contrast to prokaryotes, fungal DNA exchange originates from interspecific hybridization, where two genomes are merged into a single, often highly unstable, polyploid genome that evolves rapidly into stabler derivatives. The resulting hybrids can display novel combinations of genetic and phenotypic variation that enhance fitness and allow colonization of new niches. Interspecific hybridization led to the emergence of important pathogens of humans and plants (for example, various Candida and 'powdery mildew' species, respectively) and industrially important yeasts, such as Saccharomyces hybrids that are important in the production of cold-fermented lagers or cold-cellared Belgian ales. In this Review, we discuss the genetic processes and evolutionary implications of fungal interspecific hybridization and highlight some of the best-studied examples. In addition, we explain how hybrids can be used to study molecular mechanisms underlying evolution, adaptation and speciation, and serve as a route towards development of new variants for industrial applications.

PMID:33767366 | DOI:10.1038/s41579-021-00537-4

Sci Rep. 2021 Mar 25;11(1):6921. doi: 10.1038/s41598-021-86427-4.

ABSTRACT

Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.

PMID:33767340 | DOI:10.1038/s41598-021-86427-4

Sci Rep. 2021 Mar 25;11(1):6824. doi: 10.1038/s41598-021-86375-z.

ABSTRACT

The replication machinery of most RNA viruses lacks proofreading mechanisms. As a result, RNA virus populations harbor a large amount of genetic diversity that confers them the ability to rapidly adapt to changes in their environment. In this work, we investigate whether further increasing the initial population diversity of a model RNA virus can improve adaptation to a single selection pressure, thermal inactivation. For this, we experimentally increased the diversity of coxsackievirus B3 (CVB3) populations across the capsid region. We then compared the ability of these high diversity CVB3 populations to achieve resistance to thermal inactivation relative to standard CVB3 populations in an experimental evolution setting. We find that viral populations with high diversity are better able to achieve resistance to thermal inactivation at both the temperature employed during experimental evolution as well as at a more extreme temperature. Moreover, we identify mutations in the CVB3 capsid that confer resistance to thermal inactivation, finding significant mutational epistasis. Our results indicate that even naturally diverse RNA virus populations can benefit from experimental augmentation of population diversity for optimal adaptation and support the use of such viral populations in directed evolution efforts that aim to select viruses with desired characteristics.

PMID:33767337 | DOI:10.1038/s41598-021-86375-z

Nat Commun. 2021 Mar 25;12(1):1886. doi: 10.1038/s41467-021-22190-4.

ABSTRACT

Cells can encode information about their environment by modulating signaling dynamics and responding accordingly. Yet, the mechanisms cells use to decode these dynamics remain unknown when cells respond exclusively to transient signals. Here, we approach design principles underlying such decoding by rationally engineering a synthetic short-pulse decoder in budding yeast. A computational method for rapid prototyping, TopoDesign, allowed us to explore 4122 possible circuit architectures, design targeted experiments, and then rationally select a single circuit for implementation. This circuit demonstrates short-pulse decoding through incoherent feedforward and positive feedback. We predict incoherent feedforward to be essential for decoding transient signals, thereby complementing proposed design principles of temporal filtering, the ability to respond to sustained signals, but not to transient signals. More generally, we anticipate TopoDesign to help designing other synthetic circuits with non-intuitive dynamics, simply by assembling available biological components.

PMID:33767179 | DOI:10.1038/s41467-021-22190-4

Nat Commun. 2021 Mar 25;12(1):1756. doi: 10.1038/s41467-021-22010-9.

