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opencc-by-4.0Dec 2021View details →

The translational landscape of SARS-CoV-2 and infected cells reveals suppression of innate immune genes

SARS-CoV-2 utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2 infected model cell lines and primary airway cells grown at the air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We find that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In the highly permissive cell models, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokines, cytokines and interferon stimulated genes, many of these mRNAs were not translated efficiently. Impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function.  Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development. The processed data presented here is derived from the relevant RNA-seq and ribo-seq libraries.

opencc-by-4.0May 2024View details →

Innate immune responses against the mRNA component of mRNA vaccine promote cellular immunity through IFN-β at the injection site

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opencc-zeroDec 2018View details →

Data from: Constitutive innate immunity of tropical House Wrens varies with season and reproductive activity

In lowland Neotropical regions, where air temperature and day length remain relatively constant year-round, seasonality is determined primarily by changes in rainfall. The wet season triggers the start of breeding for many Neotropical birds, but also alters the antigenic environment, likely increasing the risk of disease transmission. We explored two hypotheses about temporal variation in constitutive innate immunity of a Neotropical bird, the House Wren (Troglodytes aedon). One hypothesis proposes that Neotropical wrens up-regulate their immune function in the wet season either in anticipation of or in response to vectors that become more prevalent. A second hypotheses proposes that during periods of putative high resource demand, such as when parents are feeding young, immune function would be compromised and downregulated. Controlling for reproductive stage, we found that microbicidal capacity of blood against Escherichia coli was higher in the wet than the dry season, consistent with the antigen response hypothesis. Phagocytosis of E.coli and Staphylococcus aureus did not differ between wet and dry seasons. Microbicidal capacity and H/L-ration of tropical House Wrens did not vary among reproductive stages, and our data offered no support for the idea that immune function is compromised during the period when parents are feeding young.

opencc-zeroJun 2021View details →

Innate and adaptive immune genes associated with MERS-CoV infection in dromedaries

The recent SARS-CoV-2 pandemic has refocused attention to the betacoronaviruses, only eight years after the emergence of another zoonotic betacoronavirus, the Middle East respiratory syndrome coronavirus (MERS-CoV). While the wild source of SARS-CoV-2 may be disputed, for MERS-CoV, dromedaries are considered as source of zoonotic human infections. Testing 100 immune- response genes in 121 dromedaries from United Arab Emirates (UAE) for potential association with present MERS-CoV infection, we identified candidate genes with important functions in the adaptive, MHC-class I (HLA-A-24-like) and II (HLA-DPB1-like), and innate immune response (PTPN4, MAGOHB), and in cilia coating the respiratory tract (DNAH7).

opencc-zeroJun 2021View details →

Supplemental tables for: A periventricular gradient of innate immune cell activation in Multiple Sclerosis

Objectives: To explore in-vivo innate immune cell activation as a function of the distance from ventricular CSF in patients with Multiple Sclerosis (MS) using [18F]-DPA714 PET, and to investigate its relationship with periventricular microstructural damage, evaluated by magnetization transfer ratio (MTR), and with trajectories of disability worsening. Methods: Thirty-seven MS patients and nineteen healthy controls underwent MRI and [18F]-DPA714 TSPO dynamic PET, from which individual maps of voxels characterized by innate immune cell activation (DPA+) were generated. White matter (WM) was divided in 3mm-thick concentric rings radiating from the ventricular surface toward the cortex, and the percentage of DPA+ voxels and mean MTR were extracted from each ring. Two-year trajectories of disability worsening were collected to identify patients with and without recent disability worsening. Results: The percentage of DPA+ voxels was higher in patients compared to controls in the periventricular WM (p=6.10e-6), and declined with increasing distance from ventricular surface, with a steeper gradient in patients compared to controls (p=0.001). This gradient was found both in periventricular lesions and normal-appearing WM. In the total WM, it correlated with a gradient of microstructural tissue damage measured by MTR (rs=-0.65, p=1.0e-3). When compared to clinically stable patients, patients with disability worsening were characterized by a higher percentage of DPA+ voxels in the periventricular normal-appearing WM (p=0.025). Conclusions: Our results demonstrate that in MS the innate immune cell activation predominates in periventricular regions and associates with microstructural damage and disability worsening. This could result from the diffusion of pro-inflammatory CSF-derived factors into surrounding tissues.

openJun 2023View details →

IL-18 couples innate and adaptive immune cell activation in acute multisystem inflammatory syndrome in children (MIS-C)

This repository contains the scRNA-Seq data (including TCR-Seq and BCR-Seq data) set used in the manuscript titled "IL-18 couples innate and adaptive immune cell activation in acute multisystem inflammatory syndrome in children (MIS-C)". This dataset is generated from 10x cell ranger software. In the study, we have 10 PBMC samples, from 5 MIS-C children at paired time points. T1 stands for admission time and T3 follow-up time, about 1 month post hospital discharge.

