GeneExpression

Gene Expression

Available public gene expression data for COVID-19.

• Search NCBI Gene Expression Omnibus by COVID-19

Interesting Bibliography to take into account (Including pre-prints, feel free to complete the list):

General RNAseq analyses

• Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses
• ...?

ACE Related RNAseq analyses

• Bulk and single-cell transcriptomics identify tobacco-use disparity in lung gene expression of ACE2 - Pre-Print
• SARS-CoV-2 Receptor ACE2 is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Enriched in Specific Cell Subsets Across Tissues
• Tissue specific expression and genetic regulation of SARS-CoV-2 receptors ACE2 and TMPRSS2
• High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa
• ...?

ACE polymorphisms from RNA-seq data: project idea

SARS-CoV and SARS-CoV-2 bind to the human target cells through angiotensin-converting enzyme 2 (ACE), which is ix expressed in e.g. the epithelial cells of the lung, intestine, kidney, and blood vessels. The genetic predisposition for an increased risk of developing severe symptoms of COVID-19 might be due to ACE2 polymorphisms, especially those that have previously been linked to COVID-19 comorbidities such as diabetes mellitus and hypertension. However, since genomic data on ACE2 is limited, one approach would be to analyze existing ACE2 RNA-seq data from healthy individuals and individuals with comorbidities associated with COVID-19 and COVID-19 itself in order to find polymorphisms associated with COVID-19 severity.

Literature

• Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection? (Lancet) Discusses the importance of ACE polymorphisms and COVID-19

Datasets

• Transcriptional response of human lung epithelial cells to SARS-CoV-2 infection (GEO 25 March 2020). Human cells infected with the virus.

Pre-prints (1021 bioRxiv and medRxiv articles screened 31st March 2020)

• Non-neural expression of SARS-CoV-2 entry genes in the olfactory epithelium suggests mechanisms underlying anosmia in COVID-19 patients (bioRxiv 28 March 2020) Analyzes enrichment of ACE2 in olfactory epithelium, same RNA-seq data could be inclued for finding polymorphisms
• ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19. Transcriptomes gathered from patients with COVID-19 comorbidites and ACE2 found to be enriched (medRxiv 27 March 2020) Same data could be analyzed for polymorphisms in ACE2 associated with these comorbidites.
• Dangers of ACE inhibitor and ARB usage in COVID-19: evaluating the evidence (30 March 2020). Lists studies that have studied ACE expression.
• Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors (bioRxiv 29 March 2020). Gathers ACE2 expression data fro scRNA-seq.
• Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing (medRxiv 27 March 2020). scRNA-seq from infected patients, could look for ACE2 transcripts.
• scRNA-seq reveals ACE2 and TMPRSS2 expression in TROP2+ Liver Progenitor Cells: Implications in COVID-19 associated Liver Dysfunction. ACE2 expression in the liver.
• SARS-CoV-2 launches a unique transcriptional signature from in vitro, ex vivo, and in vivo systems. Gene expression in infected cells.
• ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19. ACE2 expression in lungs.
• Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19 (medRxiv 17 March 2020). scRNA-seq from immune cells.
• The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2 (bioRxiv 17 March 2020). ACE2 binding mutants.
• SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches ACE2 expression in lungs.
• Exploring diseases/traits and blood proteins causally related to expression of ACE2, the putative receptor of 2019-nCov: A Mendelian Randomization analysis ACE2 association analysis.
• Highly ACE2 Expression in Pancreas May Cause Pancreas Damage After SARS-CoV-2 Infection (medRxiv 3 March 2020) ACE2 expression in pancreas.
• TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 for the pathological changes in the human host after coronavirus infection ACE2 text mining
• Bulk and single-cell transcriptomics identify tobacco-use disparity in lung gene expression of ACE2, the receptor of 2019-nCov (medRxiv 28 February 2020 ). Studies expression levels of ACE2 in different patient groups. Could be re-analyzed to find polymorphisms and to see if they correlate with expression level or are enriched in specific patient groups.
• Increasing Host Cellular Receptor—Angiotensin-Converting Enzyme 2 (ACE2) Expression by Coronavirus may Facilitate 2019-nCoV Infection ACE2 expression
• Profiling ACE2 expression in colon tissue of healthy adults and colorectal cancer patients by single-cell transcriptome analysis (medRxiv 23 Feb 2020). ACE2 expression in colon
• Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses ACE2 expression in human cells.
• Single-cell Analysis of ACE2 Expression in Human Kidneys and Bladders Reveals a Potential Route of 2019-nCoV InfectionACE2 gene expression in kidney and bladders
• ACE2 Expression in Kidney and Testis May Cause Kidney and Testis Damage After 2019-nCoV Infection ACE2 expression in kidney and testis
• Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCoV, in the nasal tissue ACE2 expression in nasal tissue
• ACE2 expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism ACE2 expression in colon.
• Specific ACE2 Expression in Cholangiocytes May Cause Liver Damage After 2019-nCoV Infection ACE2 expression in liver
• The digestive system is a potential route of 2019-nCov infection: a bioinformatics analysis based on single-cell transcriptomes ACE2 expression in human organs
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing Other potential virus-interacting partners besides ACE2

Communication channel

• https://virtualbiohac-xt62674.slack.com/ (#geneexpression)

Participants

(Feel free to add your name)

• Mariana G. Ferrarini (coordinator)
• Christophe Vanderaa (Interested in participating)
• Andreas Gruber
• Vanessa Aguiar-Pulido
• Avantika Lal
• Jakke Neiro