Systems level insights into the impact of airborne exposure on SARS-CoV-2 pathogenesis and COVID-19 outcome – A multi-omics big data study

Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China

(2020) Dawei Wang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

Cardiac dysfunction and metabolic remodeling due to seasonally ambient fine particles exposure

(2020) Jingxu Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Oxidative Stress as Key Player in Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) Infection

(2020) Livan Delgado-Roche et al.   ARCHIVES OF MEDICAL RESEARCH

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

(2020) Daniel Blanco-Melo et al.   CELL

Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2

(2020) Vanessa Monteil et al.   CELL

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

COVID-19: towards understanding of pathogenesis

(2020) Wei Cao et al.   CELL RESEARCH

Particulate Matter Toxicity Is Nrf2 and Mitochondria Dependent: The Roles of Metals and Polycyclic Aromatic Hydrocarbons

(2020) Michal Pardo et al.   CHEMICAL RESEARCH IN TOXICOLOGY

The role of the exposome in promoting resilience or susceptibility after SARS-CoV-2 infection

(2020) Sean X. Naughton et al.   Journal of Exposure Science and Environmental Epidemiology

Endothelial cell infection and endotheliitis in COVID-19

(2020) Zsuzsanna Varga et al.   LANCET

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

(2020) Denisa Bojkova et al.   NATURE

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

(2020) Waradon Sungnak et al.   NATURE MEDICINE

SPEED2: inferring upstream pathway activity from differential gene expression

(2020) Mattias Rydenfelt et al.   NUCLEIC ACIDS RESEARCH

Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease 2019 Pneumonia in Wuhan, China

(2020) Chaomin Wu et al.   JAMA Internal Medicine

Re-analysis of SARS-CoV-2-infected host cell proteomics time-course data by impact pathway analysis and network analysis: a potential link with inflammatory response

(2020) Jens-Ole Bock et al.   Aging-US

Should we unstress SARS-CoV-2 infected cells?

(2020) Fabiana Csukasi et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Can atmospheric pollution be considered a co-factor in extremely high level of SARS-CoV-2 lethality in Northern Italy?

(2020) Edoardo Conticini et al.   ENVIRONMENTAL POLLUTION

Crosstalk between endoplasmic reticulum stress and anti-viral activities: A novel therapeutic target for COVID-19

(2020) Aditi Banerjee et al.   LIFE SCIENCES

Association between short-term exposure to air pollution and COVID-19 infection: Evidence from China

(2020) Yongjian Zhu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Evidence-Based Considerations Exploring Relations between SARS-CoV-2 Pandemic and Air Pollution: Involvement of PM2.5-Mediated Up-Regulation of the Viral Receptor ACE-2

(2020) Marina Borro et al.   International Journal of Environmental Research and Public Health

Tripartite Combination of Candidate Pandemic Mitigation Agents: Vitamin D, Quercetin, and Estradiol Manifest Properties of Medicinal Agents for Targeted Mitigation of the COVID-19 Pandemic Defined by Genomics-Guided Tracing of SARS-CoV-2 Targets in Human Cells

(2020) Gennadi V. Glinsky   Biomedicines

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

(2019) Jüri Reimand et al.   Nature Protocols

Seasonal variations in the oxidative stress and inflammatory potential of PM2.5 in Tehran using an alveolar macrophage model; The role of chemical composition and sources

(2019) Ahlam H. Al Hanai et al.   ENVIRONMENT INTERNATIONAL

As a downstream target of the AKT pathway, NPTX1 inhibits proliferation and promotes apoptosis in hepatocellular carcinoma

(2019) Yue Zhao et al.   BIOSCIENCE REPORTS

Blocking TBK1 alleviated radiation-induced pulmonary fibrosis and epithelial-mesenchymal transition through Akt-Erk inactivation

(2019) Hongjin Qu et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

PM2.5 induces ferroptosis in human endothelial cells through iron overload and redox imbalance

(2019) Yan Wang et al.   ENVIRONMENTAL POLLUTION

Involvement of cigarette smoke-induced epithelial cell ferroptosis in COPD pathogenesis

(2019) Masahiro Yoshida et al.   Nature Communications

PM2.5 Exposure in the Respiratory System Induces Distinct Inflammatory Signaling in the Lung and the Liver of Mice

(2019) Soi Jeong et al.   Journal of Immunology Research

Instillation of particulate matter 2.5 induced acute lung injury and attenuated the injury recovery in ACE2 knockout mice