ABSTRACT

The levels of nuclear protein Lamin A/C are crucial for nuclear mechanotransduction. Lamin A/C levels are known to scale with tissue stiffness and extracellular matrix levels in mesenchymal tissues. But in epithelial tissues, where cells lack a strong interaction with the extracellular matrix, it is unclear how Lamin A/C is regulated. Here, we show in epithelial tissues that Lamin A/C levels scale with apico-basal cell compression, independent of tissue stiffness. Using genetic perturbations in Drosophila epithelial tissues, we show that apico-basal cell compression regulates the levels of Lamin A/C by deforming the nucleus. Further, in mammalian epithelial cells, we show that nuclear deformation regulates Lamin A/C levels by modulating the levels of phosphorylation of Lamin A/C at Serine 22, a target for Lamin A/C degradation. Taken together, our results reveal a mechanism of Lamin A/C regulation which could provide key insights for understanding nuclear mechanotransduction in epithelial tissues.

PMID:33767161 | DOI:10.1038/s41467-021-22010-9

Semin Cancer Biol. 2021 Mar 22:S1044-579X(21)00061-4. doi: 10.1016/j.semcancer.2021.03.011. Online ahead of print.

ABSTRACT

EV-miRNAs are microRNA (miRNA) molecules encapsulated in extracellular vesicles (EVs), which play crucial roles in tumor pathogenesis, progression, and metastasis. Recent studies about EV-miRNAs have gained novel insights into cancer biology and have demonstrated a great potential to develop novel liquid biopsy assays for various applications. Notably, compared to conventional liquid biomarkers, EV-miRNAs are more advantageous in representing host-cell molecular architecture and exhibiting higher stability and specificity. Despite various available techniques for EV-miRNA separation, concentration, profiling, and data analysis, a standardized approach for EV-miRNA biomarker development is yet lacking. In this review, we performed a substantial literature review and distilled an integrated workflow encompassing important steps for EV-miRNA biomarker development, including sample collection and EV isolation, EV-miRNA extraction and quantification, high-throughput data preprocessing, biomarker prioritization and model construction, functional analysis, as well as validation. With the rapid growth of "big data", we highlight the importance of efficient mining of high-throughput data for the discovery of EV-miRNA biomarkers and integrating multiple independent datasets for in silico and experimental validations to increase the robustness and reproducibility. Furthermore, as an efficient strategy in systems biology, network inference provides insights into the regulatory mechanisms and can be used to select functionally important EV-miRNAs to refine the biomarker candidates. Despite the encouraging development in the field, a number of challenges still hinder the clinical translation. We finally summarize several common challenges in various biomarker studies and discuss potential opportunities emerging in the related fields.

PMID:33766650 | DOI:10.1016/j.semcancer.2021.03.011

Anal Chim Acta. 2021 Apr 22;1155:338342. doi: 10.1016/j.aca.2021.338342. Epub 2021 Feb 19.

ABSTRACT

Spatially resolved metabolomics offers unprecedented opportunities for elucidating metabolic mechanisms during cancer progression. It facilitated the discovery of aberrant cellular metabolism with clinical application potential. Here, we developed a novel strategy to discover cancer tissue relevant metabolic signatures by high spatially resolved metabolomics combined with a multicellular tumor spheroid (MCTS) in vitro model. Esophageal cancer MCTS were generated using KYSE-30 human esophageal cancer cells to fully mimic the 3D microenvironment under physiological conditions. Then, the spatial features and temporal variation of metabolites and metabolic pathways in MCTS were accurately mapped by using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) with a spatial resolution at ∼12 μm. Metabolites, such as glutamate, tyrosine, inosine and various types of lipids displayed heterogeneous distributions in different microregions inside the MCTS, revealing the metabolic heterogenicity of cancer cells under different proliferative states. Subsequently, through joint analysis of metabolomic data of clinical cancer tissue samples, cancer tissue relevant metabolic signatures in esophageal cancer MCTS were identified, including glutamine metabolism, fatty acid metabolism, de novo synthesis phosphatidylcholine (PC) and phosphatidylethanolamine (PE), etc. In addition, the abnormal expression of the involved metabolic enzymes, i.e., GLS, FASN, CHKA and cPLA2, was further confirmed and showed similar tendencies in esophageal cancer MCTS and cancer tissues. The MALDI-MSI combined with MCTS approach offers molecular insights into cancer metabolism with real-word relevance, which would potentially benefit the biomarker discovery and metabolic mechanism studies.