opencc-zeroJul 2023View details →

Data from: Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull

Immunogenetic variation in natural vertebrate populations is expected to respond to spatial and temporal fluctuations in pathogen assemblages. While spatial heterogeneity in pathogen-driven selection enhances local immunogenetic adaptations and population divergence, different immune genes may yield contrasting responses to the environment. Here, we investigated population differentiation at the key pathogen recognition genes of the innate and adaptive immune system in a colonial bird species, the black headed gull Chroicocephalus ridibundus. We assessed genetic variation at three toll-like receptor (TLR) genes (innate immunity) and the major histocompatibility complex (MHC) class I and II genes (adaptive immunity) in gulls from seven colonies scattered across Poland. As expected, we found much greater polymorphism at the MHC than TLRs. Population differentiation at the MHC class II, but not MHC-I, was significantly stronger than at neutral microsatellite loci, suggesting local adaptation. This could reflect spatial variation in the composition of extra-cellular parasite communities (e.g. helminths), possibly driven by sharp differences in habitat structure between colonies. Despite contrasting patterns of population differentiation, both MHC classes showed similar regimes of diversifying selection. Some significant population differentiation was also observed at TLRs, suggesting that innate immune receptors may respond to fine-scale spatial variation in pathogen pressure, although this pattern could have been enhanced by drift. Our results suggested that local adaptation at the pathogen recognition immune genes can be maintained at relatively small or moderate spatial scales in species with high dispersal potential and highlighted the complexity of immunogenetic responses of animals to heterogeneous environments.

opencc-bySep 2023View details →

MAPK p38 and NFkB activity dynamics in macrophages upon innate immune stimulation

Dataset (.mat structure) containing single cell p38 and NFkB activity dynamics in macrophages (iMPDMs) upon innate immune stimulation (LPS, TNF, P3C4, CpG) (1 h baseline + app 8 h stimulation). Two biological replicates per stimulation condition are included. 6 doses per stimulus are included. Signaling dynamics are quantified using live cell microscopy followed by automated image analysis by MACKtrack. Datasets include dynamic features ('metrics'), MACKtrack quantification outputs ('measure'), info on experimental (esp. dose), tracking, and quantification parameters, and filtering outcomes ('info').

Activation Innate Immune System in Type 1 Diabetes

ClinicalTrials.gov study NCT03441919. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.

Send-In Sample Collection for Comprehensive Analyses of Innate and Adaptive Immune Responses During Acute COVID-19 and Convalescence

ClinicalTrials.gov study NCT04582903. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.

Role of Interferon-gamma 1-b (IFN-γ) on Cells of the Innate Immune System: Functional, Biochemical and Gene Expression Studies in Patients With Chronic Granulomatous Disease

ClinicalTrials.gov study NCT03548818. IPD Sharing: NO. Countries: 1. Publications: 1.

Characterization of the Innate Immune Response in Healthy NIH Employees at Baseline and After Immunization With the H1N1 Vaccine

ClinicalTrials.gov study NCT00995527. IPD Sharing: Not stated. Countries: 1. Publications: 3.

The Effects of Oral Dipyridamole Treatment on the Innate Immune Response During Human Endotoxemia

ClinicalTrials.gov study NCT01091571. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Comparison of Innate Immune Responses Induced by Allergy Immunotherapy (AIT) With Different Adjuvants

ClinicalTrials.gov study NCT04104828. IPD Sharing: NO. Countries: 1. Publications: 1.

Testing if BCG (Bacille Calmette-Guérin) Vaccination Can Induce Innate Immune Training in Adult People Above 50 Years of Age in Guinea-Bissau

ClinicalTrials.gov study NCT02953327. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Efficacy of BCG Vaccination in the Prevention of COVID19 Via the Strengthening of Innate Immunity in Health Care Workers

ClinicalTrials.gov study NCT04384549. IPD Sharing: NO. Countries: 1. Publications: 4.

Response to Tregs in Innate Immunity Receptor LRP1 (CD91) and Tregs in Periferic Blood Mononuclear Cells in Patients With Non-segmentary Vitiligo

ClinicalTrials.gov study NCT03249064. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.

In Vivo Effects of C1-esterase Inhibitor on the Innate Immune Response During Human Endotoxemia - VECTOR II

ClinicalTrials.gov study NCT01766414. IPD Sharing: Not stated. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

Innate Immunity in COPD

ClinicalTrials.gov study NCT05743582. IPD Sharing: YES. Countries: 1. Publications: 7.

The Innate Immune System and Inflammatory Bowel Disease

ClinicalTrials.gov study NCT00516776. IPD Sharing: NO. Countries: 1. Publications: 3.