(2018) Chung-I Lin et al.   International Journal of Biological Sciences

Inflammatory health effects of indoor and outdoor particulate matter

(2018) Weidong Wu et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

(2018) Daniel J B Clarke et al.   NUCLEIC ACIDS RESEARCH

PM2.5-induced oxidative stress increases intercellular adhesion molecule-1 expression in lung epithelial cells through the IL-6/AKT/STAT3/NF-κB-dependent pathway

(2018) Chen-Wei Liu et al.   Particle and Fibre Toxicology

Mitochondrial DNA damage and subsequent activation of Z-DNA binding protein 1 links oxidative stress to inflammation in epithelial cells

(2018) Bartosz Szczesny et al.   Scientific Reports

Analysis of Genes Related to Angiotensin II-Induced Arterial Injury Using a Time Series Microarray

(2018) Yun-Long Zhang et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

The Development of the Concept of Ferroptosis

(2018) Tal Hirschhorn et al.   FREE RADICAL BIOLOGY AND MEDICINE

A Dual Role of Heme Oxygenase-1 in Cancer Cells

(2018) Shih-Kai Chiang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Differential toxicities of fine particulate matters from various sources

(2018) Minhan Park et al.   Scientific Reports

Mass spectrometry-based metabolomics reveals the mechanism of ambient fine particulate matter and its components on energy metabolic reprogramming in BEAS-2B cells

(2018) Yuanyuan Song et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Crosstalk between NRF2 and HIPK2 shapes cytoprotective responses

(2017) L Torrente et al.   ONCOGENE

Industrial PM 2.5 cause pulmonary adverse effect through RhoA/ROCK pathway

(2017) Junyan Yan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity

(2017) María-José Sandí et al.   Science Signaling

MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity

(2017) María-José Sandí et al.   Science Signaling

Urban particulate matter triggers lung inflammation via the ROS-MAPK-NF-κB signaling pathway

(2017) Jian Wang et al.   Journal of Thoracic Disease

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

Heme oxygenase-1 accelerates erastin-induced ferroptotic cell death

(2015) Min-Young Kwon et al.   Oncotarget

Metabolomics reveals disturbed metabolic pathways in human lung epithelial cells exposed to airborne fine particulate matter

(2015) Qingyu Huang et al.   Toxicology Research

Long-Acting Progestin-Only Contraceptives Enhance Human Endometrial Stromal Cell Expressed Neuronal Pentraxin-1 and Reactive Oxygen Species to Promote Endothelial Cell Apoptosis

(2014) O. Guzeloglu-Kayisli et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Cell cycle alterations induced by urban PM2.5 in bronchial epithelial cells: characterization of the process and possible mechanisms involved

(2013) Eleonora Longhin et al.   Particle and Fibre Toxicology

PM2.5-induced oxidative stress triggers autophagy in human lung epithelial A549 cells

(2013) Xiaobei Deng et al.   TOXICOLOGY IN VITRO

Pulmonary Oxidative Stress, Inflammation and Cancer: Respirable Particulate Matter, Fibrous Dusts and Ozone as Major Causes of Lung Carcinogenesis through Reactive Oxygen Species Mechanisms

(2013) Athanasios Valavanidis et al.   International Journal of Environmental Research and Public Health

The Pivotal Role of TBK1 in Inflammatory Responses Mediated by Macrophages

(2012) Tao Yu et al.   MEDIATORS OF INFLAMMATION

Gene expression profiling and pathway analysis of human bronchial epithelial cells exposed to airborne particulate matter collected from Saudi Arabia

(2012) Hong Sun et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Finding disease similarity based on implicit semantic similarity

(2011) Sachin Mathur et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Particulate Matter-Induced Lung Inflammation Increases Systemic Levels of PAI-1 and Activates Coagulation Through Distinct Mechanisms

(2011) G. R. Scott Budinger et al.   PLoS One

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

(2010) V. Kaimal et al.   NUCLEIC ACIDS RESEARCH

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Urban Particulate Matter Causes ER Stress and the Unfolded Protein Response in Human Lung Cells

(2009) Todd L. Watterson et al.   TOXICOLOGICAL SCIENCES

Protein kinase A-mediated CREB phosphorylation is an oxidant-induced survival pathway in alveolar type II cells

(2008) Christy A. Barlow et al.   APOPTOSIS