PMID:33766316 | DOI:10.1016/j.aca.2021.338342

BMC Res Notes. 2021 Mar 25;14(1):117. doi: 10.1186/s13104-021-05532-9.

ABSTRACT

OBJECTIVES: Agarwood is the aromatic heartwood formed upon wounding of Aquilaria trees either naturally formed due to physical wound sustained from natural phenomena followed by microbial infection, or artificially induced using different inoculation methods. Different induction methods produce agarwoods with different aromas which have impacts on their commercial values. In lieu of elucidating the molecular mechanisms of agarwood formation under different treatment conditions, the transcriptome profiles of trunk tissues from healthy A. malaccensis tree, and naturally and artificially induced trees were obtained.

DATA DESCRIPTION: The transcriptome of trunk tissues from healthy A. malaccensis, and naturally and artificially induced trees were sequenced using Illumina HiSeq™ 4000 platform which resulted in a total of 38.4 Gb clean reads with Q30 rate of at least 91%. The transcriptome consists of 85,986 unigenes containing 1305 bases on average which were annotated against several databases. From this, 44,654 unigenes were mapped to 290 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. These transcriptome data represent considerable contribution towards Aquilaria transcriptome data and enhance current knowledge in comprehending the molecular mechanisms underlying agarwood formation in Aquilaria spp.

PMID:33766087 | DOI:10.1186/s13104-021-05532-9

BMC Bioinformatics. 2021 Mar 25;22(1):157. doi: 10.1186/s12859-021-04075-x.

ABSTRACT

BACKGROUND: Large-scale biological data sets are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell cycle and life history variation, and from exogenous technical factors like sample preparation and instrument variation.

RESULTS: We describe a general method for automatically reducing noise in large-scale biological data sets. This method uses an interaction network to identify groups of correlated or anti-correlated measurements that can be combined or "filtered" to better recover an underlying biological signal. Similar to the process of denoising an image, a single network filter may be applied to an entire system, or the system may be first decomposed into distinct modules and a different filter applied to each. Applied to synthetic data with known network structure and signal, network filters accurately reduce noise across a wide range of noise levels and structures. Applied to a machine learning task of predicting changes in human protein expression in healthy and cancerous tissues, network filtering prior to training increases accuracy up to 43% compared to using unfiltered data.

CONCLUSIONS: Network filters are a general way to denoise biological data and can account for both correlation and anti-correlation between different measurements. Furthermore, we find that partitioning a network prior to filtering can significantly reduce errors in networks with heterogenous data and correlation patterns, and this approach outperforms existing diffusion based methods. Our results on proteomics data indicate the broad potential utility of network filters to applications in systems biology.

PMID:33765911 | DOI:10.1186/s12859-021-04075-x

Immunity. 2021 Mar 11:S1074-7613(21)00117-5. doi: 10.1016/j.immuni.2021.03.005. Online ahead of print.

ABSTRACT

Immune response dynamics in coronavirus disease 2019 (COVID-19) and their severe manifestations have largely been studied in circulation. Here, we examined the relationship between immune processes in the respiratory tract and circulation through longitudinal phenotypic, transcriptomic, and cytokine profiling of paired airway and blood samples from patients with severe COVID-19 relative to heathy controls. In COVID-19 airways, T cells exhibited activated, tissue-resident, and protective profiles; higher T cell frequencies correlated with survival and younger age. Myeloid cells in COVID-19 airways featured hyperinflammatory signatures, and higher frequencies of these cells correlated with mortality and older age. In COVID-19 blood, aberrant CD163+ monocytes predominated over conventional monocytes, and were found in corresponding airway samples and in damaged alveoli. High levels of myeloid chemoattractants in airways suggest recruitment of these cells through a CCL2-CCR2 chemokine axis. Our findings provide insights into immune processes driving COVID-19 lung pathology with therapeutic implications for targeting inflammation in the respiratory tract.

PMID:33765436 | DOI:10.1016/j.immuni.2021.03.005